Index (BioJava-1.5-beta API)

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## A

a() - Static method in class org.biojava.bio.seq.DNATools
a() - Static method in class org.biojava.bio.seq.NucleotideTools
a() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Alanine
a() - Static method in class org.biojava.bio.seq.RNATools
A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `AA` indicates that a sequence contains AA (amino acid) symbols.
AAindex - Class in org.biojava.bio.proteomics.aaindex
  Symbol property table based on the Amino Acid Index Database.
AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex
  Initializes the AAindex symbol property table.
AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex
  Iterator over `AAindex` objects that are stored in a stream in the AAindex1 file format.
AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
  Initializes the iterator.
AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
  Initializes the iterator.
ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
  An abbreviation of the journal title.
ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
  The magic number for ABIF files.
ABIFChromatogram - Class in org.biojava.bio.program.abi
  An implementation of `Chromatogram` to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700.
ABIFChromatogram() - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram
ABIFChromatogram.Parser - Class in org.biojava.bio.program.abi
  An extension of `ABIFParser` that reads the particular fields from the ABIF that contain the chromatogram data and initializes the fields in its enclosing `ABIFChromatogram` instance.
ABIFChromatogram.Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
ABIFChromatogram.Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
ABIFParser - Class in org.biojava.bio.program.abi
  A general base parser for files produced by ABI software.
ABIFParser(File) - Constructor for class org.biojava.bio.program.abi.ABIFParser
  Creates a new ABIFParser for a file.
ABIFParser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFParser
  Creates a new ABIFParser for an input stream.
ABIFParser(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser
  Creates a new ABIFParser for the specified `ABIFParser.DataAccess` object.
ABIFParser.DataAccess - Interface in org.biojava.bio.program.abi
  Concatenation of the `Seekable` and `DataInput` interfaces.
ABIFParser.TaggedDataRecord - Class in org.biojava.bio.program.abi
  An aggregate immutable type for an ABIF tagged data record.
ABIFParser.TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
  Creates a new TaggedDataRecord from the next 28 bytes of `din`.
ABITools - Class in org.biojava.bio.program.abi
  Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
ABITools() - Constructor for class org.biojava.bio.program.abi.ABITools
ABITrace - Class in org.biojava.bio.program.abi
  Title: ABITrace
  ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The URL constructor opens an ABI file from any URL.
ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
  The `byte[]` constructor parses an ABI file represented as a byte array.
AbiTraceRenderer - Class in org.biojava.bio.gui.sequence
  Renders an ABI trace file as a chromatogram graph.
AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html
  Abstract implementation of `AlignmentStyler`, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
AbstractAlphabet - Class in org.biojava.bio.symbol
  An abstract implementation of `Alphabet`.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
AbstractAnnotation - Class in org.biojava.bio
  A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation
  Protected no-args constructor intended for sub-classes.
AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
  Copy-constructor.
AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
  Create a new Annotation by copying the key-value pairs from a map.
AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence
  `AbstractBeadRenderer` is a an abstract base class for the creation of `FeatureRenderer`s which use a 'string of beads' metaphor for displaying features.
AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Creates a new `AbstractBeadRenderer` with no delegates.
AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Creates a new `AbstractBeadRenderer` object.
AbstractBioEntryDB - Class in org.biojavax.bio.db
  An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
AbstractChangeable - Class in org.biojava.utils
  Useful base-class for objects implementing Changeable
AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
AbstractChromatogram - Class in org.biojava.bio.chromatogram
  A basic, abstract implementation of `Chromatogram`.
AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
  Create a new AbstractChromatogram.
AbstractCrossOverFunction - Class in org.biojavax.ga.functions
  Abstract implementation of `CrossOverFunction`.
AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
AbstractDistribution - Class in org.biojava.bio.dist
  An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
AbstractFeatureHolder - Class in org.biojava.bio.seq
  An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl
  Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
AbstractLocation - Class in org.biojava.bio.symbol
  An abstract implementation of `Location`.
AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
AbstractLocationDecorator - Class in org.biojava.bio.symbol
  Abstract `Location` decorator (wrapper).
AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
  Construct a new decorator wrapping the specified Location.
AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol
  an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
AbstractMutationFunction - Class in org.biojavax.ga.functions
  Abstract implementation of `MutationFunction` all custom implementations should inherit from here.
AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
AbstractOrderNDistribution - Class in org.biojava.bio.dist
  Simple base class for OrderNDistributions.
AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
  Construct a new NthOrderDistribution.
AbstractOrganism - Class in org.biojavax.ga.impl
  Abstract implementation of Organism.
AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene
  An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene
  represents the Homologene Group.
AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
  A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
AbstractPopulation - Class in org.biojavax.ga.impl
  Most Population implementations will want to inherit from here.
AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
AbstractRangeLocation - Class in org.biojava.bio.symbol
  Base class for simple contiguous Location implementations.
AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol
  an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
AbstractRichSequenceDB - Class in org.biojavax.bio.db
  An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
AbstractSelectionFunction - Class in org.biojavax.ga.functions
  Abstract implementation of `FitnessFunction`.
AbstractSelectionFunction() - Constructor for class org.biojavax.ga.functions.AbstractSelectionFunction
AbstractSequenceDB - Class in org.biojava.bio.seq.db
  An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
AbstractSVMClassifierModel - Class in org.biojava.stats.svm
  Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
AbstractSVMTarget - Class in org.biojava.stats.svm
  An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
AbstractSymbol - Class in org.biojava.bio.symbol
  The base-class for Symbol implementations.
AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
AbstractSymbolList - Class in org.biojava.bio.symbol
  Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol
  This adapter screens all edit events to see if they overlap with a window of interest.
AbstractSymbolList.EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
  This translates edit events that fall within a window into window co-ordinates.
AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
AbstractTaxon - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
AbstractTerm - Class in org.biojava.ontology
  Abstract implementation of term
AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
AbstractTrainer - Class in org.biojava.bio.dp
  An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
abstractType - Variable in class org.biojava.bibliography.BiblioDescription
  It specifies how `BiblioDescription.theAbstract` is coded.
AbstractULAlignment - Class in org.biojava.bio.alignment
AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
AbstractULAlignment.LeftRightLocationComparator - Class in org.biojava.bio.alignment
  Orders by location left to right.
AbstractULAlignment.LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
AbstractULAlignment.SubULAlignment(Set, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
AbstractWrapper - Class in org.biojava.bio.program.tagvalue
  An abstract TagValueWrapper that does nothing!
AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
accept(Object) - Method in interface org.biojava.bio.CollectionConstraint
  `accept` returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
  Return whether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
accept(Object) - Method in interface org.biojava.bio.PropertyConstraint
  `accept` returns true if the value fulfills the constraint.
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
  returns a TriState indicating the current outcome of evaluating this filter.
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
accept(Object) - Method in interface org.biojava.bio.search.FilterTest
accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
  This method determines whether a feature is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
  Accept a Feature if it is an instance of SimilarityPairFeature and its score is <= filter's minimum score and >= filter's maximum score.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
  Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
  Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
  Accept the Feature if it is an instance of FramedFeature and matches the value of getFrame().
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
  Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
  Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
  Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
  Accept the Feature if it is an instance of StrandedFeature and matches the value of getStrand().
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
  Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
  Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
  Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
  Returns true if the feature has a matching source property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
  Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
  Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
  Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
  Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
  Returns true if the feature overlaps this filter's location.
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
  A GFFRecordFilter that accepts everything.
ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the accession number of the AAindex entry.
AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd
  `AcnumHitReader` reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader
  Creates a new `AcnumHitReader`.
AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd
  `AcnumTrgReader` reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
  Creates a new `AcnumTrgReader`.
ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
  Use this to define acronyms for things.
ACRONYM - Static variable in interface org.biojavax.Namespace
activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener
  Notification of errors behind the scenes.
ActivityListener - Interface in org.biojava.utils
  Interface for object which monitor long-running activities.
activityProgress(Object, int, int) - Static method in class org.biojava.bio.program.das.DAS
activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
  Estimated progress of an activity.
add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Add a comment to the end of this set.
add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Add a GFFRecord to the end of this set.
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
add(int, int, int, int) - Method in class org.biojava.bio.structure.align.helper.JointFragments
add(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  add two atoms ( a + b).
add(Object) - Method in class org.biojava.utils.FileAsList
add(Object) - Method in class org.biojava.utils.MergingSet
add(Object) - Method in class org.biojava.utils.SmallSet
add(Object) - Method in class org.biojavax.ga.util.WeightedSet
  Adds a new `Object` with a weight of zero.
ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
addActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools
  Add features to a sequence that contain the same information as all those in a feature holder.
addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
  Add a new Annotation to to the end of the list to be merged.
addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
  Add a DB to be merged in this view.
addAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
addAtom(Atom) - Method in interface org.biojava.bio.structure.Group
  add an atom to this group.
addAtom(Atom) - Method in class org.biojava.bio.structure.HetatomImpl
  add an atom to this group.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Adds a sequence to the database.
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
  Add a BioEntry, the name of the BioEntry will be used as the ID
addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
addBlock(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  Add a "Block" Annotation.
addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
  Add a configuration as the most default place to look.
addChain(Chain) - Method in interface org.biojava.bio.structure.Structure
  add a new chain.
addChain(Chain, int) - Method in interface org.biojava.bio.structure.Structure
  add a new chain, if several models are available.
addChain(Chain) - Method in class org.biojava.bio.structure.StructureImpl
  add a new chain.
addChain(Chain, int) - Method in class org.biojava.bio.structure.StructureImpl
  add a new chain, if several models are available.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addChangeListener` adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addChangeListener` adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addChangeListener` adds a listener for all types of change.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addChangeListener` adds a listener for specific types of change.
addChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Add a ChangeListener to a projected feature.
addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
  Deprecated. use addChangeListener(cl, ChangeType.UNKNOWN)
addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
  Add a listener that will be informed of changes of a given type.
addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
  Add a listener that will be informed of all changes.
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
  Add a listener that will be informed of changes of a given type (and it's subtypes)
addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Add a listener that will be informed of all changes. IGNORED
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Add a listener that will be informed of changes of a given type. IGNORED
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Add a taxon as a child to a parent.
addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
  Add a cluster to a database.
addComment(Comment) - Method in interface org.biojavax.bio.BioEntry
  Adds a comment instance to this bioentry.
addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
  Adds a comment instance to this bioentry.
addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Registers that sym was counted in this state.
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Registers that sym was counted in this state.
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
  Deprecated.
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
  Add 'count' to the transition from->to.
addDasURL(URL) - Method in class org.biojava.bio.program.das.DAS
addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
  Add a distributed data source.
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
  add @param id
addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
  Adds a descriptor.
addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Adds a descriptor.
addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Extend this FeatureSetHandler to delegate certain detail elements to the specified handler type.
addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest
  Adds peptides as features to the Sequence in this class.
addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `addEnzyme` adds an enzyme to be searched for in the `Sequence`.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
  Add a silent optimisable transition to instance.
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addExtension(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
  define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
  add a known File extension.
addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
  Add a feature to the featureholder
addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Extend this FeatureSetHandler to delegate certain feature elements to the specified handler type.
addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
  Add an extra FeatureHolder to the set of FeatureHolders which are merged.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener of a feature property.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
  Add an annotation-bundle entry to the feature.
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Null implementation
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener of a feature property.
addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureHolder
  Adds a relationship to this feature holder.
addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Adds a relationship to this feature holder.
addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
  Add sequences from a file to the sequence database.
addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Add a gap at pos within the source coordinates.
addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Add a single gap at pos within the view coordintates.
addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Add length gaps at pos within the source coordinates.
addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Add length gaps at pos within the view coordinates.
addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
addGroup(Group) - Method in interface org.biojava.bio.structure.Chain
  add a group to this chain.
addGroup(Group) - Method in class org.biojava.bio.structure.ChainImpl
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Adds a feature to the Handler attribute of the StAXFeatureHandler object
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
  The `addHitProperty` method adds a key/value pair containing some property of a particular hit.
addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap
  `addHotSpot` adds a hotspot to the map.
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
  Install a new mapping from a class of Feature.Template to a class of Feature implementations.
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `addKey` adds a new identifier namespace.
addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model
  Add a key and a path to that key in the tag-value hierachy.
addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Add a piece of text to this renderer's label
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
  Add a silent persistent transition to instance.
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
  add a ChangeListener associated with given key.
addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
addMatrix(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  add Annotation of DAS alignment "matrix" type.
addModel(List) - Method in interface org.biojava.bio.structure.Structure
  add a new model.
addModel(List) - Method in class org.biojava.bio.structure.StructureImpl
  add a new model.
addName(Connection, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Adds a new name of the given `nameClass` to the taxon.
addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Adds the name to this taxon in the given name class.
addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Adds the name to this taxon in the given name class.
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton
  Add a node to the FA.
addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
  Adds a note to this annotation. You can not add Notes to the Empty RichAnnotation object.
addNote(Note) - Method in interface org.biojavax.RichAnnotation
  Adds a note to this annotation.
addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
  Adds a note to this annotation.
addObject(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  add Annotation of DAS alignment "object" type.
addOntology(Ontology) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganism(Organism) - Method in interface org.biojavax.ga.Population
  Adds an Organism to the Population
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
  Adds several organisms to the population
addOrganisms(Set) - Method in interface org.biojavax.ga.Population
  Adds several organisms to the population
addOrganisms(Population) - Method in interface org.biojavax.ga.Population
  Adds the residents of one population to this one
addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
  Add an orthologue to the set.
addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  add a property to the current Orthologue
addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  adds a specified OrthoPair relationship to this group.
addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  add a property to the current OrthoPair
addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
  Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
  Adds a parse error listener to the list of listeners.
addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz
  add the specified regex to the patterns used for searching.
addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search
  add a search pattern to the searches to be conducted by this object.
addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search
  add a search pattern to the searches to be conducted by this object.
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
  Add a value to the specified property slot.
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
  Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Adds a ranked cross reference to the existing set.
addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
  Adds a ranked cross reference to the existing set.
addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
  Adds a ranked docref instance to this bioentry.
addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
  Adds a ranked docref instance to this bioentry.
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
  Adds a relation instance to this bioentry.
addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
  Adds a relation instance to this bioentry.
addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
  `addRenderer` adds a renderer as a new track.
addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `addRenderer` adds a renderer.
addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
  Add a repository to FeatureTypes.
addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool
  `addRequest` requests that a `Runnable` be scheduled to be run by one of the threads in the pool.
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
  Add a sequence.
addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
  Adds a sequence to the database.
addScore(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  adds a "Score" Annotation.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
  The `addSearchProperty` method adds a key/value pair containing some property of the overall search result.
addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
  Add a secondary key.
addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  add a new a alignment usings a location to the reference sequence.
addSequence(Sequence) - Method in class org.biojava.bio.program.das.DASSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
  `addSequence` always throws a `ChangeVetoException` as this implementation is immutable.
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
  Add a sequence under a particular id.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
  Adds a sequence to the database.
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB
  Not supported, You can't add sequences to a WebDB!
addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Add a sequence into the tree.
addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
  As this is a dummy implementation adding a sequenceDB doesn't do anything
addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
  `addSequenceDB` adds a new `SequenceDB` under its own identifier which will additionally be recognised by the set of other identifiers.
addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  This method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  `addSequenceDB` adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
  Add an annotation-bundle entry to the sequence.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Notify the listener of a sequence-wide property.
addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener of a sequence-wide property.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerListener` adds a listener for mouse click `SequenceViewerEvent`s.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addSequenceViewerListener` adds a listener for mouse click `SequenceViewerEvent`s.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerMotionListener` adds a listener for mouse motion `SequenceViewerEvent`s.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addSequenceViewerMotionListener` adds a listener for mouse motion `SequenceViewerEvent`s.
addSet(Set) - Method in class org.biojava.utils.MergingSet
addState(State) - Method in interface org.biojava.bio.dp.MarkovModel
  Adds a state to the model.
addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
addState(State) - Method in class org.biojava.bio.dp.WMAsMM
addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Add a colour style to this Styler.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
  The `addSubHitProperty` method adds a key/value pair containing some property of a particular subhit.
addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
  Adds a symbol to this alphabet.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Add a new Symbol to the end of this list.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  `SoftMaskedAlphabet`s cannot add new `Symbol`s.
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  tool to construct the SymbolList by adding Symbols.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  Deprecated.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener of symbol data.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
  does nothing for now.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Prints out the sequences properties in order.
addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree
  Add a count for all motifs with length of up to `window` to this tree.
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener of symbol data.
addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
addSynonym(Object) - Method in interface org.biojava.ontology.Term
  Add a synonym for this term.
addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Add a synonym for this term. Synonyms are stored in the database as the results of a toString() operation on each synonym object.
addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Add a synonym for this term. NOT IMPLEMENTED
addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Adds a symbol property table to the database.
addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Add a tag to retain.
addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
  Add a configuration as the most authoritative place to look.
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory
  Register a type as being a 'container' class.
addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
  Add Variable modifications.
addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
  Add Variable modifications.
addVector(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  add Annotation of DAS alignment "vector" type.
addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Register a writer for the specified class of collection constraint
addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Register a writer for a singleton property constraint.
addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Add a writer for the specified class of filters
addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Add a writer for a singleton filter.
addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Register a writer for the specified class of property constraint
addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Register a writer for a singleton property constraint.
addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
  add @param xref
addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState
  This signals that the advance array has been altered.
advance() - Method in interface org.biojava.bio.dp.MarkovModel
  The maximum advance for this model.
advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  Advance.
advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
advance() - Method in class org.biojava.bio.dp.WMAsMM
affiliation - Variable in class org.biojava.bibliography.BiblioPerson
  Their affiliation.
Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
  Dumping the data from biojava with source of agave into agave format
AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with alternate sequence IDs
AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave
  This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <bio_sequence> element
AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <chromosome> element
AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <contig> element
AGAVEDbId - Class in org.biojava.bio.seq.io.agave
AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave
  this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with database crossreferences
AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with database crossreferences
AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave
  An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
AGAVEHandler - Class in org.biojava.bio.seq.io.agave
  Handles the root AGAVE element modified for agave format
AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with AGAVE keywords
AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with match_align
AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with match_desc
AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave
  match_region
AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with match_region
AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <mrna> element
AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with note
AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave
  Handles the AGAVE <predicted_protein> element
AGAVEProperty - Class in org.biojava.bio.seq.io.agave
AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
  construct..
AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
  sci_property
AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave
  seq_feature
AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave
  seq_location
AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave
  sequence_map
AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with sequence code
AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave
  transcript
AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave
  unordered_fragments
AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave
  Moves view attributes into annotation properties.
AgaveWriter - Class in org.biojava.bio.seq.io.agave
  Writes Sequence into AGAVE XML document.
AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
  Default constructor uses generic annotation to attribute mapping.
AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
  Construct with data source specific annotation to attribute mapping.
AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave
  Implements indenting for elements.
AgaveWriter.Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
AGAVEXref - Class in org.biojava.bio.seq.io.agave
  xref
AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave
  handle AGAVE xref
AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave
  xref_property
AGAVEXrefs - Class in org.biojava.bio.seq.io.agave
  xrefs
AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave
  Deals with database crossreferences (xrefs)
Aggregator - Class in org.biojava.bio.program.tagvalue
  Joins multipel values into single values.
Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
ala() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Alanine (A)
ALIGFACTOR - Static variable in class org.biojava.bio.structure.align.pairwise.Gotoh
AligMatEl - Class in org.biojava.bio.structure.align.helper
AligMatEl() - Constructor for class org.biojava.bio.structure.align.helper.AligMatEl
align(Structure, Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
  calculate the actual protein structure superimposition.
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.bio.structure.align.pairwise.AligNPE
  Align w/o penalizing endpags.
Alignable - Interface in org.biojava.bio.structure.align.pairwise
alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.SequenceAlignment
AlignIOConstants - Class in org.biojava.bio.seq.io
  `AlignIOConstants` contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
alignment - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
Alignment - Class in org.biojava.bio.program.das.dasalignment
  Alignment object to contain/manage a DAS alignment.
Alignment() - Constructor for class org.biojava.bio.program.das.dasalignment.Alignment
  Construct a new empty Alignment object.
ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology
  Signals that the alignment describing the homologous sequences has changed.
alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `alignment` `Alignment` field.
Alignment - Interface in org.biojava.bio.symbol
  An alignment containing multiple SymbolLists.
alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews
  Construct an alignment of the SymbolLists contained in the values collection of `labelToSymList`.
alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
  View a SymbolList over a cross-product Alphabet as an Alignment.
Alignment.SymbolListIterator - Class in org.biojava.bio.symbol
  Iterator implementation looping over symbol lists in an alignment using the labels.
Alignment.SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.symbol.Alignment.SymbolListIterator
ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
AlignmentElement - Interface in org.biojava.bio.alignment
  AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentFormat - Interface in org.biojava.bio.seq.io
AlignmentMarker - Class in org.biojava.bio.program.blast2html
  Class to do simple HTML colouring of sequence alignments.
AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker
  Creates a new `AlignmentMarker` instance.
alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
AlignmentRenderer - Class in org.biojava.bio.gui.sequence
AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
AlignmentStAXHandler - Class in org.biojava.bio.program.ssbind
  `AlignmentStAXHandler` handles the BlastLikeAlignment element of BioJava BlastLike XML.
AligNPE - Class in org.biojava.bio.structure.align.pairwise
AligNPE() - Constructor for class org.biojava.bio.structure.align.pairwise.AligNPE
AlignTools - Class in org.biojava.bio.structure.align.helper
AlignTools() - Constructor for class org.biojava.bio.structure.align.helper.AlignTools
ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
all - Static variable in interface org.biojava.bio.seq.FeatureFilter
  All features are selected by this filter.
all() - Static method in class org.biojava.bio.seq.FilterUtils
  Return a filter which matches all features.
ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
  All features are selected by this filter.
allEntryPointsDB() - Method in class org.biojava.bio.program.das.DASSequenceDB
allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  make sure that all Symbols in this range are gaps
allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  Destructive down-cast an annotation to a type.
allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  `allOut` returns a new `Annotation` containing only those values in the `Annotation` argument which are not of a type specified by the `AnnotationType`.
alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
alphabet - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
Alphabet - Interface in org.biojava.bio.symbol
  The set of AtomicSymbols which can be concatenated together to make a SymbolList.
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve the alphabet for a specific name.
AlphabetIndex - Interface in org.biojava.bio.symbol
  Map between Symbols and index numbers.
AlphabetManager - Class in org.biojava.bio.symbol
  Utility methods for working with Alphabets.
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
AlphabetResolver - Class in org.biojava.bio.program.ssbind
  `AlphabetResolver`s are helpers which determine which type of sequence `Alphabet` to expect from a search result.
AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get an iterator over all alphabets known.
AlphaCTools - Class in org.biojava.bio.structure
  AlphaCTools is a collection of static convenience methods for dealing with Alpha Carbon Backbone Phi / Psi angles.
AlphaCTools() - Constructor for class org.biojava.bio.structure.AlphaCTools
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
AlreadyExistsException - Exception in org.biojava.ontology
  Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the alternative yeast nuclear genetic code.
AltAligComparator - Class in org.biojava.bio.structure.align.pairwise
AltAligComparator() - Constructor for class org.biojava.bio.structure.align.pairwise.AltAligComparator
ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
AlternativeAlignment - Class in org.biojava.bio.structure.align.pairwise
  Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener
  Convenience implementation which vetoes every change of which it is notified.
AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `AMBIGUOUS` indicates that a sequence contains ambiguity symbols.
AminoAcid - Interface in org.biojava.bio.structure
  AminoAcid inherits most from Hetatom.
AminoAcidImpl - Class in org.biojava.bio.structure
  AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.bio.structure.AminoAcidImpl
aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
amount(Atom) - Static method in class org.biojava.bio.structure.Calc
  amount.
and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a new filter which matches the intersection of two other filters.
and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
  Constructs a new filter which matches the intersection of a set of filters.
and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
angle(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  angle.
annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
Annotatable - Interface in org.biojava.bio
  Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder - Class in org.biojava.bio
  Deprecated. use `new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)` instead
Annotatable.AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder
  Deprecated. Create a new AnnotationForwarder that will forward events for a source using a change support.
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `annotate` adds `Feature`s which represent restriction sites.
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
  Return an annotated version of a sequence.
ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
AnnotatedSequenceDB - Class in org.biojava.bio.seq.db
  SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
  Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools
  Annotates a sequence with the features from a GFF entry set.
annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
  Annotates all sequences in a sequence DB with features from a GFF entry set.
annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
ANNOTATION - Static variable in interface org.biojava.bio.Annotatable
  Signals that the associated Annotation has altered in some way.
Annotation - Interface in org.biojava.bio
  Arbitrary annotation associated with one or more objects.
annotation - Variable in class org.biojava.bio.seq.Feature.Template
annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation
  ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation
  ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation
  ChangeType of ChangeEvent fired before and after an annotation is added to MergeAnnotation.
AnnotationBuilder - Class in org.biojava.bio.program.tagvalue
  Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder
  Make a new AnnotationBuilder that will build Annotation instances of a given type.
AnnotationChanger - Class in org.biojava.bio
  `AnnotationChanger` remaps the values of an `Annotation` to new values specified by a `ValueChanger`.
AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger
  Creates a new `AnnotationChanger` using the specified `ValueChanger` to remap its values.
AnnotationDB - Interface in org.biojava.bio.annodb
  A database of Annotation instances.
AnnotationFactory - Class in org.biojava.bio.program.ssbind
  `AnnotationFactory` is a utility class for making `Annotation`s from `Map`s.
AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
annotationForwarder - Variable in class org.biojava.bio.program.das.DASSequence
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
AnnotationRenamer - Class in org.biojava.bio
  `AnnotationRenamer` remaps the keys of an `Annotation` to new keys specified by a `TagMapper`.
AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer
  Creates a new `AnnotationRenamer` using the specified `TagMapper` to remap its keys.
ANNOTATIONS - Static variable in class org.biojava.bio.program.das.DASSequence
  Change type which indicates that the set of annotation servers used by this DASSequence has been changed.
AnnotationTools - Class in org.biojava.bio
  `AnnotationTools` is a set of static utility methods for manipulating `Annotation`s and `AnnotationType`s.
AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
AnnotationType - Interface in org.biojava.bio
  A set of constraints on the data contained in an `Annotation`.
AnnotationType.Abstract - Class in org.biojava.bio
  An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
AnnotationType.Impl - Class in org.biojava.bio
  An implementation of `AnnotationType`.
AnnotationType.Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with no constraints.
AnnotationType.Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with a default property and cardinality constraint.
AnnotationType.Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl
  Create a new Impl with a default collection constraint.
ANNOTATOR - Static variable in class org.biojava.bio.program.das.ReferenceServer
ANY - Static variable in interface org.biojava.bio.AnnotationType
  The type that accepts all annotations and is the supertype of all other annotations.
ANY - Static variable in class org.biojava.bio.CardinalityConstraint
  The property can have any number of values, including none.
ANY - Static variable in interface org.biojava.bio.CollectionConstraint
  `ANY` is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in interface org.biojava.bio.PropertyConstraint
  `ANY` is a constraint which accepts a property for addition under all conditions.
ANY - Static variable in class org.biojava.ontology.OntoTools
apairs_from_idxlst(JointFragments) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  Set apairs according to a seed position.
AppBeanRunner - Class in org.biojava.utils.xml
  Create a bean from an XML file, then attempt to enter it.
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
AppEntry - Interface in org.biojava.utils.xml
AppException - Exception in org.biojava.utils.xml
AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
applicants - Variable in class org.biojava.bibliography.BiblioPatent
  Array of applicants.
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
ARAlignment - Interface in org.biojava.bio.alignment
  ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel
  Signals that the architecture of the model is changing.
arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Determines if two queries can be proven to be disjoint.
areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Compares the emission spectra of two distributions.
areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Compares the emission spectra of two distribution arrays.
areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Decide if two feature filters accept exactly the same set of features.
areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return whether two locations are equal.
areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Determines if the set of features matched by sub can be `proven` to be a proper subset of the features matched by sup.
arg() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Arginine (R)
ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
arrayLeftDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element right division in place, A = A./B
ArrayStateMachineToolkit - Class in org.biojava.utils.automata
arrayTimes(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Element-by-element multiplication in place, A = A.*B
ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence
  A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
ArrowGlyph - Class in org.biojava.bio.gui.glyph
  A Glyph that paints an arrow shape within the bounds.
ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the ascidian mitochondrial genetic code.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
asCriterion() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
  This method returns a Hibernate Criterion object that can be used to query the database.
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
asMap() - Method in class org.biojava.bio.AbstractAnnotation
asMap() - Method in interface org.biojava.bio.Annotation
  Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojava.bio.MergeAnnotation
asMap() - Method in class org.biojava.bio.OverlayAnnotation
  Return a `Map` view onto this annotation.
asMap() - Method in class org.biojavax.EmptyRichAnnotation
  Return a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojavax.ga.util.WeightedSet
  Converts the Set to a map from key `Objects` to `Double` weights.
asMap() - Method in class org.biojavax.SimpleRichAnnotation
  Return a map that contains the same key/values as this Annotation. The map is a copy of the internal structure.
asn() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Asparagine (N)
asp() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Aspartic Acid (D)
ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
AssembledSymbolList - Class in org.biojava.bio.seq.impl
  Support class for applications which need to patch together sections of sequence into a single SymbolList.
AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
AssertionFailure - Error in org.biojava.utils
  An unchecked exception representing an Assertion failure.
AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
Atom - Interface in org.biojava.bio.structure
  simple interface of an Atom.
AtomicSymbol - Interface in org.biojava.bio.symbol
  A symbol that is not ambiguous.
AtomImpl - Class in org.biojava.bio.structure
  Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.bio.structure.AtomImpl
AtomIterator - Class in org.biojava.bio.structure
  an iterator over all atoms of a structure / group.
AtomIterator(Structure) - Constructor for class org.biojava.bio.structure.AtomIterator
  Constructs an AtomIterator object.
AtomIterator(Group) - Constructor for class org.biojava.bio.structure.AtomIterator
  Constructs an AtomIterator object.
attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Attempt to close the Statement.
attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Attempt to close the ResultSet.
ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name, or a part of a vocabulary name.
ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A part of a vocabulary name.
ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name, or a part of a vocabulary name.
attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Add an attribute to an element.
attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Add an un-qualified attribute to an element.
AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORITY - Static variable in interface org.biojavax.Namespace
authors - Variable in class org.biojava.bibliography.BibRef
  The authors and contributors are responsible for creating the contents of the cited resource.
AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
automaticUpdate(Connection, DBHelper, TaxonFactory, File, File) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. This method tries to perform a complete update according to the given `TaxonFactory`, which already contains the newes taxa and the files available at the NCBI-FTP-Site.
AutomatonException - Exception in org.biojava.utils.automata
  An exception thrown by classes of this package.
AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
available() - Method in class org.biojava.utils.io.UncompressInputStream
average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Averages two or more distributions.
AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable

## B

b() - Static method in class org.biojava.bio.seq.NucleotideTools
B_TAURUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
back - Variable in class org.biojava.bio.dp.BackPointer
  The previous backpointer (towards origin of DP matrix) in traceback.
backboneAtomNames - Static variable in class org.biojava.bio.structure.StructureTools
BackMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
BackMatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
BackPointer - Class in org.biojava.bio.dp
  A backpointer.
BackPointer(State, BackPointer, double) - Constructor for class org.biojava.bio.dp.BackPointer
BackPointer(State) - Constructor for class org.biojava.bio.dp.BackPointer
backPointers - Variable in class org.biojava.bio.dp.twohead.Cell
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_recurse(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backward_termination(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
backwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
backwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
backwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
backwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat
  This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.StreamReader
  This method determines the behaviour when a bad line is processed.
BadLineParsed(ParseErrorEvent) - Method in interface org.biojava.utils.ParseErrorListener
  Method called when the parser encounters a bad line.
BarLogoPainter - Class in org.biojava.bio.gui
  A logo painter that paints in bars.
BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
BASE_COUNT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
BASE_COUNT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASE_COUNT_TAG_FULL - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
BASEPOSITION_EXTENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BASEPOSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BASEPOSITION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
BaseXMLWriter - Class in org.biojava.bio.program.xml
  Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
BaseXMLWriter() - Constructor for class org.biojava.bio.program.xml.BaseXMLWriter
BasicFeatureRenderer - Class in org.biojava.bio.gui.sequence
BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
BasicImapRenderer - Class in org.biojava.bio.gui.sequence
  `BasicImapRenderer` is a decorator for `BasicFeatureRenderer` which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the `BasicFeatureRenderer`.
BasicImapRenderer(BasicFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.BasicImapRenderer
  Creates a new `BasicImapRenderer`.
BasicXFFHelper - Class in org.biojava.bio.program.xff
BasicXFFHelper() - Constructor for class org.biojava.bio.program.xff.BasicXFFHelper
BasisSymbol - Interface in org.biojava.bio.symbol
  A symbol that can be represented as a string of Symbols.
BaumWelchSampler - Class in org.biojava.bio.dp
  Train a hidden markov model using a sampling algorithm.
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
BaumWelchTrainer - Class in org.biojava.bio.dp
  Train a hidden markov model using maximum likelihood.
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
beadDepth - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadDisplacement - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
BeadFeatureRenderer - Interface in org.biojava.bio.gui.sequence
  `BeadFeatureRenderer`s use a 'string of beads' metaphor for displaying features.
beadFill - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadOutline - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
beadStroke - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
BeanAsAnnotation - Class in org.biojava.bio
  Create an Annotation with properties matching those of a JavaBean instance.
BeanAsAnnotation(Object) - Constructor for class org.biojava.bio.BeanAsAnnotation
  Create a new BeanAsAnnotation for a bean.
BeanAsMap - Class in org.biojava.utils
BeanAsMap(Object) - Constructor for class org.biojava.utils.BeanAsMap
beginWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Informs the writer that we want to start writing.
beginWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
  Informs the writer that we want to start writing.
beginWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Informs the writer that we want to start writing.
BETWEEN_BASES - Static variable in interface org.biojavax.bio.seq.Position
  A symbol representing a position that falls in between two bases, eg.
BetweenLocation - Class in org.biojava.bio.symbol
  Between view onto an underlying Location instance.
BetweenLocation(Location) - Constructor for class org.biojava.bio.symbol.BetweenLocation
BiblioArticle - Class in org.biojava.bibliography
  It represents an article.
BiblioArticle() - Constructor for class org.biojava.bibliography.BiblioArticle
BiblioBook - Class in org.biojava.bibliography
  It represents a book.
BiblioBook() - Constructor for class org.biojava.bibliography.BiblioBook
BiblioBookArticle - Class in org.biojava.bibliography
  It represents a book article.
BiblioBookArticle() - Constructor for class org.biojava.bibliography.BiblioBookArticle
BiblioCriterion - Class in org.biojava.bibliography
  The criteria define how the matching or ordering should be done during queries.
BiblioCriterion() - Constructor for class org.biojava.bibliography.BiblioCriterion
BiblioDescription - Class in org.biojava.bibliography
  It represents an account of the content of the cited resource.
BiblioDescription() - Constructor for class org.biojava.bibliography.BiblioDescription
BiblioEntryStatus - Class in org.biojava.bibliography
  It defines information related to the citation itself rather than to the cited resource.
BiblioEntryStatus() - Constructor for class org.biojava.bibliography.BiblioEntryStatus
BiblioJournal - Class in org.biojava.bibliography
  A class describing journals.
BiblioJournal() - Constructor for class org.biojava.bibliography.BiblioJournal
BiblioJournalArticle - Class in org.biojava.bibliography
  It represents a journal article.
BiblioJournalArticle() - Constructor for class org.biojava.bibliography.BiblioJournalArticle
BiblioOrganisation - Class in org.biojava.bibliography
  It represents an organisation dealing with the bibliographic resources.
BiblioOrganisation() - Constructor for class org.biojava.bibliography.BiblioOrganisation
BiblioPatent - Class in org.biojava.bibliography
  It represents a patent.
BiblioPatent() - Constructor for class org.biojava.bibliography.BiblioPatent
BiblioPerson - Class in org.biojava.bibliography
  It represents a person dealing with the bibliographic resources.
BiblioPerson() - Constructor for class org.biojava.bibliography.BiblioPerson
BiblioProceeding - Class in org.biojava.bibliography
  It represents a conference proceeding.
BiblioProceeding() - Constructor for class org.biojava.bibliography.BiblioProceeding
BiblioProvider - Class in org.biojava.bibliography
  This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
BiblioProvider() - Constructor for class org.biojava.bibliography.BiblioProvider
BiblioScope - Class in org.biojava.bibliography
  It represent an extent or scope of the content of the cited resource.
BiblioScope() - Constructor for class org.biojava.bibliography.BiblioScope
BiblioService - Class in org.biojava.bibliography
  It represents a service dealing with the bibliographic resources.
BiblioService() - Constructor for class org.biojava.bibliography.BiblioService
BiblioSubject - Class in org.biojava.bibliography
  It represents the topic of the content of the cited resource.
BiblioSubject() - Constructor for class org.biojava.bibliography.BiblioSubject
BiblioTechReport - Class in org.biojava.bibliography
  It represents a technical report.
BiblioTechReport() - Constructor for class org.biojava.bibliography.BiblioTechReport
BiblioThesis - Class in org.biojava.bibliography
  It represents a thesis.
BiblioThesis() - Constructor for class org.biojava.bibliography.BiblioThesis
BiblioWebResource - Class in org.biojava.bibliography
  It represents a WWW resource.
BiblioWebResource() - Constructor for class org.biojava.bibliography.BiblioWebResource
BibRef - Class in org.biojava.bibliography
  This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
BibRef() - Constructor for class org.biojava.bibliography.BibRef
BibRefException - Exception in org.biojava.bibliography
  An exception raised when communciation with the BibRef APIs fails.
BibRefException(String) - Constructor for exception org.biojava.bibliography.BibRefException
  Create a new BibRefException with a message.
BibRefException(Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
  Create a new BibRefException with a root cause.
BibRefException(String, Throwable) - Constructor for exception org.biojava.bibliography.BibRefException
  Create a nw BibRefException with a message and a root cause.
BibRefQuery - Interface in org.biojava.bibliography
  The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport - Interface in org.biojava.bibliography
  This interface defines supporting utilities for working with bibliographic repositories.
binary(long) - Static method in class org.biojava.bio.symbol.PackingFactory
binary(int) - Static method in class org.biojava.bio.symbol.PackingFactory
BinarySearch - Class in org.biojava.utils.math
  solves y = f(x) = 0 by binary search.
BinarySearch() - Constructor for class org.biojava.utils.math.BinarySearch
bind(Name, Object) - Method in class org.biojava.naming.ObdaContext
bind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bind(String, Object) - Method in class org.biojava.naming.ObdaContext
bind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
bindSymbol(Symbol, char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
  Bind a Symbol to a character.
BioEntry - Interface in org.biojavax.bio
  This class relates to the bioentry table in BioSQL.
BioEntryDB - Interface in org.biojavax.bio.db
  .
BioEntryDBLite - Interface in org.biojavax.bio.db
  A database of BioEntrys.
BioEntryIterator - Interface in org.biojavax.bio
  Essentially the same as SequenceIterator.
BioEntryRelationship - Interface in org.biojavax.bio
  Represents the relation between two bioentries.
BIOENTRYS - Static variable in interface org.biojavax.bio.db.BioEntryDBLite
  Signals that sequences are being added to or remove from the database.
BioError - Error in org.biojava.bio
  A nestable biological error.
BioError(String) - Constructor for error org.biojava.bio.BioError
  Create a new BioError with a message.
BioError(Throwable) - Constructor for error org.biojava.bio.BioError
  Create a new BioError with a cause.
BioError(Throwable, String) - Constructor for error org.biojava.bio.BioError
  Deprecated. Use BioError(message, ex) instead.
BioError(String, Throwable) - Constructor for error org.biojava.bio.BioError
  Create a new BioError with a cause and a message.
BioError() - Constructor for error org.biojava.bio.BioError
  Create a new BioError.
BioException - Exception in org.biojava.bio
  A nestable biological exception.
BioException(String) - Constructor for exception org.biojava.bio.BioException
  Create a new BioException with a message.
BioException(Throwable) - Constructor for exception org.biojava.bio.BioException
  Create a new BioException with a cause.
BioException(Throwable, String) - Constructor for exception org.biojava.bio.BioException
  Deprecated. use new BioException(message, ex) instead
BioException(String, Throwable) - Constructor for exception org.biojava.bio.BioException
  Create a new BioException with a cause and a message.
BioException() - Constructor for exception org.biojava.bio.BioException
  Create a new BioException.
BioFetchSequenceDB - Class in org.biojava.bio.seq.db.biofetch
  Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
BioFetchSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
  Construct a BioFetchSequenceDB which connects to the specified BioFetch server.
BioFetchSequenceDBProvider - Class in org.biojava.bio.seq.db.biofetch
  Directory-services plugin for biofetch databases.
BioFetchSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
BioIndex - Class in org.biojava.bio.seq.db
  The original object for indexing sequence files.
BioIndex(File, String, int) - Constructor for class org.biojava.bio.seq.db.BioIndex
BioIndex(File) - Constructor for class org.biojava.bio.seq.db.BioIndex
  Load an existing index file.
biojavaToFile(String, String, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a Biojava `SequenceIterator`, `SequenceDB`, `Sequence` or `Aligment` to an `OutputStream`
biojavaToFile(int, OutputStream, Object) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Converts a Biojava object to the given filetype.
BioMatcher - Interface in org.biojava.bio.search
  Interface for things that perform matches.
BioPattern - Interface in org.biojava.bio.search
BIOPHYSICOCHEMICAL_PROPERTIES - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
BioRuntimeException - Exception in org.biojava.bio
  A nestable biological exception.
BioRuntimeException(String) - Constructor for exception org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a message.
BioRuntimeException(Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a cause.
BioRuntimeException(Throwable, String) - Constructor for exception org.biojava.bio.BioRuntimeException
  Deprecated. use new BioRuntimeException(message, ex) instead
BioRuntimeException(String, Throwable) - Constructor for exception org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException with a cause and a message.
BioRuntimeException() - Constructor for exception org.biojava.bio.BioRuntimeException
  Create a new BioRuntimeException.
BIOSEQUENCE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
BIOSEQUENCE_ORACLECLOB - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
BioSQLAcceptAllFilter - Class in org.biojavax.bio.db.biosql
  The class that accepts all features.
BioSQLAcceptAllFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
BioSQLAcceptNoneFilter - Class in org.biojavax.bio.db.biosql
  The class that accepts no features.
BioSQLAcceptNoneFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
BioSQLBioEntryDB - Class in org.biojavax.bio.db.biosql
BioSQLBioEntryDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
  Creates a new instance of BioSQLBioEntryDB
BioSQLBioEntryDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
  Creates a new instance of BioSQLBioEntryDB
BioSQLCrossReferenceResolver - Class in org.biojavax.bio.db.biosql
  A simple implementation of CrossReferenceResolver
BioSQLCrossReferenceResolver(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
  Requires a Hibernate session to work correctly.
BioSQLFeatureFilter - Interface in org.biojavax.bio.db.biosql
  A filter for accepting or rejecting a feature.
BioSQLFeatureFilter.And - Class in org.biojavax.bio.db.biosql
  A filter that returns all features accepted by both child filter.
BioSQLFeatureFilter.And(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
BioSQLFeatureFilter.ByName - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by display name.
BioSQLFeatureFilter.ByName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
  Create a ByType filter that filters in all features with type fields equal to type.
BioSQLFeatureFilter.ByNote - Class in org.biojavax.bio.db.biosql
  A filter that returns all features that have the given note, and the value and rank is checked as well.
BioSQLFeatureFilter.ByNote(Note) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
BioSQLFeatureFilter.ByNoteTermOnly - Class in org.biojavax.bio.db.biosql
  A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByNoteTermOnly(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
BioSQLFeatureFilter.ByRank - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by rank.
BioSQLFeatureFilter.ByRank(int) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
  Create a Rank filter that filters in all features with rank fields equal to rank.
BioSQLFeatureFilter.BySequenceName - Class in org.biojavax.bio.db.biosql
  Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySequenceName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
BioSQLFeatureFilter.BySourceTerm - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by source.
BioSQLFeatureFilter.BySourceTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
  Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.
BioSQLFeatureFilter.BySourceTermName - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by source (name only - parent ontology is ignored).
BioSQLFeatureFilter.BySourceTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
  Create a BySourceTerm filter that filters in all features with sourceTerm fields having name equal to sourceTermName.
BioSQLFeatureFilter.ByStrand - Class in org.biojavax.bio.db.biosql
  A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByStrand(RichLocation.Strand) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
  Creates a filter that returns everything on strand str.
BioSQLFeatureFilter.ByTypeTerm - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by type.
BioSQLFeatureFilter.ByTypeTerm(ComparableTerm) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
  Create a ByTypeTerm filter that filters in all features with typeTerm fields equal to typeTerm.
BioSQLFeatureFilter.ByTypeTermName - Class in org.biojavax.bio.db.biosql
  Construct one of these to filter features by type (name only - parent ontology is ignored).
BioSQLFeatureFilter.ByTypeTermName(String) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
  Create a ByTypeTermName filter that filters in all features with typeTerm fields having name equal to typeTermName.
BioSQLFeatureFilter.ContainedByRichLocation - Class in org.biojavax.bio.db.biosql
  A filter that returns all features contained within a location.
BioSQLFeatureFilter.ContainedByRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
  Creates a filter that returns everything contained within loc.
BioSQLFeatureFilter.HibernateFeatureFilter - Class in org.biojavax.bio.db.biosql
  A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.HibernateFeatureFilter() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
BioSQLFeatureFilter.Not - Class in org.biojavax.bio.db.biosql
  A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Not(BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
BioSQLFeatureFilter.Or - Class in org.biojavax.bio.db.biosql
  A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.Or(BioSQLFeatureFilter, BioSQLFeatureFilter) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
BioSQLFeatureFilter.OverlapsRichLocation - Class in org.biojavax.bio.db.biosql
  A filter that returns all features overlapping a location.
BioSQLFeatureFilter.OverlapsRichLocation(RichLocation) - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
  Creates a filter that returns everything overlapping loc.
BioSQLFeatureFilter.Tools - Class in org.biojavax.bio.db.biosql
  A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
BioSQLFeatureFilter.Tools() - Constructor for class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
BioSQLRichObjectBuilder - Class in org.biojavax.bio.db.biosql
  Takes requests for RichObjects and sees if it can load them from a Hibernate database.
BioSQLRichObjectBuilder(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
  Creates a new instance of SimpleRichObjectBuilder.
BioSQLRichSequenceDB - Class in org.biojavax.bio.db.biosql
BioSQLRichSequenceDB(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
  Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceDB(String, Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
  Creates a new instance of BioSQLRichSequenceDB
BioSQLRichSequenceHandler - Class in org.biojavax.bio.db.biosql
  A handler which loads sequence data from a BioSQL database, caching it where possible.
BioSQLRichSequenceHandler(Object) - Constructor for class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Requires a Hibernate session to work correctly.
BioSQLSequenceDB - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDB(String, String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated. Connect to a BioSQL database.
BioSQLSequenceDB(String, String, String, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated. Connect to a BioSQL database.
BioSQLSequenceDB(DataSource, String, boolean) - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
BioSQLSequenceDBProvider - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
  Deprecated.
BioStore - Class in org.biojava.bio.program.indexdb
  `BioStore`s represent directory and file structures which index flat files according to the OBDA specification.
BioStore(File, boolean) - Constructor for class org.biojava.bio.program.indexdb.BioStore
  Creates a new `BioStore` flatfile index at the specified location with the specified caching behaviour.
BioStoreFactory - Class in org.biojava.bio.program.indexdb
  `BioStoreFactory` creates `BioStore` instances.
BioStoreFactory() - Constructor for class org.biojava.bio.program.indexdb.BioStoreFactory
  Creates a new `BioStoreFactory`.
BIT_PACKED - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
bitsOfInformation(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Calculates the total bits of information for a distribution.
Blast2HTMLHandler - Class in org.biojava.bio.program.blast2html
  Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
Blast2HTMLHandler(HTMLRenderer) - Constructor for class org.biojava.bio.program.blast2html.Blast2HTMLHandler
  A content handler for rendering blast like outputs into HTML.
BlastLikeHomologyBuilder - Class in org.biojava.bio.program.ssbind
  `BlastLikeHomologyBuilder` populates a `List` with `Homology` instances created from SAX events supplied via a `SeqSimilarityAdapter`.
BlastLikeHomologyBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
  Creates a new `BlastLikeHomologyBuilder` which will instantiate `Homology` objects into the `List` target.
BlastLikeSAXParser - Class in org.biojava.bio.program.sax
  A facade class allowing for direct SAX2-like parsing of the native output from Blast-like bioinformatics software.
BlastLikeSAXParser() - Constructor for class org.biojava.bio.program.sax.BlastLikeSAXParser
  Initialises SAXParser, and sets default namespace prefix to "biojava".
BlastLikeSearchBuilder - Class in org.biojava.bio.program.ssbind
  `BlastLikeSearchBuilder` will create `SeqSimilaritySearchResult`s from SAX events via a `SeqSimilarityAdapter`.
BlastLikeSearchBuilder(List) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
  Creates a new `BlastLikeSearchBuilder` which will instantiate results into the `List` target.
BlastLikeSearchBuilder(List, SequenceDB, SequenceDBInstallation) - Constructor for class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
  Creates a new `BlastLikeSearchBuilder` which will instantiate results into the `List` target.
BlastLikeSearchFilter - Interface in org.biojava.bio.search
  A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter - Class in org.biojava.bio.search
BlastLikeSearchFilter.And - Class in org.biojava.bio.search
BlastLikeSearchFilter.And(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.And
BlastLikeSearchFilter.ByHitProperty - Class in org.biojava.bio.search
  Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.ByHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
BlastLikeSearchFilter.BySearchProperty - Class in org.biojava.bio.search
  Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySearchProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
BlastLikeSearchFilter.BySubHitProperty - Class in org.biojava.bio.search
  Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.BySubHitProperty(String, FilterTest) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
BlastLikeSearchFilter.Node - Interface in org.biojava.bio.search
BlastLikeSearchFilter.Not - Class in org.biojava.bio.search
BlastLikeSearchFilter.Not(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Not
BlastLikeSearchFilter.Or - Class in org.biojava.bio.search
BlastLikeSearchFilter.Or(BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.AbstractBlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.BlastLikeSearchFilter.Or
BlastLikeToXMLConverter - Class in org.biojava.bio.program
  A class that converts the raw output from a variety of bioinformatics software and converts it to XML that will validate against the biojava:BlastLikeDataSetCollection DTD.
BlastLikeToXMLConverter(String) - Constructor for class org.biojava.bio.program.BlastLikeToXMLConverter
  Creates a new `BlastToXMLConverter` instance.
BlastXMLParser - Class in org.biojava.bio.program.sax.blastxml
  This class parses NCBI Blast XML output.
BlastXMLParser() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParser
BlastXMLParserFacade - Class in org.biojava.bio.program.sax.blastxml
  A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form.
BlastXMLParserFacade() - Constructor for class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
BLEPH_MNUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the blepharisma macronuclear genetic code.
blockCount(Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the number of contiguous blocks in a location.
blockIterator() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
blockIterator() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
blockIterator() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
blockIterator() - Method in interface org.biojava.bio.symbol.Location
  Return an Iterator over the set of maximal contiguous sub-locations.
BlockIterator() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Get list of the un-gapped region of the SymbolList.
blockIterator() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Return an Iterator over the set of maximal contiguous sub-locations.

  Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.

  This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.

blockIterator() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Return an Iterator over the set of maximal contiguous sub-locations. ALWAYS RETURNS THE EMPTY SET ITERATOR
blockIterator() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Return an Iterator over the set of maximal contiguous sub-locations.
BlockPainter - Interface in org.biojava.bio.gui
BLUNT - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `BLUNT` the end type created by enzymes which leave a blunt end.
BooleanElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of an boolean.
BooleanElementHandlerBase() - Constructor for class org.biojava.utils.stax.BooleanElementHandlerBase
BOTH_FORWARD_COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
BoundaryFinder - Interface in org.biojava.bio.program.tagvalue
bPointers - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
bPointers - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  Deprecated. Converts the symbol list passed in into an array of strings.
breakSymbolArray(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Converts the symbol list passed in into an array of strings.
buildDataParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceStreamer, Packing, int, int, int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
  Build a new DataStore.
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
buildDataStore(File, SequenceDB, Packing, int, int) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
buildLibInfoParser(TagValueListener) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Generate a tag-value parser for the library info unigene files.
buildObject(Class, List) - Method in class org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder
  This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters. Attempts to look up the details of the object in the database.
buildObject(Class, List) - Method in interface org.biojavax.RichObjectBuilder
  This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters.
buildObject(Class, List) - Method in class org.biojavax.SimpleRichObjectBuilder
  This method takes a class name and some parameters, and uses that information to construct and return an equivalent object, usually by calling the constructor on the class with the supplied parameters. Instantiates and returns objects, that's all there is to it.
BumpedRenderer - Class in org.biojava.bio.gui.sequence
BumpedRenderer() - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
BumpedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
BumpedRenderer(SequenceRenderer, int, int) - Constructor for class org.biojava.bio.gui.sequence.BumpedRenderer
byAncestor(FeatureFilter.ByAncestor, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
byAncestor(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where at least one of the ancestors matches the specified filter.
byAnnotation(Object, Object) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where the annotation property named `key` is equal to `value`.
byAnnotationType(AnnotationType) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features with annotations matching the specified `AnnotationType`
byAnnotationType(Object, Class) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where the annotation property named `key` is an instance of `valClass`.
byChild(FeatureFilter.ByChild, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
byChild(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where at least one child feature matches the supplied filter.
byClass(Class) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features which are assignable to the specified class or interface.
byComponentName(String) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches all features which implement the `ComponentFeature` interface and have a `componentName` property equal to the specified value
byDescendant(FeatureFilter.ByDescendant, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
byDescendant(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where at least one decendant feature -- possibly but not necessarily an immediate child -- matches the specified filter.
byFrame(FramedFeature.ReadingFrame) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches FramedFeatures with the specified reading frame.
byHitProperty(BlastLikeSearchFilter.ByHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
ByLocationMinMaxComparator - Class in org.biojava.bio.seq
  A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
ByLocationMinMaxComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxComparator
ByLocationMinMaxFeatureComparator - Class in org.biojava.bio.seq
  Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
ByLocationMinMaxFeatureComparator() - Constructor for class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
byLocationOrder - Static variable in interface org.biojava.bio.seq.Feature
  `byLocationOrder` contains a `Feature` comparator which compares by the minimum base position of their `Location`.
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
  A simple implementation of IDMaker that hashes by sequence name.
byPairwiseScore(double, double) - Static method in class org.biojava.bio.seq.FilterUtils
  Match SeqSimilaritiy features with scores in the specified range.
byParent(FeatureFilter.ByParent, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
byParent(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where the parent feature matches the specified filter.
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
  `byScore` contains a `SeqSimilaritySearchHit` comparator which compares by their score.
byScore - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  `byScore` contains a `SeqSimilaritySearchSubHit` comparator which compares by the score of the sub-hit.
bySearchProperty(BlastLikeSearchFilter.BySearchProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
bySequenceName(String) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features attached to sequences with a specified name.
bySource(String) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with a specific `source` value.
byStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.FilterUtils
  Match StrandedFeatures on the specified strand.
bySubHitCount - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchHit
  `bySubHitCount` contains a `SeqSimilaritySearchHit` comparator which compares by their number of sub-hits.
bySubHitProperty(BlastLikeSearchFilter.BySubHitProperty) - Method in class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
bySubjectStart - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  `bySubjectStart` contains a `SeqSimilaritySearchSubHit` comparator which compares by the start position of the sub-hit on the subject sequence.
BYTE_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
  Represents the maximum unsigned value of a byte for wrapping purposes
ByteElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of a byte.
ByteElementHandlerBase() - Constructor for class org.biojava.utils.stax.ByteElementHandlerBase
BYTES_IN_BYTE - Static variable in class org.biojava.utils.Constants
BYTES_IN_CHAR - Static variable in class org.biojava.utils.Constants
BYTES_IN_DOUBLE - Static variable in class org.biojava.utils.Constants
BYTES_IN_FLOAT - Static variable in class org.biojava.utils.Constants
BYTES_IN_INT - Static variable in class org.biojava.utils.Constants
BYTES_IN_LONG - Static variable in class org.biojava.utils.Constants
BYTES_IN_SHORT - Static variable in class org.biojava.utils.Constants
byType(String) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with a specific `type` value.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
  A simple implementation of IDMaker that hashes by URN.

## C

c() - Static method in class org.biojava.bio.seq.DNATools
c() - Static method in class org.biojava.bio.seq.NucleotideTools
c() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Cysteine
c() - Static method in class org.biojava.bio.seq.RNATools
C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
caAtomName - Static variable in class org.biojava.bio.structure.StructureTools
Cache - Interface in org.biojava.utils.cache
  Interface for managing caches of objects.
cache - Variable in class org.biojava.utils.io.CachingInputStream
  The byte cache itself.
cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
CacheMap - Interface in org.biojava.utils.cache
  Interface for managing caches of objects fetchable by key.
CacheReference - Interface in org.biojava.utils.cache
  Interface for a reference to an object, analogous to `java.lang.ref.Referencce`, but more flexible.
CachingInputStream - Class in org.biojava.utils.io
  A wrapper around `InputStream` that provides in-memory caching of the input data.
CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
CachingKernel - Class in org.biojava.stats.svm
  Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
CachingSequenceDB - Class in org.biojava.bio.seq.db
  SequenceDB implementation that caches the results of another SequenceDB.
CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB
  Create a new CachingSequenceDB that caches the sequences in parent.
Calc - Class in org.biojava.bio.structure
  utility operations on Atoms, AminoAcids, etc.
Calc() - Constructor for class org.biojava.bio.structure.Calc
calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
  Calculate the 'scores' array in the cell at cells[0][0].
calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker
  Calculate the id for a sequence.
calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `calculatePrimRecLen` calculates the byte length of primary namespace records.
calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType
  Calculates the score associated with a distribution and a symbol.
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `calculateSecRecLen` calculates the byte length of secondary namespace records.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  this is the stack of handler objects for the current feature.
callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  this is the stack of handler objects for the current feature.
callboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Flag for call boxes.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
  Accepts all URLs that are of the file protocol.
canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
  Accepts all URLs that are of the jdbc protocol.
canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  Can we advance?
CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
CandyEntry - Class in org.biojava.utils.candy
  This is a basic container for a vocabulary entry.
CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry
  An empty constructor.
CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry
  It creates an entry instance with given name and empty value.
CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry
  It creates an entry instance with given name and value.
CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry
  It creates an entry instance with given name, value and additional properties.
CandyException - Exception in org.biojava.utils.candy
CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
CandyFinder - Interface in org.biojava.utils.candy
  This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary - Interface in org.biojava.utils.candy
  This interface defines functionality of a controlled vocabulary.
canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Determines whether the locations are touching or not (if they could be merged in a single Location.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in EMBL format if its name contains the word eem or edat, or the first line matches the EMBL format for the ID line.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  Check to see if a given stream is in our format. A stream is in EMBL format if its first line matches the EMBL format for the ID line.
canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Check to see if a given stream is in our format. A stream is in EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".
canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in FASTA format if the name ends with fa or fas, or the file starts with ">".
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
  Check to see if a given stream is in our format. A stream is in FASTA format if the stream starts with ">".
canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in GenBank format if the name ends with gbk, contains the letters egb, or the first line of the file starts with the word LOCUS
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  Check to see if a given stream is in our format. A stream is in GenBank format if the first line of the stream starts with the word LOCUS
canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Check to see if a given stream is in our format. A stream is in INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Check to see if a given file is in our format.
canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Check to see if a given file is in our format.
canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Check to see if a given stream is in our format.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in UniProt format if the first line matches the UniProt format for the ID line.
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  Check to see if a given stream is in our format. A stream is in UniProt format if the first line matches the UniProt format for the ID line.
canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.xsd".
canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Check to see if a given stream is in our format. A stream is in UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.xsd".
CardinalityConstraint - Class in org.biojava.bio
  A constraint on the number of values a property can have.
Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Carbon average mass
Cell - Class in org.biojava.bio.dp.twohead
  A single cell in the DP matrix.
Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
CellCalculator - Interface in org.biojava.bio.dp.twohead
  The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead
  The interface for all functions that can calculate the 'scores' array for a given cell.
centerAtoms(Atom[]) - Static method in class org.biojava.bio.structure.Calc
  center the atoms at the Centroid
CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Saccharomyces cerevisiae codon preferences
Chain - Interface in org.biojava.bio.structure
  Defines the interface for a Chain.
ChainImpl - Class in org.biojava.bio.structure
  A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.bio.structure.ChainImpl
  Constructs a ChainImpl object.
change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer
  Produce a modified value from an old value.
change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
  Deprecated. Change type to indicate that the common name of this Taxon is changing.
CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
  Deprecated. Change type to indicate that the scientific name of this Taxon is changing.
Changeable - Interface in org.biojava.utils
  This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeableCache - Class in org.biojava.utils.cache
  A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
ChangeAdapter - Class in org.biojava.utils
  This is a ChangeListener that ignores everything.
ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
ChangeEvent - Class in org.biojava.utils
  Event which encapsulates a change in any mutable BioJava object.
ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent
  Construct a ChangeEvent with no change details.
ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent
  Construct a ChangeEvent specifying a new value for a property, or an object to be added to a collection.
ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent
  Construct a ChangeEvent specifying a new value for a property, and giving the previous value.
ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent
  Construct a ChangeEvent to be fired because another ChangeEvent has been received from a property object.
ChangeForwarder - Class in org.biojava.utils
  This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder
  Create a new ChangeForwarder for forwarding events.
ChangeForwarder.Retyper - Class in org.biojava.utils
  A ChangeForwarder that systematically uses a given type and wraps the old event.
ChangeForwarder.Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper
  Create a new Retyper for forwarding events.
ChangeHub - Interface in org.biojava.utils
  Interface implemented by ChangeHubs, i.e.
ChangeListener - Interface in org.biojava.utils
  Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener - Class in org.biojava.utils
  An implementation that always vetoes everything.
ChangeListener.AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
  Private constructor.
ChangeListener.ChangeEventRecorder - Class in org.biojava.utils
  A listener that remembers the ChangeEvent of the last change.
ChangeListener.ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
ChangeListener.LoggingListener - Class in org.biojava.utils
  A listener that writes information about the event stream to a PrintStream.
ChangeListener.LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
  Create a LoggingListener that will log all events to 'out'.
ChangeListener.LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
  Create a LoggingListener that will log all events to 'out' with a prefix.
changeSupport() - Method in class org.biojava.utils.ChangeForwarder
  Return the underlying `ChangeSupport` instance that can be used to fire `ChangeEvent`s and mannage listeners.
ChangeSupport - Class in org.biojava.utils
  A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport
  Generate a new ChangeSupport instance.
ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport
  Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources.
ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport
  Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport
  Generate a new ChangeSupport instance which has room for initialSize listeners before it needs to grow any resources, and which will grow by delta each time.
ChangeTable - Class in org.biojava.bio.program.tagvalue
  A mapping between keys and actions to turn old values into new values.
ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue
  An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue
  Callback used to produce a new value from an old one.
ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue
  Callback used to produce a list of values from a single old one.
ChangeType - Class in org.biojava.utils
  Class for all constants which are used to indicate change types.
ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType
  Construct a new ChangeType.
ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType
  Construct a new ChangeType with superType UNKNOWN.
ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType
  Construct a new ChangeType with supertype UNKNOWN.
ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
  Construct a new ChangeType with supertype UNKNOWN
ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
ChangeVetoException - Exception in org.biojava.utils
  Exception which is thrown when a ChangeListener does not wish a change to take place.
ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
  Construct an exception to veto a change without explanation.
ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException
  Create an exception with a detail message
ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
  Construct an exception to veto a change for a specified reason.
ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
  Propogate an exception without (additional) explanation.
ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException
  Deprecated. use new ChangeVetoException(reason, ex);
ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
  Propogate an exception, giving a detail message
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
  Describe `characters` method here.
characters(char[], int, int) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
characters(char[], int, int) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
  Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
  Signal a span of character data in the XML input.
characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
CharacterTokenization - Class in org.biojava.bio.seq.io
  Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
CharElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of a char.
CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory
  Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for.
charValue(Symbol) - Method in class org.biojava.utils.regex.Search
checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
children - Variable in class org.biojava.bio.taxa.SimpleTaxon
  Deprecated.
chol() - Method in class org.biojava.bio.structure.jama.Matrix
  Cholesky Decomposition
CholeskyDecomposition - Class in org.biojava.bio.structure.jama
  Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.CholeskyDecomposition
  Cholesky algorithm for symmetric and positive definite matrix.
Chromatogram - Interface in org.biojava.bio.chromatogram
  Encapsulates the basic information you would want from a chromatogram.
ChromatogramFactory - Class in org.biojava.bio.chromatogram
  A factory that creates `Chromatogram` objects from files or streams.
ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
ChromatogramGraphic - Class in org.biojava.bio.chromatogram.graphic
  Encapsulates a configurable method for drawing a `Chromatogram` into a graphics context.
ChromatogramGraphic() - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Default constructor with no Chromatogram.
ChromatogramGraphic(Chromatogram) - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Creates a new `ChromatogramGraphic`, initially displaying the given chromatogram.
ChromatogramGraphic.Option - Class in org.biojava.bio.chromatogram.graphic
  A typesafe enumeration of the options available for configuring the behavior of a `ChromatogramGraphic` instance.
ChromatogramNonlinearScaler - Interface in org.biojava.bio.chromatogram.graphic
  Provides the mechanism whereby a ChromatogramGraphic can display a Chromatogram with a non-linear horizontal scale.
ChromatogramNonlinearScaler.Identity - Class in org.biojava.bio.chromatogram.graphic
  The default scaler that displays the chromatogram 1:1.
ChromatogramTools - Class in org.biojava.bio.chromatogram
  Utility class for dealing with `Chromatogram`s.
CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
ChunkedSymbolList - Class in org.biojava.bio.symbol
  SymbolList implementation using constant-size chunks.
ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io
  class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the ciliate nuclear genetic code.
CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
  `CIRCLE` indicates a circular image map hotspot.
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence
CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence
CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence
CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
CircularLocation - Class in org.biojava.bio.symbol
  Circular view onto an underlying Location instance.
CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
  Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
  Makes a CircularLocation where the 5' end of the Location is specified.
CircularMLR - Class in org.biojava.bio.gui.sequence
  Renders multiple renderers, each in their own concentric rings.
CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR
CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence
CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
CircularReferenceException - Exception in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
  Deprecated.
CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
  Deprecated.
CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
  Deprecated.
CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
  Deprecated.
CircularRenderer - Interface in org.biojava.bio.gui.sequence
  Render information from a CircularRendererContext onto a graphics context.
CircularRendererContext - Interface in org.biojava.bio.gui.sequence
  A context providing information for rendering sequences into circular coordinate systems.
CircularRendererPanel - Class in org.biojava.bio.gui.sequence
  Renders a sequence as a circle using a CircularRenderer.
CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel
CircularView - Class in org.biojava.bio.seq
  A circular view onto another Sequence object.
CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ClassifierExample - Class in org.biojava.stats.svm.tools
  A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools
  An extention of JComponent that contains the points & encapsulates the classifier.
ClassifierExample.PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Make a new PointClassifier.
classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Learn a model from the current points.
Classify - Class in org.biojava.stats.svm.tools
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
ClassTools - Class in org.biojava.utils
  Utility methods for manipulating class objects and resources.
clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
clear() - Method in interface org.biojava.stats.svm.SVMTarget
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Remove all points from the canvas, and discard any model.
clear() - Method in interface org.biojava.utils.cache.CacheReference
clear() - Method in class org.biojava.utils.FileAsList
clear() - Method in class org.biojavax.EmptyRichAnnotation
  Removes all notes from this annotation object. Does nothing as it contains nothing.
clear() - Method in class org.biojavax.ga.util.WeightedSet
clear() - Method in interface org.biojavax.RichAnnotation
  Removes all notes from this annotation object.
clear() - Method in class org.biojavax.SimpleRichAnnotation
  Removes all notes from this annotation object.
clearAtoms() - Method in interface org.biojava.bio.structure.Group
  remove all atoms from this group
clearAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
  remove all atoms
clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Clears all of the counts to zero.
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Clears all of the counts to zero.
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
  Deprecated.
clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer
  Clears all of the counts to zero.
clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper
  `clearEnzymes` removes all enzymes from those to be searched for in the `Sequence`.
clearLRUCache() - Static method in class org.biojavax.RichObjectFactory
  Removes all objects from the LRU cache.
clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory
  Removes all objects of the specified class from the LRU cache.
clearPatterns() - Method in class org.biojava.utils.regex.Search
  remove all patterns from the pattern cache.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
  `clearRenderers` removes all renderers from this renderer.
clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `clearRenderers` removes all the renderers.
clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Sets the trace data structures to null.
clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Sets all the traces to null.
clobToString(Connection, ResultSet, int) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
clone() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Performs a partial deep copy and invalidates regenerable structures.
clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
clone() - Method in class org.biojava.bio.seq.Feature.Template
clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence
  clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence.
clone() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
clone() - Method in class org.biojava.bio.structure.AminoAcidImpl
  returns and identical copy of this Group object .
clone() - Method in interface org.biojava.bio.structure.Atom
  returns and identical copy of this object .
clone() - Method in class org.biojava.bio.structure.AtomImpl
  returns and identical copy of this object .
clone() - Method in interface org.biojava.bio.structure.Chain
  returns an identical copy of this Chain.
clone() - Method in class org.biojava.bio.structure.ChainImpl
  returns an identical copy of this Chain .
clone() - Method in interface org.biojava.bio.structure.Group
  returns and identical copy of this Group object .
clone() - Method in class org.biojava.bio.structure.GroupIterator
  Creates and returns a copy of this object.
clone() - Method in class org.biojava.bio.structure.HetatomImpl
  returns and identical copy of this Group object .
clone() - Method in class org.biojava.bio.structure.jama.Matrix
  Clone the Matrix object.
clone() - Method in class org.biojava.bio.structure.NucleotideImpl
clone() - Method in interface org.biojava.bio.structure.Structure
  returns an identical copy of this structure .
clone() - Method in class org.biojava.bio.structure.StructureImpl
  returns an identical copy of this structure .
clone() - Method in class org.biojava.utils.ExecRunner
  We override the `clone` method here to prevent cloning of our class.
clone() - Method in class org.biojava.utils.TypedProperties
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `close` closes the underlying `InputStream`.
close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `close` closes the underlying `RandomAccessFile`.
close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `close` closes the underlying `EntryNamRandomAccess` which in turn closes the lower level `RandomAccessFile`.
close() - Method in interface org.biojava.bio.seq.io.StreamParser
close() - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
close() - Method in class org.biojava.naming.ObdaContext
close() - Method in class org.biojava.utils.io.CountedBufferedReader
close() - Method in class org.biojava.utils.io.RandomAccessReader
  `close` closes the underlying `RandomAccessFile`.
close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
close() - Method in interface org.biojava.utils.xml.XMLWriter
  Close this XMLWriter, and it's underlying stream.
closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Closes an element
closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Closes an un-qualified element.
CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `CLUSTAL` indicates that the alignment format is Clustal.
CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `CLUSTAL_AA` premade CLUSTAL | AA;
CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `CLUSTAL_DNA` premade CLUSTAL | DNA;
CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `CLUSTAL_RNA` premade CLUSTAL | RNA;
ClustalWAlignmentSAXParser - Class in org.biojava.bio.program.sax
  A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format.
ClustalWAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
  Initialises internal state Sets namespace prefix to "biojava"
Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Carbon monoisotopic mass
CNBr - Static variable in class org.biojava.bio.proteomics.Protease
CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
codes - Variable in class org.biojava.bibliography.BiblioSubject
  Classification code (call number) is usually either Dewey decimal or Congress classification.
CodonPref - Interface in org.biojava.bio.symbol
CodonPrefFilter - Interface in org.biojava.bio.symbol
CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
CodonPrefFilter.AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
CodonPrefFilter.ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
CodonPrefFilter.EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
CodonPrefTools - Class in org.biojava.bio.symbol
  An utility class for codon preferences
CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
CollectionConstraint - Interface in org.biojava.bio
  Used by `AnnotationType` to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn - Class in org.biojava.bio
  CollectionConstraint which validates all members of a Collection.
CollectionConstraint.AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
  Create an AllValuesIn based upon a PropertyConstraint and a cardinality.
CollectionConstraint.And - Class in org.biojava.bio
  A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
  Create a new `And` from two child constraints.
CollectionConstraint.Contains - Class in org.biojava.bio
  CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
  Create a Contains based upon a PropertyConstraint and a cardinality.
CollectionConstraint.Or - Class in org.biojava.bio
  A collection constraint that accepts items iff they are accepted by either child constraints.
CollectionConstraint.Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or
  Create a new `Or` from two child constraints.
colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  The map containing the colors for drawing traces.
ColourCommand - Interface in org.biojava.bio.program.blast2html
  Interface for specifying whether a particular pair of residues/bases should be coloured.
colSymbols - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
columns() - Method in class org.biojava.bio.dp.ProfileHMM
  Retrieve the number of columns in the model.
columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
columns() - Method in interface org.biojava.bio.dp.WeightMatrix
  The number of columns modeled by the weight matrix.
COMMENT - Static variable in interface org.biojavax.bio.BioEntry
Comment - Interface in org.biojavax
  A simple ranked comment designed to be used for BioEntry comments in BioSQL.
COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EVENT_ISOFORMS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
  A comment line has been encountered.
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter
  Prints the comment directly to the PrintWriter after adding a leading '`#`'.
commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
  A comment line has been encountered.
commit() - Method in class org.biojava.bio.program.indexdb.BioStore
  `commit` writes an index to disk.
commit() - Method in class org.biojava.bio.seq.db.BioIndex
commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `commit` commits changes.
commit() - Method in interface org.biojava.bio.seq.db.IndexStore
  Commit the stored indices to permanent storage.
commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
commit() - Method in interface org.biojava.utils.Commitable
  `commit` commits pending changes.
commit() - Method in class org.biojava.utils.FileAsList
Commitable - Interface in org.biojava.utils
  Implementations of `Commitable` support atomic changes from one known state to another via commit/rollback semantics.
CommitFailure - Exception in org.biojava.utils
CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
  Use this to define common names for things.
COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CompactedDataStore - Class in org.biojava.bio.program.ssaha
  An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha
  Builder for a data store that is backed by a java.nio.MappedByteBuffer.
CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
ComparableOntology - Interface in org.biojavax.ontology
  An Ontology that can be compared to another.
ComparableTerm - Interface in org.biojavax.ontology
  Makes Term objects comparable properly and adds some extra features to them.
ComparableTriple - Interface in org.biojavax.ontology
  Comparable triples, obviously.
comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator
  Deprecated.
compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator
  Deprecated.
compare(Object, Object) - Method in class org.biojava.bio.structure.align.pairwise.AltAligComparator
compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Empty Rich Locations return 0 when compared to other Empty ones, or -1 otherwise.
compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
  Strands are compared first by symbol, then by number.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Features are sorted by rank only.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Relations are compared first by rank, then object, subject, then finally term.
compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry
  Bioentries are ordered first by namespace, then name, accession, and finally version.
compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  A relationship is compared first by rank, then object, subject, then term.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  NCBITaxon objects are compared only by their NCBITaxID fields.
compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Taxon names are sorted by class first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Ontologies are compared only by name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Terms are sorted by ontology first, then name.
compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Triples are sorted in order of ontology, subject, object, and finally predicate.
compareTo(Object) - Method in class org.biojavax.SimpleComment
  Comments are ordered first by their rank, then by a string comparison of their text values.
compareTo(Object) - Method in class org.biojavax.SimpleCrossRef
  Compares cross references first by database name, then by accession, then by version.
compareTo(Object) - Method in class org.biojavax.SimpleDocRef
  Document references are compared first by author, then by location, then by title.
compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor
  Document authors are compared first by name, then consortium status, then editor status.
compareTo(Object) - Method in class org.biojavax.SimpleNamespace
  Namespaces are compared only by name.
compareTo(Object) - Method in class org.biojavax.SimpleNote
  Notes are compared first by rank, then by the term.
compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef
  Ranked cross references are sorted first by rank, then by cross reference.
compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef
  Ranked document references are sorted first by rank then by actual document reference.
compile(String) - Method in class org.biojava.utils.regex.PatternFactory
  Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory
  Returns a Pattern object that applies the specified regex against SymbolLists in the Alphabet that this PatternFactory was defined against.
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
  Retrieve a complement view of list.
COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
  Retrieve a complement view of list.
complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
  Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a complement view of list.
complementTable() - Static method in class org.biojava.bio.seq.DNATools
  Get a translation table for complementing DNA symbols.
complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools
  Get a translation table for complementing Nucleotide symbols.
complementTable() - Static method in class org.biojava.bio.seq.RNATools
  Get a translation table for complementing DNA symbols.
completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
  indicate that a cycle of training is completed and the emission/transition matrices should be updated.
completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
completedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
  Notification that an activity is complete.
COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ComponentFeature - Interface in org.biojava.bio.seq
  Feature which represents a component in an assembly (contig).
ComponentFeature.Template - Class in org.biojava.bio.seq
  Template for constructing a new ComponentFeature.
ComponentFeature.Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
composeName(String, String) - Method in class org.biojava.naming.ObdaContext
CompoundRichLocation - Class in org.biojavax.bio.seq
  An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
  Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
  Constructs a CompoundRichLocation from the given set of members.
CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator
  computes charge at given pH
compute(double) - Method in interface org.biojava.utils.math.ComputeObject
  workhorse method for this class.
ComputeObject - Interface in org.biojava.utils.math
  interface for classes that return a single double precision value for a single double precision argument.
cond() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix condition (2 norm)
cond() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Two norm condition number
conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution
  Get the conditioned distributions.
CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
conjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
conjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
connect() - Method in interface org.biojava.bibliography.BibRefQuery
  It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication.
connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery
  It creates a connection to a bibliographic repository, or/and it makes all necessary initialization steps needed for further communication, and it makes the collection described by `collectionId` the current collection.
connect() - Method in interface org.biojava.bibliography.BibRefSupport
  It creates a connection to an object providing the supporting utilities, or/and it makes all necessary initialization steps needed for further communication.
connect() - Method in interface org.biojava.utils.candy.CandyFinder
  It creates a connection to an object representing a vocabulary finder, or/and it makes all necessary initialization steps needed for further communication.
connectModel() - Method in class org.biojava.bio.dp.ProfileHMM
  This is called by constructor in setting up the allowed transitions in the model
connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
  This is called by constructor in setting up the allowed transitions in the model
connectToBioSQL(Object) - Static method in class org.biojavax.RichObjectFactory
  A utility method that configures the RichObjectFactory for use with a Hibernate session.
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
Constants - Class in org.biojava.utils
  Some usefull constants for working with binary files.
Constants() - Constructor for class org.biojava.utils.Constants
construct(Collection) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Constructs a RichLocation object based on the given collection of members.
constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
constructWithCopy(double[][]) - Static method in class org.biojava.bio.structure.jama.Matrix
  Construct a matrix from a copy of a 2-D array.
containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with locations wholly contained by the specified `Location`.
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
  Returns whether or not this Alphabet contains the symbol.
contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
contains(Location) - Method in interface org.biojava.bio.symbol.Location
  Checks if this location contains the other.
contains(int) - Method in interface org.biojava.bio.symbol.Location
  Checks if this location contains a point.
contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return `true` iff all indices in `locB` are also contained by `locA`.
contains(int) - Method in class org.biojava.bio.symbol.PointLocation
contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
  It checks if a given entry exists in this vocabulary.
contains(Object) - Method in class org.biojava.utils.MergingSet
contains(Object) - Method in class org.biojava.utils.SmallSet
contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Checks if this location contains a point. Recursively applies this call to all members.
contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Checks if this location contains the other.

  Abstractly, a location contains another if every point in the other location is contained within this one. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand. Recursively applies this call to all members.

contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Checks if this location contains a point. ALWAYS RETURNS FALSE
contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Checks if this location contains the other. ALWAYS RETURNS FALSE
contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Checks if this location contains a point.
contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Checks if this location contains the other. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand.
contains(Note) - Method in class org.biojavax.EmptyRichAnnotation
  Returns true if the given note exists in this annotation.
contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
contains(Note) - Method in interface org.biojavax.RichAnnotation
  Returns true if the given note exists in this annotation.
contains(Note) - Method in class org.biojavax.SimpleRichAnnotation
  Returns true if the given note exists in this annotation.
CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
containsFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
  Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
  containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature;
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Check if the feature is present in this holder.
containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Check if the feature is present in this holder.
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
containsKey(Object) - Method in class org.biojava.utils.OverlayMap
containsKey(Object) - Method in class org.biojava.utils.SmallMap
containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Tests for the presence of a name in a given class.
containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Tests for the presence of a name in a given class.
containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
containsProperty(Object) - Method in interface org.biojava.bio.Annotation
  Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
  Returns whether there the property is defined.
containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
  Returns whether there the property is defined.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Detects whether a particular table is present in the database.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
  Deprecated.
containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
containsTerm(String) - Method in interface org.biojava.ontology.Ontology
  Determines if this ontology currently contains a term named `name`
containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Determines if this ontology currently contains a term named `name`
containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
  Returns wether a transition exists or not.
containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
  See if a triple exists in this ontology
containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
  See if a triple exists in this ontology If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms.
CONTENT - Static variable in interface org.biojava.bio.symbol.Alignment
  Signals that SymbolLists will be added to or removed from an alignment.
contextForLabel(SequenceRenderContext, Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
contributors - Variable in class org.biojava.bibliography.BibRef
  The authors and contributors are responsible for creating the contents of the cited resource.
convert() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
convert() - Method in class org.biojava.bio.program.PdbToXMLConverter
convert(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
  Convert a non-BioSQL FeatureFilter into a BioSQL one.
convert_3code_1code(String) - Method in class org.biojava.bio.structure.io.PDBFileParser
  convert three character amino acid codes into single character e.g.
convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree
  Labels `Sequence` objects with their name, `Annotations` with the tag Annotations, `Features` with the tag Features and other objects with the `toString` value.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `coordinateDisplayOn` toggles the display of sequence coordinates.
copy() - Method in class org.biojava.bio.structure.jama.Matrix
  Make a deep copy of a matrix
COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
cost - Variable in class org.biojava.bibliography.BiblioWebResource
  The cost of accessing the resource.
CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
Count - Interface in org.biojava.bio.dist
  An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader - Class in org.biojava.utils.io
CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
countFeatures() - Method in class org.biojava.bio.program.das.DASSequence
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
  Count how many features are contained.
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Count how many features are contained.
countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Count how many features are contained.
COUNTS - Static variable in interface org.biojava.bio.dist.Count
  Whenever a component count changes the values that would be returned by getCount, they should fire a ChangeEvent with this object as the type.
countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools
  Make a distribution from a count.
coverage - Variable in class org.biojava.bibliography.BibRef
  It defines an extent or scope of the content of the cited resource.
coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the number of positions which are covered by a `Location`
CRC64Checksum - Class in org.biojavax.utils
  Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
  Creates a new instance of CRC64Checksum.
create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
  Creates a new `Chromatogram` object from the named file.
create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
  Creates a new `Chromatogram` object from the supplied stream.
create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
  Create a new ABIF object from a file.
create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
  Create a new ABIF object from a stream of bytes.
create(File) - Static method in class org.biojava.bio.program.scf.SCF
create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
createBinary(String) - Static method in class org.biojavax.ga.util.GATools
  Creates a `SymbolList` in the GABinary `Alphabet`
createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `createBioStore` creates a `BioStore` reflecting the current state of the factory and returns a reference to it.
createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory
  Generate a new Distribution as requested.
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory
  Creates an OrderNDistribution of the appropriate type.
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
  Return a new DNA SymbolList for dna.
createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
  Return a new DNA Sequence for dna.
createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools
  Create a new Sequence that has no annotation, no features and a zero-length symbol list.
createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools
  Create a new Sequence that contains a single symbol repeated over and over.
createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createFeature(Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence).
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder
  Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence
  createFeature() will call createFeature() on the underlying Sequence.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Deprecated. Please use new 1-arg createFeature instead.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Create a projected feature with properties matching the template.
createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Create a new projected feature.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Create a new Feature, and add it to this FeatureHolder.
createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Create a new template of the appropriate type.
createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
  Get a new dna as a GappedSequence
createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
  Get a new protein as a GappedSequence
createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Internal method to create a GFFRecord from an individual Feature.
createImmutableAlignment(Map) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  A factory method for creating new immutable alignments, particularly for use as base call alignments.
createImmutableSymbolList(Alphabet, List) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  A factory method for creating new symbol lists with a given alphabet.
createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools
createList(List) - Static method in class org.biojava.utils.ListTools
createList(Object[]) - Static method in class org.biojava.utils.ListTools
createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools
  Return a new Nucleotide SymbolList for nucleotide.
createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools
  Return a new Nucleotide Sequence for nucleotide.
createOntology(String, String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory
  Creates a new Ontology
createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Create an orthologue.
createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Create an orthologue.
createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Create a computed orthology entry.
createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Create a curated orthology entry.
createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Create a Homologene Group.
createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools
createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools
  Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
  Creates and registers a new Protease.
createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools
  Return a new Protein SymbolList for protein.
createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
  Return a new PROTEIN Sequence for protein.
createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser
  Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools
  `createRegex` creates a regular expression which matches the `SymbolList`.
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Create a new RichSequence in the default namespace.
createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Create a new RichSequence in the specified namespace.
createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Create a new RichSequence in the specified namespace.
createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Create a new RichSequence in the default namespace.
createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Create a new RichSequence in the specified namespace.
createRNA(String) - Static method in class org.biojava.bio.seq.RNATools
  Return a new RNA SymbolList for rna.
createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools
  Return a new RNA Sequence for rna.
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
  Deprecated. Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools
  Create a new SeriesList with the given leader, trailer and size.
createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generate a new AtomicSymbol instance with a name and Annotation.
createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generate a new AtomicSymbol instance with a name and an Empty Annotation.
createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. Use the two-arg version of this method instead.
createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. use the new version, without the token argument
createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generates a new Symbol instance that represents the tuple of Symbols in symList.
createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. use the three-arg version of this method instead.
createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generates a new Symbol instance that represents the tuple of Symbols in symList.
createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
  add a Taxon
createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Create a new orphan Taxon with a given scientific and common name.
createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  generates a very basic Template for the feature with SmallAnnotation in the annotation field.
createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
createTerm(String, String) - Method in interface org.biojava.ontology.Ontology
  Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology
  Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Create a new term in this ontology.
createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Create a new term in this ontology.
createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
  Makes a transition between two states legal.
createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology
  Creates a new Triple.
createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Creates a new Triple. If you call this method with plain Terms instead of ComparableTerms, it will import them into the local ontology first.
createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
  Create a new type in this repository.
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Create a new UnigeneDB instance referred to by a URL.
createURL(Object) - Method in interface org.biojava.utils.net.URLFactory
  `createURL` returns a URL which is relevant to the object in a way specified by the implementation.
createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
createVariable(String, String) - Method in interface org.biojava.ontology.Ontology
  Create a new term in this ontology that is used as a variable.
createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Create a new term in this ontology that is used as a variable. NOT IMPLEMENTED
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.bio.structure.Calc
  creates a virtual C-beta atom.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
criterionAliasMap() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
  Returns a map of property names (keys) to aliases (values), if the criterion returned by asCriterion() uses aliases at all.
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
CrosshairRenderer - Class in org.biojava.bio.gui.sequence
  `CrosshairRenderer` draws a crosshair, optionally with coordinates.
CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
  Creates a new `CrosshairRenderer` in light grey with coordinates displayed.
CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
  Creates a new `CrosshairRenderer` of the specified colour, with coordinates displayed.
CrossOverFunction - Interface in org.biojavax.ga.functions
  Crosses two chromosomes.
CrossOverFunction.NoCross - Class in org.biojavax.ga.functions
  A place holder CrossOverFunction that doesn't perform cross overs
CrossOverFunction.NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross
CrossProductTokenization - Class in org.biojava.bio.seq.io
  Tokenization for cross-product alphabets.
CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
CrossRef - Interface in org.biojavax
  Represents a cross reference to another database.
CROSSREF - Static variable in interface org.biojavax.DocRef
CrossReferenceResolutionException - Exception in org.biojavax
  An exception that indicates that an attempt to resolve a `CrossRef` has failed.
CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException
  Creates a new instance of CrossReferenceResolutionException
CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException
  Creates a new instance of CrossReferenceResolutionException with a message.
CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
  Creates a new instance of CrossReferenceResolutionException with a message and a cause.
CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
  Creates a new instance of CrossReferenceResolutionException with a cause.
CrossReferenceResolver - Interface in org.biojavax
  This interface returns symbols or sequence for a given cross-reference.
crossReferences - Variable in class org.biojava.bibliography.BibRef
  It is an array of identifiers, all of them pointing to the same cited source but usually stored in different bibliographic repositories.
crypticVariable - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the c loop state
CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The current column of the matrix.
currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The current symbol.
CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `CUT_COMPOUND` a cut type where the enzyme cuts in two positions relative to the recognition site.
CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `CUT_SIMPLE` a cut type where the enzyme cuts in one position relative to the recognition site.
cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
cys() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Cysteine (C)

## D

d() - Static method in class org.biojava.bio.seq.NucleotideTools
d() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Aspartic Acid
D_MELANOGASTER - Static variable in interface org.biojava.bio.program.homologene.Taxon
D_RERIO - Static variable in interface org.biojava.bio.program.homologene.Taxon
DAS - Class in org.biojava.bio.program.das
  A collection of DAS datasources.
DAS() - Constructor for class org.biojava.bio.program.das.DAS
DASAlignmentCall - Class in org.biojava.bio.program.das.dasalignment
  takes care of the communication with a DAS Alignment service.
DASAlignmentCall() - Constructor for class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  Constructs a DASAlignmentCall object.
DASAlignmentCall(String) - Constructor for class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  Constructs a DASAlignmentCall object.
DASAlignmentClient - Class in org.biojava.bio.program.das.dasalignment
  A DAS client that connects to a DAS aligmnent service and returns a Biojava Alignment object.
DASAlignmentClient() - Constructor for class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Constructs a DASAlignmentClient object.
DASAlignmentClient(String) - Constructor for class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Constructs a DASAlignmentClient object.
DASAlignmentXMLResponseParser - Class in org.biojava.bio.program.das.dasalignment
  A class to Parse the XML response of a DAS Alignment service.
DASAlignmentXMLResponseParser() - Constructor for class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
DASException - Exception in org.biojava.bio.program.das.dasalignment
  An exception of one of the DAS classes.
DASException(String) - Constructor for exception org.biojava.bio.program.das.dasalignment.DASException
  Constructs a DASException object.
DASException(Throwable, String) - Constructor for exception org.biojava.bio.program.das.dasalignment.DASException
  Constructs a DASException object.
DASException(Throwable) - Constructor for exception org.biojava.bio.program.das.dasalignment.DASException
  Constructs a DASException object.
DASLink - Class in org.biojava.bio.program.das
  A memento class for storing a link.
DASLink(String, String) - Constructor for class org.biojava.bio.program.das.DASLink
DASSequence - Class in org.biojava.bio.program.das
  Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
DASSequenceDB - Class in org.biojava.bio.program.das
  Collection of sequences retrieved from the DAS network.
DASSequenceDB(URL) - Constructor for class org.biojava.bio.program.das.DASSequenceDB
DASSequenceDBProvider - Class in org.biojava.bio.program.das
  Hook DAS into the OBDA directory system.
DASSequenceDBProvider() - Constructor for class org.biojava.bio.program.das.DASSequenceDBProvider
DASStructureCall - Class in org.biojava.bio.program.das.dasstructure
  Calls a DAS - Structure server.
DASStructureCall() - Constructor for class org.biojava.bio.program.das.dasstructure.DASStructureCall
  Constructs a DASStructureCall object.
DASStructureCall(String) - Constructor for class org.biojava.bio.program.das.dasstructure.DASStructureCall
  Constructs a DASStructureCall object.
DASStructureClient - Class in org.biojava.bio.structure.io
  A DAS client that connects to a DAS structure service and returns a Biojava structure class.
DASStructureClient(String) - Constructor for class org.biojava.bio.structure.io.DASStructureClient
  Constructs a DASStructureClient object.
DASStructureXMLResponseParser - Class in org.biojava.bio.program.das.dasstructure
  a class to Parse the XML response of a DAS structure service.
DASStructureXMLResponseParser() - Constructor for class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
data - Variable in class org.biojava.bio.alignment.FlexibleAlignment
DATA_TYPE_ASCII_ARRAY - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_DATE - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_FLOAT - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_INTEGER - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_PSTRING - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATA_TYPE_TIME - Static variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DATABASE - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DATABASE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
databaseID - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
DatabaseURLGenerator - Interface in org.biojava.bio.program.blast2html
  Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
dataRecord - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
DataSource - Class in org.biojava.bio.program.das
  Reflect a datasource (reference or annotation) in the DAS1 network.
DATASOURCE - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
dataSource - Variable in class org.biojava.bio.structure.io.PDBMSDReader
DATASOURCE_SELECTION - Static variable in class org.biojava.bio.seq.distributed.DistributedSequenceDB
dataSourceURLs() - Method in class org.biojava.bio.program.das.DASSequence
DataStore - Interface in org.biojava.bio.program.ssaha
  A repository that can be searched with a sequence.
DataStoreFactory - Interface in org.biojava.bio.program.ssaha
  Builder for a data store.
dataType - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
date - Variable in class org.biojava.bibliography.BibRef
  Defines a date associated with an event in the life cycle of the cited resource when this resource became available.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
DATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DATE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
DB_NUCLEOTIDE - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DB_PROTEIN - Static variable in class org.biojava.bio.seq.db.NCBISequenceDB
DBHelper - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
DBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
DBHelper.BioSequenceStyle - Class in org.biojava.bio.seq.db.biosql
  Deprecated.
DBHelper.DeleteStyle - Class in org.biojava.bio.seq.db.biosql
  Deprecated.
DBHelper.JoinStyle - Class in org.biojava.bio.seq.db.biosql
  Deprecated.
DBREF_DB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_PRIMARY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREF_SEC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
DBREFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
dbxp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DBXREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
debug(String) - Method in class org.biojava.bio.alignment.AbstractULAlignment
DebuggingRichSeqIOListener - Class in org.biojavax.bio.seq.io
  This is purely for debugging purposes.
DebuggingRichSeqIOListener(InputStream) - Constructor for class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
declareNamespace(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
declareNamespace(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Hints that a namespace is going to be used in a sub-tree.
decodeDNAToken(char) - Static method in class org.biojava.bio.program.abi.ABIFParser
  Decodes a character into a `Symbol` in the DNA alphabet.
decorate(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
decorate(Location) - Method in class org.biojava.bio.symbol.BetweenLocation
decorate(Location) - Method in class org.biojava.bio.symbol.CircularLocation
DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory
  The default DistributionFactory object.
DEFAULT - Static variable in class org.biojava.bio.dist.OrderNDistributionFactory
  Factory which used DistributionFactory.DEFAULT to create conditioned distributions.
DEFAULT - Static variable in interface org.biojava.bio.dp.DPFactory
DEFAULT - Static variable in class org.biojava.bio.program.phred.PhredFormat
DEFAULT - Static variable in class org.biojava.bio.seq.impl.FeatureImpl
  Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
DEFAULT - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.FastaFormat
  Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.io.GAMEFormat
DEFAULT - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
DEFAULT - Static variable in class org.biojava.bio.seq.projection.ProjectionEngine
  The standard projection engine object.
DEFAULT - Static variable in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
DEFAULT - Static variable in interface org.biojavax.ga.functions.SelectionFunction
  Selects all members of a population for replication
DEFAULT_CHAIN_ID - Static variable in class org.biojava.bio.structure.ChainImpl
DEFAULT_CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties
  the default string of delimiter characters used by getAsStringList()
DEFAULT_FINDER_NAME - Static variable in interface org.biojava.utils.candy.CandyFinder
  A default name of this (and any) finder.
DEFAULT_MAX_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
DEFAULT_MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
DEFAULT_TERM_CHAR - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
DefaultOps - Class in org.biojava.ontology
  Default implementation of OntologyOps.
DefaultOps() - Constructor for class org.biojava.ontology.DefaultOps
DefaultURLGeneratorFactory - Class in org.biojava.bio.program.blast2html
  A simple default `URLGeneratorFactory` which returns a single `NcbiDatabaseURLGenerator` instance.
DefaultURLGeneratorFactory() - Constructor for class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
DEFINITION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DEFINITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
delegate - Variable in class org.biojava.bio.program.tagvalue.StateMachine
delegate(StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
delegate(StAXContentHandler) - Method in interface org.biojava.utils.stax.DelegationManager
delegates - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
delegationCache - Variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
DelegationManager - Interface in org.biojava.bio.seq.io.agave
  Interface which exposes delegation services offered by a StAX event source.
DelegationManager - Interface in org.biojava.utils.stax
  Interface which exposes delegation services offered by a StAX event source.
DELETE_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
DELETE_MYSQL4 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
DELETE_POSTGRESQL - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
deleteTerm(Term) - Method in class org.biojava.ontology.IntegerOntology
deleteTerm(Term) - Method in interface org.biojava.ontology.Ontology
  Remove a term from an ontology, together with all triples which refer to it.
deleteTerm(Term) - Method in class org.biojava.ontology.Ontology.Impl
deleteTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Remove a term from an ontology, together with all triples which refer to it. If you call this method with a plain Term instead of a ComparableTerm, it may not match any of the terms in the ontology as they are all stored as ComparableTerms.
DELIMITER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
depth - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
depth - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
DEPTH - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `DEPTH` indicating a change to the depth of the renderer.
DEPTH - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
DESC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
describeSequence(Sequence) - Method in class org.biojava.bio.program.phred.PhredFormat
  Return a suitable description line for a Sequence.
describeSequence(Sequence) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Return a suitable description line for a Sequence.
description - Variable in class org.biojava.bibliography.BibRef
  An account of the content of the cited resource.
description - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
description - Variable in class org.biojava.utils.candy.CandyEntry
  A value of this entry.
DESCRIPTION - Static variable in interface org.biojavax.bio.BioEntry
DESCRIPTION - Static variable in interface org.biojavax.Namespace
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableOntology
DESCRIPTION - Static variable in interface org.biojavax.ontology.ComparableTerm
DESCRIPTOR - Static variable in interface org.biojavax.ontology.ComparableTriple
destination - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition
  the terminus of this Transition
destroy() - Method in interface org.biojava.bibliography.BibRefQuery
  It frees all resources related to this query collection.
destroy() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It frees all resources related to this vocabulary.
destroySubcontext(Name) - Method in class org.biojava.naming.ObdaContext
destroySubcontext(String) - Method in class org.biojava.naming.ObdaContext
destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
  Breaks a transition between two states legal.
destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
det() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Determinant
det() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix determinant
DfaBuilder - Class in org.biojava.utils.automata
DiagonalAddKernel - Class in org.biojava.stats.svm
  Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
DiagonalCachingKernel - Class in org.biojava.stats.svm
  Caches the leading diagonal of a kernel matrix.
DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
  Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
  Creates a new DiagonalCachingKernel that nests k.
diddleQueue() - Method in class org.biojava.utils.IndexedChangeHub
DIGEST - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
DIGEST - Static variable in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
Digest - Class in org.biojava.bio.proteomics
  This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
Digest() - Constructor for class org.biojava.bio.proteomics.Digest
  Creates a new Digest Bean
dimensionRatio - Variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
disconnect() - Method in interface org.biojava.bibliography.BibRefQuery
  It disconnects from the repository.
disconnect() - Method in interface org.biojava.bibliography.BibRefSupport
  It closes connection with a utility object.
disconnect() - Method in interface org.biojava.utils.candy.CandyFinder
  It closes connection with the finder object.
disjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
disjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
DISPLACEMENT - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `DISPLACEMENT` indicating a change to the Y-axis displacement of the features.
displayString() - Method in class org.biojava.utils.ChangeSupport
DistDataSource - Interface in org.biojava.bio.seq.distributed
  Object which contributes data to a DistributedSequenceDB.
distForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
distOverAlignment(Alignment) - Static method in class org.biojava.bio.dist.DistributionTools
  Equivalent to distOverAlignment(a, false, 0.0).
distOverAlignment(Alignment, boolean, double) - Static method in class org.biojava.bio.dist.DistributionTools
  Creates an array of distributions, one for each column of the alignment.
distOverAlignment(Alignment, boolean) - Static method in class org.biojava.bio.dist.DistributionTools
  Creates an array of distributions, one for each column of the alignment.
DistributedSequenceDB - Class in org.biojava.bio.seq.distributed
  Sequence database from the meta-DAS system.
DistributedSequenceDB() - Constructor for class org.biojava.bio.seq.distributed.DistributedSequenceDB
Distribution - Interface in org.biojava.bio.dist
  An encapsulation of a probability distribution over the Symbols within an alphabet.
DISTRIBUTION - Static variable in interface org.biojava.bio.dp.EmissionState
  This signals that the distribution associate with an EmissionState has been altered.
Distribution.NullModelForwarder - Class in org.biojava.bio.dist
  Deprecated. use `new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)` instead
Distribution.NullModelForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.dist.Distribution.NullModelForwarder
  Deprecated. Create a new forwarder.
DistributionFactory - Interface in org.biojava.bio.dist
  A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - Class in org.biojava.bio.dist
  The default DistributionFactory implementation.
DistributionFactory.DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
DistributionLogo - Class in org.biojava.bio.gui
  The GUI component for rendering a DistributionLogo.
DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo
  Create a new DistributionLogo object.
DistributionTools - Class in org.biojava.bio.dist
  A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer - Interface in org.biojava.bio.dist
  An object that can be used to train a distribution up.
DistributionTrainerContext - Interface in org.biojava.bio.dist
  A context within a group of DistributionTrainers can be trained together.
DIVISION - Static variable in interface org.biojavax.bio.BioEntry
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
DIVISION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
DIVISION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
DivisionLkpReader - Class in org.biojava.bio.seq.db.emblcd
  `DivisionLkpReader` reads the "division.lkp" file of an EMBL CD-ROM format binary index.
DivisionLkpReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
  Creates a new `DivisionLkpReader`.
DNA - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
  The sequence label for the list of called bases.
DNA - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `DNA` indicates that a sequence contains DNA (deoxyribonucleic acid) symbols.
DNAAmbPack - Class in org.biojava.bio.symbol
  Packing utility class for DNA.
DNAAmbPack() - Constructor for class org.biojava.bio.symbol.DNAAmbPack
DNANoAmbPack - Class in org.biojava.bio.symbol
  A `Packing` implementation which handles the DNA alphabet, without any support for ambiguity symbols.
DNANoAmbPack(byte) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
  Construct a new packing which returns the specified byte value for unknown Symbols (such as ambiguity symbols).
DNANoAmbPack(Symbol) - Constructor for class org.biojava.bio.symbol.DNANoAmbPack
  Construct a new packing which translates unknown symbols into the specified symbol.
DNAStyle - Class in org.biojava.bio.gui
  A simple implementation of SymbolStyle optimized for DNA.
DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
dnaSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
  Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
dnaToken(Symbol) - Static method in class org.biojava.bio.seq.DNATools
  Get a single-character token for a DNA symbol
DNATools - Class in org.biojava.bio.seq
  Useful functionality for processing DNA sequences.
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
  Apply the annotation to a sequence.
docNumber - Variable in class org.biojava.bibliography.BiblioPatent
  The document number.
docOffice - Variable in class org.biojava.bibliography.BiblioPatent
  Document office.
DocRef - Interface in org.biojavax
  Represents a documentary reference.
DocRefAuthor - Interface in org.biojavax
  Represents an author of a documentary reference.
DocRefAuthor.Tools - Class in org.biojavax
  Useful tools for working with authors.
docType - Variable in class org.biojava.bibliography.BiblioPatent
  Document type.
DOI_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
  Holds a reference to the key that must be used to store DOI references.
doLayer(SequenceRenderContext, FeatureFilter) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
domain1 - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
DOMAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
doPreProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Emit any per-sequence header information.
doPrintConnections() - Method in class org.biojava.bio.structure.io.FileConvert
  returns if the Connections should be added default is true;
doProcessFeature(Feature, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Internal method to process an individual Feature.
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Internal method to process an individual Sequence.
doRefreshRenderers() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Find out if known tags are retained or dropped.
doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
DotState - Interface in org.biojava.bio.dp
  A Dot state.
DoubleAlphabet - Class in org.biojava.bio.symbol
  An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange - Class in org.biojava.bio.symbol
  A range of double values.
DoubleAlphabet.DoubleRange(double, double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
DoubleAlphabet.DoubleSymbol - Class in org.biojava.bio.symbol
  A single double value.
DoubleAlphabet.SubDoubleAlphabet - Class in org.biojava.bio.symbol
  A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of a double.
DoubleElementHandlerBase() - Constructor for class org.biojava.utils.stax.DoubleElementHandlerBase
DoubleTokenization - Class in org.biojava.bio.seq.io
DoubleTokenization() - Constructor for class org.biojava.bio.seq.io.DoubleTokenization
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
  this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
  this method is expected to reverse-translate any symbol in the source alphabet.
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
doUntranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
DP - Class in org.biojava.bio.dp
  Objects that can perform dymamic programming operations upon sequences with HMMs.
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
dp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
dp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
dp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
DP.ReverseIterator - Class in org.biojava.bio.dp
DP.ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
DPCompiler - Class in org.biojava.bio.dp.twohead
  This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
DPCompiler(boolean) - Constructor for class org.biojava.bio.dp.twohead.DPCompiler
DPCursor - Interface in org.biojava.bio.dp.onehead
  Encapsulates the dynamic programmming matrix, and the context within algorithms work.
DPFactory - Interface in org.biojava.bio.dp
  The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory - Class in org.biojava.bio.dp
DPFactory.DefaultFactory(CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.DPFactory.DefaultFactory
DPInterpreter - Class in org.biojava.bio.dp.twohead
DPInterpreter(DP) - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter
DPInterpreter.Maker - Class in org.biojava.bio.dp.twohead
DPInterpreter.Maker() - Constructor for class org.biojava.bio.dp.twohead.DPInterpreter.Maker
DPMatrix - Interface in org.biojava.bio.dp
DR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
DRAW_CALL_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to fill in the callboxes for calls of nucleotide A.
DRAW_CALL_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to fill in the callboxes for calls of nucleotide C.
DRAW_CALL_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to fill in the callboxes for calls of nucleotide G.
DRAW_CALL_OTHER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).
DRAW_CALL_SEPARATORS - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to draw vertical lines separating the calls.
DRAW_CALL_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to fill in the callboxes for calls of nucleotide T.
DRAW_TRACE_A - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to draw the chromatogram trace for nucleotide A.
DRAW_TRACE_C - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to draw the chromatogram trace for nucleotide C.
DRAW_TRACE_G - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to draw the chromatogram trace for nucleotide G.
DRAW_TRACE_T - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to draw the chromatogram trace for nucleotide T.
drawableCallboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Flag for drawable call boxes.
drawLine(Graphics2D, SequenceRenderContext, int, StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
  draws required bar in correct translation frame.
drawTo(Graphics2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Draws the chromatogram onto the provided graphics context.
dropBoundaryValues() - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
DROSOPHILA_MELANOGASTER_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Drosophila melanogaster codon preferences
dsCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
DummyCrossReferenceResolver - Class in org.biojavax
  A simple implementation of CrossReferenceResolver.
DummyCrossReferenceResolver() - Constructor for class org.biojavax.DummyCrossReferenceResolver
DummyRichSequenceHandler - Class in org.biojavax.bio.seq
DummyRichSequenceHandler() - Constructor for class org.biojavax.bio.seq.DummyRichSequenceHandler
DummySequence - Class in org.biojava.bio.seq.impl
  A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
DummySequence(String, String) - Constructor for class org.biojava.bio.seq.impl.DummySequence
DummySequenceDB - Class in org.biojava.bio.seq.db
  `DummySequenceDB` is an implementation which contains only a `DummySequence`.
DummySequenceDB(String) - Constructor for class org.biojava.bio.seq.db.DummySequenceDB
DummySequenceDBInstallation - Class in org.biojava.bio.seq.db
  `DummySequenceDBInstallation` is an implementation which returns the same `DummySequenceDB` instance regardless of the identifier used to retrieve a database.
DummySequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.DummySequenceDBInstallation
DummySymbolList - Class in org.biojava.bio.symbol
  Symbol list which just consists of non-informative symbols.
DummySymbolList(FiniteAlphabet, int) - Constructor for class org.biojava.bio.symbol.DummySymbolList
DummySymbolList(Alphabet, int, Symbol) - Constructor for class org.biojava.bio.symbol.DummySymbolList
dumpBlocks() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Debugging method
duplicate() - Method in class org.biojava.utils.automata.NfaSubModel
  Makes a deep clone of this instance.
DuplicateTaxonException - Exception in org.biojava.bio.program.homologene
DuplicateTaxonException() - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException
DuplicateTaxonException(Throwable, String) - Constructor for exception org.biojava.bio.program.homologene.DuplicateTaxonException

## E

e() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glutamic Acid
EbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html
  Simple URL generator for EMBL at the EBI.
EbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
EbiFormat - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
EbiFormat() - Constructor for class org.biojava.bio.taxa.EbiFormat
  Deprecated.
EC_FROM_STRING - Static variable in class org.biojava.bio.program.formats.FormatTools
EC_PATTERN - Static variable in interface org.biojava.bio.EcNumber
  A Pattern that can be used to parse EC strings into the indiidual numbers.
eCache - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
eCache - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
ECHIN_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the echinoderm mitochondrial genetic code.
Echo - Class in org.biojava.bio.program.tagvalue
  A simple listener that just echoes events back to the console.
Echo() - Constructor for class org.biojava.bio.program.tagvalue.Echo
EcNumber - Interface in org.biojava.bio
  An ec (enzyme classification) number.
EcNumber.Impl - Class in org.biojava.bio
  A simple implementation of EcNumber.
EcNumber.Impl(int, int, int, int) - Constructor for class org.biojava.bio.EcNumber.Impl
  Make a new EcNumber.Impl with the data provided.
ECOLI - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Escherichia coli codon preferences
edit(Object, Edit) - Method in interface org.biojava.bio.alignment.EditableAlignment
  edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
edit(Object, Edit) - Method in class org.biojava.bio.alignment.FlexibleAlignment
edit(Edit) - Method in class org.biojava.bio.dp.SimpleStatePath
edit(Edit) - Method in class org.biojava.bio.program.das.DASSequence
edit(Edit) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
edit(Edit) - Method in class org.biojava.bio.seq.impl.DummySequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.RevCompSequence
  edit() will try to edit the underlying Sequence.
edit(Edit) - Method in class org.biojava.bio.seq.impl.SimpleSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.SubSequence
edit(Edit) - Method in class org.biojava.bio.seq.impl.ViewSequence
edit(Edit) - Method in class org.biojava.bio.seq.NewSimpleAssembly
edit(Edit) - Method in class org.biojava.bio.seq.SimpleAssembly
edit(Edit) - Method in class org.biojava.bio.symbol.AbstractSymbolList
Edit - Class in org.biojava.bio.symbol
  Encapsulates an edit operation on a SymbolList.
Edit(int, int, SymbolList) - Constructor for class org.biojava.bio.symbol.Edit
  Create a new Edit.
Edit(int, Alphabet, Symbol) - Constructor for class org.biojava.bio.symbol.Edit
  Convenience construtor for making single residue changes
edit(Edit) - Method in class org.biojava.bio.symbol.RelabeledAlignment
edit(Edit) - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Apply and edit to the SymbolList as specified by Edit.
EDIT - Static variable in interface org.biojava.bio.symbol.SymbolList
  Signals that the SymbolList is being edited.
edit(Edit) - Method in interface org.biojava.bio.symbol.SymbolList
  Apply an edit to the SymbolList as specified by the edit object.
edit(RichSequence, Edit) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Apply an edit to the Sequence as specified by the edit object.

  ## Description

  All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

  When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

  The pos and pos+length should always be valid positions on the SymbolList to:

  - be edited (between 0 and symL.length()+1).
  - To append to a sequence, pos=symL.length()+1, pos=0.
  - To insert something at the beginning of the sequence, set pos=1 and length=0.

  ## Examples

  `

       RichSequence seq = //code to initialize RichSequence
       System.out.println(seq.seqString());

       // delete 5 bases from position 4
       Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
       seq.edit(ed);
       System.out.println(seq.seqString());

       // delete one base from the start
       ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
       seq.edit(ed);

       // delete one base from the end
       ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
       seq.edit(ed);
       System.out.println(seq.seqString());

       // overwrite 2 bases from position 3 with "tt"
       ed = new Edit(3, 2, DNATools.createDNA("tt"));
       seq.edit(ed);
       System.out.println(seq.seqString());

       // add 6 bases to the start
       ed = new Edit(1, 0, DNATools.createDNA("aattgg");
       seq.edit(ed);
       System.out.println(seq.seqString());

       // add 4 bases to the end
       ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
       seq.edit(ed);
       System.out.println(seq.seqString());

       // full edit
       ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
       seq.edit(ed);
       System.out.println(seq.seqString());

  `
edit(RichSequence, Edit) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Apply an edit to the Sequence as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Apply an edit to the SymbolList as specified by the edit object. IGNORED
edit(RichSequence, Edit) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Apply an edit to the Sequence as specified by the edit object.
edit(Edit) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Apply an edit to the SymbolList as specified by the edit object.
EditableAlignment - Interface in org.biojava.bio.alignment
  EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
edition - Variable in class org.biojava.bibliography.BiblioBook
  Edition.
editor - Variable in class org.biojava.bibliography.BiblioBook
  Editor.
EDITOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EDITOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
eig() - Method in class org.biojava.bio.structure.jama.Matrix
  Eigenvalue Decomposition
EigenvalueDecomposition - Class in org.biojava.bio.structure.jama
  Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.EigenvalueDecomposition
  Check for symmetry, then construct the eigenvalue decomposition provides a way to access D and V.
elementLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
ElementRecognizer - Interface in org.biojava.bio.program.xff
  Simple interface for filtering SAX/StAX startElement events.
ElementRecognizer - Interface in org.biojava.bio.seq.io.agave
  This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer - Interface in org.biojava.bio.seq.io.game
  Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.program.xff
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.agave
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer - Class in org.biojava.bio.seq.io.game
ElementRecognizer.AllElementRecognizer() - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
ElementRecognizer.ByLocalName - Class in org.biojava.bio.program.xff
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.agave
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
ElementRecognizer.ByLocalName - Class in org.biojava.bio.seq.io.game
  Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
ElementRecognizer.ByNSName - Class in org.biojava.bio.program.xff
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.agave
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
ElementRecognizer.ByNSName - Class in org.biojava.bio.seq.io.game
  Filter elements by name and namespace.
ElementRecognizer.ByNSName(String, String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
ElementRecognizer.HasAttribute - Class in org.biojava.bio.program.xff
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.agave
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
ElementRecognizer.HasAttribute - Class in org.biojava.bio.seq.io.game
  Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute(String) - Constructor for class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
EllipticalBeadRenderer - Class in org.biojava.bio.gui.sequence
  `EllipticalBeadRenderer` renders features as simple ellipses.
EllipticalBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  Creates a new `EllipticalBeadRenderer` object with the default settings.
EllipticalBeadRenderer(double, double, Paint, Paint, Stroke, double) - Constructor for class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  Creates a new `EllipticalBeadRenderer`.
email - Variable in class org.biojava.bibliography.BiblioPerson
  Their e-mail address.
Embl - Class in org.biojava.bio.program.formats
Embl() - Constructor for class org.biojava.bio.program.formats.Embl
EMBL - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser
  A LineSplitParser pre-configured to process EMBL-style flat files.
EMBL - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `EMBL` indicates that the sequence format is EMBL.
Embl2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
  Map EMBL data into AGAVE format
EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `EMBL_AA` premade EMBL | AA.
EMBL_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `EMBL_DNA` premade EMBL | DNA.
EMBL_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
  The name of the current format
EMBL_GENBANK_FEATURE_TABLE_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
EMBL_PRE87_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
  The name of the Pre-87 format
EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `EMBL_RNA` premade EMBL | RNA.
EMBL_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
EmblCDROMIndexReader - Class in org.biojava.bio.seq.db.emblcd
  `EmblCDROMIndexReader` is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying `InputStream`.
EmblCDROMIndexReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  Creates a new `EmblCDROMIndexReader` instance.
EmblCDROMIndexStore - Class in org.biojava.bio.seq.db
  `EmblCDROMIndexStore`s implement a read-only `IndexStore` backed by EMBL CD-ROM format binary indices.
EmblCDROMIndexStore(File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore
  Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
EmblCDROMIndexStore(File, File, File, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.EmblCDROMIndexStore
  Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
EmblCDROMRandomAccess - Class in org.biojava.bio.seq.db.emblcd
  `EmblCDROMRandomAccess` is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files.
EmblCDROMRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  Creates a new `EmblCDROMRandomAccess` object.
EmblFileFormer - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblFileFormer() - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated. Creates a new `EmblFileFormer` using `System.out` stream.
EmblFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated. Creates a new `EmblFileFormer` using the specified stream.
EMBLFormat - Class in org.biojavax.bio.seq.io
  Format reader for EMBL files.
EMBLFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat
EMBLFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some EMBL-specific terms.
EMBLFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLFormat.Terms
EmblLikeFormat - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeFormat() - Constructor for class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
EmblLikeLocationParser - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.EmblProcessor
  Deprecated.
EmblProcessor.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps SequenceBuilders in an EmblProcessor
EmblProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.EmblProcessor.Factory
  Deprecated.
EmblReferenceComparator - Class in org.biojava.bio.seq.io
EmblReferenceComparator() - Constructor for class org.biojava.bio.seq.io.EmblReferenceComparator
EMBLXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
  The name of this format
EMBLxmlFormat - Class in org.biojavax.bio.seq.io
  Format reader for EMBLxml files.
EMBLxmlFormat() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat
EMBLxmlFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some EMBLxml-specific terms.
EMBLxmlFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
emissionAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
  Alphabet that is emitted by the emission states.
emissionAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
emissionAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
EmissionCache - Class in org.biojava.bio.dp.twohead
  Cache for columns of emission probabilities in pair-wise alignment algorithms.
EmissionCache(Alphabet, State[], int, ScoreType) - Constructor for class org.biojava.bio.dp.twohead.EmissionCache
emissions - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emissions - Variable in class org.biojava.bio.dp.twohead.Cell
emissionsNull - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsOdds - Variable in class org.biojava.bio.dp.onehead.SingleDP
emissionsProb - Variable in class org.biojava.bio.dp.onehead.SingleDP
EmissionState - Interface in org.biojava.bio.dp
  A state in a markov process that has an emission spectrum.
EMPTY - Static variable in interface org.biojava.bio.annodb.AnnotationDB
  An AnnotationDB that is always empty.
EMPTY - Static variable in interface org.biojava.bio.CollectionConstraint
  `EMPTY` is a constraint which only accepts the empty set.
empty - Static variable in interface org.biojava.bio.symbol.Location
  The `Location` which contains no points.
EMPTY_ALPHABET - Static variable in interface org.biojava.bio.symbol.Alphabet
  A really useful static alphabet that is always empty.
EMPTY_ANNOTATION - Static variable in interface org.biojava.bio.Annotation
  A really useful empty and immutable annotation object.
EMPTY_ANNOTATION - Static variable in interface org.biojavax.RichAnnotation
EMPTY_FEATURE_HOLDER - Static variable in interface org.biojava.bio.seq.FeatureHolder
EMPTY_LINE_EOR - Static variable in interface org.biojava.bio.program.tagvalue.TagValueParser
  `EMPTY_LINE_EOR` is a special EOR value which allows an empty line to be used as a record separator.
EMPTY_LIST - Static variable in interface org.biojava.bio.symbol.SymbolList
  A useful object that represents an empty symbol list, to avoid returning null.
EMPTY_LOCATION - Static variable in interface org.biojavax.bio.seq.RichLocation
  The empty location matches nothing.
EMPTY_PAIRWISE - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  Constant `EMPTY_PAIRWISE` is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
EMPTY_POSITION - Static variable in interface org.biojavax.bio.seq.Position
  The empty position lies nowhere.
emptyBP - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
emptyBP - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
emptyFeature - Variable in class org.biojavax.bio.seq.io.RichSeqIOAdapter
  This is a dummy feature.
emptyList(Alphabet) - Static method in class org.biojava.bio.symbol.SymbolListViews
  Get a new immutable, empty symbol list with the given alphabet.
EmptyRichAnnotation - Class in org.biojavax
  A place holder for a RichAnnotation that prevents null having to be used
EmptyRichAnnotation() - Constructor for class org.biojavax.EmptyRichAnnotation
EmptyRichLocation - Class in org.biojavax.bio.seq
  An Empty implementation of RichLocation.
EmptyRichLocation() - Constructor for class org.biojavax.bio.seq.EmptyRichLocation
end() - Method in interface org.biojava.bio.search.BioMatcher
  Get the last symbol index that matches the pattern.
end() - Method in class org.biojava.bio.search.MaxMismatchMatcher
end - Variable in class org.biojava.utils.automata.FiniteAutomaton
end() - Method in class org.biojava.utils.regex.Matcher
  Returns the index of the last character matched, plus one.
end(int) - Method in class org.biojava.utils.regex.Matcher
  Returns the index of the last Symbol, plus one, of the subsequence captured by the given group during the previous match operation.
END_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
END_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
END_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
endDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  end of data for DB
endDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endDocument() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
endDocument() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
endDocument() - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
  Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.gff.GFFFilterer
endDocument() - Method in class org.biojava.bio.program.gff.GFFWriter
  Flushes the PrintWriter to make sure that everything is written.
endDocument() - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
  Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement(String, String, String) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
  Called when the end of an element is reached.
endElement(String, String, String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
endElement(String, String, String) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
endElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.FeatureHandler
  StAX callback for element ends.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
endElement() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
endElement(String, String, String) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
endElement(String, String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Handles basic exit processing.
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.CharElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.IntElementHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.LongElementHandlerBase
endElement(String, String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.utils.stax.StAXContentHandler
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StringElementHandlerBase
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
  when exiting, put the DbXrefElement into the annotation bundle
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  Element specific exit handler Subclass to do anything useful.
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler.SeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.GAMESpanHandler
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Element specific exit handler Subclass to do anything useful.
endFeature() - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
  Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endFeature() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endFeature() - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Mark the end of data associated with one specific feature.
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endFeature() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endFeature() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Null implementation.
endFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Mark the end of data associated with one specific feature.
endGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  end of data for group
endGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
endHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
endHeader() - Method in class org.biojava.bio.search.SearchContentFilter
endHeader() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `endHeader` method indicates the end of a formatted header.
endHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endHit() - Method in class org.biojava.bio.search.SearchContentFilter
endHit() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `endHit` method indicates the end of a formatted hit.
endHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
endLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
endOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  end of data for this Orthologue
endOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  end of data for this OrthoPair
endOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
endPrefixMapping(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endPrefixMapping(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
endPrefixMapping(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
endPrefixMapping(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
endRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
endRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
  The current record has ended.
endSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
endSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
  Indicates that a sequence has been searched against a DataStore.
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
endSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
endSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
endSearch() - Method in class org.biojava.bio.search.SearchContentFilter
endSearch() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `endSearch` method indicates the end of useful search information.
endSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.OrganismParser
  Deprecated.
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
endSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
endSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
endSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Notify the listener that processing of the sequence is complete.
endSequence() - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
endSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
endSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
endSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener that processing of the sequence is complete.
endSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
endSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
endSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
endSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
endSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
endSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
endSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `endSubHit` method indicates the end of a formatted subhit.
endSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
endTag() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.Aggregator
endTag() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
endTag() - Method in class org.biojava.bio.program.tagvalue.Echo
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer
endTag() - Method in class org.biojava.bio.program.tagvalue.Indexer2
endTag() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
endTag() - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
endTag() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine
endTag() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
endTag() - Method in class org.biojava.bio.program.tagvalue.TagDropper
endTag() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
  End the current tag.
endTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
endTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
endTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
endTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
enrich(Feature) - Static method in class org.biojavax.bio.seq.RichFeature.Tools
  Takes a normal Feature and attempts to convert it into a RichFeature.
enrich(Location) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Attempts to convert a plain Location into a RichLocation.
enrich(Sequence) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Boldly attempts to convert a `Sequence` into a `RichSequence`.
entropy(Distribution, Symbol) - Static method in class org.biojava.bio.gui.DistributionLogo
  Calculate the information content of a symbol in bits.
entry - Variable in class org.biojava.utils.candy.CandyEntry
  A unique identifier of this entry.
ENTRY_ACCESSION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_CREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_DIVISION_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_NAMESPACE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
ENTRY_RELCREATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_RELUPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ENTRY_UPDATED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ENTRY_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
EntryNamIdxReader - Class in org.biojava.bio.seq.db.emblcd
  `EntryNamIdxReader` reads the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamIdxReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
  Creates a new `EntryNamIdxReader`.
EntryNamRandomAccess - Class in org.biojava.bio.seq.db.emblcd
  `EntryNamRandomAccess` objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamRandomAccess(File, int, int, long) - Constructor for class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
entrySet() - Method in class org.biojava.utils.BeanAsMap
entrySet() - Method in class org.biojava.utils.cache.WeakValueHashMap
entrySet() - Method in class org.biojava.utils.OverlayMap
entrySet() - Method in class org.biojava.utils.SmallMap
entryStatus - Variable in class org.biojava.bibliography.BibRef
  It defines information related to the citation itself rather than to the cited resource.
enzyme - Variable in class org.biojava.bio.molbio.RestrictionSite.Template
  `enzyme` `RestrictionEnzyme` field.
Enzyme - Class in org.biojava.bio.program.formats
Enzyme() - Constructor for class org.biojava.bio.program.formats.Enzyme
eof() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
  Checks if the end of the file or stream is reached.
eq - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
equals(Object) - Method in class org.biojava.bio.AbstractAnnotation
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
equals(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
equals(Object) - Method in class org.biojava.bio.dist.AbstractDistribution
equals(Object) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
equals(Object) - Method in class org.biojava.bio.dp.TrainerTransition
  Two transitions are equal if they have the same trainer, from and to states.
equals(Object) - Method in class org.biojava.bio.dp.Transition
  Two transitions are equal if they have the same from and to states.
equals(Object) - Method in class org.biojava.bio.EcNumber.Impl
equals(Object) - Method in class org.biojava.bio.gui.sequence.SequencePanel
equals(Object) - Method in class org.biojava.bio.molbio.RestrictionEnzyme
equals(Object) - Method in class org.biojava.bio.program.das.DataSource
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
equals(Object) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
equals(Object) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
equals(Object) - Method in class org.biojava.bio.seq.Feature.Template
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.And
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Not
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.Or
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
equals(Object) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
equals(Object) - Method in class org.biojava.bio.seq.impl.SimpleFeature
equals(Object) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocation
equals(Object) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
equals(Object) - Method in class org.biojava.bio.symbol.AbstractSymbolList
  Provides logical equality for two SymbolLists that share the same list of canonical symbols
equals(Object) - Method in class org.biojava.bio.symbol.CircularLocation
equals(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
equals(Object) - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
equals(Object) - Method in interface org.biojava.bio.symbol.Location
  Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
equals(Object) - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. Two taxa are equal if they have equivalent children, common and scientific names.
equals(Object) - Method in class org.biojava.ontology.Term.Impl
equals(Object) - Method in interface org.biojava.ontology.Triple
  Check to see if an object is an equivalent Triple.
equals(Object) - Method in class org.biojava.ontology.Triple.Impl
  Two triples are equal if all their fields are identical.
equals(Object) - Method in class org.biojava.utils.ListTools.Doublet
equals(Object) - Method in class org.biojava.utils.ListTools.Triplet
equals(Object) - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
equals(boolean, boolean) - Static method in class org.biojava.utils.ObjectUtil
equals(int, int) - Static method in class org.biojava.utils.ObjectUtil
equals(long, long) - Static method in class org.biojava.utils.ObjectUtil
equals(float, float) - Static method in class org.biojava.utils.ObjectUtil
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
equals(boolean[], boolean[]) - Static method in class org.biojava.utils.ObjectUtil
equals(int[], int[]) - Static method in class org.biojava.utils.ObjectUtil
equals(long[], long[]) - Static method in class org.biojava.utils.ObjectUtil
equals(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
equals(Object) - Method in class org.biojava.utils.TypedProperties
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
equals(Object) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
equals(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Checks if this location is equivalent to the other.

  Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location. Locations are equal if their term, min, max, strand, and crossref are the same, and if their rank is the same too. Compound locations are only equal to other Locations if all their components are equal.

equals(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Checks if this location is equivalent to the other. Empty Rich Locations only match other Empty Rich Locations
equals(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
  Strands are equal if their numbers and symbols match.
equals(Object) - Method in class org.biojavax.bio.seq.SimplePosition
  Two positions are equal if they share all parameters in common, eg.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Features are equal when they have the same parent, type, source and rank.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Relations are equal if their objects, subjects and terms are equal.
equals(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Checks if this location is equivalent to the other. Locations are equal if their term, min, max, strand, and crossref are the same, and if their rank is the same too.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntry
  Two bioentries are equal if they share the same namespace, name, accession and version.
equals(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Relationships are equal if they share the same object, subject, rank and term.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  NCBITaxon objects are equal if their NCBITaxID fields match.
equals(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Two taxon names are equal if their name and class match.
equals(Object) - Method in class org.biojavax.EmptyRichAnnotation
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Ontologies are equal if their names are equal.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Two terms are equal if they are in the same ontology and share the same name.
equals(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Check to see if an object is an equivalent Triple. Triples are equal only if they are from the same ontology and share the same subject, object and predicate.
equals(Object) - Method in class org.biojavax.SimpleComment
  Two comments are defined as equal if their text values and rankings are identical.
equals(Object) - Method in class org.biojavax.SimpleCrossRef
  Equality is defined as having the same database name, accession and version.
equals(Object) - Method in class org.biojavax.SimpleDocRef
  Document references are equal if they have the same author and location and title.
equals(Object) - Method in class org.biojavax.SimpleDocRefAuthor
  Document references are equal if they have all fields the same.
equals(Object) - Method in class org.biojavax.SimpleNamespace
  Namespaces are equal only by name.
equals(Object) - Method in class org.biojavax.SimpleNote
  Notes are equal if they have the same rank and term.
equals(Object) - Method in class org.biojavax.SimpleRankedCrossRef
  Ranked cross references are the same if they have the same rank and refer to the same cross reference (cross references are equal).
equals(Object) - Method in class org.biojavax.SimpleRankedDocRef
  Two ranked document references are equal if they have the same rank and refer to the same document reference.
EQUIVALENCE - Static variable in class org.biojava.ontology.OntoTools
EQUIVALENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
  Use this to define equivalent names for things.
ERROR_FEATURES_PROPERTY - Static variable in class org.biojava.bio.seq.io.SequenceBuilderBase
estimatedSize - Variable in class org.biojava.bibliography.BiblioWebResource
  An estomated size in kilobytes.
EUPL_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the euplotid nuclear genetic code.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
evaluate(BlastLikeSearchFilter.Node) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
  computes the outcome of this filter on the specified node and stores it.
evaluate(BlastLikeSearchFilter.Node) - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
evaluate(Object, Object) - Method in class org.biojava.stats.svm.CachingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
  Return the dot product of a, b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
  Returns the kernel product of two Objects.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.LinearKernel
  Deprecated. The linear kernel is equal to the dot product of a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.ListSumKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.NormalizingKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.PolynomialKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.RadialBaseKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SigmoidKernel
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Evaluate the kernel function between two SparseVectors.
evaluate(Object, Object) - Method in interface org.biojava.stats.svm.SVMKernel
  Return the dot product of two vectors in an arbitrary feature space.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
  Calculate the dot product between the SuffixTrees a and b.
EVIDENCE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_ATTRIBUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_CATEGORY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
EVIDENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
exec(String) - Method in class org.biojava.utils.ExecRunner
  The exec(String) method runs a process inside of a watched thread.
exec(String, String[]) - Method in class org.biojava.utils.ExecRunner
  Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
exec(String, OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner
  Convenience method for calling exec with OutputStreams.
exec(String, String[], OutputStream, OutputStream) - Method in class org.biojava.utils.ExecRunner
  Convenience method for calling exec with OutputStreams.
exec(String, PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner
  The `exec(String, PrintWriter, PrintWriter)` method runs a process inside of a watched thread.
exec(String, String[], PrintWriter, PrintWriter) - Method in class org.biojava.utils.ExecRunner
  The `exec(String, PrintWriter, PrintWriter)` method runs a process inside of a watched thread.
exec(String[], Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools
  Deprecated. Execute the specified command and wait for it to return.
exec(String[], String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools
  Deprecated. Execute the specified command and wait for it to return, or kill it if the specified timeout expires first.
exec(String, Reader, Writer, Writer) - Static method in class org.biojava.utils.ProcessTools
  Deprecated. Execute the specified command and wait for it to return.
exec(String, String[], File, Reader, Writer, Writer, long) - Static method in class org.biojava.utils.ProcessTools
  Deprecated. Execute the specified command and wait for it to return.
ExecRunner - Class in org.biojava.utils
  Makes running external executables easier, optionally under a watched thread.
ExecRunner() - Constructor for class org.biojava.utils.ExecRunner
  Basic ExecRunner constructor.
ExecRunner(String) - Constructor for class org.biojava.utils.ExecRunner
  ExecRunner constructor which also conveniently runs exec(String).
ExecRunner(String, String[]) - Constructor for class org.biojava.utils.ExecRunner
  ExecRunner constructor which also conveniently runs exec(String).
execute(String) - Static method in class org.biojava.utils.process.ExternalProcess
  Executes an external program.
execute(String, String, StringWriter, StringWriter) - Static method in class org.biojava.utils.process.ExternalProcess
  Executes an external program.
execute() - Method in class org.biojava.utils.process.ExternalProcess
  Executes the external process and waits for its termination.
execute(Properties) - Method in class org.biojava.utils.process.ExternalProcess
  Executes the external process and waits for its termination.
expandCache(int) - Method in class org.biojava.utils.io.CachingInputStream
  Expands the cache to hold some number of `additionalBytes`.
ExternalProcess - Class in org.biojava.utils.process
  Utility class to execute an external process and to handle the `STDOUT`, `STDERR` and `STDIN` streams in multiple threads managed by a thread pool.
ExternalProcess() - Constructor for class org.biojava.utils.process.ExternalProcess
  Initializes the external process.
ExternalProcess(ThreadPool) - Constructor for class org.biojava.utils.process.ExternalProcess
  Initializes the external process.
extractOverlappingLocation(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Try to determine the minimal location which all features matching a given filter must overlap.
extras - Variable in class org.biojava.utils.candy.CandyEntry
  A container for the additional properties represented by this entry.

## F

f() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Phenylalanine
factorize(Alphabet, Set) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet.
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SimpleSequenceBuilder
FACTORY - Static variable in class org.biojava.bio.seq.io.SmartSequenceBuilder
FACTORY - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
  Accessor for the default factory.
FALSE - Static variable in class org.biojava.utils.TriState
FASTA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `FASTA` indicates that the alignment format is Fasta.
FASTA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `FASTA` indicates that the sequence format is Fasta.
FASTA_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `FASTA_AA` premade FASTA | AA;
FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `FASTA_AA` premade FASTA | AA.
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `FASTA_DNA` premade FASTA | DNA;
FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `FASTA_DNA` premade FASTA | DNA.
FASTA_FORMAT - Static variable in class org.biojavax.bio.seq.io.FastaFormat
  The name of this format
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `FASTA_RNA` premade FASTA | RNA;
FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `FASTA_RNA` premade FASTA | RNA.
FastaAlignmentFormat - Class in org.biojava.bio.seq.io
  This class implements the AlignmentFormat interface to read FASTA alignments.
FastaAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.FastaAlignmentFormat
FastaDescriptionLineParser - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser
  Deprecated.
FastaDescriptionLineParser.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaDescriptionLineParser.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
  Deprecated.
FastaFormat - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat
  Deprecated.
FastaFormat - Class in org.biojavax.bio.seq.io
  Format object representing FASTA files.
FastaFormat() - Constructor for class org.biojavax.bio.seq.io.FastaFormat
FastaSearchSAXParser - Class in org.biojava.bio.program.sax
  `FastaSearchSAXParser` is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).
FastaSearchSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSearchSAXParser
  Creates a new `FastaSearchSAXParser` instance.
FastaSequenceSAXParser - Class in org.biojava.bio.program.sax
  A SAX2 parser for dealing with multiple sequences in FASTA format.
FastaSequenceSAXParser() - Constructor for class org.biojava.bio.program.sax.FastaSequenceSAXParser
  Initialises internal state Sets namespace prefix to "biojava"
FastXMLWriter - Class in org.biojava.utils.xml
  Simple implementation of XMLWriter, optimized for speed.
FastXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.FastXMLWriter
Feature - Interface in org.biojava.bio.seq
  A feature within a sequence, or nested within another feature.
FEATURE - Static variable in interface org.biojavax.bio.seq.RichLocation
Feature.ByLocationComparator - Class in org.biojava.bio.seq
  `ByLocationComparator` compares `Feature`s by the minimum base position of their `Location`.
Feature.ByLocationComparator() - Constructor for class org.biojava.bio.seq.Feature.ByLocationComparator
Feature.Template - Class in org.biojava.bio.seq
  Template class for a plain feature.
Feature.Template() - Constructor for class org.biojava.bio.seq.Feature.Template
FEATURE_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_COLLAPSING - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
FEATURE_DESC_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_FLAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
FEATURE_FROM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.FeatureHandler
FEATURE_HEADER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_INTERBP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_INTERVALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ISCOMP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_KEY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_LINE_PREFIX - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
FEATURE_LOC_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_OPERATOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_ORIGINAL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_PARTIAL3_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_PARTIAL5_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_POINT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_RENDERER - Static variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
FEATURE_TABLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
FEATURE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
FEATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FEATURE_TO_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATURE_VARIATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
FeatureBlockSequenceRenderer - Class in org.biojava.bio.gui.sequence
  `FeatureBlockSequenceRenderer` forms a bridge between `Sequence` rendering and `Feature` rendering.
FeatureBlockSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  Creates a new `FeatureBlockSequenceRenderer` which uses a `BasicFeatureRenderer` as its renderer.
FeatureBlockSequenceRenderer(FeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  Creates a new `FeatureBlockSequenceRenderer` which uses the specified `FeatureRenderer`.
featureData(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
  Deprecated.
FeatureFilter - Interface in org.biojava.bio.seq
  A filter for accepting or rejecting a feature.
featureFilter(FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
FeatureFilter.And - Class in org.biojava.bio.seq
  A filter that returns all features accepted by both child filter.
FeatureFilter.And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
FeatureFilter.AnnotationContains - Class in org.biojava.bio.seq
  Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.AnnotationContains(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.AnnotationContains
  Make a new AnnotationContains that will accept features with an annotation bundle where the value-set assosiated with the property `key` contains a member equal to `value`.
FeatureFilter.ByAncestor - Class in org.biojava.bio.seq
  Filter by applying a nested `FeatureFilter` to all ancestor features.
FeatureFilter.ByAncestor(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAncestor
FeatureFilter.ByAnnotation - Class in org.biojava.bio.seq
  Retrieve features that contain a given annotation with a given value.
FeatureFilter.ByAnnotation(Object, Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotation
  Make a new ByAnnotation that will accept features with an annotation bundle containing 'value' associated with 'key'.
FeatureFilter.ByAnnotationType - Class in org.biojava.bio.seq
  A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByAnnotationType() - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
FeatureFilter.ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
FeatureFilter.ByChild - Class in org.biojava.bio.seq
  Filter by applying a nested `FeatureFilter` to the child features.
FeatureFilter.ByChild(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByChild
FeatureFilter.ByClass - Class in org.biojava.bio.seq
  Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByClass(Class) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByClass
FeatureFilter.ByComponentName - Class in org.biojava.bio.seq
  Accepts features which are ComponentFeatures and have a `componentSequenceName` property of the specified value.
FeatureFilter.ByComponentName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByComponentName
FeatureFilter.ByDescendant - Class in org.biojava.bio.seq
  Filter by applying a nested `FeatureFilter` to all descendant features.
FeatureFilter.ByDescendant(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByDescendant
FeatureFilter.ByFeature - Class in org.biojava.bio.seq
  Accept only features which are equal to the specified feature
FeatureFilter.ByFeature(Feature) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByFeature
FeatureFilter.ByPairwiseScore - Class in org.biojava.bio.seq
  `ByPairwiseScore` is used to filter `SimilarityPairFeature`s by their score.
FeatureFilter.ByPairwiseScore(double, double) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
  Creates a new `ByPairwiseScore`.
FeatureFilter.ByParent - Class in org.biojava.bio.seq
  Filter by applying a nested `FeatureFilter` to the parent feature.
FeatureFilter.ByParent(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByParent
FeatureFilter.BySequenceName - Class in org.biojava.bio.seq
  Accept features that reside on a sequence with a particular name.
FeatureFilter.BySequenceName(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySequenceName
FeatureFilter.BySource - Class in org.biojava.bio.seq
  Construct one of these to filter features by source.
FeatureFilter.BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource
  Create a BySource filter that filters in all features which have sources equal to source.
FeatureFilter.ByType - Class in org.biojava.bio.seq
  Construct one of these to filter features by type.
FeatureFilter.ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType
  Create a ByType filter that filters in all features with type fields equal to type.
FeatureFilter.ContainedByLocation - Class in org.biojava.bio.seq
  A filter that returns all features contained within a location.
FeatureFilter.ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
  Creates a filter that returns everything contained within loc.
FeatureFilter.FrameFilter - Class in org.biojava.bio.seq
  Accept features with a given reading frame.
FeatureFilter.FrameFilter(FramedFeature.ReadingFrame) - Constructor for class org.biojava.bio.seq.FeatureFilter.FrameFilter
  Build a new filter that matches all features of a reading frame.
FeatureFilter.HasAnnotation - Class in org.biojava.bio.seq
  Retrieve features that contain a given annotation with any value.
FeatureFilter.HasAnnotation(Object) - Constructor for class org.biojava.bio.seq.FeatureFilter.HasAnnotation
  Make a new ByAnnotation that will accept features with an annotation bundle containing any value associated with 'key'.
FeatureFilter.Not - Class in org.biojava.bio.seq
  A filter that returns all features not accepted by a child filter.
FeatureFilter.Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not
FeatureFilter.OnlyChildren - Class in org.biojava.bio.seq
  Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyChildren(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyChildren
FeatureFilter.OnlyDescendants - Class in org.biojava.bio.seq
  Accepts features where all descendants meet the supplied filter.
FeatureFilter.OnlyDescendants(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
FeatureFilter.Or - Class in org.biojava.bio.seq
  A filter that returns all features accepted by at least one child filter.
FeatureFilter.Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or
FeatureFilter.OverlapsLocation - Class in org.biojava.bio.seq
  A filter that returns all features overlapping a location.
FeatureFilter.OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
  Creates a filter that returns everything overlapping loc.
FeatureFilter.ShadowContainedByLocation - Class in org.biojava.bio.seq
  A filter that accepts all features whose shadow is contained by a specified `Location`.
FeatureFilter.ShadowContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
  Creates a filter that returns everything contained within loc.
FeatureFilter.ShadowOverlapsLocation - Class in org.biojava.bio.seq
  A filter that accepts all features whose shadow overlaps a specified `Location`.
FeatureFilter.ShadowOverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
  Creates a filter that returns everything overlapping loc.
FeatureFilter.StrandFilter - Class in org.biojava.bio.seq
  Accept features with a given strandedness.
FeatureFilter.StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.seq.FeatureFilter.StrandFilter
  Build a new filter that matches all features of a given strand.
FeatureHandler - Class in org.biojava.bio.program.xff
  StAX handler for the basic `feature` type of XFF.
FeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.FeatureHandler
  Construct a new Feature handler, passing in an XFF-parsing environment.
FeatureHolder - Interface in org.biojava.bio.seq
  The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - Class in org.biojava.bio.seq
FeatureHolder.EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleFeature
  A utility function to find out if the feature holder delegate has been instantiated yet.
featureHolderAllocated() - Method in class org.biojava.bio.seq.impl.SimpleSequence
featureHolderAsSet(FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
  Returns a FeatureHolder as a Set of Features
FeatureHolderUtils - Class in org.biojava.bio.seq
  This class intendes to provide some FeatureHolder utilities.
FeatureHolderUtils() - Constructor for class org.biojava.bio.seq.FeatureHolderUtils
FeatureImpl - Class in org.biojava.bio.seq.impl
  Wrap up default sets of Feature implementations.
FeatureImpl() - Constructor for class org.biojava.bio.seq.impl.FeatureImpl
FeatureLabelRenderer - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
FeatureLabelRenderer(FeatureLabelRenderer.LabelMaker) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer
FeatureLabelRenderer.AnnotationLabelMaker - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer.AnnotationLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.AnnotationLabelMaker(Object) - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.LabelMaker - Interface in org.biojava.bio.gui.sequence
FeatureLabelRenderer.SourceLabelMaker - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer.SourceLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker
FeatureLabelRenderer.TypeLabelMaker - Class in org.biojava.bio.gui.sequence
FeatureLabelRenderer.TypeLabelMaker() - Constructor for class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
featureListener - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
FEATUREQUAL_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUAL_VALUE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FEATUREQUALS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureRealizer - Interface in org.biojava.bio.seq
  Interface for translators which map from Feature.Template instances to real Feature objects.
featureRelationshipSet - Variable in class org.biojavax.bio.seq.RichFeature.Template
FeatureRenderer - Interface in org.biojava.bio.gui.sequence
features() - Method in class org.biojava.bio.program.das.DASSequence
features() - Method in interface org.biojava.bio.seq.Feature
  Iterate over any child features which are held by this feature.
features() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
FEATURES - Static variable in interface org.biojava.bio.seq.FeatureHolder
  Signals that features have been added or removed directly within this FeatureHolder.
features() - Method in interface org.biojava.bio.seq.FeatureHolder
  Iterate over the features in no well defined order.
features() - Method in class org.biojava.bio.seq.impl.DummySequence
features() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
features() - Method in class org.biojava.bio.seq.impl.RevCompSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleFeature
features() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
features() - Method in class org.biojava.bio.seq.impl.SimpleSequence
features() - Method in class org.biojava.bio.seq.impl.SubSequence
features() - Method in class org.biojava.bio.seq.impl.ViewSequence
features - Variable in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
features() - Method in class org.biojava.bio.seq.LazyFeatureHolder
features() - Method in class org.biojava.bio.seq.MergeFeatureHolder
  Iterate over all the features in all child FeatureHolders.
features() - Method in class org.biojava.bio.seq.NewSimpleAssembly
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
features() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
features() - Method in class org.biojava.bio.seq.SimpleAssembly
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
features() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Iterate over any child features which are held by this feature.
features() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Iterate over the features in no well defined order. Warning this method gives access to the original Collection not a copy.
FEATURES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
FeatureSource - Interface in org.biojava.bio.gui.sequence
  A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
FeatureTableParser - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
featureTemplate - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
featureTemplate - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
FeatureTree - Class in org.biojava.bio.gui
  FeatureTree is GUI tree to display the features and annotations of the sequences in a `SequenceDB` Nested Features are displayed as expandable leaves.
FeatureTree() - Constructor for class org.biojava.bio.gui.FeatureTree
  Create a new FeatureTree
FeatureTypes - Class in org.biojava.bio.seq
  Registry of known types of features.
FeatureTypes() - Constructor for class org.biojava.bio.seq.FeatureTypes
FeatureTypes.Repository - Interface in org.biojava.bio.seq
  A named collection of Types.
FeatureTypes.RepositoryImpl - Class in org.biojava.bio.seq
  A simple implementation of a Repository.
FeatureTypes.RepositoryImpl(String) - Constructor for class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
  Create a named repository.
FeatureTypes.Type - Interface in org.biojava.bio.seq
  A type of feature.
fetch(String) - Method in class org.biojava.bio.seq.db.BioIndex
fetch(String) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
fetch(String) - Method in interface org.biojava.bio.seq.db.IndexStore
  Fetch an Index based upon an ID.
fetch(String) - Method in class org.biojava.bio.seq.db.TabIndexStore
FetchURL - Class in org.biojava.bio.seq.db
FetchURL(String, String) - Constructor for class org.biojava.bio.seq.db.FetchURL
  Constructs a fetchURL object based on the database name and specified return format of sequence.
FileAsList - Class in org.biojava.utils
  `FileAsList` creates a writable `List` implementation backed by a random access file.
FileAsList(File, int) - Constructor for class org.biojava.utils.FileAsList
  Creates a new `FileAsList` and corresponding backing file.
FileAsList(File, boolean) - Constructor for class org.biojava.utils.FileAsList
  Creates a new `FileAsList` instance from an existing backing file.
FileConvert - Class in org.biojava.bio.structure.io
  Methods to convert a structure object into different file formats.
FileConvert(Structure) - Constructor for class org.biojava.bio.structure.io.FileConvert
  Constructs a FileConvert object.
fileToBiojava(String, String, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Reads a file with the specified format and alphabet
fileToBiojava(int, BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Reads a file and returns the corresponding Biojava object.
FILL - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `FILL` indicating a change to the fill of the features.
FILL - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
FILL - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
fillBuffer(StringBuffer, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Simple method that adds spaces onto the buffer passed in.
fillColors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  The map containing the fill colors for callboxes.
fillPaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
fillPaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
fillPaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
fillPaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
  Return the fill paint for a symbol.
fillTemplate(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
fillTemplate(FramedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
fillTemplate(HomologyFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
fillTemplate(RemoteFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
fillTemplate(SimilarityPairFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
fillTemplate(StrandedFeature.Template) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
filter(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB
  Find all Annotation instances in this DB that are of a particular type.
filter(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
filter(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
FILTER - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
filter - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
FILTER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  Constant `FILTER` indicating a change to the renderer's filter.
filter - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `filter` is the filter applied to both `FeatureHolder`s.
filter(FeatureFilter) - Method in class org.biojava.bio.program.das.DASSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.program.das.DASSequence
filter(FeatureFilter) - Method in class org.biojava.bio.program.das.DASSequenceDB
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Filter this entry set into another set.
filter(OrthologueFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthologueSet
filter(OrthoPairSetFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
filter(OrthoPairFilter) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairSet
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Filter the database for a specified group.
filter(OrthologueFilter) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
  Filter the contents of a set.
filter(OrthoPairSetFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
filter(OrthoPairFilter) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  filter an OrthoPairSet
filter(FeatureFilter) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
filter(FeatureFilter) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.db.SequenceDB
  Query features attached to all sequences in this database.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
filter(FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.FeatureHolder
  Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter) - Method in interface org.biojava.bio.seq.FeatureHolder
  Query this set of features using a supplied `FeatureFilter`.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.DummySequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.RevCompSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SimpleSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.SubSequence
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.impl.ViewSequence
filter(FeatureFilter) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.LazyFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.MergeFeatureHolder
  When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.NewSimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
filter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojava.bio.seq.SimpleAssembly
filter(FeatureFilter) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
filter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Query this set of features using a supplied `FeatureFilter`.
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Query this set of features using a supplied `FeatureFilter`.
FilteringContentHandler - Class in org.biojava.bio.search
FilteringContentHandler(BlastLikeSearchFilter, SearchContentHandler) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler(BlastLikeSearchFilter) - Constructor for class org.biojava.bio.search.FilteringContentHandler
FilteringContentHandler.FilterVisitor - Class in org.biojava.bio.search
  Visitor class that parses the filter tree
FilteringContentHandler.FilterVisitor() - Constructor for class org.biojava.bio.search.FilteringContentHandler.FilterVisitor
FilteringRenderer - Class in org.biojava.bio.gui.sequence
FilteringRenderer() - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
FilteringRenderer(SequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.FilteringRenderer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.program.xff.ElementRecognizer
  Recognize an element based upon the start element parameters.
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.agave.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.AllElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByLocalName
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.ByNSName
filterStartElement(String, String, String, Attributes) - Method in interface org.biojava.bio.seq.io.game.ElementRecognizer
filterStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.ElementRecognizer.HasAttribute
FilterTest - Interface in org.biojava.bio.search
  Class for implementing tests with BlastLikeSearchFilter objects.
FilterTest.Equals - Class in org.biojava.bio.search
  Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.Equals(Object) - Constructor for class org.biojava.bio.search.FilterTest.Equals
FilterTest.FindRegex - Class in org.biojava.bio.search
  Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.FindRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.FindRegex
FilterTest.GreaterThan - Class in org.biojava.bio.search
  Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.GreaterThan(double) - Constructor for class org.biojava.bio.search.FilterTest.GreaterThan
FilterTest.LessThan - Class in org.biojava.bio.search
  Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.LessThan(double) - Constructor for class org.biojava.bio.search.FilterTest.LessThan
FilterTest.MatchRegex - Class in org.biojava.bio.search
  Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
FilterTest.MatchRegex(String) - Constructor for class org.biojava.bio.search.FilterTest.MatchRegex
FilterTransformer - Class in org.biojava.bio.seq.filter
  Base-class for visitors that re-write a filter tree.
FilterTransformer() - Constructor for class org.biojava.bio.seq.filter.FilterTransformer
FilterUtils - Class in org.biojava.bio.seq
  A set of FeatureFilter algebraic operations.
FilterUtils.DelegatingTransformer - Class in org.biojava.bio.seq
  An implementation of FilterTransformer that attempts to transform by one transformer, and if that fails, by another.
FilterUtils.DelegatingTransformer(FilterUtils.FilterTransformer, FilterUtils.FilterTransformer) - Constructor for class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
  Create a new DelegatingTransformer that will apply t1 and then t2 if t1 fails.
FilterUtils.FilterTransformer - Interface in org.biojava.bio.seq
  An object able to transform some FeatureFilter instances sytematically into others.
finalize() - Method in class org.biojava.bio.seq.io.NameTokenization
finalize() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
finalize() - Method in class org.biojava.bio.symbol.SimpleAlignment
finalize() - Method in class org.biojava.bio.symbol.SimpleSymbolList
finalize() - Method in class org.biojava.utils.process.ExternalProcess
find(String[], String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
  The easiest direct method for querying a repository.
find() - Method in interface org.biojava.bio.search.BioMatcher
  Attempt to find the next match.
find() - Method in class org.biojava.bio.search.MaxMismatchMatcher
find() - Method in class org.biojava.utils.regex.Matcher
  Attempts to find the next subsequence of the input sequence that matches the pattern.
find(int) - Method in class org.biojava.utils.regex.Matcher
  Resets this matcher and then attempts to find the next subsequence of the input sequence that matches the pattern, starting at the specified index.
findByAuthor(BiblioProvider, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
  This is a convenient method for a common query.
findById(String) - Method in interface org.biojava.bibliography.BibRefQuery
  This is a convenient method returning just one citation.
findById(String, String[]) - Method in interface org.biojava.bibliography.BibRefQuery
  This is a convenient method returning just one citation, perhaps with a limited number of attributes.
findChain(String) - Method in interface org.biojava.bio.structure.Structure
  request a particular chain from a structure.
findChain(String, int) - Method in interface org.biojava.bio.structure.Structure
  request a particular chain from a particular model
findChain(String, int) - Method in class org.biojava.bio.structure.StructureImpl
findChain(String) - Method in class org.biojava.bio.structure.StructureImpl
findFactory(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Find the UnigeneFactory that can accept a URL.
findGroup(String, String) - Method in interface org.biojava.bio.structure.Structure
  request a particular group from a structure.
findGroup(String, String, int) - Method in interface org.biojava.bio.structure.Structure
  request a particular group from a structure.
findGroup(String, String, int) - Method in class org.biojava.bio.structure.StructureImpl
findGroup(String, String) - Method in class org.biojava.bio.structure.StructureImpl
findMatches(SymbolList) - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
  This will return an int[] giving the offsets of the matches in `text` (ie the location of the first symbol of each match in the `text`).
findRecord(String) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `findRecord` performs a binary search within the file for a record specified by an identifier String.
findSourceBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Finds the index of the block containing the source coordinate indx.
findSourceGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Finds the index of the Block before the gap at indx within the following gap.
findTaxon(Object[]) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
findViewBlock(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Finds the index of the Block containing indx within the view ranges.
findViewGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Finds the index of the Block before the gap at indx within the view range.
finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
finishWriting() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Informs the writer that are done writing.
finishWriting() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
  Informs the writer that are done writing.
finishWriting() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Informs the writer that are done writing.
FiniteAlphabet - Interface in org.biojava.bio.symbol
  An alphabet over a finite set of Symbols.
FiniteAutomaton - Class in org.biojava.utils.automata
  Class for modelling finite automata.
fireEndFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Fire the endFeature event.
fireHits(int, int, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
fireMouseClicked(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
fireMouseDragged(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
fireMouseMoved(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
fireMousePressed(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
fireMouseReleased(SequenceViewerEvent) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
firePostChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub
  invoke the firePostChangeEvent on all ChangeListeners associated with a specific key.
firePostChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePostChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport
  Inform the listeners that a change has taken place using their firePostChangeEvent methods.
firePreChange(Object, ChangeEvent) - Method in interface org.biojava.utils.ChangeHub
  invoke the firePreChangeEvent on all ChangeListeners associated with a specific key.
firePreChange(Object, ChangeEvent) - Method in class org.biojava.utils.IndexedChangeHub
firePreChangeEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeSupport
  Inform the listeners that a change is about to take place using their firePreChangeEvent methods.
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.StackedLogoPainter
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.TextLogoPainter
fireStartFeature() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Fire the startFeature event.
firstName - Variable in class org.biojava.bibliography.BiblioPerson
  The person's christian name (first name).
firstNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Return the index of the first Symbol that is not a Gap character.
firstNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
firstPage - Variable in class org.biojava.bibliography.BiblioArticle
  First page of the article.
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
fitness(Organism, Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.FitnessFunction
  Calculates the fitness of `org`.
FITNESS_FUNCTION - Static variable in interface org.biojavax.ga.functions.SelectionFunction
FitnessFunction - Interface in org.biojavax.ga.functions
  Calculates the fitness of an `Organism` in a `Population` of `Organisms`
fivePrimeBlockIterator() - Method in class org.biojava.bio.symbol.CircularLocation
  Iterates over the location blocks in order starting with the most 5'
FixedBaseWidthScaler - Class in org.biojava.bio.chromatogram.graphic
  A `ChromatogramNonlinearScaler` that scales all the base calls in a chromatogram to the same width in pixels, optionally biasing the peak of the call to the center.
FixedBaseWidthScaler(float) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
  Creates a new scaler that will scale bases to the specified width without attempting to center their peaks.
FixedBaseWidthScaler(float, boolean) - Constructor for class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
  Creates a new scaler that will scale bases to the specified width and may or may not bias the peaks to the center.
FixedSizeCache - Class in org.biojava.utils.cache
  Cache which stores up to `limit` Objects.
FixedSizeCache(int) - Constructor for class org.biojava.utils.cache.FixedSizeCache
FixedSizeMap - Class in org.biojava.utils.cache
  A cache that only remembers a given number of keys.
FixedSizeMap(int) - Constructor for class org.biojava.utils.cache.FixedSizeMap
FIXEDWIDTH - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
FlatFileUnigeneFactory - Class in org.biojava.bio.program.unigene
  A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.
FlatFileUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
FlatSequenceDB - Class in org.biojava.bio.seq.db.flat
  `FlatSequenceDB` is an OBDA flatfile sequence databank implementation.
FlatSequenceDB(String, String) - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDB
FlatSequenceDBProvider - Class in org.biojava.bio.seq.db.flat
  `FlatSequenceDBProvider` directory-services plugin for flatfile databases.
FlatSequenceDBProvider() - Constructor for class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
flatten(RichLocation) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes a location and returns the set of all members.
flatten(Collection) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes a set of locations and returns the set of all members.
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
FlexibleAlignment - Class in org.biojava.bio.alignment
  FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
FlexibleAlignment(List) - Constructor for class org.biojava.bio.alignment.FlexibleAlignment
  construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String).
flip(SymbolList, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.DNATools
  Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
flip() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
  Return a strand that represents flipping this onto the opposite strand.
flip(Location, int) - Static method in class org.biojava.bio.symbol.LocationTools
  Flips a location relative to a length.
flipLocation(Location, int) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
  Flip a location.
flipStrand(StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
FloatElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of a float.
FloatElementHandlerBase() - Constructor for class org.biojava.utils.stax.FloatElementHandlerBase
flush() - Method in class org.biojava.utils.RepeatedCharSequence
flushFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
force() - Method in class org.biojava.utils.io.LargeBuffer
forIndex(int) - Static method in class org.biojava.bio.seq.DNATools
  Return the symbol for an index - compatible with `index`.
forIndex(int) - Static method in class org.biojava.bio.seq.NucleotideTools
  Return the symbol for an index - compatible with `index`.
forIndex(int) - Static method in class org.biojava.bio.seq.RNATools
  Return the symbol for an index - compatible with index.
format - Variable in class org.biojava.bibliography.BibRef
  It describes the physical or digital manifestation of the cited resource.
Format - Interface in org.biojava.bio.program.formats
  A file format supported by the tag-value event-based parsing system.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  Deprecated. `formatLocation` creates a String representation of a `Location`.
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  Deprecated. Formats the location of a feature.
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. `formatLocation` creates a String representation of a `Location`.
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Creates a string representation of the location of a feature
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. `formatLocation` creates a String representation of a `Location`.
formatOutput(String, String, String[], String, int, int, long, int, int, long, double, long) - Static method in class org.biojava.bio.alignment.SequenceAlignment
  This method provides a BLAST-like formated alignment from the given `String`s, in which the sequence coordinates and the information "Query" or "Target", respectively is added to each line.
formatPoint(int, int, boolean) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Formats the points from fuzzy locations.
Formats - Class in org.biojava.bio.program.tagvalue
  This is intended as a repository for tag-value and AnnotationType information about common file formats.
Formats() - Constructor for class org.biojava.bio.program.tagvalue.Formats
formatToFactory(SequenceFormat, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. as this essentially duplicates the operation available in the method `identifyBuilderFactory`.
FormatTools - Class in org.biojava.bio.program.formats
forName(String) - Static method in class org.biojavax.bio.seq.RichLocation.Strand
  Returns the strand object that matches the symbol given.
forSubset - Variable in class org.biojava.bibliography.BiblioCriterion
  A name of a repository subset which this criterion is valid/used for.
forSymbol(char) - Static method in class org.biojava.bio.seq.DNATools
  Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.NucleotideTools
  Retrieve the symbol for a symbol.
forSymbol(char) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve the symbol for a symbol.
forValue(int) - Static method in class org.biojavax.bio.seq.RichLocation.Strand
  Returns the strand object that matches the number given.
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forward(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
FORWARD - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
forward_initialize(DPCursor, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardChangeEvent(ChangeEvent) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
  Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.DP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
forwardMatrix(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardMatrix(SymbolList[], DPMatrix, ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
forwardRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
forwards(ScoreType) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
forwards(ScoreType) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
forwardsBackwards(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
  Returns a matrix for the specified States describing all valid Transitions between those States.
forwardTransitionScores(MarkovModel, State[], int[][], ScoreType) - Static method in class org.biojava.bio.dp.DP
  Compute the log(score) of all transitions between the specified States.
fp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
  Calculate the pairwise compatibility of fpairs.
FragmentJoiner - Class in org.biojava.bio.structure.align.pairwise
  Joins the initial Fragments together to larger Fragments
FragmentJoiner() - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentJoiner
FragmentPair - Class in org.biojava.bio.structure.align.pairwise
  a pair of fragments of two protein structures
FragmentPair(int, int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.FragmentPair
Frame - Interface in org.biojava.bio.seq
  Title: Frame.
FRAME_0 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_0 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_1 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_1 - Static variable in interface org.biojava.bio.seq.FramedFeature
FRAME_2 - Static variable in interface org.biojava.bio.seq.Frame
FRAME_2 - Static variable in interface org.biojava.bio.seq.FramedFeature
FramedFeature - Interface in org.biojava.bio.seq
  Title: FramedFeature.
FramedFeature.ReadingFrame - Class in org.biojava.bio.seq
  A singleton to hold the frame information
FramedFeature.Template - Class in org.biojava.bio.seq
FramedFeature.Template() - Constructor for class org.biojava.bio.seq.FramedFeature.Template
frequency(int) - Method in class org.biojava.bio.symbol.SuffixTree
  Return the number of motifs of a given length encoded in this SuffixTree.
from - Variable in class org.biojava.bio.dp.TrainerTransition
from - Variable in class org.biojava.bio.dp.Transition
FROM_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating the lowest (leftmost) trace sample that should be drawn.
fromArray(double[]) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve a SymbolList view of an array of doubles.
fromArray(int[]) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
  Retrieve a SymbolList view of an array of integers.
fromBook - Variable in class org.biojava.bibliography.BiblioBookArticle
  Book this is from.
fromJournal - Variable in class org.biojava.bibliography.BiblioJournalArticle
  The journal that this article is in.
FUGU_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Takifugu rubripes codon preferences
full - Static variable in interface org.biojava.bio.symbol.Location
  The `Location` which contains all points.
FULL_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
FullHmmerProfileHMM - Class in org.biojava.bio.program.hmmer
  This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
fullyLoadRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
FundamentalAtomicSymbol - Class in org.biojava.bio.symbol
  An atomic symbol consisting only of itself.
FundamentalAtomicSymbol(String, Annotation) - Constructor for class org.biojava.bio.symbol.FundamentalAtomicSymbol
FuzzyLocation - Class in org.biojava.bio.symbol
  A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyLocation(int, int, int, int, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation
  Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Constructor for class org.biojava.bio.symbol.FuzzyLocation
  Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation.RangeResolver - Interface in org.biojava.bio.symbol
  Determines how a `FuzzyLocation` should be treated when used as a normal `Location`.
FuzzyPointLocation - Class in org.biojava.bio.symbol
  `FuzzyPointLocation` represents two types of EMBL-style partially-defined locations.
FuzzyPointLocation(int, int, FuzzyPointLocation.PointResolver) - Constructor for class org.biojava.bio.symbol.FuzzyPointLocation
  Creates a new `FuzzyPointLocation` object.
FuzzyPointLocation.PointResolver - Interface in org.biojava.bio.symbol
  Determines how a `FuzzyPointLocation` should be treated when used as a normal `Location`.
FWORM_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the flatworm mitochondrial genetic code.

## G

g() - Static method in class org.biojava.bio.seq.DNATools
g() - Static method in class org.biojava.bio.seq.NucleotideTools
g() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glycine
g() - Static method in class org.biojava.bio.seq.RNATools
GACross - Interface in org.biojavax.ga.functions
  Holds the results of a CrossOver event, objects of this type are made by `CrossOverFunctions`
GACrossResult - Interface in org.biojavax.ga.functions
  Holds the results of a CrossOver event, objects of this type are made by `CrossOverFunctions`
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
  Description of the Field
GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
  Description of the Field
GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
  Description of the Field
GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
  Description of the Field
GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
  Description of the Field
GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
  Description of the Field
GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler
  Description of the Field
GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
  Description of the Field
GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler
  Description of the Field
GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <annotation> element
GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <annotation> element
GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <aspect> element
GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <aspect> element
GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <dbxref> element
GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game
  Deals with database crossreferences
GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game
GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game
  StAX handler for GAME <description> elements.
GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game
  Handles the <feature_set> element
GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game
  Handles the <feature_span> element
GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <feature_span> element
GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12
GAMEFormat - Class in org.biojava.bio.seq.io
  A rudimentary read-only GAME 1.2 Format object.
GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <annotation> element
GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <gene> element
GAMEHandler - Class in org.biojava.bio.seq.io.game
  Handles the root GAME element
GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
GAMEHandler - Class in org.biojava.bio.seq.io.game12
  Handles the root GAME element
GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler
  Constructor for the GAMEHandler object
GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler - Class in org.biojava.bio.seq.io.game
  StAX handler for the GAME <name> element.
GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <dbxref> element
GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game
  StAX handler for GAME <residues> elements.
GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
GAMESeqHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <seq> element
GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <seq> element
GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <> element
GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <aspect> element
GAMESpanHandler - Class in org.biojava.bio.seq.io.game12
  Handles the GAME <> element.
GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game
  Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game
  An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler - Class in org.biojava.bio.seq.io.game
  StAX handler for GAME <type> elements.
GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
GapArray - Class in org.biojava.bio.structure.align.helper
GapArray() - Constructor for class org.biojava.bio.structure.align.helper.GapArray
GapDistribution - Class in org.biojava.bio.dist
  This distribution emits gap symbols.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution
  Get a GapDistribution for an alphabet.
GappedRenderer - Class in org.biojava.bio.gui.sequence
  A renderer that will display a gapped sequence as a discontinuous series of regions.
GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
GappedSequence - Interface in org.biojava.bio.seq
  Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList - Interface in org.biojava.bio.symbol
  This extends SymbolList with API for manipulating, inserting and deleting gaps.
gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Translates a Location from the gapped view into the underlying sequence.
gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
  Create a new gapped sequence for a sequence.
GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment
GAStoppingCriteria - Interface in org.biojavax.ga
  Used by a `GeneticAlgorithm.run()` method to determine when the algorithm should stop
GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga
  Simple Implementation of GAStoppingCriteria, signals a `GeneticAlgorithm` to stop after n generations
GAStoppingCriteria.MaximumGeneration(int) - Constructor for class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
  Public Constructer
GATools - Class in org.biojavax.ga.util
  Utility methods for the GA library
GATools() - Constructor for class org.biojavax.ga.util.GATools
GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GCG` indicates that the sequence format is GCG.
ge - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser
  A LineSplitParser pre-configured to process GENBANK-style flat files.
GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENBANK` indicates that the sequence format is GENBANK.
GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENBANK_DNA` premade GENBANK | AA.
GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENBANK_DNA` premade GENBANK | DNA.
GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
  The name of this format
GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENBANK_DNA` premade GENBANK | RNA.
GenbankFileFormer - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated. Creates a new `GenbankFileFormer` using `System.out` stream.
GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated. Creates a new `GenbankFileFormer` using the specified stream.
GenbankFormat - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
GenbankFormat - Class in org.biojavax.bio.seq.io
  Format reader for GenBank files.
GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some GenBank-specific terms.
GenbankFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat.Terms
GenbankLocationParser - Class in org.biojavax.bio.seq.io
  Parses Genbank location strings into RichLocation objects.
GenbankProcessor - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
GenbankProcessor.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps sequence builders in a GenbankProcessor
GenbankProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory
  Deprecated.
GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi
  This class contains functions accessing DNA sequences in Genbank format.
GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  The default constructor delegates to the parent class.
GenbankSequenceDB - Class in org.biojava.bio.seq.db
  This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
GenbankXmlFormat - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat
GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat
  Deprecated.
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
GenEmblFeatureComparator - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
generate(int) - Method in class org.biojava.bio.dp.DP
  Generates an alignment from a model.
generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Generates a comment string based on the current values of the internal fields.
generateAuthorString(List) - Static method in class org.biojavax.DocRefAuthor.Tools
  Takes a set of authors and creates a comma-separated string.
generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Precomputes the `Rectangle2D`s that are the in-memory representation of the callboxes.
generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable
  Called the first time a ChangeSupport object is needed.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Generates a new CrossProductAlphabet from the give name.
generateDrawableCallboxes(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Precomputes the callboxes in screen coordinates.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder
  Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder
  Deprecated.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
  `generateEvent` generates events in response to layout change and repaint requests.
generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
  Return the new event to represent the originating event ce.
generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper
generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
  Deprecated. use generateSequence() or generateSymbolList() instead.
generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList
generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
  Produces a sequence by randomly sampling the Distribution.
generateSubpaths() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Precomputes the `GeneralPath`s used to draw the traces.
generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
  Produces a `SymbolList` by randomly sampling a Distribution.
generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a provider type.
GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
GeneticAlgorithm - Interface in org.biojavax.ga
  The class that runs the cycles of reproduction, evolution and selection, potentially on multiple `Population`s
GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
GeneticCodes - Class in org.biojava.bio.seq
  Collects the references to translation methods in one place.
GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GENPEPT` indicates that the sequence format is GENPEPT.
GenpeptFormat - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat
  Deprecated.
GenpeptSequenceDB - Class in org.biojava.bio.seq.db
GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore
get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
  `get` returns a record specified by a primary identifier.
get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
  `get` returns a list of `Record`s by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
  get the Transition associated with the specified tag.
get(int, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Get a single element.
get(int) - Method in class org.biojava.stats.svm.SparseVector
  Retrieve the value at dimension dim.
get(Object) - Method in interface org.biojava.utils.cache.CacheMap
  Retrieve the Object associated with the key, or null if either no value has been associated or if the key's value has been cleared by the cache.
get() - Method in interface org.biojava.utils.cache.CacheReference
get(Object) - Method in class org.biojava.utils.cache.ChangeableCache
get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
get(int) - Method in class org.biojava.utils.FileAsList
get(long) - Method in class org.biojava.utils.io.LargeBuffer
get() - Method in class org.biojava.utils.io.LargeBuffer
get(int) - Method in class org.biojava.utils.ListTools.Doublet
get(int) - Method in class org.biojava.utils.ListTools.SeriesList
get(int) - Method in class org.biojava.utils.ListTools.Triplet
get(Object) - Method in class org.biojava.utils.OverlayMap
get(int) - Method in class org.biojava.utils.SingletonList
get(Object) - Method in class org.biojava.utils.SmallMap
get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
  The point at which indicates the 5' end of the Location.
get_() - Method in class org.biojava.bio.proteomics.StructureTools
get_structure() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
  returns the Structure object.
getA() - Method in class org.biojava.utils.ListTools.Doublet
getA() - Method in class org.biojava.utils.ListTools.Triplet
getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property absorptionMax.
getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property absorptionNote.
getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue
  get the Accession ID associated with this orthologue.
getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAccession() - Method in interface org.biojavax.bio.BioEntry
  Returns the accession of this bioentry.
getAccession() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the accession of this bioentry.
getAccession() - Method in interface org.biojavax.CrossRef
  Returns the accession of the object that the crossref refers to.
getAccession() - Method in class org.biojavax.SimpleCrossRef
  Returns the accession of the object that the crossref refers to.
getAcronym() - Method in interface org.biojavax.Namespace
  If the namespace has an acronym, this will return it.
getAcronym() - Method in class org.biojavax.SimpleNamespace
  If the namespace has an acronym, this will return it.
getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Get the GFFDocumentHandler for adding to this set.
getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the secondary/tertiary/additional accession term
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the current value of addPos.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
  Get the URL object for locating sequence object using eutils.
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
  Get the URL object for locating sequence object using eutils.
getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Get the URL object for locating sequence object using eutils.
getAdvance() - Method in interface org.biojava.bio.dp.EmissionState
  Determine the number of symbols this state advances along one or more symbol lists.
getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
getAligMat() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getAligMat(int, int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getAligMat() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAlignment(Sequence, Sequence) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  This method is good if one wants to reuse the alignment calculated by this class in another BioJava class.
getAlignment(Sequence, Sequence) - Method in class org.biojava.bio.alignment.SequenceAlignment
  This method also performs a sequence alignment of the two given sequences but it returns an Alignment object instead of the score.
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Gets the Alignment - one of LEADING, TRAILING or CENTER.
getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools
  View a symbol list over the QUALITY alphabet as an alignment.
getAlignment(int) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
  Returns Alignment at position ...
getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology
  Retrieve the Alignment that specifies how the homologous regions are aligned.
getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  `getAlignment` returns the `Alignment` of two similar features.
getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology
  `getAlignment` returns the alignment, which uses the `HomologyFeature`s as keys.
getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
  `getAlignment` returns the alignment between the two features.
getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  connect to a DAS alignment service and retreive alignments.
getAlignments(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  connect to a DAS alignment service and retreive data.
getAlignments(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Returns the alignments.
getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Returns the alignments.
getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
  Returns the alignments.
getAlignments() - Method in class org.biojava.bio.structure.align.StructurePairAligner
  return the alternative alignments that can be found for the two structures
getAlignmentString() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
getAlignmentString() - Method in class org.biojava.bio.alignment.SequenceAlignment
getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
  All sequences that map to this cluster.
getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Return the ambiguity symbol which matches all symbols in a given alphabet.
getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns all citations from the current collection as a (possibly big) array.
getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
  It returns all citations from the current collection as a (possibly big) array, perhaps with a limited number of attributes.
getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns all citations from the current collection as an XML stream.
getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns all available vocabulary entries.
getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getAllEnzymes` returns an unmodifable set of all available enzymes.
getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery
  A convenient method returning just identifiers of all current citations.
getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It return all names (entry identifiers) available in this vocabulary.
getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAllScientificNames(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Returns all the `scientific name`s, which are currently stored in the database.
getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Return a set containing all possible symbols which can be considered members of a given alphabet, including ambiguous symbols.
getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder
  It returns all available vocabularies.
getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder
  It returns names of all vocabularies known to this vocabulary finder.
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment
getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Gives the alphabet used by this matrix.
getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getAlphabet() - Method in interface org.biojava.bio.dist.Count
  The alphabet from which this Count is over.
getAlphabet() - Method in interface org.biojava.bio.dist.Distribution
  The alphabet from which this spectrum emits symbols.
getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount
getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution
getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix
  The alphabet for the sequences that this weight matrix models.
getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle
getAlphabet() - Method in class org.biojava.bio.program.das.DASSequence
getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore
  The alphabet of symbol lists that can be searched against this DataStore.
getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB
getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence
getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. `getAlphabet` accepts a value which represents a sequence format and returns the relevant `FiniteAlphabet` object.
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader
  Find the alphabet of all symbols which may be returned by this SymbolReader.
getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  The alphabet to which this tokenization applies.
getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization
getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
  Gets the protein alphabet
getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly
getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex
  Retrieve the alphabet that this indexes.
getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack
getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList
getAlphabet() - Method in interface org.biojava.bio.symbol.Packing
  The FiniteAlphabet this packing is for.
getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleAlignment
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Get the alphabet of this SymbolList.
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree
  Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList
  The alphabet that this SymbolList is over.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getAlphabet() - Method in class org.biojava.utils.regex.Pattern
getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  The alphabet that this SymbolList is over.
getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence
  The alphabet that this SymbolList is over.
getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get an indexer for a specified alphabet.
getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get an indexer for an array of symbols.
getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence
getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet
  Return an ordered List of the alphabets which make up a compound alphabet.
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Gets the components of the `Alphabet`.
getAlphaCarbonAngleAlphabet() - Static method in class org.biojava.bio.structure.AlphaCTools
  Returns a reference to the Alphabet that contains Symbols that represent PHI, PSI angles.
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getAltAligNumber() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  returns the sequential number of this alternative alignment
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getAltLoc() - Method in interface org.biojava.bio.structure.Atom
  get set alternate Location.
getAltLoc() - Method in class org.biojava.bio.structure.AtomImpl
  get alternate Location.
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getAmbiguity(Set) - Method in interface org.biojava.bio.symbol.Alphabet
  Get a symbol that represents the set of symbols in syms.
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  This is not supported.
getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
  Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
getAminoAcid(String) - Static method in class org.biojava.bio.structure.StandardAminoAcid
  get a standard amino acid.
getAminoType() - Method in interface org.biojava.bio.structure.AminoAcid
  returns the name of the AA, in single letter code.
getAminoType() - Method in class org.biojava.bio.structure.AminoAcidImpl
  returns the name of the AA, in single letter code.
getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  Return the angle for an index into a sequence.
getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getAngleDiff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getAnnotaters() - Method in class org.biojava.bio.program.das.ReferenceServer
getAnnotation() - Method in interface org.biojava.bio.Annotatable
  Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getAnnotation` returns an immutable, static annotation describing the enzyme.
getAnnotation() - Method in class org.biojava.bio.program.das.DASSequence
getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated. `getAnnotation` returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated. `getAnnotation` returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
  `getAnnotation` returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
  `getAnnotation` returns the Annotation associated with this hit.
getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
  `getAnnotation` returns the Annotation associated with this sub-hit.
getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence
getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence
getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization
getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
getAnnotation() - Method in interface org.biojava.bio.structure.Chain
  get/set the Annotation of a Chain.
getAnnotation() - Method in class org.biojava.bio.structure.ChainImpl
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  The SoftMaskedAlphabet has no annotation
getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl
getAnnotation() - Method in class org.biojava.ontology.Term.Impl
getAnnotation() - Method in class org.biojava.ontology.Triple.Impl
getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry
  Should return the associated annotation object.
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Should return the associated annotation object. ALWAYS RETURNS AN EMPTY ANNOTATION OBJECT
getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
getAnnotation() - Method in class org.biojavax.SimpleCrossRef
  Should return the associated annotation object.
getAnnotations() - Method in class org.biojava.bio.MergeAnnotation
  Gets an unmodifiable view of the list of Annotations that are part of the MergeAnnotation.
getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
  Get the AnnotationType used as a constraint.
getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  Return the AnnotationType built by this handler
getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getArray() - Method in class org.biojava.bio.structure.jama.Matrix
  Access the internal two-dimensional array.
getArrayCopy() - Method in class org.biojava.bio.structure.jama.Matrix
  Copy the internal two-dimensional array.
getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the names of the authors which first published an article about the AAindex entry.
getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the title of the article which describes the AAindex entry.
getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getAtom(String) - Method in interface org.biojava.bio.structure.Group
  get an atom throws StructureException if atom not found.
getAtom(int) - Method in interface org.biojava.bio.structure.Group
  get at atom by position.
getAtom(String) - Method in class org.biojava.bio.structure.HetatomImpl
  get an atom throws StructureException if atom not found.
getAtom(int) - Method in class org.biojava.bio.structure.HetatomImpl
  return an atom by its position in the internal List.
getAtomArray(Structure, String[]) - Static method in class org.biojava.bio.structure.StructureTools
  returns an array of the requested Atoms from the Structure object.
getAtomCAArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
  returns an Atom array of the CA atoms
getAtoms() - Method in interface org.biojava.bio.structure.Group
  get list of atoms.
getAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
  get all atoms of this group .
getAttributes(Name) - Method in class org.biojava.naming.ObdaContext
getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext
getAttributes(String) - Method in class org.biojava.naming.ObdaContext
getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext
getAuthority() - Method in interface org.biojavax.Namespace
  This method will return the authority that governs the namespace.
getAuthority() - Method in class org.biojavax.SimpleNamespace
  This method will return the authority that governs the namespace.
getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the authority id for this identifier.
getAuthorList() - Method in interface org.biojavax.DocRef
  Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthorList() - Method in class org.biojavax.SimpleDocRef
  Returns the authors of the document reference as a set of DocRefAuthor implementation instances.
getAuthors() - Method in interface org.biojavax.DocRef
  Returns the authors of the document reference.
getAuthors() - Method in class org.biojavax.SimpleDocRef
  Returns the authors of the document reference.
getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton
getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder
getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel
getB() - Method in class org.biojava.bio.proteomics.StructureTools
getB() - Method in class org.biojava.utils.ListTools.Doublet
getB() - Method in class org.biojava.utils.ListTools.Triplet
getBackboneAtomArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
  returns an Atom array of the MainChain atoms
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Return the total number of base calls.
getBaseCalls() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns an alignment that describes the base calls for this chromatogram.
getBasecalls() - Method in class org.biojava.bio.program.abi.ABITrace
  Returns an `int[]` array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBaseColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the color that will be used to draw the trace for the given DNA symbol.
getBaseFillColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the color that will be used to fill in the callboxes for calls with the given symbol.
getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState
getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getBeadDepth` returns the depth of a single bead produced by this renderer.
getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
  `getBeadDepth` returns the depth of a single bead produced by the renderer.
getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getBeadDisplacement` returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
  `getBeadDisplacement` returns the displacement of beads from the centre line of the renderer.
getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getBeadFill` returns the bead fill paint.
getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getBeadOutline` returns the bead outline paint.
getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getBeadStroke` returns the bead outline stroke.
getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery
  A convenient utility method converting a given citation to its XML representation.
getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns the number of citations in the current collection.
getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns an enumeration of all citations from the current collection.
getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
  It returns an enumeration of all citations from the current collection, perhaps with a limited number of attributes.
getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns an enumeration of all citations from the current collection.
getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools
  Gets a Reference to the FlyWeight GA_Binary `Alphabet`.
getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Retrieve a single BioEntry by its id.
getBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB
getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB
  Returns a BioEntryIterator over all BioEntrys in the database.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Retrieve multiple BioEntry by their ids.
getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Retrieve multiple BioEntry into a specific sequence database.
getBioEntrys(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Returns the an object indicating the style of biosequence storage that this database should employ.
getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
getBlockAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the alignment Block Annotation Type.
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo
getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext
getBlocks() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  get all Annotations of type "Block".
getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph
getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
getBounds() - Method in interface org.biojava.bio.gui.LogoContext
getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. `getBuilderFactory` accepts a value which represents a sequence format and returns the relevant `SequenceBuilderFactory` object.
getC() - Method in class org.biojava.bio.proteomics.StructureTools
getC() - Method in interface org.biojava.bio.structure.AminoAcid
  get C atom.
getC() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get C atom.
getC() - Method in class org.biojava.stats.svm.SMOTrainer
getC() - Method in class org.biojava.utils.ListTools.Triplet
getCA() - Method in interface org.biojava.bio.structure.AminoAcid
  get CA atom.
getCA() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get CA atom.
getCallboxBounds(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the screen-coordinate bounds of the callbox for a given call.
getCallboxBounds(int, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the bounds of the callbox for a given call.
getCallboxCount() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the number of callboxes, regenerating them if necessary.
getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the 0-based index of the call containing a given point.
getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Synonym for `ChromatogramGraphic.getCallContaining(Point2D, boolean)` with `pointOnScreen`=true.
getCallContaining(float, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Same as `ChromatogramGraphic.getCallContaining(Point2D, boolean)`, except that only the x-coordinate of the point is specified.
getCallContaining(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Synonym for `ChromatogramGraphic.getCallContaining(float, boolean)` with `pointOnScreen`=true.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
  Get the cardinality constraint used to validate the number of property values.
getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
  Get the cardinality constraint used to validate the number of property values.
getCB() - Method in interface org.biojava.bio.structure.AminoAcid
  get CB atom.
getCB() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get CB atom.
getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
getCenter(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
  get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
getCenter1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getCenter2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getCenterVector(Atom[]) - Static method in class org.biojava.bio.structure.Calc
getCentroid(Atom[]) - Static method in class org.biojava.bio.structure.Calc
  returns the center of mass of the set of atoms
getChain(int) - Method in interface org.biojava.bio.structure.Structure
  retrieve a chain by it's position within the Structure .
getChain(int, int) - Method in interface org.biojava.bio.structure.Structure
  retrieve a chain by it's position within the Structure and model number.
getChain(int) - Method in class org.biojava.bio.structure.StructureImpl
  retrieve a chain by it's position within the Structure.
getChain(int, int) - Method in class org.biojava.bio.structure.StructureImpl
  retrieve a chain by it's position within the Structure and model number.
getChainByPDB(String) - Method in interface org.biojava.bio.structure.Structure
  request a chain by it's PDB code by default takes only the first model
getChainByPDB(String, int) - Method in interface org.biojava.bio.structure.Structure
  request a chain by it's PDB code by default takes only the first model
getChainByPDB(String, int) - Method in class org.biojava.bio.structure.StructureImpl
getChainByPDB(String) - Method in class org.biojava.bio.structure.StructureImpl
getChainedEvent() - Method in class org.biojava.utils.ChangeEvent
  Return the event which caused this to be fired, or `null` if this change was not caused by another event.
getChains(int) - Method in interface org.biojava.bio.structure.Structure
  retrieve all chains of a model.
getChains(int) - Method in class org.biojava.bio.structure.StructureImpl
  retrieve all chains of a model.
getChange() - Method in class org.biojava.utils.ChangeEvent
  Return an object which is to be the new value of some property, or is to be added to a collection.
getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException
  Return the ChangeEvent which is being vetoed.
getChanger() - Method in class org.biojava.bio.AnnotationChanger
  `getMapper` returns the `ValueChanger` being used to remap the `Annotation`.
getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
  Get the Changer currently registered to handle a tag.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState
getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getChangeSupport` lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getChangeSupport` lazily instantiates a helper for change listeners.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation
getChangeSupport(ChangeType) - Method in class org.biojava.bio.program.das.DASSequence
getChangeSupport(ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol
getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet
getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm
getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl
getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
  Called to retrieve the ChangeSupport for this object.
getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType
  Get all ChangeType objects defined within a class.
getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
getChar() - Method in class org.biojava.utils.io.LargeBuffer
getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence
getCharacterOffset() - Method in exception org.biojava.utils.ParserException
  Get the character offset in the line where an error was detected.
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree
  Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree
  Get the n'th child of a node.
getChild() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
getChild1() - Method in class org.biojava.bio.CollectionConstraint.And
  Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or
  Get the first child CollectionConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.And
  Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or
  Get the first child PropertyConstraint.
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
getChild2() - Method in class org.biojava.bio.CollectionConstraint.And
  Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or
  Get the seccond child CollectionConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.And
  Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or
  Get the seccond child PropertyConstraint.
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon
  Deprecated.
getChildren() - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. The children of this Taxon.
getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
getChildrenOf(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Returns all children of the specified taxon.
getChildrenOf(Connection, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Returns the children as a `Stack` of this given taxon.
getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Accessor for the in-use chromatogram.
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getChromosomes() - Method in interface org.biojavax.ga.functions.GACross
  Gets the chromosomes after the cross
getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult
  Gets the chromosomes after the cross
getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism
getChromosomes() - Method in interface org.biojavax.ga.Organism
  Gets the organisms 'chromosome' sequences
getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCircular() - Method in interface org.biojavax.bio.seq.RichSequence
  Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i).
getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i).
getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the circular length of this location. ALWAYS RETURNS ZERO
getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Retrieves the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. ALWAYS RETURNS ZERO
getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the circular length of this location.
getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the circular length of this location.
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools
  Get the classloader which loaded the class of `obj`.
getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools
  Get the classloader which loaded `clazz`.
getClassNumber(int) - Method in interface org.biojava.bio.EcNumber
  Get the class number associated with the particular level of the ec number.
getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl
getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease
  The list of residues that the protease will cleave at.
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
  Fetch a cluster by its cluster id.
getCluster() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools
  Gets the (DNA x DNA x DNA) Alphabet
getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools
  Gets the (RNA x RNA x RNA) Alphabet
getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
  get the specified codon preference.
getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
getCol() - Method in class org.biojava.bio.structure.align.helper.IndexPair
getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  Returns `true` if this class collapses to zero depth when there are no visible features.
getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery
  It returns an identification of the current query collection.
getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Returns the colour class for the specified colour (in hex).
getCols() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getCols() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix
  Retrieve a column as an EmissionState.
getColumnDimension() - Method in class org.biojava.bio.structure.jama.Matrix
  Get column dimension.
getColumnPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
  Make a one-dimensional column packed copy of the internal array.
getCommands() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the command line including the path or name of the external program and its command line arguments.
getComment() - Method in interface org.biojava.bio.AnnotationType
  Get the comment for the whole AnnotationType.
getComment(Object) - Method in interface org.biojava.bio.AnnotationType
  Get the comment for a particular property.
getComment() - Method in class org.biojava.bio.AnnotationType.Impl
getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The feature comment.
getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the user comment for the AAindex entry.
getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Getter for property comment.
getComment() - Method in interface org.biojavax.Comment
  Returns the comment part of this comment.
getComment() - Method in class org.biojavax.SimpleComment
  Returns the comment part of this comment.
getComments() - Method in class org.biojava.bio.program.scf.SCF
  Returns the comments fields as a `Properties` mapping.
getComments() - Method in interface org.biojavax.bio.BioEntry
  Returns a set of all comments associated with this bioentry.
getComments() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns a set of all comments associated with this bioentry. Warning this method gives access to the original Collection not a copy.
getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property commentType.
getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
getCommonName() - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. The common name of the Taxon.
getComparator() - Method in class org.biojava.utils.FileAsList
getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation
  Gets the component locations that make up this one
getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature
  Return a location which identifies a portion of the component sequence which is to be included in the assembly.
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature
  Get the sequence object which provides a component of this feature's parent sequence.
getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature
  Get the name of the component sequence.
getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
  Get the conditioned alphabet.
getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
  Get the conditioned alphabet.
getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
  Get the conditioning alphabet of this distribution.
getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
  Get the conditioning alphabet of this distribution.
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration
  `getConfigLocator` returns a locator for the configuration.
getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration
  `getConfiguration` returns a mapping of registry database names to collections of tag-value pairs.
getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
getConnections() - Method in interface org.biojava.bio.structure.Structure
  Returns the connections value.
getConnections() - Method in class org.biojava.bio.structure.StructureImpl
  Returns the connections value.
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType
  Retrieve the constraint that will be applied to all properties with a given key.
getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
getContacts() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Gets the default CONTAINS term used for defining the relationship between features.
getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
  correct this later
getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
getContig() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  See if empty tags are treated as a continuation of previous tags or as a new tag with the value of the empty string.
getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Report whether empty tags will be treated as continuations of the last non -empty tag.
getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `getCoordinates` returns the hotspot coordinates.
getCoords() - Method in interface org.biojava.bio.structure.Atom
  get the coordinates.
getCoords() - Method in class org.biojava.bio.structure.AtomImpl
  get the coordinates as a double[3] array .
getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the copyright term
getCoreOntology() - Static method in class org.biojava.ontology.OntoTools
  Get the Ontology that defines our core "central dogma".
getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count
  Return the counts for a given Symbol.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Get the current count for this state.
getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Return the number of counts of a particular symbol which will be used to train the specified distribution.
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
  Deprecated.
getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a number of entries contained in this vocabulary.
getCovered() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getCRC() - Method in interface org.biojavax.DocRef
  Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references.
getCRC() - Method in class org.biojavax.SimpleDocRef
  Returns a CRC64 checksum of this document reference, allowing for easy comparisons with other document references. The string to be checksummed is constructed by concatenating the authors, title, and location in that order, with no space between.
getCreate_co() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross
  Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult
  Returns the collection of cross over locations from the last cross
getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Attempts to create a cross product alphabet and register it under a name.
getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the crossref associated with this location. ALWAYS RETURNS NULL
getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Retrieves the crossref associated with this location. ALWAYS RETURNS NULL
getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the crossref associated with this location.
getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the crossref associated with this location.
getCrossref() - Method in interface org.biojavax.DocRef
  The document reference may refer to an object in another database.
getCrossRef() - Method in interface org.biojavax.RankedCrossRef
  Return the cross reference associated with this object.
getCrossref() - Method in class org.biojavax.SimpleDocRef
  The document reference may refer to an object in another database.
getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef
  Return the cross reference associated with this object.
getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
  Get a List containing details of all the cross over events during the run.
getCurrentChain() - Method in class org.biojava.bio.structure.GroupIterator
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Gets the feature currently being created.
getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Gets the feature currently being created.
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getCutType` returns the type of cut produced by the enzyme.
getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getD() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
  Return the block diagonal eigenvalue matrix
getDataAccess() - Method in class org.biojava.bio.program.abi.ABIFParser
  Returns the accessor for the raw data being parsed by this parser.
getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getDatabase(String) - Method in class org.biojava.directory.Registry
  `getDatabase` retrieves a database instance known by a name `String`.
getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property databaseName.
getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory
  Returns a list of 0, 1 or more `DatabaseURLGenerator` The first is used to link from the id in the summary table, all are used as a list of links in the detail section.
getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
  Getter for the Ensembl-specific 'dataClass' term
getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the DataClass term
getDataRecord(String, int) - Method in class org.biojava.bio.program.abi.ABIFParser
  Get the entry from the file TOC with the given name and tag number.
getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource
getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
  Get the current set of all currently registered data sources.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
  Get a pre-built data store associated with a file.
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the date annotated term
getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the date created term
getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the date updated term
getDB() - Method in class org.biojava.bio.program.das.ReferenceServer
getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  retrieve the DB that has just been built
getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
getDB() - Method in class org.biojava.bio.seq.db.FetchURL
getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getDBHelper(Connection) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Returns a DBHelper implementation suitable for a particular database.
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
  return a set of DbId
getDbname() - Method in interface org.biojavax.CrossRef
  Returns the name of the database the cross reference refers to.
getDbname() - Method in class org.biojavax.SimpleCrossRef
  Returns the name of the database the cross reference refers to.
getDBSearchParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
getDBTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e.
getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation
getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location
  Checks the decorator chain for an instance of decoratorClass and return it if found.
getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Checks the decorator chain for an instance of decoratorClass and return it if found.

  The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps. ALWAYS RETURNS NULL

getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Checks the decorator chain for an instance of decoratorClass and return it if found. ALWAYS RETURNS NULL
getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Checks the decorator chain for an instance of decoratorClass and return it if found.
getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
  Get the changer that will be applied to values of tags with no specific handler registered.
getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType
  Get the CollectionConstraint that will be applied to all properties without an explicit binding.
getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl
getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory
  Returns the default cross ref resolver object.
getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools
getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
  Deprecated.
getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat
  Deprecated.
getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat
  Deprecated. new implementations should only write a single format.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory
  Returns the default namespace object.
getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory
  Returns the default ontology object.
getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
getDefaultParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory
  Returns the default position resolver object.
getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory
  Returns the default sequence resolver object.
getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
  Get the splitter that will be applied to values of tags with no specific handler registered.
getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
  get listener to which all calls will be delegated
getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter
  Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
  Retrieve the delegate that is wrapped.
getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  The compound alpha that holds the symbols used by this wrapper
getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Returns the current expenses of a single delete operation.
getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM
  Retrieves the delete state for column indx.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Returns the an object indicating the style of deletion that this database should employ.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
  Deprecated.
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
  Deprecated.
getDensityCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Gets the Depth attribute of the LightPairDPCursor object
getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
  retrieve the depth of this cursor
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `getDepth` calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer
  Get the depth needed for this renderer.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  `getDepth` calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getDepth` returns the total depth of a list of `SequenceRenderer`s.
getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  `getDepth` calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
  `getDepth` calculates the depth required by this renderer to display its beads.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
  Retrieve the depth of this renderer when rendering src.
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
  Retrieve the current DepthScaler.
getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  This gives you the description of this matrix if there is one.
getDescription() - Method in class org.biojava.bio.program.das.DataSource
getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder
getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon
  returns the name of the Taxon
getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the description for the AAindex entry.
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getDescription() - Method in class org.biojava.ontology.IntegerOntology
getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getDescription() - Method in interface org.biojava.ontology.Ontology
  Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojava.ontology.Ontology.Impl
getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl
getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl
getDescription() - Method in interface org.biojava.ontology.Term
  Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojava.ontology.Term.Impl
getDescription() - Method in class org.biojava.ontology.Triple.Impl
getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a description of this vocabulary.
getDescription() - Method in interface org.biojavax.bio.BioEntry
  Returns a description of this sequence.
getDescription() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns a description of this sequence.
getDescription() - Method in interface org.biojavax.Namespace
  Returns a description of this namespace.
getDescription() - Method in interface org.biojavax.ontology.ComparableOntology
  Return a human-readable description of this ontology.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Return a human-readable description of this ontology, or the empty string if none is available
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return a human-readable description of this term, or the empty string if none is available. ALWAYS RETURNS THE EMPTY STRING
getDescription() - Method in class org.biojavax.SimpleNamespace
  Returns a description of this namespace.
getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple
  Returns all descriptors.
getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Returns all descriptors. Warning this method gives access to the original Collection not a copy.
getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Return a handler for the XFF `details` element.
getDFA() - Method in class org.biojava.utils.automata.DfaBuilder
getDiagonalAtK(Atom[], int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
getDiagonalDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getDiagonalDistance2() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
  Retrieve the dimension at a specific index.
getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  `getDimensionRatio` returns the maximum ratio of long dimension to short dimension of the bead.
getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools
  returns an RNA dinucleotide alphabet.
getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getDirection` returns the direction in which this context expects the sequence to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Retrieve the current rendering direction.
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the current rendering direction.
getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getDirection` returns the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific
getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns the name of this taxon entry in the form: scientific (common) or if there is no common name: scientific or if there are no scientific names at all, the empty string.
getDistance(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  calculate distance between two atoms.
getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
  matrix of all distances between two sets of 3d coords"
getDistDataSource() - Method in class org.biojava.bio.program.das.DataSource
getDistDataSource() - Method in class org.biojava.bio.program.das.ReferenceServer
getDistMat() - Method in class org.biojava.bio.structure.align.StructurePairAligner
  return the difference of distance matrix between the two structures
getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
getDistribution() - Method in interface org.biojava.bio.dp.EmissionState
  Get the Distribution associated with this state.
getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo
  Retrieve the currently rendered dist.
getDistribution() - Method in interface org.biojava.bio.gui.LogoContext
getDivision() - Method in interface org.biojavax.bio.BioEntry
  Returns the division of this bioentry.
getDivision() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the division of this bioentry.
getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence
  Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
getDNA() - Static method in class org.biojava.bio.seq.DNATools
  Return the DNA alphabet.
getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools
  return a SimpleDistribution of specified GC content.
getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Creates a DNA symbol tokenizer.
getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Get the called DNA sequence from a chromatogram.
getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools
  Gets the (DNA x DNA) Alphabet
getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools
  return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.
getDocumentReference() - Method in interface org.biojavax.RankedDocRef
  Represents a reference to a document.
getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef
  Represents a reference to a document.
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
getDouble() - Method in class org.biojava.utils.io.LargeBuffer
getDoublePivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Return pivot permutation vector as a one-dimensional double array
getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getDownstreamCut` returns the cut site within or downstream of the recognition site.
getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getDownstreamEndType` returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getE() - Method in class org.biojava.bio.proteomics.StructureTools
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Tree navigation methods
getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  This gives the edit distance acording to the given parameters of this certain object.
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Is the format going to emit events when comments data or remarks from bibliographic references are read?
getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Is the format going to emit events when feature data is read?
getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Is the format going to emit events when feature data is read?
getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Is the format going to emit events when bibliographic reference data is read?
getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Is the format going to emit events when bibliographic reference data is read?
getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Return a flag indicating if symbol data will be skipped when parsing streams.
getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Is the format going to emit events when sequence data is read?
getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Is the format going to emit events when sequence data is read?
getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Get a default SequenceBuilderFactory for handling EMBL files.
getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
  Getter for the EMBL term
getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
  Getter for the EMBLxml term
getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
  This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.
getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache
getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache
  Retrieve the emission scores from the cache for every EmissionState for the specified symbols.
getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The end of this feature within the source sequence.
getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton
getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder
getEnd() - Method in class org.biojava.utils.automata.NfaSubModel
getEnd() - Method in interface org.biojavax.bio.seq.Position
  Returns the end of the range of bases this base could lie in.
getEnd() - Method in class org.biojavax.bio.seq.SimplePosition
  Returns the end of the range of bases this base could lie in.
getEnd() - Method in interface org.biojavax.RankedDocRef
  The end position in the sequence that this reference is referred to from.
getEnd() - Method in class org.biojavax.SimpleRankedDocRef
  The end position in the sequence that this reference is referred to from.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Get the current string indicating that a record has ended.
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Get the explicit end-of-record string.
getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
  This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a selected vocabulary entry.
getEnvironment() - Method in class org.biojava.naming.ObdaContext
getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess
  Gets environment variables for the external process.
getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getEnzyme` returns an enzyme by name.
getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite
  `getEnzyme` returns the enzyme which cuts at this site.
getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
getEqr() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  returns the number of euqivalent residues in this alignment
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser
  Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Find the error handler used by this parser.
getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the output error handler which is responsible for the standard error output of the external process.
getErrString() - Method in class org.biojava.utils.ExecRunner
  Returns the error string if exec(String) was invoked.
getEvalCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the overall E-value of this hit.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the E-value of this sub-hit.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property events.
getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the evidence attr term
getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the evidence category term
getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the evidence date term
getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the evidence type term
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getExtendedName() - Method in interface org.biojavax.DocRefAuthor
  Returns the extended version of the authors name.
getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor
  Returns the extended version of the authors name.
getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit
getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Getter for property factory.
getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Get a default SequenceBuilderFactory for handling FASTA files.
getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The feature type filed.
getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
  Retrieve the current feature.
getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the feature this location is associated with. ALWAYS RETURNS NULL
getFeature() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the feature this location is associated with.
getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the feature this location is associated with.
getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the FeatureDesc term
getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Return the current FeatureFilter.
getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
  getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence.
getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature
  A utility function to retrieve the feature holder delegate, creating it if necessary.
getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Return the object which receives startFeature/endFeature notifications.
getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Return current feature listener
getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Return current feature listener
getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the feature original term
getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
  Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the feature ref term
getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureHolder
  Returns the set of relationships held in this feature holder.
getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Returns the set of relationships held in this feature holder. Warning this method gives access to the original Collection not a copy.
getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  `getFeatureRenderer` returns the currently active renderer.
getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getFeatures` returns all of the `Feature`s belonging to the currently rendered `Sequence`.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel
getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  The features to render.
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getFeatures` returns all of the `Feature`s belonging to the currently rendered `Sequence`.
getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get all features matching a FeatureFilter provided by this DistDataSource.
getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology
  Retrieve the set of features that mark homologous regions.
getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology
  `getFeatures` returns the constituent `HomologyFeature`s which are also used as the keys in the alignment.
getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
  Returns the list of features in this featureholder.
getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence
  The features for this sequence.
getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence
  The features for this sequence. Warning this method gives access to the original Collection not a copy.
getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the feature status term
getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Get the template for the feature being constructed.
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the feature variation term
getField() - Method in class org.biojava.utils.ChangeType
  Return a Field object where this change type is declared.
getFile() - Method in interface org.biojava.bio.program.indexdb.Record
  `getFile` returns the random access file in which the record belongs.
getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `getFile` returns the `File` wrapped.
getFile() - Method in interface org.biojava.bio.seq.db.Index
  The file to retrieve from.
getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex
getFile() - Method in class org.biojava.utils.io.RAF
getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader
getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader
  `getFilePointer` returns the effective position of the pointer in the underlying `RandomAccessFile`.
getFiles() - Method in class org.biojava.bio.seq.db.BioIndex
getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the Set of files that are currently indexed.
getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore
getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Get the background color of the label area.
getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `getFilter` returns the current filter.
getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder
  It returns a name of this vocabulary finder.
getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property firstIntActID.
getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
  gets the first orthologue in the orthology relationship.
getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getFitnessFunction() - Method in class org.biojavax.ga.functions.AbstractSelectionFunction
getFitnessFunction() - Method in interface org.biojavax.ga.functions.SelectionFunction
getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
getFloat() - Method in class org.biojava.utils.io.LargeBuffer
getFloatOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Helper method for converting a `Number`-valued option into a `float` primitive.
getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Gets the Font attribute of the SequenceRenderContext object
getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools
  Attempt to find aformat for a format identifer string.
getFormat() - Method in class org.biojava.bio.seq.db.BioIndex
getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the format of the index file.
getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore
getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getForwardRegex` returns a regular expression which matches the forward strand of the recognition site.
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
getFragCompat() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getFragment(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
  get a continue subset of Atoms based by the starting position and the length
getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
  get a subset of Atoms based by their positions
getFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getFragmentMiniDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getFragmentPairs() - Method in class org.biojava.bio.structure.align.StructurePairAligner
  get the results of step 1 - the FragmentPairs used for seeding the alignment
getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The frame of the feature.
getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
  Retrieve the reading frame this filter matches.
getFrame() - Method in interface org.biojava.bio.seq.Frame
  A method to get the frame information of the implementing object
getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref
  returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
  returns a Distribution giving the frequency of synonymous codons.
getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
  returns the frequency with which synonymous codons start with a specified pair of bases.
getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException
getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the FTId term
getFullName() - Method in interface org.biojava.bio.structure.Atom
  get full name of atom e.g.
getFullName() - Method in class org.biojava.bio.structure.AtomImpl
  get full name of atom e.g.
getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position
  Returns true if the position has a fuzzy end.
getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition
  Returns true if the position has a fuzzy end.
getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position
  Returns true if the position has a fuzzy start.
getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition
  Returns true if the position has a fuzzy start.
getG() - Method in class org.biojava.bio.proteomics.StructureTools
getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Returns the current expenses of any extension of a gap operation.
getGapExtCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getGapExtCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getGapExtension() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getGapExtRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getGapExtRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getGapOpen() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getGapOpenCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getGapOpenCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getGapOpenRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getGapOpenRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getGaps() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  return the number of gaps in this alignment
getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet
getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet
  Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get the special `gap' Symbol.
getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Get the gap symbol appropriate to this list of alphabets.
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Get a default SequenceBuilderFactory for handling GenBank files.
getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms
  Getter for the Genbank term
getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the GeneName term
getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Discover if per-sequence header lines will be generated.
getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm
getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
  The current generation
getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the GeneSynonym term
getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a TranslationTable by name.
getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref
  the genetic code that this codon preference is based on.
getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns the genetic code of this taxon, which may be null if not known.
getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns the genetic code of this taxon, which may be null if not known.
getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref
  get the name of the genetic code
getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a Set containing the name of each genetic code.
getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
  Getter for the Ensembl-specific 'genomic' term
getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Get a default SequenceBuilderFactory for handling Genpept files.
getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getGraphics() - Method in interface org.biojava.bio.gui.LogoContext
getGroup(int) - Method in interface org.biojava.bio.structure.Chain
  return the amino acid at position X.
getGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
  return the amino acid at position .
getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord
  A Map containing the group / attribute information.
getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getGroupByPDB(String) - Method in interface org.biojava.bio.structure.Chain
  get a group by its PDB residue numbering.
getGroupByPDB(String) - Method in class org.biojava.bio.structure.ChainImpl
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getGroups(String) - Method in interface org.biojava.bio.structure.Chain
  return an ArrayList of all groups of a special type (e.g.
getGroups() - Method in interface org.biojava.bio.structure.Chain
  return all groups of this chain.
getGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
  return an array of all groups of a special type (e.g.
getGroups() - Method in class org.biojava.bio.structure.ChainImpl
  return all groups of this chain .
getGroupsByPDB(String, String) - Method in interface org.biojava.bio.structure.Chain
  get all groups that are located between two PDB residue numbers
getGroupsByPDB(String, String) - Method in class org.biojava.bio.structure.ChainImpl
getH() - Method in class org.biojava.bio.proteomics.StructureTools
getH() - Method in class org.biojava.bio.structure.jama.QRDecomposition
  Return the Householder vectors
getHandler(SeqSimilarityStAXAdapter) - Method in interface org.biojava.bio.program.ssbind.StAXHandlerFactory
  `getHandler` returns an appropriate `StAXContentHandler` implementation containing a reference to a parent context.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory
  Return a suitable StAX content handler.
getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  Retrieve a `FilterHandler` for the specified tag name.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory
  Return a suitable StAX content handler.
getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory
  Return a suitable StAX content handler.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  return iterator to callbackStack
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  get iterator for current stack starting at the position below mine.
getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  return iterator to callbackStack
getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  get iterator for current stack starting at the position below mine.
getHeader() - Method in interface org.biojava.bio.structure.Structure
  get Header data .
getHeader() - Method in class org.biojava.bio.structure.StructureImpl
  get Header data.
getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
  Returns the appropriate style and javascript definitions for this renderer.
getHeight() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the height of the whole graphic (in pixels).
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  `getHeightScaling` returns the state of the height scaling policy.
getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `getHeightScaling` returns the state of the height scaling policy.
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
  Return all hits in this sequence similarity search result.
getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue
  get the Homologene ID.
getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature
getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
getHorizontalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the in-use horizontal scale factor.
getI() - Method in class org.biojava.bio.proteomics.StructureTools
getID() - Method in interface org.biojava.bio.program.indexdb.Record
  `getID` returns the primary identifier of the record.
getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
  The public unigene ID.
getID() - Method in interface org.biojava.bio.seq.db.Index
  The ID of the sequence at this position in this file.
getID() - Method in class org.biojava.bio.seq.db.SimpleIndex
getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property ID.
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable
  Return the identifier of this object.
getIdentifier() - Method in interface org.biojavax.bio.BioEntry
  Returns the identifier of this bioentry.
getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the identifier of this bioentry.
getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm
  Returns the (optional) identifier associated with this term.
getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Returns the (optional) identifier associated with this term.
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB
  Retrieve the IDMaker associated with this database.
getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB
  Retrieve the IDMaker associated with this database.
getIDs() - Method in class org.biojava.bio.seq.db.BioIndex
getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the set of all current IDs.
getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore
getIdx1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
getIdx2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
getIdxlist() - Method in class org.biojava.bio.structure.align.helper.JointFragments
getImage(int, int) - Method in class org.biojava.bio.program.abi.ABITrace
  Returns a BufferedImage that represents the entire trace.
getImagEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
  Return the imaginary parts of the eigenvalues
getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
  `getImageMap` returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `getImageMap` returns the current image map.
getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
  `getImageMap` returns the current image map.
getImplementationNames(Class) - Static method in class org.biojava.utils.Services
  Return a Set of names of implementations of the given service interface in the classloader from which BioJava was loaded.
getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services
  Return a List of names of implementations of the given service interface available in a given classloader.
getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  Calculate the position in the sequence relating to the angle.
getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getIndex() - Method in class org.biojava.bio.structure.align.helper.GapArray
getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
  Retrieve the IndexStore.
getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory
getInitialK() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getInput() - Method in interface org.biojava.utils.process.OutputHandler
  Gets the input stream.
getInput() - Method in class org.biojava.utils.process.StreamPipe
  Gets the input stream
getInput() - Method in class org.biojava.utils.process.WriterOutputHandler
  Gets the input stream.
getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the input handler which is responsible for the standard input of the external process.
getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider
  get an InputStream for this file
getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider
  get an InputStream for the file
getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
  Getter for the INSDseq term
getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Returns the current expenses of a single insert operation.
getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM
  Retrieves the insert state at column indx.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Returns the id value created during the last insert command.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
  Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
  Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
  Deprecated.
getInstance() - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
  Retrieve the singleton instance of this class.
getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer
  Returns the global singleton instance of the IgnoreCountsTrainer.
getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve the single DoubleAlphabet instance.
getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet
  Retrieve the single IntegerAlphabet instance.
getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Generates a soft masked Alphabet where lowercase tokens are assumed to be soft masked.
getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Creates a compound alphabet that is a hybrid of the alphabet that is to be soft masked and a binary alphabet that indicates if any `Symbol` is soft masked or not.
getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
getInstance() - Static method in class org.biojava.naming.ObdaUriParser
getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory
  Make a WalkerFactory that handles a Visitor for a class of type typeClazz.
getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory
getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
getInt() - Method in class org.biojava.utils.io.LargeBuffer
getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools
  Get the Ontology that defines integers.
getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property interactions.
getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence
  A special function that returns the SymbolList that this RichSequence is based around.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence
  A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.
getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence
  A special function that returns the SymbolList that this RichSequence is based around.
getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Retrieves, unwraps, and returns an `int` from a SymbolList containing `IntegerAlphabet.IntegerSymbol`s.
getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Helper method for converting a `Number`-valued option into an `int` primitive.
getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns a new AffineTransform describing the transformation from output space to chromatogram space.
getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property isoforms.
getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Getter for property isoIDs.
getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getIsoschizomers` returns an unmodifable set of the isoschizomers of this enzyme.
getItem() - Method in interface org.biojava.stats.svm.ItemValue
getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
getIterator() - Method in class org.biojava.utils.ListTools.Doublet
getIterator() - Method in class org.biojava.utils.ListTools.Triplet
getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator
getJoinRMSCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated. Returns the an object indicating the style of table joining that this database should employ.
getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
  Getter for the "join" term
getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets a reference to the journal which published the article about the AAindex entry.
getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the currently used kernel
getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation
getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference
getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the keyword term
getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property kineticsNote.
getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
  Returns the table of border lengths
getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property KMs.
getL() - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
  Return triangular factor.
getL() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Return lower triangular factor
getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement
getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  return the label of this class.
getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property label.
getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment
  getLabels will return a list of labels in left to right order
getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
getLabels() - Method in interface org.biojava.bio.symbol.Alignment
  The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
getLabels() - Method in class org.biojava.bio.symbol.SimpleAlignment
getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel
  Retrieve the scale factor.
getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
  Get the last complete annotation built.
getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
getLeader() - Method in class org.biojava.utils.ListTools.SeriesList
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getLeadingBorder` returns the leading border of the primary sequence.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Gets the LeadingBorder attribute of the SequenceRenderContext object.
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getLeadingBorder` returns the leading border.
getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Gets the left value.
getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Gets the left value.
getLength() - Method in interface org.biojava.bio.program.indexdb.Record
  `getLength` returns the length of the record in bytes.
getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getLength() - Method in class org.biojava.bio.search.SeqContentPattern
  Get the current length.
getLength() - Method in interface org.biojava.bio.seq.db.Index
  The entry can be slurped out of the file by grabbing length bytes from start.
getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex
getLength() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getLength() - Method in interface org.biojava.bio.structure.Chain
  get total length of chain, including HETATMs..
getLength() - Method in class org.biojava.bio.structure.ChainImpl
getLength() - Method in class org.biojava.bio.symbol.CircularLocation
getLength() - Method in class org.biojava.utils.RepeatedCharSequence
getLengthAminos() - Method in interface org.biojava.bio.structure.Chain
  returns the length of the AminoAcids in chain, without HETATMs.
getLengthAminos() - Method in class org.biojava.bio.structure.ChainImpl
getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  return current stack level.
getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  return current stack level.
getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache
getLine() - Method in exception org.biojava.utils.ParserException
  Get the text of the line where the exception occured.
getLineNumber() - Method in exception org.biojava.utils.ParserException
  Get the line number in the stream where this exception occured.
getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the number of lines that the sequence will be rendered over.
getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat
  Retrive the current line width.
getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Retrive the current line width.
getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Retrive the current line width.
getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Retrive the current line width.
getLinkURL() - Method in class org.biojava.bio.program.das.DASLink
getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener
  `getListener` returns the listener of the pair.
getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  return the TagValueListener assigned to this State.
getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Gets the list of literature database identifiers for the AAindex entry.
getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement
getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore
  `getLocation` returns the directory where the index is located.
getLocation() - Method in interface org.biojava.bio.seq.Feature
  The location of this feature.
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region
  Retrieve the Location of the Region.
getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  The location of this feature.
getLocation() - Method in interface org.biojavax.DocRef
  Returns a textual description of the document reference.
getLocation() - Method in interface org.biojavax.RankedDocRef
  If this object was constructed using a location instead of two integers, then this method will return that location.
getLocation() - Method in class org.biojavax.SimpleDocRef
  Returns a textual description of the document reference.
getLocation() - Method in class org.biojavax.SimpleRankedDocRef
getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the location seq term
getLocator() - Method in exception org.biojava.utils.ParserException
  Get a locator for the stream which caused this exception.
getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue
  get the locus ID associated with this orthologue.
getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getLogoFont() - Method in class org.biojava.bio.gui.TextBlock
  Retrieve the current font.
getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter
  Retrieve the current font.
getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo
  Retrieve the current logo painter.
getLong(long) - Method in class org.biojava.utils.io.LargeBuffer
getLong() - Method in class org.biojava.utils.io.LargeBuffer
getLSID() - Method in class org.biojava.bio.program.formats.Embl
getLSID() - Method in class org.biojava.bio.program.formats.Enzyme
getLSID() - Method in interface org.biojava.bio.program.formats.Format
  Retrieve the LSID associated with this format.
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getLSID() - Method in class org.biojava.bio.program.formats.Swissprot
getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine
getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper
  `getMapAll` returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapper() - Method in class org.biojava.bio.AnnotationRenamer
  `getMapper` returns the `TagMapper` being used to remap the `Annotation`.
getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer
  Retrieve the mapper used to rename tags
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getMapURL() - Method in class org.biojava.bio.program.das.DataSource
getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Gets the `Alphabet` upon which masking is being applied
getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Getter for the `MaskingDetector```
getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc
  `getMass` calculates the mass of this peptide.
getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
  Get the Mass of this peptide.
getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Returns the current expenses of a single match operation.
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM
  Retrieve the match state at column indx.
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getMatches() - Method in interface org.biojava.bio.symbol.Symbol
  The alphabet containing the symbols matched by this ambiguity symbol.
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMatrices() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  Returns the matrices.
getMatrix(int, int, int, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Get a submatrix.
getMatrix(int[], int[]) - Method in class org.biojava.bio.structure.jama.Matrix
  Get a submatrix.
getMatrix(int, int, int[]) - Method in class org.biojava.bio.structure.jama.Matrix
  Get a submatrix.
getMatrix(int[], int, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Get a submatrix.
getMatrixAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the rotation matrix annotation type
getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  The maximum score in this matrix.
getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getMax(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getMax() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Gets the max intensity from all the traces.
getMax(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Gets the max intensity on the trace for the specified nucleotide.
getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMax() - Method in class org.biojava.bio.symbol.CircularLocation
  This will give you the coordinate of the maximum point contained by this Location.
getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMax() - Method in interface org.biojava.bio.symbol.Location
  The maximum position contained.
getMax() - Method in class org.biojava.bio.symbol.PointLocation
getMax() - Method in class org.biojava.bio.symbol.RangeLocation
getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  The maximum position contained. ALWAYS RETURNS ZERO
getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  The maximum position contained.

  WARNING: The location will not contain every point between `getMin()` and `getMax()` if `isContiguous()` is false. If `isContiguous()` does return false you should use the `Iterator` returned by `blockIterator()` to iterate over the minimum set of contiguous blocks that make up this `Location` ALWAYS RETURNS COMBINED LENGTH OF MEMBERS

getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
  Resolves the maximum possible base for this position. ALWAYS RETURNS e.getStart()+e.getEnd() / 2
getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
  Resolves the maximum possible base for this position.
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
  Resolves the maximum possible base for this position. ALWAYS RETURNS e.getEnd()
getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
  Resolves the maximum possible base for this position. ALWAYS RETURNS e.getStart()
getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  The maximum position contained.
getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
  Get the maximum counts required for a symbol.
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction
getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
getMaxIter() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the end position of this location. ALWAYS RETURNS THE EMPTY POSITION
getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Retrieves the end position of this location. ALWAYS RETURNS A POINT POSITION AT POINT EQUIVALENT TO COMBINED LENGTH OF MEMBERS
getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the end position of this location.
getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the end position of this location.
getMaxrefine() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner
  Returns whether the maximum runtime was exceeded or not.
getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner
  Returns the maximum run time in seconds for this object.
getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
  `getMaxScore` returns the maximum score accepted.
getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap
getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
  Return a list of merged DBs.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  See if tags are being merged.
getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Report whether empty tags will be treated as continuations of the last non -empty tag.
getMessage() - Method in class org.biojava.utils.ParseErrorEvent
  Find the message about this event
getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore
getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore
  `getMetaData` returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
  Get the Method used.
getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  The minimum score of this matrix.
getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getMin() - Method in class org.biojava.bio.symbol.CircularLocation
  This will give you the coordinate of the minimum point contained by this Location.
getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getMin() - Method in interface org.biojava.bio.symbol.Location
  The minimum position contained.
getMin() - Method in class org.biojava.bio.symbol.PointLocation
getMin() - Method in class org.biojava.bio.symbol.RangeLocation
getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  The minimum position contained. ALWAYS RETURNS ZERO
getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  The minimum position contained.

  WARNING: The location will not contain every point between `getMin()` and `getMax()` if `isContiguous()` is false. If `isContiguous()` does return false you should use the `Iterator` returned by `blockIterator()` to iterate over the minimum set of contiguous blocks that make up this `Location` ALWAYS RETURNS ONE

getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
  Resolves the minimum possible base for this position. ALWAYS RETURNS s.getStart()+s.getEnd() / 2
getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
  Resolves the minimum possible base for this position.
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
  Resolves the minimum possible base for this position. ALWAYS RETURNS s.getStart()
getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
  Resolves the minimum possible base for this position. ALWAYS RETURNS s.getEnd()
getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  The minimum position contained.
getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
  Get the minimum counts required for a symbol.
getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  get the lowest level of identity observed in this Group
getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getMinimumLeader` returns the maximum value of getMinimumLeader() for a list of `SequenceRenderer`s.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
  Retrieve the minimum leading distance for this renderer when rendering src.
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
  `getMinimumTrailer` returns the maximum value of getMinimumTrailer() for a list of `SequenceRenderer`s.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
  Retrieve the minimum trailing distance for this renderer when rendering src.
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer
  Retrieve the minimum space required to render the label.
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the start position of this location. ALWAYS RETURNS THE EMPTY POSITION
getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Retrieves the start position of this location. ALWAYS RETURNS A POINT POSITION AT POINT 1
getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the start position of this location.
getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the start position of this location.
getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
  `getMinScore` returns the minimum score accepted.
getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern
getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns the mitochondrial genetic code of this taxon, which may be null if not known.
getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Getter for property mitoGeneticCode.
getModel() - Method in class org.biojava.bio.dp.DP
getModel() - Method in interface org.biojava.bio.dp.ModelInState
  The model that is inside this state.
getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
getModel(int) - Method in interface org.biojava.bio.structure.Structure
  retrieve all Chains belonging to a model .
getModel(int) - Method in class org.biojava.bio.structure.StructureImpl
  retrieve all Chains belonging to a model .
getModifiable() - Method in class org.biojava.utils.MergingSet
getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property molecularWeight.
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getMolTypeTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  getter for the MolType term
getMolWeightError() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property molWeightError.
getMolWeightMethod() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property molWeightMethod.
getMolWeightRangeEnd() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property molWeightRangeEnd.
getMolWeightRangeStart() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property molWeightRangeStart.
getMoreSearches() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
getMoreSearches() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentAdapter
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentFilter
getMoreSearches() - Method in interface org.biojava.bio.search.SearchContentHandler
  `getMoreSearches` returns the state of the `SearchContentHandler` with respect to further searches from its data source.
getMoreSearches() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
getMotifs() - Method in class org.biojava.bio.program.Meme
getMouseEvent() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
  Get the mouse event that caused this.
getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel
getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel
getMutationFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getMutationFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getMutationProbs() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
getMutationProbs() - Method in interface org.biojavax.ga.functions.MutationFunction
getMutationProbs() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
getMutationSpectrum() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
getMutationSpectrum() - Method in interface org.biojavax.ga.functions.MutationFunction
getMutationSpectrum() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
getMyComponents(Name) - Method in class org.biojava.naming.ObdaContext
getN() - Method in interface org.biojava.bio.structure.AminoAcid
  get N atom.
getN() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get N atom.
getName() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Every substitution matrix has a name like "BLOSUM30" or "PAM160".
getName() - Method in interface org.biojava.bio.annodb.AnnotationDB
  The name of this AnnotationDB.
getName() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
getName() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
getName() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
getName() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
getName() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
getName() - Method in class org.biojava.bio.dp.SimpleEmissionState
getName() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getName` returns the enzyme name.
getName() - Method in class org.biojava.bio.program.das.DASSequence
getName() - Method in class org.biojava.bio.program.das.DASSequenceDB
getName() - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
getName() - Method in class org.biojava.bio.program.das.DataSource
getName() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  retrieves name of this group.
getName() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getName() - Method in class org.biojava.bio.program.indexdb.BioStore
  The name of this store or null if the name has not been set.
getName() - Method in class org.biojava.bio.proteomics.Protease
  Gets the name of this Protease
getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
getName() - Method in class org.biojava.bio.seq.db.BioIndex
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
  Deprecated.
getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
getName() - Method in class org.biojava.bio.seq.db.DummySequenceDB
getName() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `getName` returns the database name as defined within the EMBL CD-ROM index.
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
getName() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
  Get the name of this sequence database.
getName() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the name of this store.
getName() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getName() - Method in interface org.biojava.bio.seq.db.SequenceDBLite
  Get the name of this sequence database.
getName() - Method in class org.biojava.bio.seq.db.SubSequenceDB
getName() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getName() - Method in class org.biojava.bio.seq.db.TabIndexStore
getName() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
getName() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
  The name of this repository.
getName() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
  Get the name of this type.
getName() - Method in class org.biojava.bio.seq.impl.DummySequence
getName() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getName() - Method in class org.biojava.bio.seq.impl.SubSequence
getName() - Method in class org.biojava.bio.seq.impl.ViewSequence
getName() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getName() - Method in interface org.biojava.bio.seq.Sequence
  The name of this sequence.
getName() - Method in class org.biojava.bio.seq.SimpleAssembly
getName() - Method in interface org.biojava.bio.structure.Atom
  get trimmed version of atom name, e.g.
getName() - Method in class org.biojava.bio.structure.AtomImpl
  Gets this object's name.
getName() - Method in interface org.biojava.bio.structure.Chain
  get and set the name of this chain (Chain id in PDB file ).
getName() - Method in class org.biojava.bio.structure.ChainImpl
  get and set the name of this chain (Chain id in PDB file ).
getName() - Method in interface org.biojava.bio.structure.Structure
  get biological name of Structure.
getName() - Method in class org.biojava.bio.structure.StructureImpl
  get biological name of Structure.
getName() - Method in interface org.biojava.bio.symbol.Alphabet
  Get the name of the alphabet.
getName() - Method in interface org.biojava.bio.symbol.CodonPref
  get name of object
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
getName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
getName() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  The name of the Alphabet
getName() - Method in interface org.biojava.bio.symbol.Symbol
  The long name for the symbol.
getName() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
getName() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
getName() - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Name for this TaxonFactory.
getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
getName() - Method in interface org.biojava.directory.SequenceDBProvider
  The name of this provider.
getName() - Method in class org.biojava.ontology.IntegerOntology
getName() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getName() - Method in interface org.biojava.ontology.Ontology
  Return the name of this ontology
getName() - Method in class org.biojava.ontology.Ontology.Impl
getName() - Method in class org.biojava.ontology.OntologyTerm.Impl
getName() - Method in class org.biojava.ontology.RemoteTerm.Impl
getName() - Method in interface org.biojava.ontology.Term
  Return the name of this term.
getName() - Method in class org.biojava.ontology.Term.Impl
getName() - Method in class org.biojava.ontology.Triple.Impl
getName() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a name of this vocabulary.
getName() - Method in class org.biojava.utils.ChangeType
  Return the name of this change.
getName() - Method in class org.biojava.utils.regex.Pattern
  return the String label associated with this pattern.
getName() - Method in interface org.biojavax.bio.BioEntry
  Returns the name of this bioentry.
getName() - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Get the name of this sequence database.
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
getName() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getName() - Method in class org.biojavax.bio.db.HashBioEntryDB
getName() - Method in class org.biojavax.bio.db.HashRichSequenceDB
getName() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
getName() - Method in interface org.biojavax.bio.seq.RichFeature
  Returns the name of this feature.
getName() - Method in class org.biojavax.bio.seq.RichLocation.Strand
  Returns the string symbol of this strand.
getName() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Returns the name of this feature.
getName() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the name of this bioentry.
getName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Returns this name.
getName() - Method in interface org.biojavax.DocRefAuthor
  Returns a textual description of the authors name.
getName() - Method in class org.biojavax.ga.impl.AbstractOrganism
getName() - Method in class org.biojavax.ga.impl.AbstractPopulation
getName() - Method in interface org.biojavax.ga.Organism
  Gets the organisms name
getName() - Method in interface org.biojavax.ga.Population
getName() - Method in interface org.biojavax.Namespace
  The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getName() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Return the name of this ontology
getName() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Return the name of this term.
getName() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return the name of this term. Returns the output of toSring()
getName() - Method in class org.biojavax.SimpleDocRefAuthor
  Returns a textual description of the authors name.
getName() - Method in class org.biojavax.SimpleNamespace
  The name of the namespace is immutable and must be set by the constructor of the instantiating class.
getNameClass() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Returns the class of this name.
getNameClasses() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns all the name classes available for a taxon.
getNameClasses() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns all the name classes available for a taxon.
getNamedIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Getter for property namedIsoforms.
getNameHierarchy() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns the taxonomy hierarchy of this taxon entry in the form: least specific; more specific; ...; most specific.
getNameHierarchy() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
getNameInNamespace() - Method in class org.biojava.naming.ObdaContext
getNameParser(Name) - Method in class org.biojava.naming.ObdaContext
getNameParser(String) - Method in class org.biojava.naming.ObdaContext
getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getNames() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Getter for property names.
getNames(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns all the names available for a taxon in a given class.
getNames(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns all the names available for a taxon in a given class.
getNameSet() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
getNamesMap() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
getNamespace() - Method in interface org.biojavax.bio.BioEntry
  Returns the namespace of this bioentry.
getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Getter for property namespace.
getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the namespace of this bioentry.
getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the namespace id for this identifier within the authority.
getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Gets the NCBI taxon ID.
getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Gets the NCBI taxon ID.
getNCutters(int) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getNCutters` returns an unmodifable set of all enzymes with a cut site of size n.
getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the shape used to represent negative points.
getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel
  Retrieve the currently nested SVMKernel.
getNewTag(Object) - Method in interface org.biojava.bio.program.tagvalue.PropertyChanger
  `getNewTag` returns the tag which substitutes the specified value.
getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
getNodeRank() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Gets the node rank of this taxon.
getNodeRank() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Gets the node rank of this taxon.
getNodes() - Method in class org.biojava.utils.automata.FiniteAutomaton
  get all Nodes within this instance.
getNodes() - Method in interface org.biojava.utils.automata.NfaBuilder
getNodes() - Method in class org.biojava.utils.automata.NfaSubModel
getNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
  returns Set containing the nonWobbleBases that occur in codons that encode this residue
getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Retrive the current normalizing vector.
getNotCleaveResidues() - Method in class org.biojava.bio.proteomics.Protease
  The list of residues that will prevent cleavage if they follow the cleavage residue.
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getNote(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getNote() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property note.
getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Getter for property note.
getNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
  Uses the term and rank to lookup a note in this annotation. There are no notes in the Empty RichAnnotation object.
getNote(Note) - Method in interface org.biojavax.RichAnnotation
  Uses the term and rank to lookup a note in this annotation.
getNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
  Uses the term and rank to lookup a note in this annotation.
getNoteSet() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
getNoteSet() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Returns the set of notes associated with this object. ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Returns the set of notes associated with this object. Warning this method gives access to the original Collection not a copy.
getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Returns the set of notes associated with this object. Warning this method gives access to the original Collection not a copy.
getNoteSet() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the set of notes associated with this object. Warning this method gives access to the original Collection not a copy.
getNoteSet() - Method in class org.biojavax.EmptyRichAnnotation
  Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in interface org.biojavax.RichAnnotatable
  Returns the set of notes associated with this object.
getNoteSet() - Method in interface org.biojavax.RichAnnotation
  Returns an immutable set of all notes in this annotation.
getNoteSet() - Method in class org.biojavax.SimpleCrossRef
  Returns the set of notes associated with this object.
getNoteSet() - Method in class org.biojavax.SimpleRichAnnotation
  Returns an immutable set of all notes in this annotation. Warning this method gives access to the original Collection not a copy.
getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools
  Return the Nucleotide alphabet.
getNucleotideParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Creates a nucleotide symbol tokenizer.
getNullModel() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
getNullModel() - Method in interface org.biojava.bio.dist.Distribution
  Retrieve the null model Distribution that this Distribution recognizes.
getNullModel() - Method in class org.biojava.bio.dist.GapDistribution
getNullModel(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution
  Get a uniform null model over a PairDistribution over [first,second].
getNullModel() - Method in class org.biojava.bio.dist.PairDistribution
getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution
getNullModel() - Method in class org.biojava.bio.dist.TranslatedDistribution
getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution
getNullModelWeight() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Return the number of pseudocounts added to the distribution when training.
getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Return a number (usually, but not always, a motif count) associated with this node of the tree.
getNumberExperiments() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property numberExperiments.
getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder
  It returns the number of available vocabularies.
getO() - Method in interface org.biojava.bio.structure.AminoAcid
  get O atom.
getO() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get O atom.
getObject() - Method in interface org.biojava.ontology.Triple
  Return the object term of this triple.
getObject() - Method in class org.biojava.ontology.Triple.Impl
getObject() - Method in interface org.biojavax.bio.BioEntryRelationship
  Returns the object of this relationship (ie.
getObject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
  Returns the object of this relationship (ie.
getObject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Returns the object of this relationship (ie.
getObject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Returns the object of this relationship (ie.
getObject() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return the object term of this triple.
getObject(Class, Object[]) - Static method in class org.biojavax.RichObjectFactory
  Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
getObjectAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the alignment object Annotation Type.
getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the object id of this identifier.
getObjects() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  Returns the Annotation of all objects in this Alignment.
getObsolete() - Method in interface org.biojavax.ontology.ComparableTerm
  Checks to see if this term is obsolete.
getObsolete() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Checks to see if this term is obsolete.
getOccupancy() - Method in interface org.biojava.bio.structure.Atom
  get occupancy.
getOccupancy() - Method in class org.biojava.bio.structure.AtomImpl
getOffset() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  Get the angle through which the origin of the sequence is rotated through.
getOffset() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
getOffset() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getOffset() - Method in interface org.biojava.bio.program.indexdb.Record
  `getOffset` returns the byte offset in the file at which the record begins.
getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl
getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getOntology(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
getOntology() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getOntology() - Method in interface org.biojava.ontology.OntologyTerm
  Get the remote ontology referenced by this term
getOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
getOntology() - Method in class org.biojava.ontology.RemoteTerm.Impl
getOntology() - Method in interface org.biojava.ontology.Term
  Return the ontology in which this term exists.
getOntology() - Method in class org.biojava.ontology.Term.Impl
getOntology() - Method in class org.biojava.ontology.Triple.Impl
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Return the ontology in which this term exists.
getOntology() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return the ontology in which this term exists.
getOps() - Method in class org.biojava.ontology.IntegerOntology
getOps() - Method in interface org.biojava.ontology.Ontology
  Return the associated OntologyOps.
getOps() - Method in class org.biojava.ontology.Ontology.Impl
getOps() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Return the associated OntologyOps.
getOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the current value for the specified option.
getOrCreateTerm(String) - Method in interface org.biojavax.ontology.ComparableOntology
  Looks for a term with the given name and returns it.
getOrCreateTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Looks for a term with the given name and returns it. If the term has to be created, it is added with the description "auto-generated by biojavax".
getOrCreateTriple(Term, Term, Term) - Method in interface org.biojavax.ontology.ComparableOntology
  Looks for a triple with the given subject object and predicate and returns it.
getOrCreateTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Looks for a triple with the given subject object and predicate and returns it.
getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
getOrderedLocusNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the OrderedLocusName term
getOrderTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
  Getter for the "order" term
getORFNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the ORFName term
getOrganelleTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Organelle term
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getOrganismByName(String) - Method in class org.biojavax.ga.impl.SimplePopulation
getOrganismByName(String) - Method in interface org.biojavax.ga.Population
  Gets the specified organism
getOrganisms() - Method in class org.biojavax.ga.impl.SimplePopulation
getOrganisms() - Method in interface org.biojavax.ga.Population
  Gets the Set of Organisms
getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getOrImportTerm(Term) - Method in interface org.biojavax.ontology.ComparableOntology
  Looks for a term with the same name as the given term and returns it.
getOrImportTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Looks for a term with the same name as the given term and returns it.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Returns an orthologue of specified ID.
getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
getOrthoPairSets() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
  Get the HomologeneGroups in this database.
getOrthoPairSets() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getOtherSeqIdTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
  Getter for the INSDseq term
getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
getOutline() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
getOutline() - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `getOutline` returns the colour used to draw the lines.
getOutline() - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `getOutline` returns the colour used to draw the lines.
getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
getOutline() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
getOutline() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
getOutput() - Method in interface org.biojava.utils.process.InputHandler
  Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.ReaderInputHandler
  Gets the output stream.
getOutput() - Method in class org.biojava.utils.process.StreamPipe
  Gets the output stream.
getOutputHandler() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the output handler which is responsible for the standard output of the external process.
getOutString() - Method in class org.biojava.utils.ExecRunner
  Returns the output string if exec(String) was invoked.
getOverlay() - Method in class org.biojava.bio.OverlayAnnotation
  Get the map used for the overlay.
getOverlayMap() - Method in class org.biojava.utils.OverlayMap
  Return the object containing the overlay mappings.
getPacking(FiniteAlphabet, boolean) - Static method in class org.biojava.bio.symbol.PackingFactory
  Get the default packing for an alphabet.
getPadding() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
  Retrieve the current padding.
getParams() - Method in class org.biojava.bio.structure.align.StructurePairAligner
  get the parameters.
getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
  Get the original sequenceDB from this annotated sequenceDB.
getParent() - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
  Return the parent SequenceDB.
getParent() - Method in interface org.biojava.bio.seq.Feature
  Return the `FeatureHolder` to which this feature has been attached.
getParent() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
getParent() - Method in class org.biojava.bio.seq.projection.ReparentContext
getParent(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getParent() - Method in interface org.biojava.bio.structure.Atom
  Returns the parent Group of the Atom returns null if the referenced object is not Group
getParent() - Method in class org.biojava.bio.structure.AtomImpl
getParent() - Method in interface org.biojava.bio.structure.Group
  Returns the parent Chain of the Group
getParent() - Method in class org.biojava.bio.structure.HetatomImpl
  Returns the parent Chain of the Group
getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon
  Deprecated.
getParent() - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. The parent of this Taxon.
getParent() - Method in class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
getParent() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Return the `FeatureHolder` to which this feature has been attached.
getParentDB() - Method in class org.biojava.bio.program.das.DASSequence
getParentMap() - Method in class org.biojava.utils.OverlayMap
  Return the object containing the fallback mappings.
getParentNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Returns the parent NCBI taxon ID, if known.
getParentNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns the parent NCBI taxon ID, if known.
getParents() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
  Get a set of URIs for parent types.
getParser() - Method in class org.biojava.bio.program.tagvalue.ParserListener
  `getParser` returns the parser of the pair.
getParser(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getParserListener(TagValueListener) - Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory
  Get the ParserListener for a TagValueListener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Embl
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Enzyme
getParserListener(TagValueListener) - Method in interface org.biojava.bio.program.formats.Format
  Retrieve a ParserListener pair for the format that will pass all events on to a listener.
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Compound
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Swissprot
getParserListenerFactory() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
  Get the ParserListenerFactory used by this IndexedAnnotationDB.
getPartHandler(XFFFeatureSetHandler) - Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory
  Return a suitable StAX content handler.
getPath() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
  Get the list of SequenceRenderer instances that were passed through to produce this event
getPath() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getPath() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getPath() - Method in class org.biojava.bio.structure.io.PDBFileReader
  Returns the path value.
getPathEnd(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getPathLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getPathPrefix() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `getPathPrefix` returns the abstract path currently being appended to the raw sequence database filenames extracted from the binary index.
getPathSize() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getPathSize() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getPattern() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Get the Pattern currently used to split lines.
getPattern() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
getPattern() - Method in class org.biojava.bio.search.MaxMismatchPattern
getPatterns(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getPatterns` returns two `Pattern` objects for an enzyme, one matches the forward strand and one the reverse.
getPDBCode() - Method in interface org.biojava.bio.structure.Group
  return the PDBcode (residue number) of this group.
getPDBCode() - Method in class org.biojava.bio.structure.HetatomImpl
  Returns the PDBCode.
getPDBCode() - Method in interface org.biojava.bio.structure.Structure
  get PDB code of structure.
getPDBCode() - Method in class org.biojava.bio.structure.StructureImpl
  get PDB code of structure .
getPDBline() - Method in interface org.biojava.bio.structure.Atom
  store the whole line.
getPDBline() - Method in class org.biojava.bio.structure.AtomImpl
  get the whole line .
getPDBName() - Method in interface org.biojava.bio.structure.Group
  set the PDB 3 character name for this group.
getPDBName() - Method in class org.biojava.bio.structure.HetatomImpl
  Returns the PDBName.
getPDBresnum1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
getPDBresnum2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
getPDBserial() - Method in interface org.biojava.bio.structure.Atom
  get PDB atom number.
getPDBserial() - Method in class org.biojava.bio.structure.AtomImpl
  get PDB atom number.
getPercentIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
  get percentage identity.
getPercentIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getPermutationSize() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getPhase() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getPhase() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getPHDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property PHDependence.
getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
  phi angle.
getPhiAngle(Symbol) - Static method in class org.biojava.bio.structure.AlphaCTools
  extracts the Phi angle from a `Symbol`.
getPhiPsiSymbol(double, double) - Static method in class org.biojava.bio.structure.AlphaCTools
  Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
getPhredAlphabet() - Static method in class org.biojava.bio.program.phred.PhredTools
  Retrieves the PHRED alphabet from the AlphabetManager.
getPhredSymbol(Symbol, Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
  Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc
  Computes isoelectric point of specified peptide.
getPivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Return pivot permutation vector
getPlasmidTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Plasmid term
getPopulation() - Method in interface org.biojavax.ga.GeneticAlgorithm
  The registered `Population`
getPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getPos() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
  Get the offset within the sequence - the symbol index.
getPos() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
getPos1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getPos2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getPosition() - Method in interface org.biojava.bio.molbio.RestrictionSite
  `getPosition` returns the common, forward strand cut site.
getPosition() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
getPosition1() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getPosition2() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Retrieve the shape used to represent positive points.
getPredicate() - Method in interface org.biojava.ontology.Triple
  Return a Term which defines the type of relationship between the subject and object terms.
getPredicate() - Method in class org.biojava.ontology.Triple.Impl
getPredicate() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return a Term which defines the type of relationship between the subject and object terms.
getPrevious() - Method in class org.biojava.utils.ChangeEvent
  Return the old value of a property being changed.
getPrimaryKey() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `getPrimaryKey` returns the primary identifier namespace.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Index2Model
  Retrieve the tag currently used as primary key.
getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Indexer
  Retrieve the tag currently used as primary key.
getPrintStream() - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  Deprecated. `getPrintStream` returns the `PrintStream` to which an instance will write the formatted data.
getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. `getPrintStream` returns the `PrintStream` to which an instance of SwissprotFileFormer will write the formatted data.
getPrintStream() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Gets the print stream currently being written to.
getPrintStream() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Gets the print stream currently being written to.
getProbabilityAlphabet() - Static method in class org.biojava.bio.program.scf.SCF
getProjectedFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getProjectionContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getProjectionContext() - Method in interface org.biojava.bio.seq.projection.Projection
getPropClass() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getProperties() - Method in class org.biojava.bio.AbstractAnnotation
  Implement this to return the Map delegate.
getProperties() - Method in class org.biojava.bio.AnnotationChanger
  `getProperties` returns the mapped contents of the underlying `Annotation` as a `Map`.
getProperties() - Method in class org.biojava.bio.AnnotationRenamer
  `getProperties` returns the mapped contents of the underlying `Annotation` as a `Map`.
getProperties() - Method in interface org.biojava.bio.AnnotationType
  Retrieve the set of properties for which constraints have been explicity specified.
getProperties() - Method in class org.biojava.bio.AnnotationType.Impl
getProperties() - Method in class org.biojava.bio.BeanAsAnnotation
getProperties() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation
  Deprecated.
getProperties() - Method in class org.biojava.bio.SimpleAnnotation
  Get the property value pairs in this annotation
getProperties() - Method in class org.biojava.bio.SmallAnnotation
getProperties() - Method in interface org.biojava.bio.structure.Group
  return properties.
getProperties() - Method in class org.biojava.bio.structure.HetatomImpl
  return properties.
getProperties(Object) - Method in class org.biojavax.EmptyRichAnnotation
  Find all the `Note`s with any rank that match the key. There are no properties in the Empty RichAnnotation object.
getProperties(Object) - Method in interface org.biojavax.RichAnnotation
  Find all the `Note`s with any rank that match the key.
getProperties(Object) - Method in class org.biojavax.SimpleRichAnnotation
  Find all the `Note`s with any rank that match the key. Strictly it will return all `Note`s which match the `key` (or a `Term` made with a `String` key)..
getProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
getProperty(Object) - Method in interface org.biojava.bio.Annotation
  Retrieve the value of a property by key.
getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
getProperty(Annotation, Object) - Method in interface org.biojava.bio.AnnotationType
  Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.
getProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
getProperty(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getProperty(Annotation, String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
  ThomasD made this a bit safer...
getProperty(Annotation, String) - Static method in class org.biojava.bio.seq.io.agave.UtilHelper
  inhibit the getProperty(key) of Annotation from throw exception when key does not exist.
getProperty(String) - Method in interface org.biojava.bio.structure.Group
  get a single property .
getProperty(String) - Method in class org.biojava.bio.structure.HetatomImpl
  get a single property .
getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation

  Retrieve the value of a property by key. There are no properties in the Empty RichAnnotation object.

getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation

  Retrieve the value of a property by key. Strictly it will return the first `Note` which matches the `key` (or a `Term` made with a `String` key)..

getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties
  Searches for the property with the specified key in this property list.
getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties
  Searches for the property with the specified key in this property list.
getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties
  Searches for the property with the specified key in this property list.
getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties
  Searches for the property with the specified key in this property list.
getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties
  Searches for the property with the specified key in this property list.
getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties
  just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab) as the possible delimiters.
getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass
  Get the Class used as the constraint.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
  Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
  Get the PropertyConstraint used to validate each property value.
getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getPropType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.Protease
  Retrieves a reference to the named Protease.
getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
  Gets a Protease instance by name.
getProteaseList() - Static method in class org.biojava.bio.proteomics.Protease
  Get the list of Protease names defined in the ProteaseManager (Internally calls ProteaseManager.
getProteinParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Creates a protein symbol tokenizer.
getProteinTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the protein type term
getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
  psi angle.
getPsiAngle(Symbol) - Static method in class org.biojava.bio.structure.AlphaCTools
  extracts the Psi angle from a `Symbol`.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the overall P-value of this hit.
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the P-value of this sub-hit.
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQ() - Method in class org.biojava.bio.structure.jama.QRDecomposition
  Generate and return the (economy-sized) orthogonal factor
getQuality() - Method in class org.biojava.bio.program.phred.PhredSequence
  Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
getQuality() - Method in interface org.biojava.bio.program.phred.Qualitative
  Retreives the list of quality symbols from the underlying object.
getQualityAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
getQualityAt(int) - Method in interface org.biojava.bio.program.phred.Qualitative
  Retreives the quality symbol for the specified index.
getQuery() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Returns the query.
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the end position of the last sub-hit in the query sequence.
getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the end position of the sub-hit in the query sequence.
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getQuerySeqHolder() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
  `getQuerySeqHolder` returns the database of query sequences used to retrieve sequences for creation of the various result objects.
getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
  Returns the query sequence which was used to perform the search.
getQuerySequence() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the start position of the first sub-hit in the query sequence.
getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the start position of the sub-hit in the query sequence.
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the strand of the hit with respect to the query sequence.
getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the strand of the sub-hit with respect to the query sequence.
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getR() - Method in class org.biojava.bio.structure.jama.QRDecomposition
  Return the upper triangular factor
getRadius() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  Get the current radius at which data should be rendered.
getRadius() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
getRadius() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getRange() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getRange` returns a `RangeLocation` representing the region of the sequence currently being rendered.
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanel
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getRange() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  The range of the SymbolList to render.
getRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getRange() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getRange() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getRange` returns a `RangeLocation` representing the region of the sequence currently being rendered.
getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
getRanges() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
getRank() - Method in interface org.biojavax.bio.BioEntryRelationship
  Returns the rank of this relationship.
getRank() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
getRank() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the rank associated with this location. ALWAYS RETURNS ZERO
getRank() - Method in interface org.biojavax.bio.seq.RichFeature
  Returns the rank of this feature.
getRank() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
  Gets the rank of this relationship.
getRank() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Returns the rank of this feature.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Gets the rank of this relationship.
getRank() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the rank associated with this location.
getRank() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Returns the rank of this relationship.
getRank() - Method in interface org.biojavax.Comment
  Returns the rank of this comment.
getRank() - Method in interface org.biojavax.Note
  Gets the rank that defines this note.
getRank() - Method in interface org.biojavax.RankedCrossRef
  Return the rank associated with the cross reference.
getRank() - Method in interface org.biojavax.RankedDocRef
  The rank of this reference.
getRank() - Method in class org.biojavax.SimpleComment
  Returns the rank of this comment.
getRank() - Method in class org.biojavax.SimpleNote
  Gets the rank that defines this note.
getRank() - Method in class org.biojavax.SimpleRankedCrossRef
  Return the rank associated with the cross reference.
getRank() - Method in class org.biojavax.SimpleRankedDocRef
  The rank of this reference.
getRankedCrossRefs() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
getRankedCrossRefs() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
getRankedCrossRefs() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
getRankedCrossRefs() - Method in interface org.biojavax.RankedCrossRefable
  Returns the set of all ranked cross references associated with an object.
getRankedDocRefs() - Method in interface org.biojavax.bio.BioEntry
  Returns a set of all bioentrydocrefs associated with this bioentry.
getRankedDocRefs() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns a set of all bioentrydocrefs associated with this bioentry. Warning this method gives access to the original Collection not a copy.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer
  Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer2
  Retrieve the reader that can be safely used to index this file.
getReader() - Method in class org.biojava.utils.process.ReaderWriterPipe
  Gets the reader.
getReadingFrame() - Method in interface org.biojava.bio.seq.FramedFeature
  return the reading frame of the feature.
getReadingFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
getRealEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
  Return the real parts of the eigenvalues
getRealScientificName(Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. This returns the true scientific name of a given taxon, if there is one.
getRecognitionSequence(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getRecognitionSequence` returns a string that describes the recognition site of this enzyme.
getRecognitionSite() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getRecognitionSite` returns the forward strand of the recognition site.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `getRecordKey` returns the field from the record on which the records were sorted in the index.
getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
  `getRecordKey` returns the field from the record on which the records were sorted in the index.
getRecordList() - Method in class org.biojava.bio.program.indexdb.BioStore
  `getRecordList` returns all the `Record`s in the index.
getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `getRecurse` returns the recursion flag of the filter.
getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Return whether features will be filtered recursively or not.
getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
getRedoxPotential() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property redoxPotential.
getRef() - Method in interface org.biojava.bio.program.homologene.OrthoPair
  get reference to evidence for orthology.
getRef() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getReferenceServers() - Method in class org.biojava.bio.program.das.DAS
getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature
  Retrieve the list of Regions that locate this feature both localy and remotely.
getRegistryConfiguration() - Method in class org.biojava.directory.Registry
  `getRegistryConfiguration` returns the configuration of the registry.
getRegistryPath() - Static method in class org.biojava.directory.SystemRegistry
  Get the list of places that will be searched for registry files.
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getRelAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the release annotated term
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getRelationships() - Method in interface org.biojavax.bio.BioEntry
  Returns a set of all relationships associated with this bioentry.
getRelationships() - Method in class org.biojavax.bio.SimpleBioEntry
  Returns a set of all relationships associated with this bioentry. Warning this method gives access to the original Collection not a copy.
getRelCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the release created term
getRelUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the release updated term
getRemark() - Method in interface org.biojavax.DocRef
  If remarks have been made about this document reference, this method will return them.
getRemark() - Method in class org.biojavax.SimpleDocRef
  If remarks have been made about this document reference, this method will return them.
getRemoteBioEntry(CrossRef) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
  Given the `CrossRef` return the corresponding `BioEntry`
getRemoteBioEntry(CrossRef) - Method in interface org.biojavax.CrossReferenceResolver
  Given the `CrossRef` return the corresponding `BioEntry`
getRemoteBioEntry(CrossRef) - Method in class org.biojavax.DummyCrossReferenceResolver
  Given the `CrossRef` return the corresponding `BioEntry` All responses are null.
getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature
  Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly.
getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
  Given a cross reference, return the corresponding symbol list.
getRemoteSymbolList(CrossRef, Alphabet) - Method in interface org.biojavax.CrossReferenceResolver
  Given a cross reference, return the corresponding symbol list.
getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.DummyCrossReferenceResolver
  Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList.
getRemoteTerm() - Method in interface org.biojava.ontology.RemoteTerm
  Return the imported term
getRemoteTerm() - Method in class org.biojava.ontology.RemoteTerm.Impl
getRemoteTerms() - Method in interface org.biojava.ontology.OntologyOps
  Get the set of all remote terms.
getRenderedWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the width of the graphic as it will be rendered.
getRenderedWidth(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the width of the graphic as it would be rendered with the specified horizontal scale.
getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
getRenderer() - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `getRenderer` return the current renderer.
getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getRenderer` returns the current `PairwiseSequenceRenderer`.
getRenderer() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getRenderer() - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
getRenderer() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getRenderer` returns the current `SequenceRenderer`.
getRenderingHints() - Method in class org.biojava.bio.gui.DistributionLogo
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getRenderingHints` returns the `RenderingHints` currently being used by the `Graphics2D` instances of delegate renderers.
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanel
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getRenderingHints` returns the `RenderingHints` currently being used by the `Graphics2D` instances of delegate renderers.
getReplace() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Returns the current expenses of a single replace operation.
getRepository(String) - Static method in class org.biojava.bio.seq.FeatureTypes
  Fetch a repository by name.
getRepositoryNames() - Static method in class org.biojava.bio.seq.FeatureTypes
  Find the names of all known repositories.
getResidue() - Method in interface org.biojava.bio.symbol.WobbleDistribution
  returns the residue encoded by this WobbleDistribution
getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature
getResolver() - Method in class org.biojava.bio.symbol.FuzzyLocation
  Retrieve the Location that this decorates.
getResolver() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getResultType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getReturnCode() - Method in exception org.biojava.utils.ProcessTimeoutException
  Get the return code from the dying child process.
getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL
getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getReverseRegex` returns a regular expression which matches the reverse strand of the recognition site.
getReverter() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
getReverter() - Method in class org.biojava.bio.seq.projection.ReparentContext
getReverter() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Return the revision id of this identifier.
getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
getRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getRichSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Given the appropriate Genbank ID, return the matching RichSequence object.
getRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
  Retrieve a single RichSequence by its id.
getRichSequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getRichSequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
  Returns a RichSequenceIterator over all sequences in the database.
getRichSequences(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
getRichSequences(Set) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.HashRichSequenceDB
getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Retrieve rich sequences from a Genbank
getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Retrieve rich sequences from a Genbank
getRichSequences(Set) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
  Retrieve multiple RichSequence by its id.
getRichSequences(Set, RichSequenceDB) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
  Retrieve multiple RichSequence into a specific sequence database.
getRightValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Gets the right value.
getRightValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Gets the right value.
getRms() - Method in class org.biojava.bio.structure.align.helper.JointFragments
getRms() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
getRms() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getRMS(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.SVDSuperimposer
  calculate the RMS (root mean square) of two sets of atoms
getRNA() - Static method in class org.biojava.bio.seq.RNATools
  Return the RNA alphabet.
getRNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Creates a RNA symbol tokenizer.
getRole() - Method in class org.biojava.bio.program.das.DASLink
getRoot() - Method in class org.biojava.bio.symbol.SuffixTree
  Return the node object which is the root of this suffix tree.
getRoot() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
getRoot() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
getRot() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getRotation() - Method in class org.biojava.bio.structure.SVDSuperimposer
getRotationMatrix() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
getRow() - Method in class org.biojava.bio.structure.align.helper.IndexPair
getRowDimension() - Method in class org.biojava.bio.structure.jama.Matrix
  Get row dimension.
getRowPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
  Make a one-dimensional row packed copy of the internal array.
getRows() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getRows() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getS() - Method in class org.biojava.bio.proteomics.StructureTools
getS() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Return the diagonal matrix of singular values
getSBFactory() - Method in class org.biojava.bio.seq.db.BioIndex
getSBFactory() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getSBFactory() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the SequenceBuilderFactory used to build Sequence instances.
getSBFactory() - Method in class org.biojava.bio.seq.db.TabIndexStore
getScale() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getScale() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getScale` returns the scale in pixels per `Symbol`.
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Retrieve the current scale.
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getScale() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the current scale.
getScale() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Gets the scale as pixels per Symbol
getScale() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getScale() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getScale() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getScale` returns the scale in pixels per `Symbol`.
getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
  Retrieve the scaling factor at a given depth
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
getSchema() - Method in interface org.biojava.bio.annodb.AnnotationDB
  Get an AnnotationType that accepts all Annotation instances in this DB.
getSchema() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
getSchema() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
getSchema() - Method in class org.biojava.bio.program.das.DASSequence
getSchema() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
getSchema() - Method in interface org.biojava.bio.seq.FeatureHolder
  Return a schema-filter for this `FeatureHolder`.
getSchema() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
  Get the schema for this type.
getSchema() - Method in class org.biojava.bio.seq.impl.DummySequence
getSchema() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getSchema() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getSchema() - Method in class org.biojava.bio.seq.impl.SubSequence
getSchema() - Method in class org.biojava.bio.seq.impl.ViewSequence
getSchema() - Method in class org.biojava.bio.seq.LazyFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder
getSchema() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
getSchema(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly
getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
getSchema(Name) - Method in class org.biojava.naming.ObdaContext
getSchema(String) - Method in class org.biojava.naming.ObdaContext
getSchema() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Return a schema-filter for this `FeatureHolder`.
getSchema() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Return a schema-filter for this `FeatureHolder`.
getSchemaClassDefinition(Name) - Method in class org.biojava.naming.ObdaContext
getSchemaClassDefinition(String) - Method in class org.biojava.naming.ObdaContext
getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
getScientificName() - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. The scientific name of this taxon.
getScore() - Method in interface org.biojava.bio.dp.DPMatrix
getScore() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
getScore() - Method in class org.biojava.bio.dp.SimpleStatePath
getScore() - Method in interface org.biojava.bio.dp.StatePath
  Return the overall score for this state-path and it's emissions.
getScore() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The score of the feature.
getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getScore() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getScore() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the overall score of this hit in the units defined by the search algorithm.
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the score of this sub-hit in the units defined by the search algorithm.
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getScore() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getScore() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  `getScore` returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
  `getScore` returns the alignment score.
getScore() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
getScore() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
getScore() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  the alignment score
getScore() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
getScoreAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the alignment Score Annotation Type.
getScores() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  get all "Score" Annotations.
getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
  Return a set of all databases that can be searched with this sequence similarity searcher.
getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
  `getSearchContentHandler` gets the handler which will recieve the method calls generated by the adapter.
getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
  `getSearchContentHandler` gets the handler which will receive the method calls generated by the adapter.
getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
  Returns the search parameters used in the search that produced this search result.
getSearchParameters() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getSearchProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getSearchProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getSecondaryDirection() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `getSecondaryDirection` returns the direction in which the secondary sequence is rendered.
getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondaryDirection` returns the direction in which this context expects the secondary sequence to be rendered - HORIZONTAL or VERTICAL.
getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getSecondaryFeatures() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `getSecondaryFeatures` returns the features on the secondary sequence.
getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondaryFeatures` returns all of the `Feature`s belonging to the currently rendered secondary `Sequence`.
getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `getSecondaryRange` returns the range of the secondary sequence currently rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondaryRange` returns a `RangeLocation` representing the region of the secondary sequence currently being rendered.
getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondarySequence` returns the entire secondary `Sequence` currently being rendered.
getSecondarySymbols() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `getSecondarySymbols` returns the symbols of the secondary sequence.
getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondarySymbols` returns all of the `Symbol`s belonging to the currently rendered secondary `Sequence`.
getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSecondarySymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
getSecondIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property secondIntActID.
getSecondOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
  gets the first orthologue in the orthology relationship.
getSecondOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getSecStruc() - Method in interface org.biojava.bio.structure.AminoAcid
  get secondary structure data .
getSecStruc() - Method in class org.biojava.bio.structure.AminoAcidImpl
  get secondary structure data .
getSeedFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getSeedRmsdCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getSegmentAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the alignment Segment Annotation Type.
getSelectionFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
getSelectionFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
getSeqDB() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
getSeqDBs() - Method in interface org.biojava.bio.seq.homol.HomologyDB
  Retrieve the SeqDBs that have been searched against each other.
getSeqID() - Method in class org.biojava.bio.seq.RemoteFeature.Region
  Return the remote Sequence ID if this Region is on another Sequence (isRemote will return true), null otherwise.
getSeqIDs() - Method in class org.biojava.bio.program.Meme
getSeqIOEvents(Sequence, SeqIOListener) - Method in class org.biojava.bio.seq.io.SeqIOEventEmitter
  Deprecated. `getSeqIOEvents` scans a `Sequence` object and sends events describing its data to the `SeqIOListener`.
getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The sequence name field.
getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
  Retrieve the current sequence name.
getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getSequence() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
getSequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSequence` returns the entire `Sequence` currently being rendered.
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanel
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getSequence() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getSequence` returns the entire `Sequence` currently being rendered.
getSequence() - Method in class org.biojava.bio.program.abi.ABITrace
  Returns the original programatically determined (unedited) sequence as a `SymbolList`.
getSequence(String) - Method in class org.biojava.bio.program.das.DASSequenceDB
getSequence() - Method in class org.biojava.bio.proteomics.Digest
getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
getSequence(int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
  Retrieve a single sequence by its id.
getSequence(String) - Method in class org.biojava.bio.seq.db.SubSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
  Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
getSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get a Sequence object for an ID.
getSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
getSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
getSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
getSequence() - Method in interface org.biojava.bio.seq.Feature
  Return the `Sequence` object to which this feature is (ultimately) attached.
getSequence() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSequence() - Method in class org.biojava.bio.seq.impl.SubSequence
  Return the parent sequence of which this is a partial view
getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the sequence for a feature.
getSequence(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
getSequence() - Method in interface org.biojava.bio.structure.Chain
  return the amino acid sequqence of this chain ( all aminos even if they do not have 3D data ...).
getSequence() - Method in class org.biojava.bio.structure.ChainImpl
  get amino acid sequence.
getSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
getSequence() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Return the `Sequence` object to which this feature is (ultimately) attached.
getSequenceDB(Map) - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
  Returns the sequence database against which the search was performed.
getSequenceDB() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
  Deprecated.
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
  Return the SequenceDB for the given identifier.
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier.
getSequenceDB(Map) - Method in interface org.biojava.directory.SequenceDBProvider
  Get a sequence database.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
  Return all sequence dbs available in this sequence db installation.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  Return a newly created set of the SequenceDB objects that were already created through method addSequenceDB().
getSequenceFormat() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `getSequenceFormat` returns the current sequence format name.
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
getSequenceFormat() - Method in class org.biojava.bio.seq.db.WebSequenceDB
getSequenceFormat(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. `getSequenceFormat` accepts a value which represents a sequence format and returns the relevant `SequenceFormat` object.
getSequenceID() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getSequenceID() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getSequenceId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getSequenceId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getSequenceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Return the sequence length.
getSequenceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded.
getSequenceLength() - Method in class org.biojava.bio.program.abi.ABITrace
  Returns the length of the sequence (number of bases) in this trace.
getSequenceLength() - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
  Gets the sequenceLength attribute of the GAMESeqHandler object
getSequenceLength() - Method in class org.biojavax.bio.seq.SimpleRichSequence
getSequenceLength() - Method in class org.biojavax.bio.seq.ThinRichSequence
getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
getSequenceName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
getSequenceOffset() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getSequenceRef() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Getter for property sequenceRef.
getSequences(Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
  Retrieve sequences from a Genbank
getSequences(Set, SequenceDB) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
  Retrieve sequences from a Genbank
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
  get all the top level sequences bio_sequence --> SimpleSequence contig --> SimpleAssembly --> SimpleSequence( if only one sequence ) chromosome -> SimpleAssembly -> SimpleSequence( if only one sequence)
getSequenceType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Getter for property sequenceType.
getSeqVersion() - Method in interface org.biojavax.bio.seq.RichSequence
  The version of the associated symbol list.
getSeqVersion() - Method in class org.biojavax.bio.seq.ThinRichSequence
  The version of the associated symbol list.
getServerurl() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  get url of alignment service.
getServerurl() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
  get url of structure service.
getShape(List, List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
getShape(List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
getShape(int[], int[]) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
getShatter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Determine if features with non-contiguous locations will be broken into multiple GFF records.
getShift() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  returns the shift vector that has to be applied on structure to to shift on structure one
getShort(long) - Method in class org.biojava.utils.io.LargeBuffer
getShort() - Method in class org.biojava.utils.io.LargeBuffer
getSibling() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  `getSibling` returns the sibling `Feature`, query for subject and vice versa.
getSibling() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
  `getSibling` returns the sibling feature of the pair.
getSignificantBits() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Return the number of significant bits.
getSignificantBits() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns the number of bits of the traces which are significant.
getSimilarity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
  gets the second orthologue in the orthology relationship.
getSimilarity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
getSingularValues() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Return the one-dimensional array of singular values
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Gets the current size of the border in pixels.
getSleepTime() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated.
getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The source, or creator of this feature.
getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
  Retrieve the current source.
getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getSource() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getSource() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getSource() - Method in interface org.biojava.bio.seq.Feature
  The source of the feature.
getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
getSource() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSource() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getSource() - Method in class org.biojava.utils.ChangeForwarder
  Retrieve the 'source' object for `ChangeEvent`s fired by this forwarder.
getSource() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  The source of the feature.
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
  The alphabet of Symbols that can be translated.
getSourceHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getSourceSymbolList() - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Return the underlying (ungapped) SymbolList.
getSourceSymbolList() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getSourceTerm() - Method in interface org.biojava.bio.seq.Feature
  An ontology term defining the source of this feature.
getSourceTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSourceTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
getSourceTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  An ontology term defining the source of this feature.
getSourceTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the current spacer value
getSpeciesForShortName(String) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Converts short species names (like Hs) to long species names (like Homo Sapiens).
getSpeciesTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Species term
getSplitOffset() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Get the current offset at which lines are split.
getSplitter(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
  Get the Splitter currently registered to handle a tag.
getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The start of this feature within the source sequence.
getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getStart() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getStart() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getStart() - Method in interface org.biojava.bio.seq.db.Index
  Skipping this number of bytes through the file should put the file pointer to the first byte of the sequence.
getStart() - Method in class org.biojava.bio.seq.db.SimpleIndex
getStart() - Method in class org.biojava.bio.seq.impl.SubSequence
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
getStart() - Method in class org.biojava.utils.automata.FiniteAutomaton
getStart() - Method in interface org.biojava.utils.automata.NfaBuilder
getStart() - Method in class org.biojava.utils.automata.NfaSubModel
getStart() - Method in interface org.biojava.utils.automata.StateMachineInstance
getStart() - Method in interface org.biojavax.bio.seq.Position
  Returns the beginning of the range of bases this base could lie in.
getStart() - Method in class org.biojavax.bio.seq.SimplePosition
  Returns the beginning of the range of bases this base could lie in.
getStart() - Method in interface org.biojavax.RankedDocRef
  The start position in the sequence that this reference is referred to from.
getStart() - Method in class org.biojavax.SimpleRankedDocRef
  The start position in the sequence that this reference is referred to from.
getState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
getStates() - Method in class org.biojava.bio.dp.DP
getStAXContentHandler() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  Return a StAXContentHandler which can deal with any FilterXML construct known to this class.
getStoreLocation() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `getStoreLocation` returns the directory of the bew index.
getStoreName() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `getStoreName` returns the name to be given to the new index.
getStrainTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Strain term
getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord
  The strand of the feature.
getStrand() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
getStrand() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getStrand() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getStrand() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
  Retrieve the strand this matches.
getStrand() - Method in interface org.biojava.bio.seq.FramedFeature
getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature
  Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
getStrand() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the strand associated with this location. ALWAYS RETURNS THE UNKNOWN STRAND
getStrand() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Retrieves the strand associated with this location.
getStrand() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the strand associated with this location.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the strand associated with this location.
getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
getStrandedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Strand term
getStringSequence() - Method in class org.biojavax.bio.seq.SimpleRichSequence
getStructure(String) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
  connect to a DAS structure service and retreive 3D data.
getStructure() - Method in class org.biojava.bio.proteomics.StructureTools
getStructure(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
  opens filename, parses it and returns aStructure object .
getStructure(File) - Method in class org.biojava.bio.structure.io.PDBFileReader
  opens filename, parses it and returns a Structure object
getStructure(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
  open filename and returns a Structure object.
getStructureById(String) - Method in class org.biojava.bio.structure.io.DASStructureClient
  if pdb code is set (setId): connect to a DAS-structure service and retreive data.
getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
  load a structure from local file system and return a PDBStructure object
getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBMSDReader
  Get a structure by providing a PDB code.
getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBSRSReader
  load a structure from from SRS installation using wgetz returns null if no structure found
getStructureById(String) - Method in interface org.biojava.bio.structure.io.StructureIO
  Get a structure by providing a PDB code.
getStyle() - Method in class org.biojava.bio.gui.DistributionLogo
  Retrieve the current style.
getStyle() - Method in interface org.biojava.bio.gui.LogoContext
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Return the styles for the two aligned characters.
getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Returns the styles for the two aligned characters in the form of predefined font classes.
getSubAlphabet(double, double) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
getSubAlphabet(int, int) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
  Construct a finite contiguous subset of the `IntegerAlphabet`.
getSubContext(PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `getSubContext` creates a new context which has `FeatureHolder`s filtered using the current filter.
getSubHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
getSubHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return all sub-hits for this sequence similarity search hit.
getSubHits() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubject() - Method in interface org.biojava.ontology.Triple
  Return the subject term of this triple
getSubject() - Method in class org.biojava.ontology.Triple.Impl
getSubject() - Method in interface org.biojavax.bio.BioEntryRelationship
  Returns the subject of this relationship (ie.
getSubject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
  Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Gets the feature that this relationship refers to.
getSubject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Returns the subject of this relationship (ie.
getSubject() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return the subject term of this triple
getSubjectDBInstallation() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
  `getSubjectDBInstallation` returns the installation in which all the databases searched may be found.
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the end position of the last sub-hit in the subject sequence.
getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the start position of the sub-hit in the subject sequence.
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubjectID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  The sequence identifier of this hit within the sequence database against which the search was performed.
getSubjectID() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getSubjectID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the start position of the first sub-hit in the subject sequence.
getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the start position of the sub-hit in the subject sequence.
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
  Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  Return the strand of the sub-hit with respect to the subject sequence.
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getSuppliers(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `getSuppliers` returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.
getSupportedCriteria() - Method in interface org.biojava.bibliography.BibRefSupport
  It returns all supported searching and sorting criteria for the whole bibliographic repository.
getSupportedCriteria(String) - Method in interface org.biojava.bibliography.BibRefSupport
  It returns all supported searching and sorting criteria in the given repository subset.
getSupportedValues(String, String) - Method in interface org.biojava.bibliography.BibRefSupport
  It returns a controlled vocabulary containing all possible values of the attribute given in `attrName` in the context given in `resourceType`.
getSwissprotBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Get a default SequenceBuilderFactory for handling Swissprot files.
getSwissprotId() - Method in interface org.biojava.bio.structure.Chain
  get the Swissprot id of this chains .
getSwissprotId() - Method in class org.biojava.bio.structure.ChainImpl
  get the Swissprot id of this chains .
getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getSymbol(List) - Method in interface org.biojava.bio.symbol.Alphabet
  Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve the Symbol for a double.
getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
  Retrieve the symbol for a range of doubles.
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getSymbol() - Method in exception org.biojava.bio.symbol.IllegalSymbolException
  Retrieve the symbol that caused this exception, or null.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet
  Retrieve the Symbol for an int.
getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getSymbol(List) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Gets the compound symbol composed of the `Symbols` in the List.
getSymbolArray() - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Return the Java Symbol[] array that backs this object.
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SimpleAlphabet
getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SingletonAlphabet
getSymbolList() - Method in interface org.biojava.bio.alignment.AlignmentElement
getSymbolList() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
getSymbolParser() - Method in class org.biojava.bio.seq.db.BioIndex
getSymbolParser() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
getSymbolParser() - Method in interface org.biojava.bio.seq.db.IndexStore
  Retrieve the symbol parser used to turn the sequence characters into Symobl objects.
getSymbolParser() - Method in class org.biojava.bio.seq.db.TabIndexStore
getSymbolPropertyTable(String) - Static method in class org.biojava.bio.seq.ProteinTools
getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState
getSymbols() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
  The SymbolList that is currently rendered by this context.
getSymbols() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getSymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Retrieve the currently rendered SymbolList
getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the currently rendered SymbolList
getSymbols() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  The SymbolList that is currently rendered by this SequenceRenderContext.
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getSymbols() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getSymbols() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
getSymbols() - Method in class org.biojava.bio.program.das.DASSequence
getSymbols() - Method in interface org.biojava.bio.seq.Feature
  Return a list of symbols that are contained in this feature.
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
getSymbols() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature
  Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.symbol.BasisSymbol
  The list of symbols that this symbol is composed from.
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
getSymbols() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
getSymbols() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
getSymbols() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Return a list of symbols that are contained in this feature.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getSymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getSymbolTranslation` returns the current translation in `Symbol`s which will be applied when rendering.
getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList
  Return the long array within which the symbols are bit-packed.
getSynonyms() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
getSynonyms() - Method in class org.biojava.ontology.OntologyTerm.Impl
getSynonyms() - Method in class org.biojava.ontology.RemoteTerm.Impl
getSynonyms() - Method in interface org.biojava.ontology.Term
  Return the synonyms for this term.
getSynonyms() - Method in class org.biojava.ontology.Term.Impl
getSynonyms() - Method in class org.biojava.ontology.Triple.Impl
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Return the synonyms for this term.
getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Return the synonyms for this term. ALWAYS RETURNS AN EMPTY LIST
getT() - Method in class org.biojava.bio.proteomics.StructureTools
getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution
  Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one.
getTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
getTagGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Get the group number that matches the tag.
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
getTags() - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Get the complete set of tags that are currently recognized.
getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
  Gets the protein alphabet including the translation termination symbols
getTarget() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
  Get the Object that was the target of the mouse gesture or null if the mouse is not gesturing over any recognizable rendered object.
getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
  The alphabet of Symbols that will be produced.
getTargetOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
getTaxa() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  get the taxa represented in this group
getTaxa() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
getTaxon(int) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
  get the Taxon corresponding to this Taxon ID
getTaxon() - Method in interface org.biojava.bio.program.homologene.Orthologue
  return the Taxon associated with this orthologue
getTaxon() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.
getTaxon(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Attempts to get a Taxon object corresponding to the specified name.
getTaxon() - Method in interface org.biojavax.bio.BioEntry
  Gets the taxon associated with this bioentry.
getTaxon() - Method in class org.biojavax.bio.SimpleBioEntry
  Gets the taxon associated with this bioentry.
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Orthologue
  a convenience method to return the TaxonID for thsi orhtologue.
getTaxonID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTaxonID() - Method in interface org.biojava.bio.program.homologene.Taxon
  returns the taxon ID
getTaxonID() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getTemperatureDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property temperatureDependence.
getTempFactor() - Method in interface org.biojava.bio.structure.Atom
  get set temp factor.
getTempFactor() - Method in class org.biojava.bio.structure.AtomImpl
getTerm(String) - Method in class org.biojava.ontology.IntegerOntology
getTerm(String) - Method in interface org.biojava.ontology.Ontology
  Fetch the term with the specified name.
getTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
getTerm() - Method in interface org.biojavax.bio.BioEntryRelationship
  Returns the term describing the relationship.
getTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
getTerm() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Retrieves the term associated with this location. ALWAYS RETURNS NULL
getTerm() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
  Gets the term that describes this relationship.
getTerm() - Method in interface org.biojavax.bio.seq.RichLocation
  Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Gets the term that describes this relationship.
getTerm() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Retrieves the term associated with this location.
getTerm() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Returns the term describing the relationship.
getTerm() - Method in interface org.biojavax.Note
  Gets the term that defines this note.
getTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Fetch the term with the specified name.
getTerm() - Method in class org.biojavax.SimpleNote
  Gets the term that defines this note.
getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc
  `getTermMass` returns the terminal mass being used by the instance methods.
getTerms() - Method in class org.biojava.ontology.IntegerOntology
getTerms() - Method in interface org.biojava.ontology.Ontology
  Return all the terms in this ontology
getTerms() - Method in class org.biojava.ontology.Ontology.Impl
getTerms() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Return all the terms in this ontology This will always return a set of ComparableTerm objects.
getTermSet() - Method in interface org.biojavax.ontology.ComparableOntology
  Returns the set of terms in this ontology.
getTermSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Returns the set of terms in this ontology. Warning this method gives access to the original Collection not a copy.
getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
getText() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property text.
getTextColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Get the color of the label text
getThreadFetches() - Static method in class org.biojava.bio.program.das.DAS
getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
getTickDirection() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
getTimeStamp() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
  Returns a time stamp .
getTimeStamp() - Method in class org.biojava.bio.structure.io.PDBFileParser
  Returns a time stamp.
getTissueTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Tissue term
getTitle() - Method in interface org.biojava.bio.program.homologene.Orthologue
  return the title used by Genbank for this protein
getTitle() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
  The cluster title.
getTitle() - Method in interface org.biojavax.DocRef
  Returns the title of the document reference.
getTitle() - Method in class org.biojavax.SimpleDocRef
  Returns the title of the document reference.
getTo() - Method in exception org.biojava.bio.dp.IllegalTransitionException
getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState
getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
  Returns the token for strandedness.
getTokenization(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet
getTokenization(String) - Method in interface org.biojava.bio.symbol.Alphabet
  Get a SymbolTokenization by name.
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet
  Creates a new parser (Mark Schreiber 3 May 2001).
getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet
getTokenization(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getTokenType() - Method in class org.biojava.bio.seq.io.CharacterTokenization
getTokenType() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  Determine the style of tokenization represented by this object.
getTokenType() - Method in class org.biojava.bio.seq.io.WordTokenization
getTokenType() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo
getTotalWeight() - Method in class org.biojavax.ga.util.WeightedSet
  The total weight that has been added to this Set.
getTrace(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getTrace(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base `nucleotide`.
getTrace() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
getTrace(AtomicSymbol) - Method in class org.biojava.bio.program.abi.ABITrace
  Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
getTraceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
getTraceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns the length of the trace of the Chromatogram.
getTraceLength() - Method in class org.biojava.bio.program.abi.ABITrace
  Returns the length of the trace (number of x-coordinate points in the graph).
getTraceOffset(Chromatogram, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Get a specific value from the trace offset sequence in the given chromatogram and extract its `int` value.
getTraceOffsetArray(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Converts the peak offsets list of the given chromatogram into a new `int` array.
getTraceOffsets(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
  Get the peak offsets for the called bases of a chromatogram.
getTrack() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
getTrackLayout() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getTrailer() - Method in class org.biojava.utils.ListTools.SeriesList
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getTrailingBorder` returns the trailing border of the primary sequence.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
getTrailingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Gets the TrailingBorder attribute of the SequenceRenderContext object.
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getTrailingBorder` returns the trailing border.
getTrailingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
getTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Return the Distribution trainer object from the current context.
getTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
getTrans() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns a new AffineTransform describing the transformation from chromatogram coordinates to output coordinates.
getTransformAndConcat(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Concatenates the chromatogram-to-output transform to the provided given AffineTransform.
getTransformer() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
getTransformer() - Method in class org.biojava.bio.seq.projection.ReparentContext
getTransformer() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getTransitions() - Method in class org.biojava.utils.automata.FiniteAutomaton
  retrieve Set of all transitions in instance.
getTransitions() - Method in interface org.biojava.utils.automata.NfaBuilder
getTransitions() - Method in class org.biojava.utils.automata.NfaSubModel
getTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  retrieve the TransitionTable for this State.
getTranslation() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
getTranslation() - Method in class org.biojava.bio.structure.SVDSuperimposer
getTransposonTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
  Getter for the Transposon term
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  See if tag trimming is enabled.
getTrimTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  See if trimming of tags is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  See if value trimming is enabled.
getTrimValue() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  See if trimming of values is enabled.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
getTriples(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
  Return all triples from this ontology which match the supplied pattern.
getTriples(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
getTriples(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Return all triples from this ontology which match the supplied pattern. If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms.
getTripleSet() - Method in interface org.biojavax.ontology.ComparableOntology
  Returns the set of triples in this ontology.
getTripleSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Returns the set of triples in this ontology. Warning this method gives access to the original Collection not a copy.
getTrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
getType() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `getType` returns the type of hotspot.
getType() - Method in class org.biojava.bio.program.formats.Embl
getType() - Method in class org.biojava.bio.program.formats.Enzyme
getType() - Method in interface org.biojava.bio.program.formats.Format
  Get the AnnotationType that constrains the events that will be fired.
getType() - Method in class org.biojava.bio.program.formats.Ligand.Compound
getType() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
getType() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
getType() - Method in class org.biojava.bio.program.formats.Swissprot
getType() - Method in interface org.biojava.bio.program.gff3.GFF3Record
getType() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
getType() - Method in interface org.biojava.bio.seq.Feature
  The type of the feature.
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes
  Get a Type by URI.
getType(String) - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
  Find the type for a name.
getType(String) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getType() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getType() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
getType() - Method in class org.biojava.bio.structure.AminoAcidImpl
getType() - Method in interface org.biojava.bio.structure.Group
  get Type of group, e.g.
getType() - Method in class org.biojava.bio.structure.HetatomImpl
  Returns the type value.
getType() - Method in class org.biojava.bio.structure.NucleotideImpl
getType() - Method in class org.biojava.utils.ChangeEvent
  Find the type of this event.
getType() - Method in class org.biojava.utils.ChangeForwarder.Retyper
getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Getter for property type.
getType() - Method in interface org.biojavax.bio.seq.Position
  Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimplePosition
  Returns the type of this position if it is not a point/single position.
getType() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  The type of the feature.
getTypeClass() - Method in class org.biojava.utils.walker.WalkerFactory
getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
getTypes(URL) - Static method in class org.biojava.bio.program.das.DAS
getTypes() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
  Get a set of all type names defined in this repository.
getTypes() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
getTypeTerm() - Method in interface org.biojava.bio.seq.Feature
  An ontology term defining the type of feature.
getTypeTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
getTypeTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
getTypeTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  An ontology term defining the type of feature.
getTypeTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
getU() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Return upper triangular factor
getU() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Return the left singular vectors
getUngappedLocation() - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Get a Location that contains exactly those positions that are not gaps.
getUngappedLocation() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
getUniProtDBNameTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
  Getter for the UniProt combined database term
getUniprotKWOnto() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the private uniprot ontology.
getUniProtTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
  Getter for the UniProt term
getUniProtXMLTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
  Getter for the UniProtXML term
getUnique() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
  The unique sequence that is used as a representative for this cluster.
getUnits() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
getUnitv() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getUnprojectedFeatures() - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Get the features before projection.
getUnprojectedFeatures() - Method in class org.biojava.bio.seq.projection.ReparentContext
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getUpstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getUpstreamCut` returns the cut site upstream of the recognition site.
getUpstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `getUpstreamEndType` returns the double-stranded end type produced by the secondary (upstream) cut.
getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
  Get the URI for this type.
getUri() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property uri.
getURI() - Method in interface org.biojavax.Namespace
  If the namespace has a URI, this will return it.
getURI() - Method in class org.biojavax.SimpleNamespace
  If the namespace has a URI, this will return it.
getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `getURL` returns the hotspot URL.
getURL() - Method in class org.biojava.bio.program.das.DASSequenceDB
  Return the URL of the reference server for this database.
getURL() - Method in class org.biojava.bio.program.das.DataSource
getURN() - Method in class org.biojava.bio.program.das.DASSequence
getURN() - Method in class org.biojava.bio.seq.impl.DummySequence
getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence
getURN() - Method in class org.biojava.bio.seq.impl.SubSequence
getURN() - Method in class org.biojava.bio.seq.impl.ViewSequence
getURN() - Method in class org.biojava.bio.seq.NewSimpleAssembly
getURN() - Method in interface org.biojava.bio.seq.Sequence
  A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getURN() - Method in class org.biojava.bio.seq.SimpleAssembly
getURN() - Method in class org.biojavax.bio.seq.ThinRichSequence
  A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
getUsed() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
getUsedAtomNames() - Method in class org.biojava.bio.structure.align.StrucAligParameters
getUserObject() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `getUserObject` returns the current user object (or null).
getV() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
  Return the eigenvector matrix
getV() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Return the right singular vectors
getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue
getValue() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
  Get the value that all properties must match.
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
getValue() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
  Returns the integer label for strandedness.
getValue() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
getValue() - Method in class org.biojava.bio.structure.align.helper.GapArray
getValue() - Method in interface org.biojava.stats.svm.ItemValue
getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
getValue() - Method in interface org.biojava.utils.walker.Walker
  If the visitor has a return value, then the result of applying the visitor to the tree can be obtained using this method, otherwise the result will be null.
getValue() - Method in interface org.biojavax.Note
  Gets the value that defines this note.
getValue() - Method in class org.biojavax.SimpleNote
  Gets the value that defines this note.
getValue() - Method in class org.biojavax.utils.CRC64Checksum
getValueAt(Symbol, Symbol) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  There are some substitution matrices containing more columns than lines.
getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
  Retrieve the value at a specific index.
getValueGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Get the group number that matches the value.
getValues() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
  `getValues` returns the set of values which constrain the property.
getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
  Get all masses including the variable mass.
getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
getVectorAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
  define the shift vector annotation type
getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated. Is VectorNTI compatable output being produced?
getVectors() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  Returns the shift vectors.
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns a vesrion of this vocabulary.
getVersion() - Method in interface org.biojavax.bio.BioEntry
  Gets the version of this bioentry.
getVersion() - Method in class org.biojavax.bio.SimpleBioEntry
  Gets the version of this bioentry.
getVersion() - Method in interface org.biojavax.CrossRef
  Returns the version of the object that the crossref refers to.
getVersion() - Method in class org.biojavax.SimpleCrossRef
  Returns the version of the object that the crossref refers to.
getVersionLineTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
  Getter for the Ensembl-specific 'versionLine' term
getVerticalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the in use vertical scale factor.
getViewedFeature() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
getViewedFeature() - Method in interface org.biojava.bio.seq.projection.Projection
getVisibleRange(SequenceRenderContext, Graphics2D) - Static method in class org.biojava.bio.gui.sequence.GUITools
getVisibleRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getVisibleSecondarySymbolCount` returns the maximum number of secondary `Symbol`s which can be rendered in the visible area (excluding all borders) of the `PairwiseSequencePanel` at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `getVisibleSymbolCount` returns the maximum number of `Symbol`s which can be rendered in the visible area (excluding all borders) of the `PairwiseSequencePanel` at the current scale.
getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `getVisibleSymbolCount` returns the maximum number of `Symbol`s which can be rendered in the visible area (excluding all borders) of the `TranslatedSequencePanel` at the current scale.
getVMaxes() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Getter for property VMaxes.
getVocabularyByName(String) - Method in interface org.biojava.utils.candy.CandyFinder
  It returns a selected vocabulary.
getVocabularyFinder() - Method in interface org.biojava.bibliography.BibRefSupport
  It returns an object representing a central place where all controlled vocabularies can be received from and shared by all users.
getWalker(Visitor) - Method in class org.biojava.utils.walker.WalkerFactory
  Get a Walker that is customosed to a particular visitor.
getWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution
  Retrieve the weight for this distribution.
getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution
  Return the probability that Symbol s is emitted by this spectrum.
getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution
getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution
getWeight(Symbol) - Method in class org.biojava.bio.dist.TranslatedDistribution
getWeight(Object) - Method in class org.biojavax.ga.util.WeightedSet
  Determines the normalized weight for `o`
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractDistribution
  Override this method to implement getting the weight for an atomic symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
  Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution
getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.UniformDistribution
getWeightMatrixID() - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
  Get the value of the weight matrix id.
getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
  Get the underlying array that stores the weights.
getWeights(State) - Method in interface org.biojava.bio.dp.MarkovModel
  Get a probability Distribution over the transition from 'source'.
getWeights(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
getWeights(State) - Method in class org.biojava.bio.dp.WMAsMM
getWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Returns the width of the whole graphic (in pixels).
getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel
getWobbleDistributionForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
  returns a WobbleDistribution for a specified residue.
getWobbleDistributionForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
getWobbleFrequency(Symbol) - Method in interface org.biojava.bio.symbol.WobbleDistribution
  returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.
getWorkingDirectory() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the working directory for the external process.
getWrap() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
getWrap() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
getWrapIncrement() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
getWrapped() - Method in class org.biojava.bio.AnnotationChanger
  `getWrapped` returns the `Annotation` being remapped.
getWrapped() - Method in class org.biojava.bio.AnnotationRenamer
  `getWrapped` returns the `Annotation` being remapped.
getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
getWriter() - Method in class org.biojava.utils.process.ReaderWriterPipe
  Gets the writer.
getX() - Method in interface org.biojava.bio.structure.Atom
  get cordinate X.
getX() - Method in class org.biojava.bio.structure.AtomImpl
  get the X coordinate.
getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler
  Return the XFF processing environment passed in when this handler was created.
getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
getXrefs() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
  return a set of AGAVEXref
getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
getY() - Method in interface org.biojava.bio.structure.Atom
  get cordinate Y.
getY() - Method in class org.biojava.bio.structure.AtomImpl
  get the Y coordinate.
getZ() - Method in interface org.biojava.bio.structure.Atom
  get cordinate Z.
getZ() - Method in class org.biojava.bio.structure.AtomImpl
  get the Z coordinate.
GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `GFF` indicates that the sequence format is GFF.
GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3
  The interface for things that listen to GFF event streams.
GFF3Parser - Class in org.biojava.bio.program.gff3
  Parse a stream of GFF text into a stream of records and comments.
GFF3Parser() - Constructor for class org.biojava.bio.program.gff3.GFF3Parser
GFF3Record - Interface in org.biojava.bio.program.gff3
  A record in a GFF3 formatted file.
GFF3Record.Impl - Class in org.biojava.bio.program.gff3
GFF3Record.Impl() - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
GFF3Record.Impl(GFF3Record) - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
GFFDataSource - Class in org.biojava.bio.seq.distributed
  Use a GFFEntrySet as a DataSource for adding annotation to sequences.
GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
GFFDocumentHandler - Interface in org.biojava.bio.program.gff
  The interface for things that listen to GFF event streams.
GFFEntrySet - Class in org.biojava.bio.program.gff
  A set of entries and comments as a representation of a GFF file.
GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet
  Make an empty GFFEntrySet.
GFFErrorHandler - Interface in org.biojava.bio.program.gff
  Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff
GFFErrorHandler.AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff
GFFErrorHandler.SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
GFFFilterer - Class in org.biojava.bio.program.gff
  An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer
  Create a new GFFFilterer that will forward to handler everything that filter accepts.
gffFromSeqDB(SequenceDB) - Static method in class org.biojava.bio.program.gff.GFFTools
  Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools
  Creates a GFFEntrySet containing one entry for each feature on a sequence.
GFFParser - Class in org.biojava.bio.program.gff
  Parse a stream of GFF text into a stream of records and comments.
GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser
GFFRecord - Interface in org.biojava.bio.program.gff
  A single GFF record.
GFFRecordFilter - Interface in org.biojava.bio.program.gff
  A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff
  Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff
  Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
GFFRecordFilter.FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff
GFFRecordFilter.FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
GFFRecordFilter.FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff
GFFRecordFilter.NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
GFFRecordFilter.NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff
  Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
GFFRecordFilter.SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff
  Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
GFFRecordFilter.SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff
GFFRecordFilter.StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
GFFRecordFilter.StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
GFFTools - Class in org.biojava.bio.program.gff
GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools
GFFWriter - Class in org.biojava.bio.program.gff
  Listens to a stream of GFF events and writes the lines to a PrintWriter.
GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter
  Create a new GFFWriter that will write to out.
GI_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
gln() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glutamine (Q)
GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated. The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
GLOBAL - Static variable in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated. The TaxonFactory that the biojava system should use for storing the taxonomy used by swissprot and embl as in-memory objects.
glu() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glutamic Acid (E)
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.Protease
GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.ProteaseManager
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.Protease
GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.ProteaseManager
gly() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glycine (G)
Glyph - Interface in org.biojava.bio.gui.glyph
  The Glyph interface for painting a shape within bounds
GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence
  A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
GlyphFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
GlyphUtils - Class in org.biojava.bio.gui.glyph
  Utils class used by Glyph implementors.
GOParser - Class in org.biojava.ontology.io
  Simple parser for the Gene Ontology (GO) flatfile format.
GOParser() - Constructor for class org.biojava.ontology.io.GOParser
Gotoh - Class in org.biojava.bio.structure.align.pairwise
  a class to perform Gotoh algorithm
Gotoh(Alignable) - Constructor for class org.biojava.bio.structure.align.pairwise.Gotoh
graphicsToSecondarySequence(double) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `graphicsToSecondarySequence` converts a graphical position to a sequence coordinate on the secondary sequence.
graphicsToSecondarySequence(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `graphicsToSecondarySequence` converts a graphical position to a secondary sequence index.
graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `graphicsToSequence` converts a graphical position to a sequence index.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `graphicsToSequence` converts a graphical position to a sequence index.
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePanel
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Converts a graphical position into a sequence coordinate.
graphicsToSequence(Point2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Converts a graphical position into a sequence coordinate.
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `graphicsToSequence` converts a graphical position to a sequence index.
graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `graphicsToSequence` converts a graphical position to a sequence index.
greater(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
group() - Method in interface org.biojava.bio.search.BioMatcher
  Get the matching region as a SymbolList.
group() - Method in class org.biojava.bio.search.MaxMismatchMatcher
Group - Interface in org.biojava.bio.structure
  This is the datastructure for a single Group of atoms.
group() - Method in class org.biojava.utils.regex.Matcher
  Returns the input subsequence matched by the previous match.
group(int) - Method in class org.biojava.utils.regex.Matcher
  Returns the input subsequence captured by the given group during the previous match operation.
groupCount() - Method in class org.biojava.utils.regex.Matcher
  Returns the number of capturing groups in this matcher's pattern.
GroupIterator - Class in org.biojava.bio.structure
  an iterator over all groups of a structure.
GroupIterator(Structure) - Constructor for class org.biojava.bio.structure.GroupIterator
  Constructs a GroupIterator object.
groups - Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
growIfNecessary() - Method in class org.biojava.utils.ChangeSupport
  Grows the internal resources if by adding one more listener they would be full.
guessFileType(File) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
guessRecLen(RandomAccessFile) - Method in class org.biojava.bio.seq.db.BioIndex
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Always returns a DNA tokenizer.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Always returns a DNA tokenizer.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Returns an dna parser if the letters DNA or RNA appear in the first line of the file.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Returns an dna parser if the letters DNA or RNA appear in the first line of the stream.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Always returns a DNA tokenizer.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a protein tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Always returns a protein tokenizer.
guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a protein tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. Always returns a protein tokenizer.
GUITools - Class in org.biojava.bio.gui.sequence
GZIP_MAGIC - Static variable in class org.biojava.utils.io.InputStreamProvider
  The magic number found at the start of a GZIP stream.

## H

h() - Static method in class org.biojava.bio.seq.NucleotideTools
h() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Histidine
H_SAPIENS - Static variable in interface org.biojava.bio.program.homologene.Taxon
H_VULGARE - Static variable in interface org.biojava.bio.program.homologene.Taxon
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler
handleEndElement(String, String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNAAmbPack
handlesAmbiguity() - Method in class org.biojava.bio.symbol.DNANoAmbPack
handlesAmbiguity() - Method in interface org.biojava.bio.symbol.Packing
  Flag to state if ambiguities are stored.
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HitStAXHandler
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPStAXHandler
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
handleStartElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
has3D() - Method in interface org.biojava.bio.structure.Group
  returns true or false, depending if this group has 3D coordinates or not.
has3D() - Method in class org.biojava.bio.structure.HetatomImpl
  returns true or false, depending if this group has 3D coordinates or not.
hasAminoAtoms() - Method in interface org.biojava.bio.structure.Group
  calculate if a groups has all atoms required for an amino acid.
hasAminoAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
  calculate if a groups has all atoms required for an amino acid this allows to include chemically modified amino acids that are labeled hetatoms into some computations ...
hasAnnotation(Object) - Static method in class org.biojava.bio.seq.FilterUtils
  Match features where the property `key` has been defined as having some value, regardless of the exact value.
hasAtom(String) - Method in interface org.biojava.bio.structure.Group
  returns flag whether a particular atom is existing within this group .
hasAtom(String) - Method in class org.biojava.bio.structure.HetatomImpl
  test is an Atom with name is existing.
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
hasBoundedMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
hasBoundedMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
hasChain(String) - Method in interface org.biojava.bio.structure.Structure
  check if a chain with the id chainId is contained in this structure.
hasChain(String) - Method in class org.biojava.bio.structure.StructureImpl
hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel
hasChangeListeners() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
hasChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
hasChild(int) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Determine if this node has a child corresponding to a given index number.
hasChild(Character) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
  Determine if this node has a child corresponding to a given character
hasFeatures(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Find out if this DistDataSource can provide features on a sequence with a particular ID.
hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
hasFeatures(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
HashBioEntryDB - Class in org.biojavax.bio.db
  An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashBioEntryDB() - Constructor for class org.biojavax.bio.db.HashBioEntryDB
  Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashBioEntryDB(String) - Constructor for class org.biojavax.bio.db.HashBioEntryDB
  Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
hashCode() - Method in class org.biojava.bio.AbstractAnnotation
hashCode() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
hashCode() - Method in class org.biojava.bio.CollectionConstraint.Contains
hashCode() - Method in class org.biojava.bio.dist.AbstractDistribution
hashCode() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
hashCode() - Method in class org.biojava.bio.dp.TrainerTransition
  The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.dp.Transition
  The hash code is from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.EcNumber.Impl
hashCode() - Method in class org.biojava.bio.gui.sequence.SequencePanel
hashCode() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
hashCode() - Method in class org.biojava.bio.program.das.DataSource
hashCode() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
hashCode() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
hashCode() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
hashCode() - Method in class org.biojava.bio.seq.Feature.Template
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.And
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Not
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.Or
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
hashCode() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
hashCode() - Method in class org.biojava.bio.seq.impl.SimpleFeature
hashCode() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
hashCode() - Method in class org.biojava.bio.symbol.AbstractLocation
hashCode() - Method in class org.biojava.bio.symbol.AbstractSymbolList
hashCode() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
hashCode() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
hashCode() - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
hashCode() - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. The hash-code of a Taxon is equal to the hash-code of it's scientific name.
hashCode() - Method in class org.biojava.ontology.Term.Impl
hashCode() - Method in interface org.biojava.ontology.Triple
  The hashcode for a Triple.
hashCode() - Method in class org.biojava.ontology.Triple.Impl
hashCode() - Method in class org.biojava.utils.ListTools.Doublet
hashCode() - Method in class org.biojava.utils.ListTools.Triplet
hashCode() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
hashCode(int, boolean) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, int) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, long) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, float) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, boolean[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, int[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, long[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, float[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, double[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, Object[]) - Static method in class org.biojava.utils.ObjectUtil
hashCode(int, Object) - Static method in class org.biojava.utils.ObjectUtil
hashCode() - Method in class org.biojava.utils.TypedProperties
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
hashCode() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
hashCode() - Method in class org.biojavax.bio.seq.CompoundRichLocation
hashCode() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  ALWAYS RETURNS 17
hashCode() - Method in class org.biojavax.bio.seq.RichLocation.Strand
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeature
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
hashCode() - Method in class org.biojavax.bio.seq.SimpleRichLocation
hashCode() - Method in class org.biojavax.bio.SimpleBioEntry
hashCode() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
hashCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
hashCode() - Method in class org.biojavax.EmptyRichAnnotation
hashCode() - Method in class org.biojavax.ontology.SimpleComparableOntology
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTerm
hashCode() - Method in class org.biojavax.ontology.SimpleComparableTriple
  The hashcode for a Triple.
hashCode() - Method in class org.biojavax.SimpleComment
hashCode() - Method in class org.biojavax.SimpleCrossRef
hashCode() - Method in class org.biojavax.SimpleDocRef
hashCode() - Method in class org.biojavax.SimpleDocRefAuthor
hashCode() - Method in class org.biojavax.SimpleNamespace
hashCode() - Method in class org.biojavax.SimpleNote
hashCode() - Method in class org.biojavax.SimpleRankedCrossRef
hashCode() - Method in class org.biojavax.SimpleRankedDocRef
HashRichSequenceDB - Class in org.biojavax.bio.db
  An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashRichSequenceDB() - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
  Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashRichSequenceDB(IDMaker) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
  Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashRichSequenceDB(String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
  Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
HashRichSequenceDB(IDMaker, String) - Constructor for class org.biojavax.bio.db.HashRichSequenceDB
  Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
HashSequenceDB - Class in org.biojava.bio.seq.db
  An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
HashSequenceDB() - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
  Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashSequenceDB(IDMaker) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
  Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashSequenceDB(String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
  Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name.
HashSequenceDB(IDMaker, String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
  Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
hasListeners() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
hasListeners() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
hasListeners() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
hasListeners() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `hasListeners` returns true if there are active listeners for BioJava events.
hasListeners() - Method in class org.biojava.bio.gui.sequence.SequencePanel
hasListeners() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `hasListeners` returns true if there are active listeners for BioJava events.
hasListeners(String) - Method in class org.biojava.bio.gui.StackedLogoPainter
hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter
hasListeners() - Method in class org.biojava.bio.program.das.ReferenceServer
hasListeners() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
hasListeners() - Method in class org.biojava.utils.AbstractChangeable
  Deprecated. use hasListeners(ChangeType) if at all possible
hasListeners(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
  Discover if we have listeners registered for a particular change type.
hasListeners() - Method in class org.biojava.utils.ChangeSupport
  Return true if we have any listeners registered at all.
hasListeners(ChangeType) - Method in class org.biojava.utils.ChangeSupport
  Return true if we have listeners registered for a particular change type.
hasMoreSymbols() - Method in interface org.biojava.bio.seq.io.SymbolReader
  Determine if there are more symbols left to read in this stream.
hasNext() - Method in class org.biojava.bio.dp.DP.ReverseIterator
hasNext() - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
hasNext() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Are there further Cells to be computed?
hasNext() - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
hasNext() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
  test wether the cursor can be advanced further
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
  are more OrthoPairSets available?
hasNext() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
hasNext() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
hasNext() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
hasNext() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
hasNext() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
  Checks if there is a further `SymbolPropertyTable` object.
hasNext() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator
  Checks if there is a further `SymbolPropertyTable` object.
hasNext() - Method in class org.biojava.bio.seq.io.StreamReader
hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator
  Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojava.bio.structure.AtomIterator
  is there a next atom ?
hasNext() - Method in class org.biojava.bio.structure.GroupIterator
  is there a group after the current one in the structure?
hasNext() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
hasNext() - Method in class org.biojava.utils.MergingIterator
hasNext() - Method in interface org.biojavax.bio.BioEntryIterator
  Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojavax.bio.seq.io.RichStreamReader
  Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
  Returns whether there are more sequences to iterate over.
hasSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Find out if this DistDataSource provides the sequence information for a sequence ID.
hasSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
hasSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
hasWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
  Indicate whether the weights array has been allocated yet.
Havg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Hydrogen average mass
HEADER_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HeaderStAXHandler
headerLine - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
headerLine - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
headerLine - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
HeaderStAXHandler - Class in org.biojava.bio.program.ssbind
  `HeaderStAXHandler` handles the Header element of BioJava BlastLike XML.
HeadlessRenderContext - Class in org.biojava.bio.gui.sequence
  A stand-alone SequenceRenderContext to make it easy to render to an image.
HeadlessRenderContext(Sequence, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.HeadlessRenderContext
heads() - Method in interface org.biojava.bio.dp.MarkovModel
  Deprecated. use `advance().length`
heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel
heads() - Method in class org.biojava.bio.dp.WMAsMM
HEIGHT_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether height or vertical scale is the authoritative measure.
HEIGHTSCALING - Static variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  Constant `HEIGHTSCALING` indicating a change to the feature height scaling policy.
HelixGlyph - Class in org.biojava.bio.gui.glyph
  A Glyph that paints a Helix within the bounds
HelixGlyph() - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph
HelixGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.HelixGlyph
HetatomImpl - Class in org.biojava.bio.structure
  Generic Implementation of a Group interface.
HetatomImpl() - Constructor for class org.biojava.bio.structure.HetatomImpl
HIDDEN - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
his() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Histidine (H)
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.HitMerger
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
hit(int, int, int, int) - Method in interface org.biojava.bio.program.ssaha.SearchListener
  There has been a hit between the query sequence and a database sequence.
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
hit(int, int, int, int) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
HIT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HitStAXHandler
HitMerger - Class in org.biojava.bio.program.ssaha
  A listener that merges overlapping hits and culls all hits under a given length.
HitMerger(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.HitMerger
  Build a new HitMerger that will pass events on to a delegate.
HitStAXHandler - Class in org.biojava.bio.program.ssbind
  `AlignmentStAXHandler` handles the Hit element of BioJava BlastLike XML.
hmm() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the inner HmmerProfileHMM state
hmm - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
HmmerProfileHMM - Class in org.biojava.bio.program.hmmer
  This is a class for representing HMMER generated Profile HMM.
HmmerProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileHMM
HmmerProfileParser - Class in org.biojava.bio.program.hmmer
  A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training note that this class is still currently experimental.
HmmerProfileParser(String) - Constructor for class org.biojava.bio.program.hmmer.HmmerProfileParser
HMMTrainer - Interface in org.biojava.bio.dp
  interface implemented by objects that train HMMs.
Hmono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Hydrogen monoisotopic mass
HOMOID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
HomologeneBuilder - Interface in org.biojava.bio.program.homologene
  an interface for Homologene dataset Builders
HomologeneDB - Interface in org.biojava.bio.program.homologene
  Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms.
HomologeneTools - Class in org.biojava.bio.program.homologene
  Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms.
HomologeneTools() - Constructor for class org.biojava.bio.program.homologene.HomologeneTools
Homology - Interface in org.biojava.bio.seq.homol
  Signifies that two or more features are homologous.
homology - Variable in class org.biojava.bio.seq.homol.HomologyFeature.Template
HOMOLOGY_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
  `HOMOLOGY_FEATURE_TYPE` is the type String used by `BlastLikeHomologyBuilder` when creating `HomologyFeature`s.
HomologyDB - Interface in org.biojava.bio.seq.homol
HomologyFeature - Interface in org.biojava.bio.seq.homol
HomologyFeature.Template - Class in org.biojava.bio.seq.homol
HomologyFeature.Template() - Constructor for class org.biojava.bio.seq.homol.HomologyFeature.Template
HORIZONTAL_NONLINEAR_SCALER - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option specifying the non-linear scaling function to apply, as embodied in a `ChromatogramNonlinearScaler` object.
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
hotSpots() - Method in interface org.biojava.bio.gui.sequence.ImageMap
  `hotSpots` iterates over the hotspots in the map
hotSpots() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
hp - Static variable in class org.biojavax.bio.seq.io.FastaFormat
HSP_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPStAXHandler
HSPStAXHandler - Class in org.biojava.bio.program.ssbind
  `HSPStAXHandler` handles the HSP element of BioJava BlastLike XML.
HSPSUMMARY_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.HSPSummaryStAXHandler
HSPSummaryStAXHandler - Class in org.biojava.bio.program.ssbind
  `HSPSummaryStAXHandler` handles the HSPSummary element of BioJava BlastLike XML.
HTMLRenderer - Class in org.biojava.bio.program.blast2html
  Renders HTML version of blast-like output.
HTMLRenderer(PrintWriter, String, int, URLGeneratorFactory, AlignmentMarker, Properties) - Constructor for class org.biojava.bio.program.blast2html.HTMLRenderer
  Creates an HTMLRenderer, that outputs the HTML to the specified PrintWriter.
HypersonicDBHelper - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
HypersonicDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
  Deprecated.
hypot(double, double) - Static method in class org.biojava.bio.structure.jama.Maths
  sqrt(a^2 + b^2) without under/overflow.

## I

i() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Isoleucine
ID_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ID_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
ID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
Identifiable - Interface in org.biojava.utils.lsid
  Marks an implementor as having a LifeScienceIdentifier.
identifier - Variable in class org.biojava.bibliography.BibRef
  It is an unambiguous reference to this citation "within the world".
IDENTIFIER - Static variable in interface org.biojavax.bio.BioEntry
IDENTIFIER - Static variable in interface org.biojavax.ontology.ComparableTerm
identifyFormat(String, String) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. `identifyFormat` performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer.
identity(int, int) - Static method in class org.biojava.bio.structure.jama.Matrix
  Generate identity matrix
IDMaker - Interface in org.biojava.bio.seq.db
  Interface for objects that define how to make an ID for a sequence.
IDMaker.ByName - Class in org.biojava.bio.seq.db
IDMaker.ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
IDMaker.ByURN - Class in org.biojava.bio.seq.db
IDMaker.ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN
ids() - Method in class org.biojava.bio.program.das.DASSequenceDB
ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
ids() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
ids() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
ids() - Method in class org.biojava.bio.seq.db.DummySequenceDB
ids() - Method in class org.biojava.bio.seq.db.HashSequenceDB
ids() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
ids() - Method in interface org.biojava.bio.seq.db.SequenceDB
  Get an immutable set of all of the IDs in the database.
ids() - Method in class org.biojava.bio.seq.db.SubSequenceDB
ids() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
ids(boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
  Get the complete set of sequence IDs provided by this DistDataSource.
ids() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
ids(boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
ids(boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
ids() - Method in interface org.biojavax.bio.db.BioEntryDB
  Get an immutable set of all of the IDs in the database.
ids() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
ids() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
ids() - Method in class org.biojavax.bio.db.HashBioEntryDB
ids() - Method in class org.biojavax.bio.db.HashRichSequenceDB
ids() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
IG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `IG` indicates that the sequence format is IG.
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
ignorableWhitespace(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
ignorableWhitespace(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
IgnoreCountsTrainer - Class in org.biojava.bio.dist
  A distribution trainer that just ignores all counts.
IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer
  Constructor intended for sub-classes.
IgnoreRecordException - Exception in org.biojava.bio.program.gff
  Ignore this record in the stream.
IgnoreRecordException() - Constructor for exception org.biojava.bio.program.gff.IgnoreRecordException
ile() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Isoleucine (I)
IllegalAlignmentEditException - Exception in org.biojava.bio.alignment
  The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.
IllegalAlignmentEditException() - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
  Just make the exception.
IllegalAlignmentEditException(String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
  Make the exception with a message.
IllegalAlignmentEditException(Throwable) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
IllegalAlignmentEditException(Throwable, String) - Constructor for exception org.biojava.bio.alignment.IllegalAlignmentEditException
IllegalAlphabetException - Exception in org.biojava.bio.symbol
  The exception to indicate that an invalid alphabet has been used.
IllegalAlphabetException() - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
  Just make the exception.
IllegalAlphabetException(String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
  Make the exception with a message.
IllegalAlphabetException(Throwable) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
IllegalAlphabetException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalAlphabetException
IllegalIDException - Exception in org.biojava.bio.seq.db
IllegalIDException() - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(Throwable) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
IllegalIDException(Throwable, String) - Constructor for exception org.biojava.bio.seq.db.IllegalIDException
IllegalOrganismException - Exception in org.biojavax.ga.exception
  Indicates an invalid organism
IllegalOrganismException() - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
IllegalOrganismException(String) - Constructor for exception org.biojavax.ga.exception.IllegalOrganismException
IllegalSymbolException - Exception in org.biojava.bio.symbol
  The exception to indicate that a symbol is not valid within a context.
IllegalSymbolException(String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
  Make the exception with a message.
IllegalSymbolException(Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
  Make the exception with a message and a symbol.
IllegalSymbolException(Throwable, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
IllegalSymbolException(Throwable, Symbol, String) - Constructor for exception org.biojava.bio.symbol.IllegalSymbolException
IllegalTransitionException - Exception in org.biojava.bio.dp
  This exception indicates that there is no transition between two states.
IllegalTransitionException(State, State, String) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
IllegalTransitionException(State, State) - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
IllegalTransitionException() - Constructor for exception org.biojava.bio.dp.IllegalTransitionException
ImageMap - Interface in org.biojava.bio.gui.sequence
  `ImageMap` represents a collection of image map hotspots.
ImageMap.ClientSide - Class in org.biojava.bio.gui.sequence
  `ClientSide` represents a client-side style image map.
ImageMap.ClientSide(String) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ClientSide
  Creates a new `ClientSide` image map.
ImageMap.HotSpot - Class in org.biojava.bio.gui.sequence
  `HotSpot`s represent an image map hotspot.
ImageMap.HotSpot(String, URL, Integer[]) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  Creates a new `HotSpot` with a null user object.
ImageMap.HotSpot(String, URL, Integer[], Object) - Constructor for class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  Creates a new `HotSpot`.
ImageMap.ServerSide - Class in org.biojava.bio.gui.sequence
  `ServerSide` represents a server-side style image map.
ImageMap.ServerSide() - Constructor for class org.biojava.bio.gui.sequence.ImageMap.ServerSide
  Creates a new `ServerSide` image map.
ImageMapRenderer - Interface in org.biojava.bio.gui.sequence
  `ImageMapRenderer`s create strings representing `Feature`s suitable for use in HTML image maps.
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
importTaxon(Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Import a Taxon and all its children into the implementation provided by this factory.
importTaxon(Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
importTerm(Term, String) - Method in class org.biojava.ontology.IntegerOntology
importTerm(Term, String) - Method in class org.biojava.ontology.Ontology.Impl
importTerm(Term, String) - Method in interface org.biojava.ontology.Ontology
  Create a view of a term from another ontology.
importTerm(Term, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Create a view of a term from another ontology. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term.
in - Variable in class org.biojava.utils.io.CachingInputStream
  The underlying input stream whose data we're caching
IN_RANGE - Static variable in interface org.biojavax.bio.seq.Position
  A symbol representing a position that occupies a single base somewhere in a range, eg.
incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree
INCLUDES_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
increaseCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
  Set the probability or odds that Symbol s is emitted by this state.
increaseCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
indent() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
INDENT - Static variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  use a two space indent
indent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  Add a level of indentation
INDETERMINATE - Static variable in class org.biojava.utils.TriState
index(State) - Method in class org.biojava.bio.dp.WMAsMM
Index - Interface in org.biojava.bio.seq.db
  This defines an index entry for an individual sequence within a set of indexed files.
index(Symbol) - Static method in class org.biojava.bio.seq.DNATools
  Return an integer index for a symbol - compatible with `forIndex`.
index(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
  Return an integer index for a symbol - compatible with `forIndex`.
index(Symbol) - Static method in class org.biojava.bio.seq.RNATools
  Return an integer index for a symbol - compatible with forIndex.
index - Variable in class org.biojava.bio.structure.align.helper.GapArray
INDEX - Static variable in interface org.biojava.bio.symbol.AlphabetIndex
  Indicates that the index is changing, probably due to the underlying alphabet changing.
Index2Model - Class in org.biojava.bio.program.tagvalue
Index2Model() - Constructor for class org.biojava.bio.program.tagvalue.Index2Model
IndexedAnnotationDB - Class in org.biojava.bio.annodb
  A database of Annotation instances backed by an indexed file set.
IndexedAnnotationDB(String, File, Index2Model, List, int, AnnotationType, IndexedAnnotationDB.ParserListenerFactory) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB
  Create a new IndexedAnnotationDB.
IndexedAnnotationDB(BioStore) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB
  Initialise the db from a store.
IndexedAnnotationDB.ParserListenerFactory - Interface in org.biojava.bio.annodb
  A factory for retrieving parsers and listeners.
IndexedAnnotationDB.StaticMethodRPFactory - Class in org.biojava.bio.annodb
  An implementation of ParserListenerFactory that uses a static method.
IndexedAnnotationDB.StaticMethodRPFactory(Method) - Constructor for class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
  Create a new StaticMethodRPFactory for a method.
IndexedChangeHub - Class in org.biojava.utils
  implements Changeable support with a ChangeHub that stores ChangeListener by key.
IndexedChangeHub() - Constructor for class org.biojava.utils.IndexedChangeHub
IndexedChangeHub.ListenerMemento - Class in org.biojava.utils
IndexedChangeHub.ListenerMemento(ChangeType, Reference) - Constructor for class org.biojava.utils.IndexedChangeHub.ListenerMemento
IndexedCount - Class in org.biojava.bio.dist
  An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
IndexedCount(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.IndexedCount
  Get a new IdexedCount for an alphabet using the default indexer.
IndexedCount(AlphabetIndex) - Constructor for class org.biojava.bio.dist.IndexedCount
  Get a new InexedCount for an alphabet indexer.
IndexedSequenceDB - Class in org.biojava.bio.seq.db
  This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
IndexedSequenceDB(IDMaker, IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB
  Create an IndexedSequenceDB by specifying both the IDMaker and IndexStore used.
IndexedSequenceDB(IndexStore) - Constructor for class org.biojava.bio.seq.db.IndexedSequenceDB
  Create an IndexedSequenceDB by specifying IndexStore used.
indexEmbl(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
  `indexEmbl` indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
Indexer - Class in org.biojava.bio.program.tagvalue
  Listens to tag-value events and passes on indexing events to an IndexStore.
Indexer(File, IndexStore) - Constructor for class org.biojava.bio.program.tagvalue.Indexer
  Build a new Indexer.
Indexer2 - Class in org.biojava.bio.program.tagvalue
  Listens to tag-value events and passes on indexing events to an IndexStore.
Indexer2(File, IndexStore, Index2Model) - Constructor for class org.biojava.bio.program.tagvalue.Indexer2
  Build a new Indexer.
indexFasta(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
  `indexFasta` indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
indexForSymbol(Symbol) - Method in interface org.biojava.bio.symbol.AlphabetIndex
  Return the unique index for a symbol.
indexGenbank(String, File, File[], int) - Static method in class org.biojava.bio.program.indexdb.IndexTools
  `indexGenbank` indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
IndexPair - Class in org.biojava.bio.structure.align.helper
IndexPair(short, short) - Constructor for class org.biojava.bio.structure.align.helper.IndexPair
IndexStore - Interface in org.biojava.bio.program.indexdb
  `IndexStore` is an interface for indexing flatfiles according to the OBDA specification.
IndexStore - Interface in org.biojava.bio.seq.db
  This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets.
indexSwissprot(String, File, File[]) - Static method in class org.biojava.bio.program.indexdb.IndexTools
  `indexSwissprot` indexes Swissprot format protein sequence files on ID as primary identifier.
IndexTools - Class in org.biojava.bio.program.indexdb
  `IndexTools` contains static utility methods for creating flatfile indices according to the OBDA standard.
inFeature() - Method in class org.biojava.bio.seq.io.FeatureTableParser
  Deprecated.
InfinitelyAmbiguousSymbolList - Class in org.biojavax.bio.seq
  A symbol list that is `Integer.MAX_VALUE`long, never gives index out of bounds and always returns ambiguity symbols for everything.
InfinitelyAmbiguousSymbolList(FiniteAlphabet) - Constructor for class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Creates a new instance of InfinitelyAmbiguousSymbolList
init() - Method in interface org.biojava.utils.xml.Initializable
INIT_PROP_LOG - Static variable in interface org.biojava.bibliography.BibRefSupport
  A property name ("log").
INIT_PROP_SUPPORT - Static variable in interface org.biojava.bibliography.BibRefSupport
  A property name ("bibrefsupport").
initComponents() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
initialiseProfileHMM(int) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
Initializable - Interface in org.biojava.utils.xml
initialize(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
  Initialize the cell at [0][0] to the recursion initial parameters.
initialize() - Method in class org.biojava.bio.seq.db.TabIndexStore
initializeVariables(int, int, int, int, boolean, boolean, FuzzyLocation.RangeResolver) - Method in class org.biojava.bio.symbol.FuzzyLocation
  Refactored initialization code from the constructors.
input - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
InputHandler - Interface in org.biojava.utils.process
  Interface to a threadable input handler for an external process.
InputStreamProvider - Class in org.biojava.utils.io
  A class that provides an InputStream from a File.
InputStreamProvider() - Constructor for class org.biojava.utils.io.InputStreamProvider
INSDSEQ_FORMAT - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
  The name of this format
INSDSEQ_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
INSDseqFormat - Class in org.biojavax.bio.seq.io
  Format reader for INSDseq files.
INSDseqFormat() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat
INSDseqFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some INSDseq-specific terms.
INSDseqFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.INSDseqFormat.Terms
INSDSEQS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
INSTANCE - Static variable in class org.biojava.bio.gui.sequence.LayeredRenderer
  Static `LayeredRenderer` `INSTANCE` used by `MultiLineRenderer`s.
INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblFeatureComparator
  Deprecated.
INSTANCE - Static variable in class org.biojava.bio.seq.io.GenEmblPropertyComparator
  Deprecated.
instance() - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. all AlphabetManager methods have become static
INSTANCE - Static variable in class org.biojava.bio.symbol.DoubleAlphabet
INSTANCE - Static variable in class org.biojava.bio.symbol.IntegerAlphabet
  The singleton instance of the IntegerAlphabet class.
instance() - Static method in class org.biojava.directory.SystemRegistry
  Get the singleton Registry instance representing the system-wide default registry.
INSTANCE - Static variable in class org.biojava.utils.xml.XMLBeans
instanceOf(Annotation) - Method in class org.biojava.bio.AnnotationType.Abstract
instanceOf(Annotation) - Method in interface org.biojava.bio.AnnotationType
  Validate an Annotation against this AnnotationType.
instantiateBean(Element) - Method in class org.biojava.utils.xml.XMLBeans
instantiateBean(Element, ClassLoader, Map) - Method in class org.biojava.utils.xml.XMLBeans
instantiateDB(URL, HomologeneBuilder) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
  instantiate a HomologeneDB.
instantiateTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
  This attempts to divine the 'best' template class for a feature and return a new instance readly for pupulating.
INTEGER - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `INTEGER` indicates that a sequence contains integer alphabet symbols, such as used to describe sequence quality data.
IntegerAlphabet - Class in org.biojava.bio.symbol
  An efficient implementation of an Alphabet over the infinite set of integer values.
IntegerAlphabet.IntegerSymbol - Class in org.biojava.bio.symbol
  A single int value.
IntegerAlphabet.IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
IntegerAlphabet.SubIntegerAlphabet - Class in org.biojava.bio.symbol
  A class to represent a finite contiguous subset of the infinite IntegerAlphabet
IntegerOntology - Class in org.biojava.ontology
IntegerOntology.IntTerm - Class in org.biojava.ontology
IntegerOntology.IntTerm(int) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
IntegerOntology.IntTerm(int, Object[]) - Constructor for class org.biojava.ontology.IntegerOntology.IntTerm
integerSymbolFromPhred(Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
  Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
IntegerTokenization - Class in org.biojava.bio.seq.io
IntegerTokenization() - Constructor for class org.biojava.bio.seq.io.IntegerTokenization
IntElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of an integer.
IntElementHandlerBase() - Constructor for class org.biojava.utils.stax.IntElementHandlerBase
INTERACTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
intersect(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
  Operator: Intersect FeatureHolder1 with FeatureHolder2
intersection(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  Calculate an AnnotationType that matches all Annotation instances matched by both types.
intersection(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Calculate the intersection of two PropertyConstraint instances.
intersection(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Return the CollectionConstraint which accept only collections accepted by both of those specified.
intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
intersection(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
intersection(Location) - Method in class org.biojava.bio.symbol.CircularLocation
intersection(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
intersection(Location) - Method in interface org.biojava.bio.symbol.Location
  Returns a Location that contains all points common to both ranges.
intersection(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the intersection of two locations.
intersection(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().
intersection(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Returns a Location that contains all points common to both ranges. ALWAYS RETURNS SELF
intersection(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned.
intValue() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
intValue() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
intValue() - Method in class org.biojavax.bio.seq.RichLocation.Strand
  Returns the numeric value of this strand.
iNumberOfColours - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  The number of unique colours.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidEnd(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
  The `end' field of the GFF entry was not a valid value.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
invalidEnd(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidFrame(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
  The `frame' field of the GFF entry was not a valid value.
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
invalidFrame(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidScore(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
  The `score' field of the GFF entry was not a valid value.
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
invalidScore(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidStart(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
  The `start' field of the GFF entry was not a valid value.
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
invalidStart(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
invalidStrand(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
  The `strand' field of the GFF entry was not a valid value.
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFWriter
InvalidTermException - Exception in org.biojava.ontology
  Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
InvalidTermException() - Constructor for exception org.biojava.ontology.InvalidTermException
InvalidTermException(String) - Constructor for exception org.biojava.ontology.InvalidTermException
InvalidTermException(Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
InvalidTermException(String, Throwable) - Constructor for exception org.biojava.ontology.InvalidTermException
inverse() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix inverse or pseudoinverse
INVERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the invertebrate mitochondrial genetic code.
IOExceptionFound - Variable in class org.biojava.bio.seq.db.GenbankSequenceDB
IS_A - Static variable in class org.biojava.ontology.OntoTools
isActive() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `isActive` returns true if both the `Sequence`s to be rendered and the `PairwiseHomologyRenderer` are not null.
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanel
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
isActive() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
isActive() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `isActive` returns true if both the `Sequence` to be rendered and the `SequenceRenderer` are not null.
isbn - Variable in class org.biojava.bibliography.BiblioBook
  ISBN number.
isBoundaryEnd(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
isBoundaryStart(Object) - Method in interface org.biojava.bio.program.tagvalue.BoundaryFinder
isCaseSensitive() - Method in interface org.biojava.utils.candy.CandyVocabulary
  It returns `true` if the vocabulary entries should be considered as case-sensitive.
isColoured(String, String) - Method in interface org.biojava.bio.program.blast2html.ColourCommand
  Returns true if the alignment pair should be coloured else false.
isComponentResolvable() - Method in interface org.biojava.bio.seq.ComponentFeature
  Determine if the sequence references by this ComponentFeature is available in this context.
isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
  test if two amino acids are connected, i.e.
isConsortium() - Method in interface org.biojavax.DocRefAuthor
  Is this author actually a consortium?
isConsortium() - Method in class org.biojavax.SimpleDocRefAuthor
  Is this author actually a consortium?
isContiguous() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
isContiguous() - Method in class org.biojava.bio.symbol.AbstractRangeLocation
isContiguous() - Method in class org.biojava.bio.symbol.CircularLocation
  Delegates to the wrapped location.
isContiguous() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
isContiguous() - Method in interface org.biojava.bio.symbol.Location
  Determine if a Location is contiguous.
isContiguous() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Determine if a Location is contiguous. ALWAYS RETURNS FALSE
isContiguous() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Determine if a Location is contiguous. ALWAYS RETURNS TRUE
isContiguous() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Determine if a Location is contiguous.
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
isDisjoint(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
isDisjoint(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter
  Returns true if this filter is disjoint from filt - that is, there is no Feature that is accepted by both filters.
isDoAngleCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
isDoDensityCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
isDoDistanceCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
isDoRMSCheck() - Method in class org.biojava.bio.structure.align.StrucAligParameters
isEditor() - Method in interface org.biojavax.DocRefAuthor
  Is this author actually an editor?
isEditor() - Method in class org.biojavax.SimpleDocRefAuthor
  Is this author actually an editor?
isEmpty() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
isEmpty() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
isEmpty() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
isEmpty() - Method in class org.biojavax.ga.util.WeightedSet
isEndoProtease() - Method in class org.biojava.bio.proteomics.Protease
isFullRank() - Method in class org.biojava.bio.structure.jama.QRDecomposition
  Is the matrix full rank?
isHaploid() - Method in class org.biojavax.ga.impl.AbstractOrganism
isHaploid() - Method in class org.biojavax.ga.impl.SimpleOrganism
  Simple Organisms are Halpoid
isHaploid() - Method in interface org.biojavax.ga.Organism
  Is the organism Haploid?
isJoinPlo() - Method in class org.biojava.bio.structure.align.StrucAligParameters
isMasked(BasisSymbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  Determines if a `Symbol` is masked.
isMasked(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
  Default Behaivour is that if the whole token is lower case it is masked.
isMasked(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
isMatchingType(ChangeType) - Method in class org.biojava.utils.ChangeType
  Return `true` iff `ct` is equal to this type or any of it's supertypes (including ChangeType.UNKNOWN).
isMaxFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
isMinFuzzy() - Method in class org.biojava.bio.symbol.FuzzyLocation
isMultiSource(Collection) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Returns false if all the locations in the set are from the same strand of the same sequence.
isMyChangeEvent(ChangeEvent, IndexedChangeHub.ListenerMemento) - Method in class org.biojava.utils.IndexedChangeHub
isNewTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
isNmr() - Method in interface org.biojava.bio.structure.Structure
  test if this structure is an nmr structure.
isNmr() - Method in class org.biojava.bio.structure.StructureImpl
  is this structure an nmr structure ?
isNonsingular() - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Is the matrix nonsingular?
IsoelectricPointCalc - Class in org.biojava.bio.proteomics
  class that computes isoelectric point for proteins
IsoelectricPointCalc() - Constructor for class org.biojava.bio.proteomics.IsoelectricPointCalc
IsoelectricPointCalc.ChargeCalculator - Class in org.biojava.bio.proteomics
isOppositeStrand() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
isOrganismsDiffer() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Getter for property organismsDiffer.
isPalindromic() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
  `isPalindromic` returns true if the recognition site is palindromic.
isParseable(Comment) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Returns true if the comment may be parseable (starts with -!-).
isParseable(String) - Static method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Returns true if the comment may be parseable (starts with -!-).
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
isProperSubset(FeatureFilter) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
isProperSubset(FeatureFilter) - Method in interface org.biojava.bio.seq.OptimizableFilter
  Returns true if this filter is a proper subset of sup - that is, for every feature that matches this, it also matches sup.
isReady() - Method in interface org.biojava.bibliography.BibRefQuery
  It checks if the repository is available.
isReady() - Method in interface org.biojava.bibliography.BibRefSupport
  It checks if a utility object is available.
isReady() - Method in interface org.biojava.utils.candy.CandyFinder
  It checks if a vocabulary finder object is available.
isRemote() - Method in class org.biojava.bio.seq.RemoteFeature.Region
  Return whether this Region is remote or local.
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
isRequired(String) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
isRequired(String) - Method in interface org.biojava.bio.symbol.CodonPrefFilter
  indicates if the current CodonPref is to be accepted
isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
isSane() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
isScaleByInformation() - Method in class org.biojava.bio.gui.DistributionLogo
issn - Variable in class org.biojava.bibliography.BiblioJournal
  A standard number for journals.
isSPD() - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
  Is the matrix symmetric and positive definite?
isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Determine if this writer is in strict mode.
isStrict() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Determine if this writer is in strict mode.
isSubTypeOf(FeatureTypes.Type, FeatureTypes.Type) - Static method in class org.biojava.bio.seq.FeatureTypes
  Work out if one type is a sub-type of another.
issue - Variable in class org.biojava.bibliography.BiblioJournalArticle
  The issue of the journal.
issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle
  Suplement.
isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon
  used in getNameHierarchy() to determine whether this taxonomy level is displayed
isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific; ...; least specific.
isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Determine is this node is terminal (has no children).
isTerminal() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
  Determine is this node is terminal (has no children).
isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria
  Decide if the training has completed.
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
isUnchanging(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
isUnchanging(ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
isUnchanging(ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
isUnchanging(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
isUnchanging(ChangeType) - Method in interface org.biojava.utils.Changeable
  A particular ChangeType can never be raised by this Changeable.
isUnchanging(ChangeType) - Method in class org.biojava.utils.ChangeSupport
isUnchanging(ChangeType) - Method in class org.biojava.utils.Unchangeable
isUnchanging(ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

  A particular ChangeType can never be raised by this Changeable. ALWAYS RETURNS TRUE

isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
isUnchanging(ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel
items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
items() - Method in class org.biojava.stats.svm.SimpleSVMTarget
items() - Method in interface org.biojava.stats.svm.SVMClassifierModel
items() - Method in interface org.biojava.stats.svm.SVMTarget
itemTargets() - Method in class org.biojava.stats.svm.SimpleSVMTarget
itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget
ItemValue - Interface in org.biojava.stats.svm
  A simple Object-double tuple.
iterator() - Method in interface org.biojava.bio.annodb.AnnotationDB
  Loop over each Annotation in this db.
iterator() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
iterator() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
iterator() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
iterator() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
iterator() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
iterator() - Method in class org.biojava.bio.dp.SimpleStatePath
iterator() - Method in class org.biojava.bio.program.das.DASSequence
iterator() - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
iterator() - Method in interface org.biojava.bio.program.homologene.OrthologueSet
  Return an iterator to the contents of the set.
iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
iterator() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  returns an iterator to the members of this set
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
iterator() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
iterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
iterator() - Method in class org.biojava.bio.seq.impl.DummySequence
iterator() - Method in class org.biojava.bio.seq.impl.SimpleSequence
iterator() - Method in class org.biojava.bio.seq.impl.SubSequence
iterator() - Method in class org.biojava.bio.seq.impl.ViewSequence
iterator() - Method in class org.biojava.bio.seq.NewSimpleAssembly
iterator() - Method in class org.biojava.bio.seq.SimpleAssembly
iterator() - Method in interface org.biojava.bio.structure.Group
  get an Atom Iterator.
iterator() - Method in class org.biojava.bio.structure.HetatomImpl
  return an AtomIterator.
iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList
iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
  Retrieve an Iterator over the AtomicSymbols in this FiniteAlphabet.
iterator() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
iterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
iterator() - Method in class org.biojava.bio.symbol.SimpleAlphabet
iterator() - Method in class org.biojava.bio.symbol.SingletonAlphabet
iterator() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
iterator() - Method in interface org.biojava.bio.symbol.SymbolList
  An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojava.utils.FileAsList
iterator() - Method in class org.biojava.utils.MergingSet
iterator() - Method in class org.biojava.utils.SmallSet
iterator(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  An Iterator over all Symbols in this SymbolList.

  This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

iterator(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  An Iterator over all Symbols in this SymbolList. ALWAYS RETURNS AN ITERATOR OVER A SINGLE AMBIGUITY SYMBOL
iterator(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojavax.bio.seq.ThinRichSequence
  An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojavax.ga.util.WeightedSet
  Returns an unmodifiable iterator over the keys of the set.

## J

JDBCConnectionPool - Class in org.biojava.utils
  Really simple connection pool for JDBC databases.
JDBCConnectionPool(String, String, String) - Constructor for class org.biojava.utils.JDBCConnectionPool
JDBCConnectionPool(String) - Constructor for class org.biojava.utils.JDBCConnectionPool
JDBCPooledDataSource - Class in org.biojava.utils
  Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages.
JDBCPooledDataSource() - Constructor for class org.biojava.utils.JDBCPooledDataSource
JOIN_GENERIC - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
JOIN_ORACLE8 - Static variable in class org.biojava.bio.seq.db.biosql.DBHelper
  Deprecated.
joinCommands(Object[]) - Static method in class org.biojava.utils.process.ExternalProcess
  Joins a command list to a single command string.
jointDistOverAlignment(Alignment, boolean, double, int[]) - Static method in class org.biojava.bio.dist.DistributionTools
  Creates a joint distribution.
JointFragments - Class in org.biojava.bio.structure.align.helper
JointFragments() - Constructor for class org.biojava.bio.structure.align.helper.JointFragments
JOURNAL_ABBREV - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
JOURNAL_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
JOURNAL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
JOURNAL_TITLES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
jState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the J loop state
jumpTo(UkkonenSuffixTree.SuffixNode, CharSequence, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  Just like walkTo, but faster when used during tree construction, as it assumes that a mismatch can only occurs with the last character of the target string.

## K

k() - Static method in class org.biojava.bio.seq.NucleotideTools
k() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Lysine
kernel - Static variable in class org.biojava.stats.svm.SparseVector
KEY_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
KEY_QUERY_ID - Static variable in interface org.biojava.bio.search.BlastLikeSearchFilter
KeyedWeakReference - Class in org.biojava.utils.cache
  Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
KeyedWeakReference(Object, Object) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.utils.cache.KeyedWeakReference
keys() - Method in class org.biojava.bio.AbstractAnnotation
keys() - Method in interface org.biojava.bio.Annotation
  Get a set of key objects.
keys() - Method in class org.biojava.bio.MergeAnnotation
keys() - Method in class org.biojava.bio.OverlayAnnotation
  Return a `Set` containing all key objects visible in this annotation.
KEYS - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  `KEYS` is the key used to identify the secondary namespaces in the OBDA config.dat files.
keys() - Method in class org.biojavax.EmptyRichAnnotation
  Get a set of key objects.
keys() - Method in class org.biojavax.SimpleRichAnnotation
  Get a set of key objects.
keySet() - Method in class org.biojava.utils.OverlayMap
keySet() - Method in class org.biojava.utils.SmallMap
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
KEYWORD_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
keywords - Variable in class org.biojava.bibliography.BiblioSubject
  The keywords are usually (but not limited to) one word long.
KEYWORDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
KEYWORDS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
KEYWORDS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
KLDistance(Distribution, Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
  A method to calculate the Kullback-Liebler Distance (relative entropy).
KnuthMorrisPrattSearch - Class in org.biojava.bio.search
  An object to find exact subsequences within a sequence.
KnuthMorrisPrattSearch(SymbolList) - Constructor for class org.biojava.bio.search.KnuthMorrisPrattSearch
  Constructs a KMP matcher to find exact occurances of `pattern` in `text` using the Knuth-Morris-Pratt algorithm.

## L

l() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Leucine
L_ESCULENTUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
label - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
LABEL - Static variable in class org.biojava.bio.gui.sequence.AlignmentRenderer
LABEL - Static variable in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
LABEL_MAKER - Static variable in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
LabelledSequenceRenderer - Class in org.biojava.bio.gui.sequence
  Renderer which draws a track of sequence with a textual label.
LabelledSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Creates new LabelledSequenceRenderer with default width and depth;
LabelledSequenceRenderer(String, SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
LabelledSequenceRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Creates new LabelledSequenceRenderer with the specified width and depth.
labelOrder - Variable in class org.biojava.bio.alignment.FlexibleAlignment
LabelRenderer - Interface in org.biojava.bio.gui.sequence
  The interface for things that can render labels for a line of information about a sequence.
LabelRenderer.RenderNothing - Class in org.biojava.bio.gui.sequence
LabelRenderer.RenderNothing() - Constructor for class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
labelsAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
labelsAt(int) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
  Returns a list labels, of all seqs that cover that column
labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
labelsInRange(Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
labelsInRange(Location) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
  Returns list of all the labels that intersect that range
LANE - Static variable in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
language - Variable in class org.biojava.bibliography.BiblioDescription
  It defines a language used for `BiblioDescription.theAbstract` and `BiblioDescription.tableOfContents`.
language - Variable in class org.biojava.bibliography.BibRef
  It defines a language of the intellectual contents of the cited resource.
LANGUAGES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
LargeBuffer - Class in org.biojava.utils.io
  Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs.
LargeBuffer(FileChannel, FileChannel.MapMode, long, long) - Constructor for class org.biojava.utils.io.LargeBuffer
lastCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The previous column.
lastCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
lastModifiedDate - Variable in class org.biojava.bibliography.BiblioEntryStatus
  It defines when the citation record was added or last modified.
lastNonGap() - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Return the index of the last Symbol that is not a Gap character.
lastNonGap() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
lastPage - Variable in class org.biojava.bibliography.BiblioArticle
  Last page of the article.
lastRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The previous symbol.
layer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
LayeredRenderer - Class in org.biojava.bio.gui.sequence
  `LayeredRenderer` handles the lane offsets for `MultiLineRender`s.
LayeredRenderer() - Constructor for class org.biojava.bio.gui.sequence.LayeredRenderer
LAYOUT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
LazyFeatureHolder - Class in org.biojava.bio.seq
  Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
LazyFeatureHolder() - Constructor for class org.biojava.bio.seq.LazyFeatureHolder
  Construct a LazyFeatureHolder with the schema of its contained featureholder
LazyFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.LazyFeatureHolder
  Construct a LazyFeatureHolder with the specified schema
LazyFilteredAnnotationDB - Class in org.biojava.bio.annodb
  An implementation of AnnotationDB that lazily applies a filter.
LazyFilteredAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazyFilteredAnnotationDB
  Create a new DB by wrapping another with a schema.
LazyFilterFeatureHolder - Class in org.biojava.bio.seq.impl
  FeatureHolder which lazily applies a specified filter to another FeatureHolder.
LazyFilterFeatureHolder(FeatureHolder, FeatureFilter) - Constructor for class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
LazySearchedAnnotationDB - Class in org.biojava.bio.annodb
  An implementation of AnnotationDB that does a JIT search on another set.
LazySearchedAnnotationDB(String, AnnotationDB, AnnotationType) - Constructor for class org.biojava.bio.annodb.LazySearchedAnnotationDB
  Create a new DB from an old one by applying a schema.
le - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
leaf - Static variable in interface org.biojava.bio.seq.FeatureFilter
  A filter which accepts features with no children
leaf() - Static method in class org.biojava.bio.seq.FilterUtils
  Return a filter which matches features with zero children.
leftIndent(String, int) - Static method in class org.biojavax.utils.StringTools
  Takes an input string and appends spaces to the left.
leftMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
  leftMost and rightMost return labels.
leftPad(String, int) - Static method in class org.biojavax.utils.StringTools
  Pads a string to be a certain width by prepending spaces.
leftPad(String, char, int) - Static method in class org.biojavax.utils.StringTools
  Pads a string to be a certain width by prepending given symbols.
LEFTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
length() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
length() - Method in class org.biojava.bio.alignment.FlexibleAlignment
length() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The length of the sequence.
length() - Method in class org.biojava.bio.dp.onehead.SmallCursor
length() - Method in class org.biojava.bio.dp.SimpleStatePath
length() - Method in class org.biojava.bio.program.das.DASSequence
length() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
length() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
length() - Method in class org.biojava.bio.seq.impl.DummySequence
length() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
length() - Method in class org.biojava.bio.seq.impl.SimpleSequence
length() - Method in class org.biojava.bio.seq.impl.SubSequence
length() - Method in class org.biojava.bio.seq.impl.ViewSequence
length() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
length() - Method in class org.biojava.bio.seq.NewSimpleAssembly
length() - Method in class org.biojava.bio.seq.SimpleAssembly
length() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
length() - Method in class org.biojava.bio.symbol.DummySymbolList
length - Variable in class org.biojava.bio.symbol.Edit
length() - Method in class org.biojava.bio.symbol.PackedSymbolList
length() - Method in class org.biojava.bio.symbol.RelabeledAlignment
length() - Method in class org.biojava.bio.symbol.SimpleAlignment
length() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
length() - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Get the length of this SymbolList.
length() - Method in interface org.biojava.bio.symbol.SymbolList
  The number of symbols in this SymbolList.
length() - Method in class org.biojava.utils.io.RandomAccessReader
  `length` returns the length of the underlying `RandomAccessFile`.
length() - Method in class org.biojava.utils.RepeatedCharSequence
length() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  The number of symbols in this SymbolList. ALWAYS RETURNS `Integer.MAX_VALUE`
length() - Method in class org.biojavax.bio.seq.SimpleRichSequence
  The number of symbols in this SymbolList.
length() - Method in class org.biojavax.bio.seq.ThinRichSequence
  The number of symbols in this SymbolList.
LENGTH_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
lesser(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
leu() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Leucine (L)
LIBRARY_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
  Annotation schema for all Unigene libraries.
LifeScienceIdentifier - Class in org.biojava.utils.lsid
  Life Science Identifier (LSID).
LifeScienceIdentifierParseException - Exception in org.biojava.utils.lsid
  Exception thrown in the event of an error in parsing a LSID-formatted string.
LifeScienceIdentifierParseException() - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException
  Construct a new parse exception with no message.
LifeScienceIdentifierParseException(String) - Constructor for exception org.biojava.utils.lsid.LifeScienceIdentifierParseException
  Construct a new parse exception with the specified error message.
Ligand - Class in org.biojava.bio.program.formats
Ligand.Compound - Class in org.biojava.bio.program.formats
Ligand.Compound() - Constructor for class org.biojava.bio.program.formats.Ligand.Compound
Ligand.Enzyme - Class in org.biojava.bio.program.formats
Ligand.Enzyme() - Constructor for class org.biojava.bio.program.formats.Ligand.Enzyme
Ligand.Reaction - Class in org.biojava.bio.program.formats
Ligand.Reaction() - Constructor for class org.biojava.bio.program.formats.Ligand.Reaction
LightPairDPCursor - Class in org.biojava.bio.dp.twohead
  A LIGHT implementation of PairDPCursor.
LightPairDPCursor(SymbolList, SymbolList, int, int, int, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.LightPairDPCursor
  Constructor for the LightPairDPCursor object
line - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `line` is the line to be drawn for each feature.
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LINEAGE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LinearKernel - Class in org.biojava.stats.svm
  Deprecated. Just use SparseVector.kernel instead...
LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel
  Deprecated.
LineInfo - Class in org.biojava.bio.gui.sequence
  Encapsulates the rendering info for a single line of the display.
LineInfo() - Constructor for class org.biojava.bio.gui.sequence.LineInfo
lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Loop over all lines in the set.
LineSplitParser - Class in org.biojava.bio.program.tagvalue
  A parser that splits a line into tag/value at a given column number.
LineSplitParser() - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
LineSplitParser(LineSplitParser) - Constructor for class org.biojava.bio.program.tagvalue.LineSplitParser
lineWidth - Variable in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. The line width for output.
list(Name) - Method in class org.biojava.naming.ObdaContext
list(String) - Method in class org.biojava.naming.ObdaContext
listBindings(Name) - Method in class org.biojava.naming.ObdaContext
listBindings(String) - Method in class org.biojava.naming.ObdaContext
listener - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
listIntersection(List, List) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
ListSumKernel - Class in org.biojava.stats.svm
  This kernel computes the sum of the dot products between items of two lists at corresponding indexes.
ListSumKernel() - Constructor for class org.biojava.stats.svm.ListSumKernel
ListTools - Class in org.biojava.utils
ListTools() - Constructor for class org.biojava.utils.ListTools
ListTools.Doublet - Class in org.biojava.utils
ListTools.Doublet() - Constructor for class org.biojava.utils.ListTools.Doublet
ListTools.Doublet(Object, Object) - Constructor for class org.biojava.utils.ListTools.Doublet
ListTools.Mapper - Interface in org.biojava.utils
  Maps one object to another.
ListTools.SeriesList - Class in org.biojava.utils
  A list that represents a series of values.
ListTools.Triplet - Class in org.biojava.utils
ListTools.Triplet() - Constructor for class org.biojava.utils.ListTools.Triplet
ListTools.Triplet(Object, Object, Object) - Constructor for class org.biojava.utils.ListTools.Triplet
load(File) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
load(InputStream) - Method in class org.biojava.bio.program.abi.ABIFChromatogram
load(File) - Method in class org.biojava.bio.program.scf.SCF
load(InputStream, long) - Method in class org.biojava.bio.program.scf.SCF
load(String) - Method in class org.biojava.utils.TypedProperties
  Reads a property list (key and element pairs) from the file with the given file name.
load(Class, String) - Method in class org.biojava.utils.TypedProperties
  Reads a property list (key and element pairs) from the given file which is interpreted as a resource of the given class.
loadAlphabets(InputSource) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Load additional Alphabets, defined in XML format, into the AlphabetManager's registry.
loadEnzymeFile(InputStream, boolean) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `loadEnzymeFile` loads a new REBASE file (or any file using REBASE format #31).
loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
loadUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
loadUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
loadUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Load a UnigeneDB instance referred to by a URL.
loc - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
LOC_ELEMENT_ACC_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOC_ELEMENT_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOC_ELEMENT_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOC_ELEMENT_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOC_FUZZY_END_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
LOC_FUZZY_START_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
LOCATION - Static variable in interface org.biojava.bio.alignment.EditableAlignment
LOCATION - Static variable in interface org.biojava.bio.seq.Feature
  The location of this feature is being altered.
location - Variable in class org.biojava.bio.seq.Feature.Template
Location - Interface in org.biojava.bio.symbol
  A set of integers, often used to represent positions on biological sequences.
LOCATION - Static variable in interface org.biojavax.bio.seq.RichFeature
LOCATION_BEGIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_COMPL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOCATION_ELEMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOCATION_END_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_POSITION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_SEQ_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
LOCATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LocationHandlerBase - Class in org.biojava.bio.program.xff
  Handler to the XFF location type.
LocationHandlerBase() - Constructor for class org.biojava.bio.program.xff.LocationHandlerBase
locationToGapped(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Translate a Location onto the gapped view, splitting blocks if necessary
LocationTools - Class in org.biojava.bio.symbol
  Tools class containing a number of operators for working with `Location` objects.
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
LOCATOR_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
locInAlignment(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
  The location of an individual SymbolList relative to overall Alignment
locInAlignment(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  The location of an individual SymbolList relative to overall Alignment
locInAlignment(Object) - Method in interface org.biojava.bio.alignment.UnequalLengthAlignment
  The location of an individual SymbolList relative to overall Alignment
locInSeq(Object, Location) - Method in class org.biojava.bio.alignment.FlexibleAlignment
lock() - Method in class org.biojava.utils.automata.PatternBlitz
lockModel() - Method in class org.biojava.bio.dp.DP
LOCUS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
LOCUS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
LOCUSID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
log2(double) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
log2(double) - Static method in class org.biojava.bio.program.hmmer.ProfileEmissionState
LOG_TO_OUT - Static variable in interface org.biojava.utils.ChangeListener
  Convenience implementation that echoes all events to out.
logger - Static variable in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
logger - Static variable in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
LogoContext - Interface in org.biojava.bio.gui
LogoPainter - Interface in org.biojava.bio.gui
  The interface for something that will draw the sequence logo for a state.
logProb(Symbol) - Method in class org.biojava.bio.program.hmmer.ProfileEmissionState
LongElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string representation of a long.
LongElementHandlerBase() - Constructor for class org.biojava.utils.stax.LongElementHandlerBase
lookingAt() - Method in class org.biojava.utils.regex.Matcher
  Attempts to match the input SymbolList, starting at the beginning, against the pattern.
lookup(String) - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Looks up an `Option` instance based on its string description.
lookup(Name) - Method in class org.biojava.naming.ObdaContext
lookup(String) - Method in class org.biojava.naming.ObdaContext
lookupLink(Name) - Method in class org.biojava.naming.ObdaContext
lookupLink(String) - Method in class org.biojava.naming.ObdaContext
lp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
lp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
lp - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
lpPre87 - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
LSID_EMBL_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_EMBL_AA` sequence format LSID for EMBL AA.
LSID_EMBL_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_EMBL_DNA` sequence format LSID for EMBL DNA.
LSID_EMBL_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_EMBL_RNA` sequence format LSID for EMBL RNA.
LSID_FASTA_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_FASTA_AA` sequence format LSID for Fasta AA.
LSID_FASTA_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_FASTA_DNA` sequence format LSID for Fasta DNA.
LSID_FASTA_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_FASTA_RNA` sequence format LSID for Fasta RNA.
LSID_GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_GENBANK_AA` sequence format LSID for Genbank AA.
LSID_GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_GENBANK_DNA` sequence format LSID for Genbank DNA.
LSID_GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_GENBANK_RNA` sequence format LSID for Genbank RNA.
LSID_SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `LSID_SWISSPROT` sequence format LSID for Swissprot.
lu() - Method in class org.biojava.bio.structure.jama.Matrix
  LU Decomposition
LUDecomposition - Class in org.biojava.bio.structure.jama
  LU Decomposition.
LUDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.LUDecomposition
  LU Decomposition provides a data structure to access L, U and piv.
lys() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Lysine (K)
LYS_C - Static variable in class org.biojava.bio.proteomics.Protease
LYS_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager

## M

m() - Static method in class org.biojava.bio.seq.NucleotideTools
m() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Methionine
M_MUSCULUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
M_TRUNCULATA - Static variable in interface org.biojava.bio.program.homologene.Taxon
MAGICAL_STATE - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
MagicalState - Class in org.biojava.bio.dp
  Start/end state for HMMs.
magicalState() - Method in interface org.biojava.bio.dp.MarkovModel
  The MagicalState for this model.
magicalState() - Method in class org.biojava.bio.dp.SimpleMarkovModel
magicalState() - Method in class org.biojava.bio.dp.WMAsMM
main(String[]) - Static method in class org.biojava.bio.search.KnuthMorrisPrattSearch
  Demo and Test method
main(String[]) - Static method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  Test this class
main(String[]) - Static method in class org.biojava.bio.seq.io.MSFAlignmentFormat
  used to quick test the code
main(String[]) - Static method in class org.biojava.bio.structure.align.StructurePairAligner
  example usage of this class
main(String[]) - Static method in class org.biojava.stats.svm.tools.ClassifierExample
  Entry point for the application.
main(String[]) - Static method in class org.biojava.stats.svm.tools.Classify
main(String[]) - Static method in class org.biojava.stats.svm.tools.Train
main(String[]) - Static method in class org.biojava.stats.svm.tools.TrainRegression
main(String[]) - Static method in class org.biojava.utils.ExecRunner
  This is for unit testing of the class.
main(String[]) - Static method in class org.biojava.utils.io.UncompressInputStream
main(String[]) - Static method in class org.biojava.utils.JDBCPooledDataSource
main(String[]) - Static method in class org.biojava.utils.process.ExternalProcess
  Runs an external program from the command line.
main(String[]) - Static method in class org.biojava.utils.xml.AppBeanRunner
make(DP) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactoryMaker
make(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
make(DP) - Method in class org.biojava.bio.dp.twohead.DPInterpreter.Maker
make(SymbolReader) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  Method to create a Sequence with a SymbolReader.
makeAnnotation(Map) - Static method in class org.biojava.bio.program.ssbind.AnnotationFactory
  `makeAnnotation` creates the annotation.
makeBatchRequest(URL, Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
  Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
makeBatchRequest(URL, Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
makeCircularLocation(int, int, int) - Static method in class org.biojava.bio.symbol.LocationTools
  A simple method to generate a RangeLocation wrapped in a CircularLocation.
makeConfigFile(File) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `makeConfigFile` returns a file which represents an OBDA "config.dat" in the specified index directory.
makeContext(SequenceRenderContext, RangeLocation) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
makeEmptyFeature() - Static method in class org.biojavax.bio.seq.RichFeature.Tools
  A way to make a dummy feature
makeFactory(FiniteAlphabet) - Static method in class org.biojava.utils.regex.PatternFactory
  Returns a factory for Patterns in the specified Alphabet.
makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
makeHandler(String, String) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
makeHandler(String, String, XMLFilterHandler) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandlerFactory
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
makeLabel(Feature) - Method in interface org.biojava.bio.gui.sequence.FeatureLabelRenderer.LabelMaker
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.SourceLabelMaker
makeLabel(Feature) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.TypeLabelMaker
makeLocation(int, int) - Static method in class org.biojava.bio.symbol.LocationTools
  Return a contiguous Location from min to max.
makeName(String, MarkovModel) - Static method in class org.biojava.bio.dp.twohead.DPCompiler
makeNewInsertState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
makeNewMatchState(String, Annotation, int[], Distribution) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
makePrimaryKeyFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `makePrimaryKeyFile` returns a file which represents an OBDA "key_<primary namespace>.key" primary key file on the specified index directory.
makeProjectionSet(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
  Called internally to construct a lightweight projected view of a set of features
makeQueryViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
makeReference(Object) - Method in interface org.biojava.utils.cache.Cache
  Construct a temporary reference to an object.
makeReference(Object) - Method in class org.biojava.utils.cache.FixedSizeCache
makeReference(Object) - Method in class org.biojava.utils.cache.SoftReferenceCache
makeRichSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder
  Build a RichSequence.
makeRichSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Build a RichSequence.
makeSearchResult() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
makeSearchResult() - Method in interface org.biojava.bio.search.SearchBuilder
  The `makeSearchResult` method returns a `SeqSimilaritySearchResult` instance created from accumulated data.
makeSecondaryFile(File, String) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `makeSecondaryFile` returns a file which represents an OBDA "id_<secondary namespace>.index" secondary key file on the specified.
makeSequence() - Method in interface org.biojava.bio.seq.io.SequenceBuilder
  Return the Sequence object which has been constructed by this builder.
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
makeSequence() - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
  create the sequence
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
makeSequence() - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
makeSequence() - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
makeSequence() - Method in interface org.biojavax.bio.seq.io.RichSequenceBuilder
  Return the Sequence object which has been constructed by this builder. Implementations of this for a RichSequenceBuilder should delegate to makeRichSequence() and return only RichSequence objects.
makeSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Return the Sequence object which has been constructed by this builder.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.EmblProcessor.Factory
  Deprecated.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
  Deprecated.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
  Deprecated.
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.GenbankProcessor.Factory
  Deprecated.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.OrganismParser.Factory
  Deprecated.
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
  Deprecated.
makeSequenceBuilder() - Method in interface org.biojava.bio.seq.io.SequenceBuilderFactory
makeSequenceBuilder() - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
  Deprecated.
makeSequenceBuilder(String) - Method in class org.biojava.bio.seq.io.SwissprotProcessor.Factory
  Deprecated.
makeSequenceBuilder() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
makeSubjectViewSequence(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
makeSymbolList() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  Converts accumulated Symbols to a SymbolList
makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.PackedSymbolListFactory
  Makes a packed SymbolList out of a list of Symbols.
makeSymbolList(Symbol[], int, Alphabet) - Method in class org.biojava.bio.symbol.SimpleSymbolListFactory
  Create a factory for SimpleSymbolLists.
makeSymbolList(Symbol[], int, Alphabet) - Method in interface org.biojava.bio.symbol.SymbolListFactory
  makes a SymbolList containing size Symbols from a Symbol array.
makeTemplate() - Method in interface org.biojava.bio.seq.Feature
  Create a new Template that could be used to generate a feature identical to this one.
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFeature
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
makeTemplate() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
makeTemplate(Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
makeTemplate() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
makeTemplate() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Create a new Template that could be used to generate a feature identical to this one.
MAN_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Homo sapiens codon preferences
mAnnotFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.
ManyToOneTranslationTable - Interface in org.biojava.bio.symbol
  A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.
map(Set) - Method in class org.biojava.bio.symbol.RelabeledAlignment
map(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
map(Object) - Method in interface org.biojava.utils.ListTools.Mapper
  Map the object.
mapList(List, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
mapLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
mapMap(Map, ListTools.Mapper, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
MappedDataStoreFactory - Class in org.biojava.bio.program.ssaha
  Builder for a data store that is backed by a java.nio.MappedByteBuffer.
MappedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.MappedDataStoreFactory
mapSet(Set, ListTools.Mapper) - Static method in class org.biojava.utils.ListTools
mark(int) - Method in class org.biojava.utils.io.CountedBufferedReader
MarkovModel - Interface in org.biojava.bio.dp
  A markov model.
markSupported() - Method in class org.biojava.utils.io.CountedBufferedReader
markSupported() - Method in class org.biojava.utils.io.UncompressInputStream
  This stream does not support mark/reset on the stream.
mask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
  Masks a token by making it lowercase
mask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
  Present the token for a `Symbol` as it would appear if masked
maskSequence(Sequence, RangeLocation) - Static method in class org.biojava.bio.seq.SequenceTools
  Mask of a sequence.
MASS_SPECTROMETRY - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
MassCalc - Class in org.biojava.bio.proteomics
  `MassCalc` calculates the mass of peptides which for our purposes are `SymbolList`s which contain `Symbol`sfrom the protein `Alphabet`.
MassCalc(String, boolean) - Constructor for class org.biojava.bio.proteomics.MassCalc
  Creates a new `MassCalc`.
matcher(SymbolList) - Method in interface org.biojava.bio.search.BioPattern
  Get a matcher that will use these parameters to search a SymbolList.
matcher(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
matcher(SymbolList) - Method in class org.biojava.bio.search.SeqContentPattern
Matcher - Class in org.biojava.utils.regex
  This class is analogous to java.util.Matcher except that it works on SymbolLists instead of Strings.
matcher(SymbolList) - Method in class org.biojava.utils.regex.Pattern
  Creates a matcher that will match the given input against this pattern.
matches() - Method in class org.biojava.utils.regex.Matcher
  Attempts to match the entire input sequence against the pattern.
matchingTypes() - Method in class org.biojava.utils.ChangeType
  Return an iterator which contains this type, and all supertypes.
mathExp(double) - Method in class org.biojava.bio.dp.BaumWelchTrainer
Maths - Class in org.biojava.bio.structure.jama
Maths() - Constructor for class org.biojava.bio.structure.jama.Maths
matrix - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
Matrix - Class in org.biojava.bio.structure.jama
  Jama = Java Matrix class.
Matrix(int, int) - Constructor for class org.biojava.bio.structure.jama.Matrix
  Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class org.biojava.bio.structure.jama.Matrix
  Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class org.biojava.bio.structure.jama.Matrix
  Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class org.biojava.bio.structure.jama.Matrix
  Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class org.biojava.bio.structure.jama.Matrix
  Construct a matrix from a one-dimensional packed array
MatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
MatrixPairDPCursor(SymbolList, SymbolList, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.MatrixPairDPCursor
max - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
max - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
MAX_ANGLE - Static variable in class org.biojava.bio.structure.AlphaCTools
  MAX_ANGLE .
MAX_CROSSES - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
maxIndex() - Method in class org.biojava.stats.svm.SparseVector
maxLength() - Method in class org.biojava.bio.symbol.SuffixTree
  Return the length of the longest motif represented in this SuffixTree
MaxMismatchMatcher - Class in org.biojava.bio.search
  A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.
MaxMismatchPattern - Class in org.biojava.bio.search
  This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches.
MaxMismatchPattern() - Constructor for class org.biojava.bio.search.MaxMismatchPattern
MaxMismatchPattern(SymbolList, int) - Constructor for class org.biojava.bio.search.MaxMismatchPattern
MEDLINE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
  Holds a reference to the key that must be used to store Medline references.
MEDLINE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
MEDLINE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
members - Variable in class org.biojavax.bio.seq.CompoundRichLocation
Meme - Class in org.biojava.bio.program
  The results of a meme run.
Meme(InputStream, SymbolTokenization) - Constructor for class org.biojava.bio.program.Meme
merge(Set, Set) - Static method in class org.biojava.utils.MergingSet
merge(Collection) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.
MergeAnnotation - Class in org.biojava.bio
  Merged view onto a list of underlying Annotation objects.
MergeAnnotation() - Constructor for class org.biojava.bio.MergeAnnotation
MergeAnnotation.PropertyForwarder - Class in org.biojava.bio
  Listener used to forward changes for any of the underlying annotations to listeners on this annotation.
MergeAnnotation.PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.MergeAnnotation.PropertyForwarder
  Create a new forwarder on behalf of a source using the change support.
MergeFeatureHolder - Class in org.biojava.bio.seq
  FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
MergeFeatureHolder() - Constructor for class org.biojava.bio.seq.MergeFeatureHolder
  Create a new, empty, MergeFeatureHolder.
MergeLocation - Class in org.biojava.bio.symbol
  Produced by LocationTools as a result of union operations.
mergeLocations(List) - Static method in class org.biojava.bio.symbol.MergeLocation
  Static Factory method for getting an instance of a `MergeLocation`
mergeLocations(Location, Location) - Static method in class org.biojava.bio.symbol.MergeLocation
MergingAnnotationDB - Class in org.biojava.bio.annodb
  An AnnotationDB that provides a merged view of a list of underlying DBs.
MergingAnnotationDB(String) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB
  Create a new MergingAnnotationDB with a name and no DBs to merge.
MergingAnnotationDB(String, List) - Constructor for class org.biojava.bio.annodb.MergingAnnotationDB
  Create a new MergingAnnotationDB with a name and a list of DBs to merge.
MergingIterator - Class in org.biojava.utils
MergingIterator(Iterator) - Constructor for class org.biojava.utils.MergingIterator
MergingSet - Class in org.biojava.utils
MergingSet() - Constructor for class org.biojava.utils.MergingSet
MergingSet(Set) - Constructor for class org.biojava.utils.MergingSet
met() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Methionine (M)
META_DATA_TYPE - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  AnnotationType that all meta-data files should fit.
mFilter - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  writes PCDATA replacing XML characters with escape entities
midInitials - Variable in class org.biojava.bibliography.BiblioPerson
  Any middle innitials.
min(double, double, double) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch
  This just computes the minimum of three double values.
min - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
min - Variable in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
MIN_ANGLE - Static variable in class org.biojava.bio.structure.AlphaCTools
  MIN_ANGLE .
mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  Base indent
mIndent - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  indent
minus(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  C = A - B
minusEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  A = A - B
mismatchCount() - Method in class org.biojava.bio.search.MaxMismatchMatcher
  Returns number of mismatches
MITOGENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
mListeners - Variable in class org.biojava.bio.seq.io.FastaFormat
  Deprecated.
model() - Method in interface org.biojava.bio.dp.DPMatrix
model - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
model() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
model() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
ModelInState - Interface in org.biojava.bio.dp
  A state that contains an entire sub-model.
ModelTrainer - Interface in org.biojava.bio.dp
  Encapsulates the training of an entire model.
modifiableMerge() - Static method in class org.biojava.utils.MergingSet
modifiableMerge(Set) - Static method in class org.biojava.utils.MergingSet
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthologueSet
MODIFY - Static variable in interface org.biojava.bio.program.homologene.OrthoPairSet
modifyAttributes(Name, int, Attributes) - Method in class org.biojava.naming.ObdaContext
modifyAttributes(Name, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
modifyAttributes(String, int, Attributes) - Method in class org.biojava.naming.ObdaContext
modifyAttributes(String, ModificationItem[]) - Method in class org.biojava.naming.ObdaContext
modulateCircularIndex(int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base.
modulateCircularLocation(int, int, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes a start and end position on a circular location of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
modulateCircularLocationPair(Location, Location, int) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
  Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
MOLD_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the mold mitochondrial genetic code.
MOLTYPE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
MONO_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
MotifTools - Class in org.biojava.bio.symbol
  `MotifTools` contains utility methods for sequence motifs.
MotifTools() - Constructor for class org.biojava.bio.symbol.MotifTools
MOUSE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Mus musculus codon preferences
mouseClicked(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
mouseDragged(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener
mouseMoved(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerMotionListener
mousePressed(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
mouseReleased(SequenceViewerEvent) - Method in interface org.biojava.bio.gui.sequence.SequenceViewerListener
mOut - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write to XML document
MSF - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `MSF` indicates that the alignment format is MSF.
MSF_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `MSF_AA` premade MSF | AA;
MSF_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `MSF_DNA` premade MSF | DNA;
MSF_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `MSF_DNA` premade MSF | RNA;
MSFAlignmentFormat - Class in org.biojava.bio.seq.io
MSFAlignmentFormat() - Constructor for class org.biojava.bio.seq.io.MSFAlignmentFormat
MultiLineRenderer - Class in org.biojava.bio.gui.sequence
  `MultiLineRenderer` is a `SequenceRenderer` which collects a number of other `SequenceRenderer`s each of which render their own view of a `Sequence`.
MultiLineRenderer() - Constructor for class org.biojava.bio.gui.sequence.MultiLineRenderer
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
MULTIPLE - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
MultiSourceCompoundRichLocation - Class in org.biojavax.bio.seq
  An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
MultiSourceCompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Constructs a MultiSourceCompoundRichLocation from the given set of members, with the default term of "join".
MultiSourceCompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Constructs a MultiSourceCompoundRichLocation from the given set of members.
MultiTagger - Class in org.biojava.bio.program.tagvalue
  Partician multiple values for a tag into their own tag groups.
MultiTagger(TagValueListener, BoundaryFinder) - Constructor for class org.biojava.bio.program.tagvalue.MultiTagger
mutate(Structure, String, String, String) - Method in class org.biojava.bio.structure.Mutator
  creates a new structure which is identical with the original one.
mutate(SymbolList) - Method in interface org.biojavax.ga.functions.MutationFunction
  Produces a new SymbolList by mutation.
mutate(SymbolList) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
mutate(SymbolList) - Method in class org.biojavax.ga.functions.SimpleMutationFunction
mutateResidue(AminoAcid, String) - Method in class org.biojava.bio.structure.Mutator
  create a new residue which is of the new type.
MUTATION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
MUTATION_PROBS - Static variable in interface org.biojavax.ga.functions.MutationFunction
MUTATION_SPECTRUM - Static variable in interface org.biojavax.ga.functions.MutationFunction
MutationFunction - Interface in org.biojavax.ga.functions
  A class that mutates a `SymbolList`
MutationFunction.NoMutation - Class in org.biojavax.ga.functions
  Place Holder class that doesn't mutate its SymbolLists
MutationFunction.NoMutation() - Constructor for class org.biojavax.ga.functions.MutationFunction.NoMutation
Mutator - Class in org.biojava.bio.structure
  A class that can change one amino acid to another.
Mutator() - Constructor for class org.biojava.bio.structure.Mutator
mutuallyExclusiveWith - Variable in class org.biojava.bibliography.BiblioCriterion
  A list of other criteria names that this criterion is mutually exclusive with.
mWriteDocType - Variable in class org.biojava.bio.seq.io.agave.AgaveWriter
  write DOCTYPE if true
myLocalName - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
MySQLDBHelper - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
MySQLDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.MySQLDBHelper
  Deprecated.

## N

n() - Static method in class org.biojava.bio.seq.DNATools
n() - Static method in class org.biojava.bio.seq.NucleotideTools
n() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Asparagine
n() - Static method in class org.biojava.bio.seq.RNATools
name - Variable in class org.biojava.bibliography.BiblioCriterion
  Each Criterion is identified by its name.
name - Variable in class org.biojava.bibliography.BiblioJournal
  A journal title.
name - Variable in class org.biojava.bibliography.BiblioOrganisation
  The name of the organisation.
name - Variable in class org.biojava.bibliography.BiblioService
  The name of a bibliographic service.
name - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
name - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
name - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
NAME - Static variable in interface org.biojavax.bio.seq.RichFeature
NAME - Static variable in interface org.biojavax.ga.Organism
NAME - Static variable in interface org.biojavax.ga.Population
NAME - Static variable in interface org.biojavax.Namespace
NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
names() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Returns the set of unique table names.
names() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
  Returns the set of unique table names.
NAMES - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
names - Variable in class org.biojavax.bio.taxa.SimpleNCBITaxon
NAMESET_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
NameSetStringValue(String) - Method in interface org.biojava.bio.seq.io.game.GAMENameCallbackItf
  Callback implemented by nesting class to allow nested class to pass string to nesting class for handling.
NameSetStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
NAMESPACE - Static variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
Namespace - Interface in org.biojavax
  The namespace of an entry in a database schema.
NameTokenization - Class in org.biojava.bio.seq.io
  Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
NameTokenization(FiniteAlphabet, boolean) - Constructor for class org.biojava.bio.seq.io.NameTokenization
NameTokenization(FiniteAlphabet) - Constructor for class org.biojava.bio.seq.io.NameTokenization
  Construct a new NameTokenization, defaulting to case-insensitive.
NATURAL_ORDER - Static variable in interface org.biojava.bio.program.gff.GFFRecord
  Comparator which defines a useful sort order for GFF records.
naturalOrder - Static variable in interface org.biojava.bio.symbol.Location
  Comparator which orders Locations naturally.
Navg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Nitrogen average mass
NBRF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `NBRF` indicates that the sequence format is NBRF.
NCBI_TAXON_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
NcbiDatabaseURLGenerator - Class in org.biojava.bio.program.blast2html
  Simple URL generator for Entrez at the NCBI.
NcbiDatabaseURLGenerator() - Constructor for class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
NCBIids(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Returns a `Set` of all NCBI-Taxon-IDs which are currently stored in the database.
NCBISequenceDB - Class in org.biojava.bio.seq.db
NCBISequenceDB() - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
  Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.
NCBISequenceDB(String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
  Parameterized constructor
NCBISequenceDB(String, String, String, SequenceFormat) - Constructor for class org.biojava.bio.seq.db.NCBISequenceDB
  Parameterized constructor
NCBITaxon - Interface in org.biojavax.bio.taxa
  Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.
NCBITaxonomyLoader - Interface in org.biojavax.bio.taxa.io
  Implementors are able to load taxonomy files and generate sets of NCBITaxon objects that represent them.
NeedlemanWunsch - Class in org.biojava.bio.alignment
  Needleman and Wunsch definied the problem of global sequence alignments, from the first till the last symbol of a sequence.
NeedlemanWunsch(double, double, double, double, double, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.NeedlemanWunsch
  Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
  Flag to indicate that a feature is on the negative strand.
NEGATIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
  The negative strand is represented by the symbol '-' and has the number -1.
NestedKernel - Class in org.biojava.stats.svm
  Encapsulates a kernel that wraps another kernel up.
NestedKernel() - Constructor for class org.biojava.stats.svm.NestedKernel
  Create a new NestedKernel.
NestedKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NestedKernel
  Create a new NestedKernel that wraps k.
NewAssembledSymbolList - Class in org.biojava.bio.seq.impl
  Support class for applications which need to patch together sections of sequence into a single SymbolList.
NewAssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.NewAssembledSymbolList
newInstance(Constructor, Object[]) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.Instantiator
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
newInstance(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
newInstance(Location) - Method in interface org.biojava.bio.symbol.Location
  Create a new instance of Location with all of the same decorators as this instance but with the data stored in `loc`.
newInstance(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Create a new instance of Location with all of the same decorators as this instance but with the data stored in `loc`.

  The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates `loc`. ALWAYS RETURNS SELF

newInstance(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Create a new instance of Location with all of the same decorators as this instance but with the data stored in `loc`. ALWAYS RETURNS PASSED LOCATION
newInstance(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Create a new instance of Location with all of the same decorators as this instance but with the data stored in `loc`.
NewSimpleAssembly - Class in org.biojava.bio.seq
  A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
NewSimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly
  Construct a new SimpleAssembly using the DNA alphabet.
NewSimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.NewSimpleAssembly
  Construct a new NewSimpleAssembly using the DNA alphabet.
next() - Method in class org.biojava.bio.dp.DP.ReverseIterator
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.BackMatrixPairDPCursor
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Method
next(Cell[][]) - Method in class org.biojava.bio.dp.twohead.MatrixPairDPCursor
next(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
  retrieve the next block of cells
next() - Method in class org.biojava.bio.structure.AtomIterator
  return next atom.
next() - Method in class org.biojava.bio.structure.GroupIterator
  get next Group.
next() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
next() - Method in class org.biojava.utils.MergingIterator
nextBioEntry() - Method in interface org.biojavax.bio.BioEntryIterator
nextBioEntry() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextBioEntry() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthologueSet.Iterator
nextOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator
nextOrthoPair() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet.Iterator
nextOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator
nextRequest() - Method in class org.biojava.utils.SimpleThreadPool
  `nextRequest` gets the next `Runnable` from the queue.
nextRichSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader
nextRichSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
nextRichSequence() - Method in interface org.biojavax.bio.seq.RichSequenceIterator
nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader
  Pull the next sequence out of the stream.
nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator
  Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojavax.bio.seq.io.RichStreamReader
  Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
  Returns the next sequence in the iterator.
nextSet() - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
  returns the next OrthoPairSet
nextSet() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator
nextTable() - Method in class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
  Returns the next `SymbolPropertyTable` object.
nextTable() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableIterator
  Returns the next `SymbolPropertyTable` object.
nextWord(SymbolList, int, int, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
Nfa - Class in org.biojava.utils.automata
  Class for modelling non-deterministic finite automata.
Nfa(String, FiniteAlphabet) - Constructor for class org.biojava.utils.automata.Nfa
NfaBuilder - Interface in org.biojava.utils.automata
NfaSubModel - Class in org.biojava.utils.automata
  This class caches a reference to all objects that it directs its delegate to make.
NIODataStoreFactory - Class in org.biojava.bio.program.ssaha
  Builder for a datastore that has no practical file size limit.
NIODataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.NIODataStoreFactory
nl() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
Nmono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Nitrogen monoisotopic mass
NO_CROSS - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
NO_FRAME - Static variable in interface org.biojava.bio.program.gff.GFFRecord
  Deprecated. Use GFFTools.NO_FRAME instead
NO_FRAME - Static variable in class org.biojava.bio.program.gff.GFFTools
  Flag to indicate that there is no frame info.
NO_MUTATION - Static variable in interface org.biojavax.ga.functions.MutationFunction
NO_SCORE - Static variable in interface org.biojava.bio.program.gff.GFFRecord
  Deprecated. Use GFFTools.NO_SCORE instead
NO_SCORE - Static variable in class org.biojava.bio.program.gff.GFFTools
  Flag to indicate that there is no score info.
NODERANK - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
nodes - Variable in class org.biojava.utils.automata.FiniteAutomaton
NONE - Static variable in interface org.biojava.bio.AnnotationType
  The type that accepts no annotations at all and is the subtype of all other annotations.
NONE - Static variable in class org.biojava.bio.CardinalityConstraint
  This cardinality contains no intengers, not even zero.
NONE - Static variable in interface org.biojava.bio.CollectionConstraint
  `NONE` is a constraint which accepts no value for a property under any condition.
NONE - Static variable in interface org.biojava.bio.PropertyConstraint
  `NONE` is a constraint which accepts no value for a property under any condition.
none - Static variable in interface org.biojava.bio.seq.FeatureFilter
  No features are selected by this filter.
none() - Static method in class org.biojava.bio.seq.FilterUtils
  Return a filter which matches no features.
NONE - Static variable in class org.biojava.ontology.OntoTools
none - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
  No features are selected by this filter.
nonRemoveIterator(Iterator) - Static method in class org.biojava.utils.ListTools
norm1() - Method in class org.biojava.bio.structure.jama.Matrix
  One norm
norm2() - Method in class org.biojava.bio.structure.jama.Matrix
  Two norm
norm2() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Two norm
normalizeMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  With this method you can get a "normalized" `SubstitutionMatrix` object; however, since this implementation uses an int matrix, the normalized matrix will be scaled by ten.
NormalizingKernel - Class in org.biojava.stats.svm
  Performs a normalization on the results of a nested kernel.
NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel
NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel
normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector
normF() - Method in class org.biojava.bio.structure.jama.Matrix
  Frobenius norm
normInf() - Method in class org.biojava.bio.structure.jama.Matrix
  Infinity norm
not(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
  Operator: FeatureHolder 1 NOT FeatureHolder2
not(FeatureFilter.Not, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
not(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a new filter which is the negation of `filter`.
not - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
NOTE - Static variable in interface org.biojavax.bio.seq.RichLocation
Note - Interface in org.biojavax
  Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
NOTE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
notifyExit() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.ExitNotification
notifyHit(String, int, int, boolean) - Method in interface org.biojava.utils.automata.PatternListener
notifyOnExit - Variable in class org.biojava.bio.program.tagvalue.StateMachine.Transition
  should the State listener be notified that this transition is leaving the state.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.program.phred.PhredFormat
  Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
notifyParseErrorEvent(ParseErrorEvent) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
nrModels() - Method in interface org.biojava.bio.structure.Structure
  return number of models .
nrModels() - Method in class org.biojava.bio.structure.StructureImpl
  return number of models.
nState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
  Gets the n loop state
NucleotideImpl - Class in org.biojava.bio.structure
  A nucleotide group is almost the same as a Hetatm group.
NucleotideImpl() - Constructor for class org.biojava.bio.structure.NucleotideImpl
nucleotideToken(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
  Get a single-character token for a Nucleotide symbol
NucleotideTools - Class in org.biojava.bio.seq
  Useful functionality for processing nucleotide sequences.
NULL_MAPPER - Static variable in class org.biojava.utils.ListTools
NULL_MODEL - Static variable in interface org.biojava.bio.dist.Distribution
  Whenever the null model distribution changes the values that would be returned by getWeight, either by being edited or by being replaced, a ChangeEvent with this object as the type should be thrown.
NULL_MODEL - Static variable in interface org.biojava.bio.dp.ScoreType
nullModelForwarder - Variable in class org.biojava.bio.dist.AbstractDistribution
  Forwarder for modifications to the null model.
numberOfElements - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
numericalEntity(char) - Method in class org.biojava.utils.xml.FastXMLWriter
numericalEntity(char) - Method in class org.biojava.utils.xml.PrettyXMLWriter
numStates - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
numStates - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
numTables() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Returns the number of symbol property tables in the database.
numTables() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
  Returns the number of symbol property tables in the database.

## O

O_SATIVA - Static variable in interface org.biojava.bio.program.homologene.Taxon
Oavg - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Oxygen average mass
OBDA_SEARCH_ENV - Static variable in class org.biojava.directory.SystemRegistry
ObdaContext - Class in org.biojava.naming
ObdaInitialContextFactory - Class in org.biojava.naming
ObdaInitialContextFactory() - Constructor for class org.biojava.naming.ObdaInitialContextFactory
OBDARegistryParser - Class in org.biojava.directory
  This class encapsulates all the parsing of the OBDA registry configuration file.
OBDARegistryParser() - Constructor for class org.biojava.directory.OBDARegistryParser
ObdaUriParser - Class in org.biojava.naming
  Singleton class for parsers that understand OBDA URIs.
ObjectUtil - Class in org.biojava.utils
  utility methods for implementing the equals() and hashCode() methods of Objects.
ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil
OBSOLETE - Static variable in interface org.biojavax.ontology.ComparableTerm
oColourClassMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Stores mapping from a Colour to a FONT Class.
oColourMap - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Map between Char and the Colour class.
oColourSet - Variable in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
  Store the unique colours for markup.
ODDS - Static variable in interface org.biojava.bio.dp.ScoreType
OFFSET - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
OffsetRulerRenderer - Class in org.biojava.bio.gui.sequence
  OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
OffsetRulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer
OffsetRulerRenderer(int, int) - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer
OFFSETS - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
  The sequence label for the trace offsets of the called bases.
Omono - Static variable in class org.biojava.bio.proteomics.MassCalc
  Constant value of Oxygen monoisotopic mass
ONE - Static variable in class org.biojava.bio.CardinalityConstraint
  The property should have exactly one value.
one() - Static method in class org.biojavax.ga.util.GATools
ONE_OR_MORE - Static variable in class org.biojava.bio.CardinalityConstraint
  The property should have one or more values.
onlyChildren(FeatureFilter.OnlyChildren, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
onlyChildren(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features whose children all match the specified filter.
onlyDescendants(FeatureFilter.OnlyDescendants, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
onlyDescendants(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features whose decendants all match the specified filter.
Ontology - Interface in org.biojava.ontology
  An ontology.
ONTOLOGY - Static variable in interface org.biojava.ontology.Term
  ChangeType which indicates that this term's ontology has been altered
Ontology.Impl - Class in org.biojava.ontology
  A basic in-memory implementation of an ontology
Ontology.Impl(String, String) - Constructor for class org.biojava.ontology.Ontology.Impl
OntologyException - Exception in org.biojava.ontology
  Thrown to indicate an error in an Ontology object
OntologyException() - Constructor for exception org.biojava.ontology.OntologyException
OntologyException(String) - Constructor for exception org.biojava.ontology.OntologyException
OntologyException(Throwable) - Constructor for exception org.biojava.ontology.OntologyException
OntologyException(String, Throwable) - Constructor for exception org.biojava.ontology.OntologyException
OntologyFactory - Interface in org.biojava.ontology
  A factory for Ontology instances.
OntologyOps - Interface in org.biojava.ontology
  This is an interface for optimizing ontology operators.
OntologyTerm - Interface in org.biojava.ontology
  A term in an ontology which identifies another ontology.
OntologyTerm.Impl - Class in org.biojava.ontology
  Simple in-memory implementation of a remote ontology term.
OntologyTerm.Impl(Ontology, Ontology) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
OntologyTerm.Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.ontology.OntologyTerm.Impl
OntoTools - Class in org.biojava.ontology
  Tools for manipulating ontologies.
open(File) - Static method in class org.biojava.bio.seq.db.TabIndexStore
  Open an existing index store.
openTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
openTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
openTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
openTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
  Open a new namespace-qualified XML tag.
openTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Open a new unqualified XML tag.
OptimizableFilter - Interface in org.biojava.bio.seq
  The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.
optimize(FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Attempts to reduce a FeatureFilter to an equivalent FeatureFilter with fewer terms.
optionIsTrue(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Helper method for converting a `Boolean`-valued option into a `boolean` primitive.
options - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  The map containing the `ChromatogramGraphic.Option`s and values for this instance.
or(FeatureFilter.Or, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
or(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a new filter which matches the union of two filters.
or(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a new filter which matches the intersection of two filters.
or - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
OracleDBHelper - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
OracleDBHelper(Connection) - Constructor for class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
orderedLables(Comparator) - Method in class org.biojava.bio.alignment.AbstractULAlignment
OrderNDistribution - Interface in org.biojava.bio.dist
  Provides an N'th order distribution.
OrderNDistributionFactory - Class in org.biojava.bio.dist
  Default factory for Order-N distributions.
OrderNDistributionFactory(DistributionFactory) - Constructor for class org.biojava.bio.dist.OrderNDistributionFactory
  Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions.
orderNSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
  An n-th order view of another SymbolList.
ORDLOCNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
ORFNAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
org.biojava.bibliography - package org.biojava.bibliography
  The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
org.biojava.bio - package org.biojava.bio
  The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment - package org.biojava.bio.alignment
  Classes to generate and describe sequence alignments.
org.biojava.bio.annodb - package org.biojava.bio.annodb
  Databases of generic structured data (annotation) objects.
org.biojava.bio.chromatogram - package org.biojava.bio.chromatogram
  Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.chromatogram.graphic - package org.biojava.bio.chromatogram.graphic
  Tools for displaying chromatograms.
org.biojava.bio.dist - package org.biojava.bio.dist
  Probability distributions over Alphabets.
org.biojava.bio.dp - package org.biojava.bio.dp
  HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead - package org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead - package org.biojava.bio.dp.twohead
org.biojava.bio.gui - package org.biojava.bio.gui
  Graphical interfaces for biojava objects.
org.biojava.bio.gui.glyph - package org.biojava.bio.gui.glyph
  Glyphs implementations that draw shapes into SequenceRenderers
org.biojava.bio.gui.sequence - package org.biojava.bio.gui.sequence
  Graphical displays of biological sequences and associated annotations.
org.biojava.bio.gui.sequence.tracklayout - package org.biojava.bio.gui.sequence.tracklayout
  Classes for the handling of the layout of a WrappedSequencePanel.
org.biojava.bio.molbio - package org.biojava.bio.molbio
  The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program - package org.biojava.bio.program
  Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.abi - package org.biojava.bio.program.abi
  ABI Trace Handling.
org.biojava.bio.program.blast2html - package org.biojava.bio.program.blast2html
  Code for generating HTML reports from blast output
org.biojava.bio.program.das - package org.biojava.bio.program.das
  Development client for the Distributed Annotation System.
org.biojava.bio.program.das.dasalignment - package org.biojava.bio.program.das.dasalignment
org.biojava.bio.program.das.dasstructure - package org.biojava.bio.program.das.dasstructure
org.biojava.bio.program.formats - package org.biojava.bio.program.formats
  Experimental parsers using the tagvalue framework.
org.biojava.bio.program.gff - package org.biojava.bio.program.gff
  GFF manipulation.
org.biojava.bio.program.gff3 - package org.biojava.bio.program.gff3
  Support for reading and writing GFF3.
org.biojava.bio.program.hmmer - package org.biojava.bio.program.hmmer
  Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.homologene - package org.biojava.bio.program.homologene
  Support classes for Homologene data.
org.biojava.bio.program.indexdb - package org.biojava.bio.program.indexdb
  A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.phred - package org.biojava.bio.program.phred
  Parser for Phred output
org.biojava.bio.program.sax - package org.biojava.bio.program.sax
  Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.sax.blastxml - package org.biojava.bio.program.sax.blastxml
  Parsers for the XML output from NCBI blast.
org.biojava.bio.program.scf - package org.biojava.bio.program.scf
  Support for the SCF chromatogram format.
org.biojava.bio.program.ssaha - package org.biojava.bio.program.ssaha
  SSAHA sequence searching API.
org.biojava.bio.program.ssbind - package org.biojava.bio.program.ssbind
  Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.tagvalue - package org.biojava.bio.program.tagvalue
  Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene - package org.biojava.bio.program.unigene
  Objects for representing Unigene clusters.
org.biojava.bio.program.xff - package org.biojava.bio.program.xff
  Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.program.xml - package org.biojava.bio.program.xml
  Utility classes for the `org.biojava.bio.program.sax` package.
org.biojava.bio.proteomics - package org.biojava.bio.proteomics
  Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.proteomics.aaindex - package org.biojava.bio.proteomics.aaindex
  Classes and interfaces to load Amino Acid Index database files.
org.biojava.bio.search - package org.biojava.bio.search
  Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq - package org.biojava.bio.seq
  Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db - package org.biojava.bio.seq.db
  Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch - package org.biojava.bio.seq.db.biofetch
  Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql - package org.biojava.bio.seq.db.biosql
  General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.emblcd - package org.biojava.bio.seq.db.emblcd
  Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.
org.biojava.bio.seq.db.flat - package org.biojava.bio.seq.db.flat
  Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed - package org.biojava.bio.seq.distributed
  Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.filter - package org.biojava.bio.seq.filter
org.biojava.bio.seq.homol - package org.biojava.bio.seq.homol
  The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl - package org.biojava.bio.seq.impl
  Standard in-memory implementations of `Sequence` and `Feature`.
org.biojava.bio.seq.io - package org.biojava.bio.seq.io
  Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave - package org.biojava.bio.seq.io.agave
  Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.filterxml - package org.biojava.bio.seq.io.filterxml
  Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.io.game - package org.biojava.bio.seq.io.game
  Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12 - package org.biojava.bio.seq.io.game12
  Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.projection - package org.biojava.bio.seq.projection
  Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.structure - package org.biojava.bio.structure
  Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align - package org.biojava.bio.structure.align
org.biojava.bio.structure.align.helper - package org.biojava.bio.structure.align.helper
org.biojava.bio.structure.align.pairwise - package org.biojava.bio.structure.align.pairwise
org.biojava.bio.structure.io - package org.biojava.bio.structure.io
org.biojava.bio.structure.jama - package org.biojava.bio.structure.jama
org.biojava.bio.symbol - package org.biojava.bio.symbol
  Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa - package org.biojava.bio.taxa
  Taxonomy object for representing species information.
org.biojava.directory - package org.biojava.directory
  Open Bio Sequence Database Access (OBDA) registry support.
org.biojava.naming - package org.biojava.naming
org.biojava.ontology - package org.biojava.ontology
  A general-purpose API for ontologies.
org.biojava.ontology.io - package org.biojava.ontology.io
  Tools for loading and saving ontologies.
org.biojava.stats.svm - package org.biojava.stats.svm
  Support Vector Machine classification and regression.
org.biojava.stats.svm.tools - package org.biojava.stats.svm.tools
  Tools for use of the SVM package.
org.biojava.utils - package org.biojava.utils
  Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.automata - package org.biojava.utils.automata
org.biojava.utils.cache - package org.biojava.utils.cache
  A simple cache system with pluggable caching behaviours.
org.biojava.utils.candy - package org.biojava.utils.candy
  The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.
org.biojava.utils.io - package org.biojava.utils.io
  I/O utility classes.
org.biojava.utils.lsid - package org.biojava.utils.lsid
  Life Science Identifier (LSID) package.
org.biojava.utils.math - package org.biojava.utils.math
  Mathematical utility classes.
org.biojava.utils.net - package org.biojava.utils.net
  Network programming utility classes.
org.biojava.utils.process - package org.biojava.utils.process
  Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
org.biojava.utils.regex - package org.biojava.utils.regex
  This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojava.utils.stax - package org.biojava.utils.stax
  The Stack API for XML (StAX).
org.biojava.utils.walker - package org.biojava.utils.walker
org.biojava.utils.xml - package org.biojava.utils.xml
  Utility classes for handling and generating XML documents.
org.biojavax - package org.biojavax
  The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio - package org.biojavax.bio
  Classes to represent biological entities and their relationships.
org.biojavax.bio.db - package org.biojavax.bio.db
  Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql - package org.biojavax.bio.db.biosql
org.biojavax.bio.db.ncbi - package org.biojavax.bio.db.ncbi
org.biojavax.bio.seq - package org.biojavax.bio.seq
  Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io - package org.biojavax.bio.seq.io
  Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.bio.taxa - package org.biojavax.bio.taxa
  Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.bio.taxa.io - package org.biojavax.bio.taxa.io
org.biojavax.ga - package org.biojavax.ga
  Classes to provide a genetic algorithm framework
org.biojavax.ga.exception - package org.biojavax.ga.exception
  Exceptions related to the GA framework
org.biojavax.ga.functions - package org.biojavax.ga.functions
  GA functions
org.biojavax.ga.impl - package org.biojavax.ga.impl
  Default implementations and abstract classes.
org.biojavax.ga.util - package org.biojavax.ga.util
  Utility functions and helper classes
org.biojavax.ontology - package org.biojavax.ontology
  Extensions to the biojava ontology model that represent BioSQL ontology.
org.biojavax.utils - package org.biojavax.utils
  Utility classes that are used by biojavax objects but could have wider utility to other applications.
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
ORGANELLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
Organism - Interface in org.biojavax.ga
  A GA 'organism' contains one or more Chromosomes
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
ORGANISM_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
ORGANISM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ORGANISM_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
OrganismParser - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.taxa framework instead
OrganismParser(SequenceBuilder, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser
  Deprecated.
OrganismParser.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps SequenceBuilders in an OrganismParser.
OrganismParser.Factory(SequenceBuilderFactory, TaxonFactory, TaxonParser, String, String, String) - Constructor for class org.biojava.bio.seq.io.OrganismParser.Factory
  Deprecated.
organisms() - Method in class org.biojavax.ga.impl.SimplePopulation
ORGANISMS - Static variable in interface org.biojavax.ga.Population
organisms() - Method in interface org.biojavax.ga.Population
origSeq - Variable in class org.biojava.bio.seq.impl.RevCompSequence
Orthologue - Interface in org.biojava.bio.program.homologene
  this entry contains data about the orthologue.
OrthologueFilter - Interface in org.biojava.bio.program.homologene
OrthologueFilter.AcceptAll - Class in org.biojava.bio.program.homologene
OrthologueFilter.AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
OrthologueFilter.And - Class in org.biojava.bio.program.homologene
OrthologueFilter.And(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.And
OrthologueFilter.ByAccession - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByAccession(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
OrthologueFilter.ByHomologeneID - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByHomologeneID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
OrthologueFilter.ByLocusID - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByLocusID(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
OrthologueFilter.ByTaxon - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
OrthologueFilter.ByTaxonID - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByTaxonID(int) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
OrthologueFilter.ByTitle - Class in org.biojava.bio.program.homologene
OrthologueFilter.ByTitle(String) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
OrthologueFilter.Not - Class in org.biojava.bio.program.homologene
OrthologueFilter.Not(OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Not
OrthologueFilter.Or - Class in org.biojava.bio.program.homologene
OrthologueFilter.Or(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Or
OrthologueFilter.Xor - Class in org.biojava.bio.program.homologene
OrthologueFilter.Xor(OrthologueFilter, OrthologueFilter) - Constructor for class org.biojava.bio.program.homologene.OrthologueFilter.Xor
OrthologueSet - Interface in org.biojava.bio.program.homologene
  Interface for classes that store and manipulate orthologues.
OrthologueSet.Iterator - Interface in org.biojava.bio.program.homologene
  An iterator for the contents of an OrthologueSet.
OrthoPair - Interface in org.biojava.bio.program.homologene
  Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
OrthoPairCollection - Interface in org.biojava.bio.program.homologene
  Interface for a Set of OrthoPairSets
OrthoPairCollection.Iterator - Interface in org.biojava.bio.program.homologene
  Iterator for a OrthoPairCollection
OrthoPairFilter - Interface in org.biojava.bio.program.homologene
OrthoPairFilter.AcceptAll - Class in org.biojava.bio.program.homologene
OrthoPairFilter.AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
OrthoPairFilter.And - Class in org.biojava.bio.program.homologene
OrthoPairFilter.And(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.And
OrthoPairFilter.ByMaxIdentity - Class in org.biojava.bio.program.homologene
OrthoPairFilter.ByMaxIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
OrthoPairFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
OrthoPairFilter.ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
OrthoPairFilter.ByRef - Class in org.biojava.bio.program.homologene
OrthoPairFilter.ByRef(String) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
OrthoPairFilter.BySimilarityType - Class in org.biojava.bio.program.homologene
OrthoPairFilter.BySimilarityType(SimilarityType) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
OrthoPairFilter.Not - Class in org.biojava.bio.program.homologene
OrthoPairFilter.Not(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Not
OrthoPairFilter.Or - Class in org.biojava.bio.program.homologene
OrthoPairFilter.Or(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Or
OrthoPairFilter.Xor - Class in org.biojava.bio.program.homologene
OrthoPairFilter.Xor(OrthoPairFilter, OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
OrthoPairSet - Interface in org.biojava.bio.program.homologene
  represents the Homologene Group.
OrthoPairSet.Iterator - Interface in org.biojava.bio.program.homologene
OrthoPairSetFilter - Interface in org.biojava.bio.program.homologene
OrthoPairSetFilter.AcceptAll - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.AcceptAll() - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
OrthoPairSetFilter.AllPairsInCollection - Class in org.biojava.bio.program.homologene
  all OrthoPairs must meet the requirement defined by filter.
OrthoPairSetFilter.AllPairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
OrthoPairSetFilter.And - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.And(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
OrthoPairSetFilter.ByMinIdentity - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.ByMinIdentity(double) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
OrthoPairSetFilter.ByTaxon - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.ByTaxon(Taxon) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
OrthoPairSetFilter.Not - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.Not(OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
OrthoPairSetFilter.Or - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.Or(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
OrthoPairSetFilter.SomePairsInCollection - Class in org.biojava.bio.program.homologene
  at least one OrthoPair must meet the requirement defined by filter.
OrthoPairSetFilter.SomePairsInCollection(OrthoPairFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
OrthoPairSetFilter.Xor - Class in org.biojava.bio.program.homologene
OrthoPairSetFilter.Xor(OrthoPairSetFilter, OrthoPairSetFilter) - Constructor for class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
OTHER_SEQID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
OTHER_SEQIDS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `OUTLINE` indicating a change to the outline paint of the features.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  Constant `OUTLINE` indicating a change to the crosshair paint.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  Constant `OUTLINE` indicating a change to the fill of the features.
outline - Variable in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `outline` is the line colour.
OUTLINE - Static variable in class org.biojava.bio.gui.sequence.TickFeatureRenderer
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
outlinePaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
  Return the outline paint for a symbol.
OutputHandler - Interface in org.biojava.utils.process
  Interface to a threadable output handler for an external process.
OVERHANG_3PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `OVERHANG_3PRIME` the sticky end type created by enzymes which leave a 3' overhang.
OVERHANG_5PRIME - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
  `OVERHANG_5PRIME` the sticky end type created by enzymes which leave a 5' overhang.
overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
overlaps(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
overlaps(Location) - Method in class org.biojava.bio.symbol.CircularLocation
overlaps(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
overlaps(Location) - Method in interface org.biojava.bio.symbol.Location
  Checks if these two locations overlap, using this location's concept of overlapping.
overlaps(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Determines whether the locations overlap or not.
overlaps(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Checks if these two locations overlap, using this location's concept of overlapping.

  Abstractly, two locations overlap if they both contain any point. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity. Recursively applies this call to all members.

overlaps(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Checks if these two locations overlap, using this location's concept of overlapping. ALWAYS RETURNS FALSE
overlaps(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Checks if these two locations overlap, using this location's concept of overlapping. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity.
overlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with locations contained by or overlapping the specified `Location`.
overlapsOrigin() - Method in class org.biojava.bio.symbol.CircularLocation
  Does the Location overlap the origin (position 1) of the sequence?
OverlayAnnotation - Class in org.biojava.bio
  Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
OverlayAnnotation(Annotation) - Constructor for class org.biojava.bio.OverlayAnnotation
  Construct an annotation which can overlay new key-value pairs onto an underlying annotation.
OverlayAnnotation.PropertyForwarder - Class in org.biojava.bio
  Forwards change events from the underlying Annotation to this one.
OverlayAnnotation.PropertyForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.OverlayAnnotation.PropertyForwarder
  Forward on behalf of source using the change support provided.
OverlayMap - Class in org.biojava.utils
  Overlap one map onto another.
OverlayMap(Map, Map) - Constructor for class org.biojava.utils.OverlayMap
  Build a new map with default key-value pairs.
OverlayMap(Map) - Constructor for class org.biojava.utils.OverlayMap
  Build a new map with default key-value pairs.
OverlayMarker - Interface in org.biojava.bio.gui.sequence
  This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern.
OverlayRendererWrapper - Class in org.biojava.bio.gui.sequence
  This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer.
OverlayRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper
OverlayRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.OverlayRendererWrapper

## P

p() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Proline
pack(Symbol) - Method in class org.biojava.bio.symbol.DNAAmbPack
pack(Symbol) - Method in class org.biojava.bio.symbol.DNANoAmbPack
pack(Symbol) - Method in interface org.biojava.bio.symbol.Packing
  Return a byte representing the packing of a symbol.
PACKED - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
  Accessor for a factory that produces builders that compress the `SymbolList` of a `RichSequence`.
PackedSymbolList - Class in org.biojava.bio.symbol
  A SymbolList that stores symbols as bit-patterns in an array of longs.
PackedSymbolList(Packing, long[], int) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
  Create a new PackedSymbolList directly from a bit pattern.
PackedSymbolList(Packing, SymbolList) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
  Create a new PackedSymbolList as a packed copy of another symbol list.
PackedSymbolList(Packing, Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.PackedSymbolList
  Create a new PackedSymbolList from an array of Symbols.
PackedSymbolListFactory - Class in org.biojava.bio.symbol
  This class makes PackedSymbolLists.
PackedSymbolListFactory() - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory
  Create a factory for PackedSymbolLists.
PackedSymbolListFactory(boolean) - Constructor for class org.biojava.bio.symbol.PackedSymbolListFactory
  Deprecated. the argumentless constructor creates a SymbolListFactory that will autoselect the packing appropriately.
Packing - Interface in org.biojava.bio.symbol
  An encapsulation of the way symbols map to bit-patterns.
PackingFactory - Class in org.biojava.bio.symbol
  A factory that is used to maintain associations between alphabets and preferred bit-packings for them.
PackingFactory() - Constructor for class org.biojava.bio.symbol.PackingFactory
PADDING - Static variable in class org.biojava.bio.gui.sequence.PaddingRenderer
  Event type for when the size of the padding changes.
PaddingRenderer - Class in org.biojava.bio.gui.sequence
  A renderer that adds padding before and after a delegate renderer.
PaddingRenderer() - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer
  Build a new PaddingRenderer with zero padding.
PaddingRenderer(SequenceRenderer, double) - Constructor for class org.biojava.bio.gui.sequence.PaddingRenderer
  Build a new PaddingRenderer that wraps `renderer` and has padding depth `padding`.
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
paint(Graphics2D, CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
paint(Graphics2D, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer
  Paint this renderer.
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer
  Render a label for the information for sp to g.
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
paint(Graphics2D, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `paint` renders the feature as a simple line.
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
paint(Graphics2D, PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `paint` applies all renderers in the order in which they were added.
paint(Graphics2D, PairwiseRenderContext) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
  `paint`s some or all of the information about the sequence pair.
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
paint(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
paint(Graphics2D, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
  Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
paint(Graphics2D, SequenceRenderContext, int, int, SequenceRenderContext.Border) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
paint(Graphics2D, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in interface org.biojava.bio.gui.BlockPainter
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.PlainBlock
paintBlock(LogoContext, Rectangle2D, AtomicSymbol) - Method in class org.biojava.bio.gui.TextBlock
paintComponent(Graphics) - Method in class org.biojava.bio.gui.DistributionLogo
  Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Paint this component.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Paint this component.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `paintComponent` paints this component.
paintComponent(Graphics) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Renders this component to display the points, and if present, the support vector machine.
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.BarLogoPainter
paintLogo(LogoContext) - Method in interface org.biojava.bio.gui.LogoPainter
  Render the state from sl onto the graphics object g.
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.StackedLogoPainter
paintLogo(LogoContext) - Method in class org.biojava.bio.gui.TextLogoPainter
pairalign - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
PairDistribution - Class in org.biojava.bio.dist
  Class for pairing up two independant distributions.
PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution
  Create a new PairDistribution that represents the product of two other distributions.
PairDPCursor - Interface in org.biojava.bio.dp.twohead
  A cursor over a DP matrix.
PairDPMatrix - Class in org.biojava.bio.dp.twohead
  Storage structure for intermediate values from a pairwise dynamic programming run.
PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.twohead.PairDPMatrix
pairwiseAlignment(Sequence, Sequence) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Global pairwise sequence alginment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
pairwiseAlignment(Sequence, Sequence) - Method in class org.biojava.bio.alignment.SequenceAlignment
  Performs a pairwise sequence alignment of the two given sequences.
pairwiseAlignment(Sequence, Sequence) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
PairwiseDiagonalRenderer - Class in org.biojava.bio.gui.sequence
  `PairwiseDiagonalRenderer` renders a region of similarity between two sequences as a straight line.
PairwiseDiagonalRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  Creates a new `PairwiseDiagonalRenderer` which will draw black lines.
PairwiseDiagonalRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  Creates a new `PairwiseDiagonalRenderer` which will draw lines using the specified `Paint`.
PairwiseDP - Class in org.biojava.bio.dp.twohead
  Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
PairwiseDP(MarkovModel, CellCalculatorFactoryMaker) - Constructor for class org.biojava.bio.dp.twohead.PairwiseDP
PairwiseFilteringRenderer - Class in org.biojava.bio.gui.sequence
  `PairwiseFilteringRenderer` wraps a `PairwiseSequenceRenderer` and filters the `PairwiseRenderContext`s passed to it.
PairwiseFilteringRenderer(PairwiseSequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  Creates a new `PairwiseFilteringRenderer` which uses a filter which accepts all features.
PairwiseFilteringRenderer(PairwiseSequenceRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  Creates a new `PairwiseFilteringRenderer`.
PairwiseOverlayRenderer - Class in org.biojava.bio.gui.sequence
  `PairwiseOverlayRenderer` allows a list of other `PairwiseSequenceRenderer`s to superimpose their output.
PairwiseOverlayRenderer() - Constructor for class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  Creates a new, empty `PairwiseOverlayRenderer`.
PairwiseRenderContext - Interface in org.biojava.bio.gui.sequence
  `PairwiseRenderContext` encapsulates information required for the rendering of a pair of sequences.
PairwiseSequencePanel - Class in org.biojava.bio.gui.sequence
  A `PairwiseSequencePanel` is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).
PairwiseSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  Creates a new `PairwiseSequencePanel` with the default settings (primary sequence direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, secondary symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).
PairwiseSequenceRenderer - Interface in org.biojava.bio.gui.sequence
  `PairwiseSequenceRenderer`s render information about the relationship between two sequences.
PairwiseSequenceRenderer.PairwiseRendererForwarder - Class in org.biojava.bio.gui.sequence
  `PairwiseRendererForwarder` forward events to other renderers.
PairwiseSequenceRenderer.PairwiseRendererForwarder(PairwiseSequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
  Creates a new `PairwiseRendererForwarder`.
PARAMETER - Static variable in interface org.biojava.bio.dp.MarkovModel
  Signals that one or more parameters have altered.
parent - Variable in class org.biojava.bio.taxa.SimpleTaxon
  Deprecated.
parent - Variable in class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
parent() - Method in interface org.biojava.utils.automata.StateMachineInstance
PARENT - Static variable in interface org.biojavax.bio.seq.RichFeature
PARENT - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
parse(BufferedReader, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFParser
  Informs handler of each line of gff read from bReader.
parse(BufferedReader, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.GFFParser
  Informs handler of each line of GFF read from bReader
parse(BufferedReader, GFF3DocumentHandler, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Informs handler of each line of gff read from bReader.
parse(BufferedReader, GFF3DocumentHandler, Ontology, String) - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Informs handler of each line of GFF read from bReader
parse(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser
  Returns a profile HMM representing the core HMMER hmm
parse(InputSource) - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
  `parse` initiates the parsing operation.
parse(InputSource) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
parse(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
parse(InputSource) - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
  Describe 'parse' method here.
parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
parse(InputSource) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser
  Describe 'parse' method here.
parse(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
parse(InputSource) - Method in class org.biojava.bio.program.sax.PdbSAXParser
  Describe 'parse' method here.
parse(InputSource) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
  Describe 'parse' method here.
parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser
parse(TaxonFactory, String) - Method in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
parse(TaxonFactory, String) - Method in interface org.biojava.bio.taxa.TaxonParser
  Deprecated. Convert a stringified Taxon into a Taxon instance.
parse(String) - Method in class org.biojava.naming.ObdaUriParser
parse(BufferedReader, OntologyFactory) - Method in class org.biojava.ontology.io.TabDelimParser
  Parse an ontology from a reader.
parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser
  Parse attValList into a Map of attributes and value lists.
parseAttribute(String, Annotation, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Parse attValList into a Map of attributes and value lists.
parseAuthorString(String) - Static method in class org.biojavax.DocRefAuthor.Tools
  Takes a list of authors and returns a set of DocRefAuthor objects.
parseComment(Comment) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Parses the comment string from the given comment and populates the internal fields appropriately.
parseComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Parses the comment string from the given comment and populates the internal fields appropriately.
parseDASResponse(InputStream) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  parse the Response of a DAS ALignment service and return a biojava Alignment object.
ParseErrorEvent - Class in org.biojava.utils
  Event which signals a bad line when parsing a record.
ParseErrorEvent(Object) - Constructor for class org.biojava.utils.ParseErrorEvent
  Construct a ParseErrorEvent with no other information.
ParseErrorEvent(Object, String) - Constructor for class org.biojava.utils.ParseErrorEvent
  Construct a ParseErrorEvent with a message.
ParseErrorListener - Interface in org.biojava.utils
  Listener for a ParseErrorEvent.
ParseErrorSource - Interface in org.biojava.utils
  Source for a ParseErrorEvent.
parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
ParseException - Exception in org.biojava.bio.seq.io
  ParseException should be thrown to indicate that there was a problem with parsing sequence information.
ParseException() - Constructor for exception org.biojava.bio.seq.io.ParseException
ParseException(String) - Constructor for exception org.biojava.bio.seq.io.ParseException
ParseException(Throwable) - Constructor for exception org.biojava.bio.seq.io.ParseException
ParseException(Throwable, String) - Constructor for exception org.biojava.bio.seq.io.ParseException
parseFull(File) - Static method in class org.biojava.bio.program.hmmer.HmmerProfileParser
  Returns the full markov model - including the core model + J,C,N loop states.
parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.ontology.io.GOParser
parseLocation(String, Feature.Template) - Method in class org.biojava.bio.seq.io.EmblLikeLocationParser
  Deprecated. `parseLocation` creates a `Location` from the String and returns a stranded location.
parseLocation(Namespace, String, String) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser
  Parses a location.
parseLocation(String) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser
  Parses a location.
parseMatrix(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Reads a String representing the contents of a substitution matrix file.
parseModel(File) - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
parsePDBFile(InputStream) - Method in class org.biojava.bio.structure.io.PDBFileParser
  parse a PDB file and return a datastructure implementing PDBStructure interface.
parsePDBFile(BufferedReader) - Method in class org.biojava.bio.structure.io.PDBFileParser
  parse a PDB file and return a datastructure implementing PDBStructure interface.
Parser - Class in org.biojava.bio.program.tagvalue
  Encapsulate the parsing of lines from a buffered reader into tag-value events.
Parser() - Constructor for class org.biojava.bio.program.tagvalue.Parser
parseRecord(byte[]) - Method in class org.biojava.utils.FileAsList
parseRegistry(BufferedReader, String) - Static method in class org.biojava.directory.OBDARegistryParser
  `parseRegistry` parses an Open Bioinformatics Database Access (OBDA) configuration file.
ParserException - Exception in org.biojava.utils
  Exception thrown when an error occurs in document parsing.
ParserException(String) - Constructor for exception org.biojava.utils.ParserException
ParserException(String, String) - Constructor for exception org.biojava.utils.ParserException
ParserException(String, String, int) - Constructor for exception org.biojava.utils.ParserException
ParserException(String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
ParserException(String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable, String) - Constructor for exception org.biojava.utils.ParserException
  Deprecated. use new ParserException(detail, t)
ParserException(String, Throwable) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable, String, String) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable, String, String, int) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable, String, String, int, String) - Constructor for exception org.biojava.utils.ParserException
ParserException(Throwable, String, String, int, String, int) - Constructor for exception org.biojava.utils.ParserException
ParserListener - Class in org.biojava.bio.program.tagvalue
  `ParserListener` is an immutable pairing of a parser and listener.
ParserListener(TagValueParser, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ParserListener
  Creates a new `ParserListener` instance.
PARSERS - Static variable in interface org.biojava.bio.symbol.Alphabet
  This signals that the available parsers have changed.
parseStrand(String) - Static method in class org.biojava.bio.seq.StrandParser
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.CharacterTokenization
parseStream(SeqIOListener) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  Return an object which can parse an arbitrary character stream into symbols.
parseStream(SeqIOListener) - Method in class org.biojava.bio.seq.io.WordTokenization
parseStream(SeqIOListener) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
  The current implementation only supports character parsing.
parseString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.CharacterTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.DoubleTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.IntegerTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.NameTokenization
parseToken(String) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
parseToken(String) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  Returns the symbol for a single token.
parseToken(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
parseTokenChar(char) - Method in class org.biojava.bio.seq.io.CharacterTokenization
parseXML(InputStream) - Method in class org.biojava.bio.dist.XMLDistributionReader
  Reads an XML representation of a Distribution from a file.
PARTIAL_ORDER - Static variable in class org.biojava.ontology.OntoTools
PATENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
pattern() - Method in class org.biojava.utils.regex.Matcher
  Returns the Pattern object that compiled this Matcher.
Pattern - Class in org.biojava.utils.regex
  A class analogous to java.util.regex.Pattern but for SymbolLists.
patternAsString() - Method in class org.biojava.utils.regex.Pattern
  returns the Pattern to be matched as a String.
PatternBlitz - Class in org.biojava.utils.automata
PatternBlitz(FiniteAlphabet, StateMachineToolkit) - Constructor for class org.biojava.utils.automata.PatternBlitz
patternExpanded() - Method in class org.biojava.utils.regex.Pattern
  returns the actual String used to construct the regex with all ambiguities expanded.
PatternFactory - Class in org.biojava.utils.regex
  A class that creates Patterns for regex matching on SymbolLists of a specific Alphabet.
PatternListener - Interface in org.biojava.utils.automata
PatternMaker - Class in org.biojava.utils.automata
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePanel.Border
pcs - Variable in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
PDB - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `PDB` indicates that the sequence format is PDB.
PDBFileParser - Class in org.biojava.bio.structure.io
  A PDB file parser.
PDBFileParser() - Constructor for class org.biojava.bio.structure.io.PDBFileParser
PDBFileReader - Class in org.biojava.bio.structure.io
  A PDB file parser.
PDBFileReader() - Constructor for class org.biojava.bio.structure.io.PDBFileReader
PDBMSDReader - Class in org.biojava.bio.structure.io
  retreive a structure from an installation of the MSD - search database ( http://www.ebi.ac.uk/msd/index.html , http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )
PDBMSDReader() - Constructor for class org.biojava.bio.structure.io.PDBMSDReader
PDBParseException - Exception in org.biojava.bio.structure.io
  An exception during the parsing of a PDB file.
PDBParseException(String) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
  Constructs a PDBParseException object.
PDBParseException(Throwable, String) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
  Deprecated. use new BioException(message, ex) instead
PDBParseException(String, Throwable) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
  Constructs a PDBParseException object.
PDBParseException(Throwable) - Constructor for exception org.biojava.bio.structure.io.PDBParseException
  Constructs a PDBParseException object.
PdbSAXParser - Class in org.biojava.bio.program.sax
  A SAX2 parser for dealing with native PDB files.
PdbSAXParser() - Constructor for class org.biojava.bio.program.sax.PdbSAXParser
  Sets namespace prefix to "biojava"
PDBSRSReader - Class in org.biojava.bio.structure.io
  reads a PDB file from a local SRS installation using getz Actually is the same as PDBFileReader, but instead of reading from a file stream, reads from a buffered stream.
PDBSRSReader() - Constructor for class org.biojava.bio.structure.io.PDBSRSReader
PdbToXMLConverter - Class in org.biojava.bio.program
  A class that converts Protein Data Bank (PDB) to XML that will validate against the biojava:MacromolecularStructure DTD.
PdbToXMLConverter(String) - Constructor for class org.biojava.bio.program.PdbToXMLConverter
  Creates a new `BlastToXMLConverter` instance.
PEPTIDE_FEATURE_TYPE - Static variable in class org.biojava.bio.proteomics.Digest
PeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
  A concrete AbstractPeptideDigestRenderer.
PeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
PeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
PeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.PeptideDigestRenderer
PERCENTIDENTITY - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
performCrossOver(SymbolList, SymbolList) - Method in interface org.biojavax.ga.functions.CrossOverFunction
  Performs a cross between the pair of chromosomes
performCrossOver(SymbolList, SymbolList) - Method in class org.biojavax.ga.functions.SimpleCrossOverFunction
PERSON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
pFromQuality(double) - Static method in class org.biojava.bio.program.phred.PhredTools
  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
pFromQuality(int) - Static method in class org.biojava.bio.program.phred.PhredTools
  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
pFromQuality(IntegerAlphabet.IntegerSymbol) - Static method in class org.biojava.bio.program.phred.PhredTools
  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
phe() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Phenylalanine (F)
PHRED - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `PHRED` indicates that the sequence format is PHRED.
phredAlignmentToDistArray(Alignment) - Static method in class org.biojava.bio.program.phred.PhredTools
  converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
PhredFormat - Class in org.biojava.bio.program.phred
  Format object representing Phred Quality files.
PhredFormat() - Constructor for class org.biojava.bio.program.phred.PhredFormat
PhredSequence - Class in org.biojava.bio.program.phred
  PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
PhredSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.program.phred.PhredSequence
  Constructs a new PhredSequence.
phredToDistArray(PhredSequence) - Static method in class org.biojava.bio.program.phred.PhredTools
  Converts a Phred sequence to an array of distributions.
PhredTools - Class in org.biojava.bio.program.phred
  PhredTools contains static methods for working with phred quality data.
PhredTools() - Constructor for class org.biojava.bio.program.phred.PhredTools
PK - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
PK_COOH - Static variable in class org.biojava.bio.proteomics.IsoelectricPointCalc
PK_NH2 - Static variable in class org.biojava.bio.proteomics.IsoelectricPointCalc
PlainBlock - Class in org.biojava.bio.gui
  A painter that just draws a block (or bar).
PlainBlock() - Constructor for class org.biojava.bio.gui.PlainBlock
PlainStyle - Class in org.biojava.bio.gui
  A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling.
PlainStyle() - Constructor for class org.biojava.bio.gui.PlainStyle
PlainStyle(Paint, Paint) - Constructor for class org.biojava.bio.gui.PlainStyle
PLASMID_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
plus(Structure, Matrix) - Static method in class org.biojava.bio.structure.Calc
  calculate structure + Matrix coodinates ...
plus(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  C = A + B
plusEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  A = A + B
point - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `point` is the current location (in sequence coordinates) of the crosshair in the X and Y sequences.
PointLocation - Class in org.biojava.bio.symbol
  A location representing a single point.
PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation
POLY - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
  `POLY` indicates a polygonal image map hotspot.
polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
PolynomialKernel - Class in org.biojava.stats.svm
  This kernel computes all possible products of order features in feature space.
PolynomialKernel() - Constructor for class org.biojava.stats.svm.PolynomialKernel
PolynomialKernel(SVMKernel, double, double, double) - Constructor for class org.biojava.stats.svm.PolynomialKernel
POMBE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Schizosaccharomyces pombe codon preferences
pop() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  pop a StAXContentHandler off the stack.
pop() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  pop a StAXContentHandler off the stack.
populate(Feature.Template, Feature) - Static method in class org.biojava.bio.seq.impl.TemplateUtils
  This attempts to populate the fields of a template using the publically accessible information in a feature.
POPULATION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
population - Variable in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
Population - Interface in org.biojavax.ga
  A collection of GA organisms
pos - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
pos - Variable in class org.biojava.bio.symbol.Edit
posInSeq(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  get the position in the sequence corresponding to the postion within the alignment
position() - Method in class org.biojava.utils.io.LargeBuffer
position(long) - Method in class org.biojava.utils.io.LargeBuffer
Position - Interface in org.biojavax.bio.seq
  Holds info about base positions.
PositionResolver - Interface in org.biojavax.bio.seq
  Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
PositionResolver.AverageResolver - Class in org.biojavax.bio.seq
  The minimal resolver returns the base which provides the average range, halfway between maximal and minimal.
PositionResolver.AverageResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.AverageResolver
PositionResolver.MaximalResolver - Class in org.biojavax.bio.seq
  The maximal resolver returns the base which provides the largest possible range.
PositionResolver.MaximalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MaximalResolver
PositionResolver.MinimalResolver - Class in org.biojavax.bio.seq
  The minimal resolver returns the base which provides the smallest possible range.
PositionResolver.MinimalResolver() - Constructor for class org.biojavax.bio.seq.PositionResolver.MinimalResolver
POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
  Flag to indicate that a feature is on the positive strand.
POSITIVE_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
  The positive strand is represented by the symbol '+' and has the number 1.
posmax(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
posmin(Position, Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
postalAddress - Variable in class org.biojava.bibliography.BiblioPerson
  Their postal address.
postChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
postChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
postChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener
  Called when a change has just taken place.
PostgreSQLDBHelper - Class in org.biojava.bio.seq.db.biosql
PostgreSQLDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
preChange(ChangeEvent) - Method in class org.biojava.bio.symbol.SimpleSymbolList
  On preChange() we convert the SymolList to a non-veiw version, giving it its own copy of symbols
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeAdapter
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.AlwaysVetoListener
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener
  Called before a change takes place.
press() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.
press() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
  press out a new correctly sized cell array
PrettyXMLWriter - Class in org.biojava.utils.xml
  Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava.utils.xml.PrettyXMLWriter
PRIMARY_KEY_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  `PRIMARY_KEY_NAME` is the key used to identify the primary namespace in the OBDA config.dat files.
PRIME - Static variable in class org.biojava.utils.ObjectUtil
  the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is added.
primeWord(SymbolList, int, Packing) - Static method in class org.biojava.bio.symbol.PackingFactory
print(int, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Print the matrix to the output stream.
print(NumberFormat, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class org.biojava.bio.structure.jama.Matrix
  Print the matrix to the output stream.
print(String) - Method in class org.biojava.utils.xml.FastXMLWriter
print(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
print(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Prints some textual content in an element.
printAlignment(String) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch
  prints the alignment String on the screen (standard output).
printAttributeValue(String) - Method in class org.biojava.utils.xml.FastXMLWriter
printAttributeValue(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
printChars(String) - Method in class org.biojava.utils.xml.FastXMLWriter
printChars(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
printCostMatrix(double[][], char[], char[]) - Static method in class org.biojava.bio.alignment.NeedlemanWunsch
  Prints a String representation of the CostMatrix for the given Alignment on the screen.
println(String) - Method in class org.biojava.utils.xml.FastXMLWriter
println(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
println(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Prints some textual content, terminated with a newline character.
printMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Just to perform some test.
printMatrix(Matrix) - Method in class org.biojava.bio.structure.SVDSuperimposer
printOutSequenceHeaderLine(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Prints out sequence header with only length data.
printRaw(String) - Method in class org.biojava.utils.xml.FastXMLWriter
printRaw(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
printRaw(String) - Method in interface org.biojava.utils.xml.XMLWriter
  Send raw data to the stream.
printTree() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
priority - Variable in class org.biojava.utils.SimpleThreadPool
pro() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Proline (P)
PROB_NUC_A - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the probability that call should be A.
PROB_NUC_C - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the probability that call should be C.
PROB_NUC_G - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the probability that call should be G.
PROB_NUC_T - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the probability that call should be T.
PROB_OVERCALL - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the overcall probability.
PROB_SUBSTITUTION - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the substitution probability.
PROB_UNDERCALL - Static variable in class org.biojava.bio.program.scf.SCF
  Base call alignment sequence label for the undercall probability.
PROBABILITY - Static variable in interface org.biojava.bio.dp.ScoreType
processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Process all Sequences within a SequenceDB, informing handler of any suitable features.
processFeatureFilter(FeatureFilter) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
processingInstruction(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
processingInstruction(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
processingInstruction(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
processingInstruction(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
processingInstruction(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
processingInstruction(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `processMouseEvent` defines the behaviour on revieving a mouse event.
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `processMouseEvent` processes any `MouseEvent`s directed to the renderer.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
processMouseEvent(List, MouseEvent, List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `processMouseEvent` acts on a mouse gesture.
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `processMouseEvent` produces a `SequenceViewerEvent` in response to a mouse gesture.
processMouseEvent(PairwiseRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.PairwiseSequenceRenderer
  `processMouseEvent` produces a `SequenceViewerEvent` in response to a mouse gesture.
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
  Produce a SequenceViewerEvent in response to a mouse gesture.
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.StopRenderer
processMouseEvent(SequenceRenderContext, MouseEvent, List) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
processMouseEvent(FeatureHolder, SequenceRenderContext, MouseEvent) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
processSequence(Sequence, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Process an individual Sequence, informing handler of any suitable features.
processSequenceLine(String, StreamParser) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Dispatch symbol data from SQ-block line of an EMBL-like file.
ProcessTimeoutException - Exception in org.biojava.utils
  Exception which is thrown if a child process managed by `ProcessTools` exceeds a specified time limit.
ProcessTimeoutException(int) - Constructor for exception org.biojava.utils.ProcessTimeoutException
ProcessTimeoutException(int, String) - Constructor for exception org.biojava.utils.ProcessTimeoutException
ProcessTools - Class in org.biojava.utils
  Deprecated. preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.
ProfileEmissionState - Class in org.biojava.bio.program.hmmer
  A state in a HMMer model.
ProfileEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.program.hmmer.ProfileEmissionState
ProfileHMM - Class in org.biojava.bio.dp
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory) - Constructor for class org.biojava.bio.dp.ProfileHMM
  Deprecated.
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory, String) - Constructor for class org.biojava.bio.dp.ProfileHMM
  Create a new ProfileHMM.
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
projectChildFeatures(Feature, FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Project all features that are children of feature so that they become children of parent.
projectChildFeatures(Feature, FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
ProjectedFeature - Class in org.biojava.bio.seq.projection
  Internal class used by ProjectionEngine to wrap Feature objects.
ProjectedFeature(Feature, ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeature
ProjectedFeatureHolder - Class in org.biojava.bio.seq.projection
  Helper class for projecting Feature objects into an alternative coordinate system.
ProjectedFeatureHolder(ProjectionContext) - Constructor for class org.biojava.bio.seq.projection.ProjectedFeatureHolder
projectFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
projectFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Project a single feature.
projectFeature(Feature, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine
  Return a projection of Feature `f` into the system defined by a given ProjectionContext.
projectFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
  Create a single projected feature using the rules of this `ProjectedFeatureHolder`.
projectFeatures(FeatureHolder) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Project all of the features in a FeatureHolder.
projectFeatures(FeatureHolder) - Method in class org.biojava.bio.seq.projection.ReparentContext
projectFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Transform a filter on unprojected features so that it applies to projected features.
projectFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
Projection - Interface in org.biojava.bio.seq.projection
  Interface implemented by all projected feature objects.
ProjectionContext - Interface in org.biojava.bio.seq.projection
  Interface that defines the projection between original features and projected features.
ProjectionEngine - Class in org.biojava.bio.seq.projection
  Factory for proxy objects which project BioJava features into alternate coordinate systems.
ProjectionEngine.Instantiator - Interface in org.biojava.bio.seq.projection
  Internal helper class.
ProjectionEngine.TemplateProjector - Interface in org.biojava.bio.seq.projection
  This is an interface for things that project feature templates.
ProjectionUtils - Class in org.biojava.bio.seq.projection
  Some common things you want to do while projecting features.
ProjectionUtils() - Constructor for class org.biojava.bio.seq.projection.ProjectionUtils
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
projectLocation(Location) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
projectLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
projectStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
PROP_CASE_SENSITIVE - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROP_CRITERIONS - Static variable in interface org.biojava.bibliography.BibRefQuery
  A property name specifying a list of searching and ordering criteria names (type of the property value should be `String[]`).
PROP_ENTRY_COUNT - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROP_EXCLUDED_ATTRS - Static variable in interface org.biojava.bibliography.BibRefQuery
  A property name specifying a list of excluded attribute names (the type of the property value should be `String[]`).
PROP_VOCAB_DESC - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROP_VOCAB_NAME - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROP_VOCAB_VERSION - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyFinder
  A property name.
PROP_VOCABULARY - Static variable in interface org.biojava.utils.candy.CandyVocabulary
  A property name.
PROPDETAIL_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.PropDetailHandler
PropDetailHandler - Class in org.biojava.bio.program.xff
  StAX handler for xff:prop detail elements.
PropDetailHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.PropDetailHandler
properties - Variable in class org.biojava.bibliography.BiblioEntryStatus
  The dynamic properties may be used to add features related to the citation itself.
properties - Variable in class org.biojava.bibliography.BiblioJournal
  Additional properties used when the explicit attributes are not sufficient.
properties - Variable in class org.biojava.bibliography.BiblioProvider
  Additional properties used when the explicit attributes of the sub-classes are not sufficient.
properties - Variable in class org.biojava.bibliography.BiblioScope
  It may contain additional properties related to the extend or scope of the cited resource.
properties - Variable in class org.biojava.bibliography.BibRef
  Additional attributes of this citation.
propertiesAllocated() - Method in class org.biojava.bio.AbstractAnnotation
  A convenience method to see if we have allocated the properties Map.
propertiesAllocated() - Method in class org.biojava.bio.AnnotationChanger
  `propertiesAllocated` is a convenience method to see if we have allocated the properties `Map`.
propertiesAllocated() - Method in class org.biojava.bio.AnnotationRenamer
  `propertiesAllocated` Javadoc FIXME - this overrides a protected method and I'm not sure why (KJ).
propertiesAllocated() - Method in class org.biojava.bio.BeanAsAnnotation
propertiesAllocated() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation
  Deprecated.
propertiesAllocated() - Method in class org.biojava.bio.SimpleAnnotation
  Test to see if any properties have been allocated
propertiesAllocated() - Method in class org.biojava.bio.SmallAnnotation
PROPERTY - Static variable in interface org.biojava.bio.Annotation
  This type symbolizes that one or more properties have changed.
PROPERTY_ANNOTATIONSERVER - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_DATA_KEY - Static variable in interface org.biojava.bio.seq.Feature
  This is used as a key in the `Annotation` where it identifies internal data.
PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.program.phred.PhredFormat
  Constant string which is the property key used to notify listeners of the description lines of Phred sequences.
PROPERTY_DESCRIPTIONLINE - Static variable in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.
PROPERTY_EMBL_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated.
PROPERTY_FEATUREID - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_FEATURELABEL - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_GENBANK_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated.
PROPERTY_GFF_SCORE - Static variable in class org.biojava.bio.program.gff.GFFEntrySet
PROPERTY_LINKS - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_NCBI_TAXON - Static variable in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
PROPERTY_ORGANISM - Static variable in class org.biojava.bio.seq.io.OrganismParser
  Deprecated.
PROPERTY_SEQUENCEVERSION - Static variable in class org.biojava.bio.program.das.DASSequence
PROPERTY_SWISSPROT_ACCESSIONS - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
PROPERTY_SWISSPROT_COMMENT - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
PROPERTY_SWISSPROT_FEATUREATTRIBUTE - Static variable in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
PROPERTY_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
PROPERTY_TAXON_NAMES - Static variable in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
PROPERTY_XFF_ID - Static variable in class org.biojava.bio.program.xff.XFFFeatureSetHandler
PropertyChanger - Interface in org.biojava.bio.program.tagvalue
  Interface for objects that change tag names or properties systematically.
PropertyConstraint - Interface in org.biojava.bio
  `PropertyConstraint`s describes a constraint applied to the members of an annotation bundle.
PropertyConstraint.And - Class in org.biojava.bio
  A property constraint that accpepts items iff they are accepted by both child constraints.
PropertyConstraint.And(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.And
  Create a new `And` from two child constraints.
PropertyConstraint.ByAnnotationType - Class in org.biojava.bio
  `ByAnnotationType` accepts a property value if it belongs to type defined by AnnotationType.
PropertyConstraint.ByAnnotationType(AnnotationType) - Constructor for class org.biojava.bio.PropertyConstraint.ByAnnotationType
  Create a new constraint by type.
PropertyConstraint.ByClass - Class in org.biojava.bio
  `ByClass` accepts a property value if it is an instance of a specific Java class.
PropertyConstraint.ByClass(Class) - Constructor for class org.biojava.bio.PropertyConstraint.ByClass
  Create a new ByClass instance.
PropertyConstraint.Enumeration - Class in org.biojava.bio
  `Enumeration` accepts a property if it is present in the specified set of values.
PropertyConstraint.Enumeration(Set) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
  Creates a new `Enumeration` using the members of the specified set as a constraint.
PropertyConstraint.Enumeration(Object[]) - Constructor for class org.biojava.bio.PropertyConstraint.Enumeration
  Creates a new `Enumeration` using the elements of the specified array as a constraint.
PropertyConstraint.ExactValue - Class in org.biojava.bio
  Matches properties if they have exactly this one value.
PropertyConstraint.ExactValue(Object) - Constructor for class org.biojava.bio.PropertyConstraint.ExactValue
  Get a PropertyConstraint that matches this object and all those that are equal to it (by the Object.equals() method).
PropertyConstraint.Or - Class in org.biojava.bio
  A property constraint that accepts items iff they are accepted by either child constraints.
PropertyConstraint.Or(PropertyConstraint, PropertyConstraint) - Constructor for class org.biojava.bio.PropertyConstraint.Or
  Create a new `Or` from two child constraints.
PropertyWriter - Class in org.biojava.bio.program.xff
PropertyWriter() - Constructor for class org.biojava.bio.program.xff.PropertyWriter
ProportionalSelection - Class in org.biojavax.ga.functions
  A Selection function that determines the proportion of individuals in a new population proportionally to their fitness.
ProportionalSelection() - Constructor for class org.biojavax.ga.functions.ProportionalSelection
Protease - Class in org.biojava.bio.proteomics
  The protease class stores parameters needed by Digest to digest a protein sequence.
Protease(SymbolList, boolean, SymbolList, String) - Constructor for class org.biojava.bio.proteomics.Protease
Protease(SymbolList, boolean, SymbolList) - Constructor for class org.biojava.bio.proteomics.Protease
  Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(String, boolean, String) - Constructor for class org.biojava.bio.proteomics.Protease
  Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
Protease(String, boolean) - Constructor for class org.biojava.bio.proteomics.Protease
  Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
ProteaseManager - Class in org.biojava.bio.proteomics
  Registry and utility methods for Proteases.
ProteaseManager() - Constructor for class org.biojava.bio.proteomics.ProteaseManager
PROTEIN - Static variable in class org.biojava.bio.seq.io.FastaAlignmentFormat
PROTEIN_ALPHABET - Static variable in class org.biojava.bio.proteomics.aaindex.AAindex
  The alphabet of the symbol property table, that is protein.
PROTEIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
PROTEIN_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ProteinRefSeqFileFormer - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqFileFormer() - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  Deprecated.
ProteinRefSeqFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  Deprecated.
ProteinRefSeqProcessor - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor
  Deprecated.
ProteinRefSeqProcessor.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps sequence builders in a ProteinRefSeqProcessor
ProteinRefSeqProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
  Deprecated.
ProteinTools - Class in org.biojava.bio.seq
  The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
PROVIDER_ORGANISATION - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a provider type.
PROVIDER_PERSON - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a provider type.
PROVIDER_SERVICE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a provider type.
ProviderNotFoundException - Exception in org.biojava.directory
  `ProviderNotFoundException` is thrown when a sequence database provider can not be located.
ProviderNotFoundException() - Constructor for exception org.biojava.directory.ProviderNotFoundException
  Creates a `ProviderNotFoundException` with no detail message.
ProviderNotFoundException(String) - Constructor for exception org.biojava.directory.ProviderNotFoundException
  Creates a `ProviderNotFoundException` with the specified detail message.
PTM - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
  A name for a comment type.
ptr - Variable in class org.biojava.utils.io.CachingInputStream
  The 0-based index into cache of the _next_ byte to return.
publisher - Variable in class org.biojava.bibliography.BibRef
  A publisher is responsible for making the resource available.
PUBMED_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
  Holds a reference to the key that must be used to store PubMed references.
PUBMED_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
PUBMED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Push StAXContentHandler object onto stack
push(StAXContentHandler) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Push StAXContentHandler object onto stack
pushParser(TagValueParser, TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueContext
  Push a parser and listener pair onto the parser stack.
put(Object, StateMachine.Transition) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
  set a Transition within this TransitionTable (2-argument form)
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
put(CodonPref) - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
put(CodonPref) - Method in interface org.biojava.bio.symbol.CodonPrefFilter
  handles storage of a CodonPref object
put(int, double) - Method in class org.biojava.stats.svm.SparseVector
  Set the value at a particular dimension.
put(Object, Object) - Method in class org.biojava.utils.BeanAsMap
put(Object, Object) - Method in interface org.biojava.utils.cache.CacheMap
  Associate a value with a key.
put(Object, Object) - Method in class org.biojava.utils.cache.ChangeableCache
put(Object, Object) - Method in class org.biojava.utils.cache.FixedSizeMap
put(Object, Object) - Method in class org.biojava.utils.cache.WeakCacheMap
put(Object, Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
put(long, byte) - Method in class org.biojava.utils.io.LargeBuffer
put(byte) - Method in class org.biojava.utils.io.LargeBuffer
put(Object, Object) - Method in class org.biojava.utils.OverlayMap
put(Object, Object) - Method in class org.biojava.utils.SmallMap
putChar(long, char) - Method in class org.biojava.utils.io.LargeBuffer
putChar(char) - Method in class org.biojava.utils.io.LargeBuffer
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
putComponent(Location, SymbolList) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
putComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
putConnection(Connection) - Method in class org.biojava.utils.JDBCConnectionPool
putDouble(long, double) - Method in class org.biojava.utils.io.LargeBuffer
putDouble(double) - Method in class org.biojava.utils.io.LargeBuffer
putFloat(long, float) - Method in class org.biojava.utils.io.LargeBuffer
putFloat(float) - Method in class org.biojava.utils.io.LargeBuffer
putInt(long, int) - Method in class org.biojava.utils.io.LargeBuffer
putInt(int) - Method in class org.biojava.utils.io.LargeBuffer
putLong(long, long) - Method in class org.biojava.utils.io.LargeBuffer
putLong(long) - Method in class org.biojava.utils.io.LargeBuffer
putShort(long, short) - Method in class org.biojava.utils.io.LargeBuffer
putShort(short) - Method in class org.biojava.utils.io.LargeBuffer
putStatement(Statement) - Method in class org.biojava.utils.JDBCConnectionPool
putTaxon(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Adds a `Taxon` (along with its parents) to the database.
putTokenization(String, SymbolTokenization) - Method in class org.biojava.bio.symbol.AbstractAlphabet
  Assigns a symbol parser to a String object.

## Q

q() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Glutamine
qr() - Method in class org.biojava.bio.structure.jama.Matrix
  QR Decomposition
QRDecomposition - Class in org.biojava.bio.structure.jama
  QR Decomposition.
QRDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.QRDecomposition
  QR Decomposition, computed by Householder reflections.
QUALIFIER - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
QUALIFIER_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
QUALIFIER_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
Qualitative - Interface in org.biojava.bio.program.phred
  Qualitative is an interface for classes wanting to hold quality data in symbolic form such as Phred scores.
QualitativeAlignment - Interface in org.biojava.bio.alignment
QUALITY - Static variable in class org.biojava.bio.program.abi.ABITools
  The quality alphabet.
qualityAt(Object, int) - Method in interface org.biojava.bio.alignment.QualitativeAlignment
  Returns a quality score for label/position
qualityFromP(double) - Static method in class org.biojava.bio.program.phred.PhredTools
  The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
query(String, Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
  It queries the current collection using a query language.
QUERY_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
  A query criterion.
QUERY_LABEL - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
  This object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence.
QUERY_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  Constant `QUERY_LABEL` is the alignment label used for all query sequences.
querySeqHolder - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
queryViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory

## R

r() - Static method in class org.biojava.bio.seq.NucleotideTools
r() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Arginine
R_NORVEGICUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
RadialBaseKernel - Class in org.biojava.stats.svm
  This kernel computes the radial base kernel that corresponds to a gausian distribution.
RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel
RadialBaseKernel(SVMKernel, double) - Constructor for class org.biojava.stats.svm.RadialBaseKernel
RAF - Class in org.biojava.utils.io
RAF(File, String) - Constructor for class org.biojava.utils.io.RAF
RAF(String, String) - Constructor for class org.biojava.utils.io.RAF
raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
random(int, int) - Static method in class org.biojava.bio.structure.jama.Matrix
  Generate matrix with random elements
RandomAccessReader - Class in org.biojava.utils.io
  `RandomAccessReader` extends `Reader` to provide a means to create buffered `Reader`s from `RandomAccessFile`s.
RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader
  Creates a new `RandomAccessReader` wrapping the `RandomAccessFile` and using a default-sized buffer (8192 bytes).
RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader
  Creates a new `RandomAccessReader` wrapping the `RandomAccessFile` and using a buffer of the specified size.
randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Randomizes the weights of a `Distribution`.
RangeLocation - Class in org.biojava.bio.symbol
  A simple implementation of Location that contains all points between getMin and getMax inclusive.
RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation
  Construct a new RangeLocation from `min` to `max`.
rank() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix rank
rank() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
  Effective numerical matrix rank
RANK - Static variable in interface org.biojavax.bio.BioEntryRelationship
RANK - Static variable in interface org.biojavax.bio.seq.RichFeature
RANK - Static variable in interface org.biojavax.bio.seq.RichFeatureRelationship
RANK - Static variable in interface org.biojavax.bio.seq.RichLocation
RANK - Static variable in interface org.biojavax.Note
RANKEDCROSSREF - Static variable in interface org.biojavax.bio.BioEntry
RANKEDCROSSREF - Static variable in interface org.biojavax.ontology.ComparableTerm
RankedCrossRef - Interface in org.biojavax
  Allows cross-references to other databases to be ranked.
RankedCrossRefable - Interface in org.biojavax
  Defines an object as being able to have ranked cross references associated with it.
rankedCrossRefs - Variable in class org.biojavax.bio.seq.RichFeature.Template
RANKEDDOCREF - Static variable in interface org.biojavax.bio.BioEntry
RankedDocRef - Interface in org.biojavax
  Represents a documentary reference.
RAT_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Rattus norvegicus codon preferences
RATIO - Static variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  Constant `RATIO` indicating a change to the minimum allowed ratio of long axis to short axis of the features.
RAW - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `RAW` indicates that the alignment format is raw (symbols only).
RAW - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `RAW` indicates that the sequence format is raw (symbols only).
RAW_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `RAW_AA` premade RAW | AA.
RAW_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `RAW_DNA` premade RAW | DNA.
RAW_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `RAW_RNA` premade RAW | RNA.
rawGet(int) - Method in class org.biojava.utils.FileAsList
  `rawGet` reads the record at the specified index as a raw byte array.
rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RC_PLASMID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RC_SPECIES_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RC_STRAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RC_TISSUE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RC_TRANSP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat
  Read in an alignment from a buffered reader object
read(BufferedReader) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
  Reads an alignment in FASTA format.
read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
  Reads an MSF Alignment File
read(BufferedReader) - Static method in class org.biojava.bio.structure.jama.Matrix
  Read a matrix from a stream.
read() - Method in class org.biojava.utils.io.CachingInputStream
read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream
read() - Method in class org.biojava.utils.io.CountedBufferedReader
read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader
read(char[], int, int) - Method in class org.biojava.utils.io.CountedBufferedReader
read() - Method in class org.biojava.utils.io.RandomAccessReader
  `read` reads one byte from the underlying `RandomAccessFile`.
read(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader
  `read` reads from the underlying `RandomAccessFile` into an array.
read() - Method in class org.biojava.utils.io.UncompressInputStream
read(byte[], int, int) - Method in class org.biojava.utils.io.UncompressInputStream
read() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat
readableFiles - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
readColourMap() - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Read the the properties file that specifies the character/colour mapping.
readColourMapFromProperties(String) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Setup styles from java property file.
readDBDate() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readDBDate` reads the date from the index header.
readDBName() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readDBName` returns the database name from the index header.
readDBRelease() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readDBRelease` returns the database release from the index header.
readEmbl(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an EMBL-format stream.
readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a EMBL file using a custom type of SymbolList.
readEMBLDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBL-format stream of DNA sequences.
readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an EMBL-format stream.
readEMBLProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBL-format stream of Protein sequences.
readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an EMBL-format stream, but for RNA.
readEMBLRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBL-format stream of RNA sequences.
readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a EMBLxml file using a custom type of SymbolList.
readEMBLxmlDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBLxml-format stream of DNA sequences.
readEMBLxmlProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBLxml-format stream of Protein sequences.
readEMBLxmlRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an EMBLxml-format stream of RNA sequences.
ReaderInputHandler - Class in org.biojava.utils.process
  Reader input handler that reads the input for an external process from a reader.
ReaderInputHandler(Reader, String) - Constructor for class org.biojava.utils.process.ReaderInputHandler
  Initializes the reader input handler.
ReaderWriterPipe - Class in org.biojava.utils.process
  A multi threaded class which pipes the contents of an input reader to an output writer.
ReaderWriterPipe(Reader, Writer, String) - Constructor for class org.biojava.utils.process.ReaderWriterPipe
  Initializes the reader writer pipe.
readFasta(BufferedReader, SymbolTokenization) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Read a fasta file.
readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Read a fasta file using a custom type of SymbolList.
readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Create a sequence database from a fasta file provided as an input stream.
readFasta(BufferedReader, SymbolTokenization, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a fasta file.
readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a fasta file building a custom type of `RichSequence`.
readFastaDNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an FASTA-format stream of DNA sequences.
readFastaDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an FASTA-format stream of DNA sequences.
readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an FASTA-format stream of Protein sequences.
readFastaProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an FASTA-format stream of Protein sequences.
readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an FASTA-format stream of RNA sequences.
readFastaRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an FASTA-format stream of RNA sequences.
readFile(File, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Guess which format a file is then attempt to read it.
readFile(File, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Guess which format a file is then attempt to read it.
readFileLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readFileLength` returns the file length in bytes (stored within the file's header by the indexing program).
readFromXML(InputStream) - Static method in class org.biojava.bio.dist.DistributionTools
  Read a distribution from XML.
readFromXML(InputStream, String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
  reads a specified CodonPref from an file.
readFromXML(InputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
readFromXML(InputStream, CodonPrefFilter) - Static method in class org.biojava.bio.symbol.CodonPrefTools
  read an CodonPref XML stream and handle it with a CodonPrefFilter object.
readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an Genbank-format stream.
readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a GenBank file using a custom type of SymbolList.
readGenbankDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an GenBank-format stream of DNA sequences.
readGenbankProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an GenBank-format stream of Protein sequences.
readGenbankRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an GenBank-format stream of RNA sequences.
readGenbankXml(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an GenbankXML-format stream.
readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an Genpept-format stream.
readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools
  Deprecated. use: readGff(File)
readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
  Deprecated. use: readGff(File,GFFRecordFilter)
readGFF(File) - Static method in class org.biojava.bio.program.gff.GFFTools
  Reads a `GFFEntrySet` from a file with no filtering.
readGFF(File, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
  Reads a GFFEntrySet from a file with the specified filter.
readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools
  Read all GFF entries from a buffered reader.
readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
  Read all GFF entries matching a filter from a buffered reader.
readingFrame - Variable in class org.biojava.bio.seq.FramedFeature.Template
readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a INSDseq file using a custom type of SymbolList.
readINSDseqDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an INSDseq-format stream of DNA sequences.
readINSDseqProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an INSDseq-format stream of Protein sequences.
readINSDseqRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an INSDseq-format stream of RNA sequences.
readLine() - Method in class org.biojava.utils.io.CountedBufferedReader
readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
readName(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
  Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
readName(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
  Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
readNode(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
  Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
readNode(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
  Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
readPhredQuality(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
  Constructs a StreamReader to read in Phred quality data in FASTA format.
readPhredSequence(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
  Calls SeqIOTools.readFastaDNA(br), added here for convinience.
readRawRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readRawRecord` returns the raw bytes of a single record from the index.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumHitReader
  `readRecord` creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
  `readRecord` creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
  `readRecord` creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readRecord` returns an array of objects parsed from a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  `readRecord` returns an array of objects parsed from a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
  `readRecord` creates an array of Objects from the raw byte array of a single record.
readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
  `readRecord` creates an array of Objects from the raw byte array of a single record.
readRecordCount() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readRecordCount` returns the number of records in the file.
readRecordLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
  `readRecordLength` returns the record length (bytes).
readResolve() - Method in class org.biojava.bio.proteomics.Protease
  Prevent duplication of the object during Serialization
readResolve() - Method in class org.biojava.bio.symbol.AbstractAlphabet
  To prevent duplication of a what should be a single instance of an existing alphabet.
readResolve() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
  To prevent duplication of a what should be a single instance of an existing alphabet.
readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.program.phred.PhredFormat
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Reads information from a flatfile to a `SeqIOListener` using a `SymbolTokenizer` to convert sequence strings to `Symbol` objects.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GAMEFormat
  this version only reads annotations (no symbols)
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
  Deprecated.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.FastaFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  Read a sequence and pass data on to a SeqIOListener.
readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Read a sequence and pass data on to a SeqIOListener.
readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Guess which format a stream is then attempt to read it.
readStream(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Guess which format a stream is then attempt to read it.
readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Iterate over the sequences in an Swissprot-format stream.
readSymbol() - Method in interface org.biojava.bio.seq.io.SymbolReader
  Return a single symbol from the stream.
readSymbols(Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SymbolReader
  Read one or more symbols from the stream.
readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a UniProt file using a custom type of SymbolList.
readUniProt(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an UniProt-format stream of RNA sequences.
readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Read a UniProt XML file using a custom type of SymbolList.
readUniProtXML(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Iterate over the sequences in an UniProt XML-format stream of RNA sequences.
readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools
readXFF(File, String) - Static method in class org.biojava.bio.program.xff.XFFTools
readXMLChunk(BufferedReader, DefaultHandler, String) - Static method in class org.biojavax.utils.XMLTools
  Attempts to read XML file in chunks, passing each chunk to a SAX parser.
ready() - Method in class org.biojava.utils.io.CountedBufferedReader
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer
  Install a feature on the specified sequence.
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder
  Realize a feature template.
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  recursively attach children features to parent
RealizingFeatureHolder - Interface in org.biojava.bio.seq
  Interface for `FeatureHolder` objects which know how to instantiate new child Features.
reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport
  Remove all references to listeners which have been cleared by the garbage collector.
REBASE_DATA_KEY - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_DATA_KEY` the ResourceBundle key which specifies the location of the REBASE flat file.
REBASE_TAG_COMM - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_COMM` the REBASE tag containing the commercial suppliers.
REBASE_TAG_ISZR - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_ISZR` the REBASE tag containing the enzyme isoschizomers.
REBASE_TAG_METH - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_METH` the REBASE tag containing the methylation site.
REBASE_TAG_NAME - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_NAME` the REBASE tag containing the enzyme name.
REBASE_TAG_ORGN - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_ORGN` the REBASE tag containing the organism.
REBASE_TAG_REFS - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_REFS` the REBASE tag containing the references.
REBASE_TAG_SITE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_SITE` the REBASE tag containing the enzyme site.
REBASE_TAG_SRCE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `REBASE_TAG_SRCE` the REBASE tag containing the source.
rebind(Name, Object) - Method in class org.biojava.naming.ObdaContext
rebind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
rebind(String, Object) - Method in class org.biojava.naming.ObdaContext
rebind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
Record - Interface in org.biojava.bio.program.indexdb
  `Record` represents a record within an indexed flat file databank as defined by the OBDA standard.
Record.Impl - Class in org.biojava.bio.program.indexdb
  `Impl` is the default implementation of Record.
Record.Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl
  Creates a new `Impl` record.
recordEmittedSymbol(State, Symbol, double) - Method in interface org.biojava.bio.dp.HMMTrainer
  record that the specified symbol was emitted from the specified state.
recordEmittedSymbol(State, Symbol, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
recordLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
  A record line has been encountered.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer
  Only forward the GFFRecords that match a filter.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter
  Prints record to the PrintWriter.
recordLine(GFF3Record) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
  A record line has been encountered.
recordTransition(State, State, double) - Method in interface org.biojava.bio.dp.HMMTrainer
  record that a transition was observed between the specified states.
recordTransition(State, State, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
  A `recParser` for implementing `readRecord()` specific to each concrete subclass.
RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
  `RECT` indicates a rectangular image map hotspot.
rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
RectangleGlyph - Class in org.biojava.bio.gui.glyph
  A Glyph that paints a rectangle shape within the bounds.
RectangleGlyph() - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
RectangleGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
RectangleGlyph(Paint) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
RectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
  `RectangularBeadRenderer` renders features as simple rectangles.
RectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  Creates a new `RectangularBeadRenderer` with the default settings.
RectangularBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  Creates a new `RectangularBeadRenderer`.
RectangularImapRenderer - Class in org.biojava.bio.gui.sequence
  `RectangularImapRenderer` is a decorator for `RectangularBeadRenderer` which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the `RectangularBeadRenderer`.
RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.RectangularImapRenderer
  Creates a new `RectangularImapRenderer`.
RECURSE - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
recurse - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
RECURSE - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  Constant `RECURSE` indicating a change to the renderer's filter recursion flag.
recurse - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `recurse` indicates whether the filter should recurse through any subfeatures.
reduceFragments(List, FragmentPair, Matrix) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
  In helices often many similar fragments can be found.
reduceInitialFragments() - Method in class org.biojava.bio.structure.align.StrucAligParameters
  if this is set to false, the time spent to joint the initial fragments (step 2) is increased.
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
REF_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
REF_POS_BEGIN_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
REF_POS_END_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
REF_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
REFERENCE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
REFERENCE_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
ReferenceAnnotation - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
ReferenceAnnotation() - Constructor for class org.biojava.bio.seq.io.ReferenceAnnotation
  Deprecated.
REFERENCES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
ReferenceServer - Class in org.biojava.bio.program.das
  Reflects a reference server on the DAS network.
refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  Refinement procedure based on superposition and dynamic programming.
REFLEXIVE - Static variable in class org.biojava.ontology.OntoTools
refp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
refp - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
refRange - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
refreshSequencePanels() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
REFSEQ - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `REFSEQ` indicates that the sequence format is REFSEQ.
REFSEQ_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `REFSEQ_AA` premade REFSEQ | AA.
REFSEQ_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `REFSEQ_DNA` premade REFSEQ | DNA.
REFSEQ_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `REFSEQ_RNA` premade REFSEQ | RNA.
RegexChanger - Class in org.biojava.bio.program.tagvalue
  A ValueChanger.Changer that returns a specific match value using a regex Pattern.
RegexChanger(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexChanger
  Create a new RegexChanger with a pattern.
RegexException - Exception in org.biojava.utils.regex
  An exception thrown by classes of this package.
RegexException(String) - Constructor for exception org.biojava.utils.regex.RegexException
RegexException(Throwable) - Constructor for exception org.biojava.utils.regex.RegexException
RegexException(Throwable, String) - Constructor for exception org.biojava.utils.regex.RegexException
RegexFieldFinder - Class in org.biojava.bio.program.tagvalue
RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder
  Creates a new RegexFiledFinder.
RegexParser - Class in org.biojava.bio.program.tagvalue
  A TagValueParser that splits a line based upon a regular expression.
RegexParser() - Constructor for class org.biojava.bio.program.tagvalue.RegexParser
  Create a new RegexParser with all boolean values set to false.
RegexSplitter - Class in org.biojava.bio.program.tagvalue
  A ValueChanger.Splitter that splits a line of text using a regular expression, returning one value per match.
RegexSplitter(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexSplitter
  Create a new RegexSplitter with a pattern.
regions - Variable in class org.biojava.bio.seq.RemoteFeature.Template
register(RestrictionEnzyme, Set) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
  `register` regisiters a new `RestrictionEnzyme` with the manager.
registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Register an alphabet by name.
registerAlphabet(String[], Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Register and Alphabet by more than one name.
registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  Register a factory used to create handlers for the specified tag in an XML AnnotationType
registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Register a distribution object with this context.
registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
registered(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
  Has a Protease been registered with that name?
registered(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Has an Alphabet been registered by that name
registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Register a UnigeneFactory.
registerFormat(Class) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Register a new format with IOTools for auto-guessing.
registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  Register a factory used to create handlers for the specified tag name
registerModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer
  Registers an HMM with this trainer.
registerModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer
registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  Register a factory used to create handlers for the specified tag in an XML AnnotationType
registerProtease(Protease) - Static method in class org.biojava.bio.proteomics.ProteaseManager
  Registers a protease and ensures its flyweight status
registerTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Register a Distribution and an associated DistributionTrainer object.
registerTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution
  Register an IgnoreCountsTrainer instance as the trainer for this distribution.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution
  Register this distribution with a training context.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution
  Register this paired distribution with a model trainer.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution
  Register an SimpleDistribution.Trainer instance as the trainer for this distribution.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.TranslatedDistribution
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UntrainableDistribution
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState
registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable
  Perform any registration that is necessary with mt.
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM
registrations() - Static method in class org.biojava.bio.symbol.AlphabetManager
  A set of names under which Alphabets have been registered.
Registry - Class in org.biojava.directory
  `Registry` is a factory which gets implementations of the BioJava `SequenceDBLite` interface.
Registry(RegistryConfiguration) - Constructor for class org.biojava.directory.Registry
  Creates a new OBDA `Registry` with the specified configuration.
RegistryConfiguration - Interface in org.biojava.directory
  The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases.
RegistryConfiguration.Composite - Class in org.biojava.directory
  A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
RegistryConfiguration.Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
RegistryConfiguration.Impl - Class in org.biojava.directory
  A simple implementation of RegistryConfiguration backed by a Map.
RegistryConfiguration.Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl
RegistryException - Exception in org.biojava.directory
  A `RegistryException` thrown when the registry cannot find an implementation of a requested `SequenceDB`.
RegistryException() - Constructor for exception org.biojava.directory.RegistryException
  Creates a new `RegistryException` with no detail message.
RegistryException(String) - Constructor for exception org.biojava.directory.RegistryException
  Creates a new `RegistryException` with the specified detail message.
RegistryException(Throwable) - Constructor for exception org.biojava.directory.RegistryException
  Creates a new `RegistryException` with no detail message, wrapping another `Throwable`.
RegistryException(Throwable, String) - Constructor for exception org.biojava.directory.RegistryException
  Deprecated. use new RegistryException(message, cause)
RegistryException(String, Throwable) - Constructor for exception org.biojava.directory.RegistryException
RelabeledAlignment - Class in org.biojava.bio.symbol
  An alignment that relabels another alignment.
RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment
RELATION - Static variable in class org.biojava.ontology.OntoTools
RELATION - Static variable in interface org.biojavax.bio.seq.RichFeature
RELATIONS - Static variable in interface org.biojavax.bio.BioEntry
REMARK - Static variable in interface org.biojavax.DocRef
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
RemoteFeature - Interface in org.biojava.bio.seq
  A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
RemoteFeature.Region - Class in org.biojava.bio.seq
  A tuple of Location and sequence ID.
RemoteFeature.Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region
  Create a new Region.
RemoteFeature.Resolver - Interface in org.biojava.bio.seq
  The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.
RemoteFeature.Template - Class in org.biojava.bio.seq
RemoteFeature.Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
RemoteFeature.Template(Feature.Template) - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
  Creates a RemoteFeature.Template that has the same values as the template passed in.
RemoteTerm - Interface in org.biojava.ontology
  A term in another ontology.
RemoteTerm.Impl - Class in org.biojava.ontology
  Simple in-memory implementation of a remote ontology term.
RemoteTerm.Impl(Ontology, Term, String) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
RemoteTerm.Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
remove() - Method in class org.biojava.bio.structure.AtomIterator
  does nothing.
remove() - Method in class org.biojava.bio.structure.GroupIterator
  does nothing .
remove() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
remove(Object) - Method in interface org.biojava.utils.cache.CacheMap
  Explicitly remove an object.
remove(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
remove(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
remove() - Method in class org.biojava.utils.MergingIterator
remove(Object) - Method in class org.biojava.utils.MergingSet
remove(Object) - Method in class org.biojavax.ga.util.WeightedSet
REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
removeActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
removeAllOrganisms() - Method in class org.biojavax.ga.impl.AbstractPopulation
removeAllOrganisms() - Method in interface org.biojavax.ga.Population
  Removes all the `Organisms` in this `Population`
removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.AbstractPopulation
removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.SimplePopulation
removeAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
  Remove an Annotation from the list.
removeAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
  Remove a DB from this view.
removeAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
removeBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
  Remove the BioEntry associated with an ID from the database.
removeBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
removeBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `removeChangeListener` removes a listener.
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Remove a ChangeListener from a projected feature.
removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
removeChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
  Deprecated. use removeChangeListener(cl, ChangeType.UNKNOWN)
removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
  Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
  Remove a listener that was interested in all types of changes.
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
  Remove a listener that was interested in a specific types of changes.
removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
removeChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Remove a listener that was interested in all types of changes. IGNORED
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Remove a listener that was interested in a specific types of changes. IGNORED
removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Remove a Taxon as a child to this one.
removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
removeComment(Comment) - Method in interface org.biojavax.bio.BioEntry
  Removes a comment instance from this bioentry.
removeComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
  Removes a comment instance from this bioentry.
removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
removeComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
  Remove a distributed data source.
removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `removeDelegateRenderer` removes any association of the given `OptimizableFilter` with a `BeadFeatureRenderer`.
removeDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
  Removes a descriptor.
removeDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Removes a descriptor.
removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `removeEnzyme` removes an enzyme from those to be searched for in the `Sequence`.
removeFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
  Remove a feature from this FeatureHolder.
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Remove a feature attached to this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
  Remove a feature from this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
removeFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
removeFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Remove the dying child.
removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Remove the dying child.
removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
removeFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Remove a feature from this FeatureHolder.
removeFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Remove a feature from this FeatureHolder.
removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
  Remove a FeatureHolder from the set of FeatureHolders which are merged.
removeFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureHolder
  Removes a relationship from this feature holder.
removeFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Removes a relationship from this feature holder.
removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
removeFromEnvironment(String) - Method in class org.biojava.naming.ObdaContext
removeGap(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Remove a single gap at position pos in this GappedSymbolList.
removeGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
removeGaps(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  because there is a bug in GappedSymbolList
removeGaps(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Remove some gaps at position pos in this GappedSymbolList.
removeGaps(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
removeGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the genetic code annotation from the taxon in the database.
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
removeKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `removeKey` removes the specified key.
removeKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
  Remove a key.
removeLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Remove a piece of text from the label
removeLeftValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the left value from the specified taxon in the database.
removeListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
  remove a ChangeListener associated with given key.
removeListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
removeMitochondrialGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon.
removeName(Connection, DBHelper, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the specified name from of the taxon from the database.
removeName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Removes the name from the given name class.
removeName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Removes the name from the given name class.
removeNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
  Removes a note from this annotation. You cannot remove notes from the Empty RichAnnotation
removeNote(Note) - Method in interface org.biojavax.RichAnnotation
  Removes a note from this annotation.
removeNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
  Removes a note from this annotation.
removeOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
removeOrganism(Organism) - Method in interface org.biojavax.ga.Population
  Kills off the organism
removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
removeOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
removeOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
removeOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
  Removes all the `Organisms` in `orgs`
removeOrganisms(Set) - Method in interface org.biojavax.ga.Population
  Removes all the `Organisms` in `orgs`
removeOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
  Remove an orthologue from the set.
removeOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
removeOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  removes a specified OrthoPair relationship from this group.
removeOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
  Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated. Removes a parse error listener from the list of listeners if it is included.
removeParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
  Removes a parse error listener from the list of listeners.
removeProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
removeProperty(Object) - Method in interface org.biojava.bio.Annotation
  Delete a property.
removeProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
removeProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
  Remove a value from the specified property slot.
removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
removeProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
  Delete a property. You cannot remove properties from the Empty RichAnnotation
removeProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
  Delete a property. Strictly it will remove the first `Note` which matches the `key` (or a `Term` made with a `String` key)..
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
removeRank(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Removes the rank persistently from the taxon in the database.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
  Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Removes a ranked cross reference from the existing set.
removeRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
  Removes a ranked cross reference from the existing set.
removeRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
  Removes a ranked docref instance from this bioentry.
removeRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
  Removes a ranked docref instance from this bioentry.
removeRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
  Removes a relation instance from this bioentry.
removeRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
  Removes a relation instance from this bioentry.
removeRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
  `removeRenderer` removes a renderer.
removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  `removeRenderer` removes a renderer.
removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
  Remove a repository from FeaturTypes.
removeRichSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
removeRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
removeRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
  Remove the RichSequence associated with an ID from the database.
removeRightValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the right value from the specified taxon in the database.
removeSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
  Remove a secondary key.
removeSequence(Object) - Method in interface org.biojava.bio.alignment.ARAlignment
removeSequence(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
removeSequence(String) - Method in class org.biojava.bio.program.das.DASSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
removeSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
  `removeSequence` always throws a `ChangeVetoException` as this implementation is immutable.
removeSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
removeSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
  Remove the sequence associated with an ID from the database.
removeSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
  Not supported, you can't remove a sequence from a WebDB!
removeSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
removeSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
removeSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `removeSequenceViewerListener` removes a listener for mouse click `SequenceViewerEvent`s.
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `removeSequenceViewerListener` removes a listener for mouse click `SequenceViewerEvent`s.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `addSequenceViewerMotionListener` removes a listener for mouse motion `SequenceViewerEvent`s.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `addSequenceViewerMotionListener` removes a listener for mouse motion `SequenceViewerEvent`s.
removeSet(Set) - Method in class org.biojava.utils.MergingSet
removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel
  Remove a state from the model.
removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
removeState(State) - Method in class org.biojava.bio.dp.WMAsMM
removeSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
  Remove a symbol from this alphabet.
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
  `SoftMaskedAlphabet`s cannot remove `Symbol`s.
removeSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
removeSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
removeSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
removeSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
removeSynonym(Object) - Method in interface org.biojava.ontology.Term
  Remove a synonym for this term.
removeSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Remove a synonym for this term.
removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Remove a synonym for this term. NOT IMPLEMENTED
removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Remove a tag so that it will not be retained.
removeTaxon(Connection, DBHelper, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database.
removeTaxon(Connection, int, DBHelper) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.
removeVariableModifications(char) - Method in class org.biojava.bio.proteomics.MassCalc
  Remove all variable modifications assocaited with this residue.
removeVariableModifications(Symbol) - Method in class org.biojava.bio.proteomics.MassCalc
  Remove all variable modifications assocaited with this residue.
rename(Name, Name) - Method in class org.biojava.naming.ObdaContext
rename(String, String) - Method in class org.biojava.naming.ObdaContext
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
render(Graphics2D) - Method in interface org.biojava.bio.gui.glyph.Glyph
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `renderBead` should be overridden by the concrete `BeadRenderer`.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
  `renderBead` should implement rendering for this bead type only.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  `renderBead` renders features as simple ellipse.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  `renderBead` renders features as simple rectangle.
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
  `renderBead` renders features as a rectangle with rounded corners.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
RENDERER - Static variable in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  Constant `RENDERER` indicating a change to the renderer.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  Constant `RENDERER` is a `ChangeType` which indicates a change to the renderer, requiring a layout update.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePanel
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
RENDERER - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  Constant `RENDERER` is a `ChangeType` which indicates a change to the renderer, requiring a layout update.
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
  Constant `RENDERERS` indicating a change to the renderers handled by the overlay.
RENDERERS - Static variable in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `renderFeature` draws a feature using the supplied graphics context.
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
renderFeature(Graphics2D, Feature, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
  `renderImageMap` writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.ImageMapRenderer
  `renderImageMap` renders the `Feature` as set of image map hotspots.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `renderImageMap` writes a set of image map coordinates corresponding to the rectangle drawn by the renderer.
renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
  `renderImageMap` writes a set of image map coordinates corresponding to the rectangle sections drawn by the renderer.
renderLocation(Graphics2D, SequenceRenderContext, Location) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
  Render another "exon" in the correct translation frame.
renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Renumber the view indexes from block, adding delta to each offset.
REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
ReparentContext - Class in org.biojava.bio.seq.projection
  A good base class to implement ProjectionContext from.
ReparentContext(FeatureHolder, FeatureHolder) - Constructor for class org.biojava.bio.seq.projection.ReparentContext
RepeatedCharSequence - Class in org.biojava.utils
RepeatedCharSequence(int, char) - Constructor for class org.biojava.utils.RepeatedCharSequence
RepeatedCharSequence() - Constructor for class org.biojava.utils.RepeatedCharSequence
replacement - Variable in class org.biojava.bio.symbol.Edit
replicate(String) - Method in class org.biojavax.ga.impl.SimpleOrganism
replicate(String) - Method in interface org.biojavax.ga.Organism
  Creates a replica of this `Organism` with a new name.
reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
reportExon(RangeLocation, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
reportExon(RangeLocation, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf
  Allows nesting class that manages a transcript template to gain information about its extent from nested elements that represent exons.
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
  Allows nesting class that manages a gene template to gain information about its extent from nested elements.
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
reportFeature(Location) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
reportFeature(Location) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
  Allows nesting class that manages a gene template to gain information about its extent from nested elements.
reportMatch(SymbolList, Pattern, int, int) - Method in interface org.biojava.utils.regex.Search.Listener
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVECallbackItf
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
repositorySubset - Variable in class org.biojava.bibliography.BiblioEntryStatus
  Some bibliographic repositories consist of several, or even many, databases.
requestsQueued() - Method in class org.biojava.utils.SimpleThreadPool
  `requestsQueued` returns the number of `Runnable`s currently queued.
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
reset() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
reset() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
  resets the internal state of this filter including any cached evaluations.
reset() - Method in class org.biojava.utils.io.CountedBufferedReader
reset() - Method in class org.biojava.utils.regex.Matcher
  Resets this matcher.
reset(SymbolList) - Method in class org.biojava.utils.regex.Matcher
  Resets this matcher with a new input SymbolList.
reset() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
reset() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms
reset() - Method in class org.biojavax.utils.CRC64Checksum
resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment
  check that begining is at 1 otherwise shift everything over
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `resizeAndValidate` sets the minimum, preferred and maximum sizes of the component according to the current visible symbol count.
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanel
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `resizeAndValidate` sets the minimum, preferred and maximum sizes of the component according to the current leading and trailing borders, renderer depth and visible symbol count.
resizeArray(Object, int) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
  Reallocates an array with a new size, and copies the contents of the old array to the new array.
resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
resolve(RemoteFeature) - Method in interface org.biojava.bio.seq.RemoteFeature.Resolver
  Resolve rFeat.
resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
  Return the actual point that the specified location should claim to occupy.
RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyLocation
  Use the arithmetic mean of the `inner' and `outer' values, unless the outer value is unbounded.
RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
RESOLVE_INNER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
  Always use the `inner' values.
RESOLVE_MAX - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
RESOLVE_MIN - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
RESOLVE_OUTER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
  Use the `outer' values, unless they are unbounded in which case the `inner' values are used.
resolveAlphabet(String) - Static method in class org.biojava.bio.program.ssbind.AlphabetResolver
  `resolveAlphabet` returns an appropriate `Alphabet` for an arbitrary identifier.
resolveCommands(String, Properties) - Static method in class org.biojava.utils.process.ExternalProcess
  Resolves the given command line by replacing all placeholder of the format `%NAME%` with the values from the given properties for the corresponding keys of the format `NAME`.
resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver
resolveInt(int) - Method in class org.biojava.ontology.IntegerOntology
resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  Delegate for the getMax() method.
resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
  Delegate for the getMin() method.
resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template
RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
ResourceEntityResolver - Class in org.biojava.utils.xml
  SAX EntityResolve which looks up system IDs as resources from a Java ClassLoader.
ResourceEntityResolver(String) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
  Construct a resolver which searches for resources in the specified path relative to the current classloader.
ResourceEntityResolver(String[]) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
  Construct a resolver which searches for resources in the specified list of directories relative to the current classloader.
ResourceEntityResolver(String[], ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
  Construct a resolver which searches for resources in the specified list of directories relative to the supplied classloader.
ResourceEntityResolver(String, ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
  Construct a resolver which searches for resources in the specified path relative to the supplied classloader.
RestrictionEnzyme - Class in org.biojava.bio.molbio
  `RestrictionEnzyme` represents a restriction enzyme according to the REBASE standard.
RestrictionEnzyme(String, SymbolList, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
  Creates a new `RestrictionEnzyme` which cuts within or downstream of the recognition site.
RestrictionEnzyme(String, SymbolList, int, int, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
  Creates a new `RestrictionEnzyme` of the unusual type which cuts both upstream and downstream of its recognition site.
RestrictionEnzymeManager - Class in org.biojava.bio.molbio
  `RestrictionEnzymeManager` manages collections of static `RestrictionEnzyme` instances.
RestrictionMapper - Class in org.biojava.bio.molbio
  `RestrictionMapper` is a class for annotating `Sequence`s with `Feature`s which represent restriction sites.
RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper
  Creates a new `RestrictionMapper` which will use the specified `ThreadPool`.
RestrictionSite - Interface in org.biojava.bio.molbio
  `RestrictionSite` represents the recognition site of a restriction enzyme.
RestrictionSite.Template - Class in org.biojava.bio.molbio
  `Template` for construction of `RestrictionSite`s.
RestrictionSite.Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template
RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
retainAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
returnData(Object) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  provides a standardised way of returning an object that represents the result of parsing the child element
RevCompSequence - Class in org.biojava.bio.seq.impl
  A reverse complement view onto `Sequence` interface.
RevCompSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
  URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.
RevCompSequence(Sequence, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
reverse(int[]) - Static method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Utility method for reversing an int[] array.
reverse(SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
  A reversed view onto a SymbolList.
reverseComplement() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
reverseComplement() - Method in interface org.biojava.bio.chromatogram.Chromatogram
  Returns a new `Chromatogram` representing the reverse complement of this one.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
  Retrieve a reverse-complement view of list.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
  Retrieve a reverse-complement view of list.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
  Retrieve a reverse-complement view of list.
reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
  Reverse-complement a sequence, and flip all of its features.
reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Return a symbol list containing the reverse complement of the base call data for the given label.
reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.program.scf.SCF
  Overrides `AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object)` to support the 7 quality values from the SCF.
reverseComplementBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Returns a new base call alignment that is the reverse complement of one in this chromatogram.
reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Returns a new instance of this AbstractChromatogram subclass for use in `AbstractChromatogram.reverseComplement()`.
reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
reverseComplementInstance() - Method in class org.biojava.bio.program.abi.ABIFChromatogram
reverseComplementInstance() - Method in class org.biojava.bio.program.scf.SCF
reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
ReversibleTranslationTable - Interface in org.biojava.bio.symbol
  A translation table that can also translate from the target to source alphabet.
revertFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
revertFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Unproject a feature.
revertFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
revertFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
  Transform a filter on projected features so that it applies to unprojected features.
revertFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
revertLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
revertLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
  Revert a location, translating and flipping as required.
revertLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
revertStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
revertTemplate(Feature.Template, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine
  Revert a template so that it can be used on the original feature-space.
revertTemplate(ProjectionContext, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector
RichAnnotatable - Interface in org.biojavax
  Annotatable objects that can have rich annotations.
RichAnnotation - Interface in org.biojavax
  An annotation collection which stores annotations as Note objects.
RichFeature - Interface in org.biojavax.bio.seq
  Represents a feature that can be given name and rank and be moved from one sequence to another.
RichFeature.Template - Class in org.biojavax.bio.seq
  Added-value extension of Feature.Template including bits we're interested in, eg.
RichFeature.Template() - Constructor for class org.biojavax.bio.seq.RichFeature.Template
RichFeature.Tools - Class in org.biojavax.bio.seq
  Some useful tools for working with features.
RichFeatureHolder - Interface in org.biojavax.bio.seq
  Holds feature relationships.
RichFeatureRelationship - Interface in org.biojavax.bio.seq
  Represents the relation between two bioentries.
RichLocation - Interface in org.biojavax.bio.seq
  Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichLocation.Strand - Class in org.biojavax.bio.seq
  This class represents a strand on which a location may lie.
RichLocation.Tools - Class in org.biojavax.bio.seq
  Some useful tools for working with Locations.
RichObjectBuilder - Interface in org.biojavax
  This interface allows a class to generate Rich objects based on a class name and some parameters.
RichObjectFactory - Class in org.biojavax
  Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc.
RichSeqIOAdapter - Class in org.biojavax.bio.seq.io
  This class implements all methods of RichSeqIOListener and takes no action.
RichSeqIOAdapter() - Constructor for class org.biojavax.bio.seq.io.RichSeqIOAdapter
  Creates a new instance of RichSeqIOAdapter
RichSeqIOListener - Interface in org.biojavax.bio.seq.io
  An interface for classes that listen to BioEntry or RichSequence I/O streams.
RichSequence - Interface in org.biojavax.bio.seq
  A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequence.IOTools - Class in org.biojavax.bio.seq
  A set of convenience methods for handling common file formats.
RichSequence.IOTools.SingleRichSeqIterator - Class in org.biojavax.bio.seq
  Used to iterate over a single rich sequence
RichSequence.IOTools.SingleRichSeqIterator(Sequence) - Constructor for class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
  Creates an iterator over a single sequence.
RichSequence.Terms - Class in org.biojavax.bio.seq
  Stores a number of useful terms used across many sequence formats for consistency's sake.
RichSequence.Terms() - Constructor for class org.biojavax.bio.seq.RichSequence.Terms
RichSequence.Tools - Class in org.biojavax.bio.seq
  Some useful tools for working with RichSequence objects.
RichSequenceBuilder - Interface in org.biojavax.bio.seq.io
  An interface for objects that can build RichSequences.
RichSequenceBuilderFactory - Interface in org.biojavax.bio.seq.io
  Simple factory for constructing new RichSequenceBuilder objects.
RichSequenceDB - Interface in org.biojavax.bio.db
  A database of RichSequences with accessible keys and iterators over all sequences.
RichSequenceDBLite - Interface in org.biojavax.bio.db
  A database of RichSequences.
RichSequenceFormat - Interface in org.biojavax.bio.seq.io
  Allows a file format to be read/written as RichSequences.
RichSequenceFormat.BasicFormat - Class in org.biojavax.bio.seq.io
  Provides a basic format with simple things like line-widths precoded.
RichSequenceFormat.BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
RichSequenceFormat.HeaderlessFormat - Class in org.biojavax.bio.seq.io
  Provides the basic implementation required for simple header/footer-less files such as Genbank.
RichSequenceFormat.HeaderlessFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
RichSequenceHandler - Interface in org.biojavax.bio.seq
  An interface for classes that know how to handle subsequence operations.
RichSequenceIterator - Interface in org.biojavax.bio.seq
  Essentially the same as SequenceIterator.
RichStreamReader - Class in org.biojavax.bio.seq.io
  Parses a stream into sequences.
RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
  Creates a new stream reader on the given input stream, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
  Creates a new stream reader on the given reader, which will attempt to read sequences in the given format, having symbols from the given tokenization, and pass them to the given factory to be transformed into RichSequence objects in the given namespace.
RichStreamWriter - Class in org.biojavax.bio.seq.io
  Writes all of the sequences from a SequenceIterator to a stream with a particular format.
RichStreamWriter(OutputStream, RichSequenceFormat) - Constructor for class org.biojavax.bio.seq.io.RichStreamWriter
  Generate a new RichStreamWriter to the stream os and using format.
rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
rightPad(String, int) - Static method in class org.biojavax.utils.StringTools
  Pads a string to be a certain width by appending spaces.
rightPad(String, char, int) - Static method in class org.biojavax.utils.StringTools
  Pads a string to be a certain width by appending given symbols.
rights - Variable in class org.biojava.bibliography.BibRef
  It specifies information about rights over the cited resource.
RIGHTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
  Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.
RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `RNA` indicates that a sequence contains RNA (ribonucleic acid) symbols.
RNATools - Class in org.biojava.bio.seq
  Useful functionality for processing DNA and RNA sequences.
ROLE_ATTR_QUERYABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A role of an attribute.
ROLE_ATTR_RETRIEVABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A role of an attribute.
rollback() - Method in class org.biojava.bio.seq.db.BioIndex
rollback() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `rollback` rolls back changes made since the last `commit`.
rollback() - Method in interface org.biojava.bio.seq.db.IndexStore
  Discard all uncommited changes.
rollback() - Method in class org.biojava.bio.seq.db.TabIndexStore
rollback() - Method in interface org.biojava.utils.Commitable
  `rollback` reverses pending changes to restore initial (or prior commit) state.
rollback() - Method in class org.biojava.utils.FileAsList
rotate(Atom, double[][]) - Static method in class org.biojava.bio.structure.Calc
  rotate a single atom aroud a rotation matrix.
rotate(Structure, double[][]) - Static method in class org.biojava.bio.structure.Calc
  rotate a structure .
rotate(Group, double[][]) - Static method in class org.biojava.bio.structure.Calc
  rotate a structure .
rotate(Atom, Matrix) - Static method in class org.biojava.bio.structure.Calc
  rotate an atom around a Matrix object
rotate(Group, Matrix) - Static method in class org.biojava.bio.structure.Calc
  rotate a group object
rotate(Structure, Matrix) - Static method in class org.biojava.bio.structure.Calc
  rotate a structure object
RoundRectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
  `RoundRectangularBeadRenderer` renders features as rectangles with rounded corners.
RoundRectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
  Creates a new `RoundRectangularBeadRenderer` object with the default settings.
RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double) - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
  Creates a new `RoundRectangularBeadRenderer`.
rowSymbols - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
rpp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
rppat - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
RulerRenderer - Class in org.biojava.bio.gui.sequence
  `RulerRenderer` renders numerical scales in sequence coordinates.
RulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
  Creates a new `RulerRenderer` with the default setting of ticks pointing downwards.
RulerRenderer(int) - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
  Creates a new `RulerRenderer` with the specified tick direction.
run() - Method in class org.biojava.utils.process.ReaderInputHandler
run() - Method in class org.biojava.utils.process.ReaderWriterPipe
run() - Method in class org.biojava.utils.process.SimpleInputHandler
run() - Method in class org.biojava.utils.process.StreamPipe
run(GAStoppingCriteria) - Method in interface org.biojavax.ga.GeneticAlgorithm
  Iterates the Algorithm until the stopping criteria are met.
run(GAStoppingCriteria) - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm

## S

s() - Static method in class org.biojava.bio.seq.NucleotideTools
s() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Serine
S_SCROFA - Static variable in interface org.biojava.bio.program.homologene.Taxon
sample() - Method in class org.biojavax.ga.util.WeightedSet
  Randomly samples an `Object` from the `Set` according to its weight.
sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution
sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution
  Sample a symbol from this state's probability distribution.
sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution
sampleSymbol() - Method in class org.biojava.bio.dist.PairDistribution
sampleSymbol() - Method in class org.biojava.bio.dist.TranslatedDistribution
SAX2StAXAdaptor - Class in org.biojava.bio.seq.io.agave
  Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
  Construct a new SAX Content handler which wraps a StAX handler.
SAX2StAXAdaptor - Class in org.biojava.utils.stax
  Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor
  Construct a new SAX Content handler which wraps a StAX handler.
sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
scale(Chromatogram, int) - Method in interface org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler
  Returns the remapped coordinate for the provided trace sample index of the given chromatogram.
scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
SCF - Class in org.biojava.bio.program.scf
  A `Chromatogram` as loaded from an SCF v2 or v3 file.
SCF() - Constructor for class org.biojava.bio.program.scf.SCF
  Creates a new, completely empty SCF.
SCF_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
  The magic number for SCF files.
SCHEMA - Static variable in interface org.biojava.bio.seq.FeatureHolder
  Signals that the schema of this FeatureHolder has changed.
SCI_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
SCIENTIFIC - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
  Use this to define scientific names for things.
SCIENTIFIC_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
SCINAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
score - Variable in class org.biojava.bio.dp.BackPointer
  The score of this element of the DP matrix.
score - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `score` of the search which produced the alignment.
scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
SCORES - Static variable in interface org.biojava.bio.dp.StatePath
  Alignment label for the likelyhood at each step.
scores - Variable in class org.biojava.bio.dp.twohead.Cell
ScoreType - Interface in org.biojava.bio.dp
  This class computes the score that is used to be used in a DP optimisation.
ScoreType.NullModel - Class in org.biojava.bio.dp
  In this class, calculateScore returns the probability of a Symbol being emitted by the null model.
ScoreType.NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel
ScoreType.Odds - Class in org.biojava.bio.dp
  In this class, calculateScore returns the odds ratio of a symbol being emitted.
ScoreType.Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds
ScoreType.Probability - Class in org.biojava.bio.dp
  In this class, calculateScore returns the probability of a Symbol being emitted.
ScoreType.Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability
scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP
  Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int) - Static method in class org.biojava.bio.dp.DP
  Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
search(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB
  Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.
search(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
search(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
search(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
search(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
search(String, SymbolList, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
search(String, SymbolList, SearchListener) - Method in interface org.biojava.bio.program.ssaha.DataStore
  Search the DataStore with a symbol list.
search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
  Using this sequence similarity searcher, search with the given sequence against the given sequence database.
search(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory
  Deprecated. Retrieve a Taxon that matches some ID.
search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
search(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
search(Name, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
search(Name, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
search(Name, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
search(String, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
search(String, Attributes) - Method in class org.biojava.naming.ObdaContext
search(String, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
search(String, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
search(SymbolList) - Method in class org.biojava.utils.automata.PatternBlitz
Search - Class in org.biojava.utils.regex
  A utility class to make searching a Sequence with many regex patterns easier.
Search(FiniteAlphabet) - Constructor for class org.biojava.utils.regex.Search
search(SymbolList) - Method in class org.biojava.utils.regex.Search
  search the Sequence with the patterns already registered with this object.
search(SymbolList, int, int) - Method in class org.biojava.utils.regex.Search
  search part of the SymbolList with the patterns already registered with this object.
Search.Listener - Interface in org.biojava.utils.regex
  Interface for a class that will recieve match information from this class.
searchAnnotation(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
SearchBuilder - Interface in org.biojava.bio.search
  The `SearchBuilder` interface is to be used by objects which accumulate state via a `SearchContentHandler` and then construct a `SeqSimilaritySearchResult` object.
SearchContentAdapter - Class in org.biojava.bio.search
  An adapter for SearchContentHandler.
SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter
SearchContentFilter - Class in org.biojava.bio.search
  Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
SearchContentFilter(SearchContentHandler) - Constructor for class org.biojava.bio.search.SearchContentFilter
SearchContentHandler - Interface in org.biojava.bio.search
  `SearchContentHandler` is a notification interface for objects which listen to search stream parsers.
SearchContentHandlerDebugger - Class in org.biojava.bio.search
  This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.
SearchContentHandlerDebugger() - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
  Create an instance that dumps to System.out.
SearchContentHandlerDebugger(PrintStream) - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
SearchException - Exception in org.biojava.bio.program.ssaha
  There has been some failure that prevents a search from completing.
SearchException(String) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
SearchException(Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
SearchException(String, Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
SearchListener - Interface in org.biojava.bio.program.ssaha
  The interface used to inform interested parties that some sequence has been searched and something found.
SearchListener.Echo - Class in org.biojava.bio.program.ssaha
  A SearchListener that prints events out to a PrintStream.
SearchListener.Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
SearchListener.FilterByLength - Class in org.biojava.bio.program.ssaha
  A simple listener that filters out all hits that are too short.
SearchListener.FilterByLength(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
SearchListener.Tee - Class in org.biojava.bio.program.ssaha
  A SearchListener that passes events on to two delegate listeners.
SearchListener.Tee(SearchListener, SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Tee
SearchListener.Wrapper - Class in org.biojava.bio.program.ssaha
  A simple wrapper implementation.
SearchListener.Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
sec() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Selenocysteine (U)
SEC_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SECONDARY_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
SECONDARY_ACCESSIONS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
secondarySequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
  `secondarySequenceToGraphics` converts a sequence coordinate on the secondary sequence to a graphical position.
secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `secondarySequenceToGraphics` converts a sequence index to a graphical position.
secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
SecondaryStructureFeatureRenderer - Class in org.biojava.bio.gui.sequence
  A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
SecondaryStructureFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer
sectp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
seek(long) - Method in class org.biojava.utils.io.CachingInputStream
seek(long) - Method in class org.biojava.utils.io.RandomAccessReader
  `seek` moves the pointer to the specified position.
seek(long) - Method in interface org.biojava.utils.io.Seekable
  Moves the pointer in the inputstream such that the byte starting at `pos` are returned by the next read.
Seekable - Interface in org.biojava.utils.io
  This interface provides a collective name for IO classes that implement a seek function (e.g., `RandomAccessFile`).
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.ProportionalSelection
select(Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.SelectionFunction
  Selects a `Population` of `Organisms` for replication based on their fitness.
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
  Selects individuals whose fitness (as determined by the `FitnessFunction`) is more than the cutoff.
SELECTION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
SelectionFunction - Interface in org.biojavax.ga.functions
  Selects Organisms for Replication and returns the offspring.
SelectionFunction.SelectAll - Class in org.biojavax.ga.functions
SelectionFunction.SelectAll() - Constructor for class org.biojavax.ga.functions.SelectionFunction.SelectAll
SelectionFunction.Threshold - Class in org.biojavax.ga.functions
  Selects individuals who's fitness exceeds a threshold value.
SelectionFunction.Threshold(double) - Constructor for class org.biojavax.ga.functions.SelectionFunction.Threshold
SEPARATED - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
SEPARATOR_COLOR - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating the color that the call separators should be.
SEPARATOR_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option providing the the stroke to use for drawing call separators.
SEPARATOR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
SeqContentPattern - Class in org.biojava.bio.search
  A pattern that can be used to find regions with given sequence content.
SeqContentPattern(FiniteAlphabet) - Constructor for class org.biojava.bio.search.SeqContentPattern
  Create a new SeqContentPattern over an alphabet.
SeqFileFormer - Interface in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOAdapter - Class in org.biojava.bio.seq.io
  Adapter class for SeqIOListener that has empty methods.
SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter
SeqIOConstants - Class in org.biojava.bio.seq.io
  `SeqIOConstants` contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.
SeqIOConstants() - Constructor for class org.biojava.bio.seq.io.SeqIOConstants
SeqIOEventEmitter - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOEventEmitter(Comparator, Comparator) - Constructor for class org.biojava.bio.seq.io.SeqIOEventEmitter
  Deprecated.
SeqIOFilter - Class in org.biojava.bio.seq.io
  Base-class for listeners that pass filtered events onto another listener.
SeqIOFilter(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.SeqIOFilter
  Create a new SeqIOFilter that will forward events on to another listener.
SeqIOListener - Interface in org.biojava.bio.seq.io
  Notification interface for objects which listen to a sequence stream parser.
SeqIOTools - Class in org.biojava.bio.seq.io
  Deprecated. use org.biojavax.bio.seq.RichSequence.IOTools
seqNameForID(int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
seqNameForID(int) - Method in interface org.biojava.bio.program.ssaha.DataStore
  Resolve an ID to a sequence name.
seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
SeqSimilarityAdapter - Class in org.biojava.bio.program.ssbind
  A `SeqSimilarityAdapter` converts SAX events into method calls on a `SearchContentHandler` implementation.
SeqSimilarityAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
SeqSimilaritySearcher - Interface in org.biojava.bio.search
  Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilaritySearchHit - Interface in org.biojava.bio.search
  Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
SeqSimilaritySearchHit.ByScoreComparator - Class in org.biojava.bio.search
  `ByScoreComparator` compares `SeqSimilaritySearchHit`s by their score.
SeqSimilaritySearchHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
SeqSimilaritySearchHit.BySubHitCountComparator - Class in org.biojava.bio.search
  `BySubHitCountComparator` compares `SeqSimilaritySearchHit`s by their number of sub-hits.
SeqSimilaritySearchHit.BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
SeqSimilaritySearchResult - Interface in org.biojava.bio.search
  Objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit - Interface in org.biojava.bio.search
  Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.
SeqSimilaritySearchSubHit.ByScoreComparator - Class in org.biojava.bio.search
  `ByScoreComparator` compares `SeqSimilaritySearchSubHit`s by their score.
SeqSimilaritySearchSubHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
SeqSimilaritySearchSubHit.BySubjectStartComparator - Class in org.biojava.bio.search
  `BySubjectStartComparator` compares `SeqSimilaritySearchSubHit`s by their start position on the subject sequence.
SeqSimilaritySearchSubHit.BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
SeqSimilarityStAXAdapter - Class in org.biojava.bio.program.ssbind
  `SeqSimilarityStAXAdapter` is a handler for XML conforming to the BioJava BlastLike DTD.
SeqSimilarityStAXAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
SeqSimilarityStAXHandler - Class in org.biojava.bio.program.ssbind
  `SeqSimilarityStAXHandler` is a base class for creating modular StAX handlers which send callbacks to a `SeqSimilarityStAXAdapter`.
SeqSimilarityStAXHandler(SeqSimilarityStAXAdapter) - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
  Creates a new `SeqSimilarityStAXHandler` which simply maintains a list of `StAXHandlerBinding`s and delegates to any suitable `StAXContentHandler` bound by one of them.
seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
seqString() - Method in class org.biojava.bio.program.das.DASSequence
seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
seqString() - Method in class org.biojava.bio.seq.impl.DummySequence
seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
seqString() - Method in class org.biojava.bio.seq.impl.SubSequence
seqString() - Method in class org.biojava.bio.seq.impl.ViewSequence
seqString() - Method in class org.biojava.bio.seq.NewSimpleAssembly
seqString() - Method in class org.biojava.bio.seq.SimpleAssembly
seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment
seqString() - Method in interface org.biojava.bio.symbol.SymbolList
  Stringify this symbol list.
seqString(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Stringify this Sequences.

  It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

seqString(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Stringify this Sequences.
seqString() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Stringify this symbol list. ALWAYS RETURNS THE AMBIGUITY SYMBOL REPRESENTED AS A STRING
seqString(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Stringify this Sequences.
seqString() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Stringify this symbol list.
SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath
  Alignment label for the emitted sequence.
SEQUENCE - Static variable in class org.biojava.bio.program.abi.ABITools
  Alignment label for the DNA sequence row.
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
Sequence - Interface in org.biojava.bio.seq
  A biological sequence.
SEQUENCE_CHECKSUM_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
SEQUENCE_FORMAT - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  `SEQUENCE_FORMAT` is the key used to identify the format of the indexed sequence files represented by the store in the OBDA config.dat files.
SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
SEQUENCE_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
SEQUENCE_MODIFIED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
SEQUENCE_TOPOLOGY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SEQUENCE_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SEQUENCE_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
SequenceAlignment - Class in org.biojava.bio.alignment
  This Interface provides methods for the alignment of biosequences.
SequenceAlignment() - Constructor for class org.biojava.bio.alignment.SequenceAlignment
SequenceAlignmentSAXParser - Class in org.biojava.bio.program.sax
  A SAX2 parser for dealing with a sequence alignments.
SequenceAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
  Initialises internal state Sets namespace prefix to "biojava"
SequenceAnnotator - Interface in org.biojava.bio.seq
  An object which adds some additional information to a Sequence.
SequenceBuilder - Interface in org.biojava.bio.seq.io
  Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.
SequenceBuilderBase - Class in org.biojava.bio.seq.io
  Basic SequenceBuilder implementation which accumulates all notified information.
SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase
SequenceBuilderFactory - Interface in org.biojava.bio.seq.io
  Simple factory for constructing new SequenceBuilder objects.
SequenceBuilderFilter - Class in org.biojava.bio.seq.io
  Base-class for builders that pass filtered events onto another builder.
SequenceBuilderFilter(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SequenceBuilderFilter
  Create a new SeqIOFilter that will forward events on to another listener.
SequenceContentHandlerBase - Class in org.biojava.bio.seq.io.game
  StAX handler for elements containing sequence
SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
SequenceDB - Interface in org.biojava.bio.seq.db
  A database of sequences with accessible keys and iterators over all sequences.
SequenceDBDataSource - Class in org.biojava.bio.seq.distributed
  Turn an entire SequenceDB instance into a DistDataSource.
SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource
SequenceDBInstallation - Interface in org.biojava.bio.seq.db
  A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.
SequenceDBLite - Interface in org.biojava.bio.seq.db
  A database of sequences.
SequenceDBProvider - Interface in org.biojava.directory
  Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard.
SequenceDBSearchHit - Class in org.biojava.bio.search
  Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated. Creates a new `SequenceDBSearchHit` object.
SequenceDBSearchResult - Class in org.biojava.bio.search
  Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated. Creates a new `SequenceDBSearchResult`.
SequenceDBSearchSubHit - Class in org.biojava.bio.search
  Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated. Creates a new `SequenceDBSearchSubHit` object.
SequenceDBSequenceBuilder - Class in org.biojava.bio.seq.io
  This SequenceBuilder has a variety of modes of operation.
SequenceDBSequenceBuilder(SequenceDB, int) - Constructor for class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
  constructor
SequenceDBWrapper - Class in org.biojava.bio.seq.db
  An abstract implementation of SequenceDB that wraps up another database.
SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper
SequenceDBWrapper.SequencesForwarder - Class in org.biojava.bio.seq.db
SequenceDBWrapper.SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
SequenceFactory - Interface in org.biojava.bio.seq
  Deprecated. use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder
SequenceFormat - Interface in org.biojava.bio.seq.io
  Defines what a sequence format does.
SequenceHandler - Interface in org.biojava.bio.seq.io.agave
  mark interface
sequenceIterator() - Method in class org.biojava.bio.program.das.DASSequenceDB
sequenceIterator() - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
sequenceIterator() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
  Deprecated.
sequenceIterator() - Method in class org.biojava.bio.seq.db.DummySequenceDB
sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB
sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB
  Returns a SequenceIterator over all sequences in the database.
SequenceIterator - Interface in org.biojava.bio.seq
  An iterator over a bag of sequences.
sequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
sequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
  Returns a SequenceIterator over all sequences in the database. Will always return an instance of RichSequenceIterator.
SequencePanel - Class in org.biojava.bio.gui.sequence
  A panel that displays a Sequence.
SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel
  Create a new SequencePanel.
SequencePanel.Border - Class in org.biojava.bio.gui.sequence
SequencePanelWrapper - Class in org.biojava.bio.gui.sequence
  Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.
SequencePanelWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequencePanelWrapper
  Creates a new instance of WrappedSequencePanel
SequencePoster - Class in org.biojava.bio.gui.sequence
  Deprecated. This doesn't handle loads of stuff. Use SequencePoster.
SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Create a new SeqeuncePanel.
SequencePoster.Border - Class in org.biojava.bio.gui.sequence
  Deprecated.
SequenceRenderContext - Interface in org.biojava.bio.gui.sequence
  A context within which sequence information may be rendered.
SequenceRenderContext.Border - Class in org.biojava.bio.gui.sequence
  The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.
SequenceRenderContext.Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
SequenceRenderer - Interface in org.biojava.bio.gui.sequence
  The interface for things that can render a line of information about a sequence.
SequenceRenderer.RendererForwarder - Class in org.biojava.bio.gui.sequence
SequenceRenderer.RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
SequenceRendererWrapper - Class in org.biojava.bio.gui.sequence
  An implementation of SequenceRenderer that delegates rendering to another renderer.
SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
  Create a new renderer with no wrapped renderer.
SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
  Create a new wrapper with a wrapped renderer
SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite
  Signals that sequences are being added to or remove from the database.
SequencesAsGFF - Class in org.biojava.bio.program.gff
  Turns a sequence database into a GFF event stream.
SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
SequenceStreamer - Interface in org.biojava.bio.program.ssaha
SequenceStreamer.FileStreamer - Class in org.biojava.bio.program.ssaha
SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
SequenceStreamer.SequenceDBStreamer - Class in org.biojava.bio.program.ssaha
SequenceStreamer.SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `sequenceToGraphics` converts a sequence index to a graphical position.
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
sequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
  Converts a sequence index into a graphical coordinate.
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `sequenceToGraphics` converts a sequence index to a graphical position.
SequenceTools - Class in org.biojava.bio.seq
  Methods for manipulating sequences.
SequenceViewerEvent - Class in org.biojava.bio.gui.sequence
  An event indicating that a mouse gesture was recognised within a widget that renders sequences.
SequenceViewerEvent(Object, Object, int, MouseEvent, List) - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerEvent
  Construct a SequenceViewerEvent with the given source, target, mouseEvent and path.
SequenceViewerListener - Interface in org.biojava.bio.gui.sequence
SequenceViewerMotionListener - Interface in org.biojava.bio.gui.sequence
SequenceViewerMotionSupport - Class in org.biojava.bio.gui.sequence
SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
SequenceViewerSupport - Class in org.biojava.bio.gui.sequence
SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport
SEQVERSION - Static variable in interface org.biojavax.bio.BioEntry
ser() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Serine (S)
serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser
  Deprecated. Convert a Taxon into a stringified representation.
serializeSource(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
serializeXRef(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
  Deprecated.
serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel
serialVersionUID - Static variable in exception org.biojava.bio.structure.io.PDBParseException
serialVersionUID - Static variable in exception org.biojava.bio.structure.StructureException
series - Variable in class org.biojava.bibliography.BiblioBook
  Book series.
SERVERS - Static variable in class org.biojava.bio.program.das.DAS
Services - Class in org.biojava.utils
  Utility methods for handling META-INF/services files
Services() - Constructor for class org.biojava.utils.Services
set(int, int, double) - Method in class org.biojava.bio.structure.jama.Matrix
  Set a single element.
set(int, Object) - Method in class org.biojava.utils.FileAsList
  This always returns null, not the previous object.
set(Object, Object) - Method in class org.biojava.utils.ListTools.Doublet
set(Object, Object, Object) - Method in class org.biojava.utils.ListTools.Triplet
setA(Object) - Method in class org.biojava.utils.ListTools.Doublet
setA(Object) - Method in class org.biojava.utils.ListTools.Triplet
setAbsorptionMax(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property absorptionMax.
setAbsorptionNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property absorptionNote.
setAccession(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setAccession(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setAccession(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the accession of the record being read.
setAccession(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the accession of the record being read. The last accession passed to this routine will always be the one used.
setAcronym(String) - Method in interface org.biojavax.Namespace
  Sets an optional acronym for the namespace.
setAcronym(String) - Method in class org.biojavax.SimpleNamespace
  Sets an optional acronym for the namespace.
setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Set a flag so that newly added points will be in the positive class or negative class, depending on wether addPos is true or false respectively.
setAdvance(int[]) - Method in interface org.biojava.bio.dp.EmissionState
  Set the advance array.
setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState
setAligMat(AligMatEl[][]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setAligMat(int, int, AligMatEl) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setAligMat(AligMatEl[][]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
  Deprecated.
setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Sets the Alignment attribute of the Border object.
setAlignment(Alignment) - Method in class org.biojava.bio.seq.homol.SimpleHomology
  `setAlignment` sets the alignment which describes the homology.
setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setAlphabetName(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
setAlphabetName(String) - Method in class org.biojavax.bio.seq.ThinRichSequence
setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setAltAligNumber(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
setAltLoc(Character) - Method in interface org.biojava.bio.structure.Atom
  get set alternate Location.
setAltLoc(Character) - Method in class org.biojava.bio.structure.AtomImpl
  set alternate Location.
setAminoType(Character) - Method in interface org.biojava.bio.structure.AminoAcid
  set the name of the AA, in single letter code .
setAminoType(Character) - Method in class org.biojava.bio.structure.AminoAcidImpl
  set the name of the AA, in single letter code .
setAngleDiff(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
setAnnotation(Annotation) - Method in interface org.biojava.bio.structure.Chain
  get/set the Annotation of a Chain.
setAnnotation(Annotation) - Method in class org.biojava.bio.structure.ChainImpl
setApplicationClass(Class, Class) - Static method in class org.biojavax.RichObjectFactory
  Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
setArrowHeadSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
setArticleAuthors(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets the names of the authors which first published an article about the AAindex entry.
setArticleTitle(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets the title of the article which describes the AAindex entry.
setAuthority(String) - Method in interface org.biojavax.Namespace
  This method sets the authority that governs the namespace.
setAuthority(String) - Method in class org.biojavax.SimpleNamespace
  This method sets the authority that governs the namespace.
setB(Object) - Method in class org.biojava.utils.ListTools.Doublet
setB(Object) - Method in class org.biojava.utils.ListTools.Triplet
setBaseCallAlignment(Alignment) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Provides the list of base calls.
setBaseColor(Symbol, Color) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Maps a color to a DNA symbol.
setBeadDepth(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setBeadDepth` sets the depth of a single bead produced by this renderer.
setBeadDisplacement(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setBeadDisplacement` sets the displacement of beads from the centre line of the renderer.
setBeadFill(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setBeadFill` sets the bead fill paint.
setBeadOutline(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setBeadOutline` sets the bead outline paint.
setBeadStroke(Stroke) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setBeadStroke` sets the bead outline stroke.
setBits(int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Sets the number of significant bits in the trace samples.
setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
setBlockPainter(BlockPainter) - Method in class org.biojava.bio.gui.DistributionLogo
setBlockWidth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
setBooleanValue(boolean) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
  Override this method to do something useful with the boolean we collect.
setBoundaryFinder(BoundaryFinder) - Method in class org.biojava.bio.program.tagvalue.Aggregator
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
setBounds(Rectangle2D.Float) - Method in interface org.biojava.bio.gui.glyph.Glyph
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
setByteValue(byte) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
  Override this method to do something useful with the byte we collect.
setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
setC(double) - Method in class org.biojava.stats.svm.SMOTrainer
setC(Object) - Method in class org.biojava.utils.ListTools.Triplet
setCenter1(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setCenter2(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setChanger(Object, ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
  Set the Changer to be used for all values of a particular tag.
setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
setCharacter(char) - Method in class org.biojava.utils.RepeatedCharSequence
setCharValue(char) - Method in class org.biojava.utils.stax.CharElementHandlerBase
  Override this method to do something useful with the char we collect.
setChildrenRaw(Set) - Method in class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
setChromatogram(Chromatogram) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the chromatogram to draw.
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.SimpleOrganism
setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setChromosomes(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
setChromosomes(SymbolList[]) - Method in interface org.biojavax.ga.Organism
  Sets the organisms 'chromosome' sequences.
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setCircular(boolean) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Defined this sequence being parser as circular.
setCircular(boolean) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Defined this sequence being parser as circular.
setCircular(boolean) - Method in interface org.biojavax.bio.seq.RichSequence
  Circularises the `Sequence`.
setCircular(boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Circularises the `Sequence`.
setCircularLength(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS
setCircularLength(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the circular length of this location. NOT IMPLEMENTED
setCircularLength(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS NOT IMPLEMENTED
setCircularLength(int) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the circular length of this location.
setCircularLength(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the circular length of this location.
setCluster(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setCol(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
setCollapsing(boolean) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  Specifies if the renderer should collapse to zero depth when no features are visible (default `true`).
setCommands(String) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the command line including the path or name of the external program and its command line arguments.
setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl
setComment(Object, String) - Method in class org.biojava.bio.AnnotationType.Impl
setComment(String) - Method in interface org.biojava.bio.AnnotationType
  Set the comment for the whole AnnotationType.
setComment(Object, String) - Method in interface org.biojava.bio.AnnotationType
  Set the comment for a particular property.
setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the comment to comment.
setComment(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets the user comment for the AAindex entry.
setComment(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setComment(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setComment(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener about a comment in the record being read.
setComment(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener about a comment in the record being read.
setComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Setter for property comment.
setComment(String) - Method in class org.biojavax.SimpleComment
setCommentType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property commentType.
setCommonName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. With this method the common name of the given taxon can be changed or created, if there was none before.
setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. Set the new common name of this Taxon.
setConnections(List) - Method in interface org.biojava.bio.structure.Structure
  sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
setConnections(List) - Method in class org.biojava.bio.structure.StructureImpl
setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel
setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel
setConstraint(Object, CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
setConstraint(Object, CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
  Specifies the constraint to apply to the specified property.
setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
  Set the constraints associated with a property.
setContacts(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
  sets the ContentHandler for this object
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
  this sets the ContentHandler that receives SAX events from the internal Blast XML parser which is the actual ContentHandler.
setContig(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Choose whether to treat empty tags as a continuation of previous tags or as a new tag with the value of the empty string.
setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Decide whether to treat empty tags as continuations of the previous non -empty tag.
setCoords(double[]) - Method in interface org.biojava.bio.structure.Atom
  set the coordinates.
setCoords(double[]) - Method in class org.biojava.bio.structure.AtomImpl
  the coordinates.
setCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
  Set the count for the Symbol s.
setCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
setCounts(Count) - Method in interface org.biojava.bio.dist.Count
  Set the counts in this Counts to be equal to the counts in c.
setCounts(Count) - Method in class org.biojava.bio.dist.IndexedCount
setCovered(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setCreate_co(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setCreateOnUnderlyingSequence(boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
setCrossOverFunction(CrossOverFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
  Changes the `CrossOverFunction` used to CrossOver Chromosomes
setCrossOverFunction(CrossOverFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
setCrossOverProbs(double[]) - Method in interface org.biojavax.ga.functions.CrossOverFunction
  Sets the probability of crossing at each base.
setCrossRef(CrossRef) - Method in class org.biojavax.bio.seq.SimpleRichLocation
setCrossref(CrossRef) - Method in interface org.biojavax.DocRef
  The document reference may refer to an object in another database.
setCrossref(CrossRef) - Method in class org.biojavax.SimpleDocRef
  The document reference may refer to an object in another database.
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Sets the cross ref resolver to use when retrieving remote symbols. If none is given, then the default from RichObjectFactory.getDefaultCrossRefResolver() is used. Recursively applies this call to all members.
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the cross ref resolver to use when retrieving remote symbols. This method is ignored in the empty location because there is nothing to resolve.
setCrossRefResolver(CrossReferenceResolver) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the cross ref resolver to use when retrieving remote symbols.
setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the cross ref resolver to use when retrieving remote symbols.
setDatabase(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
setDatabaseID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
setDatabaseID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentFilter
setDatabaseID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
  `setDatabaseID` identifies the database searched by a name, ID or URN.
setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
setDatabaseName(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property databaseName.
setDbCode(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
setDBConnection(String, String, String, String) - Method in class org.biojava.bio.structure.io.PDBMSDReader
  open a database conenction to the MSD search database
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
setDefaultChanger(ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
  The changer that will be applied to the values of tags not registered explicitly to any changer or splitter instance.
setDefaultConstraint(CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
setDefaultConstraint(CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
  Specifies the default constraint to apply to properties where no other constraint is specified.
setDefaultConstraints(PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
setDefaultConstraints(PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
  Set the constraints that will apply to all properties without an explicitly defined set of constraints.
setDefaultCrossReferenceResolver(CrossReferenceResolver) - Static method in class org.biojavax.RichObjectFactory
  Sets the default crossref resolver to use when resolving remote entries.
setDefaultNamespaceName(String) - Static method in class org.biojavax.RichObjectFactory
  Sets the default namespace name to use when loading sequences.
setDefaultOntologyName(String) - Static method in class org.biojavax.RichObjectFactory
  Sets the default ontology name to use when loading sequences.
setDefaultPaint(Paint) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
setDefaultPositionResolver(PositionResolver) - Static method in class org.biojavax.RichObjectFactory
  Sets the default position resolver to use when creating new rich feature locations.
setDefaultRichSequenceHandler(RichSequenceHandler) - Static method in class org.biojavax.RichObjectFactory
  Sets the default sequence handler to use when performing sequence manipulation.
setDefaultSplitter(ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
  The splitter that will be applied to the values of tags not registered explicitly to any changer or splitter instance.
setDefaultTransitions(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  specify fallback TransitionTable for this State
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine
  TagValueWrapper interface
setDelegate(TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
  set listener to which all calls will be delegated
setDelegateParser(TagValueParser) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  `setDelegateRenderer` associates an `OptimizableFilter` with a `BeadFeatureRenderer`.
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
  `setDelegateRenderer` associates an `OptimizableFilter` with a `BeadFeatureRenderer`.
setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `setDelegateRenderer` for the specified filter.
setDelete(double) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the penalty for a delete operation to the specified value.
setDelete(double) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a delete operation to the specified value.
setDensityCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
setDepth(double) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo
setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
  Change the current DepthScaler to depthScaler.
setDescription(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Sets the description to the given value.
setDescription(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets the description for the AAindex entry.
setDescription(String) - Method in interface org.biojavax.bio.BioEntry
  Sets the description for this bioentry.
setDescription(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setDescription(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setDescription(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the description of the record being read.
setDescription(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the description of the record being read.
setDescription(String) - Method in class org.biojavax.bio.SimpleBioEntry
  Sets the description for this bioentry.
setDescription(String) - Method in interface org.biojavax.Namespace
  This method sets a description for the namespace.
setDescription(String) - Method in interface org.biojavax.ontology.ComparableOntology
  Sets a human-readable description of this ontology.
setDescription(String) - Method in interface org.biojavax.ontology.ComparableTerm
  Sets the description associated with this term.
setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Sets a human-readable description of this ontology.
setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Sets the description associated with this term.
setDescription(String) - Method in class org.biojavax.SimpleNamespace
  This method sets a description for the namespace.
setDescriptors(Set) - Method in interface org.biojavax.ontology.ComparableTriple
  Clears the current set of descriptors and replaces it with the content of the set passed.
setDescriptors(Set) - Method in class org.biojavax.ontology.SimpleComparableTriple
  Clears the current set of descriptors and replaces it with the content of the set passed. Warning this method gives access to the original Collection not a copy.
setDiagonalDistance(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDiagonalDistance2(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDimensionRatio(double) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
  `setDimensionRatio` sets the minimum ratio of long dimension to short dimension of the bead.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setDirection` sets the direction in which this context will render the sequence - HORIZONTAL or VERTICAL.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Set the direction that this SequencePanel renders in.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Set the direction that this SequencePoster renders in.
setDirection(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setDirection` sets the direction in which this context will render sequences - HORIZONTAL or VERTICAL.
setDistanceBetweenFeatures(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution
  Set the distribution assocated with a symbol.
setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState
  Set the Distribution associated with this state.
setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState
setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo
  Set the dist to render.
setDivision(String) - Method in interface org.biojavax.bio.BioEntry
  Sets the division of this bioentry.
setDivision(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setDivision(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setDivision(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the division of the record being read.
setDivision(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the division of the record being read.
setDivision(String) - Method in class org.biojavax.bio.SimpleBioEntry
  Sets the division of this bioentry.
setDoAngleCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDocumentLocator(Locator) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
setDocumentLocator(Locator) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
setDocumentLocator(Locator) - Method in interface org.biojava.utils.stax.StAXContentHandler
setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
setDoDensityCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDoDistanceCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDoRMSCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setDoubleProperty(Symbol, String) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
  Override this method to do something useful with the double we collect.
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
setElideComments(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Use this method to toggle reading of comments data.
setElideComments(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Use this method to toggle reading of comments data.
setElideFeatures(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Use this method to toggle reading of feature data.
setElideFeatures(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Use this method to toggle reading of feature data.
setElideReferences(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Use this method to toggle reading of bibliographic reference data.
setElideReferences(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Use this method to toggle reading of bibliographic reference data.
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. Specifies whether the symbols (SQ) part of the entry should be ignored.
setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. Use this method to toggle reading of sequence data.
setElideSymbols(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Use this method to toggle reading of sequence data.
setElideSymbols(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Use this method to toggle reading of sequence data.
setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the end coordinate to end.
setEnd(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Set the string indicating that a record has ended.
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Set the explicit end-of-record string.
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
  This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
setEnvironmentProperties(String[]) - Method in class org.biojava.utils.process.ExternalProcess
  Sets environment variables for the external process.
setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser
  Set the error handler used by this parser.
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff3.GFF3Parser
  Set the error handler used by this parser.
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the output error handler which is responsible for the standard error output of the external process.
setEvalCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property events.
setExceptionOnNullDelegate(boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
  determines if an exception is thrown when an event arrives without the delegate being set.
setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Setter for property factory.
setFallback(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
  set the specified TransitionTable to be looked looked up if the Transition cannot be found in this one.
setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
  Set the feature to feature.
setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the feature type to type.
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
  by default, we set the parser to non-validating.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Sets the feature this location is associated with. If null, that's fine, but you won't be able to persist it to the database until you give it a not-null value. Passes the call on to each of its members in turn.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the feature this location is associated with. NOT IMPLEMENTED
setFeature(RichFeature) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the feature this location is associated with.
setFeature(RichFeature) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the feature this location is associated with.
setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Replace the current FeatureFilter with filter.
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Set the object which receives startFeature/endFeature notifications.
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
setFeatureProperty(Object, Object) - Method in class org.biojava.bio.program.xff.FeatureHandler
  Set a property.
setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
  Set the FeatureRealizer used by new sequences created by this factory.
setFeatureRelationshipSet(Set) - Method in interface org.biojavax.bio.seq.RichFeatureHolder
  Clears the relations from this feautre holder and replaces them with a new set.
setFeatureRelationshipSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Clears the relations from this feautre holder and replaces them with a new set. Warning this method gives access to the original Collection not a copy.
setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
  `setFeatureRenderer` sets the renderer to be used.
setFeatureSet(Set) - Method in interface org.biojavax.bio.seq.RichSequence
  Sets the features of this sequence.
setFeatureSet(Set) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Sets the features of this sequence. Warning this method gives access to the original Collection not a copy.
setFeatureSource(FeatureSource) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
setFillColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Set the background color of the label area.
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `setFilter` sets the filter.
setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
setFirstIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property firstIntActID.
setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.AbstractSelectionFunction
setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
setFitnessFunction(FitnessFunction) - Method in interface org.biojavax.ga.functions.SelectionFunction
  The fitness function that will be used by the select method.
setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
  Override this method to do something useful with the float we collect.
setFont(Font) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setFragCompat(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setFragmentMiniDistance(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.align.StructurePairAligner
setFrame(int) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the frame to frame.
setFullName(String) - Method in interface org.biojava.bio.structure.Atom
  set full name of atom e.g.
setFullName(String) - Method in class org.biojava.bio.structure.AtomImpl
  set full name of atom e.g.
setGapExt(double) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the penalty for an extension of any gap (insert or delete) to the specified value.
setGapExt(double) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an extension of any gap (insert or delete) to the specified value.
setGapExtCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setGapExtCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setGapExtension(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setGapExtRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setGapExtRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setGapOpen(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setGapOpenCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setGapOpenCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setGapOpenRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setGapOpenRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setGenerateSequenceHeader(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Specify whether a per-sequence header line, giving the length of the sequence, should be generated.
setGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the genetic code of this taxon, which may be null, which will unset it.
setGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Sets the genetic code of this taxon, which may be null, which will unset it.
setGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Updates the taxon in the database and sets its genetic code id to the specified value.
setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Replace the group-attribute Map with ga.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Sets the element name that the class responds to.
setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  Sets the element name that the class responds to.
setHeader(Map) - Method in interface org.biojava.bio.structure.Structure
  set the Header data .
setHeader(Map) - Method in class org.biojava.bio.structure.StructureImpl
  set the Header data.
setHeight(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the height (in pixels).
setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
  `setHeightScaling` sets the height scaling policy.
setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `setHeightScaling` sets the height scaling policy.
setHorizontalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the horizontal scale (proportional).
setId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
setID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property ID.
setIdentifier(String) - Method in interface org.biojavax.bio.BioEntry
  Sets the identifier of this bioentry.
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setIdentifier(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the identifier of the record being read.
setIdentifier(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the identifier of the record being read.
setIdentifier(String) - Method in class org.biojavax.bio.SimpleBioEntry
  Sets the identifier of this bioentry.
setIdentifier(String) - Method in interface org.biojavax.ontology.ComparableTerm
  Sets the (optional) identifier associated with this term.
setIdentifier(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Sets the (optional) identifier associated with this term.
setIdxlist(List) - Method in class org.biojava.bio.structure.align.helper.JointFragments
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
  `setImageMap` sets the current image map.
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
  `setImageMap` sets the current image map.
setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
  `setImageMap` sets the current image map.
setIndex(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
setInitialK(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setInput(InputStream) - Method in interface org.biojava.utils.process.OutputHandler
  Sets the input stream.
setInput(InputStream) - Method in class org.biojava.utils.process.StreamPipe
  Sets the input stream
setInput(InputStream) - Method in class org.biojava.utils.process.WriterOutputHandler
  Sets the input stream.
setInputHandler(InputHandler) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the input handler which is responsible for the standard input of the external process.
setInsert(double) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the penalty for an insert operation to the specified value.
setInsert(double) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and sets the penalty for an insert operation to the specified value.
setInteractions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property interactions.
setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
  Override this method to do something useful with the int we collect.
setIsoforms(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property isoforms.
setIsoIDs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Setter for property isoIDs.
setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Selects strict mode.
setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Selects strict mode.
setJoiner(String) - Method in class org.biojava.bio.program.tagvalue.Aggregator
setJoinPlo(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setJoinRMSCutoff(double) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setJournalReference(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets a reference to the journal which published the article about the AAindex entry.
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Set the kernel used for classification.
setKey(Object) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
setKineticsNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property kineticsNote.
setKMs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property KMs.
setLabel(Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
setLabel(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property label.
setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel
  Set the scale factor.
setLeadingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
setLeftValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Updates the taxon and sets the left value to the specified value.
setLeftValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the left value.
setLeftValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Sets the left value.
setLength(int) - Method in class org.biojava.bio.search.SeqContentPattern
  Set the pattern length.
setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
setLength(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
setLength(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setLength(int) - Method in class org.biojava.utils.RepeatedCharSequence
setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache
setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Set the absolute number of lines that the sequence will be rendered on.
setLineWidth(int) - Method in class org.biojava.bio.program.phred.PhredFormat
  Set the line width.
setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Set the line width.
setLineWidth(int) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Set the line width.
setLineWidth(int) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Set the line width.
setListener(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  set a TagValueListener for this State.
setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
setListener(PatternListener) - Method in class org.biojava.utils.automata.PatternBlitz
setListener(PatternListener) - Method in interface org.biojava.utils.automata.StateMachineFactory
setListener(Search.Listener) - Method in class org.biojava.utils.regex.Search
setLITDBEntryNumbers(String[]) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Sets the list of literature database identifiers for the AAindex entry.
setLoc(Location) - Method in interface org.biojava.bio.alignment.AlignmentElement
setLoc(Location) - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
setLocation(Location) - Method in interface org.biojava.bio.seq.Feature
  The new location for this feature.
setLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setLocation(Location) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  The new location for this feature.
setLocation(RichLocation) - Method in class org.biojavax.SimpleRankedDocRef
setLocationValue(Location) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
  Override this method to do something useful with the location we collect.
setLogoFont(Font) - Method in class org.biojava.bio.gui.TextBlock
  Set the current logo font.
setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter
  Set the current logo font.
setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo
  Set the logo painter.
setLongValue(long) - Method in class org.biojava.utils.stax.LongElementHandlerBase
  Override this method to do something useful with the long we collect.
setLRUCacheSize(int) - Static method in class org.biojavax.RichObjectFactory
  Sets the size of the LRU cache.
setLRUCacheSize(Class, int) - Static method in class org.biojavax.RichObjectFactory
  Sets the size of the LRU cache.
setMapAll(boolean) - Method in class org.biojava.bio.molbio.RestrictionMapper
  `setMapAll` sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.
setMapType(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setMatch(double) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the penalty for a match operation to the specified value.
setMatch(double) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a match operation to the specified value.
setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Set a submatrix.
setMaxCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
  Set the maximum counts required for a symbol.
setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
setMaxCrossOvers(int) - Method in interface org.biojavax.ga.functions.CrossOverFunction
  Sets an upper limit on the number of crosses.
setMaxIter(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest
  Sets the maximum number of partial digest products to be annotated.
setMaxPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
setMaxrefine(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setMaxRunTimeSecs(int) - Method in class org.biojava.utils.ExecRunner
  Sets the maximum run time in seconds.
setMergeAnnotation(Annotation) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Enable or disable treating runs of identical tags as a single tag start event with multiple values or each as a separate tag start, value, and tag end.
setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Decide if multiple examples of a single tag should be merged into a single start/endTag pair with multiple values, or multiple start/endTag pairs each with a single value.
setMinCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
  Set the minimum counts required for a symbol.
setMinPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
setMismatches(int) - Method in class org.biojava.bio.search.MaxMismatchPattern
setMitochondrialGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Updates the given taxon and sets it's so called mitochondrial genetic code id to the specified value.
setMitoGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
setMitoGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Sets the mitochondrial genetic code of this taxon, which may be null, which will unset it.
setModeLazy() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
setModeLazy() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
  Setting the mode to lazy means that, if the program is recognised, e.g.
setModeStrict() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
setModeStrict() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
  This is the default, parsing will be attempted only if both the program e.g.
setMolecularWeight(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property molecularWeight.
setMolWeightError(Integer) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property molWeightError.
setMolWeightMethod(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property molWeightMethod.
setMolWeightRangeEnd(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property molWeightRangeEnd.
setMolWeightRangeStart(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property molWeightRangeStart.
setMoreSearches(boolean) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentAdapter
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentFilter
setMoreSearches(boolean) - Method in interface org.biojava.bio.search.SearchContentHandler
  `setMoreSearches` sets the state of the `SearchContentHandler`'s expectation of receiving more results.
setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
setMutationFunction(MutationFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
  Sets the current `MutationFunction`
setMutationFunction(MutationFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
setMutationProbs(double[]) - Method in interface org.biojavax.ga.functions.MutationFunction
  Set the probability of a mutation occuring at a certain position Position 0 in the array corresponds to the probability of the first residue of `seq` mutating.
setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
setMutationSpectrum(OrderNDistribution) - Method in interface org.biojavax.ga.functions.MutationFunction
  Sets the `Distribution` of `Symbols` that will be selected from when a mutation occurs.
setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
setName(String) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  set the name of this group.
setName(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
setName(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Assign a name to this sequence
setName(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
setName(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
setName(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener that the current sequence is generally known by a particular name.
setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
setName(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. The name is printed out as part of the identifier line.
setName(String) - Method in interface org.biojava.bio.structure.Atom
  set trimmed version of atom name, e.g.
setName(String) - Method in class org.biojava.bio.structure.AtomImpl
  trimmed version of atom name, e.g.
setName(String) - Method in interface org.biojava.bio.structure.Chain
  get and set the name of this chain (Chain id in PDB file ).
setName(String) - Method in class org.biojava.bio.structure.ChainImpl
  get and set the name of this chain (Chain id in PDB file ).
setName(String) - Method in interface org.biojava.bio.structure.Structure
  set biological name of Structure .
setName(String) - Method in class org.biojava.bio.structure.StructureImpl
  set biological name of Structure.
setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet
  Assign a name to the alphabet
setName(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setName(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setName(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener that the current sequence is generally known by a particular name.
setName(String) - Method in interface org.biojavax.bio.seq.RichFeature
  Sets the name of this feature.
setName(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Sets the name of this feature.
setName(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Changes the name.
setName(String) - Method in class org.biojavax.ga.impl.AbstractOrganism
setName(String) - Method in class org.biojavax.ga.impl.AbstractPopulation
setName(String) - Method in interface org.biojavax.ga.Organism
  Sets the organisms name
setName(String) - Method in interface org.biojavax.ga.Population
  Sets the name of the population
setNameClass(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Changes the class of this name.
setNamedIsoforms(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Setter for property namedIsoforms.
setNames(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Setter for property names.
setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
  Setter for property namespace.
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setNamespace(Namespace) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the namespace of the record being read.
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the namespace of the record being read.
setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Set the Shape to represent the negative points.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
  Set the kernel to nest.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel
  Set the SVMKernel to nest to k.
setNewTag(Object, Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
  `setNewTag`.
setNmr(boolean) - Method in interface org.biojava.bio.structure.Structure
  set NMR flag.
setNmr(boolean) - Method in class org.biojava.bio.structure.StructureImpl
setNodeRank(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the node rank of this taxon.
setNodeRank(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Setter for property nodeRank.
setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Set the normalizing vector.
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Setter for property note.
setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property note.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. NOT IMPLEMENTED
setNoteSet(Set) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Clears the notes associated with this object and replaces them with the contents of this set. NOT IMPLEMENTED
setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
setNoteSet(Set) - Method in class org.biojavax.bio.SimpleBioEntry
  Clears the notes associated with this object and replaces them with the contents of this set. Warning this method gives access to the original Collection not a copy.
setNoteSet(Set) - Method in class org.biojavax.EmptyRichAnnotation
  Clears the notes from this annotation and replaces them with those from the given set. You can not add Notes to the Empty RichAnnotation object.
setNoteSet(Set) - Method in interface org.biojavax.RichAnnotatable
  Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in interface org.biojavax.RichAnnotation
  Clears the notes from this annotation and replaces them with those from the given set.
setNoteSet(Set) - Method in class org.biojavax.SimpleCrossRef
  Clears the notes associated with this object and replaces them with the contents of this set.
setNoteSet(Set) - Method in class org.biojavax.SimpleRichAnnotation
  Clears the notes from this annotation and replaces them with those from the given set. Warning this method gives access to the original Collection not a copy.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
setNullModel(Distribution) - Method in interface org.biojava.bio.dist.Distribution
  Set the null model Distribution that this Distribution recognizes.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.GapDistribution
setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution
setNullModel(Distribution) - Method in class org.biojava.bio.dist.TranslatedDistribution
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
  Implement this to set the null model.
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution
setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution
  Assign a background distribution.
setNullModelWeight(double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Set the number of pseudocounts to add when training the distribution.
setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
  Set the number associated with this node.
setNumberExperiments(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property numberExperiments.
setObsolete(Boolean) - Method in interface org.biojavax.ontology.ComparableTerm
  Sets the obsolescence flag associated with this term.
setObsolete(Boolean) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Sets the obsolescence flag associated with this term.
setOccupancy(double) - Method in interface org.biojava.bio.structure.Atom
  set occupancy.
setOccupancy(double) - Method in class org.biojava.bio.structure.AtomImpl
setOffset(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
setOption(ChromatogramGraphic.Option, Object) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets a new value for the specified option.
setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel
setOrganismsDiffer(boolean) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property organismsDiffer.
setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `setOutline` sets the the colour used to draw the lines.
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
  `setOutline` sets the the colour used to draw the lines.
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
setOutput(OutputStream) - Method in interface org.biojava.utils.process.InputHandler
  Sets the output stream.
setOutput(OutputStream) - Method in class org.biojava.utils.process.ReaderInputHandler
  Sets the output stream.
setOutput(OutputStream) - Method in class org.biojava.utils.process.StreamPipe
  Sets the output stream
setOutputHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the output handler which is responsible for the standard output of the external process.
setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
  Set the padding.
setParams(StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
  set the parameters to be used for the algorithm
setParent(Connection, Taxon, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. This updates the taxonomic tree in the database and sets the parent of the given child taxon to the parent taxon.
setParent(Group) - Method in interface org.biojava.bio.structure.Atom
  Sets the back-reference to its parent Group
setParent(Group) - Method in class org.biojava.bio.structure.AtomImpl
setParent(Chain) - Method in interface org.biojava.bio.structure.Group
  Set the back-reference (to its parent Chain)
setParent(Chain) - Method in class org.biojava.bio.structure.HetatomImpl
  Set the back-reference (to its parent Chain)
setParent(FeatureHolder) - Method in interface org.biojavax.bio.seq.RichFeature
  Sets the parent of this feature.
setParent(FeatureHolder) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Sets the parent of this feature.
setParentNCBITaxID(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the parent NCBI taxon ID.
setParentNCBITaxID(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Sets the parent NCBI taxon ID.
setParserListener(Object, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
setPath(IndexPair[]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setPath(IndexPair[]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setPath(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
  directory where to find PDB files
setPath(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
  set path to file / connection string to db.
setPathPrefix(File) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `setPathPrefix` sets the abstract path to be appended to sequence database filenames retrieved from the binary index.
setPathSize(int) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setPathSize(int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setPattern(Pattern) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Set the Pattern used to split lines.
setPattern(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
setPDBCode(String) - Method in interface org.biojava.bio.structure.Group
  Specifies the PDBCode value.
setPDBCode(String) - Method in class org.biojava.bio.structure.HetatomImpl
  set the PDB code.
setPDBCode(String) - Method in interface org.biojava.bio.structure.Structure
  set PDB code of structure .
setPDBCode(String) - Method in class org.biojava.bio.structure.StructureImpl
  set PDB code of structure .
setPDBFlag(boolean) - Method in interface org.biojava.bio.structure.Group
  flag if group has 3D data .
setPDBFlag(boolean) - Method in class org.biojava.bio.structure.HetatomImpl
  flag if group has 3D data.
setPDBline(String) - Method in interface org.biojava.bio.structure.Atom
  store the whole line.
setPDBline(String) - Method in class org.biojava.bio.structure.AtomImpl
  store the whole line.
setPDBName(String) - Method in class org.biojava.bio.structure.AminoAcidImpl
  set three character name of AminoAcid.
setPDBName(String) - Method in interface org.biojava.bio.structure.Group
  get the PDB 3 character name for this group.
setPDBName(String) - Method in class org.biojava.bio.structure.HetatomImpl
  set three character name of Group .
setPDBresnum1(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
setPDBresnum2(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
setPDBserial(int) - Method in interface org.biojava.bio.structure.Atom
  set PDB atom number.
setPDBserial(int) - Method in class org.biojava.bio.structure.AtomImpl
  set PDB atom number.
setPermutationSize(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setPhase(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setPHDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property PHDependence.
setPopulation(Population) - Method in interface org.biojavax.ga.GeneticAlgorithm
  Sets the `Population` of `Organisms` to the Algorithm.
setPopulation(Population) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
setPos1(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setPos2(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the resolver to use when working out actual base coordinates from fuzzy positions. This method is ignored in the empty location because positions are fixed an cannot be modified.
setPositionResolver(PositionResolver) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the resolver to use when working out actual base coordinates from fuzzy positions.
setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the resolver to use when working out actual base coordinates from fuzzy positions.
setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
  Set the Shape to represent the positive points.
setPrimaryKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `setPrimaryKey` sets the primary identifier namespace.
setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
  Set the tag to use as a primary key in the index.
setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
  Set the tag to use as a primary key in the index.
setPrintConnections(boolean) - Method in class org.biojava.bio.structure.io.FileConvert
  enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
  Deprecated. `setPrintStream` informs an instance which `PrintStream` to use.
setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. `setPrintStream` informs an instance which `PrintStream` to use.
setPrintStream(PrintStream) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
  Sets the stream to write to.
setPrintStream(PrintStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Sets the stream to write to.
setPrintWriter(PrintWriter) - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
  Set the `PrintWriter` to output the HTML to.
setProfileHMM() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
setProperties(Map) - Method in interface org.biojava.bio.structure.Group
  properties of this amino acid.
setProperties(Map) - Method in class org.biojava.bio.structure.HetatomImpl
  properties of this amino acid.
setProperty(Object, Object) - Method in class org.biojava.bio.AbstractAnnotation
setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation
  Set the value of a property.
setProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
setProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
  Set the property in an annotation bundle according to the type we believe it should be.
setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation
setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
setProperty(String, Object) - Method in interface org.biojava.bio.structure.Group
  set a single property .
setProperty(String, Object) - Method in class org.biojava.bio.structure.HetatomImpl
  set a single property .
setProperty(Object, Object) - Method in class org.biojavax.EmptyRichAnnotation

  Set the value of a property. You can not add properties to the Empty RichAnnotation object

setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation

  Set the value of a property.

setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest
setQuery(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
  Specifies the query.
setQueryID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
setQueryID(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
setQueryID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentFilter
setQueryID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
  `setQueryID` identifies the query sequence by a name, ID or URN.
setQueryID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
setQuerySeq(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
  Deprecated. use `setQueryID` instead.
setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
  `setQuerySeqHolder` sets the query sequence holder to a specific database.
setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
  `setQuerySeqHolder` sets the query sequence holder to a specific database.
setRadius(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
setRange(RangeLocation) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
setRank(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Updates a taxon and sets it's rank to the specified `String`.
setRank(Integer) - Method in interface org.biojavax.bio.BioEntryRelationship
  Sets the rank of this relationship.
setRank(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the rank for this location. NOT IMPLEMENTED
setRank(int) - Method in interface org.biojavax.bio.seq.RichFeature
  Sets the rank of this feature.
setRank(int) - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
  Sets the rank of this relationship.
setRank(int) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the rank for this location.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Sets the rank of this feature.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Sets the rank of this relationship.
setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the rank for this location.
setRank(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Sets the rank of this relationship.
setRank(int) - Method in interface org.biojavax.Note
  Sets the rank for this note.
setRank(int) - Method in class org.biojavax.SimpleNote
  Sets the rank for this note.
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener about a cross reference.
setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener about a cross reference.
setRankedCrossRefs(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Sets the ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
setRankedCrossRefs(Set) - Method in class org.biojavax.bio.SimpleBioEntry
setRankedCrossRefs(Set) - Method in class org.biojavax.ontology.SimpleComparableTerm
  Sets the ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy.
setRankedCrossRefs(Set) - Method in interface org.biojavax.RankedCrossRefable
  Sets the ranked cross references associated with an object.
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener about a literature reference in the record being read.
setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener about a literature reference in the record being read.
setReader(Reader) - Method in class org.biojava.utils.process.ReaderWriterPipe
  Sets the reader.
setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `setRecurse` sets the recursion flag on the filter.
setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Set whether features will be filtered recursively to recurse.
setRecursive(boolean) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
setRedoxPotential(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property redoxPotential.
setReduceInitialFragments(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
setRemark(String) - Method in interface org.biojavax.DocRef
  Set the remarks for this document reference using this method.
setRemark(String) - Method in class org.biojavax.SimpleDocRef
  Set the remarks for this document reference using this method.
setRenderer(CircularFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
setRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Set the child renderer responsible for drawing the contents of this track
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
  `setRenderer` sets the renderer.
setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setRenderer` sets the current `PairwiseSequenceRenderer`.
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setRenderer` sets the current `SequenceRenderer`.
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.DistributionLogo
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setRenderingHints` sets the `RenderingHints` which will be used by the `Graphics2D` instances of delegate renderers.
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Use this to switch on effects like Anti-aliasing etc
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Use this to switch on effects like Anti-aliasing etc
setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setRenderingHints` sets the `RenderingHints` which will be used by the `Graphics2D` instances of delegate renderers.
setReplace(double) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the penalty for a replace operation to the specified value.
setReplace(double) - Method in class org.biojava.bio.alignment.SmithWaterman
  Overrides the method inherited from the NeedlemanWunsch and sets the penalty for a replace operation to the specified value.
setRetain(boolean) - Method in class org.biojava.bio.program.tagvalue.TagDropper
  Set wether known tags are to be retained or dropped.
setRichObjectBuilder(RichObjectBuilder) - Static method in class org.biojavax.RichObjectFactory
  Sets the builder to use when instantiating new Rich objects.
setRightValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. Updates the taxon in the database and sets the right value to the specified value.
setRightValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  Sets the right value.
setRightValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Sets the right value.
setRms(double) - Method in class org.biojava.bio.structure.align.helper.JointFragments
setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  the rms in the structurally equivalent regions
setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setRot(Matrix) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setRow(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
setScale(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setScale` sets the scale in pixels per `Symbol`.
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Set the scale.
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Set the scale.
setScale(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setScale` sets the scale in pixels per `Symbol`.
setScaleByInformation(boolean) - Method in class org.biojava.bio.gui.DistributionLogo
setScientificName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated. This changes the scientific name of the given taxon and stores the new name persistent in the database.
setScientificName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon
  Deprecated. Change the scientific name of this species.
setScore(double) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the score to score.
setScore(double) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setScore(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
setScore(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
  `setSearchContentHandler` sets the handler which will recieve the method calls generated by the adapter.
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
  `setSearchContentHandler` sets the handler which will recieve the method calls generated by the adapter.
setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.search.FilteringContentHandler
setSecondarySequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setSecondarySequence` sets the secondary `Sequence` to be rendered.
setSecondarySymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setSecondarySymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.
setSecondIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
  Setter for property secondIntActID.
setSecStruc(Map) - Method in interface org.biojava.bio.structure.AminoAcid
  Specifies the secondary structure as a Map.
setSecStruc(Map) - Method in class org.biojava.bio.structure.AminoAcidImpl
  set the secondary structure data for this amino acid.
setSeedFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setSeedRmsdCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setSelectionFunction(SelectionFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
  Changes the `SelectionFunction` used to select candidates for the next generation
setSelectionFunction(SelectionFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
  Deprecated.
setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
  Set the sequence name to seqName.
setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the sequence name to seqName.
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setSequence` sets the `Sequence` to be rendered.
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.SequencePanel
  Set the SymboList to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Set the SymboList to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
setSequence(Sequence) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setSequence` sets the `Sequence` to be rendered.
setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest
setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree
  Use this method to provide the sequences for the tree to work with.
setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `setSequenceFormat` sets the sequence format name which will be indicated in the index.
setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
setSequenceID(String) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setSequenceLength(int) - Method in class org.biojavax.bio.seq.SimpleRichSequence
setSequenceLength(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
setSequenceOffset(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
setSequenceRef(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Setter for property sequenceRef.
setSequenceType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Setter for property sequenceType.
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setSeqVersion(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
setSeqVersion(Double) - Method in interface org.biojavax.bio.seq.RichSequence
  Sets the version of the associated symbol list.
setSeqVersion(Double) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Sets the version of the associated symbol list.
setServerurl(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
  set url of aligmnent service.
setServerurl(String) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
  set url of structure service.
setShatter(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
  Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block.
setSibling(SimilarityPairFeature) - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  `setSibling` sets the sibling feature of the pair.
setSibling(SimilarityPairFeature) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
setSignificantBits(int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Sets the number of significant bits in the data.
setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
  Sets the size of the border in number of pixels.
setSleepTime(int) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the number of milliseconds the ExternalProcess.execute(Properties) method should pauses after the external process is terminated.
setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
  Set the source to source.
setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the feature source to source.
setSource(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setSource(String) - Method in interface org.biojava.bio.seq.Feature
  Change the source of the Feature.
setSource(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setSource(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setSource(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Change the source of the Feature.
setSourceTerm(Term) - Method in interface org.biojava.bio.seq.Feature
  Set the source ontology-term for this feature.
setSourceTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setSourceTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Set the source ontology-term for this feature.
setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated. Set the number of pixels to leave blank between each block of sequence information.
setSplitOffset(int) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Set the offset to split lines at.
setSplitter(Object, ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
  Set the Splitter to be used for all values of a particular tag.
setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the start coordinate to start.
setStart(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
setStoreLocation(File) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `setStoreLocation` sets the directory of the new index.
setStoreName(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
  `setStoreName` sets the name to be given to the new index.
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Set the strand to strand.
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
setStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.StrandedFeature
  Set the strand that this feature lies upon.
setStrand(StrandedFeature.Strand) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Set the strand that this feature lies upon. NOT IMPLEMENTED.
setStrand(RichLocation.Strand) - Method in class org.biojavax.bio.seq.SimpleRichLocation
setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
  assign a StreamParser object to instance.
setStringSequence(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
setStringValue(String) - Method in class org.biojava.bio.program.xff.PropDetailHandler
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
setStringValue(String) - Method in class org.biojava.utils.stax.StringElementHandlerBase
  Override this method to do something useful with the string we collect.
setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo
  Set the symbol style.
setSubjectDB(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
  Deprecated. use `setDatabaseID` instead.
setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
  `setSubjectDBInstallation` sets the subject database holder to a specific installation.
setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
  `setSubjectDBInstallation` sets the subject database holder to a specific installation.
setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setSubstitutionMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
  Sets the substitution matrix to be used to the specified one.
setSwissprotId(String) - Method in interface org.biojava.bio.structure.Chain
  set the Swissprot id of this chains .
setSwissprotId(String) - Method in class org.biojava.bio.structure.ChainImpl
  set the Swissprot id of this chains .
setSymbolLists(SymbolList, SymbolList) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Set the DNA and OFFSETS symbol lists for the basecall alignment.
setSymbolModification(char, double) - Method in class org.biojava.bio.proteomics.MassCalc
  Use this to set a post translational modification for the `Symbol` represented by this character.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  `setSymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.
setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  `setSymbolTranslation` sets the translation in `Symbol`s which will be applied when rendering.
setTagGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Set the group number that will match the tag.
setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.BioEntry
  Sets the taxon for this bioentry.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the Taxon of the record being read.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the Taxon of the record being read.
setTaxon(NCBITaxon) - Method in class org.biojavax.bio.SimpleBioEntry
  Sets the taxon for this bioentry.
setTaxonHidden(boolean) - Method in interface org.biojavax.bio.taxa.NCBITaxon
  determines whether this taxonomy level is displayed in etNameHierarchy()
setTaxonHidden(boolean) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
setTemperatureDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property temperatureDependence.
setTempFactor(double) - Method in interface org.biojava.bio.structure.Atom
  get set temp factor .
setTempFactor(double) - Method in class org.biojava.bio.structure.AtomImpl
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Sets the term for this location.
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sets the term for this location. NOT IMPLEMENTED
setTerm(ComparableTerm) - Method in interface org.biojavax.bio.seq.RichLocation
  Sets the term for this location.
setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sets the term for this location.
setTerm(ComparableTerm) - Method in interface org.biojavax.Note
  Sets the term for this note.
setTerm(ComparableTerm) - Method in class org.biojavax.SimpleNote
  Sets the term for this note.
setTermSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
  Clears out all the terms and populates the ontology with the contents of the set passed.
setTermSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Clears out all the terms and populates the ontology with the contents of the set passed. Warning this method gives access to the original Collection not a copy.
setText(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property text.
setTextColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
  Set the color of the label text
setThreadFetches(boolean) - Static method in class org.biojava.bio.program.das.DAS
setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
setTickDirection(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
setTitle(String) - Method in interface org.biojava.bio.program.homologene.Orthologue
setTitle(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
setTrace(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
  Provides the trace samples for a particular nucleotide.
setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
setTraceValues(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
  Sets the trace array for one of the DNA nucleotides.
setTrack(IndexPair) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
setTrackLayout(TrackLayout) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
setTrans(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  set a Transition for this State
setTransition(Object, StateMachine.State) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  set a Transition for this State setting notifyOnExit to false.
setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
  set a Transition within this TransitionTable (3-argument form)
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
  Alter the translation mapping.
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
  Alter the translation mapping.
setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
  Alter the translation mapping.
setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Enable or disable trimming of tags.
setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Enable trimming of the tag using String.trim().
setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
  Enable or disable trimming of values.
setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Enable trimming of the value using String.trim().
setTripleSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
  Clears out all the triples and populates the ontology with the contents of the set passed.
setTripleSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
  Clears out all the triples and populates the ontology with the contents of the set passed. Warning this method gives access to the original Collection not a copy.
setType(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
setType(String) - Method in interface org.biojava.bio.seq.Feature
  Change the type of this feature.
setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
  Setter for property type.
setType(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Change the type of this feature.
setTypeTerm(Term) - Method in interface org.biojava.bio.seq.Feature
  Set the type ontology-term for this feature.
setTypeTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
setTypeTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Set the type ontology-term for this feature.
setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
setUnitv(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
setURI(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener of a URI identifying the current sequence.
setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
setURI(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Null implementation.
setURI(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setURI(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setURI(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Deprecated. There is no clear mapping between URI and BioSQL. This method is no longer used or supported in biojavax. Don't use it. Calling it may result in exceptions. Use instead setName(String name), setAccession(String accession), setVersion(int version) etc as appropriate.
setURI(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener of a URI identifying the current sequence. NOT IMPLEMENTED
setUri(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property uri.
setURI(URI) - Method in interface org.biojavax.Namespace
  Sets an optional URI for the namespace.
setURI(URI) - Method in class org.biojavax.SimpleNamespace
  Sets an optional URI for the namespace.
setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
  Provide the URN for this sequence
setUsed(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
setUsedAtomNames(String[]) - Method in class org.biojava.bio.structure.align.StrucAligParameters
setUserObject(Object) - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
  `setUserObject` sets the user object.
setValue(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
setValue(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
setValue(double) - Method in interface org.biojava.stats.svm.ItemValue
setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue
setValue(String) - Method in interface org.biojavax.Note
  Sets the value for this note, or null for no value.
setValue(String) - Method in class org.biojavax.SimpleNote
  Sets the value for this note, or null for no value.
setValueGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
  Set the group number that will match the value.
setVectorNTISupport(boolean) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated. VectorNTI requires GenBank format to be a little more specific than required by the GenBank definition.
setVersion(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
setVersion(int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
setVersion(int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
setVersion(int) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
  Call back method so the event emitter can tell the listener the version of the record being read.
setVersion(int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Call back method so the event emitter can tell the listener the version of the record being read.
setVerticalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the vertical scale (proportional).
setVMaxes(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
  Setter for property VMaxes.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
  Set the weight of a given symbol in this distribution.
setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution
  Set the probability or odds that Symbol s is emitted by this state.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.PairDistribution
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.TranslatedDistribution
setWeight(Object, double) - Method in class org.biojavax.ga.util.WeightedSet
  Sets the weight of an `Object`.
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
  Implement this to actually set the weight.
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
  Set a weight in one of the conditioned distributions.
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution
setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.UniformDistribution
setWeightMatrixID(String) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
  Set the weight matrix id.
setWeights(State, Distribution) - Method in interface org.biojava.bio.dp.MarkovModel
  Set the probability distribution over the transitions from 'source'.
setWeights(State, Distribution) - Method in class org.biojava.bio.dp.SimpleMarkovModel
  Use this methods to customize the transition probabilities.
setWeights(State, Distribution) - Method in class org.biojava.bio.dp.WMAsMM
setWidth(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Sets the width of the whole graphic (in pixels).
setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
setWorkingDirectory(File) - Method in class org.biojava.utils.process.ExternalProcess
  Sets the working directory for the external process.
setWrap(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
setWrap(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
setWrapIncrement(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel
setWriteDocType(boolean) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Set flag that determines if XML DOCTYPE is written or not.
setWriter(Writer) - Method in class org.biojava.utils.process.ReaderWriterPipe
  Sets the writer.
setX(double) - Method in interface org.biojava.bio.structure.Atom
  set the X coordinate
setX(double) - Method in class org.biojava.bio.structure.AtomImpl
setY(double) - Method in interface org.biojava.bio.structure.Atom
  set the Y coordinate
setY(double) - Method in class org.biojava.bio.structure.AtomImpl
setZ(double) - Method in interface org.biojava.bio.structure.Atom
  set the Z coordinate
setZ(double) - Method in class org.biojava.bio.structure.AtomImpl
shadow(Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return a contiguous location running from the minimum to the maximum points of the specified location.
shadowContainedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with locations where the interval between the `min` and `max` positions are contained by the specified `Location`.
shadowOverlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
  Construct a filter which matches features with locations where the interval between the `min` and `max` positions are contained by or overlap the specified `Location`.
shannonEntropy(Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
  A method to calculate the Shannon Entropy for a Distribution.
shift(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  moves the whole sequence
shift(Structure, Atom) - Static method in class org.biojava.bio.structure.Calc
  shift a structure with a vector.
shift(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  shift a vector
shift(Group, Atom) - Static method in class org.biojava.bio.structure.Calc
  shift a Group with a vector.
shiftAll(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
shiftAtAlignmentLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
  loc in this case is the Alignment Location
shiftAtAlignmentLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  loc in this case is the Alignment Location
shiftAtSequenceLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
  loc in this case is the SymbolList Location
shiftAtSequenceLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  loc in this case is the SymbolList Location
SHORT_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
  Represents the maximum unsigned value of a short for wrapping purposes
SHOW_ALL - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Return default styles
SHOW_DIFF - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  As NORMAL except only return if the two colour classes for query and subject are the different
SHOW_SAME - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Only return if the two colour classes for query and subject are the same
SIBLING - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  The sibling of this feature has altered.
sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
  `sibling` `SimilarityPairFeature` field.
SigmoidKernel - Class in org.biojava.stats.svm
  This kernel implements a three layer neural net.
SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
similarEntries() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
  Returns a map with the names of similar AAindex entries and its correlation coefficients.
SIMILARITY_PAIR_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
  Constant `SIMILARITY_PAIR_FEATURE_TYPE` the type String used by `SimilarityPairBuilder` when creating `SimilarityPairFeature`s.
SimilarityPairBuilder - Class in org.biojava.bio.program.ssbind
  `SimilarityPairBuilder` annotates query and subject `Sequence` with `SimilarityPairFeature`s created from SAX events supplied via a `SeqSimilarityAdapter`.
SimilarityPairBuilder() - Constructor for class org.biojava.bio.program.ssbind.SimilarityPairBuilder
SimilarityPairFeature - Interface in org.biojava.bio.seq.homol
  `SimilarityPairFeature` describes a pairwise similarity between two nucleotide sequences (as it extends `StrandedFeature`).
SimilarityPairFeature.EmptyPairwiseAlignment - Class in org.biojava.bio.seq.homol
  `EmptyPairwiseAlignment` empty pairwise alignment which has labels to empty symbol lists.
SimilarityPairFeature.Template - Class in org.biojava.bio.seq.homol
  `Template` for construction of `SimilarityPairFeature`s.
SimilarityPairFeature.Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
SIMILARITYTYPE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
SimilarityType - Interface in org.biojava.bio.program.homologene
  Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
SimilarityType.PlaceHolder - Class in org.biojava.bio.program.homologene
SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
SimpleAlignment - Class in org.biojava.bio.symbol
  A simple implementation of an Alignment.
SimpleAlignment(Map) - Constructor for class org.biojava.bio.symbol.SimpleAlignment
  Generate an alignment from a list of SymbolLists.
SimpleAlignmentElement - Class in org.biojava.bio.alignment
  SimpleSimpleAlignment is a simple implementation of AlignmentElement.
SimpleAlignmentElement(Object, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement
SimpleAlignmentStyler - Class in org.biojava.bio.program.blast2html
  Simple implementation for specifying markup styles.
SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
  Creates a new `SimpleAlignmentStyler` instance.
SimpleAlphabet - Class in org.biojava.bio.symbol
  A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
SimpleAnnotation - Class in org.biojava.bio
  A no-frills implementation of Annotation that is just a wrapper around a `LinkedHashMap`.
SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new, empty SimpleAnnotation instance.
SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new SimpleAnnotation by copying the properties from another one.
SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation
  Create a new SimpleAnnotation using the values in a Map.
SimpleAnnotationDB - Class in org.biojava.bio.annodb
  A no-frills implementation of AnnotationDB.
SimpleAnnotationDB(String, Set, AnnotationType) - Constructor for class org.biojava.bio.annodb.SimpleAnnotationDB
  Create a no-frills AnnotationDB instancec.
SimpleAnnotFilter - Class in org.biojava.bio.seq.io.agave
  Basic implementation of AGAVEAnnotFilter
SimpleAssembly - Class in org.biojava.bio.seq
  A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
SimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
  Construct a new SimpleAssembly using the DNA alphabet.
SimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
  Construct a new SimpleAssembly using the DNA alphabet.
SimpleAssemblyBuilder - Class in org.biojava.bio.seq.io
  Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder
SimpleAtomicSymbol - Class in org.biojava.bio.symbol
  A basic implementation of AtomicSymbol.
SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
SimpleBioEntry - Class in org.biojavax.bio
  Reference implementation of a BioEntry object which has no features or sequence.
SimpleBioEntry(Namespace, String, String, int) - Constructor for class org.biojavax.bio.SimpleBioEntry
  Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version.
SimpleBioEntry() - Constructor for class org.biojavax.bio.SimpleBioEntry
SimpleBioEntryRelationship - Class in org.biojavax.bio
  Represents a relationship between two bioentries that is described by a term and given a rank.
SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer) - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
  Creates a new instance of SimpleBioEntryRelationship.
SimpleBioEntryRelationship() - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
SimpleChromatogram - Class in org.biojava.bio.chromatogram
  A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.
SimpleChromatogram() - Constructor for class org.biojava.bio.chromatogram.SimpleChromatogram
  Creates a new instance of SimpleChromatogram.
SimpleCodonPref - Class in org.biojava.bio.symbol
  a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
SimpleCodonPref(String, Distribution, String) - Constructor for class org.biojava.bio.symbol.SimpleCodonPref
SimpleComment - Class in org.biojavax
  An implementaion of Comment.
SimpleComment(String, int) - Constructor for class org.biojavax.SimpleComment
  Constructs a new, immutable comment, given some text and a rank.
SimpleComment() - Constructor for class org.biojavax.SimpleComment
SimpleComparableOntology - Class in org.biojavax.ontology
  Represents an ontology that can be compared to other ontologies.
SimpleComparableOntology(String) - Constructor for class org.biojavax.ontology.SimpleComparableOntology
  Creates a new instance of SimpleComparableOntology with the given, immutable, non-nullable name.
SimpleComparableOntology() - Constructor for class org.biojavax.ontology.SimpleComparableOntology
SimpleComparableTerm - Class in org.biojavax.ontology
  A Term object that can be compared and thus sorted.
SimpleComparableTerm() - Constructor for class org.biojavax.ontology.SimpleComparableTerm
SimpleComparableTriple - Class in org.biojavax.ontology
  Basic comparable triple, BioSQL style.
SimpleComparableTriple() - Constructor for class org.biojavax.ontology.SimpleComparableTriple
SimpleCrossOverFunction - Class in org.biojavax.ga.functions
  Simple Implementation of the `CrossOverFunction` interface
SimpleCrossOverFunction() - Constructor for class org.biojavax.ga.functions.SimpleCrossOverFunction
SimpleCrossRef - Class in org.biojavax
  A basic CrossRef implementation.
SimpleCrossRef(String, String, int) - Constructor for class org.biojavax.SimpleCrossRef
  Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
SimpleCrossRef(String, String, Integer) - Constructor for class org.biojavax.SimpleCrossRef
  Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
SimpleCrossRef() - Constructor for class org.biojavax.SimpleCrossRef
SimpleDistribution - Class in org.biojava.bio.dist
  A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution
  make an instance of SimpleDistribution for the specified Alphabet.
SimpleDistribution(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistribution
  make an instance of SimpleDistribution with weights identical to the specified Distribution.
SimpleDistribution.Trainer - Class in org.biojava.bio.dist
  A simple implementation of a trainer for this class.
SimpleDistribution.Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer
  Create a new trainer.
SimpleDistributionTrainer - Class in org.biojava.bio.dist
  Deprecated. Distribution impls should be providing custom trainers.
SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer
  Deprecated.
SimpleDistributionTrainerContext - Class in org.biojava.bio.dist
  A no-frills implementation of DistributionTrainerContext.
SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext
  Create a new context with no initial distributions or trainers.
SimpleDocRef - Class in org.biojavax
  A basic DocRef implementation.
SimpleDocRef(List, String) - Constructor for class org.biojavax.SimpleDocRef
  Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef(List, String, String) - Constructor for class org.biojavax.SimpleDocRef
  Creates a new document reference from the given immutable authors and location and title.
SimpleDocRef() - Constructor for class org.biojavax.SimpleDocRef
SimpleDocRefAuthor - Class in org.biojavax
  Represents an author of a documentary reference.
SimpleDocRefAuthor(String, boolean, boolean) - Constructor for class org.biojavax.SimpleDocRefAuthor
  Constructs a new author instance.
SimpleDocRefAuthor(String) - Constructor for class org.biojavax.SimpleDocRefAuthor
  Constructs a new author instance from a string.
SimpleDotState - Class in org.biojava.bio.dp
  A Dot state that you can make and use.
SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
  Deprecated. token is ignored since 1.2. Use the 2-arg constructor instead.
SimpleDotState(String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
  Construct a new state with the specified name and annotation
SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
SimpleEmissionState - Class in org.biojava.bio.dp
SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
SimpleFeature - Class in org.biojava.bio.seq.impl
  A no-frills implementation of a feature.
SimpleFeature(Sequence, FeatureHolder, Feature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFeature
  Create a `SimpleFeature` on the given sequence.
SimpleFeatureHolder - Class in org.biojava.bio.seq
  A no-frills implementation of FeatureHolder.
SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
  Construct a new SimpleFeatureHolder with a non-informative schema.
SimpleFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
  Construct a new SimpleFeatureHolder with the specified schema.
SimpleFeatureRealizer - Class in org.biojava.bio.seq
  FeatureRealizer which uses a lookup table to map template classes to implementations.
SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
SimpleFramedFeature - Class in org.biojava.bio.seq.impl
  Title: SimpleFramedFeature.
SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature
SimpleGACrossResult - Class in org.biojavax.ga.functions
  Simple implementation of the `GACross` interface.
SimpleGACrossResult(PointLocation[], SymbolList[]) - Constructor for class org.biojavax.ga.functions.SimpleGACrossResult
SimpleGappedSequence - Class in org.biojava.bio.seq.impl
  Simple implementation of GappedSequence.
SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
SimpleGappedSequence.GappedContext - Class in org.biojava.bio.seq.impl
SimpleGappedSequence.GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
SimpleGappedSymbolList - Class in org.biojava.bio.symbol
  This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
  Create a new SimpleGappedSymbolList that will view source.
SimpleGappedSymbolList.Block - Class in org.biojava.bio.symbol
  An aligned block.
SimpleGappedSymbolList.Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
SimpleGappedSymbolList.Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
SimpleGeneticAlgorithm - Class in org.biojavax.ga.impl
  A simple implementation of the `GeneticAlgorithm` interface it is not intended that this class be overidden, hence it is final.
SimpleGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction) - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
SimpleGFFRecord - Class in org.biojava.bio.program.gff
  A no-frills implementation of a GFFRecord.
SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a new SimpleGFFRecord from GFFRecord object
SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a new SimpleGFFRecord with values set to null or zero
SimpleHMMTrainer - Class in org.biojava.bio.dp
SimpleHMMTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleHMMTrainer
SimpleHomologeneBuilder - Class in org.biojava.bio.program.homologene
  A simple no-frills implementation of the HomologeneBuilder interface.
SimpleHomologeneBuilder() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
SimpleHomologeneDB - Class in org.biojava.bio.program.homologene
SimpleHomologeneDB() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneDB
SimpleHomology - Class in org.biojava.bio.seq.homol
  A no-frills implementation of Homology.
SimpleHomology() - Constructor for class org.biojava.bio.seq.homol.SimpleHomology
  Creates a new empty `SimpleHomology` containing no `Alignment` and no `FeatureHolder`.
SimpleHomologyFeature - Class in org.biojava.bio.seq.impl
SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature
SimpleIndex - Class in org.biojava.bio.seq.db
  This is a no-frills implementation of the Index interface.
SimpleIndex(File, long, int, String) - Constructor for class org.biojava.bio.seq.db.SimpleIndex
  Build the index using the given file, start and id
SimpleInputHandler - Class in org.biojava.utils.process
  Simple input handler that reads the input for an external process from an input stream.
SimpleInputHandler(InputStream, String) - Constructor for class org.biojava.utils.process.SimpleInputHandler
  Initializes the simple input handler.
SimpleItemValue - Class in org.biojava.stats.svm
  A no-frills implementation of ItemValue.
SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
SimpleLabelRenderer - Class in org.biojava.bio.gui.sequence
SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer
SimpleManyToOneTranslationTable - Class in org.biojava.bio.symbol
  A no-frills implementation of a translation table that maps between two alphabets.
SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
  Construct a new translation table.
SimpleMarkovModel - Class in org.biojava.bio.dp
SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
  Deprecated.
SimpleModelInState - Class in org.biojava.bio.dp
SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
SimpleModelTrainer - Class in org.biojava.bio.dp
SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
SimpleMutationFunction - Class in org.biojavax.ga.functions
  Simple no frills Implementation of the MutationFunction interface
SimpleMutationFunction() - Constructor for class org.biojavax.ga.functions.SimpleMutationFunction
SimpleNamespace - Class in org.biojavax
  A basic Namespace implemenation.
SimpleNamespace(String) - Constructor for class org.biojavax.SimpleNamespace
  Creates a new instance of SimpleNamespace with the given name, which cannot be null.
SimpleNamespace() - Constructor for class org.biojavax.SimpleNamespace
SimpleNCBITaxon - Class in org.biojavax.bio.taxa
  Reference implementation of NCBITaxon.
SimpleNCBITaxon(int) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
  Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
SimpleNCBITaxon(Integer) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
  Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
SimpleNCBITaxon() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
SimpleNCBITaxonName - Class in org.biojavax.bio.taxa
  Represents a name class plus name combination for an NCBITaxon object.
SimpleNCBITaxonName() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
SimpleNCBITaxonName(String, String) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Creates a new taxon name based on the given class and name, both of which cannot be null.
SimpleNCBITaxonomyLoader - Class in org.biojavax.bio.taxa.io
  Loads NCBI taxon information from names.dmp and nodes.dmp, which are two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .
SimpleNCBITaxonomyLoader() - Constructor for class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
SimpleNote - Class in org.biojavax
  Simple implementation of Note.
SimpleNote(ComparableTerm, String, int) - Constructor for class org.biojavax.SimpleNote
  Creates a new instance of SimpleNote with a given term, value and rank.
SimpleNote() - Constructor for class org.biojavax.SimpleNote
SimpleOrganism - Class in org.biojavax.ga.impl
  A Simple Haploid Organism implementation
SimpleOrganism() - Constructor for class org.biojavax.ga.impl.SimpleOrganism
SimpleOrganism(String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
SimpleOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
SimpleOrthologue - Class in org.biojava.bio.program.homologene
  this entry contains data about the orthologue.
SimpleOrthologue(Taxon, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
SimpleOrthologue(int, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
  this constructor does the Taxon lookup for you too
SimpleOrthologueSet - Class in org.biojava.bio.program.homologene
SimpleOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologueSet
SimpleOrthologueSet.Iterator - Class in org.biojava.bio.program.homologene
SimpleOrthoPair - Class in org.biojava.bio.program.homologene
  A no-frills implementation of the OrthoPair interface
SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
  constructor for the computed form of an orthology relationship.
SimpleOrthoPair(Orthologue, Orthologue, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
  constructor for the curated form of an orthology relationship
SimpleOrthoPairCollection - Class in org.biojava.bio.program.homologene
SimpleOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
SimpleOrthoPairCollection.Iterator - Class in org.biojava.bio.program.homologene
SimpleOrthoPairSet - Class in org.biojava.bio.program.homologene
  a no-frills implementation of a Homologene Group
SimpleOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairSet
SimpleOrthoPairSet.Iterator - Class in org.biojava.bio.program.homologene
SimpleOutputHandler - Class in org.biojava.utils.process
  Simple output handler that pipes the output of an external process to an output stream.
SimpleOutputHandler(OutputStream, String) - Constructor for class org.biojava.utils.process.SimpleOutputHandler
  Initializes the simple output handler.
SimplePopulation - Class in org.biojavax.ga.impl
  Simple concrete implementation of the `Population` interface
SimplePopulation(String) - Constructor for class org.biojavax.ga.impl.SimplePopulation
SimplePopulation() - Constructor for class org.biojavax.ga.impl.SimplePopulation
SimplePosition - Class in org.biojavax.bio.seq
  A simple implementation of the Position interface.
SimplePosition(int) - Constructor for class org.biojavax.bio.seq.SimplePosition
  Constructs a point position, with no fuzzy start or end.
SimplePosition(int, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
  Constructs a range position, with no fuzzy start or end.
SimplePosition(boolean, boolean, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
  Constructs a point position, with optionally fuzzy start and end.
SimplePosition(boolean, boolean, int, int, String) - Constructor for class org.biojavax.bio.seq.SimplePosition
  Constructs a range position, with optionally fuzzy start and end.
SimplePosition() - Constructor for class org.biojavax.bio.seq.SimplePosition
SimpleRankedCrossRef - Class in org.biojavax
  Simple implementation of RankedCrossRef.
SimpleRankedCrossRef(CrossRef, int) - Constructor for class org.biojavax.SimpleRankedCrossRef
  Constructs a new crossref with a rank.
SimpleRankedCrossRef() - Constructor for class org.biojavax.SimpleRankedCrossRef
SimpleRankedDocRef - Class in org.biojavax
  Represents a documentary reference.
SimpleRankedDocRef(DocRef, Integer, Integer, int) - Constructor for class org.biojavax.SimpleRankedDocRef
  Constructs a new docref for a given location.
SimpleRankedDocRef(DocRef, RichLocation, int) - Constructor for class org.biojavax.SimpleRankedDocRef
  Constructs a new docref for a given location.
SimpleRankedDocRef() - Constructor for class org.biojavax.SimpleRankedDocRef
SimpleRemoteFeature - Class in org.biojava.bio.seq.impl
  A no-frills implementation of a remote feature.
SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature
SimpleRemoteFeature.DBResolver - Class in org.biojava.bio.seq.impl
SimpleRemoteFeature.DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
SimpleRestrictionSite - Class in org.biojava.bio.seq.impl
  `SimpleRestrictionSite` represents the recognition site of a restriction enzyme.
SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRestrictionSite
  Creates a new `SimpleRestrictionSite`.
SimpleReversibleTranslationTable - Class in org.biojava.bio.symbol
  A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable
  Construct a new translation table.
SimpleRichAnnotation - Class in org.biojavax
  Simple annotation wrapper.
SimpleRichAnnotation() - Constructor for class org.biojavax.SimpleRichAnnotation
  Creates a new, empty instance of SimpleRichAnnotation
SimpleRichFeature - Class in org.biojavax.bio.seq
  A simple implementation of RichFeature.
SimpleRichFeature(FeatureHolder, Feature.Template) - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
  Creates a new instance of SimpleRichFeature based on a template.
SimpleRichFeature() - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
SimpleRichFeatureRelationship - Class in org.biojavax.bio.seq
  Represents a relationship between two features that is described by a term.
SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int) - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Creates a new instance of SimpleRichFeatureRelationship.
SimpleRichFeatureRelationship() - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
SimpleRichLocation - Class in org.biojavax.bio.seq
  A simple implementation of RichLocation.
SimpleRichLocation(Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand.
SimpleRichLocation(Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a single position.
SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.
SimpleRichLocation(Position, Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.
SimpleRichLocation(Position, Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a range position.
SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
  Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.
SimpleRichLocation() - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
SimpleRichObjectBuilder - Class in org.biojavax
  Creates objects and returns them, and stores them in an internal map of singletons for reference.
SimpleRichObjectBuilder() - Constructor for class org.biojavax.SimpleRichObjectBuilder
SimpleRichSequence - Class in org.biojavax.bio.seq
  A simple implementation of RichSequence.
SimpleRichSequence(Namespace, String, String, int, SymbolList, Double) - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
  Creates a new instance of SimpleRichSequence.
SimpleRichSequence() - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
SimpleRichSequenceBuilder - Class in org.biojavax.bio.seq.io
  Constructs BioEntry objects by listening to events.
SimpleRichSequenceBuilder() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory with a threshold of zero.
SimpleRichSequenceBuilder(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold of zero.
SimpleRichSequenceBuilder(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Creates a new instance of SimpleRichSequenceBuilder with the desired symbollistfactory and threshold.
SimpleRichSequenceBuilderFactory - Class in org.biojavax.bio.seq.io
  Generates RichSequenceBuilder objects.
SimpleRichSequenceBuilderFactory() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
  Creates a new instance of SimpleRichSequenceBuilderFactory
SimpleRichSequenceBuilderFactory(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
  Creates a new instance of SimpleRichSequenceBuilderFactory
SimpleRichSequenceBuilderFactory(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
  Creates a new instance of SimpleRichSequenceBuilderFactory that uses a specified factory for `SymbolLists` longer than a specified length.
SimpleSeqSimilaritySearchHit - Class in org.biojava.bio.search
  `SimpleSeqSimilaritySearchHit` objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
  Creates a new `SimpleSeqSimilaritySearchHit` object.
SimpleSeqSimilaritySearchResult - Class in org.biojava.bio.search
  `SimpleSeqSimilaritySearchResult` objects represent a result of a search of a `SymbolList` against the sequences within a `SequenceDB` object.
SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
  Creates a new `SimpleSeqSimilaritySearchResult`.
SimpleSeqSimilaritySearchSubHit - Class in org.biojava.bio.search
  `SimpleSeqSimilaritySearchSubHit` objects represent sub-hits which make up a hit.
SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
  Creates a new `SimpleSeqSimilaritySearchSubHit` object.
SimpleSequence - Class in org.biojava.bio.seq.impl
  A basic implementation of the `Sequence` interface.
SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
  Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
  Create a SimpleSequence using a specified FeatureRealizer.
SimpleSequenceBuilder - Class in org.biojava.bio.seq.io
  Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder
SimpleSequenceDBInstallation - Class in org.biojava.bio.seq.db
  This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects.
SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
  create an initially empty SimpleSequenceDBInstallation
SimpleSequenceFactory - Class in org.biojava.bio.seq.impl
  A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory
SimpleSimilarityPairFeature - Class in org.biojava.bio.seq.impl
  `SimpleSimilarityPairFeature` represents a similarity between a query sequence and a subject sequence as produced by a search program.
SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
  Creates a new `SimpleSimilarityPairFeature`.
SimpleStatePath - Class in org.biojava.bio.dp
  A no-frills implementation of StatePath.
SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
SimpleStrandedFeature - Class in org.biojava.bio.seq.impl
  A no-frills implementation of StrandedFeature.
SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature
SimpleSVMClassifierModel - Class in org.biojava.stats.svm
  A no-frills implementation of an SVM classifier model.
SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
SimpleSVMTarget - Class in org.biojava.stats.svm
  No-frills implementation of SVMTarget.
SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
SimpleSymbolList - Class in org.biojava.bio.symbol
  Basic implementation of SymbolList.
SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct an empty SimpleSymbolList.
SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a SymbolList containing the symbols in the specified list.
SimpleSymbolList(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a SymbolList from a string.
SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a copy of an existing SymbolList.
SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
  Construct a SimpleSymbolList given the Symbol array that backs it.
SimpleSymbolListFactory - Class in org.biojava.bio.symbol
  This class makes SimpleSymbolLists.
SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory
SimpleSymbolPropertyTable - Class in org.biojava.bio.symbol
  Class that implements the SymbolPropertyTable interface
SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable
SimpleSymbolPropertyTableDB - Class in org.biojava.bio.proteomics.aaindex
  A simple implementation of a symbol property table database.
SimpleSymbolPropertyTableDB() - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Initializes the database.
SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator) - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Initializes the database by copying all symbol property tables from a given iterator into the database.
SimpleSymbolStyle - Class in org.biojava.bio.gui
  A no-frills implementation of SymbolStyle.
SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle
SimpleTagValueWrapper - Class in org.biojava.bio.program.tagvalue
  Helper class to wrap one TagValueListener inside another one.
SimpleTagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
  Build a SimpleTagValueWrapper that will forward everything to a delegate.
SimpleTagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
SimpleTaxon - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon
  Deprecated.
SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon
  Deprecated. Create a new instance with no parent, no children and given scientific and common names.
SimpleTaxonFactory - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory
  Deprecated.
SimpleThreadPool - Class in org.biojava.utils
  `SimpleThreadPool` is a basic implementation of `ThreadPool` for use where we don't wish to introduce a dependency on a 3rd-party pool.
SimpleThreadPool() - Constructor for class org.biojava.utils.SimpleThreadPool
  Creates a new `SimpleThreadPool` containing 4 non-daemon threads and starts them.
SimpleThreadPool(int, boolean) - Constructor for class org.biojava.utils.SimpleThreadPool
  Creates a new `SimpleThreadPool` containing the specified number of threads and starts them.
SimpleThreadPool(int, boolean, int) - Constructor for class org.biojava.utils.SimpleThreadPool
  Creates a new `SimpleThreadPool` containing the specified number of threads and starts them.
SimpleTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout
  A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues
SimpleTrackLayout() - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
SimpleTrackLayout(Sequence, int) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
SimpleTranslationTable - Class in org.biojava.bio.symbol
  A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
  Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
  Create a new translation table that will translate symbols from source to target.
SimpleWeightMatrix - Class in org.biojava.bio.dp
SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
SimpleXMLEmitter - Class in org.biojava.bio.program.xml
  A simple XML DocumentHandler that processes SAX2 events to create a sensibly formatted XML as it parsed without populating objects with data.
SimpleXMLEmitter() - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
SimpleXMLEmitter(boolean) - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
SingleDP - Class in org.biojava.bio.dp.onehead
  An implementation of DP that aligns a single sequence against a single model.
SingleDP(MarkovModel) - Constructor for class org.biojava.bio.dp.onehead.SingleDP
SingleDPMatrix - Class in org.biojava.bio.dp.onehead
  The dynamic programming matrix for a single sequence.
SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler
singleSequenceIteration(ModelTrainer, SymbolList, ScoreType) - Method in class org.biojava.bio.dp.BaumWelchSampler
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer
SingletonAlphabet - Class in org.biojava.bio.symbol
  An alphabet that contains a single atomic symbol.
SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
SingletonList - Class in org.biojava.utils
SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList
SingularValueDecomposition - Class in org.biojava.bio.structure.jama
  Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.SingularValueDecomposition
  Construct the singular value decomposition.
site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
SITE_FEATURE_SOURCE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
  `SITE_FEATURE_SOURCE` the source `String` used by `RestrictionMapper` when creating restriction site `Feature`s.
SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
  `SITE_FEATURE_TYPE` the type `String` used by `RestrictionMapper` when creating restriction site `Feature`s.
SixFrameRenderer - Class in org.biojava.bio.gui.sequence
  Class that handles drawing in six frames for other classes.
SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer
SixFrameZiggyRenderer - Class in org.biojava.bio.gui.sequence
  A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
SixFrameZiggyRenderer(SixFrameRenderer) - Constructor for class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
size() - Method in interface org.biojava.bio.annodb.AnnotationDB
  The number of Annotation instances in the DB.
size() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
size() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
size() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
size() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
size() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
size() - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Return how many lines are in this set.
size() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
  returns an iterator to the contents of the set.
size() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
size() - Method in interface org.biojava.bio.structure.Group
  getnumber of atoms.
size() - Method in class org.biojava.bio.structure.HetatomImpl
  getnumber of atoms.
size() - Method in interface org.biojava.bio.structure.Structure
  return number of Chains in this Structure.
size(int) - Method in interface org.biojava.bio.structure.Structure
  return number of chains of model.
size() - Method in class org.biojava.bio.structure.StructureImpl
  return number of chains , if NMR return number of chains of first model .
size(int) - Method in class org.biojava.bio.structure.StructureImpl
  return number of chains of model.
size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
  The number of symbols in the alphabet.
size() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
size() - Method in class org.biojava.bio.symbol.SimpleAlphabet
size() - Method in class org.biojava.bio.symbol.SingletonAlphabet
size() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
size() - Method in class org.biojava.stats.svm.SparseVector
  The number of used dimensions.
size() - Method in class org.biojava.stats.svm.SVMRegressionModel
size() - Method in class org.biojava.utils.BeanAsMap
size() - Method in class org.biojava.utils.FileAsList
size() - Method in class org.biojava.utils.ListTools.Doublet
size() - Method in class org.biojava.utils.ListTools.SeriesList
size() - Method in class org.biojava.utils.ListTools.Triplet
size() - Method in class org.biojava.utils.MergingSet
size() - Method in class org.biojava.utils.SingletonList
size() - Method in class org.biojava.utils.SmallMap
size() - Method in class org.biojava.utils.SmallSet
size - Variable in class org.biojavax.bio.seq.CompoundRichLocation
size() - Method in class org.biojavax.ga.impl.SimplePopulation
size() - Method in interface org.biojavax.ga.Population
  Gets the Size of the population
size() - Method in class org.biojavax.ga.util.WeightedSet
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
SIZE_THRESHOLD - Static variable in class org.biojava.bio.program.das.DASSequence
skalarProduct(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  skalar product.
skip(long) - Method in class org.biojava.utils.io.CachingInputStream
skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader
skip(long) - Method in class org.biojava.utils.io.UncompressInputStream
SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
skippedEntity(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
skippedEntity(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
skippedEntity(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
skippedEntity(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
skippedEntity(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
SLEEP_TIME - Static variable in class org.biojava.utils.process.ExternalProcess
  Number of milliseconds the execute method should pauses after the external process has finished the execution.
SmallAnnotation - Class in org.biojava.bio
  Annotation that is optimized for memory usage.
SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation
  Return a new SmallAnnotation optimised for small sets of properties.
SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation
  Return a new SmallAnnotation that copies all values from another annoation.
SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation
  Return a new SmallAnnotation that copies all values from a Map.
SmallCursor - Class in org.biojava.bio.dp.onehead
  Constant-memory implementation of single-head DP cursor.
SmallCursor(State[], SymbolList, Iterator) - Constructor for class org.biojava.bio.dp.onehead.SmallCursor
SmallMap - Class in org.biojava.utils
  Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.
SmallMap() - Constructor for class org.biojava.utils.SmallMap
SmallMap(int) - Constructor for class org.biojava.utils.SmallMap
SmallMap(Map) - Constructor for class org.biojava.utils.SmallMap
SmallSet - Class in org.biojava.utils
  Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability.
SmallSet() - Constructor for class org.biojava.utils.SmallSet
SmallSet(int) - Constructor for class org.biojava.utils.SmallSet
SmallSet(Collection) - Constructor for class org.biojava.utils.SmallSet
SmartSequenceBuilder - Class in org.biojava.bio.seq.io
  Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
SmithWaterman - Class in org.biojava.bio.alignment
  Smith and Waterman developed an efficient dynamic programing algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longes common substring with modifications).
SmithWaterman(double, double, double, double, double, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.SmithWaterman
  Constructs the new SmithWaterman alignment object.
SMORegressionTrainer - Class in org.biojava.stats.svm
  Train a regression support vector machine using the Sequential Minimal Optimization algorithm.
SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
SMOTrainer - Class in org.biojava.stats.svm
  Train a support vector machine using the Sequential Minimal Optimization algorithm.
SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
SoftMaskedAlphabet - Class in org.biojava.bio.symbol
  Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
SoftMaskedAlphabet.CaseSensitiveTokenization - Class in org.biojava.bio.symbol
  This `SymbolTokenizer` works with a delegate to softmask symbol tokenization as appropriate.
SoftMaskedAlphabet.MaskingDetector - Interface in org.biojava.bio.symbol
  Implementations will define how soft masking looks.
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector - Class in org.biojava.bio.symbol
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
SoftReferenceCache - Class in org.biojava.utils.cache
  Cache which is cleared according to memory pressure.
SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache
solve(Matrix) - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
  Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.LUDecomposition
  Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Solve A*X = B
solve(Matrix) - Method in class org.biojava.bio.structure.jama.QRDecomposition
  Least squares solution of A*X = B
solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch
  method that will attempt solving the equation.
solveTranspose(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Solve X*A = B, which is also A'*X' = B'
sort(String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
  It sorts the current collection and returns another collection which is a sorted copy of the current collection.
sort() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Sorts the member locations of a compound location. Does nothing for non-compound locations. Sorting depends on the compareTo() method of the member locations - usually they will be sorted by their start position. This might be useful when used with the location returned by a union or intersection, or when setting the term of a compound location to ORDER_TERM.
sort() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Sorts the member locations of a compound location. DOES NOTHING
sort() - Method in interface org.biojavax.bio.seq.RichLocation
  Sorts the member locations of a compound location.
sort() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Sorts the member locations of a compound location.
SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
  A sort criterion.
sortPeptidesIntoLanes() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
SOURCE - Static variable in interface org.biojava.bio.seq.Feature
  The source of this feature has altered
source - Variable in class org.biojava.bio.seq.Feature.Template
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
SOURCETERM - Static variable in interface org.biojava.bio.seq.Feature
  The ontological source of this feature has altered
sourceTerm - Variable in class org.biojava.bio.seq.Feature.Template
SOURCETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Coordinate conversion from source to view.
sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Coordinate conversion from source to view.
sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
SparseVector - Class in org.biojava.stats.svm
  An implementation of a sparse vector.
SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector
SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector
SparseVector.NormalizingKernel - Class in org.biojava.stats.svm
  A version of the standard dot-product kernel that scales each column independently.
SparseVector.NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Generate a normalizing kernel with the normalizing vector s.
SparseVector.NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
  Generate a normalizing kernel defined by the SparseVectors in vectors.
spatialLocation - Variable in class org.biojava.bibliography.BiblioScope
  It defines a spatial location of the cited resource.
SPECIES_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
split(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter
  Produce a list of values from an old value.
split(Object) - Method in class org.biojava.bio.program.tagvalue.RegexSplitter
splitString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
SQLUnigeneFactory - Class in org.biojava.bio.program.unigene
  An implementatoin of UnigeneFactory that manages it's data in an SQL database.
SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory
ssContext - Variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
StackedFeatureRenderer - Class in org.biojava.bio.gui.sequence
  Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout.
StackedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.StackedFeatureRenderer
StackedLogoPainter - Class in org.biojava.bio.gui
  A logo painter that paints in stacked areas.
StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter
stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
StandardAminoAcid - Class in org.biojava.bio.structure
  A class that provides a set of standard amino acids
StandardAminoAcid() - Constructor for class org.biojava.bio.structure.StandardAminoAcid
standardMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools
  Makes a mutation `Distribution` where the probability of a `Symbol` being mutated to itself is zero and the probability of it being changed to any other `Symbol` in the `Alphabet a` is `1.0 / (a.size() - 1.0)`
start() - Method in interface org.biojava.bio.search.BioMatcher
  Get the first symbol index that matches the pattern.
start() - Method in class org.biojava.bio.search.MaxMismatchMatcher
start - Variable in class org.biojava.utils.automata.FiniteAutomaton
start() - Method in class org.biojava.utils.regex.Matcher
  Returns the start index of the previous match.
start(int) - Method in class org.biojava.utils.regex.Matcher
  Returns the start index of the subsequence captured by the given group during the previous match operation.
start(String[]) - Method in interface org.biojava.utils.xml.AppEntry
START_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
startCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
  called to put the trainer into an initial state for a new round of training.
startCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
startDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  indicates start of data for a HomologeneDB
startDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
startDocument() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
startDocument() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
  Indicates that a new GFF document has been started.
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter
startDocument(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
  Indicates that a new GFF document has been started.
startDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
startDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
startDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
startedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
  Notification that an activity has started.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.dist.XMLDistributionReader
  Required by SAXParser to be public.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
  This is called when an element is entered.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
  we override the superclass startElement method so we can determine the the start tag type and use it to set up delegation for the superclass.
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.FeatureHandler
  StAX callback for element starts.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.PropDetailHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
startElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
startElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  Override this to do any processing required but call this prior to returning.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  Override this to do any processing required but call this prior to returning.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Handles basic entry processing for all feature handlers.
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.CharElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.IntElementHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.LongElementHandlerBase
startElement(String, String, String, Attributes) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.utils.stax.StAXContentHandler
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
  currently we do not handler >computation< as subtag of sciobj yet
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
  Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
  Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
  Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
  Element-specific handler.
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
  Description of the Method
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Element-specific handler.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
  Deprecated.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
  Deprecated.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOFilter
startFeature(Feature.Template) - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Notify the listener that a new feature object is starting.
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Null implementation.
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Notify the listener that a new feature object is starting.
startGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  indicates start of data for a OrthoPairSet
startGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
startHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
startHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
startHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
startHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
startHeader() - Method in class org.biojava.bio.search.SearchContentFilter
startHeader() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `startHeader` method indicates the start of a formatted header.
startHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
startHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
startHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
startHit() - Method in class org.biojava.bio.search.FilteringContentHandler
startHit() - Method in class org.biojava.bio.search.SearchContentAdapter
startHit() - Method in class org.biojava.bio.search.SearchContentFilter
startHit() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `startHit` method indicates the start of a formatted hit.
startHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
startInstance(int, int) - Method in interface org.biojava.utils.automata.StateMachineFactory
  Return a StateMachineInstance if the Symbol represented by the symbol index is valid as the initial symbol of the pattern.
startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
startOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  indicates start of data for an orthologue
startOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
startOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
  indicates start of data for an OrthoPair
startOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
startPrefixMapping(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
startPrefixMapping(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
startPrefixMapping(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
startRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
startRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
startRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
startRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
startRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
  A new record is about to start.
startSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
  Indicates that a sequence is about to be searched against a DataStore.
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
startSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
startSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
startSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
startSearch() - Method in class org.biojava.bio.search.SearchContentFilter
startSearch() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `startSearch` method indicates the start of useful search information.
startSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
  Deprecated.
startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
  Deprecated.
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
startSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
startSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener
  Start the processing of a sequence.
startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
startSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Start the processing of a sequence.
startSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
startSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
startSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
  Start the processing of a sequence.
startSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
startSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
startSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
startSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
startSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
startSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler
  The `startSubHit` method indicates the start of a formatted subhit.
startSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Echo
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
  TagValueListener interface
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagRenamer
startTag(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
  Start a new tag.
startTag(Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
startThreads() - Method in class org.biojava.utils.SimpleThreadPool
startThreads() - Method in interface org.biojava.utils.ThreadPool
  `startThreads` starts all the threads running and opens the pool to requests.
startTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
startTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
startTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
startTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
startZiggy(StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
  Used to initialise the spliced transcript renderer for a CDS feature where the ends of the feature define the frame of the feature.
startZiggy(StrandedFeature.Strand, int) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
  This method is called to initialise the renderer for a spliced transcript.
state - Variable in class org.biojava.bio.dp.BackPointer
  The state with which this backpointer is associated.
State - Interface in org.biojava.bio.dp
  A state in a markov process.
stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
  FiniteAlphabet of the states.
stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
stateList(MarkovModel) - Method in class org.biojava.bio.dp.DP
StateMachine - Class in org.biojava.bio.program.tagvalue
  This class implements a state machine for parsing events from the Parser class.
StateMachine() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine
StateMachine.BasicState - Class in org.biojava.bio.program.tagvalue
  Implementation of a State in a state machine
StateMachine.BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  This is the default constructor
StateMachine.BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  when this constructor is used, a fixed listener is used with this state.
StateMachine.ExitNotification - Interface in org.biojava.bio.program.tagvalue
  Interface implemented by State listeners that want notification when a transition leaves the State.
StateMachine.SimpleStateListener - Class in org.biojava.bio.program.tagvalue
  a basic listener for a State.
StateMachine.SimpleStateListener() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
StateMachine.State - Interface in org.biojava.bio.program.tagvalue
  Interface for a State within this StateMachine
StateMachine.Transition - Class in org.biojava.bio.program.tagvalue
  class to represent a State Transition
StateMachine.TransitionTable - Class in org.biojava.bio.program.tagvalue
  Table of Transition destination States and their corresponding Tags.
StateMachine.TransitionTable() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
StateMachineFactory - Interface in org.biojava.utils.automata
  Class that produces StateMachineInstance objects.
StateMachineInstance - Interface in org.biojava.utils.automata
StatePath - Interface in org.biojava.bio.dp
  Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.
states() - Method in interface org.biojava.bio.dp.DPMatrix
states - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
states() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
STATES - Static variable in interface org.biojava.bio.dp.StatePath
  Alignment label for the state path.
states() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
StaticMemberPlaceHolder - Class in org.biojava.utils
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
StAXContentHandler - Interface in org.biojava.bio.seq.io.agave
  Interface for StAX content handlers.
StAXContentHandler - Interface in org.biojava.utils.stax
  Interface for StAX content handlers.
StAXContentHandlerBase - Class in org.biojava.bio.seq.io.agave
  Simple implementation of the `StAXContentHandler` interface, with empty implementations for all the methods.
StAXContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
StAXContentHandlerBase - Class in org.biojava.utils.stax
  Simple implementation of the `StAXContentHandler` interface, with empty implementations for all the methods.
StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
staxenv - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
staxenv - Variable in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
  Nesting class that provides callback interfaces to nested class
StAXFeatureHandler - Class in org.biojava.bio.seq.io.agave
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler - Class in org.biojava.bio.seq.io.game
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler
StAXFeatureHandler - Class in org.biojava.bio.seq.io.game12
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXHandlerBinding - Class in org.biojava.bio.program.ssbind
  `StAXHandlerBinding`s associates an `ElementRecognizer` with a factory which creates `StAXContentHandler`s for elements which it the `ElementRecognizer` accepts.
StAXHandlerFactory - Interface in org.biojava.bio.program.ssbind
  `StAXHandlerFactory` is an interface for factories producing `StAXContentHandler`s which are used by the `SeqSimilarityStAXAdapter`.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.agave
  Factory for StAX content handlers.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game
  Factory for StAX content handlers.
StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game12
  Factory for StAX content handlers.
StAXPropertyHandler - Class in org.biojava.bio.seq.io.agave
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler - Class in org.biojava.bio.seq.io.game
  StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
stop(GeneticAlgorithm) - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
  Stops the Algorithm if the iterations are >= `maxGenerations`
stop(GeneticAlgorithm) - Method in interface org.biojavax.ga.GAStoppingCriteria
  Determines if an Algorithm should stop spawning new generations
StoppingCriteria - Interface in org.biojava.bio.dp
  A callback that is invoked during the training of an HMM.
StopRenderer - Class in org.biojava.bio.gui.sequence
  Compute sites of stop codons.
StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer
stopThreads() - Method in class org.biojava.utils.SimpleThreadPool
stopThreads() - Method in interface org.biojava.utils.ThreadPool
  `stopThreads` causes all running threads to stop when their current task is complete.
store(Index) - Method in class org.biojava.bio.seq.db.BioIndex
store(Index) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
  `store` adds an `Index` to the store.
store(Index) - Method in interface org.biojava.bio.seq.db.IndexStore
  Add the Index to the store.
store(Index) - Method in class org.biojava.bio.seq.db.TabIndexStore
STORE_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
  `STORE_NAME` is the key used to identify the arbitrary name of the store in the OBDA config.dat files.
STRAIN_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
STRAND - Static variable in interface org.biojava.bio.seq.StrandedFeature
  The strand of this feature is being altered.
strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
STRANDED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
StrandedFeature - Interface in org.biojava.bio.seq
  Adds the concept of 'strand' to features.
StrandedFeature.Strand - Class in org.biojava.bio.seq
  Class to represent the 'strandedness' of a feature.
StrandedFeature.Template - Class in org.biojava.bio.seq
  Template class for parameterizing the creation of a new `StrandedFeature`.
StrandedFeature.Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler
StrandedFeatureHandler - Class in org.biojava.bio.program.xff
  StAX handler for XFF strandedFeature type.
StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler
StrandParser - Class in org.biojava.bio.seq
  Process strings and return strand objects.
StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
StrCompAlignment - Class in org.biojava.bio.structure.align.pairwise
StrCompAlignment(int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.StrCompAlignment
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
streamNext(SeqIOListener) - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
StreamParser - Interface in org.biojava.bio.seq.io
  Parse a stream of characters into BioJava symbols.
StreamPipe - Class in org.biojava.utils.process
  A multi threaded class which pipes the contents of an input stream to an output stream.
StreamPipe(InputStream, OutputStream, String) - Constructor for class org.biojava.utils.process.StreamPipe
  Initializes the stream pipe.
StreamReader - Class in org.biojava.bio.seq.io
  Parses a stream into sequences.
StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet
  Write all records in this set out to a handler.
StreamWriter - Class in org.biojava.bio.seq.io
  Writes all of the sequences from a SequenceIterator to a stream with a particular format.
StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter
  Generate a new StreamWriter to the stream os and using format.
STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable
StringElementHandlerBase - Class in org.biojava.utils.stax
  StAX handler for any element which just contains a string.
StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase
stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord
  Create a String representation of attMap.
stringnifyDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Stringnifies the description of the matrix.
stringnifyMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Creates a `String` representation of this matrix.
stringToClob(Connection, ResultSet, int, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
  Deprecated.
StringTools - Class in org.biojavax.utils
  Utility class for formatting strings into regular-sized blocks.
STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
  Constant `STROKE` indicating a change to the outline stroke of the features.
StrucAligParameters - Class in org.biojava.bio.structure.align
StrucAligParameters() - Constructor for class org.biojava.bio.structure.align.StrucAligParameters
Structure - Interface in org.biojava.bio.structure
  Interface for a structure object.
StructureException - Exception in org.biojava.bio.structure
  An exception during the parsing of a PDB file.
StructureException(String) - Constructor for exception org.biojava.bio.structure.StructureException
  Constructs a StructureException object.
StructureException(String, Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
  Constructs a StructureException object.
StructureException(Throwable, String) - Constructor for exception org.biojava.bio.structure.StructureException
  Deprecated. use new StructureException(message, ex) instead
StructureException(Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
  Constructs a StructureException object.
StructureImpl - Class in org.biojava.bio.structure
  Implementation of a PDB Structure.
StructureImpl() - Constructor for class org.biojava.bio.structure.StructureImpl
  Constructs a StructureImpl object.
StructureImpl(Group) - Constructor for class org.biojava.bio.structure.StructureImpl
  construct a Structure object that only contains a single group
StructureImpl(Chain) - Constructor for class org.biojava.bio.structure.StructureImpl
  construct a Structure object that contains a particular chain
StructureIO - Interface in org.biojava.bio.structure.io
  Defines the interface how to access Structure (- PDB file) input,output readers, writers.
StructureIOFile - Interface in org.biojava.bio.structure.io
  interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
StructurePairAligner - Class in org.biojava.bio.structure.align
StructurePairAligner() - Constructor for class org.biojava.bio.structure.align.StructurePairAligner
StructureTools - Class in org.biojava.bio.proteomics
  Simple access to protein seccondary structure assignments.
StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools
StructureTools - Class in org.biojava.bio.structure
  a class that provides some tool methods
StructureTools() - Constructor for class org.biojava.bio.structure.StructureTools
subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
  Retrieves a subalignment specified by the location.
subAlignment(Set, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
  Retreives a subAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
subAlignment(Set, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
subAlignment(Set, Location) - Method in interface org.biojava.bio.symbol.Alignment
  Make a view onto this alignment.
subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment
subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.SimpleAlignment
SubCircularRendererContext - Class in org.biojava.bio.gui.sequence
  A renderer context that allows some or all properties of another context to be over-ridden.
SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double) - Constructor for class org.biojava.bio.gui.sequence.SubCircularRendererContext
  Create a new sub context.
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.And
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Contains
subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Or
subConstraintOf(CollectionConstraint) - Method in interface org.biojava.bio.CollectionConstraint
  `subConstraintOf` returns true if the constraint is a sub-constraint.
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.And
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByClass
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Or
subConstraintOf(PropertyConstraint) - Method in interface org.biojava.bio.PropertyConstraint
  `subConstraintOf` returns true if the constraint is a sub-constraint.
subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
SubIntegerTokenization - Class in org.biojava.bio.seq.io
SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet) - Constructor for class org.biojava.bio.seq.io.SubIntegerTokenization
subject - Variable in class org.biojava.bibliography.BibRef
  It defines the topic of the content of the cited resource.
SUBJECT_HEADINGS - Static variable in interface org.biojava.bibliography.BibRefSupport
  A vocabulary name.
SUBJECT_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
  Constant `SUBJECT_LABEL` is the alignment label used for all subject sequences.
subjectDBs - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
subjectHeadings - Variable in class org.biojava.bibliography.BiblioSubject
  The subject headings usually come from standard lists such as Sears List of Subject Headings, or Library of Congress Subject Headings (LCSH).
subjectHeadingsSource - Variable in class org.biojava.bibliography.BiblioSubject
  The source of `subject headings`.
subjectViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
subList(int, int) - Method in class org.biojava.bio.program.das.DASSequence
subList(int, int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
subList(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
subList(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
subList(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
subList(int, int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
subList(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
subList(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
subList(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
subList(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
subList(int, int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
subList(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
subList(int, int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
  create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return a new SymbolList for the symbols start to end inclusive.
subList(SymbolList, int, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
  View a portion of a SymbolList.
subList(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Return a new SymbolList for the symbols start to end inclusive.

  The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

subList(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Return a new SymbolList for the symbols start to end inclusive.
subList(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Return a new SymbolList for the symbols start to end inclusive. ALWAYS RETURNS SELF
subList(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Return a new SymbolList for the symbols start to end inclusive.
subList(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Return a new SymbolList for the symbols start to end inclusive.
subMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
SubPairwiseRenderContext - Class in org.biojava.bio.gui.sequence
  `SubPairwiseRenderContext` is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
  Creates a new `SubPairwiseRenderContext`.
SUBPATH_LENGTH - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  To improve performance, the drawing objects for the chromatogram traces are precomputed.
subpathsValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
  Flag for subpaths.
SubSequence - Class in org.biojava.bio.seq.impl
  View a sub-section of a given sequence object, including all the features intersecting that region.
SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.impl.SubSequence
  Construct a new SubSequence of the specified sequence.
SubSequence(Sequence, int, int) - Constructor for class org.biojava.bio.seq.impl.SubSequence
  Construct a new SubSequence of the specified sequence.
subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools
  Extract a sub-sequence from a sequence.
subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools
  Extract a sub-sequence from a sequence.
subSequence(Sequence, int, int, String, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.SequenceTools
  Extract a sub-sequence from a sequence.
subSequence(int, int) - Method in class org.biojava.utils.RepeatedCharSequence
subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
  Creates a new sequence from a subregion of another sequence.
SubSequence.SubProjectedFeatureContext - Class in org.biojava.bio.seq.impl
  TargetContext that implements the mapping between the parent sequence and this sub-sequence.
SubSequenceDB - Class in org.biojava.bio.seq.db
SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB
SubSequenceRenderContext - Class in org.biojava.bio.gui.sequence
  Allows a new renderer to "wrap" another one, replacing one or more values.
SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
SubstitutionMatrix - Class in org.biojava.bio.alignment
  This object is able to read a substitution matrix file and constructs an int matrix to store the matrix.
SubstitutionMatrix(FiniteAlphabet, File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
  This constructs a `SubstitutionMatrix`-object that contains two `Map` data structures having biojava symbols as key and the value being the index of the matrix containing the substitution score.
SubstitutionMatrix(FiniteAlphabet, String, String) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
  With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.
SubstitutionMatrix(FiniteAlphabet, int, int) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
  Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.
subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
subStr(int, int) - Method in class org.biojava.bio.program.das.DASSequence
subStr(int, int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
subStr(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
subStr(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
subStr(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
subStr(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
subStr(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
subStr(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
subStr(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return a region of this symbol list as a String.
subStr(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Return a region of this sequence as a String.

  This should use the same rules as seqString.

subStr(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Return a region of this sequence as a String.
subStr(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Return a region of this symbol list as a String. ALWAYS RETURNS THE CORRECT LENGTH STRING MADE UP OF AMBIGUITY SYMBOLS
subStr(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Return a region of this sequence as a String.
subStr(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Return a region of this symbol list as a String.
substract(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  substract two atoms ( a - b).
subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Subtract one location from another.
subTypeOf(AnnotationType) - Method in class org.biojava.bio.AnnotationType.Abstract
subTypeOf(AnnotationType) - Method in interface org.biojava.bio.AnnotationType
  See if an AnnotationType is a specialisation of this type.
SuffixTree - Class in org.biojava.bio.symbol
  Suffix tree implementation.
SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree
  Construct a new SuffixTree to contain motifs over the specified alphabet.
SuffixTree.SuffixNode - Class in org.biojava.bio.symbol
  A node in the suffix tree.
SuffixTree.SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
SuffixTreeKernel - Class in org.biojava.stats.svm.tools
  Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.
SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel
SuffixTreeKernel.DepthScaler - Interface in org.biojava.stats.svm.tools
  Encapsulates the scale factor to apply at a given depth.
SuffixTreeKernel.MultipleScalar - Class in org.biojava.stats.svm.tools
  Scale using a multiple of two DepthScalers.
SuffixTreeKernel.MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
SuffixTreeKernel.NullModelScaler - Class in org.biojava.stats.svm.tools
  Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
SuffixTreeKernel.NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
SuffixTreeKernel.SelectionScalar - Class in org.biojava.stats.svm.tools
  Scale using a BitSet to allow/disallow depths.
SuffixTreeKernel.SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
  Make a new SelectionScalar that masks in different depths.
SuffixTreeKernel.UniformScaler - Class in org.biojava.stats.svm.tools
  Scale all depths by 1.0
SuffixTreeKernel.UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
SUPPORT - Static variable in class org.biojava.bio.program.abi.ABITools
  Alignment label for the support row.
surname - Variable in class org.biojava.bibliography.BiblioPerson
  The person's sirname (family name).
svd() - Method in class org.biojava.bio.structure.jama.Matrix
  Singular Value Decomposition
SVDSuperimposer - Class in org.biojava.bio.structure
  a class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...
SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.bio.structure.SVDSuperimposer
SVM_Light - Class in org.biojava.stats.svm.tools
SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
SVM_Light.LabelledVector - Class in org.biojava.stats.svm.tools
SVM_Light.LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
SVM_Light.LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
SVMClassifierModel - Interface in org.biojava.stats.svm
  An SVM classifier model.
SVMKernel - Interface in org.biojava.stats.svm
  Kernel for support vector machines and related methods.
SVMRegressionModel - Class in org.biojava.stats.svm
SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
SVMTarget - Interface in org.biojava.stats.svm
  An SVM classifier model.
Swissprot - Class in org.biojava.bio.program.formats
Swissprot() - Constructor for class org.biojava.bio.program.formats.Swissprot
SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `SWISSPROT` indicates that the sequence format is SWISSPROT.
SWISSPROT_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
SwissprotFileFormer - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Creates a new `SwissprotFileFormer` using `System.out` stream.
SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
  Deprecated. Creates a new `SwissprotFileFormer` using the specified stream.
SwissprotProcessor - Class in org.biojava.bio.seq.io
  Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated. Constructor that sets the source of the feature to theSource.
SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
  Deprecated.
SwissprotProcessor.Factory - Class in org.biojava.bio.seq.io
  Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor
SwissprotProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory
  Deprecated.
SwissprotSequenceDB - Class in org.biojava.bio.seq.db
  This class contains functions accessing sequences in swiss-prot.
SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB
Symbol - Interface in org.biojava.bio.symbol
  A single symbol.
symbolAt(Object, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
  this will return the ambiguity symbol associated with all symbols in that column
symbolAt(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
  This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null
symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolAt(Object, int) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolAt(int) - Method in class org.biojava.bio.program.das.DASSequence
symbolAt(int) - Method in class org.biojava.bio.seq.CircularView
  Over rides ViewSequence.
symbolAt(Object, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolAt(int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolAt(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
symbolAt(int) - Method in class org.biojava.bio.seq.impl.DummySequence
symbolAt(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
symbolAt(int) - Method in class org.biojava.bio.seq.impl.SubSequence
symbolAt(int) - Method in class org.biojava.bio.seq.impl.ViewSequence
symbolAt(int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly
symbolAt(Object, int) - Method in interface org.biojava.bio.symbol.Alignment
  Retrieve a symbol by label and column.
symbolAt(int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList
symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList
symbolAt(Object, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolAt(Object, int) - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
  Find a symbol at a specified offset in the SymbolList.
symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList
  Return the symbol at index, counting from 1.
symbolAt(RichSequence, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Return the symbol at index, counting from 1.
symbolAt(RichSequence, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Return the symbol at index, counting from 1.
symbolAt(int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Return the symbol at index, counting from 1. ALWAYS RETURNS THE AMBIGUITY SYMBOL
symbolAt(RichSequence, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Return the symbol at index, counting from 1.
symbolAt(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
  Return the symbol at index, counting from 1.
symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex
  Retrieve the symbol for an index.
symbolForLifeScienceID(LifeScienceIdentifier) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Retreives the Symbol for the LSID
symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
  Deprecated. use symbolForLifeScienceID() instead
SymbolList - Interface in org.biojava.bio.symbol
  A sequence of symbols that belong to an alphabet.
SymbolListCharSequence - Class in org.biojava.bio.seq.io
  `SymbolListCharSequence` is a `CharSequence` implementation which wraps a `SymbolList`.
SymbolListCharSequence(SymbolList) - Constructor for class org.biojava.bio.seq.io.SymbolListCharSequence
  Creates a new `SymbolListCharSequence` wrapping a `SymbolList`.
SymbolListFactory - Interface in org.biojava.bio.symbol
  This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.dp.SimpleStatePath
symbolListForLabel(Object) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolListForLabel(Object) - Method in interface org.biojava.bio.symbol.Alignment
  Retrieve a single row of the alignment by label.
symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.SimpleAlignment
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment
symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath
symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
symbolListIterator() - Method in interface org.biojava.bio.symbol.Alignment
  Creates an Iterator over the SymbolLists in the alignment.
symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
symbolListIterator() - Method in class org.biojava.bio.symbol.SimpleAlignment
SymbolListViews - Class in org.biojava.bio.symbol
  Tools class for constructing views of `SymbolList` objects.
SymbolPropertyTable - Interface in org.biojava.bio.symbol
  class for maintaining properties associated with a symbol
SymbolPropertyTableDB - Interface in org.biojava.bio.proteomics.aaindex
  Database of `SymbolPropertyTable` objects.
SymbolPropertyTableIterator - Interface in org.biojava.bio.proteomics.aaindex
  Iterator over `SymbolPropertyTable` objects.
SymbolReader - Interface in org.biojava.bio.seq.io
  Encapsulate a stream of Symbols being parsed from some input stream.
symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet
  This ChangeType indicates that some symbols have been added or removed from the alphabet.
symbols(SymbolList) - Method in class org.biojava.bio.symbol.CircularLocation
symbols(SymbolList) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location
  Return the symbols in a sequence that fall within this range.
symbols(SymbolList) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown. This function concatenates the symbols of all its child locations.
symbols(SymbolList) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
symbols(SymbolList) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown.
SymbolSequenceRenderer - Class in org.biojava.bio.gui.sequence
  `SymbolSequenceRenderer` renders symbols of a `SymbolList`.
SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
SymbolStyle - Interface in org.biojava.bio.gui
  The interface for things that say how to paint a symbol.
SymbolTokenization - Interface in org.biojava.bio.seq.io
  Encapsulate a mapping between BioJava Symbol objects and some string representation.
SymbolTokenization.TokenType - Class in org.biojava.bio.seq.io
symList() - Method in interface org.biojava.bio.dp.DPMatrix
symList() - Method in interface org.biojava.bio.dp.onehead.DPCursor
  The symbol list being looped over.
symList - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
symList() - Method in class org.biojava.bio.dp.onehead.SmallCursor
symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
SYMLISTVERSION - Static variable in interface org.biojavax.bio.seq.RichSequence
SYMMETRIC - Static variable in class org.biojava.ontology.OntoTools
SYNONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
  Use this to define common names for things.
SYNONYM_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
SystemRegistry - Class in org.biojava.directory
  A registry that loads up the standard biodirectory files.
SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry

## T

t() - Static method in class org.biojava.bio.seq.DNATools
t() - Static method in class org.biojava.bio.seq.NucleotideTools
t() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Threonine
T_AESTIVUM - Static variable in interface org.biojava.bio.program.homologene.Taxon
TabDelimParser - Class in org.biojava.ontology.io
  Parse tab-delimited ontology files into Ontology objects.
TabDelimParser() - Constructor for class org.biojava.ontology.io.TabDelimParser
TabIndexStore - Class in org.biojava.bio.seq.db
  Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
TabIndexStore(File, File, String, SequenceFormat, SequenceBuilderFactory, SymbolTokenization) - Constructor for class org.biojava.bio.seq.db.TabIndexStore
  Create a new TabIndexStore.
table(String) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Returns the table with the specified name.
table(String) - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
  Returns the table with the specified name.
tableIterator() - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
  Returns an iterator over `SymbolPropertyTable` objects.
tableIterator() - Method in interface org.biojava.bio.proteomics.aaindex.SymbolPropertyTableDB
  Returns an iterator over `SymbolPropertyTable` objects.
tableOfContents - Variable in class org.biojava.bibliography.BiblioDescription
  It is a table of contents of the cited resource.
tableOfContentsType - Variable in class org.biojava.bibliography.BiblioDescription
  It specifies how `BiblioDescription.tableOfContents` is coded.
TagDelegator - Class in org.biojava.bio.program.tagvalue
  Pushes a new parser and listener, or delegate to a listener depending on the tag.
TagDelegator() - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
TagDelegator(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDelegator
TagDropper - Class in org.biojava.bio.program.tagvalue
  Silently drop all tags except those specified, and pass the rest onto a delegate.
TagDropper() - Constructor for class org.biojava.bio.program.tagvalue.TagDropper
TagDropper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.TagDropper
  Create a new TagDropper that will pass on all retained tags and values to tvl.
TagMapper - Class in org.biojava.bio.program.tagvalue
  `TagMapper` maps arbitrary object keys to new keys.
TagMapper() - Constructor for class org.biojava.bio.program.tagvalue.TagMapper
  Creates a new, empty `TagMapper`.
tagName - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
tagNumber - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
TagRenamer - Class in org.biojava.bio.program.tagvalue
  Rename tags using a TagMapper.
TagRenamer(TagValueListener, PropertyChanger) - Constructor for class org.biojava.bio.program.tagvalue.TagRenamer
  Build a new TagRenamer with a delegate and mapper.
TagValue - Class in org.biojava.bio.program.tagvalue
  Utility class for representing tag-value pairs for TagValueParser implementors.
TagValue(Object, Object, boolean) - Constructor for class org.biojava.bio.program.tagvalue.TagValue
  Build a new TagValue with a tag, a value and a flag indicating if this is a new example of this tag or a continuation of an old example.
TagValueContext - Interface in org.biojava.bio.program.tagvalue
  Communication interface between Parser and a TagValueListener that allows listeners to request that a parser/listener pair be pushed onto the stack to handle the current tag.
TagValueListener - Interface in org.biojava.bio.program.tagvalue
  An object that wishes to be informed of events during the parsing of a file.
TagValueParser - Interface in org.biojava.bio.program.tagvalue
  Tokenize single records (lines of text, objects) into a tag and a value.
TagValueWrapper - Interface in org.biojava.bio.program.tagvalue
  Interface for TagValueListeners that wrap other TagValueListeners
takeConnection() - Method in class org.biojava.utils.JDBCConnectionPool
takeStatement() - Method in class org.biojava.utils.JDBCConnectionPool
tanh(double) - Method in class org.biojava.stats.svm.SigmoidKernel
taxa - Static variable in interface org.biojava.bio.program.homologene.Taxon
TAXID_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
Taxon - Interface in org.biojava.bio.program.homologene
Taxon - Interface in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
TAXON - Static variable in interface org.biojavax.bio.BioEntry
Taxon.TaxonStub - Class in org.biojava.bio.program.homologene
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
TAXON_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
TaxonFactory - Interface in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
TAXONID - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
TAXONOMY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
TaxonParser - Interface in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
TaxonSQL - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
TaxonSQL() - Constructor for class org.biojava.bio.seq.db.biosql.TaxonSQL
  Deprecated.
TemplateUtils - Class in org.biojava.bio.seq.impl
  Common things you may want to do with feature templates.
temporalPeriod - Variable in class org.biojava.bibliography.BiblioScope
  It defines temporal period of the cited resource.
ter() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the termination (*) placeholder
TERM - Static variable in interface org.biojava.ontology.Ontology
Term - Interface in org.biojava.ontology
  A term in an ontology.
TERM - Static variable in interface org.biojavax.bio.seq.RichLocation
term - Variable in class org.biojavax.bio.seq.SimpleRichLocation
TERM - Static variable in interface org.biojavax.Note
TERM - Static variable in interface org.biojavax.ontology.ComparableOntology
Term.Impl - Class in org.biojava.ontology
  Simple in-memory implementation of an ontology term.
Term.Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Term.Impl
Term.Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Term.Impl
TEXT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
TextBlock - Class in org.biojava.bio.gui
  A BlockPainter that renders letters in proportion to the size of the signal.
TextBlock() - Constructor for class org.biojava.bio.gui.TextBlock
TextLogoPainter - Class in org.biojava.bio.gui
  A logo painter that paints in stacked letters.
TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter
theAbstract - Variable in class org.biojava.bibliography.BiblioDescription
  It is an abstract of the cited resource.
ThinRichSequence - Class in org.biojavax.bio.seq
  A simple implementation of RichSequence.
ThinRichSequence(Namespace, String, String, int, Alphabet, Double) - Constructor for class org.biojavax.bio.seq.ThinRichSequence
  Creates a new instance of ThinRichSequence.
ThinRichSequence() - Constructor for class org.biojavax.bio.seq.ThinRichSequence
thr() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Threonine (T)
THREAD_POOL_SIZE - Static variable in class org.biojava.utils.process.ExternalProcess
  Size of the thread pool for the static execute methods.
threadPool() - Method in class org.biojava.utils.process.ExternalProcess
  Gets the thread pool which is used for the input and output handlers.
ThreadPool - Interface in org.biojava.utils
  `ThreadPool` specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
threads - Variable in class org.biojava.utils.SimpleThreadPool
threadsAlive() - Method in class org.biojava.utils.SimpleThreadPool
  `threadsAlive` returns the number of threads currently alive.
threadsIdle() - Method in class org.biojava.utils.SimpleThreadPool
  `threadsIdle` returns the number of threads currently waiting for work.
threadsWorking() - Method in class org.biojava.utils.SimpleThreadPool
  `threadsWorking` returns the number of threads currently performing work.
THRESHOLD - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
  Accessor for a factory that produces builders that compress the `SymbolList` of a `RichSequence` when the length of the `SymbolList` exceeds `THRESHOLD`.
THRESHOLD_VALUE - Static variable in interface org.biojavax.bio.seq.io.RichSequenceBuilderFactory
  The value that will be used as a threshold for the `THRESHOLD` builder.
TickFeatureRenderer - Class in org.biojava.bio.gui.sequence
TickFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.TickFeatureRenderer
TICKS - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
TICKS_DOWN - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer
  `TICKS_DOWN` indicates that the ticks will point downwards from a baseline.
TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
TICKS_UP - Static variable in class org.biojava.bio.gui.sequence.RulerRenderer
  `TICKS_UP` indicates that the ticks will point upwards from a baseline.
times(double) - Method in class org.biojava.bio.structure.jama.Matrix
  Multiply a matrix by a scalar, C = s*A
times(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
  Linear algebraic matrix multiplication, A * B
timesEquals(double) - Method in class org.biojava.bio.structure.jama.Matrix
  Multiply a matrix by a scalar in place, A = s*A
TISSUE_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
title - Variable in class org.biojava.bibliography.BibRef
  A title given to the cited resource (a name by which the resource is formally known).
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
TITLE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
to - Variable in class org.biojava.bio.dp.TrainerTransition
to - Variable in class org.biojava.bio.dp.Transition
TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
TO_TRACE_SAMPLE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating the highest (rightmost) trace sample that should be drawn.
toArray() - Method in class org.biojavax.ga.util.WeightedSet
toDASStructure(XMLWriter) - Method in class org.biojava.bio.structure.io.FileConvert
  convert a protein Structure to a DAS Structure XML response .
toggleSelectionStatus() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CharacterTokenization
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.CrossProductTokenization
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.DoubleTokenization
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.IntegerTokenization
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.NameTokenization
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.seq.io.SubIntegerTokenization
tokenizeSymbol(Symbol) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  Return a token representing a single symbol.
tokenizeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.CharacterTokenization
tokenizeSymbolList(SymbolList) - Method in interface org.biojava.bio.seq.io.SymbolTokenization
  Return a string representation of a list of symbols.
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.seq.io.WordTokenization
tokenizeSymbolList(SymbolList) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
toLink(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator
  Returns a full retrieve item anchor for the given database id.
toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
toLink(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
toList() - Method in class org.biojava.bio.dp.SimpleStatePath
toList() - Method in class org.biojava.bio.program.das.DASSequence
toList() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
toList() - Method in class org.biojava.bio.seq.impl.DummySequence
toList() - Method in class org.biojava.bio.seq.impl.SimpleSequence
toList() - Method in class org.biojava.bio.seq.impl.SubSequence
toList() - Method in class org.biojava.bio.seq.impl.ViewSequence
toList() - Method in class org.biojava.bio.seq.NewSimpleAssembly
toList() - Method in class org.biojava.bio.seq.SimpleAssembly
toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList
toList() - Method in class org.biojava.bio.symbol.RelabeledAlignment
toList() - Method in interface org.biojava.bio.symbol.SymbolList
  Returns a List of symbols.
toList(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
  Returns a List of symbols.

  This should be an immutable list of symbols or a copy.

toList(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
  Returns a List of symbols.
toList() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
  Returns a List of symbols. ALWAYS RETURNS A LIST CONTAINING THE AMBIGUITY SYMBOL
toList(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
  Returns a List of symbols.
toList() - Method in class org.biojavax.bio.seq.ThinRichSequence
  Returns a List of symbols.
top_level - Static variable in interface org.biojava.bio.seq.FeatureFilter
  A filter which accepts only top-level Features.
toPDB(Structure, Structure) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  converts th alignment to a PDB file each of the structures will be represented as a model.
toPDB() - Method in class org.biojava.bio.structure.io.FileConvert
  Convert a structure into a PDB file.
toPDB() - Method in interface org.biojava.bio.structure.Structure
  create a String that contains the contents of a PDB file .
toPDB() - Method in class org.biojava.bio.structure.StructureImpl
  create a String that contains the contents of a PDB file.
topLevel() - Static method in class org.biojava.bio.seq.FilterUtils
  Return a filter which matches all top-level features.
TOPOLOGY_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
toRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
  Converts a `SymbolList` from the DNA `Alphabet` to the RNA `Alphabet`.
torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  torsion angle = angle between the normal vectors of the two plains a-b-c and b-c-d.
toString() - Method in class org.biojava.bio.AbstractAnnotation
toString() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
  Overides the inherited method.
toString() - Method in class org.biojava.bio.AnnotationType.Abstract
toString() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
toString() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
toString() - Method in class org.biojava.bio.CollectionConstraint.And
toString() - Method in class org.biojava.bio.CollectionConstraint.Contains
toString() - Method in class org.biojava.bio.CollectionConstraint.Or
toString() - Method in class org.biojava.bio.dp.SimpleMarkovModel
toString() - Method in class org.biojava.bio.EcNumber.Impl
toString() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
toString() - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
toString() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
toString() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
toString() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
toString() - Method in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
  A very verbose `toString` that dumps all of the data in this record in a human-readable format.
toString() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
  convert to String.
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.AllElementRecognizer
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByLocalName
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.ByNSName
toString() - Method in class org.biojava.bio.program.xff.ElementRecognizer.HasAttribute
toString() - Method in class org.biojava.bio.PropertyConstraint.And
toString() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
toString() - Method in class org.biojava.bio.PropertyConstraint.ByClass
toString() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
toString() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
toString() - Method in class org.biojava.bio.PropertyConstraint.Or
toString() - Method in class org.biojava.bio.search.SequenceDBSearchHit
  Deprecated.
toString() - Method in class org.biojava.bio.search.SequenceDBSearchResult
  Deprecated.
toString() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
  Deprecated.
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.BioSequenceStyle
  Deprecated.
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.DeleteStyle
  Deprecated.
toString() - Method in class org.biojava.bio.seq.db.biosql.DBHelper.JoinStyle
  Deprecated.
toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
toString() - Method in class org.biojava.bio.seq.Feature.Template
toString() - Method in class org.biojava.bio.seq.FeatureFilter.And
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
toString() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Not
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
toString() - Method in class org.biojava.bio.seq.FeatureFilter.Or
toString() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
toString() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
toString() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
toString() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
toString() - Method in class org.biojava.bio.seq.homol.SimpleHomology
toString() - Method in class org.biojava.bio.seq.impl.SimpleFeature
toString() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
toString() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
toString() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
toString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
toString() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
toString() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
toString() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  Return the current indent
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
  return the agave xml representation of this instance
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
  return the agave xml representation of this instance
toString(String, String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
toString() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
  the agave xml representation of xrefs
toString() - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
toString() - Method in class org.biojava.bio.seq.io.SymbolTokenization.TokenType
toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
toString() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
toString() - Method in class org.biojava.bio.structure.align.helper.IndexPair
toString() - Method in class org.biojava.bio.structure.align.helper.JointFragments
toString() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
  print the idx positions of this alignment
toString() - Method in interface org.biojava.bio.structure.AminoAcid
  string representation.
toString() - Method in class org.biojava.bio.structure.AminoAcidImpl
  string representation.
toString() - Method in class org.biojava.bio.structure.AtomImpl
  string representation.
toString() - Method in interface org.biojava.bio.structure.Chain
  string representation.
toString() - Method in class org.biojava.bio.structure.ChainImpl
  string representation.
toString() - Method in class org.biojava.bio.structure.HetatomImpl
toString() - Method in class org.biojava.bio.structure.NucleotideImpl
toString() - Method in interface org.biojava.bio.structure.Structure
  String representation of object.
toString() - Method in class org.biojava.bio.structure.StructureImpl
  string representation.
toString() - Method in class org.biojava.bio.symbol.AbstractAlphabet
toString() - Method in class org.biojava.bio.symbol.AbstractSymbol
toString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
toString() - Method in class org.biojava.bio.symbol.CircularLocation
toString() - Method in class org.biojava.bio.symbol.FuzzyLocation
toString() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
toString() - Method in class org.biojava.bio.symbol.PointLocation
toString() - Method in class org.biojava.bio.symbol.RangeLocation
toString() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
toString() - Method in class org.biojava.bio.taxa.AbstractTaxon
  Deprecated.
toString() - Method in class org.biojava.ontology.Ontology.Impl
toString() - Method in class org.biojava.ontology.OntologyTerm.Impl
toString() - Method in class org.biojava.ontology.RemoteTerm.Impl
toString() - Method in class org.biojava.ontology.Term.Impl
toString() - Method in class org.biojava.ontology.Triple.Impl
toString() - Method in class org.biojava.stats.svm.CachingKernel
toString() - Method in class org.biojava.stats.svm.DiagonalAddKernel
toString() - Method in class org.biojava.stats.svm.DiagonalCachingKernel
toString() - Method in class org.biojava.stats.svm.ListSumKernel
toString() - Method in class org.biojava.stats.svm.NormalizingKernel
toString() - Method in class org.biojava.stats.svm.PolynomialKernel
toString() - Method in class org.biojava.stats.svm.RadialBaseKernel
toString() - Method in class org.biojava.stats.svm.SigmoidKernel
toString() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
toString() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
toString() - Method in class org.biojava.utils.automata.FiniteAutomaton
  dumps internal data of Nodes and Transitions that describe this FiniteAutomaton.
toString() - Method in interface org.biojava.utils.automata.NfaBuilder
toString() - Method in class org.biojava.utils.automata.NfaSubModel
toString() - Method in class org.biojava.utils.candy.CandyEntry
  It prints the entry contents.
toString() - Method in class org.biojava.utils.ChangeEvent
toString() - Method in class org.biojava.utils.ChangeType
  Return a string representation of this change.
toString() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
toString() - Method in class org.biojava.utils.ParseErrorEvent
toString() - Method in exception org.biojava.utils.ParserException
  Represent this exception as a string.
toString() - Method in class org.biojava.utils.RepeatedCharSequence
toString() - Method in class org.biojava.utils.TypedProperties
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
toString() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
toString() - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Form: "start..end" or just "point" for point locations Form: "term:[location,location...]"
toString() - Method in class org.biojavax.bio.seq.EmptyRichLocation
  ALWAYS RETURNS "empty"
toString() - Method in class org.biojavax.bio.seq.RichLocation.Strand
  Form: "symbol" (eg.
toString() - Method in class org.biojavax.bio.seq.SimplePosition
toString() - Method in class org.biojavax.bio.seq.SimpleRichFeature
  Form: "(#rank) parent:type,source(location)"
toString() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
  Form: "(#rank) term(object,subject)"
toString() - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Form: "start..end" or just "point" for point locations
toString() - Method in class org.biojavax.bio.SimpleBioEntry
  Form: namespace:name/accession.version
toString() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
  Form is "(#rank) term(object,subject)"
toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
  Form: "taxid:[name,name...]"
toString() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
  Form: "class:name"
toString() - Method in class org.biojavax.ontology.SimpleComparableOntology
  Form: "name"
toString() - Method in class org.biojavax.ontology.SimpleComparableTerm
  Form: "ontology:name [obsolete]" where [obsolete] is optional
toString() - Method in class org.biojavax.ontology.SimpleComparableTriple
  Form: "ontology:predicate(subject,object)"
toString() - Method in class org.biojavax.SimpleComment
  Form: "(#rank) comment"
toString() - Method in class org.biojavax.SimpleCrossRef
  Form: "dbname:accession.version"
toString() - Method in class org.biojavax.SimpleDocRef
  Form: "authors; location"
toString() - Method in class org.biojavax.SimpleDocRefAuthor
  Form: "name (consortium) (ed.)" where sections in brackets are optional.
toString() - Method in class org.biojavax.SimpleNamespace
  Form: "name"
toString() - Method in class org.biojavax.SimpleNote
  Form: "(#rank) term: value"
toString() - Method in class org.biojavax.SimpleRankedCrossRef
  Form: "(#rank) crossref"
toString() - Method in class org.biojavax.SimpleRankedDocRef
  Form: "(#rank) docref"
toString() - Method in class org.biojavax.SimpleRichAnnotation
  Form: list of "[note]" values separated by commas
toString() - Method in class org.biojavax.utils.CRC64Checksum
  Form: the current CRC64Checksum checksum as a 16-digit hex string.
totalBits(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo
  Retrieve the maximal number of bits possible for this type of dist.
totalEntropy(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
  Calculates the total Entropy for a Distribution.
totalInformation(Distribution) - Static method in class org.biojava.bio.gui.DistributionLogo
  Calculates the total information of the dist in bits.
toURL(String, Properties) - Method in interface org.biojava.bio.program.blast2html.DatabaseURLGenerator
  Returns a string representation of a URL to the specified ID.
toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.EbiDatabaseURLGenerator
toURL(String, Properties) - Method in class org.biojava.bio.program.blast2html.NcbiDatabaseURLGenerator
TPA_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
TRACE - Static variable in class org.biojava.bio.gui.sequence.AbiTraceRenderer
trace() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix trace.
TRACE_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option providing the the stroke to use for drawing the chromatogram traces.
TrackLayout - Interface in org.biojava.bio.gui.sequence.tracklayout
  An interface for the handling of the layout of a WrappedSequencePanel.
train(DistributionTrainerContext, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
  Trains the Distribution, given a null model.
train() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
  Trains the Distribution, given a null model.
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
train(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
  Deprecated.
train() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
train(SequenceDB, double, StoppingCriteria) - Method in class org.biojava.bio.dp.AbstractTrainer
  Trains the sequences in db until stopper says to finnish.
train(SequenceDB, double, StoppingCriteria) - Method in interface org.biojava.bio.dp.TrainingAlgorithm
  Trains the sequences in db untill stopper says to finnish.
train(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
  Trains the transition, given an expected probability, and a weight for that probability.
Train - Class in org.biojava.stats.svm.tools
Train() - Constructor for class org.biojava.stats.svm.tools.Train
Trainable - Interface in org.biojava.bio.dp
  Flags an object as being able to register itself with a model trainer.
trainer - Variable in class org.biojava.bio.dp.TrainerTransition
trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
TrainerTransition - Class in org.biojava.bio.dp
  This is a small and ugly class for storing a trainer and a transition.
TrainerTransition(TransitionTrainer, State, State) - Constructor for class org.biojava.bio.dp.TrainerTransition
trainImpl(DistributionTrainerContext, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
TrainingAlgorithm - Interface in org.biojava.bio.dp
trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
TrainingContext - Interface in org.biojava.stats.svm
trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
TrainingEvent - Class in org.biojava.stats.svm
TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent
TrainingListener - Interface in org.biojava.stats.svm
trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer
trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer
TrainRegression - Class in org.biojava.stats.svm.tools
TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression
transcribe(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
  Transcribe DNA into RNA.
transcribe(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
  Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
transcribeToRNA(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
  Transcribes DNA to RNA.
transcriptionTable() - Static method in class org.biojava.bio.seq.RNATools
  Get a translation table for converting DNA to RNA.
transform(FeatureFilter) - Method in class org.biojava.bio.seq.FilterUtils.DelegatingTransformer
transform(FeatureFilter) - Method in interface org.biojava.bio.seq.FilterUtils.FilterTransformer
  Transform a filter, or return null if it can not be transformed.
transformFilter(FeatureFilter, FilterUtils.FilterTransformer) - Static method in class org.biojava.bio.seq.FilterUtils
  This is a general framework method for transforming one filter into another.
transformLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
  Transform a location, translating and flipping as required.
transit(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
  Find the destination State when the specified tag is encountered.
transit(Object) - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
transit(int) - Method in interface org.biojava.utils.automata.StateMachineInstance
  invoke transition from current state indicated by Symbol represented by symbol index.
Transition - Class in org.biojava.bio.dp
  This is a small and ugly class for storing a transition.
Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition
transitions - Variable in class org.biojava.utils.automata.FiniteAutomaton
transitionsFrom(State) - Method in interface org.biojava.bio.dp.MarkovModel
  Returns the FiniteAlphabet of all states that have a transition from 'source'.
transitionsFrom(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
transitionsFrom(State) - Method in class org.biojava.bio.dp.WMAsMM
transitionsTo(State) - Method in interface org.biojava.bio.dp.MarkovModel
  Returns the FiniteAlphabet of all states that have a transition to 'dest'.
transitionsTo(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
transitionsTo(State) - Method in class org.biojava.bio.dp.WMAsMM
TransitionTrainer - Interface in org.biojava.bio.dp
  An object that can be used to train the transitions within a MarkovModel.
TRANSITIVE - Static variable in class org.biojava.ontology.OntoTools
translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
  Translate RNA into protein (with termination symbols).
translate(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
  Translate RNA into protein (with termination symbols).
translate(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
translate(int) - Method in class org.biojava.bio.symbol.FuzzyLocation
translate(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
translate(int) - Method in interface org.biojava.bio.symbol.Location
  Create a location that is a translation of this location.
translate(int) - Method in class org.biojava.bio.symbol.PointLocation
translate(int) - Method in class org.biojava.bio.symbol.RangeLocation
translate(SymbolList, TranslationTable) - Static method in class org.biojava.bio.symbol.SymbolListViews
  Provides a 'translated' view of an underlying SymbolList.
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
  Translate a single symbol from source alphabet to the target alphabet.
translate(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Create a location that is a translation of this location. Recursively translates all members of this location.
translate(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Create a location that is a translation of this location. ALWAYS RETURNS SELF
translate(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
  Create a location that is a translation of this location. Recursively translates all members of this location. Recursively translates all members of this location.
translate(int) - Method in interface org.biojavax.bio.seq.Position
  Takes this position and returns a copy translated by 'distance' bases.
translate(int) - Method in class org.biojavax.bio.seq.SimplePosition
  Takes this position and returns a copy translated by 'distance' bases.
translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Create a location that is a translation of this location.
translateCUD(InputStream, OutputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
  reads in a file in Codon Usage Database format and translate it into our XML format These can be obtained from the Codon Usage Database.
TranslatedDistribution - Class in org.biojava.bio.dist
  A translated view of some underlying distribution.
TranslatedDistribution(ReversibleTranslationTable, Distribution, DistributionFactory) - Constructor for class org.biojava.bio.dist.TranslatedDistribution
  Create a new TranslatedDistribution.
TranslatedSequencePanel - Class in org.biojava.bio.gui.sequence
  `TranslatedSequencePanel` is a panel that displays a Sequence.
TranslatedSequencePanel() - Constructor for class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  Creates a new `TranslatedSequencePanel` with the default settings (direction HORIZONTAL, scale 10.0 pixels per symbol, symbol translation 0, leading border 0.0, trailing border 0.0, 12 point sanserif font).
TranslateFlipContext - Class in org.biojava.bio.seq.projection
  A ProjectionContext that translates and optionaly flips features.
TranslateFlipContext(FeatureHolder, FeatureHolder, int, boolean) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
  Create a new TranslateFlipContext with explicit translation and flip.
TranslateFlipContext(FeatureHolder, FeatureHolder, int, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
  Create a new TranslateFlipContext that flips all featurs arround min and max.
TranslateFlipContext(FeatureHolder, FeatureHolder, int) - Constructor for class org.biojava.bio.seq.projection.TranslateFlipContext
  Create a new TranslateFlipContext with translation only.
TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
  Constant `TRANSLATION` is a `ChangeType` which indicates a change to the translation, requiring a paint update.
TRANSLATION - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
  Constant `TRANSLATION` is a `ChangeType` which indicates a change to the translation, requiring a paint update.
TranslationTable - Interface in org.biojava.bio.symbol
  Encapsulates the mapping from a source to a destination alphabet.
transpose() - Method in class org.biojava.bio.structure.jama.Matrix
  Matrix transpose.
TRANSPOSON_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
transScore(State, State, Symbol, Symbol) - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
TRIPLE - Static variable in interface org.biojava.ontology.Ontology
Triple - Interface in org.biojava.ontology
  A triple in an ontology.
TRIPLE - Static variable in interface org.biojavax.ontology.ComparableOntology
Triple.Impl - Class in org.biojava.ontology
  Basic in-memory implementation of a Triple in an ontology
Triple.Impl(Term, Term, Term) - Constructor for class org.biojava.ontology.Triple.Impl
Triple.Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
Triple.Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.ontology.Triple.Impl
Triple.Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.ontology.Triple.Impl
TriState - Class in org.biojava.utils
  Class that represents the tristate values possible in a logical operation: true, false and indeterminate.
trp() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Tryptophan (W)
TRUE - Static variable in class org.biojava.utils.TriState
TRYPSIN - Static variable in class org.biojava.bio.proteomics.Protease
TRYPSIN - Static variable in class org.biojava.bio.proteomics.ProteaseManager
TurnGlyph - Class in org.biojava.bio.gui.glyph
  A Glyph that paints a wide 'H' line within the bounds
TurnGlyph() - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
TurnGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
TurnGlyph(Paint, Stroke) - Constructor for class org.biojava.bio.gui.glyph.TurnGlyph
TWIN - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
TWIN - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
TwoHeadedArrowGlyph - Class in org.biojava.bio.gui.glyph
  A Glyph that paints a two headed arrow within the bounds
TwoHeadedArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
TwoHeadedArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
type - Variable in class org.biojava.bibliography.BiblioCriterion
  The criteria can be used for defining rules for matching (type `BiblioCriterion.QUERY_CRITERION`), or for ordering (type `BiblioCriterion.SORT_CRITERION`).
type - Variable in class org.biojava.bibliography.BibRef
  It defines the nature or genre of the cited resource.
type - Variable in class org.biojava.bio.seq.Feature.Template
TYPE - Static variable in interface org.biojava.bio.seq.Feature
  The type of this feature has altered.
type - Static variable in class org.biojava.bio.structure.AminoAcidImpl
  this is an Amino acid.
type - Static variable in class org.biojava.bio.structure.HetatomImpl
  this is a "hetatm".
type - Static variable in class org.biojava.bio.structure.NucleotideImpl
  this is a "nucleotide", a special occurance of a Hetatom.
type - Variable in class org.biojava.utils.IndexedChangeHub.ListenerMemento
TYPE_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
TYPE_BOOK - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_BOOK_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_JOURNAL_ARTICLE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_PATENT - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_PROCEEDING - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
TYPE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
TYPE_TECH_REPORT - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_THESIS - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TYPE_WEB_RESOURCE - Static variable in interface org.biojava.bibliography.BibRefSupport
  A name of a bibliographic resource type.
TypedProperties - Class in org.biojava.utils
  a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of type XXX.
TypedProperties() - Constructor for class org.biojava.utils.TypedProperties
  Creates an empty property list with no default values.
TypedProperties(Properties) - Constructor for class org.biojava.utils.TypedProperties
  Creates an empty property list with the specified defaults.
typeTerm - Variable in class org.biojava.bio.seq.Feature.Template
TYPETERM - Static variable in interface org.biojava.bio.seq.Feature
  The ontological type of this feature has altered.
TYPETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
tyr() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Tyrosine (Y)

## U

u() - Static method in class org.biojava.bio.seq.NucleotideTools
u() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Selenocysteine
u() - Static method in class org.biojava.bio.seq.RNATools
UkkonenSuffixTree - Class in org.biojava.bio.symbol
  A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence.
UkkonenSuffixTree() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
  Initializes a new `UkkonenSuffixTree` instance.
UkkonenSuffixTree(String) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
UkkonenSuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree
UkkonenSuffixTree.SuffixNode - Class in org.biojava.bio.symbol
  end Tree modification methods
UkkonenSuffixTree.SuffixNode() - Constructor for class org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
uminus() - Method in class org.biojava.bio.structure.jama.Matrix
  Unary minus
unbind(Name) - Method in class org.biojava.naming.ObdaContext
unbind(String) - Method in class org.biojava.naming.ObdaContext
Unchangeable - Class in org.biojava.utils
  This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
Unchangeable() - Constructor for class org.biojava.utils.Unchangeable
UNCLASSIFIED - Static variable in interface org.biojava.bio.EcNumber
  Constant that represents EC number components that are as yet unclassified.
uncompress(String, FileOutputStream) - Static method in class org.biojava.utils.io.UncompressInputStream
UncompressInputStream - Class in org.biojava.utils.io
  This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.biojava.utils.io.UncompressInputStream
UNDEFINED - Static variable in interface org.biojava.bio.EcNumber
  Constant that represents EC number components that are not defined.
UnequalLengthAlignment - Interface in org.biojava.bio.alignment
  UnequalLengthAlignment has the following behavior.
UniformDistribution - Class in org.biojava.bio.dist
  An implementation of an uniform distribution
UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution
  Create a new UniformDistribution.
uniformMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools
  Makes a 1st order distribution which is infact uniform (equivalent to a uniform zero order distribution).
UNIGENE_ANNOTATION - Static variable in class org.biojava.bio.program.unigene.UnigeneTools
  Annotation schema for all UnigeneCluster instances.
UnigeneCluster - Interface in org.biojava.bio.program.unigene
  A single unigene cluster.
UnigeneDB - Interface in org.biojava.bio.program.unigene
  A database of Unigene clusters.
UnigeneFactory - Interface in org.biojava.bio.program.unigene
  Objects that can be used to produce a `UnigeneDB` instance given a URL.
UnigeneTools - Class in org.biojava.bio.program.unigene
  Usefull tools for working with Unigene.
UnigeneTools() - Constructor for class org.biojava.bio.program.unigene.UnigeneTools
unIndent() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  Remove a level of indentation
union(BibRefQuery[], Hashtable) - Method in interface org.biojava.bibliography.BibRefSupport
  It merges all given collections together.
union(AnnotationType, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
  Create an AnnotationType that matches all Anntotations that are accepted by two others.
union(PropertyConstraint, PropertyConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Create a PropertyConstraint that matches all Objects that are accepted by two others.
union(CollectionConstraint, CollectionConstraint) - Static method in class org.biojava.bio.AnnotationTools
  Calculate a CollectionConstaint that will accept all items accepted by either constraint.
union(FeatureHolder, FeatureHolder) - Static method in class org.biojava.bio.seq.FeatureHolderUtils
  Operator: Union of FeatureHolder1 and FeatureHolder2
union(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
union(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
union(Location) - Method in class org.biojava.bio.symbol.CircularLocation
union(Location) - Method in interface org.biojava.bio.symbol.Location
  Return a Location containing all points in either ranges.
union(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
  Return the union of two locations.
union(Collection) - Static method in class org.biojava.bio.symbol.LocationTools
  The n-way union of a Collection of locations.
union(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
  Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().
union(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
  Return a Location containing all points in either ranges. ALWAYS RETURNS PASSED LOCATION
union(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
  Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand.
UNIPROT_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
  The name of this format
UniProtCommentParser - Class in org.biojavax.bio.seq.io
UniProtCommentParser() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser
  Creates a new instance of UniProtCommentParser.
UniProtCommentParser.Event - Class in org.biojavax.bio.seq.io
  A class to describe events for alternative product comments.
UniProtCommentParser.Event() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Event
UniProtCommentParser.Interaction - Class in org.biojavax.bio.seq.io
  A class to describe protein-protein interactions.
UniProtCommentParser.Interaction() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
UniProtCommentParser.Isoform - Class in org.biojavax.bio.seq.io
  A class to describe isoforms for alternative product comments.
UniProtCommentParser.Isoform() - Constructor for class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
  Creates a new instance.
UniProtFormat - Class in org.biojavax.bio.seq.io
  Format reader for UniProt files.
UniProtFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat
UniProtFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some UniProt-specific terms.
UniProtFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtFormat.Terms
UniProtLocationParser - Class in org.biojavax.bio.seq.io
  Parses UniProt location strings into RichLocation objects.
UNIPROTXML_FORMAT - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
  The name of this format
UniProtXMLFormat - Class in org.biojavax.bio.seq.io
  Format reader for UniProtXML files.
UniProtXMLFormat() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat
UniProtXMLFormat.Terms - Class in org.biojavax.bio.seq.io
  Implements some UniProtXML-specific terms.
UniProtXMLFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
unitVector(Atom) - Static method in class org.biojava.bio.structure.Calc
  return the unit vector of vector a .
UNIVERSAL - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the universal genetic code.
UNKNOWN - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
  `UNKNOWN` indicates that the alignment format is unknown.
UNKNOWN - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
  `UNKNOWN` indicates that the sequence format is unknown.
UNKNOWN - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
UNKNOWN - Static variable in interface org.biojava.bio.seq.StrandedFeature
  Flag to indicate that a feature has an unknown strand.
UNKNOWN - Static variable in class org.biojava.utils.ChangeType
  Constant ChangeType field which indicates that a change has occured which can't otherwise be represented.
UNKNOWN_STRAND - Static variable in class org.biojavax.bio.seq.RichLocation.Strand
  The unknown strand is represented by the symbol '?' and has the number 0.
UnknownDBHelper - Class in org.biojava.bio.seq.db.biosql
  Deprecated. Use hibernate and org.biojavax.bio.db.*
UnknownDBHelper() - Constructor for class org.biojava.bio.seq.db.biosql.UnknownDBHelper
  Deprecated.
unlockModel() - Method in class org.biojava.bio.dp.DP
unmask(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
  Un-masks the token by making it upper case.
unmask(String) - Method in interface org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
  Present the token for a `Symbol` as it would appear if it wasn't softmasked
unpack(byte) - Method in class org.biojava.bio.symbol.DNAAmbPack
unpack(byte) - Method in class org.biojava.bio.symbol.DNANoAmbPack
unpack(byte) - Method in interface org.biojava.bio.symbol.Packing
  Return the symbol for a packing.
unregisterFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
  Register a UnigeneFactory.
UnsupportedChromatogramFormatException - Exception in org.biojava.bio.chromatogram
  Exception indicating that some provided data does not represent a supported chromatogram format.
UnsupportedChromatogramFormatException() - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
  Create a new UnsupportedChromatogramFormatException.
UnsupportedChromatogramFormatException(String) - Constructor for exception org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
  Create a new UnsupportedChromatogramFormatException with a message.
UntrainableDistribution - Class in org.biojava.bio.dist
  A distribution which does not interact with the training framework.
UntrainableDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UntrainableDistribution
  Construct a new untrainable distribution over the specified alphabet.
untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
  returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet.
untranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ManyToOneTranslationTable
  Translate a single symbol from target alphabet to the source alphabet.
untranslate(Symbol) - Method in interface org.biojava.bio.symbol.ReversibleTranslationTable
  Translate a single symbol from target alphabet to the source alphabet.
update() - Method in class org.biojava.bio.dp.DP
update() - Method in class org.biojava.bio.dp.onehead.SingleDP
update() - Method in class org.biojava.bio.dp.twohead.PairwiseDP
update(int) - Method in class org.biojavax.utils.CRC64Checksum
update(byte[], int, int) - Method in class org.biojavax.utils.CRC64Checksum
UPDATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
UPDATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
uri - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
URI - Static variable in interface org.biojavax.Namespace
URI_PREFIX - Static variable in class org.biojava.bio.seq.FeatureTypes
  The standard prefix for all type URIs
url - Variable in class org.biojava.bibliography.BiblioWebResource
  The URL of the resource.
urlBatchSequences - Static variable in class org.biojava.bio.seq.db.GenbankSequenceDB
urlBatchSequences - Static variable in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
URLFactory - Interface in org.biojava.utils.net
  `URLFactory` defines a means of obtaining a URL associated with an object.
URLGeneratorFactory - Interface in org.biojava.bio.program.blast2html
  Interface for a factory method to return a list of 0, 1 or more `DatabaseURLGenerator` instances.
usCutPositions - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
USE_CUSTOM_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to use custom strokes when drawing traces and separators.
USE_PER_SHAPE_TRANSFORM - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether to apply scaling and translation transforms to each shape individually or to apply a single transform to the graphics context.
UserDefinedTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout
  An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges
UserDefinedTrackLayout(RangeLocation[]) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
useSuppliedSymListFactory() - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
  Call this to convert from default SymbolList implementation to user-supplied implementation.
UtilHelper - Class in org.biojava.bio.seq.io.agave
  Just make the property follow the common case
UtilHelper() - Constructor for class org.biojava.bio.seq.io.agave.UtilHelper

## V

v() - Static method in class org.biojava.bio.seq.NucleotideTools
v() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Valine
val() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Valine (V)
validate(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
validate(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
  Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
validate(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
validate(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
validateAddValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
validateAddValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint
  Return `true` iff the Collection formed by adding `newValue` to `current` would be accepted by this constraint.
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.And
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
validateRemoveValue(Collection, Object) - Method in class org.biojava.bio.CollectionConstraint.Or
validateRemoveValue(Collection, Object) - Method in interface org.biojava.bio.CollectionConstraint
  Return `true` iff the Collection formed by removing `newValue` from `current` would be accepted by this constraint.
validLen - Variable in class org.biojava.utils.io.CachingInputStream
  A count of the number of bytes in `CachingInputStream.cache` that contain data read from the stream.
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Echo
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
value(TagValueContext, Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
  A value has been seen.
value(TagValueContext, Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
value - Variable in class org.biojava.bio.structure.align.helper.GapArray
VALUE - Static variable in interface org.biojavax.Note
VALUE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
ValueChanger - Class in org.biojava.bio.program.tagvalue
  Intercept the values associated with some tags and change them systematically.
ValueChanger(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger
ValueChanger(TagValueListener, ChangeTable) - Constructor for class org.biojava.bio.program.tagvalue.ValueChanger
  Create a new changer that will pass the modified event stream to a delegate.
valueOf(String) - Static method in class org.biojava.bio.EcNumber.Impl
  Process a string into an EcNumber.
valueOf(String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier parsed from the properly formatted string `lsid`.
valueOf(String, String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier from the specified parameters.
valueOf(String, String, String) - Static method in class org.biojava.utils.lsid.LifeScienceIdentifier
  Create a new LifeScienceIdentifier from the specified parameters.
VALUES - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
Variable - Interface in org.biojava.ontology
Variable.Impl - Class in org.biojava.ontology
Variable.Impl(Ontology, String, String) - Constructor for class org.biojava.ontology.Variable.Impl
Variable.Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.ontology.Variable.Impl
vectorProduct(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
  Vector product .
vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
VERSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
VERT_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the vertebrate mitochondrial genetic code.
view(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
  Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
view(Sequence, String) - Static method in class org.biojava.bio.seq.SequenceTools
  Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
view(Sequence, FeatureRealizer) - Static method in class org.biojava.bio.seq.SequenceTools
  Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.
viewEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
ViewingSequenceDB - Class in org.biojava.bio.seq.db
  SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
ViewingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.ViewingSequenceDB
  Create a new ViewingSequenceDB that views the sequences in parent.
ViewSequence - Class in org.biojava.bio.seq.impl
  A view onto another Sequence object.
ViewSequence(Sequence, String) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
  Construct a view onto an existing sequence and give it a new name.
ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
  Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.ViewSequence
  Construct a view onto a sequence, using a specific FeatureRealizer.
ViewSequenceFactory - Class in org.biojava.bio.program.ssbind
  `ViewSequenceFactory` is a base class for creating search handlers which create and cache views on the query and subject sequences.
ViewSequenceFactory() - Constructor for class org.biojava.bio.program.ssbind.ViewSequenceFactory
viewStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
viewToSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
  Coordinate conversion from view to source.
viewToSource(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
  Coordinate conversion from view to source.
viewToSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
visitFilter(FeatureFilter, Visitor) - Static method in class org.biojava.bio.seq.FilterUtils
  Applies a visitor to a filter, and returns the visitor's result or null.
Visitor - Interface in org.biojava.utils.walker
  Things that will be shown filters.
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.DP
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
viterbi(ScoreType, BackPointer) - Method in interface org.biojava.bio.dp.twohead.CellCalculatorFactory
viterbi(ScoreType, BackPointer) - Method in class org.biojava.bio.dp.twohead.DPInterpreter
viterbi(SymbolList[], ScoreType) - Method in class org.biojava.bio.dp.twohead.PairwiseDP
volume - Variable in class org.biojava.bibliography.BiblioBook
  Book volume.
volume - Variable in class org.biojava.bibliography.BiblioJournalArticle
  The journal volume.
vp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
vp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat

## W

w() - Static method in class org.biojava.bio.seq.NucleotideTools
w() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Tryptophan
waitForThreads() - Method in class org.biojava.utils.SimpleThreadPool
waitForThreads() - Method in interface org.biojava.utils.ThreadPool
  `waitForThreads` temporarily closes the pool to new requests until such time as the current request queue has been emptied and all running tasks completed.
walk(Object, Visitor) - Method in interface org.biojava.utils.walker.Walker
  This walks the feature tree, showing the visitor each filter in the expression.
Walker - Interface in org.biojava.utils.walker
  Objects that can walk over a filter expression, showing each element to a visitor.
WalkerFactory - Class in org.biojava.utils.walker
walkTo(UkkonenSuffixTree.SuffixNode, String, int, int) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
  This method is used to walk down the tree, from a given node.
wasEmpty() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
  Returns true if no HitSummary and no Hit elements were encountered
WeakCacheMap - Class in org.biojava.utils.cache
  A cache which retains weak references to objects
WeakCacheMap() - Constructor for class org.biojava.utils.cache.WeakCacheMap
WeakTaxon - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
WeakTaxon() - Constructor for class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
WeakTaxon(String, String) - Constructor for class org.biojava.bio.taxa.WeakTaxon
  Deprecated.
WeakTaxonFactory - Class in org.biojava.bio.taxa
  Deprecated. replaced by classes in `org.biojavax.bio.taxa`
WeakTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.WeakTaxonFactory
  Deprecated.
WeakValueHashMap - Class in org.biojava.utils.cache
  Map implementation which keeps weak references to values.
WeakValueHashMap() - Constructor for class org.biojava.utils.cache.WeakValueHashMap
WebSequenceDB - Class in org.biojava.bio.seq.db
  Functions for access to a web based database that returns sequences in a variety of formats.
WebSequenceDB() - Constructor for class org.biojava.bio.seq.db.WebSequenceDB
WeightedSet - Class in org.biojavax.ga.util
  Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight.
WeightedSet() - Constructor for class org.biojavax.ga.util.WeightedSet
weightForwarder - Variable in class org.biojava.bio.dist.AbstractOrderNDistribution
  The listener that will forward events from the underlying distributions to listeners for this distribution.
WeightMatrix - Interface in org.biojava.bio.dp
  A log odds weight matrix.
WeightMatrixAnnotator - Class in org.biojava.bio.dp
  Annotates a sequence with hits to a weight-matrix.
WeightMatrixAnnotator(WeightMatrix, ScoreType, double, String) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
  Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix.
WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
  Create a new annotator that uses PROBABILITY score type.
WeightMatrixAnnotator(WeightMatrix, ScoreType, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
  Create a new annotator that uses a specific score type.
WEIGHTS - Static variable in interface org.biojava.bio.dist.Distribution
  Whenever a distribution changes the values that would be returned by getWeight, they should fire a ChangeEvent with this object as the type.
WIDTH_IS_AUTHORITATIVE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
  Option indicating whether width or horizontal scale is the authoritative measure.
windowedSymbolList(SymbolList, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
  A view of windows onto another SymbolList.
WMAsMM - Class in org.biojava.bio.dp
  Wraps a weight matrix up so that it appears to be a very simple HMM.
WMAsMM(WeightMatrix) - Constructor for class org.biojava.bio.dp.WMAsMM
WobbleDistribution - Interface in org.biojava.bio.symbol
  an object to return statistics about the frequency of the wobble base in a set of synonymous codons.
wordSize() - Method in class org.biojava.bio.symbol.DNAAmbPack
wordSize() - Method in class org.biojava.bio.symbol.DNANoAmbPack
wordSize() - Method in interface org.biojava.bio.symbol.Packing
  The number of bits required to pack a symbol.
WordTokenization - Class in org.biojava.bio.seq.io
  Base class for tokenizations which accept whitespace-separated `words'.
WordTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.WordTokenization
wordWrap(String, String, int) - Static method in class org.biojavax.utils.StringTools
  Word-wraps a string into an array of lines of no more than the given width.
WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
  Caenorhabditis elegans codon preferences
write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Writing Sequence.
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
  Writes out the alignment to an FASTA file.
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
writeAnnotations(FeatureHolder) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeAnnotationType(AnnotationType, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Write an `AnnotationType` to the specified XMLWriter.
writeAssembly(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeBioSequence(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeClassification(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeCollectionConstraint(CollectionConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
writeCompResult(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeContig(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
writeDetails(XMLWriter, Feature) - Method in class org.biojava.bio.program.xff.PropertyWriter
writeDetails(XMLWriter, Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
writeDistribution(Distribution, OutputStream) - Method in class org.biojava.bio.dist.XMLDistributionWriter
  Writes an OrderNDistribution or simple Distribution to an XML file.
writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
writeDna(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
writeEmbl(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a stream of Sequences to an OutputStream in EMBL format.
writeEmbl(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a single Sequence to an OutputStream in EMBL format.
writeEMBL(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in EMBL Format.
writeEMBL(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in EMBL format.
writeEMBLxml(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in EMBLxml Format.
writeEMBLxml(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in EMBLxml format.
writeEmptyElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
writeEmptyElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
writeFasta(OutputStream, SequenceDB) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Write a sequenceDB to an output stream in fasta format.
writeFasta(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes sequences from a SequenceIterator to an OutputStream in Fasta Format.
writeFasta(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a single Sequence to an OutputStream in Fasta format.
writeFasta(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes `Sequence`s from a `SequenceIterator` to an `OutputStream` in Fasta Format.
writeFasta(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in Fasta format.
writeFeatureSet(FeatureHolder, XMLWriter) - Method in class org.biojava.bio.program.xff.XFFWriter
writeFilter(FeatureFilter, XMLWriter, XMLFilterWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterWriter.FilterWriter
writeFilter(FeatureFilter, XMLWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Write a FeatureFilter to the supplied XMLWriter
writeFooter() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write </sciobj>
writeGenbank(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a stream of Sequences to an OutputStream in Genbank format.
writeGenbank(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a single Sequence to an OutputStream in Genbank format.
writeGenbank(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in GenBank Format.
writeGenbank(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in GenBank format.
writeGene(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeGenpept(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a stream of Sequences to an OutputStream in Genpept format.
writeGenpept(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a single Sequence to an OutputStream in Genpept format.
writeGFF(String, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
  Writes a GFFEntrySet to a file.
writeGFF(File, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
  Writes a GFFEntrySet to a file.
writeGFF(PrintWriter, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
  Writes a GFFEntrySet to a PrintWriter.
writeHeader() - Method in class org.biojava.bio.program.xml.BaseXMLWriter
writeHeader() - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write <sciobj>
writeIndent() - Method in class org.biojava.utils.xml.PrettyXMLWriter
writeINSDseq(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in INSDseq Format.
writeINSDseq(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in INSDseq format.
writeKeyValueLine(String, String, int, int, PrintStream) - Static method in class org.biojavax.utils.StringTools
  Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of whitespace.
writeKeyValueLine(String, String, int, int, String, PrintStream) - Static method in class org.biojavax.utils.StringTools
  Writes some text to the output stream in the following format: key text continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep.
writeKeyValueLine(String, String, int, int, String, String, PrintStream) - Static method in class org.biojavax.utils.StringTools
  Writes some text to the output stream in the following format: key text wrappedKey continuation of text where the key/wrappedKey column is keyWidth wide, and the total line width is lineWidth, and the text is split over multiple lines at the nearest occurrence of separator sep.
writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.GenbankLocationParser
  Writes a location in Genbank format.
writeLocation(RichLocation) - Static method in class org.biojavax.bio.seq.io.UniProtLocationParser
  Writes a location in UniProt format.
writeMatrix(WeightMatrix, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
writeModel(MarkovModel, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
writeModelFile(SVMClassifierModel, String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
writePCData(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
writePhredQuality(OutputStream, OutputStream, SequenceDB) - Static method in class org.biojava.bio.program.phred.PhredTools
  Writes Phred quality data in a Fasta type format.
writePropertyConstraint(PropertyConstraint, XMLWriter, XMLAnnotationTypeWriter) - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
writeProtein(OutputStream, Alignment) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
writeRecord(RAF, long, int, String, Map) - Method in class org.biojava.bio.program.indexdb.BioStore
writeRecord(RAF, long, int, String, Map) - Method in interface org.biojava.bio.program.indexdb.IndexStore
  `writeRecord` creates and writes a new `Record`
WriterOutputHandler - Class in org.biojava.utils.process
  Simple output handler that writes the output of an external process to an writer.
WriterOutputHandler(Writer, String) - Constructor for class org.biojava.utils.process.WriterOutputHandler
  Initializes the writer output handler.
writeSeqFeature(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write SeqFeature XML
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat
  This method will print symbols to the line width followed by a new line etc.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.program.phred.PhredFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write sequence into AGAVE XML format.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. Writes a `Sequence` or `RichSequence` to a `PrintStream` in FASTA format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GAMEFormat
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
  Deprecated. use writeSequence(Sequence seq, PrintStream os)
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as EMBL has no concept of it.
writeSequence(Sequence, String, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
  As per `EMBLFormat.writeSequence(Sequence, Namespace)`, except that it also takes a format parameter.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as EMBLxml has no concept of it.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is null, then the sequence's own namespace is used.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as Genbank has no concept of it.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as INSDseq has no concept of it.
writeSequence(Sequence, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as UniProt has no concept of it.
writeSequence(Sequence, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  `writeSequence` writes a sequence to the specified PrintStream, using the default format.
writeSequence(Sequence, String, PrintStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.
writeSequence(Sequence, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
  Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is null, then the sequence's own namespace is used.
writeSequenceMap(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  group sequence_map by getSource()
writeSequenceMap2(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
  Write SequenceMap XML
writeStream(SequenceIterator) - Method in class org.biojava.bio.seq.io.StreamWriter
  Write each of the sequences in ss to the stream in the given format.
writeStream(SequenceIterator, Namespace) - Method in class org.biojavax.bio.seq.io.RichStreamWriter
  Write each of the sequences in ss to the stream in the given format.
writeSwissprot(OutputStream, SequenceIterator) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a stream of Sequences to an OutputStream in SwissProt format.
writeSwissprot(OutputStream, Sequence) - Static method in class org.biojava.bio.seq.io.SeqIOTools
  Deprecated. Writes a single Sequence to an OutputStream in SwissProt format.
writeToXML(Distribution, OutputStream) - Static method in class org.biojava.bio.dist.DistributionTools
  Writes a Distribution to XML that can be read with the readFromXML method.
writeToXML(CodonPref, PrintWriter) - Static method in class org.biojava.bio.symbol.CodonPrefTools
  write out a specified CodonPref object in XML format.
writeTranscript(Annotatable) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
writeUniProt(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in UniProt Format.
writeUniProt(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in UniProt format.
writeUniProtXML(OutputStream, SequenceIterator, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes sequences from a `SequenceIterator` to an `OutputStream` in UniProt XML Format.
writeUniProtXML(OutputStream, Sequence, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
  Writes a single `Sequence` to an `OutputStream` in UniProt XML format.
writeXFF(File, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
writeXFF(PrintWriter, FeatureHolder) - Static method in class org.biojava.bio.program.xff.XFFTools
writeXML(XMLWriter) - Method in interface org.biojava.utils.xml.XMLWritable

## X

X_LAEVIS - Static variable in interface org.biojava.bio.program.homologene.Taxon
XFF_BIOJAVA_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
XFF_NS - Static variable in class org.biojava.bio.program.xff.XFFTools
XFFFeatureSetHandler - Class in org.biojava.bio.program.xff
  StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events.
XFFFeatureSetHandler() - Constructor for class org.biojava.bio.program.xff.XFFFeatureSetHandler
  Construct a new XFFFeatureSetHandler with the default set of handlers.
XFFHelper - Interface in org.biojava.bio.program.xff
XFFPartHandlerFactory - Interface in org.biojava.bio.program.xff
  Factory for StAX content handlers.
XFFTools - Class in org.biojava.bio.program.xff
  Common functionality for manipulating XFF.
XFFTools() - Constructor for class org.biojava.bio.program.xff.XFFTools
XFFWriter - Class in org.biojava.bio.program.xff
  Simple XFF writing code, ripped off from Dazzle 0.08.
XFFWriter() - Constructor for class org.biojava.bio.program.xff.XFFWriter
XFFWriter(XFFHelper) - Constructor for class org.biojava.bio.program.xff.XFFWriter
xHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `xHair` is the vertical line positioned along the X-axis.
XML_ANNOTATIONTYPE_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  XML namespace string used to the AnnotationType representation
XML_FILTER_NS - Static variable in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
XMLAnnotationTypeHandler - Class in org.biojava.bio.seq.io.filterxml
  StAX handler for parsing AnnotationTypes in FilterXML documents.
XMLAnnotationTypeHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
  Construct a new XMLAnnotationTypeHandler which can parse the builtin PropertyConstraints.
XMLAnnotationTypeHandler.CollectionConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml
  Handler for an individual `CollectionConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
  Handler Factory for a `CollectionConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandler - Interface in org.biojava.bio.seq.io.filterxml
  Handler for an individual `PropertyConstraint` in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
  Handler Factory for a `PropertyConstraint` in an AnnotationType.
XMLAnnotationTypeWriter - Class in org.biojava.bio.seq.io.filterxml
  Main class for writing AnnotationTypes as XML.
XMLAnnotationTypeWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
  Construct a new AnnotationTypeWriter which knows about the builtin types of PropertyConstraint
XMLAnnotationTypeWriter.XMLCollectionConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml
  Writer for types of CollectionConstraint.
XMLAnnotationTypeWriter.XMLPropertyConstraintWriter - Interface in org.biojava.bio.seq.io.filterxml
  Writer for types of PropertyConstraint.
XMLBeans - Class in org.biojava.utils.xml
  Construct java beans from XML elements
XMLBeans() - Constructor for class org.biojava.utils.xml.XMLBeans
XMLDistributionReader - Class in org.biojava.bio.dist
  A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object.
XMLDistributionReader() - Constructor for class org.biojava.bio.dist.XMLDistributionReader
XMLDistributionWriter - Class in org.biojava.bio.dist
  Writes an OrderNDistribution or simple Distribution to an XML file.
XMLDistributionWriter() - Constructor for class org.biojava.bio.dist.XMLDistributionWriter
XMLFilterHandler - Class in org.biojava.bio.seq.io.filterxml
  Factory producing content handlers for parsing FilterXML elements.
XMLFilterHandler() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
  Construct a new XMLFilterHandler which can parse the builtin types of `FeatureFilter`.
XMLFilterHandler.FilterHandler - Interface in org.biojava.bio.seq.io.filterxml
  StAXContentHandler for a particular type of FeatureFilter.
XMLFilterHandler.FilterHandlerFactory - Interface in org.biojava.bio.seq.io.filterxml
  Factory of StAXContentHandlers for a particular type of FeatureFilter.
XMLFilterWriter - Class in org.biojava.bio.seq.io.filterxml
  Write FeatureFilters in XML format.
XMLFilterWriter() - Constructor for class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
  Construct a new `XMLFilterWriter` which can serialize the buildin types of `FeatureFilter`.
XMLFilterWriter.FilterWriter - Interface in org.biojava.bio.seq.io.filterxml
  Interface for an object which can write a FeatureFilter as XML.
XmlMarkovModel - Class in org.biojava.bio.dp
XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel
xmlSchema - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
xmlSchema - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
xmlSchema - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
XMLTools - Class in org.biojavax.utils
  Utility class for reading chunks of XML files and feeding them to SAX.
XMLWritable - Interface in org.biojava.utils.xml
  Object which knows how to represent itself as an XML element.
XMLWriter - Interface in org.biojava.utils.xml
  Simple interface for building XML documents.
XREF_DBNAME_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
XREF_ID_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
XREF_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
XREF_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat

## Y

y() - Static method in class org.biojava.bio.seq.NucleotideTools
y() - Static method in class org.biojava.bio.seq.ProteinTools
  Returns the `AtomicSymbol` for the amino acid Tyrosine
YEAST_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
  Translation table name for the yeast mitochondrial genetic code.
yHair - Variable in class org.biojava.bio.gui.sequence.CrosshairRenderer
  `yHair` is the horizontal line positioned along the Y-axis.

## Z

Z_MAYS - Static variable in interface org.biojava.bio.program.homologene.Taxon
ZERO - Static variable in class org.biojava.bio.CardinalityConstraint
  The property should have zero values.
zero() - Static method in class org.biojavax.ga.util.GATools
ZERO_OR_ONE - Static variable in class org.biojava.bio.CardinalityConstraint
  The property should have zero or one values.
zeroCol - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
zeroCol - Variable in class org.biojava.bio.dp.twohead.LightPairDPCursor
  Description of the Field
zeroCounts() - Method in interface org.biojava.bio.dist.Count
  Reset all the counts to zero.
zeroCounts() - Method in class org.biojava.bio.dist.IndexedCount
ZiggyFeatureRenderer - Class in org.biojava.bio.gui.sequence
  A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.
ZiggyFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
ZiggyImapRenderer - Class in org.biojava.bio.gui.sequence
  `ZiggyImapRenderer` is a decorator for `ZiggyFeatureRenderer` which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the `ZiggyFeatureRenderer`.
ZiggyImapRenderer(ZiggyFeatureRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.ZiggyImapRenderer
  Creates a new `ZiggyImapRenderer`.

## _

_0 - Static variable in class org.biojava.bio.program.abi.ABITools
  The poorly supported symbol.
_1 - Static variable in class org.biojava.bio.program.abi.ABITools
  The well supported symbol.
_addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
_addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
_addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
_removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
_removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
_setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
  Deprecated.

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