Serialized Form (biojava-legacy 1.9.2 API)

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<K,V> properties
```
- Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - wrapped
```
Annotation wrapped
```
    - mapper
```
PropertyChanger mapper
```
    - properties
```
Map<K,V> properties
```
- Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
```
Map<K,V> 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<E> mergeSet
```
- Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable
  - Serialized Fields
    - parent
```
Annotation parent
```
    - overlay
```
Map<K,V> overlay
```
- Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
```
Map<K,V> 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<K,V> 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
    - queryStart
```
int queryStart
```
      Start position in the query
    - queryEnd
```
int queryEnd
```
      End position in the query
    - nGapsQ
```
int nGapsQ
```
      Number of gaps in query
    - nGapsS
```
int nGapsS
```
      Number of gaps in subject
    - query
```
Sequence query
```
      Length of the query sequence
    - subjectStart
```
int subjectStart
```
      Start position in the subject
    - subjectEnd
```
int subjectEnd
```
      End position in the subject
    - similars
```
int similars
```
      Number of similar symbols
    - subject
```
Sequence subject
```
      The subject sequence.
    - 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
    - labelToSymbolList
```
LinkedHashMap<K,V> labelToSymbolList
```
    - labels
```
List<E> labels
```
    - alphabet
```
Alphabet alphabet
```
    - length
```
int length
```
    - score
```
int score
```
- Class org.biojava.bio.alignment.SubstitutionMatrix extends Object implements Serializable
  - Serialized Fields
    - rowSymbols
```
Map<K,V> rowSymbols
```
    - colSymbols
```
Map<K,V> colSymbols
```
    - matrix
```
short[][] matrix
```
    - min
```
short min
```
      Minimal and maximal entry in this matrix
    - max
```
short max
```
      Minimal and maximal entry in this matrix
    - alphabet
```
FiniteAlphabet alphabet
```
      The alphabet used by this matrix.
    - description
```
String description
```
      Name and description of this matrix.
    - name
```
String name
```
      Name and description of this matrix.
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
    - first
```
Distribution first
```
    - second
```
Distribution second
```
    - alphabet
```
Alphabet alphabet
```
- 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<K,V> c
```
      Deprecated.
- Class org.biojava.bio.dist.SimpleDistributionTrainerContext extends Object implements Serializable
  - Serialized Fields
    - distToTrainer
```
Map<K,V> distToTrainer
```
    - trainers
```
Set<E> 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<K,V> transFrom
```
    - transTo
```
Map<K,V> transTo
```
    - transWeights
```
Map<K,V> 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<E> 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<K,V> transFrom
```
    - transTo
```
Map<K,V> transTo
```
    - transWeights
```
Map<K,V> transWeights
```
Package org.biojava.bio.dp.onehead
- Class org.biojava.bio.dp.onehead.SingleDP extends DP implements Serializable
  - Serialized Fields
    - emissionsProb
```
HashMap<K,V> emissionsProb
```
    - emissionsOdds
```
HashMap<K,V> emissionsOdds
```
    - emissionsNull
```
HashMap<K,V> 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.DPInterpreter extends Object implements Serializable
  - Serialized Fields
    - dp
```
DP dp
```
- Class org.biojava.bio.dp.twohead.EmissionCache extends Object implements Serializable
  - Serialized Fields
    - eMap
```
Map<K,V> eMap
```
    - alpha
```
Alphabet alpha
```
    - states
```
State[] states
```
    - dsi
```
int dsi
```
    - scoreType
```
ScoreType scoreType
```
    - gap
```
Symbol[] gap
```
- 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<K,V> 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<E> 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<K,V> delegates
```
    - delegationCache
```
Map<K,V> delegationCache
```
- Class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer extends MultiLineRenderer implements Serializable
  - Serialized Fields
    - source
```
FeatureSource source
```
    - digestFilter
```
FeatureFilter digestFilter
```
    - laneMap
```
Map<K,V> laneMap
```
    - laneCount
```
int laneCount
```
    - distanceBetween
```
int distanceBetween
```
- 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
    - 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<E> 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<E> flushers
```
- 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<E> fList
```
    - gList
```
List<E> gList
```
- Class org.biojava.bio.gui.sequence.ImageMap.ClientSide extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
    - hotSpots
```
List<E> 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<E> hotSpots
```
- Class org.biojava.bio.gui.sequence.MultiLineRenderer extends AbstractChangeable implements Serializable
  - Serialized Fields
    - renderers
```
List<E> 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 FeatureHolders.
    - recurse
```
boolean recurse
```
      recurse indicates whether the filter should recurse through any subfeatures.
    - subContextCache
```
CacheMap subContextCache
```
    - cacheFlushers
```
Set<E> cacheFlushers
```
    - renderer
```
PairwiseSequenceRenderer renderer
```
- Class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer extends AbstractChangeable implements Serializable
  - Serialized Fields
    - renderers
```
List<E> 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
  
  serialVersionUID:
  
  8749249181471157230L
  - Serialized Fields
    - seqPanels
```
SequencePanel[] seqPanels
```
    - range
```
RangeLocation range
```
    - sequence
```
Sequence sequence
```
    - renderer
```
SequenceRenderer renderer
```
    - scale
```
double scale
```
    - hints
```
RenderingHints hints
```
    - direction
```
int direction
```
    - trackLayout
```
TrackLayout trackLayout
```
    - viewerListeners
```
List<E> viewerListeners
```
    - motionListeners
```
List<E> 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<E> 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
  
  serialVersionUID:
  
  3269477379497205817L
  - 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
```
    - size
```
double size
```
    - forwardRegex
```
String forwardRegex
```
    - reverseRegex
```
String reverseRegex
```
    - summary
```
String summary
```
    - prototype
```
RestrictionEnzyme prototype
```
- 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
    - 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<E> 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<T> 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<E> featureHolders
```
- Class org.biojava.bio.seq.RemoteFeature.Template extends StrandedFeature.Template implements Serializable
  - Serialized Fields
    - regions
```
List<E> regions
```
    - resolver
```
RemoteFeature.Resolver resolver
```
- Class org.biojava.bio.seq.SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable
  - Serialized Fields
    - features
```
List<E> features
```
      The child features.
    - schema
```
FeatureFilter schema
```
- Class org.biojava.bio.seq.SimpleFeatureRealizer extends Object implements Serializable
  - Serialized Fields
    - templateToImpl
```
List<E> 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<K,V> 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<E> 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<E> 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
  
  serialVersionUID:
  
  -791305118810523245L
  - 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
  
  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<E> 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
    - 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.AlternateTokenization extends Unchangeable implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet alphabet
```
    - symbolsToStrings
```
Map<K,V> symbolsToStrings
```
    - caseSensitive
```
boolean caseSensitive
```
    - initiated
```
boolean initiated
```
    - width
```
int width
```
- Class org.biojava.bio.seq.io.CharacterTokenization extends Unchangeable implements Serializable
  - Serialized Fields
    - alphabet
```
Alphabet alphabet
```
    - symbolsToCharacters
```
Map<K,V> symbolsToCharacters
```
    - charactersToSymbols
```
Map<K,V> charactersToSymbols
```
    - caseSensitive
```
boolean caseSensitive
```
- Class org.biojava.bio.seq.io.CrossProductTokenization extends WordTokenization implements Serializable
  - Serialized Fields
    - subTokenizations
```
List<E> 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<E> 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<E> 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<E> 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<K,V> 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.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
    - tokenizationsByName
```
Map<K,V> tokenizationsByName
```
    - ambCache
```
Map<K,V> ambCache
```
    - registered
```
boolean registered
```
- 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<E> 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<E> 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.SimpleAlphabet extends AbstractAlphabet implements Serializable
  
  serialVersionUID:
  
  216254146L
  - Serialized Fields
    - name
```
String name
```
    - annotation
```
Annotation annotation
```
    - symbols
```
Set<E> symbols
```
    - alphabets
```
List<E> 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
```
List<E> 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.SimpleGeneticCodeTable extends SimpleManyToOneTranslationTable implements Serializable
  - Serialized Fields
    - table_num
```
int table_num
```
    - description
```
String description
```
- Class org.biojava.bio.symbol.SimpleManyToOneTranslationTable extends AbstractManyToOneTranslationTable implements Serializable
  - Serialized Fields
    - transMap
```
Map<K,V> transMap
```
    - revMap
```
Map<K,V> revMap
```
    - source
```
FiniteAlphabet source
```
    - target
```
Alphabet target
```
- Class org.biojava.bio.symbol.SimpleReversibleTranslationTable extends AbstractReversibleTranslationTable implements Serializable
  - Serialized Fields
    - transMap
```
Map<K,V> transMap
```
    - revMap
```
Map<K,V> 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<K,V> transMap
```
    - source
```
FiniteAlphabet source
```
    - target
```
Alphabet target
```
- Class org.biojava.bio.symbol.SingletonAlphabet extends AbstractAlphabet implements Serializable
  - Serialized Fields
    - sym
```
AtomicSymbol sym
```
    - alphabets
```
List<E> 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<E> 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
  
  serialVersionUID:
  
  -8064461497813727957L
  - Serialized Fields
    - terms
```
Map<K,V> terms
```
    - triples
```
Set<E> triples
```
    - subjectTriples
```
Map<K,V> subjectTriples
```
    - objectTriples
```
Map<K,V> objectTriples
```
    - relationTriples
```
Map<K,V> relationTriples
```
    - remoteTerms
```
Map<K,V> remoteTerms
```
    - localRemoteTerms
```
Set<E> 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<E> synonyms
```
- Class org.biojava.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  922700041939183676L
  - Serialized Fields
    - ontology
```
Ontology ontology
```
    - remoteTerm
```
Term remoteTerm
```
    - name
```
String name
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.ontology.Term.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  6561668917514377417L
  - Serialized Fields
    - name
```
String name
```
    - ontology
```
Ontology ontology
```
    - annotation
```
Annotation annotation
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.ontology.Triple.Impl extends Unchangeable implements Serializable
  
  serialVersionUID:
  
  3807331980372839221L
  - Serialized Fields
    - subject
```
Term subject
```
    - object
```
Term object
```
    - predicate
```
Term predicate
```
    - name
```
String name
```
    - description
```
String description
```
    - synonyms
```
Set<E> 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<E> posClass
```
    - negClass
```
Set<E> 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 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
    - 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.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<K,V> param
```
- Class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - out
```
HashMap<K,V> out
```
    - outFormat
```
String outFormat
```
    - alignFormat
```
String alignFormat
```
    - descNumbers
```
int descNumbers
```
    - alignNumbers
```
int alignNumbers
```
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<E> featureRelationshipSet
```
    - rankedCrossRefs
```
Set<E> 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<K,V> key2Weight
```
    - totalWeight
```
double totalWeight
```

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

changer

properties

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

Serialized Fields

wrapped

mapper

properties

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

Serialized Fields

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

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

Serialized Fields

parent

overlay

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

Serialized Fields

properties

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

Serialized Fields

properties

Package org.biojava.bio.alignment

Class org.biojava.bio.alignment.AlignmentPair extends SimpleAlignment implements Serializable

Serialized Fields

identicals

queryStart

queryEnd

nGapsQ

nGapsS

query

subjectStart

subjectEnd

similars

subject

subMatrix

time

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

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

Serialized Fields

labelToSymbolList

labels

alphabet

length

score

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

Serialized Fields

rowSymbols

colSymbols

matrix

min

max

alphabet

description

name

Package org.biojava.bio.annodb

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

Serialized Fields

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

Serialized Fields

alphabet

firstA

lastA

nullModel