Serialized Form (BioJava-1.5-beta API)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

# Serialized Form

Package org.biojava.bibliography

Class org.biojava.bibliography.BibRefException extends Exception implements Serializable

Package org.biojava.bio

Class org.biojava.bio.AbstractAnnotation extends AbstractChangeable implements Serializable

Class org.biojava.bio.AnnotationChanger extends AbstractAnnotation implements Serializable

Serialized Fields

### wrapped

    Annotation wrapped

### changer

    ChangeTable changer

### properties

    Map properties

Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable

Serialized Fields

### wrapped

    Annotation wrapped

### mapper

    PropertyChanger mapper

### properties

    Map properties

Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

### properties

    Map properties

Class org.biojava.bio.BioError extends Error implements Serializable

Class org.biojava.bio.BioException extends Exception implements Serializable

Class org.biojava.bio.BioRuntimeException extends RuntimeException implements Serializable

Class org.biojava.bio.MergeAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

### mergeSet

    List mergeSet

Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable

Serialized Fields

### parent

    Annotation parent

### overlay

    Map overlay

Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

### properties

    Map properties

  The properties map. This may be null if no property values have yet been set.

Class org.biojava.bio.SmallAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

### properties

    Map properties

Package org.biojava.bio.alignment

Class org.biojava.bio.alignment.IllegalAlignmentEditException extends BioRuntimeException implements Serializable

Package org.biojava.bio.annodb

Class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory extends Object implements Serializable

Serialized Fields

### method

    Method method

Package org.biojava.bio.chromatogram

Class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException extends BioException implements Serializable

Package org.biojava.bio.dist

Class org.biojava.bio.dist.AbstractOrderNDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 1406135308618188893L

Serialized Fields

### alphabet

    Alphabet alphabet

### firstA

    Alphabet firstA

### lastA

    Alphabet lastA

### nullModel

    Distribution nullModel

Class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory extends Object implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Class org.biojava.bio.dist.GapDistribution extends Unchangeable implements Serializable

serialVersionUID: 88622317L

Serialized Fields

### alpha

    Alphabet alpha

Class org.biojava.bio.dist.IndexedCount extends AbstractChangeable implements Serializable

serialVersionUID: -1764931829553447679L

Serialization Methods

### readObject

    private void readObject(ObjectInputStream stream)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

### writeObject

    private void writeObject(ObjectOutputStream oos)
                      throws IOException

  Throws:
    `IOException`

Serialized Fields

### symbolIndices

    Map symbolIndices

### alpha

    FiniteAlphabet alpha

Class org.biojava.bio.dist.PairDistribution extends AbstractChangeable implements Serializable

Serialized Fields

### first

    Distribution first

### second

    Distribution second

### alphabet

    Alphabet alphabet

### nullModel

    Distribution nullModel

Class org.biojava.bio.dist.SimpleDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 7252850540926095728L

Serialization Methods

### readObject

    private void readObject(ObjectInputStream stream)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

### writeObject

    private void writeObject(ObjectOutputStream oos)
                      throws IOException

  Throws:
    `IOException`

Serialized Fields

### nullModel

    Distribution nullModel

### alpha

    FiniteAlphabet alpha

Class org.biojava.bio.dist.SimpleDistributionTrainer extends Object implements Serializable

Serialized Fields

### dis

    Distribution dis

  Deprecated.

### c

    Map c

  Deprecated.

Class org.biojava.bio.dist.SimpleDistributionTrainerContext extends Object implements Serializable

Serialized Fields

### distToTrainer

    Map distToTrainer

### trainers

    Set trainers

### nullModelWeight

    double nullModelWeight

Class org.biojava.bio.dist.TranslatedDistribution extends AbstractChangeable implements Serializable

Serialized Fields

### other

    Distribution other

### delegate

    Distribution delegate

### table

    ReversibleTranslationTable table

Class org.biojava.bio.dist.UniformDistribution extends AbstractDistribution implements Serializable

serialVersionUID: 88454038L

Serialized Fields

### alphabet

    FiniteAlphabet alphabet

### nullModel

    Distribution nullModel

Class org.biojava.bio.dist.UntrainableDistribution extends SimpleDistribution implements Serializable

Package org.biojava.bio.dp

Class org.biojava.bio.dp.BaumWelchSampler extends AbstractTrainer implements Serializable

Class org.biojava.bio.dp.BaumWelchTrainer extends AbstractTrainer implements Serializable

Class org.biojava.bio.dp.DP.ReverseIterator extends Object implements Serializable

Serialized Fields

### sym

    SymbolList sym

### index

    int index

Class org.biojava.bio.dp.IllegalTransitionException extends BioException implements Serializable

Serialized Fields

### from

    State from

### to

    State to

Class org.biojava.bio.dp.MagicalState extends SimpleEmissionState implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Class org.biojava.bio.dp.ProfileHMM extends SimpleMarkovModel implements Serializable

Serialized Fields

### columns

    int columns

  The number of columns in this model.

### matchStates

    EmissionState[] matchStates

  Match states array.

  matchStates[0] == matchStates[columns+1] == magicalState().

### insertStates

    EmissionState[] insertStates

  Insert states array.

  From 0 .. columns().

### deleteStates

    DotState[] deleteStates

  Delete states array.

  From 0 .. columns()-1 corresponding to indexes 1..columns().

Class org.biojava.bio.dp.ScoreType.NullModel extends Object implements Serializable

Class org.biojava.bio.dp.ScoreType.Odds extends Object implements Serializable

Class org.biojava.bio.dp.ScoreType.Probability extends Object implements Serializable

Class org.biojava.bio.dp.SimpleDotState extends FundamentalAtomicSymbol implements Serializable

Class org.biojava.bio.dp.SimpleEmissionState extends AbstractChangeable implements Serializable

Serialized Fields

### dis

    Distribution dis

### name

    String name

### ann

    Annotation ann

### advance

    int[] advance

### matches

    Alphabet matches

Class org.biojava.bio.dp.SimpleMarkovModel extends AbstractChangeable implements Serializable

serialVersionUID: -3043028839927615753L

Serialized Fields

### emissionAlpha

    Alphabet emissionAlpha

### stateAlpha

    FiniteAlphabet stateAlpha

### magicalState

    MagicalState magicalState

### transFrom

    Map transFrom

### transTo

    Map transTo

### transWeights

    Map transWeights

Class org.biojava.bio.dp.SimpleModelInState extends FundamentalAtomicSymbol implements Serializable

Serialized Fields

### model

    MarkovModel model

Class org.biojava.bio.dp.SimpleModelTrainer extends SimpleDistributionTrainerContext implements Serializable

Serialized Fields

### models

    Set models

Class org.biojava.bio.dp.SimpleStatePath extends Unchangeable implements Serializable

Serialized Fields

### score

    double score

### delegate

    Alignment delegate

Class org.biojava.bio.dp.SimpleWeightMatrix extends Object implements Serializable

serialVersionUID: 73394340224964858L

Serialized Fields

### columns

    Distribution[] columns

### alpha

    Alphabet alpha

Class org.biojava.bio.dp.TrainerTransition extends Object implements Serializable

Serialized Fields

### trainer

    TransitionTrainer trainer

### from

    State from

### to

    State to

Class org.biojava.bio.dp.Transition extends Object implements Serializable

Serialized Fields

### from

    State from

### to

    State to

Class org.biojava.bio.dp.WeightMatrixAnnotator extends Object implements Serializable

Serialized Fields

### matrix

    WeightMatrix matrix

### threshold

    double threshold

### scoreType

    ScoreType scoreType

### wmID

    String wmID

Class org.biojava.bio.dp.WMAsMM extends AbstractChangeable implements Serializable

Serialized Fields

### wm

    WeightMatrix wm

### stateAlpha

    FiniteAlphabet stateAlpha

### magicalState

    MagicalState magicalState

### states

    EmissionState[] states

### transFrom

    Map transFrom

### transTo

    Map transTo

### transWeights

    Map transWeights

Package org.biojava.bio.dp.onehead

Class org.biojava.bio.dp.onehead.SingleDP extends DP implements Serializable

Serialized Fields

### emissionsProb

    HashMap emissionsProb

### emissionsOdds

    HashMap emissionsOdds

### emissionsNull

    HashMap emissionsNull

Class org.biojava.bio.dp.onehead.SingleDPMatrix extends Object implements Serializable

Serialized Fields

### states

    State[] states

### model

    MarkovModel model

### symList

    SymbolList[] symList

### scores

    double[][] scores

### score

    double score

Package org.biojava.bio.dp.twohead

Class org.biojava.bio.dp.twohead.PairDPMatrix extends Object implements Serializable

Serialized Fields

### states

    State[] states

### seqs

    SymbolList[] seqs

### scores

    double[][][] scores

### model

    MarkovModel model

### finalScore

    double finalScore

Class org.biojava.bio.dp.twohead.PairwiseDP extends DP implements Serializable

Serialized Fields

### emissionCache

    HashMap emissionCache

### ccFactory

    CellCalculatorFactory ccFactory

Package org.biojava.bio.gui

Class org.biojava.bio.gui.DistributionLogo extends JComponent implements Serializable

Serialized Fields

### dist

    Distribution dist

  The dist to render.

### logoPainter

    LogoPainter logoPainter

  The logoPainter property.

### style

    SymbolStyle style

  The style property.

### scaleByInformation

    boolean scaleByInformation

  The information/plain property

### blockPainter

    BlockPainter blockPainter

### renderingHints

    RenderingHints renderingHints

Class org.biojava.bio.gui.FeatureTree extends JTree implements Serializable

Serialized Fields

### root

    String root

### seqs

    ArrayList seqs

Package org.biojava.bio.gui.sequence

Class org.biojava.bio.gui.sequence.AbstractBeadRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### beadDepth

    double beadDepth

### beadDisplacement

    double beadDisplacement

### beadOutline

    Paint beadOutline

### beadFill

    Paint beadFill

### beadStroke

    Stroke beadStroke

### delegates

    Map delegates

### delegationCache

    Map delegationCache

Class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer extends MultiLineRenderer implements Serializable

Serialized Fields

### source

    FeatureSource source

### digestFilter

    FeatureFilter digestFilter

### laneMap

    Map laneMap

### laneCount

    int laneCount

### distanceBetween

    int distanceBetween

Class org.biojava.bio.gui.sequence.AlignmentRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

### label

    Object label

Class org.biojava.bio.gui.sequence.BasicImapRenderer extends Object implements Serializable

Serialized Fields

### renderer

    BasicFeatureRenderer renderer

### imageMap

    ImageMap imageMap

### urlFactory

    URLFactory urlFactory

Class org.biojava.bio.gui.sequence.BumpedRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

### leadingPixles

    int leadingPixles

### trailingPixles

    int trailingPixles

### contextCache

    CacheMap contextCache

### flushers

    Set flushers

Class org.biojava.bio.gui.sequence.CircularRendererPanel extends JComponent implements Serializable

Serialized Fields

### ctxt

    CircularRendererContext ctxt

### symList

    SymbolList symList

### radius

    double radius

### renderer

    CircularRenderer renderer

### offset

    double offset

Class org.biojava.bio.gui.sequence.EllipticalBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

### dimensionRatio

    double dimensionRatio

Class org.biojava.bio.gui.sequence.FilteringRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

### recurse

    boolean recurse

### contextCache

    CacheMap contextCache

### flushers

    Set flushers

Class org.biojava.bio.gui.sequence.GappedRenderer extends SequenceRendererWrapper implements Serializable

Class org.biojava.bio.gui.sequence.GlyphFeatureRenderer extends FilteringRenderer implements Serializable

Serialized Fields

### depth

    double depth

### fList

    List fList

### gList

    List gList

Class org.biojava.bio.gui.sequence.ImageMap.ClientSide extends Object implements Serializable

Serialized Fields

### name

    String name

### url

    URL url

### hotSpots

    List hotSpots

Class org.biojava.bio.gui.sequence.ImageMap.HotSpot extends Object implements Serializable

Serialized Fields

### type

    String type

### url

    URL url

### coordinates

    Integer[] coordinates

### userObject

    Object userObject

Class org.biojava.bio.gui.sequence.ImageMap.ServerSide extends Object implements Serializable

Serialized Fields

### hotSpots

    List hotSpots

Class org.biojava.bio.gui.sequence.MultiLineRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### renderers

    List renderers

Class org.biojava.bio.gui.sequence.OverlayRendererWrapper extends AbstractChangeable implements Serializable

Serialized Fields

### renderer

    SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.PaddingRenderer extends SequenceRendererWrapper implements Serializable

Serialized Fields

### padding

    double padding

Class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### line

    Line2D.Float line

  `line` is the line to be drawn for each feature.

### outline

    Paint outline

  `outline` is the line colour.

Class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

  `filter` is the filter applied to both `FeatureHolder`s.

### recurse

    boolean recurse

  `recurse` indicates whether the filter should recurse through any subfeatures.

### subContextCache

    CacheMap subContextCache

### cacheFlushers

    Set cacheFlushers

### renderer

    PairwiseSequenceRenderer renderer

Class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### renderers

    List renderers

Class org.biojava.bio.gui.sequence.PairwiseSequencePanel extends JComponent implements Serializable

Serialized Fields

### sequence

    Sequence sequence

### translation

    int translation

### direction

    int direction

### secSequence

    Sequence secSequence

### secTranslation

    int secTranslation

### secDirection

    int secDirection

### scale

    double scale

### renderer

    PairwiseSequenceRenderer renderer

### hints

    RenderingHints hints

### leadingBorder

    SequenceRenderContext.Border leadingBorder

### trailingBorder

    SequenceRenderContext.Border trailingBorder

### propertyListener

    PropertyChangeListener propertyListener

### repaintListener

    ChangeListener repaintListener

### layoutListener

    ChangeListener layoutListener

### svSupport

    SequenceViewerSupport svSupport

### mouseListener

    MouseListener mouseListener

### svmSupport

    SequenceViewerMotionSupport svmSupport

### mouseMotionListener

    MouseMotionListener mouseMotionListener

Class org.biojava.bio.gui.sequence.PeptideDigestRenderer extends AbstractPeptideDigestRenderer implements Serializable

Serialized Fields

### defaultPaint

    Paint defaultPaint

Class org.biojava.bio.gui.sequence.RectangularBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

### rect

    Rectangle2D rect

### scaleHeight

    boolean scaleHeight

Class org.biojava.bio.gui.sequence.RectangularImapRenderer extends Object implements Serializable

Serialized Fields

### renderer

    RectangularBeadRenderer renderer

### imageMap

    ImageMap imageMap

### urlFactory

    URLFactory urlFactory

Class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer extends AbstractBeadRenderer implements Serializable

Serialized Fields

### rect

    RoundRectangle2D rect

### arcWidth

    double arcWidth

### arcHeight

    double arcHeight

Class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer extends GlyphFeatureRenderer implements Serializable

Class org.biojava.bio.gui.sequence.SequencePanel extends JComponent implements Serializable

Serialized Fields

### sequence

    SymbolList sequence

### range

    RangeLocation range

### direction

    int direction

### scale

    double scale

### pixelOffset

    double pixelOffset

### leadingBorder

    SequenceRenderContext.Border leadingBorder

### trailingBorder

    SequenceRenderContext.Border trailingBorder

### renderer

    SequenceRenderer renderer

### theMonitor

    org.biojava.bio.gui.sequence.SequencePanel.RendererMonitor theMonitor

### hints

    RenderingHints hints

### svSupport

    SequenceViewerSupport svSupport

### mouseListener

    MouseListener mouseListener

### svmSupport

    SequenceViewerMotionSupport svmSupport

### mouseMotionListener

    MouseMotionListener mouseMotionListener

### layoutListener

    ChangeListener layoutListener

### repaintListener

    ChangeListener repaintListener

Class org.biojava.bio.gui.sequence.SequencePanel.Border extends Object implements Serializable

Serialized Fields

### pcs

    PropertyChangeSupport pcs

### size

    double size

### alignment

    int alignment

Class org.biojava.bio.gui.sequence.SequencePanelWrapper extends JPanel implements Serializable

Serialized Fields

### range

    RangeLocation range

### sequence

    Sequence sequence

### ranges

    RangeLocation[] ranges

### seqPanels

    SequencePanel[] seqPanels

### renderer

    SequenceRenderer renderer

### scale

    double scale

### hints

    RenderingHints hints

### direction

    int direction

### trackLayout

    TrackLayout trackLayout

### viewerListeners

    List viewerListeners

### motionListeners

    List motionListeners

Class org.biojava.bio.gui.sequence.SequencePoster extends JComponent implements Serializable

Serialized Fields

### sequence

    Sequence sequence

  Deprecated.

### direction

    int direction

  Deprecated.

### scale

    double scale

  Deprecated.

### lines

    int lines

  Deprecated.

### spacer

    int spacer

  Deprecated.

### leadingBorder

    SequenceRenderContext.Border leadingBorder

  Deprecated.

### trailingBorder

    SequenceRenderContext.Border trailingBorder

  Deprecated.

### renderer

    SequenceRenderer renderer

  Deprecated.

### offsets

    double[] offsets

  Deprecated.

### realLines

    int realLines

  Deprecated.

### alongDim

    double alongDim

  Deprecated.

### acrossDim

    double acrossDim

  Deprecated.

### symbolsPerLine

    int symbolsPerLine

  Deprecated.

### theMonitor

    org.biojava.bio.gui.sequence.SequencePoster.RendererMonitor theMonitor

  Deprecated.

### renderingHints

    RenderingHints renderingHints

  Deprecated.

### svSupport

    SequenceViewerSupport svSupport

  Deprecated.

### mouseListener

    MouseListener mouseListener

  Deprecated.

### svmSupport

    SequenceViewerMotionSupport svmSupport

  Deprecated.

### mouseMotionListener

    MouseMotionListener mouseMotionListener

  Deprecated.

### layoutListener

    ChangeListener layoutListener

  Deprecated.

### repaintListener

    ChangeListener repaintListener

  Deprecated.

Class org.biojava.bio.gui.sequence.SequencePoster.Border extends Object implements Serializable

Serialized Fields

### pcs

    PropertyChangeSupport pcs

### size

    double size

### alignment

    int alignment

Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border extends Object implements Serializable

Serialized Fields

### size

    double size

### alignment

    int alignment

Class org.biojava.bio.gui.sequence.SequenceRendererWrapper extends AbstractChangeable implements Serializable

Serialized Fields

### renderer

    SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.SequenceViewerEvent extends EventObject implements Serializable

Serialized Fields

### path

    List path

### target

    Object target

### mouseEvent

    MouseEvent mouseEvent

### pos

    int pos

Class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### pane

    SixFrameRenderer pane

Class org.biojava.bio.gui.sequence.TranslatedSequencePanel extends JComponent implements Serializable

Serialized Fields

### sequence

    SymbolList sequence

### translation

    int translation

### direction

    int direction

### scale

    double scale

### renderer

    SequenceRenderer renderer

### rendererBorders

    double rendererBorders

### hints

    RenderingHints hints

### leadingBorder

    SequenceRenderContext.Border leadingBorder

### trailingBorder

    SequenceRenderContext.Border trailingBorder

### propertyListener

    PropertyChangeListener propertyListener

### repaintListener

    ChangeListener repaintListener

### layoutListener

    ChangeListener layoutListener

### svSupport

    SequenceViewerSupport svSupport

### mouseListener

    MouseListener mouseListener

### svmSupport

    SequenceViewerMotionSupport svmSupport

### mouseMotionListener

    MouseMotionListener mouseMotionListener

Class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer extends AbstractChangeable implements Serializable

Serialized Fields

### outline

    Paint outline

### fill

    Paint fill

### blockDepth

    double blockDepth

Class org.biojava.bio.gui.sequence.ZiggyImapRenderer extends Object implements Serializable

Serialized Fields

### renderer

    ZiggyFeatureRenderer renderer

### imageMap

    ImageMap imageMap

### urlFactory

    URLFactory urlFactory

Package org.biojava.bio.molbio

Class org.biojava.bio.molbio.RestrictionEnzyme extends Object implements Serializable

Serialized Fields

### name

    String name

### site

    SymbolList site

### cutType

    int cutType

### dsCutPositions

    int[] dsCutPositions

### usCutPositions

    int[] usCutPositions

### forwardRegex

    String forwardRegex

### reverseRegex

    String reverseRegex

### summary

    String summary

Class org.biojava.bio.molbio.RestrictionSite.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### enzyme

    RestrictionEnzyme enzyme

  `enzyme` `RestrictionEnzyme` field.

Package org.biojava.bio.program.abi

Class org.biojava.bio.program.abi.ABIFChromatogram extends AbstractChromatogram implements Serializable

Package org.biojava.bio.program.das.dasalignment

Class org.biojava.bio.program.das.dasalignment.DASException extends BioException implements Serializable

Package org.biojava.bio.program.gff

Class org.biojava.bio.program.gff.IgnoreRecordException extends Exception implements Serializable

Package org.biojava.bio.program.hmmer

Class org.biojava.bio.program.hmmer.FullHmmerProfileHMM extends SimpleMarkovModel implements Serializable

Serialized Fields

### j

    EmissionState j

### c

    EmissionState c

### n

    EmissionState n

### hmmState

    ModelInState hmmState

Class org.biojava.bio.program.hmmer.HmmerProfileHMM extends ProfileHMM implements Serializable

Class org.biojava.bio.program.hmmer.ProfileEmissionState extends SimpleEmissionState implements Serializable

Package org.biojava.bio.program.homologene

Class org.biojava.bio.program.homologene.DuplicateTaxonException extends BioException implements Serializable

Package org.biojava.bio.program.phred

Class org.biojava.bio.program.phred.PhredFormat extends Object implements Serializable

Serialized Fields

### mListeners

    Vector mListeners

### lineWidth

    int lineWidth

  The line width for output.

Class org.biojava.bio.program.phred.PhredSequence extends SimpleSequence implements Serializable

Package org.biojava.bio.program.ssaha

Class org.biojava.bio.program.ssaha.SearchException extends Exception implements Serializable

Package org.biojava.bio.proteomics

Class org.biojava.bio.proteomics.Protease extends Object implements Serializable

Serialization Methods

### readResolve

    protected Object readResolve()
                          throws ObjectStreamException

  Prevent duplication of the object during Serialization

  Throws:
    `ObjectStreamException`

Serialized Fields

### cleavageResidues

    SymbolList cleavageResidues

### notCleaveResidues

    SymbolList notCleaveResidues

### endoProtease

    boolean endoProtease

### name

    String name

Package org.biojava.bio.search

Class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter extends Object implements Serializable

Serialized Fields

### cachedOutcome

    TriState cachedOutcome

Class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable

Serialized Fields

### key

    Object key

### test

    FilterTest test

Class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable

Serialized Fields

### key

    Object key

### test

    FilterTest test

Class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable

Serialized Fields

### key

    Object key

### test

    FilterTest test

Class org.biojava.bio.search.BlastLikeSearchFilter.Not extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable

Serialized Fields

### filter

    BlastLikeSearchFilter.AbstractBlastLikeSearchFilter filter

Package org.biojava.bio.seq

Class org.biojava.bio.seq.CircularView extends ViewSequence implements Serializable

Class org.biojava.bio.seq.ComponentFeature.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### componentSequenceName

    String componentSequenceName

### componentSequence

    Sequence componentSequence

### componentLocation

    Location componentLocation

Class org.biojava.bio.seq.Feature.Template extends Object implements Serializable

Serialized Fields

### location

    Location location

### type

    String type

### source

    String source

### typeTerm

    Term typeTerm

### sourceTerm

    Term sourceTerm

### annotation

    Annotation annotation

Class org.biojava.bio.seq.FeatureFilter.And extends Object implements Serializable

Serialized Fields

### c1

    FeatureFilter c1

### c2

    FeatureFilter c2

Class org.biojava.bio.seq.FeatureFilter.AnnotationContains extends FeatureFilter.ByAnnotationType implements Serializable

Serialized Fields

### key

    Object key

### value

    Object value

Class org.biojava.bio.seq.FeatureFilter.ByAncestor extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByAnnotation extends FeatureFilter.ByAnnotationType implements Serializable

Serialized Fields

### key

    Object key

### value

    Object value

Class org.biojava.bio.seq.FeatureFilter.ByAnnotationType extends Object implements Serializable

Serialized Fields

### type

    AnnotationType type

Class org.biojava.bio.seq.FeatureFilter.ByChild extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByClass extends Object implements Serializable

Serialized Fields

### clazz

    Class clazz

Class org.biojava.bio.seq.FeatureFilter.ByComponentName extends Object implements Serializable

Serialized Fields

### cname

    String cname

Class org.biojava.bio.seq.FeatureFilter.ByDescendant extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByFeature extends Object implements Serializable

Serialized Fields

### feature

    Feature feature

Class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore extends Object implements Serializable

Serialized Fields

### minScore

    double minScore

### maxScore

    double maxScore

### score

    double score

### hashCode

    int hashCode

Class org.biojava.bio.seq.FeatureFilter.ByParent extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.BySequenceName extends Object implements Serializable

Serialized Fields

### seqName

    String seqName

Class org.biojava.bio.seq.FeatureFilter.BySource extends Object implements Serializable

Serialized Fields

### source

    String source

Class org.biojava.bio.seq.FeatureFilter.ByType extends Object implements Serializable

Serialized Fields

### type

    String type

Class org.biojava.bio.seq.FeatureFilter.ContainedByLocation extends Object implements Serializable

Serialized Fields

### loc

    Location loc

Class org.biojava.bio.seq.FeatureFilter.FrameFilter extends Object implements Serializable

Serialized Fields

### frame

    FramedFeature.ReadingFrame frame

Class org.biojava.bio.seq.FeatureFilter.HasAnnotation extends FeatureFilter.ByAnnotationType implements Serializable

Serialized Fields

### key

    Object key

Class org.biojava.bio.seq.FeatureFilter.Not extends Object implements Serializable

Serialized Fields

### child

    FeatureFilter child

Class org.biojava.bio.seq.FeatureFilter.OnlyChildren extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.OnlyDescendants extends Object implements Serializable

Serialized Fields

### filter

    FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.Or extends Object implements Serializable

Serialized Fields

### c1

    FeatureFilter c1

### c2

    FeatureFilter c2

Class org.biojava.bio.seq.FeatureFilter.OverlapsLocation extends Object implements Serializable

Serialized Fields

### loc

    Location loc

Class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation extends Object implements Serializable

Serialized Fields

### loc

    Location loc

Class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation extends Object implements Serializable

Serialized Fields

### loc

    Location loc

Class org.biojava.bio.seq.FeatureFilter.StrandFilter extends Object implements Serializable

Serialized Fields

### strand

    StrandedFeature.Strand strand

Class org.biojava.bio.seq.FramedFeature.ReadingFrame extends Object implements Serializable

Serialized Fields

### text

    String text

### frame

    int frame

Class org.biojava.bio.seq.FramedFeature.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### readingFrame

    FramedFeature.ReadingFrame readingFrame

Class org.biojava.bio.seq.MergeFeatureHolder extends AbstractFeatureHolder implements Serializable

Serialized Fields

### featureHolders

    List featureHolders

Class org.biojava.bio.seq.RemoteFeature.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### regions

    List regions

### resolver

    RemoteFeature.Resolver resolver

Class org.biojava.bio.seq.SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable

Serialized Fields

### features

    List features

  The child features.

### schema

    FeatureFilter schema

Class org.biojava.bio.seq.SimpleFeatureRealizer extends Object implements Serializable

Serialized Fields

### templateToImpl

    List templateToImpl

### fallBack

    FeatureRealizer fallBack

Class org.biojava.bio.seq.StrandedFeature.Strand extends Object implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Serialized Fields

### text

    String text

### value

    int value

### token

    char token

Class org.biojava.bio.seq.StrandedFeature.Template extends Feature.Template implements Serializable

Serialized Fields

### strand

    StrandedFeature.Strand strand

Package org.biojava.bio.seq.db

Class org.biojava.bio.seq.db.AnnotatedSequenceDB extends AbstractSequenceDB implements Serializable

Serialized Fields

### parent

    SequenceDB parent

### annotator

    SequenceAnnotator annotator

Class org.biojava.bio.seq.db.CachingSequenceDB extends SequenceDBWrapper implements Serializable

Serialization Methods

### readObject

    private void readObject(ObjectInputStream in)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

Class org.biojava.bio.seq.db.HashSequenceDB extends AbstractSequenceDB implements Serializable

Serialized Fields

### sequenceByID

    Map sequenceByID

  The sequence-by-id map.

### idMaker

    IDMaker idMaker

  An object to extract an ID for a sequence.

### name

    String name

  The name of this sequence database.

Class org.biojava.bio.seq.db.IDMaker.ByName extends Object implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws IOException

  Throws:
    `IOException`

Class org.biojava.bio.seq.db.IDMaker.ByURN extends Object implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws IOException

  Throws:
    `IOException`

Class org.biojava.bio.seq.db.IllegalIDException extends BioException implements Serializable

Class org.biojava.bio.seq.db.IndexedSequenceDB extends AbstractSequenceDB implements Serializable

Serialized Fields

### idMaker

    IDMaker idMaker

### indexStore

    IndexStore indexStore

Class org.biojava.bio.seq.db.SequenceDBWrapper extends AbstractSequenceDB implements Serializable

Serialized Fields

### parent

    SequenceDB parent

Class org.biojava.bio.seq.db.SubSequenceDB extends SequenceDBWrapper implements Serializable

Serialized Fields

### ids

    Set ids

Class org.biojava.bio.seq.db.TabIndexStore extends Object implements Serializable

Serialization Methods

### readObject

    private void readObject(ObjectInputStream in)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

Serialized Fields

### storeFile

    File storeFile

### indexFile

    File indexFile

### name

    String name

### files

    Set files

### seqFileIndex

    File[] seqFileIndex

### format

    SequenceFormat format

### sbFactory

    SequenceBuilderFactory sbFactory

### symbolParser

    SymbolTokenization symbolParser

Class org.biojava.bio.seq.db.ViewingSequenceDB extends SequenceDBWrapper implements Serializable

Package org.biojava.bio.seq.homol

Class org.biojava.bio.seq.homol.HomologyFeature.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### homology

    Homology homology

Class org.biojava.bio.seq.homol.SimilarityPairFeature.Template extends StrandedFeature.Template implements Serializable

Serialized Fields

### sibling

    SimilarityPairFeature sibling

  `sibling` `SimilarityPairFeature` field. May be null if the reciprocal `SimilarityPairFeature` has not yet been created.

### alignment

    Alignment alignment

  `alignment` `Alignment` field.

### score

    double score

  `score` of the search which produced the alignment.

Package org.biojava.bio.seq.impl

Class org.biojava.bio.seq.impl.RevCompSequence extends SimpleSequence implements Serializable

Serialized Fields

### pfh

    ProjectedFeatureHolder pfh

### origSeq

    Sequence origSeq

Class org.biojava.bio.seq.impl.SimpleFeature extends AbstractChangeable implements Serializable

Serialized Fields

### featureHolder

    SimpleFeatureHolder featureHolder

  The FeatureHolder that we will delegate the FeatureHolder interface too. This is lazily instantiated.

### loc

    Location loc

  The location of this feature.

### type

    String type

  The type of this feature - something like Exon. This is included for cheap interoperability with GFF.

### source

    String source

  The source of this feature - the program that generated it. This is included for cheap interoperability with GFF.

### parent

    FeatureHolder parent

  Our parent FeatureHolder.

### annotation

    Annotation annotation

  The annotation object. This is lazily instantiated.

### typeTerm

    Term typeTerm

### sourceTerm

    Term sourceTerm

Class org.biojava.bio.seq.impl.SimpleFramedFeature extends SimpleStrandedFeature implements Serializable

Serialized Fields

### readingFrame

    FramedFeature.ReadingFrame readingFrame

Class org.biojava.bio.seq.impl.SimpleGappedSequence extends SimpleGappedSymbolList implements Serializable

Serialized Fields

### sequence

    Sequence sequence

### features

    MergeFeatureHolder features

### localFeatures

    SimpleFeatureHolder localFeatures

### projectedFeatures

    FeatureHolder projectedFeatures

### createOnUnderlying

    boolean createOnUnderlying

Class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext extends ReparentContext implements Serializable

Class org.biojava.bio.seq.impl.SimpleHomologyFeature extends SimpleStrandedFeature implements Serializable

Serialized Fields

### homology

    Homology homology

Class org.biojava.bio.seq.impl.SimpleRemoteFeature extends SimpleStrandedFeature implements Serializable

Serialized Fields

### regions

    List regions

### resolver

    RemoteFeature.Resolver resolver

Class org.biojava.bio.seq.impl.SimpleRestrictionSite extends SimpleStrandedFeature implements Serializable

Serialized Fields

### enzyme

    RestrictionEnzyme enzyme

### position

    int position

Class org.biojava.bio.seq.impl.SimpleSequence extends AbstractChangeable implements Serializable

Serialized Fields

### symList

    SymbolList symList

  Delegate SymbolList.

### urn

    String urn

### name

    String name

### annotation

    Annotation annotation

### featureHolder

    SimpleFeatureHolder featureHolder

Class org.biojava.bio.seq.impl.SimpleSequenceFactory extends Object implements Serializable

Serialized Fields

### realizer

    FeatureRealizer realizer

Class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature extends SimpleStrandedFeature implements Serializable

Serialized Fields

### sibling

    SimilarityPairFeature sibling

### alignment

    Alignment alignment

### score

    double score

Class org.biojava.bio.seq.impl.SimpleStrandedFeature extends SimpleFeature implements Serializable

Serialized Fields

### strand

    StrandedFeature.Strand strand

Class org.biojava.bio.seq.impl.SubSequence extends Object implements Serializable

Serialized Fields

### parent

    Sequence parent

### symbols

    SymbolList symbols

### name

    String name

### uri

    String uri

### annotation

    Annotation annotation

### parentLocation

    RangeLocation parentLocation

Class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext extends ReparentContext implements Serializable

Serialized Fields

### parentLocation

    RangeLocation parentLocation

### remoteLocationFilter

    FeatureFilter remoteLocationFilter

### clippingFilter

    FeatureFilter clippingFilter

Class org.biojava.bio.seq.impl.ViewSequence extends Unchangeable implements Serializable

serialVersionUID: 9866447L

Serialization Methods

### readObject

    private void readObject(ObjectInputStream s)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

Serialized Fields

### seqDelegate

    Sequence seqDelegate

  Delegate Sequence.

### exposedFeatures

    MergeFeatureHolder exposedFeatures

  FeatureHolder support

### addedFeatures

    SimpleFeatureHolder addedFeatures

### name

    String name

  IDs

### urn

    String urn

### anno

    Annotation anno

  Our annotation.

Package org.biojava.bio.seq.io

Class org.biojava.bio.seq.io.CharacterTokenization extends Unchangeable implements Serializable

Serialized Fields

### alphabet

    Alphabet alphabet

### symbolsToCharacters

    Map symbolsToCharacters

### charactersToSymbols

    Map charactersToSymbols

### caseSensitive

    boolean caseSensitive

Class org.biojava.bio.seq.io.CrossProductTokenization extends WordTokenization implements Serializable

Serialized Fields

### subTokenizations

    List subTokenizations

Class org.biojava.bio.seq.io.DoubleTokenization extends WordTokenization implements Serializable

Class org.biojava.bio.seq.io.EmblLikeFormat extends Object implements Serializable

Serialized Fields

### elideSymbols

    boolean elideSymbols

  Deprecated.

### mListeners

    Vector mListeners

  Deprecated.

Class org.biojava.bio.seq.io.EmblProcessor.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.FastaFormat extends Object implements Serializable

Serialized Fields

### mListeners

    Vector mListeners

  Deprecated.

### lineWidth

    int lineWidth

  Deprecated.
  The line width for output.

Class org.biojava.bio.seq.io.GenbankFormat extends Object implements Serializable

Serialized Fields

### mListeners

    Vector mListeners

  Deprecated.

### elideSymbols

    boolean elideSymbols

  Deprecated.

Class org.biojava.bio.seq.io.GenbankProcessor.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.GenbankXmlFormat extends GenbankFormat implements Serializable

Serialized Fields

### m_xmlParser

    SAXParser m_xmlParser

  Deprecated.

### m_handler

    org.biojava.bio.seq.io.GenbankXmlFormat.GenbankXmlHandler m_handler

  Deprecated.

### m_parsed

    boolean m_parsed

  Deprecated.

### m_sequenceIndex

    int m_sequenceIndex

  Deprecated.

Class org.biojava.bio.seq.io.GenpeptFormat extends GenbankFormat implements Serializable

Class org.biojava.bio.seq.io.IntegerTokenization extends WordTokenization implements Serializable

Class org.biojava.bio.seq.io.NameTokenization extends WordTokenization implements Serializable

Serialized Fields

### caseSensitive

    boolean caseSensitive

Class org.biojava.bio.seq.io.OrganismParser.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

### sciNameKey

    String sciNameKey

### commonNameKey

    String commonNameKey

### ncbiTaxonKey

    String ncbiTaxonKey

### taxonFactory

    TaxonFactory taxonFactory

### taxonParser

    TaxonParser taxonParser

Class org.biojava.bio.seq.io.ParseException extends BioException implements Serializable

Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.ReferenceAnnotation extends AbstractAnnotation implements Serializable

Serialized Fields

### properties

    Map properties

  Deprecated.
  The properties map. This may be null if no property values have yet been set.

Class org.biojava.bio.seq.io.SubIntegerTokenization extends WordTokenization implements Serializable

Class org.biojava.bio.seq.io.SwissprotProcessor.Factory extends Object implements Serializable

Serialized Fields

### delegateFactory

    SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.WordTokenization extends Unchangeable implements Serializable

Serialized Fields

### alphabet

    Alphabet alphabet

Package org.biojava.bio.seq.projection

Class org.biojava.bio.seq.projection.ProjectedFeatureHolder extends AbstractFeatureHolder implements Serializable

Serialized Fields

### context

    ProjectionContext context

### topLevelFeatures

    FeatureHolder topLevelFeatures

Class org.biojava.bio.seq.projection.ReparentContext extends Object implements Serializable

Serialized Fields

### parent

    FeatureHolder parent

### wrapped

    FeatureHolder wrapped

Class org.biojava.bio.seq.projection.TranslateFlipContext extends ReparentContext implements Serializable

Serialized Fields

### translation

    int translation

### oppositeStrand

    boolean oppositeStrand

Package org.biojava.bio.structure

Class org.biojava.bio.structure.StructureException extends BioException implements Serializable

serialVersionUID: 62946250941673093L

Package org.biojava.bio.structure.io

Class org.biojava.bio.structure.io.PDBParseException extends BioException implements Serializable

serialVersionUID: 219047230178423923L

Package org.biojava.bio.structure.jama

Class org.biojava.bio.structure.jama.CholeskyDecomposition extends Object implements Serializable

serialVersionUID: 224348942390823L

Serialized Fields

### L

    double[][] L

  Array for internal storage of decomposition.

  internal array storage.

### n

    int n

  Row and column dimension (square matrix).

  matrix dimension.

### isspd

    boolean isspd

  Symmetric and positive definite flag.

  is symmetric and positive definite flag.

Class org.biojava.bio.structure.jama.EigenvalueDecomposition extends Object implements Serializable

serialVersionUID: 93489734879234789L

Serialized Fields

### n

    int n

  Row and column dimension (square matrix).

  matrix dimension.

### issymmetric

    boolean issymmetric

  Symmetry flag.

  internal symmetry flag.

### d

    double[] d

  Arrays for internal storage of eigenvalues.

  internal storage of eigenvalues.

### e

    double[] e

  Arrays for internal storage of eigenvalues.

  internal storage of eigenvalues.

### V

    double[][] V

  Array for internal storage of eigenvectors.

  internal storage of eigenvectors.

### H

    double[][] H

  Array for internal storage of nonsymmetric Hessenberg form.

  internal storage of nonsymmetric Hessenberg form.

### ort

    double[] ort

  Working storage for nonsymmetric algorithm.

  working storage for nonsymmetric algorithm.

Class org.biojava.bio.structure.jama.LUDecomposition extends Object implements Serializable

serialVersionUID: 9271028462937843L

Serialized Fields

### LU

    double[][] LU

  Array for internal storage of decomposition.

  internal array storage.

### m

    int m

  Row and column dimensions, and pivot sign.

  column dimension.

### n

    int n

  Row and column dimensions, and pivot sign.

  column dimension.

### pivsign

    int pivsign

  Row and column dimensions, and pivot sign.

  column dimension.

### piv

    int[] piv

  Internal storage of pivot vector.

  pivot vector.

Class org.biojava.bio.structure.jama.Matrix extends Object implements Serializable

serialVersionUID: 8492558293015348719L

Serialized Fields

### A

    double[][] A

  Array for internal storage of elements.

  internal array storage.

### m

    int m

  Row and column dimensions.

  row dimension.

### n

    int n

  Row and column dimensions.

  row dimension.

Class org.biojava.bio.structure.jama.QRDecomposition extends Object implements Serializable

serialVersionUID: 10293720387423L

Serialized Fields

### QR

    double[][] QR

  Array for internal storage of decomposition.

  internal array storage.

### m

    int m

  Row and column dimensions.

  column dimension.

### n

    int n

  Row and column dimensions.

  column dimension.

### Rdiag

    double[] Rdiag

  Array for internal storage of diagonal of R.

  diagonal of R.

Class org.biojava.bio.structure.jama.SingularValueDecomposition extends Object implements Serializable

serialVersionUID: 640239472093534756L

Serialized Fields

### U

    double[][] U

  Arrays for internal storage of U and V.

  internal storage of U.

### V

    double[][] V

  Arrays for internal storage of U and V.

  internal storage of U.

### s

    double[] s

  Array for internal storage of singular values.

  internal storage of singular values.

### m

    int m

  Row and column dimensions.

  row dimension.

### n

    int n

  Row and column dimensions.

  row dimension.

Package org.biojava.bio.symbol

Class org.biojava.bio.symbol.AbstractAlphabet extends AbstractChangeable implements Serializable

Serialization Methods

### readResolve

    protected Object readResolve()
                          throws ObjectStreamException

  To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.

  Throws:
    `ObjectStreamException`

Serialized Fields

### tokenizationsByName

    Map tokenizationsByName

### ambCache

    Map ambCache

Class org.biojava.bio.symbol.AbstractLocation extends Object implements Serializable

Class org.biojava.bio.symbol.AbstractRangeLocation extends AbstractLocation implements Serializable

Class org.biojava.bio.symbol.ChunkedSymbolList extends AbstractSymbolList implements Serializable

Serialization Methods

### readObject

    private void readObject(ObjectInputStream stream)
                     throws IOException,
                            ClassNotFoundException

  Throws:
    `IOException`
    `ClassNotFoundException`

Serialized Fields

### chunks

    SymbolList[] chunks

### chunkSize

    int chunkSize

### alpha

    Alphabet alpha

### length

    int length

Class org.biojava.bio.symbol.DNAAmbPack extends Object implements Serializable

Serialized Fields

### syms

    Symbol[] syms

Class org.biojava.bio.symbol.DNANoAmbPack extends Object implements Serializable

Serialized Fields

### placeHolder

    byte placeHolder

Class org.biojava.bio.symbol.DoubleAlphabet extends Unchangeable implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Serialized Fields

### alphabets

    List alphabets

### doubleToSym

    WeakValueHashMap doubleToSym

Class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange extends Unchangeable implements Serializable

Serialized Fields

### minVal

    double minVal

### maxVal

    double maxVal

### matches

    Alphabet matches

Class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol extends Unchangeable implements Serializable

Serialized Fields

### val

    double val

### matches

    Alphabet matches

Class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet extends Unchangeable implements Serializable

Serialization Methods

### readResolve

    protected Object readResolve()
                          throws ObjectStreamException

  To prevent duplication of a what should be a single instance of an existing alphabet. This method was written as protected so that subclasses even from other packages will inherit it. It should only be overridden with care.

  Throws:
    `ObjectStreamException`

Serialized Fields

### min

    double min

### max

    double max

### name

    String name

Class org.biojava.bio.symbol.DummySymbolList extends AbstractSymbolList implements Serializable

Serialized Fields

### sym

    Symbol sym

### alpha

    Alphabet alpha

### length

    int length

Class org.biojava.bio.symbol.Edit extends Object implements Serializable

Serialized Fields

### pos

    int pos

### length

    int length

### replacement

    SymbolList replacement

Class org.biojava.bio.symbol.FundamentalAtomicSymbol extends AbstractSymbol implements Serializable

Serialized Fields

### name

    String name

### annotation

    Annotation annotation

Class org.biojava.bio.symbol.FuzzyLocation extends AbstractRangeLocation implements Serializable

Serialized Fields

### outerMin

    int outerMin

### innerMin

    int innerMin

### innerMax

    int innerMax

### outerMax

    int outerMax

### mIsMinFuzzy

    boolean mIsMinFuzzy

### mIsMaxFuzzy

    boolean mIsMaxFuzzy

### resolver

    FuzzyLocation.RangeResolver resolver

Class org.biojava.bio.symbol.FuzzyPointLocation extends AbstractLocation implements Serializable

Serialized Fields

### min

    int min

### max

    int max

### resolver

    FuzzyPointLocation.PointResolver resolver

Class org.biojava.bio.symbol.IllegalAlphabetException extends BioException implements Serializable

Class org.biojava.bio.symbol.IllegalSymbolException extends BioException implements Serializable

Serialized Fields

### sym

    Symbol sym

Class org.biojava.bio.symbol.IntegerAlphabet extends Unchangeable implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Serialized Fields

### intToSym

    WeakValueHashMap intToSym

  Canonicalization map for ints and references to symbols.

Class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol extends Unchangeable implements Serializable

Serialized Fields

### val

    int val

### matches

    Alphabet matches

Class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet extends AbstractAlphabet implements Serializable

Serialized Fields

### min

    int min

### max

    int max

### name

    String name

Class org.biojava.bio.symbol.MergeLocation extends RangeLocation implements Serializable

Serialized Fields

### componentLocations

    List componentLocations

Class org.biojava.bio.symbol.PackedSymbolList extends AbstractSymbolList implements Serializable

Serialized Fields

### packing

    Packing packing

### syms

    long[] syms

### length

    int length

### symsPerElement

    byte symsPerElement

### mask

    byte mask

### currentMin

    int currentMin

### currentMax

    int currentMax

### currentWord

    long currentWord

### wordsize

    int wordsize

Class org.biojava.bio.symbol.PointLocation extends AbstractRangeLocation implements Serializable

Serialized Fields

### point

    int point

  The actual index contained.

Class org.biojava.bio.symbol.RangeLocation extends AbstractRangeLocation implements Serializable

Serialized Fields

### min

    int min

  The minimum point contained.

### max

    int max

  The maximum point contained.

Class org.biojava.bio.symbol.SimpleAlignment extends AbstractSymbolList implements Serializable

serialVersionUID: -1760075176220928440L

Serialized Fields

### labelToSymbolList

    LinkedHashMap labelToSymbolList

### labels

    List labels

### alphabet

    Alphabet alphabet

### length

    int length

Class org.biojava.bio.symbol.SimpleAlphabet extends AbstractAlphabet implements Serializable

serialVersionUID: 216254146L

Serialized Fields

### name

    String name

### annotation

    Annotation annotation

### symbols

    Set symbols

### ambig

    Set ambig

### alphabets

    List alphabets

  A list of alphabets that make up this one - a singleton list containing this.

Class org.biojava.bio.symbol.SimpleAtomicSymbol extends org.biojava.bio.symbol.AbstractSimpleBasisSymbol implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()

Class org.biojava.bio.symbol.SimpleGappedSymbolList extends AbstractSymbolList implements Serializable

serialVersionUID: 4258621048300499709L

Serialized Fields

### alpha

    Alphabet alpha

  The Alphabet - the same as source but guaranteed to include the gap character.

### source

    SymbolList source

  The SymbolList to view.

### blocks

    ArrayList blocks

  The list of ungapped blocks that align between source and this view.

### length

    int length

  The total length of the alignment - necessary to allow leading & trailing gaps.

Class org.biojava.bio.symbol.SimpleGappedSymbolList.Block extends Object implements Serializable

serialVersionUID: 4090888450309921439L

Serialized Fields

### sourceStart

    int sourceStart

### sourceEnd

    int sourceEnd

### viewStart

    int viewStart

### viewEnd

    int viewEnd

Class org.biojava.bio.symbol.SimpleManyToOneTranslationTable extends AbstractManyToOneTranslationTable implements Serializable

Serialized Fields

### transMap

    Map transMap

### revMap

    Map revMap

### source

    FiniteAlphabet source

### target

    Alphabet target

Class org.biojava.bio.symbol.SimpleReversibleTranslationTable extends AbstractReversibleTranslationTable implements Serializable

Serialized Fields

### transMap

    Map transMap

### revMap

    Map revMap

### source

    FiniteAlphabet source

### target

    Alphabet target

Class org.biojava.bio.symbol.SimpleSymbolList extends AbstractSymbolList implements Serializable

serialVersionUID: -9015317520644706924L

Serialized Fields

### alphabet

    Alphabet alphabet

### symbols

    Symbol[] symbols

### length

    int length

### isView

    boolean isView

### viewOffset

    int viewOffset

### referenceSymbolList

    SymbolList referenceSymbolList

Class org.biojava.bio.symbol.SimpleTranslationTable extends org.biojava.bio.symbol.AbstractTranslationTable implements Serializable

Serialized Fields

### transMap

    Map transMap

### source

    FiniteAlphabet source

### target

    Alphabet target

Class org.biojava.bio.symbol.SingletonAlphabet extends AbstractAlphabet implements Serializable

Serialized Fields

### sym

    AtomicSymbol sym

### alphabets

    List alphabets

Class org.biojava.bio.symbol.SuffixTree extends Object implements Serializable

Serialized Fields

### alphabet

    FiniteAlphabet alphabet

### root

    SuffixTree.SuffixNode root

### indexer

    AlphabetIndex indexer

### counts

    List counts

Class org.biojava.bio.symbol.SuffixTree.SuffixNode extends Object implements Serializable

Package org.biojava.bio.taxa

Class org.biojava.bio.taxa.CircularReferenceException extends BioException implements Serializable

Package org.biojava.directory

Class org.biojava.directory.ProviderNotFoundException extends RegistryException implements Serializable

Class org.biojava.directory.RegistryException extends Exception implements Serializable

Package org.biojava.ontology

Class org.biojava.ontology.AlreadyExistsException extends OntologyException implements Serializable

Class org.biojava.ontology.DefaultOps extends Object implements Serializable

Class org.biojava.ontology.InvalidTermException extends OntologyException implements Serializable

Class org.biojava.ontology.Ontology.Impl extends AbstractChangeable implements Serializable

Serialized Fields

### terms

    Map terms

### triples

    Set triples

### subjectTriples

    Map subjectTriples

### objectTriples

    Map objectTriples

### relationTriples

    Map relationTriples

### remoteTerms

    Map remoteTerms

### localRemoteTerms

    Set localRemoteTerms

### name

    String name

### description

    String description

### ops

    OntologyOps ops

Class org.biojava.ontology.OntologyException extends Exception implements Serializable

Class org.biojava.ontology.OntologyTerm.Impl extends AbstractChangeable implements Serializable

Serialized Fields

### ontology

    Ontology ontology

### target

    Ontology target

### synonyms

    Set synonyms

Class org.biojava.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable

Serialized Fields

### ontology

    Ontology ontology

### remoteTerm

    Term remoteTerm

### name

    String name

### synonyms

    Set synonyms

Class org.biojava.ontology.Term.Impl extends AbstractTerm implements Serializable

Serialized Fields

### name

    String name

### description

    String description

### ontology

    Ontology ontology

### annotation

    Annotation annotation

### synonyms

    Set synonyms

Class org.biojava.ontology.Triple.Impl extends Unchangeable implements Serializable

Serialized Fields

### subject

    Term subject

### object

    Term object

### predicate

    Term predicate

### name

    String name

### description

    String description

### synonyms

    Set synonyms

Class org.biojava.ontology.Variable.Impl extends Term.Impl implements Serializable

Package org.biojava.stats.svm

Class org.biojava.stats.svm.CachingKernel extends NestedKernel implements Serializable

Class org.biojava.stats.svm.DiagonalAddKernel extends NestedKernel implements Serializable

Serialized Fields

### posClass

    Set posClass

### negClass

    Set negClass

### lambda

    double lambda

  The scale vactor.

Class org.biojava.stats.svm.DiagonalCachingKernel extends NestedKernel implements Serializable

Class org.biojava.stats.svm.LinearKernel extends Object implements Serializable

Class org.biojava.stats.svm.ListSumKernel extends NestedKernel implements Serializable

Class org.biojava.stats.svm.NestedKernel extends Object implements Serializable

Serialized Fields

### nested

    SVMKernel nested

  The SVMKernel being wrapped.

Class org.biojava.stats.svm.NormalizingKernel extends NestedKernel implements Serializable

Class org.biojava.stats.svm.PolynomialKernel extends NestedKernel implements Serializable

Serialized Fields

### order

    double order

### a

    double a

### c

    double c

Class org.biojava.stats.svm.RadialBaseKernel extends NestedKernel implements Serializable

Serialized Fields

### width

    double width

Class org.biojava.stats.svm.SparseVector extends Object implements Serializable

Serialized Fields

### size

    int size

### keys

    int[] keys

### values

    double[] values

Class org.biojava.stats.svm.SparseVector.NormalizingKernel extends Object implements Serializable

Serialized Fields

### s

    SparseVector s

  The sparse vector that performes the normalization.

Class org.biojava.stats.svm.TrainingEvent extends EventObject implements Serializable

Package org.biojava.stats.svm.tools

Class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier extends JComponent implements Serializable

Serialized Fields

### target

    SVMTarget target

### model

    SVMClassifierModel model

### addPos

    boolean addPos

### posShape

    Shape posShape

### negShape

    Shape negShape

### svPaint

    Paint svPaint

### plainPaint

    Paint plainPaint

### posPaint

    Paint posPaint

### negPaint

    Paint negPaint

### kernel

    SVMKernel kernel

Class org.biojava.stats.svm.tools.SuffixTreeKernel extends Object implements Serializable

Serialized Fields

### depthScaler

    SuffixTreeKernel.DepthScaler depthScaler

  The DepthScaler that will scale each sub-space. This defaults to UniformScaler.

Class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar extends Object implements Serializable

Serialized Fields

### a

    SuffixTreeKernel.DepthScaler a

### b

    SuffixTreeKernel.DepthScaler b

Class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler extends Object implements Serializable

Class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar extends Object implements Serializable

Serialized Fields

### bSet

    BitSet bSet

Class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler extends Object implements Serializable

Package org.biojava.utils

Class org.biojava.utils.AssertionFailure extends AssertionError implements Serializable

Class org.biojava.utils.ChangeEvent extends EventObject implements Serializable

Serialized Fields

### type

    ChangeType type

### change

    Object change

### previous

    Object previous

### chain

    ChangeEvent chain

Class org.biojava.utils.ChangeType extends Object implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()

  Make a placeholder for this object in a serialized stream.

Serialized Fields

### name

    String name

### ourField

    Field ourField

### superType

    ChangeType superType

Class org.biojava.utils.ChangeVetoException extends Exception implements Serializable

Serialized Fields

### change

    ChangeEvent change

Class org.biojava.utils.CommitFailure extends Exception implements Serializable

Class org.biojava.utils.ListTools extends Object implements Serializable

Class org.biojava.utils.ListTools.Doublet extends AbstractList implements Serializable

Serialized Fields

### a

    Object a

### b

    Object b

Class org.biojava.utils.ListTools.Triplet extends AbstractList implements Serializable

Serialized Fields

### a

    Object a

### b

    Object b

### c

    Object c

Class org.biojava.utils.ParseErrorEvent extends EventObject implements Serializable

Serialized Fields

### mMessage

    String mMessage

Class org.biojava.utils.ParserException extends Exception implements Serializable

Serialized Fields

### locator

    String locator

### lineNumber

    int lineNumber

### character

    int character

### line

    String line

Class org.biojava.utils.ProcessTimeoutException extends Exception implements Serializable

Serialized Fields

### returnCode

    int returnCode

Class org.biojava.utils.SingletonList extends AbstractList implements Serializable

Serialized Fields

### obj

    Object obj

Class org.biojava.utils.SmallMap extends AbstractMap implements Serializable

Serialized Fields

### mappings

    Object[] mappings

### numMappings

    int numMappings

Class org.biojava.utils.StaticMemberPlaceHolder extends Object implements Serializable

Serialization Methods

### readResolve

    public Object readResolve()
                       throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Serialized Fields

### className

    String className

### fieldName

    String fieldName

Class org.biojava.utils.TypedProperties extends Properties implements Serializable

Package org.biojava.utils.automata

Class org.biojava.utils.automata.AutomatonException extends BioException implements Serializable

Package org.biojava.utils.candy

Class org.biojava.utils.candy.CandyException extends Exception implements Serializable

Package org.biojava.utils.lsid

Class org.biojava.utils.lsid.LifeScienceIdentifier extends Object implements Serializable

serialVersionUID: 8478038493421763123L

Serialized Fields

### authorityId

    String authorityId

### namespaceId

    String namespaceId

### objectId

    String objectId

### revisionId

    String revisionId

Class org.biojava.utils.lsid.LifeScienceIdentifierParseException extends Exception implements Serializable

Package org.biojava.utils.regex

Class org.biojava.utils.regex.RegexException extends BioException implements Serializable

Package org.biojava.utils.xml

Class org.biojava.utils.xml.AppException extends Exception implements Serializable

Package org.biojavax

Class org.biojavax.CrossReferenceResolutionException extends Exception implements Serializable

Class org.biojavax.EmptyRichAnnotation extends Unchangeable implements Serializable

Serialization Methods

### writeReplace

    private Object writeReplace()
                         throws ObjectStreamException

  Throws:
    `ObjectStreamException`

Serialized Fields

### emptyNotes

    Note[] emptyNotes

Package org.biojavax.bio.db.biosql

Class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter extends Object implements Serializable

Serialized Fields

### isNotNull

    Method isNotNull

Class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter extends Object implements Serializable

Serialized Fields

### isNull

    Method isNull

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### c1

    BioSQLFeatureFilter c1

### c2

    BioSQLFeatureFilter c2

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### name

    String name

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### note

    Note note

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### term

    ComparableTerm term

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### rank

    int rank

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### seqName

    String seqName

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### sourceTerm

    ComparableTerm sourceTerm

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### sourceTermName

    String sourceTermName

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### str

    RichLocation.Strand str

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### typeTerm

    ComparableTerm typeTerm

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### typeTermName

    String typeTermName

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### loc

    RichLocation loc

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter extends Object implements Serializable

Serialized Fields

### not

    Method not

### and

    Method and

### or

    Method or

### eq

    Method eq

### le

    Method le

### ge

    Method ge

### conjunction

    Method conjunction

### disjunction

    Method disjunction

### conjunctAdd

    Method conjunctAdd

### disjunctAdd

    Method disjunctAdd

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### child

    BioSQLFeatureFilter child

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### c1

    BioSQLFeatureFilter c1

### c2

    BioSQLFeatureFilter c2

Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable

Serialized Fields

### loc

    RichLocation loc

Package org.biojavax.bio.seq

Class org.biojavax.bio.seq.RichFeature.Template extends Feature.Template implements Serializable

Serialized Fields

### featureRelationshipSet

    Set featureRelationshipSet

### rankedCrossRefs

    Set rankedCrossRefs

Package org.biojavax.ga.exception

Class org.biojavax.ga.exception.IllegalOrganismException extends Exception implements Serializable

Package org.biojavax.ga.util

Class org.biojavax.ga.util.WeightedSet extends AbstractSet implements Serializable

Serialized Fields

### key2Weight

    HashMap key2Weight

### totalWeight

    double totalWeight

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES