Serialized Form

Package org.biojava.bio

Class org.biojava.bio.AbstractAnnotation implements Serializable

Class org.biojava.bio.AnnotationChanger implements Serializable

Serialized Fields

wrapped

Annotation wrapped

changer

ChangeTable changer

properties

java.util.Map properties

Class org.biojava.bio.AnnotationRenamer implements Serializable

Serialized Fields

wrapped

Annotation wrapped

mapper

TagMapper mapper

properties

java.util.Map properties

Class org.biojava.bio.BeanAsAnnotation implements Serializable

Serialized Fields

properties

java.util.Map properties

Class org.biojava.bio.BioError implements Serializable

Class org.biojava.bio.BioException implements Serializable

Class org.biojava.bio.BioRuntimeException implements Serializable

Class org.biojava.bio.MergeAnnotation implements Serializable

Serialized Fields

mergeSet

java.util.List mergeSet

Class org.biojava.bio.OverlayAnnotation implements Serializable

Serialized Fields

parent

Annotation parent

overlay

java.util.Map overlay

Class org.biojava.bio.SimpleAnnotation 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 implements Serializable

Serialized Fields

properties

java.util.Map properties

Package org.biojava.bio.seq

Class org.biojava.bio.seq.CircularView implements Serializable

Class org.biojava.bio.seq.ComponentFeature.Template implements Serializable

Serialized Fields

componentSequenceName

java.lang.String componentSequenceName

componentSequence

Sequence componentSequence

componentLocation

Location componentLocation

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

Serialized Fields

location

Location location

type

java.lang.String type

source

java.lang.String source

annotation

Annotation annotation

Class org.biojava.bio.seq.FeatureFilter.And implements Serializable

Serialized Fields

c1

FeatureFilter c1

c2

FeatureFilter c2

Class org.biojava.bio.seq.FeatureFilter.AnnotationContains implements Serializable

Serialized Fields

key

java.lang.Object key

value

java.lang.Object value

Class org.biojava.bio.seq.FeatureFilter.ByAncestor implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByAnnotation implements Serializable

Serialized Fields

key

java.lang.Object key

value

java.lang.Object value

Class org.biojava.bio.seq.FeatureFilter.ByAnnotationType implements Serializable

Serialized Fields

type

AnnotationType type

Class org.biojava.bio.seq.FeatureFilter.ByChild implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByClass implements Serializable

Serialized Fields

clazz

java.lang.Class clazz

Class org.biojava.bio.seq.FeatureFilter.ByComponentName implements Serializable

Serialized Fields

cname

java.lang.String cname

Class org.biojava.bio.seq.FeatureFilter.ByDescendant implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.ByFeature implements Serializable

Serialized Fields

feature

Feature feature

Class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore implements Serializable

Serialized Fields

minScore

double minScore

maxScore

double maxScore

score

double score

hashCode

int hashCode

Class org.biojava.bio.seq.FeatureFilter.ByParent implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.BySequenceName implements Serializable

Serialized Fields

seqName

java.lang.String seqName

Class org.biojava.bio.seq.FeatureFilter.BySource implements Serializable

Serialized Fields

source

java.lang.String source

Class org.biojava.bio.seq.FeatureFilter.ByType implements Serializable

Serialized Fields

type

java.lang.String type

Class org.biojava.bio.seq.FeatureFilter.ContainedByLocation implements Serializable

Serialized Fields

loc

Location loc

Class org.biojava.bio.seq.FeatureFilter.FrameFilter implements Serializable

Serialized Fields

frame

FramedFeature.ReadingFrame frame

Class org.biojava.bio.seq.FeatureFilter.HasAnnotation implements Serializable

Serialized Fields

key

java.lang.Object key

Class org.biojava.bio.seq.FeatureFilter.Not implements Serializable

Serialized Fields

child

FeatureFilter child

Class org.biojava.bio.seq.FeatureFilter.OnlyChildren implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.OnlyDescendants implements Serializable

Serialized Fields

filter

FeatureFilter filter

Class org.biojava.bio.seq.FeatureFilter.Or implements Serializable

Serialized Fields

c1

FeatureFilter c1

c2

FeatureFilter c2

Class org.biojava.bio.seq.FeatureFilter.OverlapsLocation implements Serializable

Serialized Fields

loc

Location loc

Class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation implements Serializable

Serialized Fields

loc

Location loc

Class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation implements Serializable

Serialized Fields

loc

Location loc

Class org.biojava.bio.seq.FeatureFilter.StrandFilter implements Serializable

Serialized Fields

strand

StrandedFeature.Strand strand

Class org.biojava.bio.seq.FramedFeature.ReadingFrame implements Serializable

Serialized Fields

text

java.lang.String text

frame

int frame

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

Class org.biojava.bio.seq.RemoteFeature.Template implements Serializable

Serialized Fields

regions

java.util.List regions

resolver

RemoteFeature.Resolver resolver

Class org.biojava.bio.seq.SimpleFeatureRealizer implements Serializable

Serialized Fields

templateToImpl

java.util.List templateToImpl

fallBack

FeatureRealizer fallBack

Class org.biojava.bio.seq.SimpleGappedSequence implements Serializable

Serialized Fields

sequence

Sequence sequence

features

MergeFeatureHolder features

localFeatures

SimpleFeatureHolder localFeatures

projectedFeatures

FeatureHolder projectedFeatures

createOnUnderlying

boolean createOnUnderlying

Class org.biojava.bio.seq.StrandedFeature.Strand implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Serialized Fields

text

java.lang.String text

value

int value

token

char token

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

Serialized Fields

strand

StrandedFeature.Strand strand

Class org.biojava.bio.seq.ViewSequence implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream s)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Serialized Fields

seqDelegate

Sequence seqDelegate

Delegate Sequence.

exposedFeatures

org.biojava.bio.seq.ViewSequence.ViewSeqMergeFeatureHolder exposedFeatures

FeatureHolder support

addedFeatures

org.biojava.bio.seq.ViewSequence.ViewSeqSimpleFeatureHolder 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 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 implements Serializable

Serialized Fields

subTokenizations

java.util.List subTokenizations

Class org.biojava.bio.seq.io.DoubleTokenization implements Serializable

Class org.biojava.bio.seq.io.EmblLikeFormat implements Serializable

Serialized Fields

elideSymbols

boolean elideSymbols

mListeners

java.util.Vector mListeners

Class org.biojava.bio.seq.io.EmblProcessor.Factory implements Serializable

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.FastaDescriptionLineParser.Factory implements Serializable

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.FastaFormat implements Serializable

Serialized Fields

mListeners

java.util.Vector mListeners

lineWidth

int lineWidth

The line width for output.

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

Serialized Fields

mListeners

java.util.Vector mListeners

elideSymbols

boolean elideSymbols

Class org.biojava.bio.seq.io.GenbankProcessor.Factory implements Serializable

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

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

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

Serialized Fields

caseSensitive

boolean caseSensitive

Class org.biojava.bio.seq.io.OrganismParser.Factory 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 implements Serializable

Class org.biojava.bio.seq.io.ProteinRefSeqProcessor.Factory implements Serializable

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

Class org.biojava.bio.seq.io.SwissprotProcessor.Factory implements Serializable

Serialized Fields

delegateFactory

SequenceBuilderFactory delegateFactory

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

Serialized Fields

alphabet

Alphabet alphabet

Package org.biojava.bio.seq.db

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

Serialized Fields

parent

SequenceDB parent

annotator

SequenceAnnotator annotator

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

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Class org.biojava.bio.seq.db.HashSequenceDB 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 implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.IOException

Class org.biojava.bio.seq.db.IDMaker.ByURN implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.IOException

Class org.biojava.bio.seq.db.IllegalIDException implements Serializable

Class org.biojava.bio.seq.db.IndexedSequenceDB implements Serializable

Serialized Fields

idMaker

IDMaker idMaker

indexStore

IndexStore indexStore

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

Serialized Fields

parent

SequenceDB parent

Class org.biojava.bio.seq.db.SubSequenceDB implements Serializable

Serialized Fields

ids

java.util.Set ids

Class org.biojava.bio.seq.db.TabIndexStore implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 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 implements Serializable

Package org.biojava.bio.seq.impl

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

Serialized Fields

pfh

ProjectedFeatureHolder pfh

origSeq

Sequence origSeq

Class org.biojava.bio.seq.impl.SimpleFeature 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.

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

Serialized Fields

readingFrame

FramedFeature.ReadingFrame readingFrame

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

Serialized Fields

homology

Homology homology

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

Serialized Fields

regions

java.util.List regions

resolver

RemoteFeature.Resolver resolver

Class org.biojava.bio.seq.impl.SimpleRestrictionSite implements Serializable

Serialized Fields

enzyme

RestrictionEnzyme enzyme

position

int position

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

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream s)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Serialized Fields

symList

SymbolList symList

Delegate SymbolList.

urn

java.lang.String urn

name

java.lang.String name

annotation

Annotation annotation

featureHolder

org.biojava.bio.seq.impl.SimpleSequence.SimpleSequenceFeatureHolder featureHolder

Class org.biojava.bio.seq.impl.SimpleSequenceFactory implements Serializable

Serialized Fields

realizer

FeatureRealizer realizer

Class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature implements Serializable

Serialized Fields

sibling

SimilarityPairFeature sibling

alignment

Alignment alignment

score

double score

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

Serialized Fields

strand

StrandedFeature.Strand strand

Package org.biojava.bio.seq.homol

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

Serialized Fields

homology

Homology homology

Class org.biojava.bio.seq.homol.SimilarityPairFeature.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.program.phred

Class org.biojava.bio.program.phred.PhredFormat implements Serializable

Serialized Fields

lineWidth

int lineWidth

The line width for output.

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

Package org.biojava.bio.program.gff

Class org.biojava.bio.program.gff.IgnoreRecordException implements Serializable

Package org.biojava.bio.program.hmmer

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

Serialized Fields

j

EmissionState j

c

EmissionState c

n

EmissionState n

hmmState

ModelInState hmmState

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

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

Package org.biojava.bio.gui

Class org.biojava.bio.gui.DistributionLogo 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 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 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.AlignmentRenderer implements Serializable

Serialized Fields

label

java.lang.Object label

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

Serialized Fields

leadingPixles

int leadingPixles

trailingPixles

int trailingPixles

contextCache

CacheMap contextCache

flushers

java.util.Set flushers

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

Serialized Fields

dimensionRatio

double dimensionRatio

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

Serialized Fields

filter

FeatureFilter filter

recurse

boolean recurse

contextCache

CacheMap contextCache

flushers

java.util.Set flushers

Class org.biojava.bio.gui.sequence.ImageMap.ClientSide implements Serializable

Serialized Fields

name

java.lang.String name

url

java.net.URL url

hotSpots

java.util.List hotSpots

Class org.biojava.bio.gui.sequence.ImageMap.HotSpot 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 implements Serializable

Serialized Fields

hotSpots

java.util.List hotSpots

Class org.biojava.bio.gui.sequence.MultiLineRenderer implements Serializable

Serialized Fields

renderers

java.util.List renderers

Class org.biojava.bio.gui.sequence.OverlayRendererWrapper implements Serializable

Serialized Fields

renderer

SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.PaddingRenderer implements Serializable

Serialized Fields

padding

double padding

Class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer 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 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 implements Serializable

Serialized Fields

renderers

java.util.List renderers

Class org.biojava.bio.gui.sequence.PairwiseSequencePanel 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.RectangularBeadRenderer implements Serializable

Serialized Fields

rect

java.awt.geom.Rectangle2D rect

scaleHeight

boolean scaleHeight

Class org.biojava.bio.gui.sequence.RectangularImapRenderer implements Serializable

Serialized Fields

renderer

RectangularBeadRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

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

Serialized Fields

rect

java.awt.geom.RoundRectangle2D rect

arcWidth

double arcWidth

arcHeight

double arcHeight

Class org.biojava.bio.gui.sequence.SequencePanel implements Serializable

Serialized Fields

sequence

Sequence 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 implements Serializable

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequencePoster implements Serializable

Serialized Fields

sequence

Sequence sequence

direction

int direction

scale

double scale

lines

int lines

spacer

int spacer

leadingBorder

SequenceRenderContext.Border leadingBorder

trailingBorder

SequenceRenderContext.Border trailingBorder

renderer

SequenceRenderer renderer

offsets

double[] offsets

realLines

int realLines

alongDim

double alongDim

acrossDim

double acrossDim

symbolsPerLine

int symbolsPerLine

theMonitor

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

renderingHints

java.awt.RenderingHints renderingHints

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.SequencePoster.Border implements Serializable

Serialized Fields

pcs

java.beans.PropertyChangeSupport pcs

size

double size

alignment

int alignment

Class org.biojava.bio.gui.sequence.SequenceRenderContext.Border implements Serializable

Serialized Fields

size

double size

alignment

int alignment

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

Serialized Fields

renderer

SequenceRenderer renderer

Class org.biojava.bio.gui.sequence.SequenceViewerEvent 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 implements Serializable

Serialized Fields

pane

SixFrameRenderer pane

Class org.biojava.bio.gui.sequence.TranslatedSequencePanel implements Serializable

Serialized Fields

sequence

Sequence 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 implements Serializable

Serialized Fields

outline

java.awt.Paint outline

fill

java.awt.Paint fill

blockDepth

double blockDepth

Class org.biojava.bio.gui.sequence.ZiggyImapRenderer implements Serializable

Serialized Fields

renderer

ZiggyFeatureRenderer renderer

imageMap

ImageMap imageMap

urlFactory

URLFactory urlFactory

Package org.biojava.bio.symbol

Class org.biojava.bio.symbol.AbstractAlphabet 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.

Serialized Fields

tokenizationsByName

java.util.Map tokenizationsByName

ambCache

java.util.Map ambCache

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

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

Class org.biojava.bio.symbol.DNAAmbPack implements Serializable

Serialized Fields

syms

Symbol[] syms

Class org.biojava.bio.symbol.DNANoAmbPack implements Serializable

Serialized Fields

placeHolder

byte placeHolder

Class org.biojava.bio.symbol.DoubleAlphabet implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Serialized Fields

alphabets

java.util.List alphabets

doubleToSym

WeakValueHashMap doubleToSym

Class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange implements Serializable

Serialized Fields

minVal

double minVal

maxVal

double maxVal

matches

Alphabet matches

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

Serialized Fields

val

double val

matches

Alphabet matches

Class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet 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.

Serialized Fields

min

double min

max

double max

name

java.lang.String name

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

Serialized Fields

sym

Symbol sym

alpha

FiniteAlphabet alpha

length

int length

Class org.biojava.bio.symbol.Edit implements Serializable

Serialized Fields

pos

int pos

length

int length

replacement

SymbolList replacement

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

Serialized Fields

name

java.lang.String name

annotation

Annotation annotation

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

Serialized Fields

min

int min

max

int max

resolver

FuzzyPointLocation.PointResolver resolver

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

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

Serialized Fields

sym

Symbol sym

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

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Serialized Fields

intToSym

WeakValueHashMap intToSym

Canonicalization map for ints and references to symbols.

Class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol implements Serializable

Serialized Fields

val

int val

matches

Alphabet matches

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

Serialized Fields

min

int min

max

int max

name

java.lang.String name

Class org.biojava.bio.symbol.MergeLocation implements Serializable

Serialized Fields

componentLocations

java.util.List componentLocations

Class org.biojava.bio.symbol.PackedDnaSymbolList implements Serializable

Serialized Fields

length

int length

log2PackedSymsPerStorageUnit

int log2PackedSymsPerStorageUnit

packedSymsPerStorageUnit

int packedSymsPerStorageUnit

storageUnitOffsetMask

int storageUnitOffsetMask

storageUnitSize

int storageUnitSize

packedSymbolArray

byte[] packedSymbolArray

log2SymsPerCacheLine

int log2SymsPerCacheLine

cacheLineOffsetMask

int cacheLineOffsetMask

symbolCache

Symbol[] symbolCache

currCacheIndex

int currCacheIndex

cacheLineCount

int cacheLineCount

symsInFinalStorageUnit

int symsInFinalStorageUnit

symsInFinalCacheLine

int symsInFinalCacheLine

fullStorageUnitsInFinalCacheLine

int fullStorageUnitsInFinalCacheLine

log2StorageUnitsPerCacheLine

int log2StorageUnitsPerCacheLine

storageUnitsPerCacheLine

int storageUnitsPerCacheLine

Class org.biojava.bio.symbol.PackedSymbolList implements Serializable

Serialized Fields

bitsPerElement

byte bitsPerElement

See Also:

Constant Field Values

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 implements Serializable

Serialized Fields

point

int point

The actual index contained.

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

Serialized Fields

min

int min

The minimum point contained.

max

int max

The maximum point contained.

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

Serialized Fields

labelToSymbolList

java.util.Map labelToSymbolList

labels

java.util.List labels

alphabet

Alphabet alphabet

length

int length

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

Serialized Fields

name

java.lang.String name

annotation

Annotation annotation

symbols

java.util.Set symbols

ambig

java.util.Set ambig

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 implements Serializable

Class org.biojava.bio.symbol.SimpleGappedSymbolList implements Serializable

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 implements Serializable

Serialized Fields

sourceStart

int sourceStart

sourceEnd

int sourceEnd

viewStart

int viewStart

viewEnd

int viewEnd

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

Serialized Fields

revMap

java.util.Map revMap

Map from targets to source symbols

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

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 implements Serializable

Serialized Fields

transMap

java.util.Map transMap

source

FiniteAlphabet source

target

Alphabet target

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

Serialized Fields

sym

AtomicSymbol sym

alphabets

java.util.List alphabets

Class org.biojava.bio.symbol.SuffixTree 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 implements Serializable

Class org.biojava.bio.symbol.SymbolList.EmptySymbolList implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Package org.biojava.bio.dist

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

Serialization Methods

writeObject

private void writeObject(java.io.ObjectOutputStream stream)
                  throws java.io.IOException

Governs serialization behaivour.

Serialized Fields

symbolIndices

java.util.Map symbolIndices

Class org.biojava.bio.dist.AbstractOrderNDistribution implements Serializable

Serialized Fields

alphabet

Alphabet alphabet

firstA

Alphabet firstA

lastA

Alphabet lastA

nullModel

Distribution nullModel

Class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory implements Serializable

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Class org.biojava.bio.dist.GapDistribution implements Serializable

Serialized Fields

alpha

Alphabet alpha

Class org.biojava.bio.dist.IndexedCount implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream stream)
                  throws java.io.IOException

Serialized Fields

symbolIndices

java.util.Map symbolIndices

alpha

FiniteAlphabet alpha

Class org.biojava.bio.dist.PairDistribution implements Serializable

Serialized Fields

first

Distribution first

second

Distribution second

alphabet

Alphabet alphabet

nullModel

Distribution nullModel

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

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Serialized Fields

nullModel

Distribution nullModel

alpha

FiniteAlphabet alpha

Class org.biojava.bio.dist.SimpleDistributionTrainer implements Serializable

Serialized Fields

dis

Distribution dis

c

java.util.Map c

Class org.biojava.bio.dist.SimpleDistributionTrainerContext implements Serializable

Serialized Fields

distToTrainer

java.util.Map distToTrainer

trainers

java.util.Set trainers

nullModelWeight

double nullModelWeight

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

Serialized Fields

other

Distribution other

delegate

Distribution delegate

table

ReversibleTranslationTable table

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

Serialized Fields

alphabet

FiniteAlphabet alphabet

nullModel

Distribution nullModel

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

Package org.biojava.bio.chromatogram

Class org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException implements Serializable

Package org.biojava.bio.proteomics

Class org.biojava.bio.proteomics.Protease 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.alignment

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

Package org.biojava.bio.dp

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

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

Class org.biojava.bio.dp.DP.ReverseIterator implements Serializable

Serialized Fields

sym

SymbolList sym

index

int index

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

Serialized Fields

from

State from

to

State to

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

Serialization Methods

writeReplace

private java.lang.Object writeReplace()
                               throws java.io.ObjectStreamException

Class org.biojava.bio.dp.ProfileHMM 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.SimpleDotState implements Serializable

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

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

_tran

Transition _tran

Class org.biojava.bio.dp.SimpleModelInState implements Serializable

Serialized Fields

model

MarkovModel model

Class org.biojava.bio.dp.SimpleModelTrainer implements Serializable

Serialized Fields

models

java.util.Set models

Class org.biojava.bio.dp.SimpleStatePath implements Serializable

Serialized Fields

score

double score

delegate

Alignment delegate

Class org.biojava.bio.dp.SimpleWeightMatrix implements Serializable

Serialized Fields

columns

Distribution[] columns

alpha

Alphabet alpha

Class org.biojava.bio.dp.TrainerTransition implements Serializable

Serialized Fields

trainer

TransitionTrainer trainer

from

State from

to

State to

Class org.biojava.bio.dp.Transition implements Serializable

Serialized Fields

from

State from

to

State to

Class org.biojava.bio.dp.WeightMatrixAnnotator implements Serializable

Serialized Fields

matrix

WeightMatrix matrix

threshold

double threshold

Class org.biojava.bio.dp.WMAsMM 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.twohead

Class org.biojava.bio.dp.twohead.PairDPMatrix 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 implements Serializable

Serialized Fields

emissionCache

java.util.HashMap emissionCache

ccFactory

CellCalculatorFactory ccFactory

Package org.biojava.bio.dp.onehead

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

Serialized Fields

states

State[] states

model

MarkovModel model

symList

SymbolList[] symList

scores

double[][] scores

score

double score

Package org.biojava.bio.taxa

Class org.biojava.bio.taxa.CircularReferenceException implements Serializable

Package org.biojava.bio.molbio

Class org.biojava.bio.molbio.RestrictionEnzyme 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 implements Serializable

Serialized Fields

enzyme

RestrictionEnzyme enzyme

enzyme RestrictionEnzyme field.

Package org.biojava.utils

Class org.biojava.utils.ChangeEvent 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 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 implements Serializable

Serialized Fields

change

ChangeEvent change

Class org.biojava.utils.ListTools implements Serializable

Class org.biojava.utils.ListTools.Doublet implements Serializable

Serialized Fields

a

java.lang.Object a

b

java.lang.Object b

Class org.biojava.utils.ListTools.Triplet implements Serializable

Serialized Fields

a

java.lang.Object a

b

java.lang.Object b

c

java.lang.Object c

Class org.biojava.utils.NestedError implements Serializable

Serialized Fields

subException

java.lang.Throwable subException

The wrapped Throwable object

Class org.biojava.utils.NestedException implements Serializable

Serialized Fields

subThrowable

java.lang.Throwable subThrowable

Class org.biojava.utils.NestedRuntimeException implements Serializable

Serialized Fields

subThrowable

java.lang.Throwable subThrowable

Class org.biojava.utils.ParseErrorEvent implements Serializable

Serialized Fields

mMessage

java.lang.String mMessage

Class org.biojava.utils.ParserException implements Serializable

Serialized Fields

locator

java.lang.String locator

lineNumber

int lineNumber

character

int character

line

java.lang.String line

Class org.biojava.utils.SingletonList implements Serializable

Serialized Fields

obj

java.lang.Object obj

Class org.biojava.utils.SmallMap implements Serializable

Serialized Fields

mappings

java.lang.Object[] mappings

numMappings

int numMappings

Class org.biojava.utils.StaticMemberPlaceHolder implements Serializable

Serialization Methods

readResolve

public java.lang.Object readResolve()
                             throws java.io.ObjectStreamException

Serialized Fields

className

java.lang.String className

fieldName

java.lang.String fieldName

Class org.biojava.utils.TypedProperties implements Serializable

Package org.biojava.utils.xml

Class org.biojava.utils.xml.AppException implements Serializable

Package org.biojava.utils.lsid

Class org.biojava.utils.lsid.LifeScienceIdentifier implements Serializable

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 implements Serializable

Package org.biojava.directory

Class org.biojava.directory.ProviderNotFoundException implements Serializable

Class org.biojava.directory.RegistryException implements Serializable

Package org.biojava.stats.svm

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

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

Class org.biojava.stats.svm.LinearKernel implements Serializable

Class org.biojava.stats.svm.ListSumKernel implements Serializable

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

Serialized Fields

nested

SVMKernel nested

The SVMKernel being wrapped.

Class org.biojava.stats.svm.NormalizingKernel implements Serializable

Class org.biojava.stats.svm.PolynomialKernel implements Serializable

Serialized Fields

order

double order

a

double a

c

double c

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

Serialized Fields

width

double width

Class org.biojava.stats.svm.SparseVector implements Serializable

Serialized Fields

size

int size

keys

int[] keys

values

double[] values

Class org.biojava.stats.svm.SparseVector.NormalizingKernel implements Serializable

Serialized Fields

s

SparseVector s

The sparse vector that performes the normalization.

Class org.biojava.stats.svm.TrainingEvent implements Serializable

Package org.biojava.stats.svm.tools

Class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier 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 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 implements Serializable

Serialized Fields

a

SuffixTreeKernel.DepthScaler a

b

SuffixTreeKernel.DepthScaler b

Class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler implements Serializable

Class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar implements Serializable

Serialized Fields

bSet

java.util.BitSet bSet

Class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler implements Serializable