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

    • changer

      ChangeTable changer

    • properties

      Map properties

    • wrapped

      Annotation wrapped

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

  • Serialized Fields

    • mapper

      PropertyChanger mapper

    • properties

      Map properties

    • wrapped

      Annotation wrapped

• 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

    • overlay

      Map overlay

    • parent

      Annotation parent

• 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.AlignmentPair extends SimpleAlignment implements Serializable

  serialVersionUID:

  -8834131912021612261L

  • Serialized Fields

    • identicals

      int identicals

      Number of identical elements in both sequences

    • nGapsQ

      int nGapsQ

      Number of gaps in query

    • nGapsS

      int nGapsS

      Number of gaps in subject

    • query

      Sequence query

      Length of the query sequence

    • queryEnd

      int queryEnd

      End position in the query

    • queryStart

      int queryStart

      Start position in the query

    • similars

      int similars

      Number of similar symbols

    • subject

      Sequence subject

      The subject sequence.

    • subjectEnd

      int subjectEnd

      End position in the subject

    • subjectStart

      int subjectStart

      Start position in the subject

    • subMatrix

      SubstitutionMatrix subMatrix

      Reference to the underlying substitution matrix of this alignment.

    • time

      long time

      Time consumption to create this alignment.

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

  serialVersionUID:

  4662428071284597336L

• Class org.biojava.bio.alignment.SimpleAlignment extends AbstractSymbolList implements Serializable

  serialVersionUID:

  -1760075176220928440L

  • Serialized Fields

    • alphabet

      Alphabet alphabet

    • labels

      List<String> labels

    • labelToSymbolList

      LinkedHashMap<String,​SymbolList> labelToSymbolList

    • length

      int length

    • score

      int score

• Class org.biojava.bio.alignment.SubstitutionMatrix extends Object implements Serializable

  • Serialized Fields

    • alphabet

      FiniteAlphabet alphabet

      The alphabet used by this matrix.

    • colSymbols

      Map<Symbol,​Integer> colSymbols

    • description

      String description

      Name and description of this matrix.

    • matrix

      short[][] matrix

    • max

      short max

      Minimal and maximal entry in this matrix

    • min

      short min

      Minimal and maximal entry in this matrix

    • name

      String name

      Name and description of this matrix.

    • rowSymbols

      Map<Symbol,​Integer> rowSymbols

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

    • alpha

      FiniteAlphabet alpha

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

  • Serialized Fields

    • alphabet

      Alphabet alphabet

    • first

      Distribution first

    • second

      Distribution second

• 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

    • alpha

      FiniteAlphabet alpha

    • nullModel

      Distribution nullModel

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

  • Serialized Fields

    • c

      Map c

      Deprecated.

    • dis

      Distribution dis

      Deprecated.

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

  • Serialized Fields

    • distToTrainer

      Map distToTrainer

    • nullModelWeight

      double nullModelWeight

    • trainers

      Set trainers

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

  • Serialized Fields

    • delegate

      Distribution delegate

    • other

      Distribution other

    • 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

    • index

      int index

    • sym

      SymbolList sym

• 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.

    • deleteStates

      DotState[] deleteStates

      Delete states array.

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

    • insertStates

      EmissionState[] insertStates

      Insert states array.

      From 0 .. columns().

    • matchStates

      EmissionState[] matchStates

      Match states array.

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

• 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

    • advance

      int[] advance

    • ann

      Annotation ann

    • dis

      Distribution dis

    • matches

      Alphabet matches

    • name

      String name

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

  serialVersionUID:

  -3043028839927615753L

  • Serialized Fields

    • emissionAlpha

      Alphabet emissionAlpha

    • magicalState

      MagicalState magicalState

    • stateAlpha

      FiniteAlphabet stateAlpha

    • 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

    • delegate

      Alignment delegate

    • score

      double score

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

  serialVersionUID:

  73394340224964858L

  • Serialized Fields

    • alpha

      Alphabet alpha

    • columns

      Distribution[] columns

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

  • Serialized Fields

    • from

      State from

    • to

      State to

    • trainer

      TransitionTrainer trainer

• 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

    • scoreType

      ScoreType scoreType

    • threshold

      double threshold

    • wmID

      String wmID

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

  • Serialized Fields

    • magicalState

      MagicalState magicalState

    • stateAlpha

      FiniteAlphabet stateAlpha

    • states

      EmissionState[] states

    • transFrom

      Map transFrom

    • transTo

      Map transTo

    • transWeights

      Map transWeights

    • wm

      WeightMatrix wm

Package org.biojava.bio.dp.onehead

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

  • Serialized Fields

    • emissionsNull

      HashMap emissionsNull

    • emissionsOdds

      HashMap emissionsOdds

    • emissionsProb

      HashMap emissionsProb

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

  • Serialized Fields

    • model

      MarkovModel model

    • score

      double score

    • scores

      double[][] scores

    • states

      State[] states

    • symList

      SymbolList[] symList

Package org.biojava.bio.dp.twohead

• Class org.biojava.bio.dp.twohead.DPInterpreter extends Object implements Serializable

  • Serialized Fields

    • dp

      DP dp

• Class org.biojava.bio.dp.twohead.EmissionCache extends Object implements Serializable

  • Serialized Fields

    • alpha

      Alphabet alpha

    • dsi

      int dsi

    • eMap

      Map eMap

    • gap

      Symbol[] gap

    • scoreType

      ScoreType scoreType

    • states

      State[] states

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

  • Serialized Fields

    • finalScore

      double finalScore

    • model

      MarkovModel model

    • scores

      double[][][] scores

    • seqs

      SymbolList[] seqs

    • states

      State[] states

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

  • Serialized Fields

    • ccFactory

      CellCalculatorFactory ccFactory

    • emissionCache

      HashMap emissionCache

Package org.biojava.bio.gui

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

  • Serialized Fields

    • blockPainter

      BlockPainter blockPainter

    • dist

      Distribution dist

      The dist to render.

    • logoPainter

      LogoPainter logoPainter

      The logoPainter property.

    • renderingHints

      RenderingHints renderingHints

    • scaleByInformation

      boolean scaleByInformation

      The information/plain property

    • style

      SymbolStyle style

      The style property.

• 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

    • beadFill

      Paint beadFill

    • beadOutline

      Paint beadOutline

    • beadStroke

      Stroke beadStroke

    • delegates

      Map delegates

    • delegationCache

      Map delegationCache

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

  • Serialized Fields

    • digestFilter

      FeatureFilter digestFilter

    • distanceBetween

      int distanceBetween

    • laneCount

      int laneCount

    • laneMap

      Map laneMap

    • source

      FeatureSource source

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

  • Serialized Fields

    • label

      String label

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

  • Serialized Fields

    • imageMap

      ImageMap imageMap

    • renderer

      BasicFeatureRenderer renderer

    • urlFactory

      URLFactory urlFactory

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

  • Serialized Fields

    • contextCache

      CacheMap contextCache

    • flushers

      Set flushers

    • leadingPixles

      int leadingPixles

    • trailingPixles

      int trailingPixles

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

  • Serialized Fields

    • ctxt

      CircularRendererContext ctxt

    • offset

      double offset

    • radius

      double radius

    • renderer

      CircularRenderer renderer

    • symList

      SymbolList symList

• 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

    • contextCache

      CacheMap contextCache

    • filter

      FeatureFilter filter

    • flushers

      Set flushers

    • recurse

      boolean recurse

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

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

  serialVersionUID:

  7005846487574725181L

  • Serialized Fields

    • depth

      double depth

    • fList

      List<FeatureFilter> fList

    • gList

      List<Glyph> gList

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

  • Serialized Fields

    • hotSpots

      List hotSpots

    • name

      String name

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

  • Serialized Fields

    • coordinates

      Integer[] coordinates

    • type

      String type

    • url

      URL url

    • 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

    • cacheFlushers

      Set cacheFlushers

    • filter

      FeatureFilter filter

      filter is the filter applied to both FeatureHolders.

    • recurse

      boolean recurse

      recurse indicates whether the filter should recurse through any subfeatures.

    • renderer

      PairwiseSequenceRenderer renderer

    • subContextCache

      CacheMap subContextCache

• 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

    • direction

      int direction

    • hints

      RenderingHints hints

    • layoutListener

      ChangeListener layoutListener

    • leadingBorder

      SequenceRenderContext.Border leadingBorder

    • mouseListener

      MouseListener mouseListener

    • mouseMotionListener

      MouseMotionListener mouseMotionListener

    • propertyListener

      PropertyChangeListener propertyListener

    • renderer

      PairwiseSequenceRenderer renderer

    • repaintListener

      ChangeListener repaintListener

    • scale

      double scale

    • secDirection

      int secDirection

    • secSequence

      Sequence secSequence

    • secTranslation

      int secTranslation

    • sequence

      Sequence sequence

    • svmSupport

      SequenceViewerMotionSupport svmSupport

    • svSupport

      SequenceViewerSupport svSupport

    • trailingBorder

      SequenceRenderContext.Border trailingBorder

    • translation

      int translation

• 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

    • imageMap

      ImageMap imageMap

    • renderer

      RectangularBeadRenderer renderer

    • urlFactory

      URLFactory urlFactory

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

  • Serialized Fields

    • arcHeight

      double arcHeight

    • arcWidth

      double arcWidth

    • rect

      RoundRectangle2D rect

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

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

  • Serialized Fields

    • direction

      int direction

    • hints

      RenderingHints hints

    • layoutListener

      ChangeListener layoutListener

    • leadingBorder

      SequenceRenderContext.Border leadingBorder

    • mouseListener

      MouseListener mouseListener

    • mouseMotionListener

      MouseMotionListener mouseMotionListener

    • pixelOffset

      double pixelOffset

    • range

      RangeLocation range

    • renderer

      SequenceRenderer renderer

    • repaintListener

      ChangeListener repaintListener

    • scale

      double scale

    • sequence

      SymbolList sequence

    • svmSupport

      SequenceViewerMotionSupport svmSupport

    • svSupport

      SequenceViewerSupport svSupport

    • theMonitor

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

    • trailingBorder

      SequenceRenderContext.Border trailingBorder

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

  • Serialized Fields

    • alignment

      int alignment

    • pcs

      PropertyChangeSupport pcs

    • size

      double size

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

  serialVersionUID:

  8749249181471157230L

  • Serialized Fields

    • direction

      int direction

    • hints

      RenderingHints hints

    • motionListeners

      List<SequenceViewerMotionListener> motionListeners

    • range

      RangeLocation range

    • renderer

      SequenceRenderer renderer

    • scale

      double scale

    • seqPanels

      SequencePanel[] seqPanels

    • sequence

      Sequence sequence

    • trackLayout

      TrackLayout trackLayout

    • viewerListeners

      List<SequenceViewerListener> viewerListeners

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

  • Serialized Fields

    • acrossDim

      double acrossDim

      Deprecated.

    • alongDim

      double alongDim

      Deprecated.

    • direction

      int direction

      Deprecated.

    • layoutListener

      ChangeListener layoutListener

      Deprecated.

    • leadingBorder

      SequenceRenderContext.Border leadingBorder

      Deprecated.

    • lines

      int lines

      Deprecated.

    • mouseListener

      MouseListener mouseListener

      Deprecated.

    • mouseMotionListener

      MouseMotionListener mouseMotionListener

      Deprecated.

    • offsets

      double[] offsets

      Deprecated.

    • realLines

      int realLines

      Deprecated.

    • renderer

      SequenceRenderer renderer

      Deprecated.

    • renderingHints

      RenderingHints renderingHints

      Deprecated.

    • repaintListener

      ChangeListener repaintListener

      Deprecated.

    • scale

      double scale

      Deprecated.

    • sequence

      Sequence sequence

      Deprecated.

    • spacer

      int spacer

      Deprecated.

    • svmSupport

      SequenceViewerMotionSupport svmSupport

      Deprecated.

    • svSupport

      SequenceViewerSupport svSupport

      Deprecated.

    • symbolsPerLine

      int symbolsPerLine

      Deprecated.

    • theMonitor

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

      Deprecated.

    • trailingBorder

      SequenceRenderContext.Border trailingBorder

      Deprecated.

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

  • Serialized Fields

    • alignment

      int alignment

    • pcs

      PropertyChangeSupport pcs

    • size

      double size

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

  • Serialized Fields

    • alignment

      int alignment

    • size

      double size

• 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

    • mouseEvent

      MouseEvent mouseEvent

    • path

      List path

    • pos

      int pos

    • target

      Object target

• 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

  serialVersionUID:

  3269477379497205817L

  • Serialized Fields

    • direction

      int direction

    • hints

      RenderingHints hints

    • layoutListener

      ChangeListener layoutListener

    • leadingBorder

      SequenceRenderContext.Border leadingBorder

    • mouseListener

      MouseListener mouseListener

    • mouseMotionListener

      MouseMotionListener mouseMotionListener

    • propertyListener

      PropertyChangeListener propertyListener

    • renderer

      SequenceRenderer renderer

    • rendererBorders

      double rendererBorders

    • repaintListener

      ChangeListener repaintListener

    • scale

      double scale

    • sequence

      SymbolList sequence

    • svmSupport

      SequenceViewerMotionSupport svmSupport

    • svSupport

      SequenceViewerSupport svSupport

    • trailingBorder

      SequenceRenderContext.Border trailingBorder

    • translation

      int translation

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

  • Serialized Fields

    • blockDepth

      double blockDepth

    • fill

      Paint fill

    • outline

      Paint outline

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

  • Serialized Fields

    • imageMap

      ImageMap imageMap

    • renderer

      ZiggyFeatureRenderer renderer

    • urlFactory

      URLFactory urlFactory

Package org.biojava.bio.molbio

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

  • Serialized Fields

    • cutType

      int cutType

    • dsCutPositions

      int[] dsCutPositions

    • forwardRegex

      String forwardRegex

    • name

      String name

    • prototype

      RestrictionEnzyme prototype

    • reverseRegex

      String reverseRegex

    • site

      SymbolList site

    • size

      double size

    • summary

      String summary

    • usCutPositions

      int[] usCutPositions

• 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.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

    • c

      EmissionState c

    • hmmState

      ModelInState hmmState

    • j

      EmissionState j

    • n

      EmissionState n

• 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

    • lineWidth

      int lineWidth

      The line width for output.

    • mListeners

      Vector mListeners

• 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

    • endoProtease

      boolean endoProtease

    • name

      String name

    • notCleaveResidues

      SymbolList notCleaveResidues

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

    • componentLocation

      Location componentLocation

    • componentSequence

      Sequence componentSequence

    • componentSequenceName

      String componentSequenceName

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

  • Serialized Fields

    • annotation

      Annotation annotation

    • location

      Location location

    • source

      String source

    • sourceTerm

      Term sourceTerm

    • type

      String type

    • typeTerm

      Term typeTerm

• 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

    • hashCode

      int hashCode

    • maxScore

      double maxScore

    • minScore

      double minScore

    • score

      double score

• 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

    • frame

      int frame

    • text

      String text

• 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

    • fallBack

      FeatureRealizer fallBack

    • templateToImpl

      List templateToImpl

• 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

    • token

      char token

    • value

      int value

• 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

    • annotator

      SequenceAnnotator annotator

    • parent

      SequenceDB parent

• 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

    • idMaker

      IDMaker idMaker

      An object to extract an ID for a sequence.

    • name

      String name

      The name of this sequence database.

    • sequenceByID

      Map sequenceByID

      The sequence-by-id map.

• 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

    • files

      Set files

    • format

      SequenceFormat format

    • indexFile

      File indexFile

    • name

      String name

    • sbFactory

      SequenceBuilderFactory sbFactory

    • seqFileIndex

      File[] seqFileIndex

    • storeFile

      File storeFile

    • 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

    • alignment

      Alignment alignment

      alignment Alignment field.

    • score

      double score

      score of the search which produced the alignment.

    • sibling

      SimilarityPairFeature sibling

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

Package org.biojava.bio.seq.impl

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

  • Serialized Fields

    • origSeq

      Sequence origSeq

    • pfh

      ProjectedFeatureHolder pfh

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

  • Serialized Fields

    • annotation

      Annotation annotation

      The annotation object. This is lazily instantiated.

    • 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.

    • parent

      FeatureHolder parent

      Our parent FeatureHolder.

    • source

      String source

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

    • sourceTerm

      Term sourceTerm

    • type

      String type

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

    • typeTerm

      Term typeTerm

• 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

  serialVersionUID:

  -791305118810523245L

  • Serialized Fields

    • createOnUnderlying

      boolean createOnUnderlying

    • features

      MergeFeatureHolder features

    • localFeatures

      SimpleFeatureHolder localFeatures

    • projectedFeatures

      FeatureHolder projectedFeatures

    • sequence

      Sequence sequence

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

  serialVersionUID:

  8878073952684354286L

• 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

  serialVersionUID:

  -8681680737943980721L

  • Serialized Fields

    • annotation

      Annotation annotation

    • featureHolder

      SimpleFeatureHolder featureHolder

    • name

      String name

    • symList

      SymbolList symList

      Delegate SymbolList.

    • urn

      String urn

• 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

    • alignment

      Alignment alignment

    • score

      double score

    • sibling

      SimilarityPairFeature sibling

• 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

    • annotation

      Annotation annotation

    • name

      String name

    • parent

      Sequence parent

    • parentLocation

      RangeLocation parentLocation

    • symbols

      SymbolList symbols

    • uri

      String uri

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

  • Serialized Fields

    • clippingFilter

      FeatureFilter clippingFilter

    • parentLocation

      RangeLocation parentLocation

    • remoteLocationFilter

      FeatureFilter remoteLocationFilter

• 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

    • addedFeatures

      SimpleFeatureHolder addedFeatures

    • anno

      Annotation anno

      Our annotation.

    • exposedFeatures

      MergeFeatureHolder exposedFeatures

      FeatureHolder support

    • name

      String name

      IDs

    • seqDelegate

      Sequence seqDelegate

      Delegate Sequence.

    • urn

      String urn

Package org.biojava.bio.seq.io

• Class org.biojava.bio.seq.io.AlternateTokenization extends Unchangeable implements Serializable

  • Serialized Fields

    • alphabet

      Alphabet alphabet

    • caseSensitive

      boolean caseSensitive

    • initiated

      boolean initiated

    • symbolsToStrings

      Map symbolsToStrings

    • width

      int width

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

  • Serialized Fields

    • alphabet

      Alphabet alphabet

    • caseSensitive

      boolean caseSensitive

    • charactersToSymbols

      Map charactersToSymbols

    • symbolsToCharacters

      Map symbolsToCharacters

• 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

    • lineWidth

      int lineWidth

      Deprecated.

      The line width for output.

    • mListeners

      Vector mListeners

      Deprecated.

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

  • Serialized Fields

    • elideSymbols

      boolean elideSymbols

      Deprecated.

    • mListeners

      Vector mListeners

      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_handler

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

      Deprecated.

    • m_parsed

      boolean m_parsed

      Deprecated.

    • m_sequenceIndex

      int m_sequenceIndex

      Deprecated.

    • m_xmlParser

      SAXParser m_xmlParser

      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

    • commonNameKey

      String commonNameKey

    • delegateFactory

      SequenceBuilderFactory delegateFactory

    • ncbiTaxonKey

      String ncbiTaxonKey

    • sciNameKey

      String sciNameKey

    • 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

    • oppositeStrand

      boolean oppositeStrand

    • translation

      int translation

Package org.biojava.bio.symbol

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

  serialVersionUID:

  -3043128839927615753L

  • 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

    • ambCache

      Map ambCache

    • registered

      boolean registered

    • tokenizationsByName

      Map tokenizationsByName

• 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

    • alpha

      Alphabet alpha

    • chunks

      SymbolList[] chunks

    • chunkSize

      int chunkSize

    • 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

    • matches

      Alphabet matches

    • maxVal

      double maxVal

    • minVal

      double minVal

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

  • Serialized Fields

    • matches

      Alphabet matches

    • val

      double val

• 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

    • max

      double max

    • min

      double min

    • name

      String name

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

  • Serialized Fields

    • alpha

      Alphabet alpha

    • length

      int length

    • sym

      Symbol sym

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

  • Serialized Fields

    • length

      int length

    • pos

      int pos

    • props

      Map<String,​Object> props

    • replacement

      SymbolList replacement

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

  • Serialized Fields

    • annotation

      Annotation annotation

    • name

      String name

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

  • Serialized Fields

    • innerMax

      int innerMax

    • innerMin

      int innerMin

    • mIsMaxFuzzy

      boolean mIsMaxFuzzy

    • mIsMinFuzzy

      boolean mIsMinFuzzy

    • outerMax

      int outerMax

    • outerMin

      int outerMin

    • resolver

      FuzzyLocation.RangeResolver resolver

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

  • Serialized Fields

    • max

      int max

    • min

      int min

    • 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

    • matches

      Alphabet matches

    • val

      int val

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

  • Serialized Fields

    • max

      int max

    • min

      int min

    • 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

    • currentMax

      int currentMax

    • currentMin

      int currentMin

    • currentWord

      long currentWord

    • length

      int length

    • mask

      byte mask

    • packing

      Packing packing

    • syms

      long[] syms

    • symsPerElement

      byte symsPerElement

    • 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

    • max

      int max

      The maximum point contained.

    • min

      int min

      The minimum point contained.

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

  serialVersionUID:

  216254146L

  • Serialized Fields

    • alphabets

      List alphabets

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

    • annotation

      Annotation annotation

    • name

      String name

    • symbols

      Set symbols

• 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.

    • blocks

      List<SimpleGappedSymbolList.Block> 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.

    • source

      SymbolList source

      The SymbolList to view.

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

  serialVersionUID:

  4090888450309921439L

  • Serialized Fields

    • sourceEnd

      int sourceEnd

    • sourceStart

      int sourceStart

    • viewEnd

      int viewEnd

    • viewStart

      int viewStart

• Class org.biojava.bio.symbol.SimpleGeneticCodeTable extends SimpleManyToOneTranslationTable implements Serializable

  • Serialized Fields

    • description

      String description

    • table_num

      int table_num

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

  • Serialized Fields

    • revMap

      Map revMap

    • source

      FiniteAlphabet source

    • target

      Alphabet target

    • transMap

      Map transMap

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

  • Serialized Fields

    • revMap

      Map revMap

    • source

      FiniteAlphabet source

    • target

      Alphabet target

    • transMap

      Map transMap

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

  serialVersionUID:

  -9015317520644706924L

  • Serialized Fields

    • alphabet

      Alphabet alphabet

    • isView

      boolean isView

    • length

      int length

    • referenceSymbolList

      SymbolList referenceSymbolList

    • symbols

      Symbol[] symbols

    • viewOffset

      int viewOffset

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

  • Serialized Fields

    • source

      FiniteAlphabet source

    • target

      Alphabet target

    • transMap

      Map transMap

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

  • Serialized Fields

    • alphabets

      List alphabets

    • sym

      AtomicSymbol sym

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

  • Serialized Fields

    • alphabet

      FiniteAlphabet alphabet

    • counts

      List counts

    • indexer

      AlphabetIndex indexer

    • root

      SuffixTree.SuffixNode root

• 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

  serialVersionUID:

  -8064461497813727957L

  • Serialized Fields

    • description

      String description

    • localRemoteTerms

      Set<Term> localRemoteTerms

    • name

      String name

    • objectTriples

      Map<Term,​Set<Triple>> objectTriples

    • ops

      OntologyOps ops

    • relationTriples

      Map<Term,​Set<Triple>> relationTriples

    • remoteTerms

      Map<Term,​RemoteTerm> remoteTerms

    • subjectTriples

      Map<Term,​Set<Triple>> subjectTriples

    • terms

      Map<String,​Term> terms

    • triples

      Set<Triple> triples

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

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

  • Serialized Fields

    • ontology

      Ontology ontology

    • synonyms

      Set synonyms

    • target

      Ontology target

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

  serialVersionUID:

  922700041939183676L

  • Serialized Fields

    • name

      String name

    • ontology

      Ontology ontology

    • remoteTerm

      Term remoteTerm

    • synonyms

      Set synonyms

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

  serialVersionUID:

  6561668917514377417L

  • Serialized Fields

    • annotation

      Annotation annotation

    • name

      String name

    • ontology

      Ontology ontology

    • synonyms

      Set<Object> synonyms

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

  serialVersionUID:

  3807331980372839221L

  • Serialized Fields

    • description

      String description

    • name

      String name

    • object

      Term object

    • predicate

      Term predicate

    • subject

      Term subject

    • synonyms

      Set<Object> 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

    • lambda

      double lambda

      The scale vactor.

    • negClass

      Set negClass

    • posClass

      Set posClass

• 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

    • a

      double a

    • c

      double c

    • order

      double order

• 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

    • keys

      int[] keys

    • size

      int size

    • 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

    • addPos

      boolean addPos

    • kernel

      SVMKernel kernel

    • model

      SVMClassifierModel model

    • negPaint

      Paint negPaint

    • negShape

      Shape negShape

    • plainPaint

      Paint plainPaint

    • posPaint

      Paint posPaint

    • posShape

      Shape posShape

    • svPaint

      Paint svPaint

    • target

      SVMTarget target

• 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

    • chain

      ChangeEvent chain

    • change

      Object change

    • previous

      Object previous

    • type

      ChangeType type

• 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 RuntimeException 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

    • character

      int character

    • line

      String line

    • lineNumber

      int lineNumber

    • locator

      String locator

• 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.bytecode

• Class org.biojava.utils.bytecode.CodeException extends Exception 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.alignment

Package org.biojavax.bio.alignment.blast

• Class org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • param

      HashMap<String,​String> param

• Class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties extends Object implements Serializable

  serialVersionUID:

  1L

  • Serialized Fields

    • alignFormat

      String alignFormat

    • alignNumbers

      int alignNumbers

    • descNumbers

      int descNumbers

    • out

      HashMap<String,​String> out

    • outFormat

      String outFormat

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

    • and

      Method and

    • conjunctAdd

      Method conjunctAdd

    • conjunction

      Method conjunction

    • disjunctAdd

      Method disjunctAdd

    • disjunction

      Method disjunction

    • eq

      Method eq

    • ge

      Method ge

    • le

      Method le

    • not

      Method not

    • or

      Method or

• 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