Uses of Interface org.biojava.bio.symbol.SymbolList (BioJava-1.5-beta API)

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## Uses of Interface
org.biojava.bio.symbol.SymbolList

Packages that use SymbolList
org.biojava.bio.alignment | Classes to generate and describe sequence alignments.
org.biojava.bio.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist | Probability distributions over Alphabets.
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead |
org.biojava.bio.dp.twohead |
org.biojava.bio.gui.sequence | Graphical displays of biological sequences and associated annotations.
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.abi | ABI Trace Handling.
org.biojava.bio.program.das | Development client for the Distributed Annotation System.
org.biojava.bio.program.phred | Parser for Phred output
org.biojava.bio.program.scf | Support for the SCF chromatogram format.
org.biojava.bio.program.ssaha | SSAHA sequence searching API.
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl | Standard in-memory implementations of `Sequence` and `Feature`.
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection | Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.automata |
org.biojava.utils.regex | This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojavax | The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.db.biosql |
org.biojavax.bio.seq | Rich implementations of Sequences, Locations and Features.
org.biojavax.ga | Classes to provide a genetic algorithm framework
org.biojavax.ga.functions | GA functions
org.biojavax.ga.impl | Default implementations and abstract classes.
org.biojavax.ga.util | Utility functions and helper classes

Uses of SymbolList in org.biojava.bio.alignment

Subinterfaces of SymbolList in org.biojava.bio.alignment
`interface` | `ARAlignment` ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
`interface` | `UnequalLengthAlignment` UnequalLengthAlignment has the following behavior.

Classes in org.biojava.bio.alignment that implement SymbolList
`class` | `AbstractULAlignment`
`class` | `AbstractULAlignment.SubULAlignment`
`class` | `FlexibleAlignment` 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.

Fields in org.biojava.bio.alignment declared as SymbolList
`protected SymbolList` | `SimpleAlignmentElement.seq`

Methods in org.biojava.bio.alignment that return SymbolList
`SymbolList` | `SimpleAlignmentElement.getSymbolList()`
`SymbolList` | `AlignmentElement.getSymbolList()`
`SymbolList` | `AbstractULAlignment.SubULAlignment.symbolListForLabel(Object label)`
`SymbolList` | `FlexibleAlignment.symbolListForLabel(Object label)`

Methods in org.biojava.bio.alignment with parameters of type SymbolList
`protected boolean` | `FlexibleAlignment.allGaps(SymbolList seq, int start, int end)` make sure that all Symbols in this range are gaps

Constructors in org.biojava.bio.alignment with parameters of type SymbolList
`SimpleAlignmentElement(Object label, SymbolList seq, Location loc)`

Uses of SymbolList in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that return SymbolList
`protected SymbolList` | `AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms)` A factory method for creating new symbol lists with a given alphabet.
`static SymbolList` | `ChromatogramTools.getDNASequence(Chromatogram chromat)` Get the called DNA sequence from a chromatogram.
`static SymbolList` | `ChromatogramTools.getTraceOffsets(Chromatogram chromat)` Get the peak offsets for the called bases of a chromatogram.
`protected SymbolList` | `AbstractChromatogram.reverseComplementBaseCallList(Object label)` Return a symbol list containing the reverse complement of the base call data for the given label.

Methods in org.biojava.bio.chromatogram with parameters of type SymbolList
`static int` | `ChromatogramTools.getIntFromSymbolList(SymbolList list, int which)` Retrieves, unwraps, and returns an `int` from a SymbolList containing `IntegerAlphabet.IntegerSymbol`s.
`void` | `SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets)` Set the DNA and OFFSETS symbol lists for the basecall alignment.

Uses of SymbolList in org.biojava.bio.dist

Methods in org.biojava.bio.dist that return SymbolList
`static SymbolList` | `DistributionTools.generateSymbolList(Distribution d, int length)` Produces a `SymbolList` by randomly sampling a Distribution.

Uses of SymbolList in org.biojava.bio.dp

Subinterfaces of SymbolList in org.biojava.bio.dp
`interface` | `StatePath` 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.

Classes in org.biojava.bio.dp that implement SymbolList
`class` | `SimpleStatePath` A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return SymbolList
`SymbolList` | `SimpleStatePath.subList(int start, int end)`
`SymbolList` | `SimpleStatePath.symbolListForLabel(Object label)`
`SymbolList[]` | `DPMatrix.symList()`

Methods in org.biojava.bio.dp with parameters of type SymbolList
`abstract double` | `DP.backward(SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix` | `DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract DPMatrix` | `DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)`
`abstract double` | `DP.forward(SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix` | `DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract DPMatrix` | `DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)`
`DPMatrix` | `DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)`
`static double` | `DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, int start)` Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
`static double` | `DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, ScoreType scoreType, int start)` Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.
`protected abstract double` | `AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected double` | `BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected double` | `BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected double` | `BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)`
`abstract StatePath` | `DP.viterbi(SymbolList[] symList, ScoreType scoreType)`

Constructors in org.biojava.bio.dp with parameters of type SymbolList
`DP.ReverseIterator(SymbolList sym)`
`SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)`

Uses of SymbolList in org.biojava.bio.dp.onehead

Fields in org.biojava.bio.dp.onehead declared as SymbolList
`protected SymbolList[]` | `SingleDPMatrix.symList`

Methods in org.biojava.bio.dp.onehead that return SymbolList
`SymbolList` | `DPCursor.symList()` The symbol list being looped over.
`SymbolList[]` | `SingleDPMatrix.symList()`
`SymbolList` | `SmallCursor.symList()`

Methods in org.biojava.bio.dp.onehead with parameters of type SymbolList
`double` | `SingleDP.backward(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` | `SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)`
`DPMatrix` | `SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)`
`double` | `SingleDP.forward(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` | `SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)`
`DPMatrix` | `SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)`
`StatePath` | `SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)`

Constructors in org.biojava.bio.dp.onehead with parameters of type SymbolList
`SingleDPMatrix(DP dp, SymbolList symList)`
`SmallCursor(State[] states, SymbolList symList, Iterator symIterator)`

Uses of SymbolList in org.biojava.bio.dp.twohead

Fields in org.biojava.bio.dp.twohead declared as SymbolList
`protected SymbolList[]` | `AbstractMatrixPairDPCursor.seqs`

Methods in org.biojava.bio.dp.twohead that return SymbolList
`SymbolList[]` | `PairDPMatrix.symList()`

Methods in org.biojava.bio.dp.twohead with parameters of type SymbolList
`double` | `PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` | `PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)`
`DPMatrix` | `PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)`
`double` | `PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` | `PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)`
`DPMatrix` | `PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)`
`StatePath` | `PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)`

Constructors in org.biojava.bio.dp.twohead with parameters of type SymbolList
`AbstractMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int start1, int start2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)`
`BackMatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)`
`LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache)` Constructor for the LightPairDPCursor object
`MatrixPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, PairDPMatrix matrix, EmissionCache eCache)`
`PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)`

Uses of SymbolList in org.biojava.bio.gui.sequence

Methods in org.biojava.bio.gui.sequence that return SymbolList
`SymbolList` | `PairwiseRenderContext.getSecondarySymbols()` `getSecondarySymbols` returns the symbols of the secondary sequence.
`SymbolList` | `PairwiseSequencePanel.getSecondarySymbols()` `getSecondarySymbols` returns all of the `Symbol`s belonging to the currently rendered secondary `Sequence`.
`SymbolList` | `SubPairwiseRenderContext.getSecondarySymbols()`
`SymbolList` | `CircularRendererPanel.getSequence()`
`SymbolList` | `SequencePanel.getSequence()`
`SymbolList` | `TranslatedSequencePanel.getSequence()` `getSequence` returns the entire `Sequence` currently being rendered.
`SymbolList` | `SubCircularRendererContext.getSymbols()`
`SymbolList` | `SubSequenceRenderContext.getSymbols()`
`SymbolList` | `SequencePanel.getSymbols()` Retrieve the currently rendered SymbolList
`SymbolList` | `HeadlessRenderContext.getSymbols()`
`SymbolList` | `PairwiseSequencePanel.getSymbols()` `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
`SymbolList` | `SequenceRenderContext.getSymbols()` The SymbolList that is currently rendered by this SequenceRenderContext.
`SymbolList` | `SequencePoster.getSymbols()` Deprecated. Retrieve the currently rendered SymbolList
`SymbolList` | `CircularRendererContext.getSymbols()` The SymbolList that is currently rendered by this context.
`SymbolList` | `TranslatedSequencePanel.getSymbols()` `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
`SymbolList` | `SubPairwiseRenderContext.getSymbols()`

Methods in org.biojava.bio.gui.sequence with parameters of type SymbolList
`void` | `CircularRendererPanel.setSequence(SymbolList symList)`
`void` | `SequencePanel.setSequence(SymbolList s)` Set the SymboList to be rendered.
`void` | `TranslatedSequencePanel.setSequence(SymbolList sequence)` `setSequence` sets the `Sequence` to be rendered.

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList
`SubCircularRendererContext(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius)` Create a new sub context.
`SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)` Creates a new `SubPairwiseRenderContext`.
`SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)`
`SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)`

Uses of SymbolList in org.biojava.bio.molbio

Fields in org.biojava.bio.molbio declared as SymbolList
`protected SymbolList` | `RestrictionEnzyme.site`

Methods in org.biojava.bio.molbio that return SymbolList
`SymbolList` | `RestrictionEnzyme.getRecognitionSite()` `getRecognitionSite` returns the forward strand of the recognition site.

Constructors in org.biojava.bio.molbio with parameters of type SymbolList
`RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse)` Creates a new `RestrictionEnzyme` which cuts within or downstream of the recognition site.
`RestrictionEnzyme(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse)` Creates a new `RestrictionEnzyme` of the unusual type which cuts both upstream and downstream of its recognition site.

Uses of SymbolList in org.biojava.bio.program.abi

Methods in org.biojava.bio.program.abi that return SymbolList
`SymbolList` | `ABITrace.getSequence()` Returns the original programatically determined (unedited) sequence as a `SymbolList`.

Methods in org.biojava.bio.program.abi with parameters of type SymbolList
`static Alignment` | `ABITools.getAlignment(SymbolList abiSeq)` View a symbol list over the QUALITY alphabet as an alignment.

Uses of SymbolList in org.biojava.bio.program.das

Methods in org.biojava.bio.program.das that return SymbolList
`protected SymbolList` | `DASSequence.getSymbols()`
`SymbolList` | `DASSequence.subList(int start, int end)`

Uses of SymbolList in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement SymbolList
`class` | `PhredSequence` PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Methods in org.biojava.bio.program.phred that return SymbolList
`static SymbolList` | `PhredTools.createPhred(SymbolList dna, SymbolList quality)` 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.
`SymbolList` | `PhredSequence.getDNA()` Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
`SymbolList` | `PhredSequence.getQuality()` Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
`SymbolList` | `Qualitative.getQuality()` Retreives the list of quality symbols from the underlying object.

Methods in org.biojava.bio.program.phred with parameters of type SymbolList
`static SymbolList` | `PhredTools.createPhred(SymbolList dna, SymbolList quality)` 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.

Constructors in org.biojava.bio.program.phred with parameters of type SymbolList
`PhredSequence(SymbolList phredSequence, String name, String urn, Annotation anno)` Constructs a new PhredSequence.

Uses of SymbolList in org.biojava.bio.program.scf

Methods in org.biojava.bio.program.scf that return SymbolList
`protected SymbolList` | `SCF.reverseComplementBaseCallList(Object label)` Overrides `AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object)` to support the 7 quality values from the SCF.

Uses of SymbolList in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type SymbolList
`void` | `CompactedDataStore.search(String seqID, SymbolList symList, SearchListener listener)`
`void` | `DataStore.search(String id, SymbolList symList, SearchListener listener)` Search the DataStore with a symbol list.

Uses of SymbolList in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return SymbolList
`SymbolList` | `Protease.getCleaveageResidues()` The list of residues that the protease will cleave at.
`SymbolList` | `Protease.getNotCleaveResidues()` The list of residues that will prevent cleavage if they follow the cleavage residue.

Methods in org.biojava.bio.proteomics with parameters of type SymbolList
`static Protease` | `ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)`
`static Protease` | `ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)` Creates and registers a new Protease.
`double` | `MassCalc.getMass(SymbolList proteinSeq)` Get the Mass of this peptide.
`static double` | `MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS)` `getMass` calculates the mass of this peptide.
`double` | `IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)` Computes isoelectric point of specified peptide.
`double[]` | `MassCalc.getVariableMasses(SymbolList peptide)` Get all masses including the variable mass.

Constructors in org.biojava.bio.proteomics with parameters of type SymbolList
`Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes)` Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())
`Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name)`

Uses of SymbolList in org.biojava.bio.search

Methods in org.biojava.bio.search that return SymbolList
`SymbolList` | `MaxMismatchPattern.getPattern()`
`SymbolList` | `KnuthMorrisPrattSearch.getPattern()`
`SymbolList` | `MaxMismatchMatcher.group()`
`SymbolList` | `BioMatcher.group()` Get the matching region as a SymbolList.

Methods in org.biojava.bio.search with parameters of type SymbolList
`int[]` | `KnuthMorrisPrattSearch.findMatches(SymbolList text)` 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`).
`BioMatcher` | `MaxMismatchPattern.matcher(SymbolList symList)`
`BioMatcher` | `SeqContentPattern.matcher(SymbolList symList)`
`BioMatcher` | `BioPattern.matcher(SymbolList symList)` Get a matcher that will use these parameters to search a SymbolList.
`SeqSimilaritySearchResult` | `SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters)` Using this sequence similarity searcher, search with the given sequence against the given sequence database.
`void` | `MaxMismatchPattern.setPattern(SymbolList pattern)`

Constructors in org.biojava.bio.search with parameters of type SymbolList
`KnuthMorrisPrattSearch(SymbolList pattern)` Constructs a KMP matcher to find exact occurances of `pattern` in `text` using the Knuth-Morris-Pratt algorithm.
`MaxMismatchPattern(SymbolList pattern, int mismatches)`

Uses of SymbolList in org.biojava.bio.seq

Subinterfaces of SymbolList in org.biojava.bio.seq
`interface` | `GappedSequence` Extension of GappedSymbolList which also projects features into the gapped coordinate system.
`interface` | `Sequence` A biological sequence.

Classes in org.biojava.bio.seq that implement SymbolList
`class` | `CircularView` A circular view onto another Sequence object.
`class` | `NewSimpleAssembly` A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
`class` | `SimpleAssembly` A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

Methods in org.biojava.bio.seq that return SymbolList
`static SymbolList` | `DNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` | `NucleotideTools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` | `RNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` | `DNATools.createDNA(String dna)` Return a new DNA SymbolList for dna.
`static SymbolList` | `NucleotideTools.createNucleotide(String nucleotide)` Return a new Nucleotide SymbolList for nucleotide.
`static SymbolList` | `ProteinTools.createProtein(String theProtein)` Return a new Protein SymbolList for protein.
`static SymbolList` | `RNATools.createRNA(String rna)` Return a new RNA SymbolList for rna.
`static SymbolList` | `DNATools.flip(SymbolList list, StrandedFeature.Strand strand)` Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
`SymbolList` | `StrandedFeature.getSymbols()` Return a list of symbols that are contained in this feature.
`SymbolList` | `Feature.getSymbols()` Return a list of symbols that are contained in this feature.
`static SymbolList` | `DNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `NucleotideTools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `RNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`SymbolList` | `SimpleAssembly.subList(int start, int end)`
`SymbolList` | `CircularView.subList(int start, int end)` Over rides ViewSequence.
`SymbolList` | `NewSimpleAssembly.subList(int start, int end)`
`static SymbolList` | `DNATools.toRNA(SymbolList syms)` Converts a `SymbolList` from the DNA `Alphabet` to the RNA `Alphabet`.
`static SymbolList` | `GeneticCodes.transcribe(SymbolList theList)` Transcribe DNA into RNA.
`static SymbolList` | `RNATools.transcribe(SymbolList list)` 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.
`static SymbolList` | `DNATools.transcribeToRNA(SymbolList syms)` Transcribes DNA to RNA.
`static SymbolList` | `GeneticCodes.translate(SymbolList theList)` Translate RNA into protein (with termination symbols).
`static SymbolList` | `RNATools.translate(SymbolList syms)` Translate RNA into protein (with termination symbols).

Methods in org.biojava.bio.seq with parameters of type SymbolList
`static SymbolList` | `DNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` | `NucleotideTools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` | `RNATools.complement(SymbolList list)` Retrieve a complement view of list.
`Sequence` | `SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)` Deprecated. Creates a sequence using these parameters.
`static Sequence` | `SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)`
`static SymbolList` | `DNATools.flip(SymbolList list, StrandedFeature.Strand strand)` Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
`static SymbolList` | `DNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `NucleotideTools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `RNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `DNATools.toRNA(SymbolList syms)` Converts a `SymbolList` from the DNA `Alphabet` to the RNA `Alphabet`.
`static SymbolList` | `GeneticCodes.transcribe(SymbolList theList)` Transcribe DNA into RNA.
`static SymbolList` | `RNATools.transcribe(SymbolList list)` 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.
`static SymbolList` | `DNATools.transcribeToRNA(SymbolList syms)` Transcribes DNA to RNA.
`static SymbolList` | `GeneticCodes.translate(SymbolList theList)` Translate RNA into protein (with termination symbols).
`static SymbolList` | `RNATools.translate(SymbolList syms)` Translate RNA into protein (with termination symbols).

Uses of SymbolList in org.biojava.bio.seq.homol

Classes in org.biojava.bio.seq.homol that implement SymbolList
`static class` | `SimilarityPairFeature.EmptyPairwiseAlignment` `EmptyPairwiseAlignment` empty pairwise alignment which has labels to empty symbol lists.

Methods in org.biojava.bio.seq.homol that return SymbolList
`SymbolList` | `SimilarityPairFeature.EmptyPairwiseAlignment.subList(int index1, int index2)`
`SymbolList` | `SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(Object label)`

Uses of SymbolList in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement SymbolList
`class` | `AssembledSymbolList` Support class for applications which need to patch together sections of sequence into a single SymbolList.
`class` | `DummySequence` A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
`class` | `NewAssembledSymbolList` Support class for applications which need to patch together sections of sequence into a single SymbolList.
`class` | `RevCompSequence` A reverse complement view onto `Sequence` interface.
`class` | `SimpleGappedSequence` Simple implementation of GappedSequence.
`class` | `SimpleSequence` A basic implementation of the `Sequence` interface.
`class` | `SubSequence` View a sub-section of a given sequence object, including all the features intersecting that region.
`class` | `ViewSequence` A view onto another Sequence object.

Methods in org.biojava.bio.seq.impl that return SymbolList
`SymbolList` | `SimpleFeature.getSymbols()`
`SymbolList` | `SimpleStrandedFeature.getSymbols()`
`SymbolList` | `SimpleSequence.subList(int start, int end)`
`SymbolList` | `DummySequence.subList(int start, int end)`
`SymbolList` | `ViewSequence.subList(int start, int end)`
`SymbolList` | `AssembledSymbolList.subList(int start, int end)`
`SymbolList` | `NewAssembledSymbolList.subList(int start, int end)`
`SymbolList` | `SubSequence.subList(int start, int end)`

Methods in org.biojava.bio.seq.impl with parameters of type SymbolList
`Sequence` | `SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)`
`void` | `AssembledSymbolList.putComponent(Location l, SymbolList sl)`

Constructors in org.biojava.bio.seq.impl with parameters of type SymbolList
`SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation)` Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
`SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation, FeatureRealizer realizer)` Create a SimpleSequence using a specified FeatureRealizer.

Uses of SymbolList in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return SymbolList
`SymbolList` | `ChunkedSymbolListFactory.make(SymbolReader sr)` Method to create a Sequence with a SymbolReader.
`SymbolList` | `ChunkedSymbolListFactory.makeSymbolList()` Converts accumulated Symbols to a SymbolList

Methods in org.biojava.bio.seq.io with parameters of type SymbolList
`String` | `SymbolTokenization.tokenizeSymbolList(SymbolList symList)` Return a string representation of a list of symbols.
`String` | `WordTokenization.tokenizeSymbolList(SymbolList sl)`
`String` | `CharacterTokenization.tokenizeSymbolList(SymbolList sl)`

Constructors in org.biojava.bio.seq.io with parameters of type SymbolList
`SymbolListCharSequence(SymbolList syms)` Creates a new `SymbolListCharSequence` wrapping a `SymbolList`.

Uses of SymbolList in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return SymbolList
`SymbolList` | `ProjectedFeature.getSymbols()`

Uses of SymbolList in org.biojava.bio.symbol

Subinterfaces of SymbolList in org.biojava.bio.symbol
`interface` | `Alignment` An alignment containing multiple SymbolLists.
`interface` | `GappedSymbolList` This extends SymbolList with API for manipulating, inserting and deleting gaps.

Classes in org.biojava.bio.symbol that implement SymbolList
`class` | `AbstractSymbolList` Abstract helper implementation of the SymbolList core interface.
`class` | `ChunkedSymbolList` SymbolList implementation using constant-size chunks.
`class` | `DummySymbolList` Symbol list which just consists of non-informative symbols.
`class` | `PackedSymbolList` A SymbolList that stores symbols as bit-patterns in an array of longs.
`class` | `RelabeledAlignment` An alignment that relabels another alignment.
`class` | `SimpleAlignment` A simple implementation of an Alignment.
`class` | `SimpleGappedSymbolList` This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
`class` | `SimpleSymbolList` Basic implementation of SymbolList.

Fields in org.biojava.bio.symbol declared as SymbolList
`static SymbolList` | `SymbolList.EMPTY_LIST` A useful object that represents an empty symbol list, to avoid returning null.
`SymbolList` | `Edit.replacement`

Methods in org.biojava.bio.symbol that return SymbolList
`static SymbolList` | `SymbolListViews.emptyList(Alphabet alpha)` Get a new immutable, empty symbol list with the given alphabet.
`static SymbolList` | `DoubleAlphabet.fromArray(double[] dArray)` Retrieve a SymbolList view of an array of doubles.
`static SymbolList` | `IntegerAlphabet.fromArray(int[] iArray)` Retrieve a SymbolList view of an array of integers.
`SymbolList` | `SimpleGappedSymbolList.getSourceSymbolList()`
`SymbolList` | `GappedSymbolList.getSourceSymbolList()` Return the underlying (ungapped) SymbolList.
`SymbolList` | `SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Create a factory for SimpleSymbolLists.
`SymbolList` | `SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` makes a SymbolList containing size Symbols from a Symbol array.
`SymbolList` | `PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Makes a packed SymbolList out of a list of Symbols.
`static SymbolList` | `SymbolListViews.orderNSymbolList(SymbolList source, int order)` An n-th order view of another SymbolList.
`static SymbolList` | `SymbolListViews.reverse(SymbolList symbols)` A reversed view onto a SymbolList.
`SymbolList` | `AbstractSymbolList.subList(int start, int end)`
`SymbolList` | `RelabeledAlignment.subList(int min, int max)`
`SymbolList` | `SymbolList.subList(int start, int end)` Return a new SymbolList for the symbols start to end inclusive.
`SymbolList` | `SimpleSymbolList.subList(int start, int end)` create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
`SymbolList` | `ChunkedSymbolList.subList(int start, int end)`
`static SymbolList` | `SymbolListViews.subList(SymbolList parent, int start, int end)` View a portion of a SymbolList.
`SymbolList` | `RelabeledAlignment.symbolListForLabel(Object label)`
`SymbolList` | `Alignment.symbolListForLabel(Object label)` Retrieve a single row of the alignment by label.
`SymbolList` | `SimpleAlignment.symbolListForLabel(Object label)`
`SymbolList` | `CircularLocation.symbols(SymbolList seq)`
`SymbolList` | `FuzzyPointLocation.symbols(SymbolList slist)`
`SymbolList` | `AbstractRangeLocation.symbols(SymbolList seq)`
`SymbolList` | `AbstractLocationDecorator.symbols(SymbolList seq)`
`SymbolList` | `Location.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range.
`static SymbolList` | `SymbolListViews.translate(SymbolList symbols, TranslationTable table)` Provides a 'translated' view of an underlying SymbolList.
`static SymbolList` | `SymbolListViews.windowedSymbolList(SymbolList source, int wsize)` A view of windows onto another SymbolList.

Methods in org.biojava.bio.symbol with parameters of type SymbolList
`void` | `UkkonenSuffixTree.addSymbolList(SymbolList list, String name, boolean doNotTerminate)`
`void` | `SuffixTree.addSymbols(SymbolList sList, int window)` Add a count for all motifs with length of up to `window` to this tree.
`static Alignment` | `SymbolListViews.alignment(List labels, SymbolList symList)` View a SymbolList over a cross-product Alphabet as an Alignment.
`static String` | `MotifTools.createRegex(SymbolList motif)` `createRegex` creates a regular expression which matches the `SymbolList`.
`static int` | `PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)`
`static SymbolList` | `SymbolListViews.orderNSymbolList(SymbolList source, int order)` An n-th order view of another SymbolList.
`static int` | `PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)`
`static SymbolList` | `SymbolListViews.reverse(SymbolList symbols)` A reversed view onto a SymbolList.
`static SymbolList` | `SymbolListViews.subList(SymbolList parent, int start, int end)` View a portion of a SymbolList.
`SymbolList` | `CircularLocation.symbols(SymbolList seq)`
`SymbolList` | `FuzzyPointLocation.symbols(SymbolList slist)`
`SymbolList` | `AbstractRangeLocation.symbols(SymbolList seq)`
`SymbolList` | `AbstractLocationDecorator.symbols(SymbolList seq)`
`SymbolList` | `Location.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range.
`String` | `SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)`
`static SymbolList` | `SymbolListViews.translate(SymbolList symbols, TranslationTable table)` Provides a 'translated' view of an underlying SymbolList.
`static SymbolList` | `SymbolListViews.windowedSymbolList(SymbolList source, int wsize)` A view of windows onto another SymbolList.

Constructors in org.biojava.bio.symbol with parameters of type SymbolList
`ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)`
`Edit(int pos, int length, SymbolList replacement)` Create a new Edit.
`PackedSymbolList(Packing packing, SymbolList symList)` Create a new PackedSymbolList as a packed copy of another symbol list.
`SimpleGappedSymbolList(SymbolList source)` Create a new SimpleGappedSymbolList that will view source.
`SimpleSymbolList(SymbolList sl)` Construct a copy of an existing SymbolList.

Uses of SymbolList in org.biojava.utils.automata

Methods in org.biojava.utils.automata with parameters of type SymbolList
`void` | `PatternBlitz.search(SymbolList sl)`

Uses of SymbolList in org.biojava.utils.regex

Methods in org.biojava.utils.regex that return SymbolList
`SymbolList` | `Matcher.group()` Returns the input subsequence matched by the previous match.
`SymbolList` | `Matcher.group(int group)` Returns the input subsequence captured by the given group during the previous match operation.

Methods in org.biojava.utils.regex with parameters of type SymbolList
`Matcher` | `Pattern.matcher(SymbolList sl)` Creates a matcher that will match the given input against this pattern.
`boolean` | `Search.Listener.reportMatch(SymbolList seq, Pattern pattern, int start, int end)`
`Matcher` | `Matcher.reset(SymbolList sl)` Resets this matcher with a new input SymbolList.
`void` | `Search.search(SymbolList seq)` search the Sequence with the patterns already registered with this object.
`void` | `Search.search(SymbolList seq, int loLimit, int hiLimit)` search part of the SymbolList with the patterns already registered with this object.

Uses of SymbolList in org.biojavax

Methods in org.biojavax that return SymbolList
`SymbolList` | `CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list.
`SymbolList` | `DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList.

Uses of SymbolList in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return SymbolList
`SymbolList` | `BioSQLCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a)` Given a cross reference, return the corresponding symbol list.
`SymbolList` | `BioSQLRichSequenceHandler.subList(RichSequence seq, int start, int end)` 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.

Uses of SymbolList in org.biojavax.bio.seq

Subinterfaces of SymbolList in org.biojavax.bio.seq
`interface` | `RichSequence` A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement SymbolList
`class` | `InfinitelyAmbiguousSymbolList` A symbol list that is `Integer.MAX_VALUE`long, never gives index out of bounds and always returns ambiguity symbols for everything.
`class` | `SimpleRichSequence` A simple implementation of RichSequence.
`class` | `ThinRichSequence` A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return SymbolList
`SymbolList` | `SimpleRichSequence.getInternalSymbolList()` 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.
`SymbolList` | `ThinRichSequence.getInternalSymbolList()` A special function that returns the SymbolList that this RichSequence is based around.
`SymbolList` | `RichSequence.getInternalSymbolList()` A special function that returns the SymbolList that this RichSequence is based around.
`SymbolList` | `SimpleRichFeature.getSymbols()` Return a list of symbols that are contained in this feature.
`SymbolList` | `ThinRichSequence.subList(int start, int end)` Return a new SymbolList for the symbols start to end inclusive.
`SymbolList` | `InfinitelyAmbiguousSymbolList.subList(int start, int end)` Return a new SymbolList for the symbols start to end inclusive. ALWAYS RETURNS SELF
`SymbolList` | `RichSequenceHandler.subList(RichSequence seq, int start, int end)` Return a new SymbolList for the symbols start to end inclusive.
`SymbolList` | `DummyRichSequenceHandler.subList(RichSequence seq, int start, int end)` Return a new SymbolList for the symbols start to end inclusive.
`SymbolList` | `SimpleRichLocation.symbols(SymbolList seq)` 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.
`SymbolList` | `EmptyRichLocation.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
`SymbolList` | `CompoundRichLocation.symbols(SymbolList seq)` 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.

Methods in org.biojavax.bio.seq with parameters of type SymbolList
`static RichSequence` | `RichSequence.Tools.createRichSequence(Namespace ns, String name, SymbolList syms)` Create a new RichSequence in the specified namespace.
`static RichSequence` | `RichSequence.Tools.createRichSequence(String name, SymbolList syms)` Create a new RichSequence in the default namespace.
`SymbolList` | `SimpleRichLocation.symbols(SymbolList seq)` 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.
`SymbolList` | `EmptyRichLocation.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range. ALWAYS RETURNS THE EMPTY SYMBOL LIST
`SymbolList` | `CompoundRichLocation.symbols(SymbolList seq)` 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.

Constructors in org.biojavax.bio.seq with parameters of type SymbolList
`SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion)` Creates a new instance of SimpleRichSequence.

Uses of SymbolList in org.biojavax.ga

Methods in org.biojavax.ga that return SymbolList
`SymbolList[]` | `Organism.getChromosomes()` Gets the organisms 'chromosome' sequences

Methods in org.biojavax.ga with parameters of type SymbolList
`void` | `Organism.setChromosomes(SymbolList[] chromosomes)` Sets the organisms 'chromosome' sequences.

Uses of SymbolList in org.biojavax.ga.functions

Methods in org.biojavax.ga.functions that return SymbolList
`SymbolList[]` | `GACrossResult.getChromosomes()` Gets the chromosomes after the cross
`SymbolList[]` | `GACross.getChromosomes()` Gets the chromosomes after the cross
`SymbolList[]` | `SimpleGACrossResult.getChromosomes()`
`SymbolList` | `MutationFunction.mutate(SymbolList seq)` Produces a new SymbolList by mutation.
`SymbolList` | `MutationFunction.NoMutation.mutate(SymbolList syml)`
`SymbolList` | `SimpleMutationFunction.mutate(SymbolList seq)`

Methods in org.biojavax.ga.functions with parameters of type SymbolList
`SymbolList` | `MutationFunction.mutate(SymbolList seq)` Produces a new SymbolList by mutation.
`SymbolList` | `MutationFunction.NoMutation.mutate(SymbolList syml)`
`SymbolList` | `SimpleMutationFunction.mutate(SymbolList seq)`
`GACrossResult` | `SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)`
`GACrossResult` | `CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)` Performs a cross between the pair of chromosomes
`GACrossResult` | `CrossOverFunction.NoCross.performCrossOver(SymbolList chromA, SymbolList chromB)`

Constructors in org.biojavax.ga.functions with parameters of type SymbolList
`SimpleGACrossResult(PointLocation[] crossOverPositions, SymbolList[] chromosomes)`

Uses of SymbolList in org.biojavax.ga.impl

Methods in org.biojavax.ga.impl that return SymbolList
`SymbolList[]` | `AbstractOrganism.getChromosomes()`

Methods in org.biojavax.ga.impl with parameters of type SymbolList
`protected abstract void` | `AbstractOrganism.setChromImpl(SymbolList[] chromosomes)`
`protected void` | `SimpleOrganism.setChromImpl(SymbolList[] chromosomes)`
`void` | `AbstractOrganism.setChromosomes(SymbolList[] chromosomes)`

Uses of SymbolList in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return SymbolList
`static SymbolList` | `GATools.createBinary(String binarySequence)` Creates a `SymbolList` in the GABinary `Alphabet`

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