Serialized Form
-
Package org.biojava.bibliography
-
Class org.biojava.bibliography.BibRefException extends java.lang.Exception implements Serializable
-
-
Package org.biojava.bio
-
Class org.biojava.bio.AbstractAnnotation extends AbstractChangeable implements Serializable
-
Class org.biojava.bio.AnnotationChanger extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
changer
ChangeTable changer
-
properties
java.util.Map properties
-
wrapped
Annotation wrapped
-
-
-
Class org.biojava.bio.AnnotationRenamer extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
mapper
PropertyChanger mapper
-
properties
java.util.Map properties
-
wrapped
Annotation wrapped
-
-
-
Class org.biojava.bio.BeanAsAnnotation extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
properties
java.util.Map properties
-
-
-
Class org.biojava.bio.BioError extends java.lang.Error implements Serializable
-
Class org.biojava.bio.BioException extends java.lang.Exception implements Serializable
-
Class org.biojava.bio.BioRuntimeException extends java.lang.RuntimeException implements Serializable
-
Class org.biojava.bio.MergeAnnotation extends AbstractChangeable implements Serializable
-
Serialized Fields
-
mergeSet
java.util.List mergeSet
-
-
-
Class org.biojava.bio.OverlayAnnotation extends AbstractChangeable implements Serializable
-
Serialized Fields
-
overlay
java.util.Map overlay
-
parent
Annotation parent
-
-
-
Class org.biojava.bio.SimpleAnnotation extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
properties
java.util.Map properties
The properties map. This may be null if no property values have yet been set.
-
-
-
Class org.biojava.bio.SmallAnnotation extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
properties
java.util.Map properties
-
-
-
-
Package org.biojava.bio.alignment
-
Class org.biojava.bio.alignment.AlignmentPair extends SimpleAlignment implements Serializable
- serialVersionUID:
- -8834131912021612261L
-
Serialized Fields
-
identicals
int identicals
Number of identical elements in both sequences -
nGapsQ
int nGapsQ
Number of gaps in query -
nGapsS
int nGapsS
Number of gaps in subject -
query
Sequence query
Length of the query sequence -
queryEnd
int queryEnd
End position in the query -
queryStart
int queryStart
Start position in the query -
similars
int similars
Number of similar symbols -
subject
Sequence subject
The subject sequence. -
subjectEnd
int subjectEnd
End position in the subject -
subjectStart
int subjectStart
Start position in the subject -
subMatrix
SubstitutionMatrix subMatrix
Reference to the underlying substitution matrix of this alignment. -
time
long time
Time consumption to create this alignment.
-
-
Class org.biojava.bio.alignment.IllegalAlignmentEditException extends BioRuntimeException implements Serializable
- serialVersionUID:
- 4662428071284597336L
-
Class org.biojava.bio.alignment.SimpleAlignment extends AbstractSymbolList implements Serializable
- serialVersionUID:
- -1760075176220928440L
-
Serialized Fields
-
alphabet
Alphabet alphabet
-
labels
java.util.List<java.lang.String> labels
-
labelToSymbolList
java.util.LinkedHashMap<java.lang.String,SymbolList> labelToSymbolList
-
length
int length
-
score
int score
-
-
Class org.biojava.bio.alignment.SubstitutionMatrix extends java.lang.Object implements Serializable
-
Serialized Fields
-
alphabet
FiniteAlphabet alphabet
The alphabet used by this matrix. -
colSymbols
java.util.Map<Symbol,java.lang.Integer> colSymbols
-
description
java.lang.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
java.lang.String name
Name and description of this matrix. -
rowSymbols
java.util.Map<Symbol,java.lang.Integer> rowSymbols
-
-
-
-
Package org.biojava.bio.annodb
-
Class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory extends java.lang.Object implements Serializable
-
Serialized Fields
-
method
java.lang.reflect.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 java.lang.Object implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.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(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
alpha
FiniteAlphabet alpha
-
-
Class org.biojava.bio.dist.PairDistribution extends AbstractChangeable implements Serializable
-
Serialized Fields
-
alphabet
Alphabet alphabet
-
first
Distribution first
-
second
Distribution second
-
-
-
Class org.biojava.bio.dist.SimpleDistribution extends AbstractDistribution implements Serializable
- serialVersionUID:
- 7252850540926095728L
-
Serialization Methods
-
readObject
private void readObject(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream oos) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
alpha
FiniteAlphabet alpha
-
nullModel
Distribution nullModel
-
-
Class org.biojava.bio.dist.SimpleDistributionTrainer extends java.lang.Object implements Serializable
-
Serialized Fields
-
c
java.util.Map c
Deprecated. -
dis
Distribution dis
Deprecated.
-
-
-
Class org.biojava.bio.dist.SimpleDistributionTrainerContext extends java.lang.Object implements Serializable
-
Serialized Fields
-
distToTrainer
java.util.Map distToTrainer
-
nullModelWeight
double nullModelWeight
-
trainers
java.util.Set trainers
-
-
-
Class org.biojava.bio.dist.TranslatedDistribution extends AbstractChangeable implements Serializable
-
Serialized Fields
-
delegate
Distribution delegate
-
other
Distribution other
-
table
ReversibleTranslationTable table
-
-
-
Class org.biojava.bio.dist.UniformDistribution extends AbstractDistribution implements Serializable
- serialVersionUID:
- 88454038L
-
Serialized Fields
-
alphabet
FiniteAlphabet alphabet
-
nullModel
Distribution nullModel
-
-
Class org.biojava.bio.dist.UntrainableDistribution extends SimpleDistribution implements Serializable
-
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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
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Class org.biojava.bio.dp.DP.ReverseIterator extends java.lang.Object implements Serializable
-
Serialized Fields
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index
int index
-
sym
SymbolList sym
-
-
-
Class org.biojava.bio.dp.IllegalTransitionException extends BioException implements Serializable
-
Class org.biojava.bio.dp.MagicalState extends SimpleEmissionState implements Serializable
-
Serialization Methods
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writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
-
Class org.biojava.bio.dp.ProfileHMM extends SimpleMarkovModel implements Serializable
-
Serialized Fields
-
columns
int columns
The number of columns in this model. -
deleteStates
DotState[] deleteStates
Delete states array.From 0 .. columns()-1 corresponding to indexes 1..columns().
-
insertStates
EmissionState[] insertStates
Insert states array.From 0 .. columns().
-
matchStates
EmissionState[] matchStates
Match states array.matchStates[0] == matchStates[columns+1] == magicalState().
-
-
-
Class org.biojava.bio.dp.ScoreType.NullModel extends java.lang.Object implements Serializable
-
Class org.biojava.bio.dp.ScoreType.Odds extends java.lang.Object implements Serializable
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Class org.biojava.bio.dp.ScoreType.Probability extends java.lang.Object implements Serializable
-
Class org.biojava.bio.dp.SimpleDotState extends FundamentalAtomicSymbol implements Serializable
-
Class org.biojava.bio.dp.SimpleEmissionState extends AbstractChangeable implements Serializable
-
Serialized Fields
-
advance
int[] advance
-
ann
Annotation ann
-
dis
Distribution dis
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matches
Alphabet matches
-
name
java.lang.String name
-
-
-
Class org.biojava.bio.dp.SimpleMarkovModel extends AbstractChangeable implements Serializable
- serialVersionUID:
- -3043028839927615753L
-
Serialized Fields
-
emissionAlpha
Alphabet emissionAlpha
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magicalState
MagicalState magicalState
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stateAlpha
FiniteAlphabet stateAlpha
-
transFrom
java.util.Map transFrom
-
transTo
java.util.Map transTo
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transWeights
java.util.Map transWeights
-
-
Class org.biojava.bio.dp.SimpleModelInState extends FundamentalAtomicSymbol implements Serializable
-
Serialized Fields
-
model
MarkovModel model
-
-
-
Class org.biojava.bio.dp.SimpleModelTrainer extends SimpleDistributionTrainerContext implements Serializable
-
Serialized Fields
-
models
java.util.Set models
-
-
-
Class org.biojava.bio.dp.SimpleStatePath extends Unchangeable implements Serializable
-
Serialized Fields
-
delegate
Alignment delegate
-
score
double score
-
-
-
Class org.biojava.bio.dp.SimpleWeightMatrix extends java.lang.Object implements Serializable
- serialVersionUID:
- 73394340224964858L
-
Serialized Fields
-
alpha
Alphabet alpha
-
columns
Distribution[] columns
-
-
Class org.biojava.bio.dp.TrainerTransition extends java.lang.Object implements Serializable
-
Serialized Fields
-
from
State from
-
to
State to
-
trainer
TransitionTrainer trainer
-
-
-
Class org.biojava.bio.dp.Transition extends java.lang.Object implements Serializable
-
Class org.biojava.bio.dp.WeightMatrixAnnotator extends java.lang.Object implements Serializable
-
Serialized Fields
-
matrix
WeightMatrix matrix
-
scoreType
ScoreType scoreType
-
threshold
double threshold
-
wmID
java.lang.String wmID
-
-
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Class org.biojava.bio.dp.WMAsMM extends AbstractChangeable implements Serializable
-
Serialized Fields
-
magicalState
MagicalState magicalState
-
stateAlpha
FiniteAlphabet stateAlpha
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states
EmissionState[] states
-
transFrom
java.util.Map transFrom
-
transTo
java.util.Map transTo
-
transWeights
java.util.Map transWeights
-
wm
WeightMatrix wm
-
-
-
-
Package org.biojava.bio.dp.onehead
-
Class org.biojava.bio.dp.onehead.SingleDP extends DP implements Serializable
-
Serialized Fields
-
emissionsNull
java.util.HashMap emissionsNull
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emissionsOdds
java.util.HashMap emissionsOdds
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emissionsProb
java.util.HashMap emissionsProb
-
-
-
Class org.biojava.bio.dp.onehead.SingleDPMatrix extends java.lang.Object implements Serializable
-
Serialized Fields
-
model
MarkovModel model
-
score
double score
-
scores
double[][] scores
-
states
State[] states
-
symList
SymbolList[] symList
-
-
-
-
Package org.biojava.bio.dp.twohead
-
Class org.biojava.bio.dp.twohead.DPInterpreter extends java.lang.Object implements Serializable
-
Serialized Fields
-
dp
DP dp
-
-
-
Class org.biojava.bio.dp.twohead.EmissionCache extends java.lang.Object implements Serializable
-
Class org.biojava.bio.dp.twohead.PairDPMatrix extends java.lang.Object implements Serializable
-
Serialized Fields
-
finalScore
double finalScore
-
model
MarkovModel model
-
scores
double[][][] scores
-
seqs
SymbolList[] seqs
-
states
State[] states
-
-
-
Class org.biojava.bio.dp.twohead.PairwiseDP extends DP implements Serializable
-
Serialized Fields
-
ccFactory
CellCalculatorFactory ccFactory
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emissionCache
java.util.HashMap emissionCache
-
-
-
-
Package org.biojava.bio.gui
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Class org.biojava.bio.gui.DistributionLogo extends javax.swing.JComponent implements Serializable
-
Serialized Fields
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blockPainter
BlockPainter blockPainter
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dist
Distribution dist
The dist to render. -
logoPainter
LogoPainter logoPainter
The logoPainter property. -
renderingHints
java.awt.RenderingHints renderingHints
-
scaleByInformation
boolean scaleByInformation
The information/plain property -
style
SymbolStyle style
The style property.
-
-
-
Class org.biojava.bio.gui.FeatureTree extends javax.swing.JTree implements Serializable
-
Serialized Fields
-
root
java.lang.String root
-
seqs
java.util.ArrayList seqs
-
-
-
-
Package org.biojava.bio.gui.sequence
-
Class org.biojava.bio.gui.sequence.AbstractBeadRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
beadDepth
double beadDepth
-
beadDisplacement
double beadDisplacement
-
beadFill
java.awt.Paint beadFill
-
beadOutline
java.awt.Paint beadOutline
-
beadStroke
java.awt.Stroke beadStroke
-
delegates
java.util.Map delegates
-
delegationCache
java.util.Map delegationCache
-
-
-
Class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer extends MultiLineRenderer implements Serializable
-
Serialized Fields
-
digestFilter
FeatureFilter digestFilter
-
distanceBetween
int distanceBetween
-
laneCount
int laneCount
-
laneMap
java.util.Map laneMap
-
source
FeatureSource source
-
-
-
Class org.biojava.bio.gui.sequence.AlignmentRenderer extends SequenceRendererWrapper implements Serializable
-
Serialized Fields
-
label
java.lang.String label
-
-
-
Class org.biojava.bio.gui.sequence.BasicImapRenderer extends java.lang.Object implements Serializable
-
Serialized Fields
-
imageMap
ImageMap imageMap
-
renderer
BasicFeatureRenderer renderer
-
urlFactory
URLFactory urlFactory
-
-
-
Class org.biojava.bio.gui.sequence.BumpedRenderer extends SequenceRendererWrapper implements Serializable
-
Serialized Fields
-
contextCache
CacheMap contextCache
-
flushers
java.util.Set flushers
-
leadingPixles
int leadingPixles
-
trailingPixles
int trailingPixles
-
-
-
Class org.biojava.bio.gui.sequence.CircularRendererPanel extends javax.swing.JComponent implements Serializable
-
Serialized Fields
-
ctxt
CircularRendererContext ctxt
-
offset
double offset
-
radius
double radius
-
renderer
CircularRenderer renderer
-
symList
SymbolList symList
-
-
-
Class org.biojava.bio.gui.sequence.EllipticalBeadRenderer extends AbstractBeadRenderer implements Serializable
-
Serialized Fields
-
dimensionRatio
double dimensionRatio
-
-
-
Class org.biojava.bio.gui.sequence.FilteringRenderer extends SequenceRendererWrapper implements Serializable
-
Serialized Fields
-
contextCache
CacheMap contextCache
-
filter
FeatureFilter filter
-
flushers
java.util.Set flushers
-
recurse
boolean recurse
-
-
-
Class org.biojava.bio.gui.sequence.GappedRenderer extends SequenceRendererWrapper implements Serializable
-
Class org.biojava.bio.gui.sequence.GlyphFeatureRenderer extends FilteringRenderer implements Serializable
- serialVersionUID:
- 7005846487574725181L
-
Serialized Fields
-
depth
double depth
-
fList
java.util.List<FeatureFilter> fList
-
gList
java.util.List<Glyph> gList
-
-
Class org.biojava.bio.gui.sequence.ImageMap.ClientSide extends java.lang.Object implements Serializable
-
Serialized Fields
-
hotSpots
java.util.List hotSpots
-
name
java.lang.String name
-
-
-
Class org.biojava.bio.gui.sequence.ImageMap.HotSpot extends java.lang.Object implements Serializable
-
Serialized Fields
-
coordinates
java.lang.Integer[] coordinates
-
type
java.lang.String type
-
url
java.net.URL url
-
userObject
java.lang.Object userObject
-
-
-
Class org.biojava.bio.gui.sequence.ImageMap.ServerSide extends java.lang.Object implements Serializable
-
Serialized Fields
-
hotSpots
java.util.List hotSpots
-
-
-
Class org.biojava.bio.gui.sequence.MultiLineRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
renderers
java.util.List renderers
-
-
-
Class org.biojava.bio.gui.sequence.OverlayRendererWrapper extends AbstractChangeable implements Serializable
-
Serialized Fields
-
renderer
SequenceRenderer renderer
-
-
-
Class org.biojava.bio.gui.sequence.PaddingRenderer extends SequenceRendererWrapper implements Serializable
-
Serialized Fields
-
padding
double padding
-
-
-
Class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
line
java.awt.geom.Line2D.Float line
line
is the line to be drawn for each feature. -
outline
java.awt.Paint outline
outline
is the line colour.
-
-
-
Class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
cacheFlushers
java.util.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 extends AbstractChangeable implements Serializable
-
Serialized Fields
-
renderers
java.util.List renderers
-
-
-
Class org.biojava.bio.gui.sequence.PairwiseSequencePanel extends javax.swing.JComponent implements Serializable
-
Serialized Fields
-
direction
int direction
-
hints
java.awt.RenderingHints hints
-
layoutListener
ChangeListener layoutListener
-
leadingBorder
SequenceRenderContext.Border leadingBorder
-
mouseListener
java.awt.event.MouseListener mouseListener
-
mouseMotionListener
java.awt.event.MouseMotionListener mouseMotionListener
-
propertyListener
java.beans.PropertyChangeListener propertyListener
-
renderer
PairwiseSequenceRenderer renderer
-
repaintListener
ChangeListener repaintListener
-
scale
double scale
-
secDirection
int secDirection
-
secSequence
Sequence secSequence
-
secTranslation
int secTranslation
-
sequence
Sequence sequence
-
svmSupport
SequenceViewerMotionSupport svmSupport
-
svSupport
SequenceViewerSupport svSupport
-
trailingBorder
SequenceRenderContext.Border trailingBorder
-
translation
int translation
-
-
-
Class org.biojava.bio.gui.sequence.PeptideDigestRenderer extends AbstractPeptideDigestRenderer implements Serializable
-
Serialized Fields
-
defaultPaint
java.awt.Paint defaultPaint
-
-
-
Class org.biojava.bio.gui.sequence.RectangularBeadRenderer extends AbstractBeadRenderer implements Serializable
-
Serialized Fields
-
rect
java.awt.geom.Rectangle2D rect
-
scaleHeight
boolean scaleHeight
-
-
-
Class org.biojava.bio.gui.sequence.RectangularImapRenderer extends java.lang.Object implements Serializable
-
Serialized Fields
-
imageMap
ImageMap imageMap
-
renderer
RectangularBeadRenderer renderer
-
urlFactory
URLFactory urlFactory
-
-
-
Class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer extends AbstractBeadRenderer implements Serializable
-
Serialized Fields
-
arcHeight
double arcHeight
-
arcWidth
double arcWidth
-
rect
java.awt.geom.RoundRectangle2D rect
-
-
-
Class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer extends GlyphFeatureRenderer implements Serializable
-
Class org.biojava.bio.gui.sequence.SequencePanel extends javax.swing.JComponent implements Serializable
-
Serialized Fields
-
direction
int direction
-
hints
java.awt.RenderingHints hints
-
layoutListener
ChangeListener layoutListener
-
leadingBorder
SequenceRenderContext.Border leadingBorder
-
mouseListener
java.awt.event.MouseListener mouseListener
-
mouseMotionListener
java.awt.event.MouseMotionListener mouseMotionListener
-
pixelOffset
double pixelOffset
-
range
RangeLocation range
-
renderer
SequenceRenderer renderer
-
repaintListener
ChangeListener repaintListener
-
scale
double scale
-
sequence
SymbolList sequence
-
svmSupport
SequenceViewerMotionSupport svmSupport
-
svSupport
SequenceViewerSupport svSupport
-
theMonitor
org.biojava.bio.gui.sequence.SequencePanel.RendererMonitor theMonitor
-
trailingBorder
SequenceRenderContext.Border trailingBorder
-
-
-
Class org.biojava.bio.gui.sequence.SequencePanel.Border extends java.lang.Object implements Serializable
-
Serialized Fields
-
alignment
int alignment
-
pcs
java.beans.PropertyChangeSupport pcs
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequencePanelWrapper extends javax.swing.JPanel implements Serializable
- serialVersionUID:
- 8749249181471157230L
-
Serialized Fields
-
direction
int direction
-
hints
java.awt.RenderingHints hints
-
motionListeners
java.util.List<SequenceViewerMotionListener> motionListeners
-
range
RangeLocation range
-
renderer
SequenceRenderer renderer
-
scale
double scale
-
seqPanels
SequencePanel[] seqPanels
-
sequence
Sequence sequence
-
trackLayout
TrackLayout trackLayout
-
viewerListeners
java.util.List<SequenceViewerListener> viewerListeners
-
-
Class org.biojava.bio.gui.sequence.SequencePoster extends javax.swing.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
java.awt.event.MouseListener mouseListener
Deprecated. -
mouseMotionListener
java.awt.event.MouseMotionListener mouseMotionListener
Deprecated. -
offsets
double[] offsets
Deprecated. -
realLines
int realLines
Deprecated. -
renderer
SequenceRenderer renderer
Deprecated. -
renderingHints
java.awt.RenderingHints renderingHints
Deprecated. -
repaintListener
ChangeListener repaintListener
Deprecated. -
scale
double scale
Deprecated. -
sequence
Sequence sequence
Deprecated. -
spacer
int spacer
Deprecated. -
svmSupport
SequenceViewerMotionSupport svmSupport
Deprecated. -
svSupport
SequenceViewerSupport svSupport
Deprecated. -
symbolsPerLine
int symbolsPerLine
Deprecated. -
theMonitor
org.biojava.bio.gui.sequence.SequencePoster.RendererMonitor theMonitor
Deprecated. -
trailingBorder
SequenceRenderContext.Border trailingBorder
Deprecated.
-
-
-
Class org.biojava.bio.gui.sequence.SequencePoster.Border extends java.lang.Object implements Serializable
-
Serialized Fields
-
alignment
int alignment
-
pcs
java.beans.PropertyChangeSupport pcs
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border extends java.lang.Object implements Serializable
-
Serialized Fields
-
alignment
int alignment
-
size
double size
-
-
-
Class org.biojava.bio.gui.sequence.SequenceRendererWrapper extends AbstractChangeable implements Serializable
-
Serialized Fields
-
renderer
SequenceRenderer renderer
-
-
-
Class org.biojava.bio.gui.sequence.SequenceViewerEvent extends java.util.EventObject implements Serializable
-
Serialized Fields
-
mouseEvent
java.awt.event.MouseEvent mouseEvent
-
path
java.util.List path
-
pos
int pos
-
target
java.lang.Object target
-
-
-
Class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
pane
SixFrameRenderer pane
-
-
-
Class org.biojava.bio.gui.sequence.TranslatedSequencePanel extends javax.swing.JComponent implements Serializable
- serialVersionUID:
- 3269477379497205817L
-
Serialized Fields
-
direction
int direction
-
hints
java.awt.RenderingHints hints
-
layoutListener
ChangeListener layoutListener
-
leadingBorder
SequenceRenderContext.Border leadingBorder
-
mouseListener
java.awt.event.MouseListener mouseListener
-
mouseMotionListener
java.awt.event.MouseMotionListener mouseMotionListener
-
propertyListener
java.beans.PropertyChangeListener propertyListener
-
renderer
SequenceRenderer renderer
-
rendererBorders
double rendererBorders
-
repaintListener
ChangeListener repaintListener
-
scale
double scale
-
sequence
SymbolList sequence
-
svmSupport
SequenceViewerMotionSupport svmSupport
-
svSupport
SequenceViewerSupport svSupport
-
trailingBorder
SequenceRenderContext.Border trailingBorder
-
translation
int translation
-
-
Class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer extends AbstractChangeable implements Serializable
-
Serialized Fields
-
blockDepth
double blockDepth
-
fill
java.awt.Paint fill
-
outline
java.awt.Paint outline
-
-
-
Class org.biojava.bio.gui.sequence.ZiggyImapRenderer extends java.lang.Object implements Serializable
-
Serialized Fields
-
imageMap
ImageMap imageMap
-
renderer
ZiggyFeatureRenderer renderer
-
urlFactory
URLFactory urlFactory
-
-
-
-
Package org.biojava.bio.molbio
-
Class org.biojava.bio.molbio.RestrictionEnzyme extends java.lang.Object implements Serializable
-
Serialized Fields
-
cutType
int cutType
-
dsCutPositions
int[] dsCutPositions
-
forwardRegex
java.lang.String forwardRegex
-
name
java.lang.String name
-
prototype
RestrictionEnzyme prototype
-
reverseRegex
java.lang.String reverseRegex
-
site
SymbolList site
-
size
double size
-
summary
java.lang.String summary
-
usCutPositions
int[] usCutPositions
-
-
-
Class org.biojava.bio.molbio.RestrictionSite.Template extends StrandedFeature.Template implements Serializable
-
Serialized Fields
-
enzyme
RestrictionEnzyme enzyme
enzyme
RestrictionEnzyme
field.
-
-
-
-
Package org.biojava.bio.program.abi
-
Class org.biojava.bio.program.abi.ABIFChromatogram extends AbstractChromatogram implements Serializable
-
-
Package org.biojava.bio.program.gff
-
Class org.biojava.bio.program.gff.IgnoreRecordException extends java.lang.Exception implements Serializable
-
-
Package org.biojava.bio.program.hmmer
-
Class org.biojava.bio.program.hmmer.FullHmmerProfileHMM extends SimpleMarkovModel implements Serializable
-
Serialized Fields
-
c
EmissionState c
-
hmmState
ModelInState hmmState
-
j
EmissionState j
-
n
EmissionState n
-
-
-
Class org.biojava.bio.program.hmmer.HmmerProfileHMM extends ProfileHMM implements Serializable
-
Class org.biojava.bio.program.hmmer.ProfileEmissionState extends SimpleEmissionState implements Serializable
-
-
Package org.biojava.bio.program.homologene
-
Class org.biojava.bio.program.homologene.DuplicateTaxonException extends BioException implements Serializable
-
-
Package org.biojava.bio.program.phred
-
Class org.biojava.bio.program.phred.PhredFormat extends java.lang.Object implements Serializable
-
Serialized Fields
-
lineWidth
int lineWidth
The line width for output. -
mListeners
java.util.Vector mListeners
-
-
-
Class org.biojava.bio.program.phred.PhredSequence extends SimpleSequence implements Serializable
-
-
Package org.biojava.bio.program.ssaha
-
Class org.biojava.bio.program.ssaha.SearchException extends java.lang.Exception implements Serializable
-
-
Package org.biojava.bio.proteomics
-
Class org.biojava.bio.proteomics.Protease extends java.lang.Object implements Serializable
-
Serialization Methods
-
readResolve
protected java.lang.Object readResolve() throws java.io.ObjectStreamException
Prevent duplication of the object during Serialization- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
cleavageResidues
SymbolList cleavageResidues
-
endoProtease
boolean endoProtease
-
name
java.lang.String name
-
notCleaveResidues
SymbolList notCleaveResidues
-
-
-
-
Package org.biojava.bio.search
-
Class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter extends java.lang.Object implements Serializable
-
Serialized Fields
-
cachedOutcome
TriState cachedOutcome
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.ByHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
-
Serialized Fields
-
key
java.lang.Object key
-
test
FilterTest test
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.BySearchProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
-
Serialized Fields
-
key
java.lang.Object key
-
test
FilterTest test
-
-
-
Class org.biojava.bio.search.BlastLikeSearchFilter.BySubHitProperty extends BlastLikeSearchFilter.AbstractBlastLikeSearchFilter implements Serializable
-
Serialized Fields
-
key
java.lang.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
-
Class org.biojava.bio.seq.Feature.Template extends java.lang.Object implements Serializable
-
Serialized Fields
-
annotation
Annotation annotation
-
location
Location location
-
source
java.lang.String source
-
sourceTerm
Term sourceTerm
-
type
java.lang.String type
-
typeTerm
Term typeTerm
-
-
-
Class org.biojava.bio.seq.FeatureFilter.And extends java.lang.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
java.lang.Object key
-
value
java.lang.Object value
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByAncestor extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByAnnotation extends FeatureFilter.ByAnnotationType implements Serializable
-
Serialized Fields
-
key
java.lang.Object key
-
value
java.lang.Object value
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByAnnotationType extends java.lang.Object implements Serializable
-
Serialized Fields
-
type
AnnotationType type
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByChild extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByClass extends java.lang.Object implements Serializable
-
Serialized Fields
-
clazz
java.lang.Class clazz
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByComponentName extends java.lang.Object implements Serializable
-
Serialized Fields
-
cname
java.lang.String cname
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByDescendant extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByFeature extends java.lang.Object implements Serializable
-
Serialized Fields
-
feature
Feature feature
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore extends java.lang.Object implements Serializable
-
Serialized Fields
-
hashCode
int hashCode
-
maxScore
double maxScore
-
minScore
double minScore
-
score
double score
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByParent extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.BySequenceName extends java.lang.Object implements Serializable
-
Serialized Fields
-
seqName
java.lang.String seqName
-
-
-
Class org.biojava.bio.seq.FeatureFilter.BySource extends java.lang.Object implements Serializable
-
Serialized Fields
-
source
java.lang.String source
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ByType extends java.lang.Object implements Serializable
-
Serialized Fields
-
type
java.lang.String type
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ContainedByLocation extends java.lang.Object implements Serializable
-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.FrameFilter extends java.lang.Object implements Serializable
-
Serialized Fields
-
frame
FramedFeature.ReadingFrame frame
-
-
-
Class org.biojava.bio.seq.FeatureFilter.HasAnnotation extends FeatureFilter.ByAnnotationType implements Serializable
-
Serialized Fields
-
key
java.lang.Object key
-
-
-
Class org.biojava.bio.seq.FeatureFilter.Not extends java.lang.Object implements Serializable
-
Serialized Fields
-
child
FeatureFilter child
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OnlyChildren extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OnlyDescendants extends java.lang.Object implements Serializable
-
Serialized Fields
-
filter
FeatureFilter filter
-
-
-
Class org.biojava.bio.seq.FeatureFilter.Or extends java.lang.Object implements Serializable
-
Serialized Fields
-
c1
FeatureFilter c1
-
c2
FeatureFilter c2
-
-
-
Class org.biojava.bio.seq.FeatureFilter.OverlapsLocation extends java.lang.Object implements Serializable
-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation extends java.lang.Object implements Serializable
-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation extends java.lang.Object implements Serializable
-
Serialized Fields
-
loc
Location loc
-
-
-
Class org.biojava.bio.seq.FeatureFilter.StrandFilter extends java.lang.Object implements Serializable
-
Serialized Fields
-
strand
StrandedFeature.Strand strand
-
-
-
Class org.biojava.bio.seq.FramedFeature.ReadingFrame extends java.lang.Object implements Serializable
-
Serialized Fields
-
frame
int frame
-
text
java.lang.String text
-
-
-
Class org.biojava.bio.seq.FramedFeature.Template extends StrandedFeature.Template implements Serializable
-
Serialized Fields
-
readingFrame
FramedFeature.ReadingFrame readingFrame
-
-
-
Class org.biojava.bio.seq.MergeFeatureHolder extends AbstractFeatureHolder implements Serializable
-
Serialized Fields
-
featureHolders
java.util.List featureHolders
-
-
-
Class org.biojava.bio.seq.RemoteFeature.Template extends StrandedFeature.Template implements Serializable
-
Serialized Fields
-
regions
java.util.List regions
-
resolver
RemoteFeature.Resolver resolver
-
-
-
Class org.biojava.bio.seq.SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable
-
Serialized Fields
-
features
java.util.List features
The child features. -
schema
FeatureFilter schema
-
-
-
Class org.biojava.bio.seq.SimpleFeatureRealizer extends java.lang.Object implements Serializable
-
Serialized Fields
-
fallBack
FeatureRealizer fallBack
-
templateToImpl
java.util.List templateToImpl
-
-
-
Class org.biojava.bio.seq.StrandedFeature.Strand extends java.lang.Object implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
text
java.lang.String text
-
token
char token
-
value
int value
-
-
-
Class org.biojava.bio.seq.StrandedFeature.Template extends Feature.Template implements Serializable
-
Serialized Fields
-
strand
StrandedFeature.Strand strand
-
-
-
-
Package org.biojava.bio.seq.db
-
Class org.biojava.bio.seq.db.AnnotatedSequenceDB extends AbstractSequenceDB implements Serializable
-
Serialized Fields
-
annotator
SequenceAnnotator annotator
-
parent
SequenceDB parent
-
-
-
Class org.biojava.bio.seq.db.CachingSequenceDB extends SequenceDBWrapper implements Serializable
-
Serialization Methods
-
readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
-
-
Class org.biojava.bio.seq.db.HashSequenceDB extends AbstractSequenceDB implements Serializable
-
Serialized Fields
-
idMaker
IDMaker idMaker
An object to extract an ID for a sequence. -
name
java.lang.String name
The name of this sequence database. -
sequenceByID
java.util.Map sequenceByID
The sequence-by-id map.
-
-
-
Class org.biojava.bio.seq.db.IDMaker.ByName extends java.lang.Object implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.IOException
- Throws:
java.io.IOException
-
-
-
Class org.biojava.bio.seq.db.IDMaker.ByURN extends java.lang.Object implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.IOException
- Throws:
java.io.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
java.util.Set ids
-
-
-
Class org.biojava.bio.seq.db.TabIndexStore extends java.lang.Object implements Serializable
-
Serialization Methods
-
readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
-
Serialized Fields
-
files
java.util.Set files
-
format
SequenceFormat format
-
indexFile
java.io.File indexFile
-
name
java.lang.String name
-
sbFactory
SequenceBuilderFactory sbFactory
-
seqFileIndex
java.io.File[] seqFileIndex
-
storeFile
java.io.File storeFile
-
symbolParser
SymbolTokenization symbolParser
-
-
-
Class org.biojava.bio.seq.db.ViewingSequenceDB extends SequenceDBWrapper implements Serializable
-
-
Package org.biojava.bio.seq.homol
-
Class org.biojava.bio.seq.homol.HomologyFeature.Template extends StrandedFeature.Template implements Serializable
-
Serialized Fields
-
homology
Homology homology
-
-
-
Class org.biojava.bio.seq.homol.SimilarityPairFeature.Template extends StrandedFeature.Template implements Serializable
-
Serialized Fields
-
alignment
Alignment alignment
alignment
Alignment
field. -
score
double score
score
of the search which produced the alignment. -
sibling
SimilarityPairFeature sibling
sibling
SimilarityPairFeature
field. May be null if the reciprocalSimilarityPairFeature
has not yet been created.
-
-
-
-
Package org.biojava.bio.seq.impl
-
Class org.biojava.bio.seq.impl.RevCompSequence extends SimpleSequence implements Serializable
-
Serialized Fields
-
origSeq
Sequence origSeq
-
pfh
ProjectedFeatureHolder pfh
-
-
-
Class org.biojava.bio.seq.impl.SimpleFeature extends AbstractChangeable implements Serializable
-
Serialized Fields
-
annotation
Annotation annotation
The annotation object. This is lazily instantiated. -
featureHolder
SimpleFeatureHolder featureHolder
The FeatureHolder that we will delegate the FeatureHolder interface too. This is lazily instantiated. -
loc
Location loc
The location of this feature. -
parent
FeatureHolder parent
Our parent FeatureHolder. -
source
java.lang.String source
The source of this feature - the program that generated it. This is included for cheap interoperability with GFF. -
sourceTerm
Term sourceTerm
-
type
java.lang.String type
The type of this feature - something like Exon. This is included for cheap interoperability with GFF. -
typeTerm
Term typeTerm
-
-
-
Class org.biojava.bio.seq.impl.SimpleFramedFeature extends SimpleStrandedFeature implements Serializable
-
Serialized Fields
-
readingFrame
FramedFeature.ReadingFrame readingFrame
-
-
-
Class org.biojava.bio.seq.impl.SimpleGappedSequence extends SimpleGappedSymbolList implements Serializable
- serialVersionUID:
- -791305118810523245L
-
Serialized Fields
-
createOnUnderlying
boolean createOnUnderlying
-
features
MergeFeatureHolder features
-
localFeatures
SimpleFeatureHolder localFeatures
-
projectedFeatures
FeatureHolder projectedFeatures
-
sequence
Sequence sequence
-
-
Class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext extends ReparentContext implements Serializable
- serialVersionUID:
- 8878073952684354286L
-
Class org.biojava.bio.seq.impl.SimpleHomologyFeature extends SimpleStrandedFeature implements Serializable
-
Serialized Fields
-
homology
Homology homology
-
-
-
Class org.biojava.bio.seq.impl.SimpleRemoteFeature extends SimpleStrandedFeature implements Serializable
-
Serialized Fields
-
regions
java.util.List regions
-
resolver
RemoteFeature.Resolver resolver
-
-
-
Class org.biojava.bio.seq.impl.SimpleRestrictionSite extends SimpleStrandedFeature implements Serializable
-
Serialized Fields
-
enzyme
RestrictionEnzyme enzyme
-
position
int position
-
-
-
Class org.biojava.bio.seq.impl.SimpleSequence extends AbstractChangeable implements Serializable
- serialVersionUID:
- -8681680737943980721L
-
Serialized Fields
-
annotation
Annotation annotation
-
featureHolder
SimpleFeatureHolder featureHolder
-
name
java.lang.String name
-
symList
SymbolList symList
Delegate SymbolList. -
urn
java.lang.String urn
-
-
Class org.biojava.bio.seq.impl.SimpleSequenceFactory extends java.lang.Object implements Serializable
-
Serialized Fields
-
realizer
FeatureRealizer realizer
-
-
-
Class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature extends SimpleStrandedFeature implements Serializable
-
Serialized Fields
-
alignment
Alignment alignment
-
score
double score
-
sibling
SimilarityPairFeature sibling
-
-
-
Class org.biojava.bio.seq.impl.SimpleStrandedFeature extends SimpleFeature implements Serializable
-
Serialized Fields
-
strand
StrandedFeature.Strand strand
-
-
-
Class org.biojava.bio.seq.impl.SubSequence extends java.lang.Object implements Serializable
-
Serialized Fields
-
annotation
Annotation annotation
-
name
java.lang.String name
-
parent
Sequence parent
-
parentLocation
RangeLocation parentLocation
-
symbols
SymbolList symbols
-
uri
java.lang.String uri
-
-
-
Class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext extends ReparentContext implements Serializable
-
Serialized Fields
-
clippingFilter
FeatureFilter clippingFilter
-
parentLocation
RangeLocation parentLocation
-
remoteLocationFilter
FeatureFilter remoteLocationFilter
-
-
-
Class org.biojava.bio.seq.impl.ViewSequence extends Unchangeable implements Serializable
- serialVersionUID:
- 9866447L
-
Serialization Methods
-
readObject
private void readObject(java.io.ObjectInputStream s) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
-
Serialized Fields
-
addedFeatures
SimpleFeatureHolder addedFeatures
-
anno
Annotation anno
Our annotation. -
exposedFeatures
MergeFeatureHolder exposedFeatures
FeatureHolder support -
name
java.lang.String name
IDs -
seqDelegate
Sequence seqDelegate
Delegate Sequence. -
urn
java.lang.String urn
-
-
-
Package org.biojava.bio.seq.io
-
Class org.biojava.bio.seq.io.AlternateTokenization extends Unchangeable implements Serializable
-
Serialized Fields
-
alphabet
Alphabet alphabet
-
caseSensitive
boolean caseSensitive
-
initiated
boolean initiated
-
symbolsToStrings
java.util.Map symbolsToStrings
-
width
int width
-
-
-
Class org.biojava.bio.seq.io.CharacterTokenization extends Unchangeable implements Serializable
-
Serialized Fields
-
alphabet
Alphabet alphabet
-
caseSensitive
boolean caseSensitive
-
charactersToSymbols
java.util.Map charactersToSymbols
-
symbolsToCharacters
java.util.Map symbolsToCharacters
-
-
-
Class org.biojava.bio.seq.io.CrossProductTokenization extends WordTokenization implements Serializable
-
Serialized Fields
-
subTokenizations
java.util.List subTokenizations
-
-
-
Class org.biojava.bio.seq.io.DoubleTokenization extends WordTokenization implements Serializable
-
Class org.biojava.bio.seq.io.EmblLikeFormat extends java.lang.Object implements Serializable
-
Serialized Fields
-
elideSymbols
boolean elideSymbols
Deprecated. -
mListeners
java.util.Vector mListeners
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.EmblProcessor.Factory extends java.lang.Object implements Serializable
-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory extends java.lang.Object implements Serializable
-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.FastaFormat extends java.lang.Object implements Serializable
-
Serialized Fields
-
lineWidth
int lineWidth
Deprecated.The line width for output. -
mListeners
java.util.Vector mListeners
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.GenbankFormat extends java.lang.Object implements Serializable
-
Serialized Fields
-
elideSymbols
boolean elideSymbols
Deprecated. -
mListeners
java.util.Vector mListeners
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.GenbankProcessor.Factory extends java.lang.Object implements Serializable
-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.GenbankXmlFormat extends GenbankFormat implements Serializable
-
Serialized Fields
-
m_handler
org.biojava.bio.seq.io.GenbankXmlFormat.GenbankXmlHandler m_handler
Deprecated. -
m_parsed
boolean m_parsed
Deprecated. -
m_sequenceIndex
int m_sequenceIndex
Deprecated. -
m_xmlParser
javax.xml.parsers.SAXParser m_xmlParser
Deprecated.
-
-
-
Class org.biojava.bio.seq.io.GenpeptFormat extends GenbankFormat implements Serializable
-
Class org.biojava.bio.seq.io.IntegerTokenization extends WordTokenization implements Serializable
-
Class org.biojava.bio.seq.io.NameTokenization extends WordTokenization implements Serializable
-
Serialized Fields
-
caseSensitive
boolean caseSensitive
-
-
-
Class org.biojava.bio.seq.io.OrganismParser.Factory extends java.lang.Object implements Serializable
-
Serialized Fields
-
commonNameKey
java.lang.String commonNameKey
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
ncbiTaxonKey
java.lang.String ncbiTaxonKey
-
sciNameKey
java.lang.String sciNameKey
-
taxonFactory
TaxonFactory taxonFactory
-
taxonParser
TaxonParser taxonParser
-
-
-
Class org.biojava.bio.seq.io.ParseException extends BioException implements Serializable
-
Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory extends java.lang.Object implements Serializable
-
Serialized Fields
-
delegateFactory
SequenceBuilderFactory delegateFactory
-
-
-
Class org.biojava.bio.seq.io.ReferenceAnnotation extends AbstractAnnotation implements Serializable
-
Serialized Fields
-
properties
java.util.Map properties
Deprecated.The properties map. This may be null if no property values have yet been set.
-
-
-
Class org.biojava.bio.seq.io.SubIntegerTokenization extends WordTokenization implements Serializable
-
Class org.biojava.bio.seq.io.SwissprotProcessor.Factory extends java.lang.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 java.lang.Object implements Serializable
-
Serialized Fields
-
parent
FeatureHolder parent
-
wrapped
FeatureHolder wrapped
-
-
-
Class org.biojava.bio.seq.projection.TranslateFlipContext extends ReparentContext implements Serializable
-
Serialized Fields
-
oppositeStrand
boolean oppositeStrand
-
translation
int translation
-
-
-
-
Package org.biojava.bio.symbol
-
Class org.biojava.bio.symbol.AbstractAlphabet extends AbstractChangeable implements Serializable
- serialVersionUID:
- -3043128839927615753L
-
Serialization Methods
-
readResolve
protected java.lang.Object readResolve() throws java.io.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:
java.io.ObjectStreamException
-
-
Serialized Fields
-
ambCache
java.util.Map ambCache
-
registered
boolean registered
-
tokenizationsByName
java.util.Map tokenizationsByName
-
-
Class org.biojava.bio.symbol.AbstractLocation extends java.lang.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(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
-
Serialized Fields
-
alpha
Alphabet alpha
-
chunks
SymbolList[] chunks
-
chunkSize
int chunkSize
-
length
int length
-
-
-
Class org.biojava.bio.symbol.DNAAmbPack extends java.lang.Object implements Serializable
-
Serialized Fields
-
syms
Symbol[] syms
-
-
-
Class org.biojava.bio.symbol.DNANoAmbPack extends java.lang.Object implements Serializable
-
Serialized Fields
-
placeHolder
byte placeHolder
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet extends Unchangeable implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
alphabets
java.util.List alphabets
-
doubleToSym
WeakValueHashMap doubleToSym
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange extends Unchangeable implements Serializable
-
Serialized Fields
-
matches
Alphabet matches
-
maxVal
double maxVal
-
minVal
double minVal
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol extends Unchangeable implements Serializable
-
Serialized Fields
-
matches
Alphabet matches
-
val
double val
-
-
-
Class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet extends Unchangeable implements Serializable
-
Serialization Methods
-
readResolve
protected java.lang.Object readResolve() throws java.io.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:
java.io.ObjectStreamException
-
-
Serialized Fields
-
max
double max
-
min
double min
-
name
java.lang.String name
-
-
-
Class org.biojava.bio.symbol.DummySymbolList extends AbstractSymbolList implements Serializable
-
Class org.biojava.bio.symbol.Edit extends java.lang.Object implements Serializable
-
Serialized Fields
-
length
int length
-
pos
int pos
-
props
java.util.Map<java.lang.String,java.lang.Object> props
-
replacement
SymbolList replacement
-
-
-
Class org.biojava.bio.symbol.FundamentalAtomicSymbol extends AbstractSymbol implements Serializable
-
Serialized Fields
-
annotation
Annotation annotation
-
name
java.lang.String name
-
-
-
Class org.biojava.bio.symbol.FuzzyLocation extends AbstractRangeLocation implements Serializable
-
Serialized Fields
-
innerMax
int innerMax
-
innerMin
int innerMin
-
mIsMaxFuzzy
boolean mIsMaxFuzzy
-
mIsMinFuzzy
boolean mIsMinFuzzy
-
outerMax
int outerMax
-
outerMin
int outerMin
-
resolver
FuzzyLocation.RangeResolver resolver
-
-
-
Class org.biojava.bio.symbol.FuzzyPointLocation extends AbstractLocation implements Serializable
-
Serialized Fields
-
max
int max
-
min
int min
-
resolver
FuzzyPointLocation.PointResolver resolver
-
-
-
Class org.biojava.bio.symbol.IllegalAlphabetException extends BioException implements Serializable
-
Class org.biojava.bio.symbol.IllegalSymbolException extends BioException implements Serializable
-
Serialized Fields
-
sym
Symbol sym
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet extends Unchangeable implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
intToSym
WeakValueHashMap intToSym
Canonicalization map for ints and references to symbols.
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol extends Unchangeable implements Serializable
-
Serialized Fields
-
matches
Alphabet matches
-
val
int val
-
-
-
Class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet extends AbstractAlphabet implements Serializable
-
Serialized Fields
-
max
int max
-
min
int min
-
name
java.lang.String name
-
-
-
Class org.biojava.bio.symbol.MergeLocation extends RangeLocation implements Serializable
-
Serialized Fields
-
componentLocations
java.util.List componentLocations
-
-
-
Class org.biojava.bio.symbol.PackedSymbolList extends AbstractSymbolList implements Serializable
-
Serialized Fields
-
currentMax
int currentMax
-
currentMin
int currentMin
-
currentWord
long currentWord
-
length
int length
-
mask
byte mask
-
packing
Packing packing
-
syms
long[] syms
-
symsPerElement
byte symsPerElement
-
wordsize
int wordsize
-
-
-
Class org.biojava.bio.symbol.PointLocation extends AbstractRangeLocation implements Serializable
-
Serialized Fields
-
point
int point
The actual index contained.
-
-
-
Class org.biojava.bio.symbol.RangeLocation extends AbstractRangeLocation implements Serializable
-
Serialized Fields
-
max
int max
The maximum point contained. -
min
int min
The minimum point contained.
-
-
-
Class org.biojava.bio.symbol.SimpleAlphabet extends AbstractAlphabet implements Serializable
- serialVersionUID:
- 216254146L
-
Serialized Fields
-
alphabets
java.util.List alphabets
A list of alphabets that make up this one - a singleton list containing this. -
annotation
Annotation annotation
-
name
java.lang.String name
-
symbols
java.util.Set symbols
-
-
Class org.biojava.bio.symbol.SimpleAtomicSymbol extends org.biojava.bio.symbol.AbstractSimpleBasisSymbol implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace()
-
-
-
Class org.biojava.bio.symbol.SimpleGappedSymbolList extends AbstractSymbolList implements Serializable
- serialVersionUID:
- 4258621048300499709L
-
Serialized Fields
-
alpha
Alphabet alpha
The Alphabet - the same as source but guaranteed to include the gap character. -
blocks
java.util.List<SimpleGappedSymbolList.Block> blocks
The list of ungapped blocks that align between source and this view. -
length
int length
The total length of the alignment - necessary to allow leading & trailing gaps. -
source
SymbolList source
The SymbolList to view.
-
-
Class org.biojava.bio.symbol.SimpleGappedSymbolList.Block extends java.lang.Object implements Serializable
- serialVersionUID:
- 4090888450309921439L
-
Serialized Fields
-
sourceEnd
int sourceEnd
-
sourceStart
int sourceStart
-
viewEnd
int viewEnd
-
viewStart
int viewStart
-
-
Class org.biojava.bio.symbol.SimpleGeneticCodeTable extends SimpleManyToOneTranslationTable implements Serializable
-
Serialized Fields
-
description
java.lang.String description
-
table_num
int table_num
-
-
-
Class org.biojava.bio.symbol.SimpleManyToOneTranslationTable extends AbstractManyToOneTranslationTable implements Serializable
-
Serialized Fields
-
revMap
java.util.Map revMap
-
source
FiniteAlphabet source
-
target
Alphabet target
-
transMap
java.util.Map transMap
-
-
-
Class org.biojava.bio.symbol.SimpleReversibleTranslationTable extends AbstractReversibleTranslationTable implements Serializable
-
Serialized Fields
-
revMap
java.util.Map revMap
-
source
FiniteAlphabet source
-
target
Alphabet target
-
transMap
java.util.Map transMap
-
-
-
Class org.biojava.bio.symbol.SimpleSymbolList extends AbstractSymbolList implements Serializable
- serialVersionUID:
- -9015317520644706924L
-
Serialized Fields
-
alphabet
Alphabet alphabet
-
isView
boolean isView
-
length
int length
-
referenceSymbolList
SymbolList referenceSymbolList
-
symbols
Symbol[] symbols
-
viewOffset
int viewOffset
-
-
Class org.biojava.bio.symbol.SimpleTranslationTable extends org.biojava.bio.symbol.AbstractTranslationTable implements Serializable
-
Serialized Fields
-
source
FiniteAlphabet source
-
target
Alphabet target
-
transMap
java.util.Map transMap
-
-
-
Class org.biojava.bio.symbol.SingletonAlphabet extends AbstractAlphabet implements Serializable
-
Serialized Fields
-
alphabets
java.util.List alphabets
-
sym
AtomicSymbol sym
-
-
-
Class org.biojava.bio.symbol.SuffixTree extends java.lang.Object implements Serializable
-
Serialized Fields
-
alphabet
FiniteAlphabet alphabet
-
counts
java.util.List counts
-
indexer
AlphabetIndex indexer
-
root
SuffixTree.SuffixNode root
-
-
-
Class org.biojava.bio.symbol.SuffixTree.SuffixNode extends java.lang.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 java.lang.Exception implements Serializable
-
-
Package org.biojava.ontology
-
Class org.biojava.ontology.AlreadyExistsException extends OntologyException implements Serializable
-
Class org.biojava.ontology.DefaultOps extends java.lang.Object implements Serializable
-
Class org.biojava.ontology.InvalidTermException extends OntologyException implements Serializable
-
Class org.biojava.ontology.Ontology.Impl extends AbstractChangeable implements Serializable
- serialVersionUID:
- -8064461497813727957L
-
Serialized Fields
-
description
java.lang.String description
-
localRemoteTerms
java.util.Set<Term> localRemoteTerms
-
name
java.lang.String name
-
objectTriples
java.util.Map<Term,java.util.Set<Triple>> objectTriples
-
ops
OntologyOps ops
-
relationTriples
java.util.Map<Term,java.util.Set<Triple>> relationTriples
-
remoteTerms
java.util.Map<Term,RemoteTerm> remoteTerms
-
subjectTriples
java.util.Map<Term,java.util.Set<Triple>> subjectTriples
-
terms
java.util.Map<java.lang.String,Term> terms
-
triples
java.util.Set<Triple> triples
-
-
Class org.biojava.ontology.OntologyException extends java.lang.Exception implements Serializable
-
Class org.biojava.ontology.OntologyTerm.Impl extends AbstractChangeable implements Serializable
-
Class org.biojava.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
- serialVersionUID:
- 922700041939183676L
-
Class org.biojava.ontology.Term.Impl extends AbstractTerm implements Serializable
- serialVersionUID:
- 6561668917514377417L
-
Serialized Fields
-
annotation
Annotation annotation
-
name
java.lang.String name
-
ontology
Ontology ontology
-
synonyms
java.util.Set<java.lang.Object> synonyms
-
-
Class org.biojava.ontology.Triple.Impl extends Unchangeable implements Serializable
- serialVersionUID:
- 3807331980372839221L
-
Class org.biojava.ontology.Variable.Impl extends Term.Impl implements Serializable
-
-
Package org.biojava.stats.svm
-
Class org.biojava.stats.svm.CachingKernel extends NestedKernel implements Serializable
-
Class org.biojava.stats.svm.DiagonalAddKernel extends NestedKernel implements Serializable
-
Serialized Fields
-
lambda
double lambda
The scale vactor. -
negClass
java.util.Set negClass
-
posClass
java.util.Set posClass
-
-
-
Class org.biojava.stats.svm.DiagonalCachingKernel extends NestedKernel implements Serializable
-
Class org.biojava.stats.svm.LinearKernel extends java.lang.Object implements Serializable
-
Class org.biojava.stats.svm.ListSumKernel extends NestedKernel implements Serializable
-
Class org.biojava.stats.svm.NestedKernel extends java.lang.Object implements Serializable
-
Serialized Fields
-
nested
SVMKernel nested
The SVMKernel being wrapped.
-
-
-
Class org.biojava.stats.svm.NormalizingKernel extends NestedKernel implements Serializable
-
Class org.biojava.stats.svm.PolynomialKernel extends NestedKernel implements Serializable
-
Serialized Fields
-
a
double a
-
c
double c
-
order
double order
-
-
-
Class org.biojava.stats.svm.RadialBaseKernel extends NestedKernel implements Serializable
-
Serialized Fields
-
width
double width
-
-
-
Class org.biojava.stats.svm.SparseVector extends java.lang.Object implements Serializable
-
Serialized Fields
-
keys
int[] keys
-
size
int size
-
values
double[] values
-
-
-
Class org.biojava.stats.svm.SparseVector.NormalizingKernel extends java.lang.Object implements Serializable
-
Serialized Fields
-
s
SparseVector s
The sparse vector that performes the normalization.
-
-
-
Class org.biojava.stats.svm.TrainingEvent extends java.util.EventObject implements Serializable
-
-
Package org.biojava.stats.svm.tools
-
Class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier extends javax.swing.JComponent implements Serializable
-
Serialized Fields
-
addPos
boolean addPos
-
kernel
SVMKernel kernel
-
model
SVMClassifierModel model
-
negPaint
java.awt.Paint negPaint
-
negShape
java.awt.Shape negShape
-
plainPaint
java.awt.Paint plainPaint
-
posPaint
java.awt.Paint posPaint
-
posShape
java.awt.Shape posShape
-
svPaint
java.awt.Paint svPaint
-
target
SVMTarget target
-
-
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel extends java.lang.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 java.lang.Object implements Serializable
-
Serialized Fields
-
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler extends java.lang.Object implements Serializable
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar extends java.lang.Object implements Serializable
-
Serialized Fields
-
bSet
java.util.BitSet bSet
-
-
-
Class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler extends java.lang.Object implements Serializable
-
-
Package org.biojava.utils
-
Class org.biojava.utils.AssertionFailure extends java.lang.AssertionError implements Serializable
-
Class org.biojava.utils.ChangeEvent extends java.util.EventObject implements Serializable
-
Serialized Fields
-
chain
ChangeEvent chain
-
change
java.lang.Object change
-
previous
java.lang.Object previous
-
type
ChangeType type
-
-
-
Class org.biojava.utils.ChangeType extends java.lang.Object implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace()
Make a placeholder for this object in a serialized stream.
-
-
Serialized Fields
-
name
java.lang.String name
-
ourField
java.lang.reflect.Field ourField
-
superType
ChangeType superType
-
-
-
Class org.biojava.utils.ChangeVetoException extends java.lang.RuntimeException implements Serializable
-
Serialized Fields
-
change
ChangeEvent change
-
-
-
Class org.biojava.utils.CommitFailure extends java.lang.Exception implements Serializable
-
Class org.biojava.utils.ListTools extends java.lang.Object implements Serializable
-
Class org.biojava.utils.ListTools.Doublet extends java.util.AbstractList implements Serializable
-
Serialized Fields
-
a
java.lang.Object a
-
b
java.lang.Object b
-
-
-
Class org.biojava.utils.ListTools.Triplet extends java.util.AbstractList implements Serializable
-
Serialized Fields
-
a
java.lang.Object a
-
b
java.lang.Object b
-
c
java.lang.Object c
-
-
-
Class org.biojava.utils.ParseErrorEvent extends java.util.EventObject implements Serializable
-
Serialized Fields
-
mMessage
java.lang.String mMessage
-
-
-
Class org.biojava.utils.ParserException extends java.lang.Exception implements Serializable
-
Serialized Fields
-
character
int character
-
line
java.lang.String line
-
lineNumber
int lineNumber
-
locator
java.lang.String locator
-
-
-
Class org.biojava.utils.ProcessTimeoutException extends java.lang.Exception implements Serializable
-
Serialized Fields
-
returnCode
int returnCode
-
-
-
Class org.biojava.utils.SingletonList extends java.util.AbstractList implements Serializable
-
Serialized Fields
-
obj
java.lang.Object obj
-
-
-
Class org.biojava.utils.SmallMap extends java.util.AbstractMap implements Serializable
-
Serialized Fields
-
mappings
java.lang.Object[] mappings
-
numMappings
int numMappings
-
-
-
Class org.biojava.utils.StaticMemberPlaceHolder extends java.lang.Object implements Serializable
-
Serialization Methods
-
readResolve
public java.lang.Object readResolve() throws java.io.ObjectStreamException
- Throws:
java.io.ObjectStreamException
-
-
Serialized Fields
-
className
java.lang.String className
-
fieldName
java.lang.String fieldName
-
-
-
Class org.biojava.utils.TypedProperties extends java.util.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 java.lang.Exception implements Serializable
-
-
Package org.biojava.utils.candy
-
Class org.biojava.utils.candy.CandyException extends java.lang.Exception implements Serializable
-
-
Package org.biojava.utils.lsid
-
Class org.biojava.utils.lsid.LifeScienceIdentifier extends java.lang.Object implements Serializable
- serialVersionUID:
- 8478038493421763123L
-
Serialized Fields
-
authorityId
java.lang.String authorityId
-
namespaceId
java.lang.String namespaceId
-
objectId
java.lang.String objectId
-
revisionId
java.lang.String revisionId
-
-
Class org.biojava.utils.lsid.LifeScienceIdentifierParseException extends java.lang.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 java.lang.Exception implements Serializable
-
-
Package org.biojavax
-
Class org.biojavax.CrossReferenceResolutionException extends java.lang.Exception implements Serializable
-
Class org.biojavax.EmptyRichAnnotation extends Unchangeable implements Serializable
-
Serialization Methods
-
writeReplace
private java.lang.Object writeReplace() throws java.io.ObjectStreamException
- Throws:
java.io.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 java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
param
java.util.HashMap<java.lang.String,java.lang.String> param
-
-
Class org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties extends java.lang.Object implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
alignFormat
java.lang.String alignFormat
-
alignNumbers
int alignNumbers
-
descNumbers
int descNumbers
-
out
java.util.HashMap<java.lang.String,java.lang.String> out
-
outFormat
java.lang.String outFormat
-
-
-
Package org.biojavax.bio.db.biosql
-
Class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter extends java.lang.Object implements Serializable
-
Serialized Fields
-
isNotNull
java.lang.reflect.Method isNotNull
-
-
-
Class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter extends java.lang.Object implements Serializable
-
Serialized Fields
-
isNull
java.lang.reflect.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
java.lang.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
java.lang.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
java.lang.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
java.lang.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 java.lang.Object implements Serializable
-
Serialized Fields
-
and
java.lang.reflect.Method and
-
conjunctAdd
java.lang.reflect.Method conjunctAdd
-
conjunction
java.lang.reflect.Method conjunction
-
disjunctAdd
java.lang.reflect.Method disjunctAdd
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disjunction
java.lang.reflect.Method disjunction
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eq
java.lang.reflect.Method eq
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ge
java.lang.reflect.Method ge
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le
java.lang.reflect.Method le
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not
java.lang.reflect.Method not
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or
java.lang.reflect.Method or
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-
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Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable
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Serialized Fields
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child
BioSQLFeatureFilter child
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-
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Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable
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Serialized Fields
-
c1
BioSQLFeatureFilter c1
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c2
BioSQLFeatureFilter c2
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-
-
Class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation extends BioSQLFeatureFilter.HibernateFeatureFilter implements Serializable
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Serialized Fields
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loc
RichLocation loc
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-
-
-
Package org.biojavax.bio.seq
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Class org.biojavax.bio.seq.RichFeature.Template extends Feature.Template implements Serializable
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Serialized Fields
-
featureRelationshipSet
java.util.Set featureRelationshipSet
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rankedCrossRefs
java.util.Set rankedCrossRefs
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-
-
-
Package org.biojavax.ga.exception
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Class org.biojavax.ga.exception.IllegalOrganismException extends java.lang.Exception implements Serializable
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-
Package org.biojavax.ga.util
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Class org.biojavax.ga.util.WeightedSet extends java.util.AbstractSet implements Serializable
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Serialized Fields
-
key2Weight
java.util.HashMap key2Weight
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totalWeight
double totalWeight
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-
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