Serialized Form


Package GNOME

Class GNOME._Unknown_Tie implements Serializable

Serialized Fields

servant

_Unknown_Operations servant

Class GNOME._UnknownImplBase implements Serializable

Class GNOME._UnknownStub implements Serializable


Package org.acedb

Class org.acedb.AceError implements Serializable

Class org.acedb.AceException implements Serializable

Serialized Fields

recoverable

boolean recoverable

Class org.acedb.AceURLException implements Serializable


Package org.Biocorba.Seqcore

Class org.Biocorba.Seqcore._AnonymousSeq_Tie implements Serializable

Serialized Fields

servant

_AnonymousSeq_Operations servant

Class org.Biocorba.Seqcore._AnonymousSeqImplBase implements Serializable

Class org.Biocorba.Seqcore._AnonymousSeqStub implements Serializable

Class org.Biocorba.Seqcore._PrimarySeq_Tie implements Serializable

Serialized Fields

servant

_PrimarySeq_Operations servant

Class org.Biocorba.Seqcore._PrimarySeqDB_Tie implements Serializable

Serialized Fields

servant

_PrimarySeqDB_Operations servant

Class org.Biocorba.Seqcore._PrimarySeqDBImplBase implements Serializable

Class org.Biocorba.Seqcore._PrimarySeqDBStub implements Serializable

Class org.Biocorba.Seqcore._PrimarySeqImplBase implements Serializable

Class org.Biocorba.Seqcore._PrimarySeqIterator_Tie implements Serializable

Serialized Fields

servant

_PrimarySeqIterator_Operations servant

Class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase implements Serializable

Class org.Biocorba.Seqcore._PrimarySeqIteratorStub implements Serializable

Class org.Biocorba.Seqcore._PrimarySeqStub implements Serializable

Class org.Biocorba.Seqcore._Seq_Tie implements Serializable

Serialized Fields

servant

_Seq_Operations servant

Class org.Biocorba.Seqcore._SeqDB_Tie implements Serializable

Serialized Fields

servant

_SeqDB_Operations servant

Class org.Biocorba.Seqcore._SeqDBImplBase implements Serializable

Class org.Biocorba.Seqcore._SeqDBStub implements Serializable

Class org.Biocorba.Seqcore._SeqFeature_Tie implements Serializable

Serialized Fields

servant

_SeqFeature_Operations servant

Class org.Biocorba.Seqcore._SeqFeatureImplBase implements Serializable

Class org.Biocorba.Seqcore._SeqFeatureIterator_Tie implements Serializable

Serialized Fields

servant

_SeqFeatureIterator_Operations servant

Class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase implements Serializable

Class org.Biocorba.Seqcore._SeqFeatureIteratorStub implements Serializable

Class org.Biocorba.Seqcore._SeqFeatureStub implements Serializable

Class org.Biocorba.Seqcore._SeqImplBase implements Serializable

Class org.Biocorba.Seqcore._SeqStub implements Serializable

Class org.Biocorba.Seqcore.EndOfStream implements Serializable

Class org.Biocorba.Seqcore.NameValueSet implements Serializable

Serialized Fields

name

java.lang.String name

values

java.lang.String[] values

Class org.Biocorba.Seqcore.OutOfRange implements Serializable

Serialized Fields

reason

java.lang.String reason

Class org.Biocorba.Seqcore.RequestTooLarge implements Serializable

Serialized Fields

reason

java.lang.String reason

suggested_size

int suggested_size

Class org.Biocorba.Seqcore.SeqType implements Serializable

Serialized Fields

_value

int _value

Class org.Biocorba.Seqcore.UnableToProcess implements Serializable

Serialized Fields

reason

java.lang.String reason


Package org.biojava.bio

Class org.biojava.bio.Annotation.EmptyAnnotation implements Serializable

Class org.biojava.bio.BioError implements Serializable

Serialized Fields

subException

java.lang.Throwable subException
The wrapped Throwable object

Class org.biojava.bio.BioException implements Serializable

Serialized Fields

subThrowable

java.lang.Throwable subThrowable

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.


Package org.biojava.bio.dist

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

Serialized Fields

other

Distribution other

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

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

Serialized Fields

nullModel

Distribution nullModel

scores

double[] scores

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

Serialized Fields

alphabet

CrossProductAlphabet alphabet

first

Distribution first

nullModel

Distribution nullModel

second

Distribution second

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

Serialized Fields

alphabet

FiniteAlphabet alphabet

nullModel

Distribution nullModel

weight

java.util.Map weight

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

Serialized Fields

c

java.util.Map c

dis

Distribution dis

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

Serialized Fields

distToTrainer

java.util.Map distToTrainer

nullModel

Distribution nullModel

nullModelWeight

double nullModelWeight

trainers

java.util.Set trainers

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

Serialized Fields

alphabet

FiniteAlphabet alphabet

nullModel

Distribution nullModel

weight

double weight


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

index

int index

res

SymbolList res

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

Serialized Fields

from

State from

to

State to

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

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

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

Serialized Fields

mce

ModelChangeEvent mce

Class org.biojava.bio.dp.ModelView.ViewTransitionTrainer implements Serializable

Serialized Fields

this$0

ModelView this$0

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

Serialized Fields

finalScore

double finalScore

model

MarkovModel model

scores

double[][][] scores

seqs

SymbolList[] seqs

states

State[] states

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

Serialized Fields

emissions

java.util.HashMap emissions

gopher

AlphabetManager.ListWrapper gopher

magicalState

EmissionState magicalState

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

Serialized Fields

columns

int columns
The number of columns in this model.

deleteStates

DotState[] deleteStates
Delete states array.

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


insertStates

EmissionState[] insertStates
Insert states array.

From 0 .. columns().


matchStates

EmissionState[] matchStates
Match states array.

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

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

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

Serialized Fields

advance

int[] advance

ann

Annotation ann

dis

Distribution dis

matches

Alphabet matches

name

java.lang.String name

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

Serialized Fields

_tran

Transition _tran

emissionAlpha

Alphabet emissionAlpha

magicalState

MagicalState magicalState

stateAlpha

FiniteAlphabet stateAlpha

transFrom

java.util.Map transFrom

transitionScores

java.util.Map transitionScores

transTo

java.util.Map transTo

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

Serialized Fields

_tran

Transition _tran

allTransitionTrainers

java.util.Set allTransitionTrainers
The set of all TransitionTrainers.

model

MarkovModel model

modelToTrainer

java.util.Map modelToTrainer
MarkovModel -> TransitionTrainer

nullModel

Distribution nullModel

nullModelWeight

double nullModelWeight

transCounts

double transCounts

transCountWeight

double transCountWeight

transitionToCount

java.util.Map transitionToCount
Transition -> Double count

Optimization so that transition counts only need be distributed to all listeners just prior to training.


transitionToTrainer

java.util.Map transitionToTrainer
Transition -> Set

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

Serialized Fields

delegate

Alignment delegate

score

double score

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

Serialized Fields

_tran

Transition _tran

model

MarkovModel model

transCounts

java.util.Map transCounts

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

Serialized Fields

alpha

Alphabet alpha

columns

Distribution[] columns

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

Serialized Fields

from

State from

to

State to

trainer

TransitionTrainer trainer

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

Serialized Fields

from

State from

to

State to

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

Serialized Fields

end

State end

newScore

double newScore

oldScore

double oldScore

start

State start

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

magicalState

MagicalState magicalState

stateAlpha

FiniteAlphabet stateAlpha

states

EmissionState[] states

wm

WeightMatrix wm


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.

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

Serialized Fields

acrossDim

double acrossDim

alongDim

double alongDim

depths

java.util.Map depths

direction

int direction

leadingBorder

SequencePanel.Border leadingBorder

lineDepth

double lineDepth

lines

int lines

realLines

int realLines

scale

double scale

sequence

Sequence sequence

spacer

int spacer

theMonitor

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

trailingBorder

SequencePanel.Border trailingBorder

views

java.util.List views

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

Serialized Fields

alignment

int alignment

pcs

java.beans.PropertyChangeSupport pcs

size

double size

this$0

SequencePanel this$0


Package org.biojava.bio.program.gff

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


Package org.biojava.bio.seq

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

Serialized Fields

annotation

Annotation annotation

location

Location location

source

java.lang.String source

type

java.lang.String type

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

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

Serialized Fields

c1

FeatureFilter c1

c2

FeatureFilter c2

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.Not implements Serializable

Serialized Fields

child

FeatureFilter child

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.SimpleFeatureRealizer implements Serializable

Serialized Fields

fallBack

FeatureRealizer fallBack

templateToImpl

java.util.List templateToImpl

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

Serialized Fields

realizer

FeatureRealizer realizer

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

Serialized Fields

text

java.lang.String text

token

char token

value

int value

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

Serialized Fields

strand

StrandedFeature.Strand strand


Package org.biojava.bio.seq.db

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

Serialized Fields

annotator

SequenceAnnotator annotator

parent

SequenceDB parent

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

Serialized Fields

parent

SequenceDB parent

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

Serialized Fields

idMaker

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

name

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

sequenceByID

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

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

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

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

Serialized Fields

files

java.util.Set files

format

SequenceFormat format

idMaker

IDMaker idMaker

idToSource

java.util.Map idToSource

indexFile

java.io.File indexFile

name

java.lang.String name

sFact

SequenceFactory sFact

symParser

SymbolParser symParser


Package org.biojava.bio.seq.io

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

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

Serialized Fields

featureBuilder

FeatureBuilder featureBuilder

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

Serialized Fields

fdr

FastaDescriptionReader fdr
The description reader.

lineWidth

int lineWidth
The line width for output.

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

Serialized Fields

featureBuilder

FeatureBuilder featureBuilder

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


Package org.biojava.bio.symbol

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

Serialized Fields

annotation

Annotation annotation

name

java.lang.String name

nameToSymbol

java.util.Map nameToSymbol

symbols

java.util.Set symbols

tokenToSymbol

java.util.Map tokenToSymbol

Class org.biojava.bio.symbol.Alphabet.EmptyAlphabet implements Serializable

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

Serialized Fields

locations

java.util.List locations
The list of child locations in order. Should contain only RangeLocation instances.

max

int max
Maximum index contained.

min

int min
Minimum index contained.

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

Serialized Fields

alpha

CrossProductAlphabet alpha

parser

SymbolParser[] parser

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

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

Serialized Fields

matches

Alphabet matches

val

double val

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

Serialized Fields

alpha

Alphabet alpha
The alphabet for this parser.

tokenLength

int tokenLength
The length of each token.

tokenToSymbol

java.util.Map tokenToSymbol
Map from token to Symbol.

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

Serialized Fields

alpha

Alphabet alpha
The Alphabet - the same as source but guaranteed to include the gap character.

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 - necisary to allow leading & trailing gaps.

source

SymbolList source
The SymbolList to view.

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

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

Serialized Fields

res

Symbol res

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

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

Serialized Fields

matches

Alphabet matches

val

int val

Class org.biojava.bio.symbol.Location.EmptyLocation implements Serializable

Class org.biojava.bio.symbol.Location.LocationComparator implements Serializable

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

Serialized Fields

alphabet

FiniteAlphabet alphabet
The alphabet to parse names to.

nameToSymbol

java.util.Map nameToSymbol
The map of name to symbols.

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

Serialized Fields

alpha

CrossProductAlphabet alpha
The alphabet for each overlapping tuple.

order

int order
The view order.

source

SymbolList source
The source sequence that we will transliterate.

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

max

int max
The maximum point contained.

min

int min
The minimum point contained.

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

Serialized Fields

source

SymbolList source
The source sequence that we will transliterate.

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

Serialized Fields

alphabet

CrossProductAlphabet alphabet

labels

java.util.List labels

labelToSymbolList

java.util.Map labelToSymbolList

length

int length

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

Serialized Fields

ambig

java.util.Set ambig
A set of well-known ambiguity symbols.

annotation

Annotation annotation
The annotation associated with this alphabet.

name

java.lang.String name
The name of this alphabet.

symbols

java.util.Set symbols
A set of the non-ambiguity symbols within the alphabet.

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

Serialized Fields

annotation

Annotation annotation

matches

Alphabet matches

name

java.lang.String name

token

char token

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

Serialized Fields

alphabet

Alphabet alphabet

length

int length

symbols

Symbol[] symbols

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

Serialized Fields

source

FiniteAlphabet source

target

Alphabet target

transMap

java.util.Map transMap

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

Serialized Fields

sym

AtomicSymbol sym

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

Serialized Fields

alphabet

FiniteAlphabet alphabet

counts

java.util.List counts

resList

java.util.List resList

root

SuffixTree.SuffixNode root

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

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

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

Serialized Fields

alphabet

FiniteAlphabet alphabet
The alphabet to parse into.

tokenToSymbol

java.util.Map tokenToSymbol
The map from token to symbol.

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

Serialized Fields

alpha

CrossProductAlphabet alpha
The alphabet of window Symbols.

source

SymbolList source
The source sequence that we will transliterate.

width

int width
The width of the window.


Package org.biojava.stats.svm

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

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

Serialized Fields

lambda

double lambda
The scale vactor.

negClass

java.util.Set negClass

posClass

java.util.Set posClass

Class org.biojava.stats.svm.DiagonalCachingKernel 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

a

double a

c

double c

order

double order

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

Serialized Fields

width

double width

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

Serialized Fields

keys

int[] keys

size

int size

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

addPos

boolean addPos

kernel

SVMKernel kernel

model

SVMClassifierModel model

negPaint

java.awt.Paint negPaint

negShape

java.awt.Shape negShape

plainPaint

java.awt.Paint plainPaint

posPaint

java.awt.Paint posPaint

posShape

java.awt.Shape posShape

svPaint

java.awt.Paint svPaint

target

SVMTarget target

Class org.biojava.stats.svm.tools.SuffixTreeKernel 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


Package org.biojava.utils

Class org.biojava.utils.ParserException implements Serializable

Serialized Fields

character

int character

line

java.lang.String line

lineNumber

int lineNumber

locator

java.lang.String locator

Class org.biojava.utils.StaticMemberPlaceHolder implements Serializable

Serialized Fields

className

java.lang.String className

fieldName

java.lang.String fieldName

Class org.biojava.utils.TypedProperties implements Serializable


Package org.biojava.utils.contract

Class org.biojava.utils.contract.AssertionFailedException implements Serializable

Class org.biojava.utils.contract.PostconditionNotMetException implements Serializable

Class org.biojava.utils.contract.PreconditionNotMetException implements Serializable