Serialized Form
-
Package org.biojava.bibliography
-
Exception Class org.biojava.bibliography.BibRefException
class BibRefException extends Exception implements Serializable
-
-
Package org.biojava.bio
-
Class org.biojava.bio.AbstractAnnotation
class AbstractAnnotation extends AbstractChangeable implements Serializable -
Class org.biojava.bio.AnnotationChanger
class AnnotationChanger extends AbstractAnnotation implements Serializable-
Serialized Fields
-
changer
ChangeTable changer
-
properties
Map properties
-
wrapped
Annotation wrapped
-
-
-
Class org.biojava.bio.AnnotationRenamer
class AnnotationRenamer extends AbstractAnnotation implements Serializable-
Serialized Fields
-
mapper
PropertyChanger mapper
-
properties
Map properties
-
wrapped
Annotation wrapped
-
-
-
Class org.biojava.bio.BeanAsAnnotation
class BeanAsAnnotation extends AbstractAnnotation implements Serializable-
Serialized Fields
-
properties
Map properties
-
-
-
Exception Class org.biojava.bio.BioError
class BioError extends Error implements Serializable -
Exception Class org.biojava.bio.BioException
class BioException extends Exception implements Serializable -
Exception Class org.biojava.bio.BioRuntimeException
class BioRuntimeException extends RuntimeException implements Serializable -
Class org.biojava.bio.MergeAnnotation
class MergeAnnotation extends AbstractChangeable implements Serializable-
Serialized Fields
-
mergeSet
List mergeSet
-
-
-
Class org.biojava.bio.OverlayAnnotation
class OverlayAnnotation extends AbstractChangeable implements Serializable-
Serialized Fields
-
overlay
Map overlay
-
parent
Annotation parent
-
-
-
Class org.biojava.bio.SimpleAnnotation
class 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
class SmallAnnotation extends AbstractAnnotation implements Serializable-
Serialized Fields
-
properties
Map properties
-
-
-
-
Package org.biojava.bio.alignment
-
Class org.biojava.bio.alignment.AlignmentPair
class 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.
-
-
Exception Class org.biojava.bio.alignment.IllegalAlignmentEditException
class IllegalAlignmentEditException extends BioRuntimeException implements Serializable- serialVersionUID:
- 4662428071284597336L
-
Class org.biojava.bio.alignment.SimpleAlignment
class 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
class 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
class StaticMethodRPFactory extends Object implements Serializable-
Serialized Fields
-
method
Method method
-
-
-
-
Package org.biojava.bio.chromatogram
-
Exception Class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException
class UnsupportedChromatogramFormatException extends BioException implements Serializable
-
-
Package org.biojava.bio.dist
-
Class org.biojava.bio.dist.AbstractOrderNDistribution
class 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
class DefaultDistributionFactory extends Object implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
ObjectStreamException
-
-
-
Class org.biojava.bio.dist.GapDistribution
class GapDistribution extends Unchangeable implements Serializable- serialVersionUID:
- 88622317L
-
Serialized Fields
-
alpha
Alphabet alpha
-
-
Class org.biojava.bio.dist.IndexedCount
class IndexedCount extends AbstractChangeable implements Serializable- serialVersionUID:
- -1764931829553447679L
-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
alpha
FiniteAlphabet alpha
-
-
Class org.biojava.bio.dist.PairDistribution
class PairDistribution extends AbstractChangeable implements Serializable-
Serialized Fields
-
alphabet
Alphabet alphabet
-
first
Distribution first
-
second
Distribution second
-
-
-
Class org.biojava.bio.dist.SimpleDistribution
class SimpleDistribution extends AbstractDistribution implements Serializable- serialVersionUID:
- 7252850540926095728L
-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
writeObject
- Throws:
IOException
-
-
Serialized Fields
-
alpha
FiniteAlphabet alpha
-
nullModel
Distribution nullModel
-
-
Class org.biojava.bio.dist.SimpleDistributionTrainer
class SimpleDistributionTrainer extends Object implements Serializable-
Serialized Fields
-
c
Map c
Deprecated. -
dis
Distribution dis
Deprecated.
-
-
-
Class org.biojava.bio.dist.SimpleDistributionTrainerContext
class SimpleDistributionTrainerContext extends Object implements Serializable -
Class org.biojava.bio.dist.TranslatedDistribution
class TranslatedDistribution extends AbstractChangeable implements Serializable-
Serialized Fields
-
delegate
Distribution delegate
-
other
Distribution other
-
table
ReversibleTranslationTable table
-
-
-
Class org.biojava.bio.dist.UniformDistribution
class UniformDistribution extends AbstractDistribution implements Serializable- serialVersionUID:
- 88454038L
-
Serialized Fields
-
alphabet
FiniteAlphabet alphabet
-
nullModel
Distribution nullModel
-
-
Class org.biojava.bio.dist.UntrainableDistribution
class UntrainableDistribution extends SimpleDistribution implements Serializable
-
-
Package org.biojava.bio.dp
-
Class org.biojava.bio.dp.BaumWelchSampler
class BaumWelchSampler extends AbstractTrainer implements Serializable -
Class org.biojava.bio.dp.BaumWelchTrainer
class BaumWelchTrainer extends AbstractTrainer implements Serializable -
Class org.biojava.bio.dp.DP.ReverseIterator
class ReverseIterator extends Object implements Serializable-
Serialized Fields
-
index
int index
-
sym
SymbolList sym
-
-
-
Exception Class org.biojava.bio.dp.IllegalTransitionException
class IllegalTransitionException extends BioException implements Serializable -
Class org.biojava.bio.dp.MagicalState
class MagicalState extends SimpleEmissionState implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
ObjectStreamException
-
-
-
Class org.biojava.bio.dp.ProfileHMM
class 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
class NullModel extends Object implements Serializable -
Class org.biojava.bio.dp.ScoreType.Odds
class Odds extends Object implements Serializable -
Class org.biojava.bio.dp.ScoreType.Probability
class Probability extends Object implements Serializable -
Class org.biojava.bio.dp.SimpleDotState
class SimpleDotState extends FundamentalAtomicSymbol implements Serializable -
Class org.biojava.bio.dp.SimpleEmissionState
class 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
class 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
class SimpleModelInState extends FundamentalAtomicSymbol implements Serializable-
Serialized Fields
-
model
MarkovModel model
-
-
-
Class org.biojava.bio.dp.SimpleModelTrainer
class SimpleModelTrainer extends SimpleDistributionTrainerContext implements Serializable-
Serialized Fields
-
models
Set models
-
-
-
Class org.biojava.bio.dp.SimpleStatePath
class SimpleStatePath extends Unchangeable implements Serializable-
Serialized Fields
-
delegate
Alignment delegate
-
score
double score
-
-
-
Class org.biojava.bio.dp.SimpleWeightMatrix
class SimpleWeightMatrix extends Object implements Serializable- serialVersionUID:
- 73394340224964858L
-
Serialized Fields
-
alpha
Alphabet alpha
-
columns
Distribution[] columns
-
-
Class org.biojava.bio.dp.TrainerTransition
class TrainerTransition extends Object implements Serializable-
Serialized Fields
-
from
State from
-
to
State to
-
trainer
TransitionTrainer trainer
-
-
-
Class org.biojava.bio.dp.Transition
class Transition extends Object implements Serializable -
Class org.biojava.bio.dp.WeightMatrixAnnotator
class 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
class 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
class SingleDP extends DP implements Serializable -
Class org.biojava.bio.dp.onehead.SingleDPMatrix
class 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
class DPInterpreter extends Object implements Serializable-
Serialized Fields
-
dp
DP dp
-
-
-
Class org.biojava.bio.dp.twohead.EmissionCache
class EmissionCache extends Object implements Serializable -
Class org.biojava.bio.dp.twohead.PairDPMatrix
class 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
class PairwiseDP extends DP implements Serializable-
Serialized Fields
-
ccFactory
CellCalculatorFactory ccFactory
-
emissionCache
HashMap emissionCache
-
-
-
-
Package org.biojava.bio.gui
-
Class org.biojava.bio.gui.DistributionLogo
class 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
class FeatureTree extends JTree implements Serializable
-
-
Package org.biojava.bio.gui.sequence
-
Class org.biojava.bio.gui.sequence.AbstractBeadRenderer
class AbstractBeadRenderer extends AbstractChangeable implements Serializable -
Class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
class 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
class AlignmentRenderer extends SequenceRendererWrapper implements Serializable-
Serialized Fields
-
label
String label
-
-
-
Class org.biojava.bio.gui.sequence.BasicImapRenderer
class BasicImapRenderer extends Object implements Serializable-
Serialized Fields
-
imageMap
ImageMap imageMap
-
renderer
BasicFeatureRenderer renderer
-
urlFactory
URLFactory urlFactory
-
-
-
Class org.biojava.bio.gui.sequence.BumpedRenderer
class BumpedRenderer extends SequenceRendererWrapper implements Serializable -
Class org.biojava.bio.gui.sequence.CircularRendererPanel
class 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
class EllipticalBeadRenderer extends AbstractBeadRenderer implements Serializable-
Serialized Fields
-
dimensionRatio
double dimensionRatio
-
-
-
Class org.biojava.bio.gui.sequence.FilteringRenderer
class 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
class GappedRenderer extends SequenceRendererWrapper implements Serializable -
Class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
class 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
class ClientSide extends Object implements Serializable -
Class org.biojava.bio.gui.sequence.ImageMap.HotSpot
class HotSpot extends Object implements Serializable -
Class org.biojava.bio.gui.sequence.ImageMap.ServerSide
class ServerSide extends Object implements Serializable-
Serialized Fields
-
hotSpots
List hotSpots
-
-
-
Class org.biojava.bio.gui.sequence.MultiLineRenderer
class MultiLineRenderer extends AbstractChangeable implements Serializable-
Serialized Fields
-
renderers
List renderers
-
-
-
Class org.biojava.bio.gui.sequence.OverlayRendererWrapper
class OverlayRendererWrapper extends AbstractChangeable implements Serializable-
Serialized Fields
-
renderer
SequenceRenderer renderer
-
-
-
Class org.biojava.bio.gui.sequence.PaddingRenderer
class PaddingRenderer extends SequenceRendererWrapper implements Serializable-
Serialized Fields
-
padding
double padding
-
-
-
Class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
class 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
class PairwiseFilteringRenderer extends AbstractChangeable implements Serializable-
Serialized Fields
-
cacheFlushers
Set cacheFlushers
-
filter
FeatureFilter filter
filter
is the filter applied to bothFeatureHolder
s. -
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
class PairwiseOverlayRenderer extends AbstractChangeable implements Serializable-
Serialized Fields
-
renderers
List renderers
-
-
-
Class org.biojava.bio.gui.sequence.PairwiseSequencePanel
class 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
class PeptideDigestRenderer extends AbstractPeptideDigestRenderer implements Serializable-
Serialized Fields
-
defaultPaint
Paint defaultPaint
-
-
-
Class org.biojava.bio.gui.sequence.RectangularBeadRenderer
class RectangularBeadRenderer extends AbstractBeadRenderer implements Serializable-
Serialized Fields
-
rect
Rectangle2D rect
-
scaleHeight
boolean scaleHeight
-
-
-
Class org.biojava.bio.gui.sequence.RectangularImapRenderer
class RectangularImapRenderer extends Object implements Serializable-
Serialized Fields
-
imageMap
ImageMap imageMap
-
renderer
RectangularBeadRenderer renderer
-
urlFactory
URLFactory urlFactory
-
-
-
Class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
class RoundRectangularBeadRenderer extends AbstractBeadRenderer implements Serializable-
Serialized Fields
-
arcHeight
double arcHeight
-
arcWidth
double arcWidth
-
rect
RoundRectangle2D rect
-
-
-
Class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer
class SecondaryStructureFeatureRenderer extends GlyphFeatureRenderer implements Serializable -
Class org.biojava.bio.gui.sequence.SequencePanel
class 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
class Border extends Object implements Serializable-
Serialized Fields
-
alignment
int alignment
-
pcs
PropertyChangeSupport pcs
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequencePanelWrapper
class 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
class 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
class Border extends Object implements Serializable-
Serialized Fields
-
alignment
int alignment
-
pcs
PropertyChangeSupport pcs
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
class Border extends Object implements Serializable-
Serialized Fields
-
alignment
int alignment
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequenceRendererWrapper
class SequenceRendererWrapper extends AbstractChangeable implements Serializable-
Serialized Fields
-
renderer
SequenceRenderer renderer
-
-
-
Class org.biojava.bio.gui.sequence.SequenceViewerEvent
class 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
class SixFrameZiggyRenderer extends AbstractChangeable implements Serializable-
Serialized Fields
-
pane
SixFrameRenderer pane
-
-
-
Class org.biojava.bio.gui.sequence.TranslatedSequencePanel
class 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
class ZiggyFeatureRenderer extends AbstractChangeable implements Serializable -
Class org.biojava.bio.gui.sequence.ZiggyImapRenderer
class 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
class 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
class 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
class ABIFChromatogram extends AbstractChromatogram implements Serializable
-
-
Package org.biojava.bio.program.gff
-
Exception Class org.biojava.bio.program.gff.IgnoreRecordException
class IgnoreRecordException extends Exception implements Serializable
-
-
Package org.biojava.bio.program.hmmer
-
Class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
class 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
class HmmerProfileHMM extends ProfileHMM implements Serializable -
Class org.biojava.bio.program.hmmer.ProfileEmissionState
class ProfileEmissionState extends SimpleEmissionState implements Serializable
-
-
Package org.biojava.bio.program.homologene
-
Exception Class org.biojava.bio.program.homologene.DuplicateTaxonException
class DuplicateTaxonException extends BioException implements Serializable
-
-
Package org.biojava.bio.program.phred
-
Class org.biojava.bio.program.phred.PhredFormat
class 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
class PhredSequence extends SimpleSequence implements Serializable
-
-
Package org.biojava.bio.program.ssaha
-
Exception Class org.biojava.bio.program.ssaha.SearchException
class SearchException extends Exception implements Serializable
-
-
Package org.biojava.bio.proteomics
-
Class org.biojava.bio.proteomics.Protease
class Protease extends Object implements Serializable-
Serialization Methods
-
readResolve
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
class AbstractBlastLikeSearchFilter extends Object implements Serializable-
Serialized Fields
-
cachedOutcome
TriState cachedOutcome
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty
class ByHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable-
Serialized Fields
-
key
Object key
-
test
FilterTest test
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty
class BySearchProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable-
Serialized Fields
-
key
Object key
-
test
FilterTest test
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty
class BySubHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable-
Serialized Fields
-
key
Object key
-
test
FilterTest test
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.Not
class Not extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable-
Serialized Fields
-
filter
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter filter
-
-
-
-
Package org.biojava.bio.seq
-
Class org.biojava.bio.seq.CircularView
class CircularView extends ViewSequence implements Serializable -
Class org.biojava.bio.seq.ComponentFeature.Template
class Template extends StrandedFeature.Template implements Serializable -
Class org.biojava.bio.seq.Feature.Template
class Template extends Object implements Serializable -
Class org.biojava.bio.seq.FeatureFilter.And
class And extends Object implements Serializable-
Serialized Fields
-
c1
FeatureFilter c1
-
c2
FeatureFilter c2
-
-
-
Class org.biojava.bio.seq.FeatureFilter.AnnotationContains
class AnnotationContains extends FeatureFilter.ByAnnotationType implements Serializable -
Class org.biojava.bio.seq.FeatureFilter.ByAncestor
class ByAncestor extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByAnnotation
class ByAnnotation extends FeatureFilter.ByAnnotationType implements Serializable -
Class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
class ByAnnotationType extends Object implements Serializable-
Serialized Fields
-
type
AnnotationType type
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByChild
class ByChild extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByClass
class ByClass extends Object implements Serializable-
Serialized Fields
-
clazz
Class clazz
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByComponentName
class ByComponentName extends Object implements Serializable-
Serialized Fields
-
cname
String cname
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByDescendant
class ByDescendant extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByFeature
class ByFeature extends Object implements Serializable-
Serialized Fields
-
feature
Feature feature
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
class 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
class ByParent extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.BySequenceName
class BySequenceName extends Object implements Serializable-
Serialized Fields
-
seqName
String seqName
-
-
-
Class org.biojava.bio.seq.FeatureFilter.BySource
class BySource extends Object implements Serializable-
Serialized Fields
-
source
String source
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByType
class ByType extends Object implements Serializable-
Serialized Fields
-
type
String type
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
class ContainedByLocation extends Object implements Serializable-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.FrameFilter
class FrameFilter extends Object implements Serializable-
Serialized Fields
-
frame
FramedFeature.ReadingFrame frame
-
-
-
Class org.biojava.bio.seq.FeatureFilter.HasAnnotation
class HasAnnotation extends FeatureFilter.ByAnnotationType implements Serializable-
Serialized Fields
-
key
Object key
-
-
-
Class org.biojava.bio.seq.FeatureFilter.Not
class Not extends Object implements Serializable-
Serialized Fields
-
child
FeatureFilter child
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OnlyChildren
class OnlyChildren extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
class OnlyDescendants extends Object implements Serializable-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.Or
class Or extends Object implements Serializable-
Serialized Fields
-
c1
FeatureFilter c1
-
c2
FeatureFilter c2
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
class OverlapsLocation extends Object implements Serializable-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
class ShadowContainedByLocation extends Object implements Serializable-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
class ShadowOverlapsLocation extends Object implements Serializable-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.StrandFilter
class StrandFilter extends Object implements Serializable-
Serialized Fields
-
strand
StrandedFeature.Strand strand
-
-
-
Class org.biojava.bio.seq.FramedFeature.ReadingFrame
class ReadingFrame extends Object implements Serializable-
Serialized Fields
-
frame
int frame
-
text
String text
-
-
-
Class org.biojava.bio.seq.FramedFeature.Template
class Template extends StrandedFeature.Template implements Serializable-
Serialized Fields
-
readingFrame
FramedFeature.ReadingFrame readingFrame
-
-
-
Class org.biojava.bio.seq.MergeFeatureHolder
class MergeFeatureHolder extends AbstractFeatureHolder implements Serializable-
Serialized Fields
-
featureHolders
List featureHolders
-
-
-
Class org.biojava.bio.seq.RemoteFeature.Template
class Template extends StrandedFeature.Template implements Serializable-
Serialized Fields
-
regions
List regions
-
resolver
RemoteFeature.Resolver resolver
-
-
-
Class org.biojava.bio.seq.SimpleFeatureHolder
class SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable-
Serialized Fields
-
features
List features
The child features. -
schema
FeatureFilter schema
-
-
-
Class org.biojava.bio.seq.SimpleFeatureRealizer
class SimpleFeatureRealizer extends Object implements Serializable-
Serialized Fields
-
fallBack
FeatureRealizer fallBack
-
templateToImpl
List templateToImpl
-
-
-
Class org.biojava.bio.seq.StrandedFeature.Strand
class Strand extends Object implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
ObjectStreamException
-
-
Serialized Fields
-
text
String text
-
token
char token
-
value
int value
-
-
-
Class org.biojava.bio.seq.StrandedFeature.Template
class 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
class AnnotatedSequenceDB extends AbstractSequenceDB implements Serializable-
Serialized Fields
-
annotator
SequenceAnnotator annotator
-
parent
SequenceDB parent
-
-
-
Class org.biojava.bio.seq.db.CachingSequenceDB
class CachingSequenceDB extends SequenceDBWrapper implements Serializable-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
-
-
Class org.biojava.bio.seq.db.HashSequenceDB
class HashSequenceDB extends AbstractSequenceDB implements Serializable -
Class org.biojava.bio.seq.db.IDMaker.ByName
class ByName extends Object implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
IOException
-
-
-
Class org.biojava.bio.seq.db.IDMaker.ByURN
class ByURN extends Object implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
IOException
-
-
-
Exception Class org.biojava.bio.seq.db.IllegalIDException
class IllegalIDException extends BioException implements Serializable -
Class org.biojava.bio.seq.db.IndexedSequenceDB
class IndexedSequenceDB extends AbstractSequenceDB implements Serializable-
Serialized Fields
-
idMaker
IDMaker idMaker
-
indexStore
IndexStore indexStore
-
-
-
Class org.biojava.bio.seq.db.SequenceDBWrapper
class SequenceDBWrapper extends AbstractSequenceDB implements Serializable-
Serialized Fields
-
parent
SequenceDB parent
-
-
-
Class org.biojava.bio.seq.db.SubSequenceDB
class SubSequenceDB extends SequenceDBWrapper implements Serializable-
Serialized Fields
-
ids
Set ids
-
-
-
Class org.biojava.bio.seq.db.TabIndexStore
class TabIndexStore extends Object implements Serializable-
Serialization Methods
-
readObject
- 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
class ViewingSequenceDB extends SequenceDBWrapper implements Serializable
-
-
Package org.biojava.bio.seq.homol
-
Class org.biojava.bio.seq.homol.HomologyFeature.Template
class Template extends StrandedFeature.Template implements Serializable-
Serialized Fields
-
homology
Homology homology
-
-
-
Class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
class 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 reciprocalSimilarityPairFeature
has not yet been created.
-
-
-
-
Package org.biojava.bio.seq.impl
-
Class org.biojava.bio.seq.impl.RevCompSequence
class RevCompSequence extends SimpleSequence implements Serializable-
Serialized Fields
-
origSeq
Sequence origSeq
-
pfh
ProjectedFeatureHolder pfh
-
-
-
Class org.biojava.bio.seq.impl.SimpleFeature
class 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
class SimpleFramedFeature extends SimpleStrandedFeature implements Serializable-
Serialized Fields
-
readingFrame
FramedFeature.ReadingFrame readingFrame
-
-
-
Class org.biojava.bio.seq.impl.SimpleGappedSequence
class 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
class GappedContext extends ReparentContext implements Serializable- serialVersionUID:
- 8878073952684354286L
-
Class org.biojava.bio.seq.impl.SimpleHomologyFeature
class SimpleHomologyFeature extends SimpleStrandedFeature implements Serializable-
Serialized Fields
-
homology
Homology homology
-
-
-
Class org.biojava.bio.seq.impl.SimpleRemoteFeature
class SimpleRemoteFeature extends SimpleStrandedFeature implements Serializable-
Serialized Fields
-
regions
List regions
-
resolver
RemoteFeature.Resolver resolver
-
-
-
Class org.biojava.bio.seq.impl.SimpleRestrictionSite
class SimpleRestrictionSite extends SimpleStrandedFeature implements Serializable-
Serialized Fields
-
enzyme
RestrictionEnzyme enzyme
-
position
int position
-
-
-
Class org.biojava.bio.seq.impl.SimpleSequence
class 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
class SimpleSequenceFactory extends Object implements Serializable-
Serialized Fields
-
realizer
FeatureRealizer realizer
-
-
-
Class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
class SimpleSimilarityPairFeature extends SimpleStrandedFeature implements Serializable-
Serialized Fields
-
alignment
Alignment alignment
-
score
double score
-
sibling
SimilarityPairFeature sibling
-
-
-
Class org.biojava.bio.seq.impl.SimpleStrandedFeature
class SimpleStrandedFeature extends SimpleFeature implements Serializable-
Serialized Fields
-
strand
StrandedFeature.Strand strand
-
-
-
Class org.biojava.bio.seq.impl.SubSequence
class 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
class SubProjectedFeatureContext extends ReparentContext implements Serializable-
Serialized Fields
-
clippingFilter
FeatureFilter clippingFilter
-
parentLocation
RangeLocation parentLocation
-
remoteLocationFilter
FeatureFilter remoteLocationFilter
-
-
-
Class org.biojava.bio.seq.impl.ViewSequence
class ViewSequence extends Unchangeable implements Serializable- serialVersionUID:
- 9866447L
-
Serialization Methods
-
readObject
- 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
class AlternateTokenization extends Unchangeable implements Serializable -
Class org.biojava.bio.seq.io.CharacterTokenization
class CharacterTokenization extends Unchangeable implements Serializable -
Class org.biojava.bio.seq.io.CrossProductTokenization
class CrossProductTokenization extends WordTokenization implements Serializable-
Serialized Fields
-
subTokenizations
List subTokenizations
-
-
-
Class org.biojava.bio.seq.io.DoubleTokenization
class DoubleTokenization extends WordTokenization implements Serializable -
Class org.biojava.bio.seq.io.EmblLikeFormat
class EmblLikeFormat extends Object implements Serializable-
Serialized Fields
-
elideSymbols
boolean elideSymbols
Deprecated. -
mListeners
Vector mListeners
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.EmblProcessor.Factory
class Factory extends Object implements Serializable-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory
class Factory extends Object implements Serializable-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.FastaFormat
class 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
class GenbankFormat extends Object implements Serializable-
Serialized Fields
-
elideSymbols
boolean elideSymbols
Deprecated. -
mListeners
Vector mListeners
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.GenbankProcessor.Factory
class Factory extends Object implements Serializable-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.GenbankXmlFormat
class 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
class GenpeptFormat extends GenbankFormat implements Serializable -
Class org.biojava.bio.seq.io.IntegerTokenization
class IntegerTokenization extends WordTokenization implements Serializable -
Class org.biojava.bio.seq.io.NameTokenization
class NameTokenization extends WordTokenization implements Serializable-
Serialized Fields
-
caseSensitive
boolean caseSensitive
-
-
-
Class org.biojava.bio.seq.io.OrganismParser.Factory
class 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
-
-
-
Exception Class org.biojava.bio.seq.io.ParseException
class ParseException extends BioException implements Serializable -
Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory
class Factory extends Object implements Serializable-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.ReferenceAnnotation
class 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
class SubIntegerTokenization extends WordTokenization implements Serializable -
Class org.biojava.bio.seq.io.SwissprotProcessor.Factory
class Factory extends Object implements Serializable-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.WordTokenization
class WordTokenization extends Unchangeable implements Serializable-
Serialized Fields
-
alphabet
Alphabet alphabet
-
-
-
-
Package org.biojava.bio.seq.projection
-
Class org.biojava.bio.seq.projection.ProjectedFeatureHolder
class ProjectedFeatureHolder extends AbstractFeatureHolder implements Serializable-
Serialized Fields
-
context
ProjectionContext context
-
topLevelFeatures
FeatureHolder topLevelFeatures
-
-
-
Class org.biojava.bio.seq.projection.ReparentContext
class ReparentContext extends Object implements Serializable-
Serialized Fields
-
parent
FeatureHolder parent
-
wrapped
FeatureHolder wrapped
-
-
-
Class org.biojava.bio.seq.projection.TranslateFlipContext
class TranslateFlipContext extends ReparentContext implements Serializable-
Serialized Fields
-
oppositeStrand
boolean oppositeStrand
-
translation
int translation
-
-
-
-
Package org.biojava.bio.symbol
-
Class org.biojava.bio.symbol.AbstractAlphabet
class AbstractAlphabet extends AbstractChangeable implements Serializable- serialVersionUID:
- -3043128839927615753L
-
Serialization Methods
-
readResolve
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
-
Class org.biojava.bio.symbol.AbstractLocation
class AbstractLocation extends Object implements Serializable -
Class org.biojava.bio.symbol.AbstractRangeLocation
class AbstractRangeLocation extends AbstractLocation implements Serializable -
Class org.biojava.bio.symbol.ChunkedSymbolList
class ChunkedSymbolList extends AbstractSymbolList implements Serializable-
Serialization Methods
-
readObject
- Throws:
IOException
ClassNotFoundException
-
-
Serialized Fields
-
alpha
Alphabet alpha
-
chunks
SymbolList[] chunks
-
chunkSize
int chunkSize
-
length
int length
-
-
-
Class org.biojava.bio.symbol.DNAAmbPack
class DNAAmbPack extends Object implements Serializable-
Serialized Fields
-
syms
Symbol[] syms
-
-
-
Class org.biojava.bio.symbol.DNANoAmbPack
class DNANoAmbPack extends Object implements Serializable-
Serialized Fields
-
placeHolder
byte placeHolder
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet
class DoubleAlphabet extends Unchangeable implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
ObjectStreamException
-
-
Serialized Fields
-
alphabets
List alphabets
-
doubleToSym
WeakValueHashMap doubleToSym
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
class DoubleRange extends Unchangeable implements Serializable-
Serialized Fields
-
matches
Alphabet matches
-
maxVal
double maxVal
-
minVal
double minVal
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
class DoubleSymbol extends Unchangeable implements Serializable-
Serialized Fields
-
matches
Alphabet matches
-
val
double val
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
class SubDoubleAlphabet extends Unchangeable implements Serializable-
Serialization Methods
-
readResolve
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
class DummySymbolList extends AbstractSymbolList implements Serializable -
Class org.biojava.bio.symbol.Edit
class 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
class FundamentalAtomicSymbol extends AbstractSymbol implements Serializable-
Serialized Fields
-
annotation
Annotation annotation
-
name
String name
-
-
-
Class org.biojava.bio.symbol.FuzzyLocation
class 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
class FuzzyPointLocation extends AbstractLocation implements Serializable-
Serialized Fields
-
max
int max
-
min
int min
-
resolver
FuzzyPointLocation.PointResolver resolver
-
-
-
Exception Class org.biojava.bio.symbol.IllegalAlphabetException
class IllegalAlphabetException extends BioException implements Serializable -
Exception Class org.biojava.bio.symbol.IllegalSymbolException
class IllegalSymbolException extends BioException implements Serializable-
Serialized Fields
-
sym
Symbol sym
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet
class IntegerAlphabet extends Unchangeable implements Serializable-
Serialization Methods
-
writeReplace
- Throws:
ObjectStreamException
-
-
Serialized Fields
-
intToSym
WeakValueHashMap intToSym
Canonicalization map for ints and references to symbols.
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
class IntegerSymbol extends Unchangeable implements Serializable-
Serialized Fields
-
matches
Alphabet matches
-
val
int val
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
class SubIntegerAlphabet extends AbstractAlphabet implements Serializable-
Serialized Fields
-
max
int max
-
min
int min
-
name
String name
-
-
-
Class org.biojava.bio.symbol.MergeLocation
class MergeLocation extends RangeLocation implements Serializable-
Serialized Fields
-
componentLocations
List componentLocations
-
-
-
Class org.biojava.bio.symbol.PackedSymbolList
class 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
class PointLocation extends AbstractRangeLocation implements Serializable-
Serialized Fields
-
point
int point
The actual index contained.
-
-
-
Class org.biojava.bio.symbol.RangeLocation
class 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
class 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
class SimpleAtomicSymbol extends org.biojava.bio.symbol.AbstractSimpleBasisSymbol implements Serializable-
Serialization Methods
-
writeReplace
-
-
-
Class org.biojava.bio.symbol.SimpleGappedSymbolList
class 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 invalid input: '&' trailing gaps. -
source
SymbolList source
The SymbolList to view.
-
-
Class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
class 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
class SimpleGeneticCodeTable extends SimpleManyToOneTranslationTable implements Serializable-
Serialized Fields
-
description
String description
-
table_num
int table_num
-
-
-
Class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
class 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
class 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
class 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
class 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
class SingletonAlphabet extends AbstractAlphabet implements Serializable-
Serialized Fields
-
alphabets
List alphabets
-
sym
AtomicSymbol sym
-
-
-
Class org.biojava.bio.symbol.SuffixTree
class 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
class SuffixNode extends Object implements Serializable
-
-
Package org.biojava.bio.taxa
-
Exception Class org.biojava.bio.taxa.CircularReferenceException
class CircularReferenceException extends BioException implements Serializable
-
-
Package org.biojava.directory
-
Exception Class org.biojava.directory.ProviderNotFoundException
class ProviderNotFoundException extends RegistryException implements Serializable -
Exception Class org.biojava.directory.RegistryException
class RegistryException extends Exception implements Serializable
-
-
Package org.biojava.ontology
-
Exception Class org.biojava.ontology.AlreadyExistsException
class AlreadyExistsException extends OntologyException implements Serializable -
Class org.biojava.ontology.DefaultOps
class DefaultOps extends Object implements Serializable -
Exception Class org.biojava.ontology.InvalidTermException
class InvalidTermException extends OntologyException implements Serializable -
Class org.biojava.ontology.Ontology.Impl
class 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
-
-
Exception Class org.biojava.ontology.OntologyException
class OntologyException extends Exception implements Serializable -
Class org.biojava.ontology.OntologyTerm.Impl
class Impl extends AbstractChangeable implements Serializable -
Class org.biojava.ontology.RemoteTerm.Impl
class Impl extends AbstractTerm implements Serializable- serialVersionUID:
- 922700041939183676L
-
Class org.biojava.ontology.Term.Impl
class 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
class Impl extends Unchangeable implements Serializable- serialVersionUID:
- 3807331980372839221L
-
Class org.biojava.ontology.Variable.Impl
class Impl extends Term.Impl implements Serializable
-
-
Package org.biojava.stats.svm
-
Class org.biojava.stats.svm.CachingKernel
class CachingKernel extends NestedKernel implements Serializable -
Class org.biojava.stats.svm.DiagonalAddKernel
class DiagonalAddKernel extends NestedKernel implements Serializable -
Class org.biojava.stats.svm.DiagonalCachingKernel
class DiagonalCachingKernel extends NestedKernel implements Serializable -
Class org.biojava.stats.svm.LinearKernel
class LinearKernel extends Object implements Serializable -
Class org.biojava.stats.svm.ListSumKernel
class ListSumKernel extends NestedKernel implements Serializable -
Class org.biojava.stats.svm.NestedKernel
class NestedKernel extends Object implements Serializable-
Serialized Fields
-
nested
SVMKernel nested
The SVMKernel being wrapped.
-
-
-
Class org.biojava.stats.svm.NormalizingKernel
class NormalizingKernel extends NestedKernel implements Serializable -
Class org.biojava.stats.svm.PolynomialKernel
class PolynomialKernel extends NestedKernel implements Serializable-
Serialized Fields
-
a
double a
-
c
double c
-
order
double order
-
-
-
Class org.biojava.stats.svm.RadialBaseKernel
class RadialBaseKernel extends NestedKernel implements Serializable-
Serialized Fields
-
width
double width
-
-
-
Class org.biojava.stats.svm.SparseVector
class SparseVector extends Object implements Serializable-
Serialized Fields
-
keys
int[] keys
-
size
int size
-
values
double[] values
-
-
-
Class org.biojava.stats.svm.SparseVector.NormalizingKernel
class NormalizingKernel extends Object implements Serializable-
Serialized Fields
-
s
SparseVector s
The sparse vector that performes the normalization.
-
-
-
Class org.biojava.stats.svm.TrainingEvent
class TrainingEvent extends EventObject implements Serializable
-
-
Package org.biojava.stats.svm.tools
-
Class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
class PointClassifier extends JComponent implements Serializable -
Class org.biojava.stats.svm.tools.SuffixTreeKernel
class 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
class MultipleScalar extends Object implements Serializable-
Serialized Fields
-
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
class NullModelScaler extends Object implements Serializable -
Class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
class SelectionScalar extends Object implements Serializable-
Serialized Fields
-
bSet
BitSet bSet
-
-
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
class UniformScaler extends Object implements Serializable
-
-
Package org.biojava.utils
-
Exception Class org.biojava.utils.AssertionFailure
class AssertionFailure extends AssertionError implements Serializable -
Class org.biojava.utils.ChangeEvent
class ChangeEvent extends EventObject implements Serializable-
Serialized Fields
-
chain
ChangeEvent chain
-
change
Object change
-
previous
Object previous
-
type
ChangeType type
-
-
-
Class org.biojava.utils.ChangeType
class ChangeType extends Object implements Serializable-
Serialization Methods
-
writeReplace
Make a placeholder for this object in a serialized stream.
-
-
Serialized Fields
-
name
String name
-
ourField
Field ourField
-
superType
ChangeType superType
-
-
-
Exception Class org.biojava.utils.ChangeVetoException
class ChangeVetoException extends RuntimeException implements Serializable-
Serialized Fields
-
change
ChangeEvent change
-
-
-
Exception Class org.biojava.utils.CommitFailure
class CommitFailure extends Exception implements Serializable -
Class org.biojava.utils.ListTools
class ListTools extends Object implements Serializable -
Class org.biojava.utils.ListTools.Doublet
class Doublet extends AbstractList implements Serializable -
Class org.biojava.utils.ListTools.Triplet
class Triplet extends AbstractList implements Serializable -
Class org.biojava.utils.ParseErrorEvent
class ParseErrorEvent extends EventObject implements Serializable-
Serialized Fields
-
mMessage
String mMessage
-
-
-
Exception Class org.biojava.utils.ParserException
class ParserException extends Exception implements Serializable -
Exception Class org.biojava.utils.ProcessTimeoutException
class ProcessTimeoutException extends Exception implements Serializable-
Serialized Fields
-
returnCode
int returnCode
-
-
-
Class org.biojava.utils.SingletonList
class SingletonList extends AbstractList implements Serializable-
Serialized Fields
-
obj
Object obj
-
-
-
Class org.biojava.utils.SmallMap
class SmallMap extends AbstractMap implements Serializable-
Serialized Fields
-
mappings
Object[] mappings
-
numMappings
int numMappings
-
-
-
Class org.biojava.utils.StaticMemberPlaceHolder
class StaticMemberPlaceHolder extends Object implements Serializable-
Serialization Methods
-
readResolve
- Throws:
ObjectStreamException
-
-
Serialized Fields
-
-
Class org.biojava.utils.TypedProperties
class TypedProperties extends Properties implements Serializable
-
-
Package org.biojava.utils.automata
-
Exception Class org.biojava.utils.automata.AutomatonException
class AutomatonException extends BioException implements Serializable
-
-
Package org.biojava.utils.bytecode
-
Exception Class org.biojava.utils.bytecode.CodeException
class CodeException extends Exception implements Serializable
-
-
Package org.biojava.utils.candy
-
Exception Class org.biojava.utils.candy.CandyException
class CandyException extends Exception implements Serializable
-
-
Package org.biojava.utils.lsid
-
Class org.biojava.utils.lsid.LifeScienceIdentifier
class LifeScienceIdentifier extends Object implements Serializable- serialVersionUID:
- 8478038493421763123L
-
Exception Class org.biojava.utils.lsid.LifeScienceIdentifierParseException
class LifeScienceIdentifierParseException extends Exception implements Serializable
-
-
Package org.biojava.utils.regex
-
Exception Class org.biojava.utils.regex.RegexException
class RegexException extends BioException implements Serializable
-
-
Package org.biojava.utils.xml
-
Exception Class org.biojava.utils.xml.AppException
class AppException extends Exception implements Serializable
-
-
Package org.biojavax
-
Exception Class org.biojavax.CrossReferenceResolutionException
class CrossReferenceResolutionException extends Exception implements Serializable -
Class org.biojavax.EmptyRichAnnotation
class EmptyRichAnnotation extends Unchangeable implements Serializable-
Serialization Methods
-
writeReplace
- 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
class RemoteQBlastAlignmentProperties extends Object implements Serializable- serialVersionUID:
- 1L
-
Class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
class RemoteQBlastOutputProperties extends Object implements Serializable- serialVersionUID:
- 1L
-
-
Package org.biojavax.bio.db.biosql
-
Class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
class BioSQLAcceptAllFilter extends Object implements Serializable-
Serialized Fields
-
isNotNull
Method isNotNull
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
class BioSQLAcceptNoneFilter extends Object implements Serializable-
Serialized Fields
-
isNull
Method isNull
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
class And extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
c1
BioSQLFeatureFilter c1
-
c2
BioSQLFeatureFilter c2
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
class ByName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
name
String name
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
class ByNote extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
note
Note note
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
class ByNoteTermOnly extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
term
ComparableTerm term
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
class ByRank extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
rank
int rank
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
class BySequenceName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
seqName
String seqName
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
class BySourceTerm extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
sourceTerm
ComparableTerm sourceTerm
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
class BySourceTermName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
sourceTermName
String sourceTermName
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
class ByStrand extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
str
RichLocation.Strand str
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
class ByTypeTerm extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
typeTerm
ComparableTerm typeTerm
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
class ByTypeTermName extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
typeTermName
String typeTermName
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
class ContainedByRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
loc
RichLocation loc
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
class HibernateFeatureFilter extends Object implements Serializable -
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
class Not extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
child
BioSQLFeatureFilter child
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
class Or extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
c1
BioSQLFeatureFilter c1
-
c2
BioSQLFeatureFilter c2
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
class OverlapsRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable-
Serialized Fields
-
loc
RichLocation loc
-
-
-
-
Package org.biojavax.bio.seq
-
Class org.biojavax.bio.seq.RichFeature.Template
class Template extends Feature.Template implements Serializable
-
-
Package org.biojavax.ga.exception
-
Exception Class org.biojavax.ga.exception.IllegalOrganismException
class IllegalOrganismException extends Exception implements Serializable
-
-
Package org.biojavax.ga.util
-
Class org.biojavax.ga.util.WeightedSet
class WeightedSet extends AbstractSet implements Serializable-
Serialized Fields
-
key2Weight
HashMap key2Weight
-
totalWeight
double totalWeight
-
-
-