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

wrapped

Annotation wrapped

changer

ChangeTable changer

properties

java.util.Map properties

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

Serialized Fields

wrapped

Annotation wrapped

mapper

PropertyChanger mapper

properties

java.util.Map properties

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

parent

Annotation parent

overlay

java.util.Map overlay

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.IllegalAlignmentEditException extends BioRuntimeException implements Serializable


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

first

Distribution first

second

Distribution second

alphabet

Alphabet alphabet

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

serialVersionUID: 7252850540926095728L

Serialization Methods

readObject

private void readObject(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

nullModel

Distribution nullModel

alpha

FiniteAlphabet alpha

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

Serialized Fields

dis

Distribution dis
Deprecated. 

c

java.util.Map c
Deprecated. 

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

Serialized Fields

distToTrainer

java.util.Map distToTrainer

trainers

java.util.Set trainers

nullModelWeight

double nullModelWeight

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

Serialized Fields

other

Distribution other

delegate

Distribution delegate

table

ReversibleTranslationTable table

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

serialVersionUID: 88454038L

Serialized Fields

alphabet

FiniteAlphabet alphabet

nullModel

Distribution nullModel

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


Package org.biojava.bio.dp

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

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

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

Serialized Fields

sym

SymbolList sym

index

int index

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

Serialized Fields

from

State from

to

State to

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

Serialization Methods

writeReplace

private 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.


matchStates

EmissionState[] matchStates
Match states array.

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


insertStates

EmissionState[] insertStates
Insert states array.

From 0 .. columns().


deleteStates

DotState[] deleteStates
Delete states array.

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

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

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

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

dis

Distribution dis

name

java.lang.String name

ann

Annotation ann

advance

int[] advance

matches

Alphabet matches

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

serialVersionUID: -3043028839927615753L

Serialized Fields

emissionAlpha

Alphabet emissionAlpha

stateAlpha

FiniteAlphabet stateAlpha

magicalState

MagicalState magicalState

transFrom

java.util.Map transFrom

transTo

java.util.Map transTo

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

score

double score

delegate

Alignment delegate

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

serialVersionUID: 73394340224964858L

Serialized Fields

columns

Distribution[] columns

alpha

Alphabet alpha

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

Serialized Fields

trainer

TransitionTrainer trainer

from

State from

to

State to

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

Serialized Fields

from

State from

to

State to

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

Serialized Fields

matrix

WeightMatrix matrix

threshold

double threshold

scoreType

ScoreType scoreType

wmID

java.lang.String wmID

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

Serialized Fields

wm

WeightMatrix wm

stateAlpha

FiniteAlphabet stateAlpha

magicalState

MagicalState magicalState

states

EmissionState[] states

transFrom

java.util.Map transFrom

transTo

java.util.Map transTo

transWeights

java.util.Map transWeights

Package org.biojava.bio.dp.onehead

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

Serialized Fields

emissionsProb

java.util.HashMap emissionsProb

emissionsOdds

java.util.HashMap emissionsOdds

emissionsNull

java.util.HashMap emissionsNull

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

Serialized Fields

states

State[] states

model

MarkovModel model

symList

SymbolList[] symList

scores

double[][] scores

score

double score

Package org.biojava.bio.dp.twohead

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

Serialized Fields

states

State[] states

seqs

SymbolList[] seqs

scores

double[][][] scores

model

MarkovModel model

finalScore

double finalScore

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

Serialized Fields

emissionCache

java.util.HashMap emissionCache

ccFactory

CellCalculatorFactory ccFactory

Package org.biojava.bio.gui

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

Serialized Fields

dist

Distribution dist
The dist to render.


logoPainter

LogoPainter logoPainter
The logoPainter property.


style

SymbolStyle style
The style property.


scaleByInformation

boolean scaleByInformation
The information/plain property


blockPainter

BlockPainter blockPainter

renderingHints

java.awt.RenderingHints renderingHints

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

beadOutline

java.awt.Paint beadOutline

beadFill

java.awt.Paint beadFill

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

source

FeatureSource source

digestFilter

FeatureFilter digestFilter

laneMap

java.util.Map laneMap

laneCount

int laneCount

distanceBetween

int distanceBetween

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

Serialized Fields

label

java.lang.Object label

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

Serialized Fields

renderer

BasicFeatureRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

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

Serialized Fields

leadingPixles

int leadingPixles

trailingPixles

int trailingPixles

contextCache

CacheMap contextCache

flushers

java.util.Set flushers

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

Serialized Fields

ctxt

CircularRendererContext ctxt

symList

SymbolList symList

radius

double radius

renderer

CircularRenderer renderer

offset

double offset

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

Serialized Fields

dimensionRatio

double dimensionRatio

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

Serialized Fields

filter

FeatureFilter filter

recurse

boolean recurse

contextCache

CacheMap contextCache

flushers

java.util.Set flushers

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

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

Serialized Fields

depth

double depth

fList

java.util.List fList

gList

java.util.List gList

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

Serialized Fields

name

java.lang.String name

hotSpots

java.util.List hotSpots

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

Serialized Fields

type

java.lang.String type

url

java.net.URL url

coordinates

java.lang.Integer[] coordinates

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

filter

FeatureFilter filter
filter is the filter applied to both FeatureHolders.


recurse

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


subContextCache

CacheMap subContextCache

cacheFlushers

java.util.Set cacheFlushers

renderer

PairwiseSequenceRenderer renderer

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

sequence

Sequence sequence

translation

int translation

direction

int direction

secSequence

Sequence secSequence

secTranslation

int secTranslation

secDirection

int secDirection

scale

double scale

renderer

PairwiseSequenceRenderer renderer

hints

java.awt.RenderingHints hints

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

propertyListener

java.beans.PropertyChangeListener propertyListener

repaintListener

ChangeListener repaintListener

layoutListener

ChangeListener layoutListener

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

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

renderer

RectangularBeadRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

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

Serialized Fields

rect

java.awt.geom.RoundRectangle2D rect

arcWidth

double arcWidth

arcHeight

double arcHeight

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

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

Serialized Fields

sequence

SymbolList sequence

range

RangeLocation range

direction

int direction

scale

double scale

pixelOffset

double pixelOffset

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

renderer

SequenceRenderer renderer

theMonitor

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

hints

java.awt.RenderingHints hints

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

layoutListener

ChangeListener layoutListener

repaintListener

ChangeListener repaintListener

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

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

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

Serialized Fields

range

RangeLocation range

sequence

Sequence sequence

seqPanels

SequencePanel[] seqPanels

renderer

SequenceRenderer renderer

scale

double scale

hints

java.awt.RenderingHints hints

direction

int direction

trackLayout

TrackLayout trackLayout

viewerListeners

java.util.List viewerListeners

motionListeners

java.util.List motionListeners

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

Serialized Fields

sequence

Sequence sequence
Deprecated. 

direction

int direction
Deprecated. 

scale

double scale
Deprecated. 

lines

int lines
Deprecated. 

spacer

int spacer
Deprecated. 

leadingBorder

SequenceRenderContext.Border leadingBorder
Deprecated. 

trailingBorder

SequenceRenderContext.Border trailingBorder
Deprecated. 

renderer

SequenceRenderer renderer
Deprecated. 

offsets

double[] offsets
Deprecated. 

realLines

int realLines
Deprecated. 

alongDim

double alongDim
Deprecated. 

acrossDim

double acrossDim
Deprecated. 

symbolsPerLine

int symbolsPerLine
Deprecated. 

theMonitor

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

renderingHints

java.awt.RenderingHints renderingHints
Deprecated. 

svSupport

SequenceViewerSupport svSupport
Deprecated. 

mouseListener

java.awt.event.MouseListener mouseListener
Deprecated. 

svmSupport

SequenceViewerMotionSupport svmSupport
Deprecated. 

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener
Deprecated. 

layoutListener

ChangeListener layoutListener
Deprecated. 

repaintListener

ChangeListener repaintListener
Deprecated. 

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

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

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

Serialized Fields

size

double size

alignment

int alignment

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

Serialized Fields

renderer

SequenceRenderer renderer

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

Serialized Fields

path

java.util.List path

target

java.lang.Object target

mouseEvent

java.awt.event.MouseEvent mouseEvent

pos

int pos

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

Serialized Fields

pane

SixFrameRenderer pane

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

Serialized Fields

sequence

SymbolList sequence

translation

int translation

direction

int direction

scale

double scale

renderer

SequenceRenderer renderer

rendererBorders

double rendererBorders

hints

java.awt.RenderingHints hints

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

propertyListener

java.beans.PropertyChangeListener propertyListener

repaintListener

ChangeListener repaintListener

layoutListener

ChangeListener layoutListener

svSupport

SequenceViewerSupport svSupport

mouseListener

java.awt.event.MouseListener mouseListener

svmSupport

SequenceViewerMotionSupport svmSupport

mouseMotionListener

java.awt.event.MouseMotionListener mouseMotionListener

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

Serialized Fields

outline

java.awt.Paint outline

fill

java.awt.Paint fill

blockDepth

double blockDepth

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

Serialized Fields

renderer

ZiggyFeatureRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

Package org.biojava.bio.molbio

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

Serialized Fields

name

java.lang.String name

site

SymbolList site

cutType

int cutType

dsCutPositions

int[] dsCutPositions

usCutPositions

int[] usCutPositions

forwardRegex

java.lang.String forwardRegex

reverseRegex

java.lang.String reverseRegex

summary

java.lang.String summary

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

Serialized Fields

enzyme

RestrictionEnzyme enzyme
enzyme RestrictionEnzyme field.


Package org.biojava.bio.program.abi

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


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

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


Package org.biojava.bio.program.gff

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


Package org.biojava.bio.program.hmmer

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

Serialized Fields

j

EmissionState j

c

EmissionState c

n

EmissionState n

hmmState

ModelInState hmmState

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

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


Package org.biojava.bio.program.homologene

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


Package org.biojava.bio.program.phred

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

Serialized Fields

mListeners

java.util.Vector mListeners

lineWidth

int lineWidth
The line width for output.

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


Package org.biojava.bio.program.ssaha

Class org.biojava.bio.program.ssaha.SearchException extends 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

notCleaveResidues

SymbolList notCleaveResidues

endoProtease

boolean endoProtease

name

java.lang.String name

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

Serialized Fields

componentSequenceName

java.lang.String componentSequenceName

componentSequence

Sequence componentSequence

componentLocation

Location componentLocation

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

Serialized Fields

location

Location location

type

java.lang.String type

source

java.lang.String source

typeTerm

Term typeTerm

sourceTerm

Term sourceTerm

annotation

Annotation annotation

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

minScore

double minScore

maxScore

double maxScore

score

double score

hashCode

int hashCode

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

text

java.lang.String text

frame

int frame

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

Serialized Fields

readingFrame

FramedFeature.ReadingFrame readingFrame

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

Serialized Fields

featureHolders

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

templateToImpl

java.util.List templateToImpl

fallBack

FeatureRealizer fallBack

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

value

int value

token

char token

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

Serialized Fields

strand

StrandedFeature.Strand strand

Package org.biojava.bio.seq.db

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

Serialized Fields

parent

SequenceDB parent

annotator

SequenceAnnotator annotator

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

Serialization Methods

readObject

private void readObject(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

sequenceByID

java.util.Map sequenceByID
The sequence-by-id map.


idMaker

IDMaker idMaker
An object to extract an ID for a sequence.


name

java.lang.String name
The name of this sequence database.

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

storeFile

java.io.File storeFile

indexFile

java.io.File indexFile

name

java.lang.String name

files

java.util.Set files

seqFileIndex

java.io.File[] seqFileIndex

format

SequenceFormat format

sbFactory

SequenceBuilderFactory sbFactory

symbolParser

SymbolTokenization symbolParser

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


Package org.biojava.bio.seq.homol

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

Serialized Fields

homology

Homology homology

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

Serialized Fields

sibling

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


alignment

Alignment alignment
alignment Alignment field.


score

double score
score of the search which produced the alignment.


Package org.biojava.bio.seq.impl

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

Serialized Fields

pfh

ProjectedFeatureHolder pfh

origSeq

Sequence origSeq

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

Serialized Fields

featureHolder

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


loc

Location loc
The location of this feature.


type

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


source

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


parent

FeatureHolder parent
Our parent FeatureHolder.


annotation

Annotation annotation
The annotation object. This is lazily instantiated.


typeTerm

Term typeTerm

sourceTerm

Term sourceTerm

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

Serialized Fields

readingFrame

FramedFeature.ReadingFrame readingFrame

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

Serialized Fields

sequence

Sequence sequence

features

MergeFeatureHolder features

localFeatures

SimpleFeatureHolder localFeatures

projectedFeatures

FeatureHolder projectedFeatures

createOnUnderlying

boolean createOnUnderlying

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

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

Serialized Fields

homology

Homology homology

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

Serialized Fields

regions

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

Serialized Fields

symList

SymbolList symList
Delegate SymbolList.


urn

java.lang.String urn

name

java.lang.String name

annotation

Annotation annotation

featureHolder

SimpleFeatureHolder featureHolder

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

sibling

SimilarityPairFeature sibling

alignment

Alignment alignment

score

double score

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

Serialized Fields

strand

StrandedFeature.Strand strand

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

Serialized Fields

parent

Sequence parent

symbols

SymbolList symbols

name

java.lang.String name

uri

java.lang.String uri

annotation

Annotation annotation

parentLocation

RangeLocation parentLocation

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

Serialized Fields

parentLocation

RangeLocation parentLocation

remoteLocationFilter

FeatureFilter remoteLocationFilter

clippingFilter

FeatureFilter clippingFilter

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

serialVersionUID: 9866447L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream s)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
Throws:
java.io.IOException
java.lang.ClassNotFoundException
Serialized Fields

seqDelegate

Sequence seqDelegate
Delegate Sequence.


exposedFeatures

MergeFeatureHolder exposedFeatures
FeatureHolder support


addedFeatures

SimpleFeatureHolder addedFeatures

name

java.lang.String name
IDs


urn

java.lang.String urn

anno

Annotation anno
Our annotation.


Package org.biojava.bio.seq.io

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

Serialized Fields

alphabet

Alphabet alphabet

symbolsToCharacters

java.util.Map symbolsToCharacters

charactersToSymbols

java.util.Map charactersToSymbols

caseSensitive

boolean caseSensitive

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

mListeners

java.util.Vector mListeners
Deprecated. 

lineWidth

int lineWidth
Deprecated. 
The line width for output.

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

Serialized Fields

mListeners

java.util.Vector mListeners
Deprecated. 

elideSymbols

boolean elideSymbols
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_xmlParser

javax.xml.parsers.SAXParser m_xmlParser
Deprecated. 

m_handler

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

m_parsed

boolean m_parsed
Deprecated. 

m_sequenceIndex

int m_sequenceIndex
Deprecated. 

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

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

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

Serialized Fields

caseSensitive

boolean caseSensitive

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

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

sciNameKey

java.lang.String sciNameKey

commonNameKey

java.lang.String commonNameKey

ncbiTaxonKey

java.lang.String ncbiTaxonKey

taxonFactory

TaxonFactory taxonFactory

taxonParser

TaxonParser taxonParser

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

Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory extends 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

translation

int translation

oppositeStrand

boolean oppositeStrand

Package org.biojava.bio.structure

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

serialVersionUID: 62946250941673093L


Package org.biojava.bio.structure.io

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

serialVersionUID: 219047230178423923L


Package org.biojava.bio.structure.jama

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

serialVersionUID: 224348942390823L

Serialized Fields

L

double[][] L
Array for internal storage of decomposition.

internal array storage.

n

int n
Row and column dimension (square matrix).

matrix dimension.

isspd

boolean isspd
Symmetric and positive definite flag.

is symmetric and positive definite flag.

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

serialVersionUID: 93489734879234789L

Serialized Fields

n

int n
Row and column dimension (square matrix).

matrix dimension.

issymmetric

boolean issymmetric
Symmetry flag.

internal symmetry flag.

d

double[] d
Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

e

double[] e
Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

V

double[][] V
Array for internal storage of eigenvectors.

internal storage of eigenvectors.

H

double[][] H
Array for internal storage of nonsymmetric Hessenberg form.

internal storage of nonsymmetric Hessenberg form.

ort

double[] ort
Working storage for nonsymmetric algorithm.

working storage for nonsymmetric algorithm.

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

serialVersionUID: 9271028462937843L

Serialized Fields

LU

double[][] LU
Array for internal storage of decomposition.

internal array storage.

m

int m
Row and column dimensions, and pivot sign.

column dimension.

n

int n
Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign
Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv
Internal storage of pivot vector.

pivot vector.

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

serialVersionUID: 8492558293015348719L

Serialized Fields

A

double[][] A
Array for internal storage of elements.

internal array storage.

m

int m
Row and column dimensions.

row dimension.

n

int n
Row and column dimensions.

row dimension.

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

serialVersionUID: 10293720387423L

Serialized Fields

QR

double[][] QR
Array for internal storage of decomposition.

internal array storage.

m

int m
Row and column dimensions.

column dimension.

n

int n
Row and column dimensions.

column dimension.

Rdiag

double[] Rdiag
Array for internal storage of diagonal of R.

diagonal of R.

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

serialVersionUID: 640239472093534756L

Serialized Fields

U

double[][] U
Arrays for internal storage of U and V.

internal storage of U.

V

double[][] V
Arrays for internal storage of U and V.

internal storage of U.

s

double[] s
Array for internal storage of singular values.

internal storage of singular values.

m

int m
Row and column dimensions.

row dimension.

n

int n
Row and column dimensions.

row dimension.

Package org.biojava.bio.symbol

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

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

tokenizationsByName

java.util.Map tokenizationsByName

ambCache

java.util.Map ambCache

registered

boolean registered

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

chunks

SymbolList[] chunks

chunkSize

int chunkSize

alpha

Alphabet alpha

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

minVal

double minVal

maxVal

double maxVal

matches

Alphabet matches

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

Serialized Fields

val

double val

matches

Alphabet matches

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

Serialization Methods

readResolve

protected 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

min

double min

max

double max

name

java.lang.String name

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

Serialized Fields

sym

Symbol sym

alpha

Alphabet alpha

length

int length

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

Serialized Fields

pos

int pos

length

int length

replacement

SymbolList replacement

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

Serialized Fields

name

java.lang.String name

annotation

Annotation annotation

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

Serialized Fields

outerMin

int outerMin

innerMin

int innerMin

innerMax

int innerMax

outerMax

int outerMax

mIsMinFuzzy

boolean mIsMinFuzzy

mIsMaxFuzzy

boolean mIsMaxFuzzy

resolver

FuzzyLocation.RangeResolver resolver

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

Serialized Fields

min

int min

max

int max

resolver

FuzzyPointLocation.PointResolver resolver

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

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

Serialized Fields

sym

Symbol sym

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

Serialization Methods

writeReplace

private 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

val

int val

matches

Alphabet matches

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

Serialized Fields

min

int min

max

int max

name

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

packing

Packing packing

syms

long[] syms

length

int length

symsPerElement

byte symsPerElement

mask

byte mask

currentMin

int currentMin

currentMax

int currentMax

currentWord

long currentWord

wordsize

int wordsize

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

Serialized Fields

point

int point
The actual index contained.

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

Serialized Fields

min

int min
The minimum point contained.


max

int max
The maximum point contained.

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

serialVersionUID: -1760075176220928440L

Serialized Fields

labelToSymbolList

java.util.LinkedHashMap labelToSymbolList

labels

java.util.List labels

alphabet

Alphabet alphabet

length

int length

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

serialVersionUID: 216254146L

Serialized Fields

name

java.lang.String name

annotation

Annotation annotation

symbols

java.util.Set symbols

alphabets

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

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

Serialization Methods

writeReplace

private 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.


source

SymbolList source
The SymbolList to view.


blocks

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


length

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

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

serialVersionUID: 4090888450309921439L

Serialized Fields

sourceStart

int sourceStart

sourceEnd

int sourceEnd

viewStart

int viewStart

viewEnd

int viewEnd

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

Serialized Fields

table_num

int table_num

description

java.lang.String description

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

Serialized Fields

transMap

java.util.Map transMap

revMap

java.util.Map revMap

source

FiniteAlphabet source

target

Alphabet target

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

Serialized Fields

transMap

java.util.Map transMap

revMap

java.util.Map revMap

source

FiniteAlphabet source

target

Alphabet target

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

serialVersionUID: -9015317520644706924L

Serialized Fields

alphabet

Alphabet alphabet

symbols

Symbol[] symbols

length

int length

isView

boolean isView

viewOffset

int viewOffset

referenceSymbolList

SymbolList referenceSymbolList

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

Serialized Fields

transMap

java.util.Map transMap

source

FiniteAlphabet source

target

Alphabet target

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

Serialized Fields

sym

AtomicSymbol sym

alphabets

java.util.List alphabets

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

Serialized Fields

alphabet

FiniteAlphabet alphabet

root

SuffixTree.SuffixNode root

indexer

AlphabetIndex indexer

counts

java.util.List counts

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

Serialized Fields

terms

java.util.Map terms

triples

java.util.Set triples

subjectTriples

java.util.Map subjectTriples

objectTriples

java.util.Map objectTriples

relationTriples

java.util.Map relationTriples

remoteTerms

java.util.Map remoteTerms

localRemoteTerms

java.util.Set localRemoteTerms

name

java.lang.String name

description

java.lang.String description

ops

OntologyOps ops

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

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

Serialized Fields

ontology

Ontology ontology

target

Ontology target

synonyms

java.util.Set synonyms

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

Serialized Fields

ontology

Ontology ontology

remoteTerm

Term remoteTerm

name

java.lang.String name

synonyms

java.util.Set synonyms

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

Serialized Fields

name

java.lang.String name

description

java.lang.String description

ontology

Ontology ontology

annotation

Annotation annotation

synonyms

java.util.Set synonyms

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

Serialized Fields

subject

Term subject

object

Term object

predicate

Term predicate

name

java.lang.String name

description

java.lang.String description

synonyms

java.util.Set synonyms

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


Package org.biojava.stats.svm

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

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

Serialized Fields

posClass

java.util.Set posClass

negClass

java.util.Set negClass

lambda

double lambda
The scale vactor.

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

Class org.biojava.stats.svm.LinearKernel extends 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

order

double order

a

double a

c

double c

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

Serialized Fields

width

double width

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

Serialized Fields

size

int size

keys

int[] keys

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

target

SVMTarget target

model

SVMClassifierModel model

addPos

boolean addPos

posShape

java.awt.Shape posShape

negShape

java.awt.Shape negShape

svPaint

java.awt.Paint svPaint

plainPaint

java.awt.Paint plainPaint

posPaint

java.awt.Paint posPaint

negPaint

java.awt.Paint negPaint

kernel

SVMKernel kernel

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

a

SuffixTreeKernel.DepthScaler a

b

SuffixTreeKernel.DepthScaler b

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

type

ChangeType type

change

java.lang.Object change

previous

java.lang.Object previous

chain

ChangeEvent chain

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

locator

java.lang.String locator

lineNumber

int lineNumber

character

int character

line

java.lang.String line

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.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.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

not

java.lang.reflect.Method not

and

java.lang.reflect.Method and

or

java.lang.reflect.Method or

eq

java.lang.reflect.Method eq

le

java.lang.reflect.Method le

ge

java.lang.reflect.Method ge

conjunction

java.lang.reflect.Method conjunction

disjunction

java.lang.reflect.Method disjunction

conjunctAdd

java.lang.reflect.Method conjunctAdd

disjunctAdd

java.lang.reflect.Method disjunctAdd

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

Serialized Fields

child

BioSQLFeatureFilter child

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

Serialized Fields

c1

BioSQLFeatureFilter c1

c2

BioSQLFeatureFilter c2

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

Serialized Fields

loc

RichLocation loc

Package org.biojavax.bio.seq

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

Serialized Fields

featureRelationshipSet

java.util.Set featureRelationshipSet

rankedCrossRefs

java.util.Set rankedCrossRefs

Package org.biojavax.ga.exception

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


Package org.biojavax.ga.util

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

Serialized Fields

key2Weight

java.util.HashMap key2Weight

totalWeight

double totalWeight