A B C D E F G H I K L M N O P Q R S T U V W X _

A

a() - Static method in class org.biojava.bio.seq.DNATools
 
ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
AbstractAlphabet - class org.biojava.bio.symbol.AbstractAlphabet.
An abstract implementation of Alphabet.
AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
 
AbstractDistribution - class org.biojava.bio.dist.AbstractDistribution.
An abstract implementation of Distribution.
AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
 
AbstractFeatureHolder - class org.biojava.bio.seq.AbstractFeatureHolder.
An abstract implementation of FeatureHolder.
AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
 
AbstractSVMClassifierModel - class org.biojava.stats.svm.AbstractSVMClassifierModel.
Abstract implementation of SVMClassifierModel.
AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
 
AbstractSVMTarget - class org.biojava.stats.svm.AbstractSVMTarget.
An abstract implementation of an SVMModel.
AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
 
AbstractSymbolList - class org.biojava.bio.symbol.AbstractSymbolList.
Abstract helper implementation of the SymbolList core interface.
AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
 
AbstractTrainer - class org.biojava.bio.dp.AbstractTrainer.
 
AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
 
ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
A GFFRecordFilter that accepts everything.
accept(AceURL) - Method in class org.acedb.socket.SocketDriver
 
accept(AceURL) - Method in interface org.acedb.Driver
Returns whether this driver can handle this url type.
accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
This method determines whether a fetaure is to be accepted.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.AcceptAllFilter
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
Returns true if the feature has a matching type property.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
Returns true if the feature is within this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
Returns true if the feature overlaps this filter's location.
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
 
accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
Return wether or not to accept record.
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
accession_number() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
accession_number() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
accession_number() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
accession_number() - Method in interface org.Biocorba.Seqcore.PrimarySeq
 
accession_number() - Method in class org.Biocorba.Seqcore._SeqStub
 
accession_number(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeq_Operations
 
accession_number(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
Ace - class org.acedb.Ace.
 
AceAnnotation - class org.acedb.seq.AceAnnotation.
 
AceAnnotation(AceNode) - Constructor for class org.acedb.seq.AceAnnotation
 
AceElement - interface org.acedb.AceElement.
An element within an AceObject.
AceError - error org.acedb.AceError.
 
AceError() - Constructor for class org.acedb.AceError
 
AceError(String) - Constructor for class org.acedb.AceError
 
AceError(Throwable) - Constructor for class org.acedb.AceError
 
AceError(Throwable, String) - Constructor for class org.acedb.AceError
 
AceException - exception org.acedb.AceException.
 
AceException() - Constructor for class org.acedb.AceException
 
AceException(String) - Constructor for class org.acedb.AceException
 
AceException(String, boolean) - Constructor for class org.acedb.AceException
 
AceException(Throwable) - Constructor for class org.acedb.AceException
 
AceException(Throwable, String) - Constructor for class org.acedb.AceException
 
AceNode - interface org.acedb.AceNode.
A node within the tree data structure.
AceObject - interface org.acedb.AceObject.
A top level object in an ACeDB database.
AcePerlParser - class org.acedb.AcePerlParser.
Parse the `Perl' representation of ACeDB objects.
AcePerlParser(Database) - Constructor for class org.acedb.AcePerlParser
 
AceSequence - class org.acedb.seq.AceSequence.
Sequence extracted from an ACeDB database.
AceSequence(AceObject) - Constructor for class org.acedb.seq.AceSequence
 
AceSequenceDB - class org.acedb.seq.AceSequenceDB.
An implementation of SequenceDB that lets either an entire ACeDB database, or some sub-set of its sequences be viewed as a native BioJava sequence database.
AceSequenceDB(AceURL) - Constructor for class org.acedb.seq.AceSequenceDB
 
AceSequenceDB(AceURL, String) - Constructor for class org.acedb.seq.AceSequenceDB
 
AceSet - interface org.acedb.AceSet.
A generalized set of named objects used within the ACeDB system.
AceURL - class org.acedb.AceURL.
 
AceURL(String) - Constructor for class org.acedb.AceURL
 
AceURL(String, String, int, String, String, String, String, String) - Constructor for class org.acedb.AceURL
 
AceURL(URL, String, String, String) - Constructor for class org.acedb.AceURL
 
AceURLException - exception org.acedb.AceURLException.
 
AceURLException() - Constructor for class org.acedb.AceURLException
 
AceURLException(String) - Constructor for class org.acedb.AceURLException
 
AceURLException(Throwable) - Constructor for class org.acedb.AceURLException
 
AceURLException(Throwable, String) - Constructor for class org.acedb.AceURLException
 
AceUtils - class org.acedb.AceUtils.
General utility methods for ACeDBC.
AceUtils() - Constructor for class org.acedb.AceUtils
 
AceValue - interface org.acedb.AceValue.
A node in an ACeDB object which represents a value.
add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Add a GFFRecord to the end of this set.
add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Add a comment to the end of this set.
add(String, AceSet) - Method in class org.acedb.staticobj.StaticAceSet
 
addAmbiguity(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
Add a commonly recognized ambiguiy symbol to this alphabet.
addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Registers that sym was counted in this state.
addCount(DistributionTrainerContext, Symbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
addCount(DistributionTrainerContext, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
 
addCount(DistributionTrainerContext, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Registers that sym was counted in this state.
addCount(State, State, double) - Method in class org.biojava.bio.dp.ModelView.ViewTransitionTrainer
 
addCount(State, State, double) - Method in class org.biojava.bio.dp.SimpleTransitionTrainer
 
addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
Add 'count' to the transition from->to.
addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
Add a feature to the featureholder
addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
Merges a featureholder to the current featureholder
addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Add sequences from a file to the sequence database.
addGapInSource(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Add a gap at pos within the source coordinates.
addGapInView(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Add a single gap at pos within the view coordintates.
addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Add length gaps at pos within the source coordinates.
addGapsInView(int, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Add length gaps at pos within the view coordinates.
addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
Install a new mapping from a class of Feature.Template to a class of Feature implementations.
addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
 
addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
addNode(AceNode) - Method in class org.acedb.staticobj.StaticAceNode
 
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.SequencePanel.Border
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.SequencePanel
 
addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
Add a sequence under its default id.
addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
Add a sequence under a particular id.
addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
this method creates a new (and empty) HashSequenceDB with the given name that will be accessible through this sequence db installation through this name and all given other identifiers.
addState(State) - Method in class org.biojava.bio.dp.WMAsMM
 
addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
addState(State) - Method in class org.biojava.bio.dp.ModelView
 
addState(State) - Method in interface org.biojava.bio.dp.MarkovModel
Adds a state to the model.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
Adds a symbol to this alphabet.
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList
Deprecated. Can we make SimpleSymbolList immutable [Thomas Down]
addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree
Add a count for all motifs with length of up to window to this tree.
addTokenMap(String, Symbol) - Method in class org.biojava.bio.symbol.FixedWidthParser
Maps a string (one or more characters) onto a symbol
addTransitionCount(State, State, double) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
addTransitionCount(State, State, double) - Method in interface org.biojava.bio.dp.ModelTrainer
Adds some counts to the transition between two states.
addTransitionListener(TransitionListener) - Method in class org.biojava.bio.dp.WMAsMM
 
addTransitionListener(TransitionListener) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
addTransitionListener(TransitionListener) - Method in interface org.biojava.bio.dp.MarkovModel
Register a TransitionListener with the model.
addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
Alignment - interface org.biojava.bio.symbol.Alignment.
An alignment containing multiple SymbolLists.
AlignmentFormat - interface org.biojava.bio.seq.io.AlignmentFormat.
 
all - Static variable in interface org.biojava.bio.seq.FeatureFilter
All features are selected in with this filter.
all_features_iterator() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
all_features_iterator() - Method in class org.Biocorba.Seqcore._SeqStub
 
all_features_iterator() - Method in interface org.Biocorba.Seqcore.Seq
 
all_features_iterator(ObjectImpl) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
all_features_iterator(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
all_features() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
all_features() - Method in class org.Biocorba.Seqcore._SeqStub
 
all_features() - Method in interface org.Biocorba.Seqcore.Seq
 
all_features(ObjectImpl) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
all_features(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
AllTokensAlphabet - class org.biojava.bio.symbol.AllTokensAlphabet.
An implementation of FiniteAlphabet that grows the alphabet to accomodate all the characters seen while parsing a file.
AllTokensAlphabet(String) - Constructor for class org.biojava.bio.symbol.AllTokensAlphabet
 
Alphabet - interface org.biojava.bio.symbol.Alphabet.
The set of AtomicSymbols which can be concatanated together to make a SymbolList.
Alphabet.EmptyAlphabet - class org.biojava.bio.symbol.Alphabet.EmptyAlphabet.
The class that implements Alphabet and is empty.
Alphabet.EmptyAlphabet() - Constructor for class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve the alphabet for a specific name.
AlphabetManager - class org.biojava.bio.symbol.AlphabetManager.
The first port of call for retrieving standard alphabets.
AlphabetManager.ListWrapper - class org.biojava.bio.symbol.AlphabetManager.ListWrapper.
Simple wrapper to assist in list-comparisons.
AlphabetManager.ListWrapper() - Constructor for class org.biojava.bio.symbol.AlphabetManager.ListWrapper
 
AlphabetManager.ListWrapper(List) - Constructor for class org.biojava.bio.symbol.AlphabetManager.ListWrapper
 
AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
 
alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
Get an iterator over all alphabets known.
ambiguities() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
Annotatable - interface org.biojava.bio.Annotatable.
Flags an object as having associated annotation.
annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
 
annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
Return an annotated version of a sequence.
AnnotatedSequenceDB - class org.biojava.bio.seq.db.AnnotatedSequenceDB.
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
annotation - Variable in class org.biojava.bio.seq.Feature.Template
 
Annotation - interface org.biojava.bio.Annotation.
Arbitrary annotation associated with one or more objects.
Annotation.EmptyAnnotation - class org.biojava.bio.Annotation.EmptyAnnotation.
The empty and immutable implementation.
Annotation.EmptyAnnotation() - Constructor for class org.biojava.bio.Annotation.EmptyAnnotation
 
AnonymousSeq - interface org.Biocorba.Seqcore.AnonymousSeq.
 
AnonymousSeqHelper - class org.Biocorba.Seqcore.AnonymousSeqHelper.
 
AnonymousSeqHolder - class org.Biocorba.Seqcore.AnonymousSeqHolder.
 
AnonymousSeqHolder() - Constructor for class org.Biocorba.Seqcore.AnonymousSeqHolder
 
AnonymousSeqHolder(AnonymousSeq) - Constructor for class org.Biocorba.Seqcore.AnonymousSeqHolder
 
AnonymousSeqImpl - class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl.
 
AnonymousSeqImpl(SymbolList) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
areEqual(Location, Location) - Method in class org.biojava.bio.symbol.Location.LocationComparator
Test whether two locations are equal or not
asMap() - Method in class org.acedb.seq.AceAnnotation
 
asMap() - Method in interface org.biojava.bio.Annotation
Retern a map that contains the same key/values as this Annotation.
asMap() - Method in class org.biojava.bio.Annotation.EmptyAnnotation
 
asMap() - Method in class org.biojava.bio.OverlayAnnotation
Return a Map view onto this annotation.
asMap() - Method in class org.biojava.bio.SimpleAnnotation
 
assert(boolean, String) - Static method in class org.biojava.utils.contract.Contract
check if a condition is met and throw an exception if not.
AssertionFailedException - exception org.biojava.utils.contract.AssertionFailedException.
Exception class that is thrown if an assertion failed.
AssertionFailedException() - Constructor for class org.biojava.utils.contract.AssertionFailedException
construct with no particular message
AssertionFailedException(String) - Constructor for class org.biojava.utils.contract.AssertionFailedException
construct with the given message
AtomicSymbol - interface org.biojava.bio.symbol.AtomicSymbol.
A symbol that is indivisible.

B

backward(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
backward(SymbolList[]) - Method in class org.biojava.bio.dp.PairwiseDP
 
backwardMatrix(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[]) - Method in class org.biojava.bio.dp.PairwiseDP
 
backwardMatrix(SymbolList[], DPMatrix) - Method in class org.biojava.bio.dp.DP
 
backwardMatrix(SymbolList[], DPMatrix) - Method in class org.biojava.bio.dp.PairwiseDP
 
backwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
 
backwardTransitionScores(MarkovModel, State[], int[][]) - Static method in class org.biojava.bio.dp.DP
 
BarLogoPainter - class org.biojava.bio.gui.BarLogoPainter.
A logo painter that paints in bars.
BarLogoPainter() - Constructor for class org.biojava.bio.gui.BarLogoPainter
 
BasicFeatureRenderer - class org.biojava.bio.gui.sequence.BasicFeatureRenderer.
 
BasicFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
BaumWelchSampler - class org.biojava.bio.dp.BaumWelchSampler.
 
BaumWelchSampler(DP) - Constructor for class org.biojava.bio.dp.BaumWelchSampler
 
BaumWelchTrainer - class org.biojava.bio.dp.BaumWelchTrainer.
 
BaumWelchTrainer(DP) - Constructor for class org.biojava.bio.dp.BaumWelchTrainer
 
BioError - error org.biojava.bio.BioError.
A general purpose Error that can wrap another Throwable object.
BioError() - Constructor for class org.biojava.bio.BioError
 
BioError(String) - Constructor for class org.biojava.bio.BioError
 
BioError(Throwable) - Constructor for class org.biojava.bio.BioError
 
BioError(Throwable, String) - Constructor for class org.biojava.bio.BioError
 
BioException - exception org.biojava.bio.BioException.
A general perpose Exception that can wrap another exception.
BioException() - Constructor for class org.biojava.bio.BioException
 
BioException(String) - Constructor for class org.biojava.bio.BioException
 
BioException(Throwable) - Constructor for class org.biojava.bio.BioException
 
BioException(Throwable, String) - Constructor for class org.biojava.bio.BioException
 
blockIterator() - Method in class org.biojava.bio.symbol.PointLocation
 
blockIterator() - Method in class org.biojava.bio.symbol.RangeLocation
 
blockIterator() - Method in class org.biojava.bio.symbol.CompoundLocation
 
blockIterator() - Method in interface org.biojava.bio.symbol.Location
Return an Iterator over the set of maximal contiguous sub-locations.
blockIterator() - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
buildFeatureTemplate(String, Location, StrandedFeature.Strand, Map) - Method in interface org.biojava.bio.seq.io.FeatureBuilder
Return a latent (template) feature object to represent a feature in some database.
buildFeatureTemplate(String, Location, StrandedFeature.Strand, Map) - Method in class org.biojava.bio.seq.io.SimpleFeatureBuilder
 
byName - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by sequence name.
byURN - Static variable in interface org.biojava.bio.seq.db.IDMaker
A simple implementation of IDMaker that hashes by URN.

C

c() - Static method in class org.biojava.bio.seq.DNATools
 
CachingKernel - class org.biojava.stats.svm.CachingKernel.
Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
 
CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
 
CachingSequenceDB - class org.biojava.bio.seq.db.CachingSequenceDB.
SequenceDB implementation that caches the results of another SequenceDB.
CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB
Create a new CachingSequenceDB that caches the sequences in parent.
calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker
Calculate the id for a sequence.
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
 
calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
 
calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
characters(char[], int, int) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
ClassifierExample - class org.biojava.stats.svm.tools.ClassifierExample.
A simple toy example that allows you to put points on a canvas, and find a polynomeal hyperplane to seperate them.
ClassifierExample.PointClassifier - class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier.
An extention of JComponent that contains the points & encapsulates the classifier.
ClassifierExample.PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Make a new PointClassifier.
ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
 
Classify - class org.biojava.stats.svm.tools.Classify.
 
classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Learn a model from the current points.
Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
 
classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Remove all points from the canvas, and discard any model.
clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
clear() - Method in interface org.biojava.stats.svm.SVMTarget
 
clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
clearCounts() - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
clearCounts() - Method in class org.biojava.bio.dp.ModelView.ViewTransitionTrainer
 
clearCounts() - Method in interface org.biojava.bio.dp.ModelTrainer
Clears all of the counts, ready for re-training.
clearCounts() - Method in class org.biojava.bio.dp.SimpleTransitionTrainer
 
clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer
Clears all of the counts to zero.
clearCounts() - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
 
clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainer
Clears all of the counts to zero.
clearDistributionCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
clearDistributionCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Clears all of the counts to zero.
clone() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
 
clone() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
clone() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
clone() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
 
clone() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
clone() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
 
clone() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
 
clone() - Method in class org.biojava.utils.TypedProperties
 
columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
columns() - Method in interface org.biojava.bio.dp.WeightMatrix
The number of columns modeled by the weight matrix.
columns() - Method in class org.biojava.bio.dp.ProfileHMM
Retrieve the number of columns in the model.
commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
A comment line has been encountered.
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
 
commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter
Prints the comment directly to the PrintWriter after adding a leading '#'.
compare(Object, Object) - Method in class org.biojava.bio.symbol.Location.LocationComparator
 
complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
Complement the symbol.
complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Retrieve a complement view of list.
ComplementaryDistribution - class org.biojava.bio.dist.ComplementaryDistribution.
Creates a complementary distribution from a given distribution.
ComplementaryDistribution(Distribution) - Constructor for class org.biojava.bio.dist.ComplementaryDistribution
 
CompoundLocation - class org.biojava.bio.symbol.CompoundLocation.
A complex location.
CompoundLocation(List) - Constructor for class org.biojava.bio.symbol.CompoundLocation
Generate a new CompoundLocation from a list of locations.
connect(AceURL) - Method in class org.acedb.socket.SocketDriver
 
connect(AceURL) - Method in interface org.acedb.Driver
Return a database that is connected to this url.
Connection - interface org.acedb.Connection.
A call-level connection to an ACeDB object.
contains(int) - Method in class org.biojava.bio.symbol.PointLocation
 
contains(int) - Method in class org.biojava.bio.symbol.RangeLocation
 
contains(int) - Method in class org.biojava.bio.symbol.CompoundLocation
 
contains(int) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains a point.
contains(int) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.PointLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.RangeLocation
 
contains(Location) - Method in class org.biojava.bio.symbol.CompoundLocation
 
contains(Location) - Method in interface org.biojava.bio.symbol.Location
Checks if this location contains the other.
contains(Location) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
contains(String) - Method in class org.acedb.staticobj.StaticAceNode
 
contains(String) - Method in class org.acedb.staticobj.StaticAceSet
 
contains(String) - Method in class org.acedb.socket.SocketResultSet
 
contains(String) - Method in interface org.acedb.AceSet
Returns whether an object is contained under a given name.
contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
Returns whether or not this Alphabet contains the symbol.
contains(Symbol) - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
contains(Symbol) - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
containsTransition(State, State) - Method in class org.biojava.bio.dp.ModelView
 
containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns whether a transition is possible in the model.
Contract - class org.biojava.utils.contract.Contract.
Some minimal support for "design by contract" with pre-conditions, post-conditions and integrity rules (assertions).
countFeatures() - Method in class org.acedb.seq.AceSequence
 
countFeatures() - Method in class org.biojava.bio.seq.ViewSequence
 
countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
 
countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
Count how many features are contained.
countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
countFeatures() - Method in class org.biojava.bio.seq.SimpleSequence
 
countFeatures() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
countFeatures() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
createDB(String, File, SequenceFormat, SequenceFactory, SymbolParser, IDMaker) - Static method in class org.biojava.bio.seq.db.IndexedSequenceDB
Create a sequence database
createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory
Generate a new Distribution as requested.
createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
 
createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
Return a new DNA SymbolList for dna.
createDP(MarkovModel) - Static method in class org.biojava.bio.dp.DPFactory
 
createFeature(Feature.Template) - Method in class org.acedb.seq.AceSequence
Add a new feature to this sequence.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.ViewSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder
Create a new Feature, and add it to this FeatureHolder.
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleSequence
 
createFeature(Feature.Template) - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
createFeature(Feature.Template) - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
createFeature(FeatureHolder, Feature.Template) - Method in class org.acedb.seq.AceSequence
Add a new feature to this sequence.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.ViewSequence
Deprecated. Please use 1-arg createFeature instead.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleSequence
Deprecated. Please use new 1-arg createFeature instead.
createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser
Actualy turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
Creates a sequence using these parameters.
createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.SimpleSequenceFactory
 
createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Makes a transition between two states legal.
createTransition(State, State, MarkovModel, State, State) - Method in class org.biojava.bio.dp.ModelView
 
CrossProductAlphabet - interface org.biojava.bio.symbol.CrossProductAlphabet.
Cross product of a list of alphabets.
CrossProductSymbol - interface org.biojava.bio.symbol.CrossProductSymbol.
Symbol in a CrossProductAlphabet.
CrossProductSymbolNameParser - class org.biojava.bio.symbol.CrossProductSymbolNameParser.
Allows Symbol objects to be created from Strings assuming that they follow the guide-lines layed down in CrossProductAlphabet for naming.
CrossProductSymbolNameParser(CrossProductAlphabet) - Constructor for class org.biojava.bio.symbol.CrossProductSymbolNameParser
 

D

Database - interface org.acedb.Database.
An encapsulation of an ACeDB Database server.
database_name() - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
database_name() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
database_name() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
database_name() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
database_name() - Method in interface org.Biocorba.Seqcore.PrimarySeqDB
 
database_name(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeqDB_Operations
 
database_name(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
database_version() - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
database_version() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
database_version() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
database_version() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
database_version() - Method in interface org.Biocorba.Seqcore.PrimarySeqDB
 
database_version(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeqDB_Operations
 
database_version(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
DateValue - interface org.acedb.DateValue.
A date value.
decode(String) - Static method in class org.acedb.AceUtils
 
DEFAULT - Static variable in class org.biojava.bio.seq.SimpleFeatureRealizer
Default implementation of FeatureRealizer, which wraps simple implementations of Feature and StrandedFeature.
DEFAULT - Static variable in interface org.biojava.bio.dist.DistributionFactory
The default DistributionFactory object.
DEFAULT_DELIMITERS - Static variable in class org.biojava.utils.TypedProperties
the default string of delimiter characters used by getAsStringList()
DEFAULT_DESCRIPTION_READER - Static variable in class org.biojava.bio.seq.io.FastaFormat
The default description reader.
DefaultDescriptionReader - class org.biojava.bio.seq.io.DefaultDescriptionReader.
Assumes that the description is of the form 'id\s*desc'.
DefaultDescriptionReader() - Constructor for class org.biojava.bio.seq.io.DefaultDescriptionReader
 
destroyTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
destroyTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
destroyTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Breaks a transition between two states legal.
DiagonalAddKernel - class org.biojava.stats.svm.DiagonalAddKernel.
Adds a class specific constant to k(x, x).
DiagonalAddKernel() - Constructor for class org.biojava.stats.svm.DiagonalAddKernel
 
DiagonalCachingKernel - class org.biojava.stats.svm.DiagonalCachingKernel.
Caches the leading diagonal of a kernel matrix.
DiagonalCachingKernel() - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.DiagonalCachingKernel
Creates a new DiagonalCachingKernel that nests k.
display_id() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
display_id() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
display_id() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
display_id() - Method in interface org.Biocorba.Seqcore.PrimarySeq
 
display_id() - Method in class org.Biocorba.Seqcore._SeqStub
 
display_id(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeq_Operations
 
display_id(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
dispose() - Method in interface org.acedb.Connection
Safely dispose of this connection.
Distribution - interface org.biojava.bio.dist.Distribution.
An encapsulation of a probability distribution over the Symbols within an alphabet.
DistributionFactory - interface org.biojava.bio.dist.DistributionFactory.
A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory - class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory.
The default DistributionFactory implementation.
DistributionFactory.DefaultDistributionFactory() - Constructor for class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
 
DistributionLogo - class org.biojava.bio.gui.DistributionLogo.
The gui component for rendering a DistributionLogo.
DistributionLogo() - Constructor for class org.biojava.bio.gui.DistributionLogo
Create a new DistributionLogo object.
DistributionTrainer - interface org.biojava.bio.dist.DistributionTrainer.
An object that can be used to train a distribution up.
DistributionTrainerContext - interface org.biojava.bio.dist.DistributionTrainerContext.
A context within a group of DistributionTrainers can be trained together.
DNA - Static variable in class org.Biocorba.Seqcore.SeqType
 
DNADistribution - class org.biojava.bio.dist.DNADistribution.
A state in a markov process.
DNADistribution() - Constructor for class org.biojava.bio.dist.DNADistribution
 
DNAStyle - class org.biojava.bio.gui.DNAStyle.
A simple implementation of SymbolStyle optimized for DNA.
DNAStyle() - Constructor for class org.biojava.bio.gui.DNAStyle
 
DNATools - class org.biojava.bio.seq.DNATools.
Usefull functionality for processing DNA sequences.
DNATools() - Constructor for class org.biojava.bio.seq.DNATools
 
doAnnotation(Sequence) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
Apply the annotation to a sequence.
doProcessSequence(Sequence, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Internal method to process an individual Sequence.
DotState - interface org.biojava.bio.dp.DotState.
A Dot state.
DoubleAlphabet - class org.biojava.bio.symbol.DoubleAlphabet.
An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleSymbol - class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol.
A single double value.
DoubleAlphabet.DoubleSymbol(double) - Constructor for class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
DoubleAlphabet() - Constructor for class org.biojava.bio.symbol.DoubleAlphabet
 
doubleValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
DP - class org.biojava.bio.dp.DP.
 
DP.ReverseIterator - class org.biojava.bio.dp.DP.ReverseIterator.
 
DP.ReverseIterator(SymbolList) - Constructor for class org.biojava.bio.dp.DP.ReverseIterator
 
DP(MarkovModel) - Constructor for class org.biojava.bio.dp.DP
 
DPFactory - class org.biojava.bio.dp.DPFactory.
 
DPFactory() - Constructor for class org.biojava.bio.dp.DPFactory
 
DPMatrix - interface org.biojava.bio.dp.DPMatrix.
 
Driver - interface org.acedb.Driver.
A driver which provides a transport for connecting to an ACeDB server.
dumpBlocks() - Method in class org.biojava.bio.symbol.GappedSymbolList
Debugging method

E

EmblFormat - class org.biojava.bio.seq.io.EmblFormat.
Format reader for EMBL files.
EmblFormat() - Constructor for class org.biojava.bio.seq.io.EmblFormat
Constuct and EMBL format processor using a default FeatureBuilder object.
EmblFormat(FeatureBuilder) - Constructor for class org.biojava.bio.seq.io.EmblFormat
Construct an EMBL format processor using the specified FeatureBuilder object.
emissionAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
 
emissionAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
emissionAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
Alphabet that is emitted by the emission states.
EmissionState - interface org.biojava.bio.dp.EmissionState.
A state in a markov process that has an emission spectrum.
empty - Static variable in interface org.biojava.bio.symbol.Location
The empty range.
EMPTY_ALPHABET - Static variable in interface org.biojava.bio.symbol.Alphabet
A really useful static alphabet that is always empty.
EMPTY_ANNOTATION - Static variable in interface org.biojava.bio.Annotation
A realy useful empty and immutable annotation object.
EMPTY_FEATURE_HOLDER - Static variable in interface org.biojava.bio.seq.FeatureHolder
 
EMPTY_LIST - Static variable in interface org.biojava.bio.symbol.SymbolList
A useful object that represents an empty symbol list, to avoid returning null.
encode(String) - Static method in class org.acedb.AceUtils
 
end() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
end() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
end() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
end(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
end(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
endDocument() - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
Indicates that the current GFF document has now ended.
endDocument() - Method in class org.biojava.bio.program.gff.GFFFilterer
 
endDocument() - Method in class org.biojava.bio.program.gff.GFFWriter
Flushes the PrintWriter to make sure that everything is written.
endDocument() - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
endElement(String) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
EndOfStream - exception org.Biocorba.Seqcore.EndOfStream.
 
EndOfStream() - Constructor for class org.Biocorba.Seqcore.EndOfStream
 
EndOfStreamHelper - class org.Biocorba.Seqcore.EndOfStreamHelper.
 
EndOfStreamHolder - class org.Biocorba.Seqcore.EndOfStreamHolder.
 
EndOfStreamHolder() - Constructor for class org.Biocorba.Seqcore.EndOfStreamHolder
 
EndOfStreamHolder(EndOfStream) - Constructor for class org.Biocorba.Seqcore.EndOfStreamHolder
 
entropy(Symbol) - Method in class org.biojava.bio.gui.DistributionLogo
Calculate the information content of a symbol in bits.
equals(boolean[], boolean[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(boolean, boolean) - Static method in class org.biojava.utils.ObjectUtil
 
equals(double[], double[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(double, double) - Static method in class org.biojava.utils.ObjectUtil
 
equals(float[], float[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(float, float) - Static method in class org.biojava.utils.ObjectUtil
 
equals(int[], int[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(int, int) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Location) - Method in class org.biojava.bio.symbol.PointLocation
Test for equality with another Location object
equals(Location) - Method in class org.biojava.bio.symbol.RangeLocation
Tests for object equality against another location
equals(long[], long[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(long, long) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Object) - Method in class org.acedb.AceURL
 
equals(Object) - Method in class org.biojava.bio.dp.TrainerTransition
Two transitions are equal if they have the same trainer, from and to states.
equals(Object) - Method in class org.biojava.bio.dp.Transition
Two transitions are equal if they have the same from and to states.
equals(Object) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
equals(Object) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
equals(Object) - Method in class org.biojava.bio.symbol.AlphabetManager.ListWrapper
 
equals(Object) - Method in class org.biojava.bio.symbol.CompoundLocation
 
equals(Object) - Method in interface org.biojava.bio.symbol.Location
Checks if this location is equivalent to the other.
equals(Object) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
equals(Object) - Method in class org.biojava.bio.symbol.Location.LocationComparator
 
equals(Object) - Method in class org.biojava.utils.TypedProperties
 
equals(Object[], Object[]) - Static method in class org.biojava.utils.ObjectUtil
 
equals(Object, Object) - Static method in class org.biojava.utils.ObjectUtil
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Calculate the dot product between the SuffixTrees a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.NormalizingKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
Returns the kernel product of two Objects.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
Return the dot product of a, b.
evaluate(Object, Object) - Method in interface org.biojava.stats.svm.SVMKernel
Return the dot product of two vectors in an arbitrary feature space.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Evaluate the kernel function between two SparseVectors.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.CachingKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.LinearKernel
Deprecated. The linear kernel is equal to the dot product of a and b.
evaluate(Object, Object) - Method in class org.biojava.stats.svm.PolynomialKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.RadialBaseKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.ListSumKernel
 
evaluate(Object, Object) - Method in class org.biojava.stats.svm.SigmoidKernel
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.stringListHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
extract(Any) - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
extract(Any) - Static method in class GNOME.UnknownHelper
 

F

FastaDescriptionReader - interface org.biojava.bio.seq.io.FastaDescriptionReader.
Converts the description line of a fasta entry into useful information.
FastaFormat - class org.biojava.bio.seq.io.FastaFormat.
Format for Fasta files.
FastaFormat() - Constructor for class org.biojava.bio.seq.io.FastaFormat
 
Feature - interface org.biojava.bio.seq.Feature.
A feature within a sequence, or nested within another feature.
Feature.Template - class org.biojava.bio.seq.Feature.Template.
Template class for a plain feature.
Feature.Template() - Constructor for class org.biojava.bio.seq.Feature.Template
 
FeatureAdapter - class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter.
 
FeatureAdapter(SequenceAdapter, SeqFeature) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
FeatureBlockSequenceRenderer - class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.
 
FeatureBlockSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
FeatureBuilder - interface org.biojava.bio.seq.io.FeatureBuilder.
Factory for new latent features.
FeatureFilter - interface org.biojava.bio.seq.FeatureFilter.
A filter for accepting or rejecting a feature.
FeatureFilter.AcceptAllFilter - class org.biojava.bio.seq.FeatureFilter.AcceptAllFilter.
The class that accepts all features.
FeatureFilter.AcceptAllFilter() - Constructor for class org.biojava.bio.seq.FeatureFilter.AcceptAllFilter
 
FeatureFilter.And - class org.biojava.bio.seq.FeatureFilter.And.
A filter that returns all features accepted by both child filter.
FeatureFilter.And(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.And
 
FeatureFilter.BySource - class org.biojava.bio.seq.FeatureFilter.BySource.
Construct one of these to filter features by source.
FeatureFilter.BySource(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.BySource
Create a BySource filter that filters in all features which have sources equal to source.
FeatureFilter.ByType - class org.biojava.bio.seq.FeatureFilter.ByType.
Construct one of these to filter features by type.
FeatureFilter.ByType(String) - Constructor for class org.biojava.bio.seq.FeatureFilter.ByType
Create a ByType filter that filters in all features with type fields equal to type.
FeatureFilter.ContainedByLocation - class org.biojava.bio.seq.FeatureFilter.ContainedByLocation.
A filter that returns all features contained within a location.
FeatureFilter.ContainedByLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
Creates a filter that returns everything contained within loc.
FeatureFilter.Not - class org.biojava.bio.seq.FeatureFilter.Not.
A filter that returns all features not accepted by a child filter.
FeatureFilter.Not(FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Not
 
FeatureFilter.Or - class org.biojava.bio.seq.FeatureFilter.Or.
A filter that returns all features accepted by at least one child filter.
FeatureFilter.Or(FeatureFilter, FeatureFilter) - Constructor for class org.biojava.bio.seq.FeatureFilter.Or
 
FeatureFilter.OverlapsLocation - class org.biojava.bio.seq.FeatureFilter.OverlapsLocation.
A filter that returns all features overlapping a location.
FeatureFilter.OverlapsLocation(Location) - Constructor for class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
Creates a filter that returns everything overlapping loc.
FeatureHolder - interface org.biojava.bio.seq.FeatureHolder.
The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder - class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder.
 
FeatureHolder.EmptyFeatureHolder() - Constructor for class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
featureHolderAllocated() - Method in class org.biojava.bio.seq.SimpleSequence
 
FeatureRealizer - interface org.biojava.bio.seq.FeatureRealizer.
Interface for translators which map from Feature.Template instances to real Feature objects.
FeatureRenderer - interface org.biojava.bio.gui.sequence.FeatureRenderer.
 
features_region_iterator(int, int) - Method in class org.Biocorba.Seqcore._Seq_Tie
 
features_region_iterator(int, int) - Method in class org.Biocorba.Seqcore._SeqStub
 
features_region_iterator(int, int) - Method in interface org.Biocorba.Seqcore.Seq
 
features_region_iterator(ObjectImpl, int, int) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
features_region_iterator(ObjectImpl, int, int) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
features_region(int, int) - Method in class org.Biocorba.Seqcore._Seq_Tie
 
features_region(int, int) - Method in class org.Biocorba.Seqcore._SeqStub
 
features_region(int, int) - Method in interface org.Biocorba.Seqcore.Seq
 
features_region(ObjectImpl, int, int) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
features_region(ObjectImpl, int, int) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
features() - Method in class org.acedb.seq.AceSequence
 
features() - Method in class org.biojava.bio.seq.ViewSequence
 
features() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
features() - Method in class org.biojava.bio.seq.MergeFeatureHolder
Iterate over all the features in all child FeatureHolders.
features() - Method in interface org.biojava.bio.seq.FeatureHolder
Iterate over the features in no well defined order.
features() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
features() - Method in class org.biojava.bio.seq.SimpleSequence
 
features() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
features() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
fetch(AceURL) - Method in interface org.acedb.Database
Return objects from the database.
fetch(AceURL) - Static method in class org.acedb.Ace
Get an entity from an ACeDB database.
fillPaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
 
fillPaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
 
fillPaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
Return the fill paint for a symbol.
fillPaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
filter(FeatureFilter, boolean) - Method in class org.acedb.seq.AceSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.ViewSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
filter(FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.FeatureHolder
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bio.seq.SimpleSequence
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
filter(FeatureFilter, boolean) - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
filter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFEntrySet
Filter this entry set into another set.
filter(String) - Method in class org.acedb.staticobj.StaticAceNode
 
filter(String) - Method in class org.acedb.staticobj.StaticAceSet
 
filter(String) - Method in class org.acedb.socket.SocketResultSet
 
filter(String) - Method in interface org.acedb.AceSet
Retrieve a sub-set of members by a filter string.
findSourceBlock(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Finds the index of the block containing the source coordinate indx.
findSourceGap(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Finds the index of the Block before the gap at indx within the following gap.
findViewBlock(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Finds the index of the Block containing indx within the view ranges.
findViewGap(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Finds the index of the Block before the gap at indx within the view range.
FiniteAlphabet - interface org.biojava.bio.symbol.FiniteAlphabet.
An alphabet over a finite set of Symbols.
firePropertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, boolean, boolean) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, int, int) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firePropertyChange(String, Object, Object) - Method in class org.biojava.bio.gui.TextLogoPainter
 
firstNonGap() - Method in class org.biojava.bio.symbol.GappedSymbolList
Return the index of the first Symbol that is not a Gap character.
firstToken(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
FixedWidthParser - class org.biojava.bio.symbol.FixedWidthParser.
A parser that uses a fixed width window of characters to look up the associated symbol.
FixedWidthParser(Alphabet, int) - Constructor for class org.biojava.bio.symbol.FixedWidthParser
 
flatView(MarkovModel) - Static method in class org.biojava.bio.dp.DP
 
FloatValue - interface org.acedb.FloatValue.
A float value.
forIndex(int) - Static method in class org.biojava.bio.seq.DNATools
Return the symbol for an index - compatible with index.
forSymbol(char) - Static method in class org.biojava.bio.seq.DNATools
Retrieve the symbol for a symbol.
forward(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
forward(SymbolList[]) - Method in class org.biojava.bio.dp.PairwiseDP
 
forwardMatrix(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
forwardMatrix(SymbolList[]) - Method in class org.biojava.bio.dp.PairwiseDP
 
forwardMatrix(SymbolList[], DPMatrix) - Method in class org.biojava.bio.dp.DP
 
forwardMatrix(SymbolList[], DPMatrix) - Method in class org.biojava.bio.dp.PairwiseDP
 
forwardsBackwards(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
forwardTransitions(MarkovModel, State[]) - Static method in class org.biojava.bio.dp.DP
 
forwardTransitionScores(MarkovModel, State[], int[][]) - Static method in class org.biojava.bio.dp.DP
 
frequency(int) - Method in class org.biojava.bio.symbol.SuffixTree
Return the number of motifs of a given length encoded in this SuffixTree.
from - Variable in class org.biojava.bio.dp.TrainerTransition
 
from - Variable in class org.biojava.bio.dp.Transition
 
from_int(int) - Static method in class org.Biocorba.Seqcore.SeqType
 
fromArray(double[]) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve a SymbolList view of an array of doubles.
fromArray(int[]) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve a SymbolList view of an array of integers.

G

g() - Static method in class org.biojava.bio.seq.DNATools
 
GapDistribution - class org.biojava.bio.dist.GapDistribution.
This distribution emits only the gap symbol.
GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution
 
GappedSymbolList - class org.biojava.bio.symbol.GappedSymbolList.
This implementation of SymbolList wraps another one, allowing you to insert gaps.
GappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.GappedSymbolList
Create a new GappedSymbolList that will view source.
GenbankFormat - class org.biojava.bio.seq.io.GenbankFormat.
Format reader for EMBL files.
GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat
Constuct a GENBANK format processor using a default FeatureBuilder object.
GenbankFormat(FeatureBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankFormat
Construct a GENBANK format processor using the specified FeatureBuilder object.
generate(int) - Method in class org.biojava.bio.dp.DP
Generates an alignment from a model.
generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new CrossProductAlphabet from the give name.
GeneticCode - class org.biojava.bio.seq.GeneticCode.
Constant TranslationTable instances that embody the genetic code.
GeneticCode() - Constructor for class org.biojava.bio.seq.GeneticCode
 
get_primaryidList() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
get_primaryidList() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
get_primaryidList() - Method in interface org.Biocorba.Seqcore.SeqDB
 
get_primaryidList(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqDB_Operations
 
get_primaryidList(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqDBImpl
 
get_PrimarySeq() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
get_PrimarySeq() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
get_PrimarySeq() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
get_PrimarySeq() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
get_PrimarySeq() - Method in class org.Biocorba.Seqcore._SeqStub
 
get_PrimarySeq() - Method in interface org.Biocorba.Seqcore.Seq
 
get_PrimarySeq(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
get_PrimarySeq(ObjectImpl) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
get_PrimarySeq(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
get_PrimarySeq(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
get_PrimarySeq(ObjectImpl, String) - Method in interface org.Biocorba.Seqcore._PrimarySeqDB_Operations
 
get_PrimarySeq(ObjectImpl, String) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
get_PrimarySeq(String) - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
get_PrimarySeq(String) - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
get_PrimarySeq(String) - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
get_PrimarySeq(String) - Method in class org.Biocorba.Seqcore._SeqDBStub
 
get_PrimarySeq(String) - Method in interface org.Biocorba.Seqcore.PrimarySeqDB
 
get_seq() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
get_seq() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
get_seq() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
get_seq() - Method in interface org.Biocorba.Seqcore.AnonymousSeq
 
get_seq() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
get_seq() - Method in class org.Biocorba.Seqcore._SeqStub
 
get_seq() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
get_seq(ObjectImpl) - Method in interface org.Biocorba.Seqcore._AnonymousSeq_Operations
 
get_seq(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
get_Seq(ObjectImpl, String) - Method in interface org.Biocorba.Seqcore._SeqDB_Operations
 
get_Seq(ObjectImpl, String) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqDBImpl
 
get_Seq(String) - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
get_Seq(String) - Method in class org.Biocorba.Seqcore._SeqDBStub
 
get_Seq(String) - Method in interface org.Biocorba.Seqcore.SeqDB
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._Seq_Tie
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
get_subseq(int, int) - Method in interface org.Biocorba.Seqcore.AnonymousSeq
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._SeqStub
 
get_subseq(int, int) - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
get_subseq(ObjectImpl, int, int) - Method in interface org.Biocorba.Seqcore._AnonymousSeq_Operations
 
get_subseq(ObjectImpl, int, int) - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
get(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the value at dimension dim.
getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Get the GFFDocumentHandler for adding to this set.
getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the current value of addPos.
getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getAdvance() - Method in interface org.biojava.bio.dp.EmissionState
Determine the number of symbols this state advances along one or more symbol lists.
getAlignment() - Method in class org.biojava.bio.gui.SequencePanel.Border
 
getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
getAllTransitionTrainers() - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getAlphabet() - Method in class org.acedb.seq.AceSequence
 
getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix
The alphabet for the sequences that this weight matrix models.
getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getAlphabet() - Method in class org.biojava.bio.seq.ViewSequence
 
getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
Gets the protein alphabet
getAlphabet() - Method in class org.biojava.bio.seq.SimpleSequence
 
getAlphabet() - Method in class org.biojava.bio.dist.ComplementaryDistribution
 
getAlphabet() - Method in interface org.biojava.bio.dist.Distribution
The alphabet from which this spectrum emits symbols.
getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.DNADistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
 
getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
 
getAlphabet() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.GappedSymbolList
 
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList
The alphabet that this SymbolList is over.
getAlphabet() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.CrossProductSymbolNameParser
 
getAlphabet() - Method in class org.biojava.bio.symbol.FixedWidthParser
 
getAlphabet() - Method in class org.biojava.bio.symbol.TokenParser
 
getAlphabet() - Method in class org.biojava.bio.symbol.ReverseSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList
Get the alphabet of this SymbolList.
getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolParser
The alphabet that all Symbols produced will belong to.
getAlphabet() - Method in class org.biojava.bio.symbol.TranslatedSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.NameParser
 
getAlphabet() - Method in class org.biojava.bio.symbol.WindowedSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.OrderNSymbolList
 
getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree
Return the Alphabet containing all Symbols which might be found in this SuffixTree.
getAlphabet() - Method in class org.biojava.bio.symbol.SimpleAlignment
 
getAlphabet() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
getAlphabets() - Method in interface org.biojava.bio.symbol.CrossProductAlphabet
Return an ordered List of the alphabets which make up this compound alphabet.
getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getAmbiguitySymbol(char, String, Annotation, Collection) - Static method in class org.biojava.bio.symbol.AlphabetManager
Create a specific ambiguity symbol for a collection of symbols.
getAmbiguitySymbol(Collection) - Static method in class org.biojava.bio.symbol.AlphabetManager
Obtain the default ambiguity symbol to represent the symbols passed in as parameters e.g.
getAmbiguityWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution
Performs the standard munge to handle ambiguity symbols.
getAnnotation() - Method in class org.acedb.seq.AceSequence
 
getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getAnnotation() - Method in class org.biojava.bio.seq.ViewSequence
 
getAnnotation() - Method in class org.biojava.bio.seq.SimpleSequence
 
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getAnnotation() - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getAnnotation() - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
getAnnotation() - Method in interface org.biojava.bio.Annotatable
Should return the associated annotation object.
getAnnotation() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getAnnotation() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet.
getAnonymousSeq() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getAuthority() - Method in class org.acedb.AceURL
 
getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
 
getBackwardTransitionScores() - Method in class org.biojava.bio.dp.DP
 
getC() - Method in class org.biojava.stats.svm.SMOTrainer
 
getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
 
getCell(int[]) - Method in class org.biojava.bio.dp.PairDPMatrix
 
getCharacterOffset() - Method in class org.biojava.utils.ParserException
Get the character offset in the line where an error was detected.
getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
 
getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree
Get the n'th child of a node.
getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree
Get a child of a SuffixTree.SuffixNode, constructing a new one if need be.
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
 
getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
 
getClassName() - Method in class org.acedb.staticobj.StaticAceObject
 
getClassName() - Method in interface org.acedb.AceObject
 
getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
 
getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix
Retrieve a column as an EmissionState.
getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord
The feature comment.
getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getConnection() - Method in interface org.acedb.Database
Return a connection object which allows ACeDB commands to be executed directly on the server.
getConnection(AceURL) - Static method in class org.acedb.Ace
 
getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
 
getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductAlphabet(List, CrossProductAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
getCrossProductSymbol(char, List) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new CrossProductSymbol instance.
getCrossProductSymbol(char, List, CrossProductAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Generates a new CrossProductSymbol instance.
getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
 
getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieves the delete state for column indx.
getDepth(SequencePanel) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the depth of this renderer when rendering sp.
getDepth(SequencePanel) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getDepth(SequencePanel) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Retrieve the current DepthScaler.
getDescriptionReader() - Method in class org.biojava.bio.seq.io.FastaFormat
Retrieve the current description reader.
getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the dimension at a specific index.
getDirection() - Method in class org.biojava.bio.gui.SequencePanel
 
getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getDistribution() - Method in interface org.biojava.bio.dp.EmissionState
Get the Distribution associated with this state.
getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the currently rendered dist.
getDistributionTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
getDistributionTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Return the Distribution trainer object from the current context.
getDNA() - Static method in class org.biojava.bio.seq.DNATools
Return the DNA alphabet.
getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
 
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getEmission(List, CrossProductAlphabet) - Method in class org.biojava.bio.dp.PairwiseDP
 
getEnd() - Method in class org.biojava.bio.dp.TransitionEvent
 
getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord
The end of this feature within the source sequence.
getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
 
getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser
Find the error handler used by this parser.
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
return the overall E-value of this hit.
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
return the E-value of this sub-hit.
getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
Retrieve the current feature.
getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord
The feature type filed.
getFeature() - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Return the current FeatureFilter.
getFeatureHolder() - Method in class org.biojava.bio.seq.SimpleSequence
 
getFeatureRealizer() - Method in class org.biojava.bio.seq.SimpleSequenceFactory
Returns the FeatureRealizer set by "setFeatureRealizer".
getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
Returns the list of features in this featureholder.
getFeatures(SequencePanel) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getFile() - Method in class org.acedb.AceURL
 
getFiles() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Retrieve an unmodifiable set of files.
getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getFilter() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getForwardTransitions() - Method in class org.biojava.bio.dp.DP
 
getForwardTransitionScores() - Method in class org.biojava.bio.dp.DP
 
getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord
The frame of the feature.
getFrom() - Method in class org.biojava.bio.dp.IllegalTransitionException
 
getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager
Get the special `gap' Symbol.
getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord
A Map containing the group / attribute information.
getHit() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getHit() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
return the ssequence similarity search hit to which this sequence similarity search sub-hit belongs.
getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
return an unmodifiable view of the hits list.
getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
return all hits in this sequence similarity search result.
getHost() - Method in class org.acedb.AceURL
 
getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB
Retrieve the IDMaker associated with this database.
getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieves the insert state at column indx.
getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer
Returns the global singleton instance of the IgnoreCountsTrainer
getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve the single IntegerAlphabet instance.
getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve the single DoubleAlphabet instance.
getItem() - Method in interface org.biojava.stats.svm.ItemValue
 
getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
 
getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the currently used kernel
getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getLabel() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getLabels() - Method in interface org.biojava.bio.symbol.Alignment
The list of SymbolLists in the alignment.
getLabels() - Method in class org.biojava.bio.symbol.SimpleAlignment
 
getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel
Retrieve the scale factor.
getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
 
getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
 
getLeadingBorder() - Method in class org.biojava.bio.gui.SequencePanel
 
getLine() - Method in class org.biojava.utils.ParserException
Get the text of the line where the exception occured.
getLineNumber() - Method in class org.biojava.utils.ParserException
Get the line number in the stream where this exception occured.
getLines() - Method in class org.biojava.bio.gui.SequencePanel
 
getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat
Retrive the current line width.
getLocation() - Method in interface org.biojava.bio.seq.Feature
The location of this feature.
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
 
getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
 
getLocation() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getLocator() - Method in class org.biojava.utils.ParserException
Get a locator for the stream which caused this exception.
getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter
Retrieve the current font.
getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the current logo painter.
getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
 
getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM
Retrieve the match state at column indx.
getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
getMatches() - Method in class org.biojava.bio.symbol.SimpleSymbol
 
getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getMatches() - Method in interface org.biojava.bio.symbol.AtomicSymbol
Return an alphabet containing only this symbol.
getMatches() - Method in interface org.biojava.bio.symbol.Symbol
The alphabet containing the symbols matched by this ambiguity symbol.
getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getMax() - Method in class org.biojava.bio.symbol.PointLocation
 
getMax() - Method in class org.biojava.bio.symbol.RangeLocation
 
getMax() - Method in class org.biojava.bio.symbol.CompoundLocation
 
getMax() - Method in interface org.biojava.bio.symbol.Location
The maximum position contained.
getMax() - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
getMessage() - Method in class org.Biocorba.Seqcore.UnableToProcess
 
getMin() - Method in class org.biojava.bio.symbol.PointLocation
 
getMin() - Method in class org.biojava.bio.symbol.RangeLocation
 
getMin() - Method in class org.biojava.bio.symbol.CompoundLocation
 
getMin() - Method in interface org.biojava.bio.symbol.Location
The minimum position contained.
getMin() - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
getMinimumLeader(SequencePanel) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the minimum leading distance for this renderer when rendering sp.
getMinimumLeader(SequencePanel) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getMinimumLeader(SequencePanel) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getMinimumTrailer(SequencePanel) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Retrieve the minimum trailing distance for this renderer when rendering sp.
getMinimumTrailer(SequencePanel) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
getMinimumTrailer(SequencePanel) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
getModel() - Method in interface org.biojava.bio.dp.ModelInState
The model that is inside this state.
getModel() - Method in class org.biojava.bio.dp.DP
 
getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
 
getModelChangeEvent() - Method in class org.biojava.bio.dp.ModelVetoException
 
getMotifs() - Method in class org.biojava.bio.program.Meme
 
getMT(State, State) - Method in class org.biojava.bio.dp.ModelView
 
getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getName() - Method in class org.acedb.seq.AceSequence
 
getName() - Method in class org.acedb.seq.AceSequenceDB
 
getName() - Method in class org.acedb.staticobj.StaticAceNode
 
getName() - Method in class org.acedb.staticobj.StaticAceSet
 
getName() - Method in class org.acedb.socket.SocketResultSet
 
getName() - Method in interface org.acedb.AceSet
The name of this node - possibly null.
getName() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
getName() - Method in interface org.biojava.bio.seq.db.SequenceDB
Get the name of this sequence database.
getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
getName() - Method in class org.biojava.bio.seq.ViewSequence
 
getName() - Method in class org.biojava.bio.seq.SimpleSequence
 
getName() - Method in interface org.biojava.bio.seq.Sequence
The name of this sequence.
getName() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
getName() - Method in class org.biojava.bio.symbol.SimpleSymbol
 
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
getName() - Method in interface org.biojava.bio.symbol.Symbol
The long name for the symbol.
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getName() - Method in interface org.biojava.bio.symbol.Alphabet
Get the name of the alphabet.
getName() - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getName() - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
getName() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
getName() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the shape used to represent negative points.
getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel
Retrieve the currently nested SVMKernel.
getNewScore() - Method in class org.biojava.bio.dp.TransitionEvent
 
getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Retrive the current normalizing vector.
getNullModel() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
Retrieve the background distribution
getNullModel() - Method in class org.biojava.bio.dist.AbstractDistribution
Retrieve the null model Distribution that this Distribution recognizes.
getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.DNADistribution
 
getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution
 
getNullModel() - Method in class org.biojava.bio.dist.PairDistribution
 
getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
Retrieve the weight of the background distribution
getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Return a number (usually, but not always, a motif count) associated with this node of the tree.
getOldScore() - Method in class org.biojava.bio.dp.TransitionEvent
 
getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
 
getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
getParent() - Method in class org.acedb.staticobj.StaticAceNode
 
getParent() - Method in class org.acedb.staticobj.StaticAceSet
 
getParent() - Method in class org.acedb.socket.SocketResultSet
 
getParent() - Method in interface org.acedb.AceSet
The logical parent of this object or null if there is no logical parent.
getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
Get the original sequenceDB from this annotated sequenceDB.
getParent() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
Return the parent SequenceDB.
getParent() - Method in interface org.biojava.bio.seq.Feature
Return the FeatureHolder to which this feature has been attached.
getParent() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getParentSeq() - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl
 
getParser(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
getParser(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet
 
getParser(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
getParser(String) - Method in interface org.biojava.bio.symbol.Alphabet
Get a parser by name.
getParser(String) - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
getParser(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
getParser(String) - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
getPath() - Method in class org.acedb.AceURL
 
getPort() - Method in class org.acedb.AceURL
 
getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Retrieve the shape used to represent positive points.
getPrimarySeq() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
getPrimarySeqDB() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
getPrimarySeqIterator() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter
 
getProperties() - Method in class org.biojava.bio.SimpleAnnotation
Retrieves properties, potentialy creating it if it was null.
getProperty(Object) - Method in class org.acedb.seq.AceAnnotation
 
getProperty(Object) - Method in interface org.biojava.bio.Annotation
Retrieve the value of a property by key.
getProperty(Object) - Method in class org.biojava.bio.Annotation.EmptyAnnotation
 
getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
 
getProperty(Object) - Method in class org.biojava.bio.SimpleAnnotation
 
getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties
just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab) as the possible delimiters.
getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties
Searches for the property with the specified key in this property list.
getProtocol() - Method in class org.acedb.AceURL
 
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
return the overall P-value of this hit.
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
return the P-value of this sub-hit.
getQuery() - Method in class org.acedb.AceURL
 
getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
return the sequence with which the search that produced this search result was performed.
getReader() - Method in class org.biojava.bio.seq.io.StreamReader.Context
Get a Reader object for accessing data from the stream.
getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Return whether features will be filtered recursively or not.
getRef() - Method in class org.acedb.AceURL
 
getRoot() - Method in class org.biojava.bio.symbol.SuffixTree
Return the node object which is the root of this suffix tree.
getScale() - Method in class org.biojava.bio.gui.SequencePanel
 
getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
Retrieve the scaling factor at a given depth
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
 
getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
 
getScore() - Method in class org.biojava.bio.dp.SimpleStatePath
 
getScore() - Method in interface org.biojava.bio.dp.StatePath
Return the overall score for this state-path and it's emissions.
getScore() - Method in interface org.biojava.bio.dp.DPMatrix
 
getScore() - Method in class org.biojava.bio.dp.PairDPMatrix
 
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
return the overall score of this hit in the units defined by the search algorithm.
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
return the score of this sub-hit in the units defined by the search algorithm.
getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord
The score of the feature.
getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
return a set of all databases that can be searched with this sequence similarity searcher.
getSearcher() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getSearcher() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
return the sequence similarity searcher that produced this sequence similarity search result.
getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
return an unmodifiable view of the search parameters map.
getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
return the search parameters used in the search that produced this search result.
getSearchResult() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
return the ssequence similarity search result to which this sequence similarity search hit belongs.
getSearchResult() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSeq() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
getSeqIDs() - Method in class org.biojava.bio.program.Meme
 
getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
Retrieve the current sequence name.
getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord
The sequence name field.
getSequence() - Method in class org.biojava.bio.gui.SequencePanel
 
getSequence() - Method in interface org.biojava.bio.seq.Feature
Return the Sequence object to which this feature is (ultimately) attached.
getSequence() - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
getSequence() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getSequence(String) - Method in class org.acedb.seq.AceSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDB
Retrieve a single sequence by its id.
getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
getSequence(String) - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
return the sequence database against which the search that produced this search result was performed.
getSequenceDB() - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
if the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier.
getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
return the SequenceDB for the given identifier.
getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
return a newly created set of the SequenceDB objects that were already created through method addSequenceDB().
getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
return all sequence dbs available in this sequence db installation.
getSequenceID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
the sequence identifier of this hit within the sequence database against which the search was performed.
getSequenceID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
getSize() - Method in class org.biojava.bio.gui.SequencePanel.Border
 
getSource() - Method in class org.biojava.bio.dp.ModelView
 
getSource() - Method in interface org.biojava.bio.seq.Feature
The source of the feature.
getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
 
getSource() - Method in class org.biojava.bio.symbol.ReverseSymbolList
Retrieve the underlying SymbolList being viewed.
getSource() - Method in class org.biojava.bio.symbol.TranslatedSymbolList
Returns the symbol list associated with this translated symbol list.
getSource() - Method in class org.biojava.bio.symbol.WindowedSymbolList
Retrieve the underlying SymbolList being viewed.
getSource() - Method in class org.biojava.bio.symbol.OrderNSymbolList
Retrieve the underlying SymbolList being viewed.
getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
Retrieve the current source.
getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord
The source, or creator of this feature.
getSource() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
The alphabet of Symbols that can be translated.
getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
getSourceModel() - Method in class org.biojava.bio.dp.ModelChangeEvent
 
getSpacer() - Method in class org.biojava.bio.gui.SequencePanel
 
getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
 
getStart() - Method in class org.biojava.bio.dp.TransitionEvent
 
getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord
The start of this feature within the source sequence.
getStates() - Method in class org.biojava.bio.dp.DP
 
getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature
Retrieve the strand that this feature lies upon.
getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
 
getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord
The strand of the feature.
getStyle() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the current style.
getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
return all sub-hits for this sequence similarity search hit.
getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
return an unmodifiable view of the sub-hits list.
getSymbol() - Method in class org.biojava.bio.symbol.IllegalSymbolException
Retrieve the symbol that caused this exception, or null.
getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
Retrieve the Symbol for a double.
getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet
Retrieve the Symbol for an int.
getSymbol(List) - Method in interface org.biojava.bio.symbol.CrossProductAlphabet
Get a symbol from the CrossProductAlphabet which corresponds to the specified ordered list of symbols.
getSymbolList() - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature
Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.seq.Feature
Return a list of symbols that are contained in this feature.
getSymbols() - Method in interface org.biojava.bio.symbol.CrossProductSymbol
Return an immutable ordered list of symbols which are represented by this CrossProductSymbol.
getSymbols() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
Gets the protein alphabet including the translation termination symbols
getTarget() - Method in class org.acedb.staticobj.StaticReference
 
getTarget() - Method in interface org.acedb.Reference
Return a url to the object on the other end of the reference.
getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
The alphabet of Symbols that will be produced.
getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
getTo() - Method in class org.biojava.bio.dp.IllegalTransitionException
 
getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState
 
getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
Returns the token for strandedness, i.e.
getToken() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
 
getToken() - Method in class org.biojava.bio.symbol.SimpleSymbol
 
getToken() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
getToken() - Method in interface org.biojava.bio.symbol.Symbol
The token for the symbol.
getToken() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
 
getTopLevelObject() - Method in class org.biojava.utils.xml.XMLPeerBuilder
Once the XMLPeerBuilder has been used, return an Object which represents the whole document.
getTrailingBorder() - Method in class org.biojava.bio.gui.SequencePanel
 
getTrainerForModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
getTrainerForModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer
Retrieve the TransitionTrainer associated with a model, or null if none is registered.
getTransitionListeners() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
getTransitionScore(State, State) - Method in class org.biojava.bio.dp.WMAsMM
 
getTransitionScore(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
getTransitionScore(State, State) - Method in class org.biojava.bio.dp.ModelView
 
getTransitionScore(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
Probability of the transition between from and to.
getTranslationTable() - Method in class org.biojava.bio.symbol.TranslatedSymbolList
Obtain the translation table associated with this symbol list
getType() - Method in interface org.biojava.bio.seq.Feature
The type of the feature.
getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
 
getType() - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
getURN() - Method in class org.acedb.seq.AceSequence
 
getURN() - Method in class org.biojava.bio.seq.ViewSequence
 
getURN() - Method in class org.biojava.bio.seq.SimpleSequence
 
getURN() - Method in interface org.biojava.bio.seq.Sequence
The URN for this sequence.
getURN() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
getUserInfo() - Method in class org.acedb.AceURL
 
getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
Returns the integer label for strandedness, i.e.
getValue() - Method in interface org.biojava.stats.svm.ItemValue
 
getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
 
getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
Retrieve the value at a specific index.
getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.ComplementaryDistribution
 
getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution
Return the probability that Symbol s is emited by this spectrum.
getWeight(Symbol) - Method in class org.biojava.bio.dist.UniformDistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.DNADistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.SimpleDistribution
 
getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution
 
getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel
 
getWrappedException() - Method in class org.biojava.bio.BioError
 
getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
 
getXMLPeer(String, List, AttributeList) - Method in interface org.biojava.utils.xml.XMLPeerFactory
Return a Java object to reflect an XML element.
getXMLPeer(String, List, AttributeList) - Method in class org.biojava.utils.xml.XMLDispatcher
 
GFFDocumentHandler - interface org.biojava.bio.program.gff.GFFDocumentHandler.
The interface for things that listen to GFF event streams.
GFFEntrySet - class org.biojava.bio.program.gff.GFFEntrySet.
A set of entries and comments as a representation of a GFF file.
GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet
Make an empty GFFEntrySet.
GFFErrorHandler - interface org.biojava.bio.program.gff.GFFErrorHandler.
Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler - class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler.
 
GFFErrorHandler.AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
GFFErrorHandler.SkipRecordErrorHandler - class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler.
 
GFFErrorHandler.SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
GFFFilterer - class org.biojava.bio.program.gff.GFFFilterer.
An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer
Create a new GFFFilterer that will forward to handler everything that filter accepts.
GFFParser - class org.biojava.bio.program.gff.GFFParser.
Parse a stream of GFF text into a stream of records and comments.
GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser
 
GFFRecord - interface org.biojava.bio.program.gff.GFFRecord.
A single GFF record.
GFFRecordFilter - interface org.biojava.bio.program.gff.GFFRecordFilter.
A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll - class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll.
Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
 
GFFRecordFilter.FeatureFilter - class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter.
Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
 
GFFRecordFilter.SequenceFilter - class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter.
Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
 
GFFRecordFilter.SourceFilter - class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter.
Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
 
GFFWriter - class org.biojava.bio.program.gff.GFFWriter.
Listens to a stream of GFF events and writes the lines to a PrintWriter.
GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter
Create a new GFFWriter that will write to out.
GNOME - package GNOME
 
graphicsToSequence(double) - Method in class org.biojava.bio.gui.SequencePanel
 

H

Handler - class org.acedb.Handler.
Simple URLStreamHandler for acedb: URLs, so that we can use URL objects as appropriate.
Handler() - Constructor for class org.acedb.Handler
 
has_more() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
has_more() - Method in interface org.Biocorba.Seqcore.SeqFeatureIterator
 
has_more() - Method in interface org.Biocorba.Seqcore.PrimarySeqIterator
 
has_more() - Method in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
has_more() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
has_more() - Method in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
has_more(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeatureIterator_Operations
 
has_more(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeqIterator_Operations
 
has_more(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqIteratorImpl
 
has_more(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl
 
hasChild(int) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Determine if this node has a child corresponding to a given index number.
hashCode() - Method in class org.acedb.AceURL
 
hashCode() - Method in class org.biojava.bio.dp.TrainerTransition
The hash code is model.hashCode() ^ from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.dp.Transition
The hash code is from.hashCode() ^ to.hashCode()
hashCode() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
hashCode() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
hashCode() - Method in class org.biojava.bio.symbol.AlphabetManager.ListWrapper
 
hashCode() - Method in class org.biojava.utils.TypedProperties
 
hashCode(int, boolean) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, boolean[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, double[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, float[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, int[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, long[]) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object) - Static method in class org.biojava.utils.ObjectUtil
 
hashCode(int, Object[]) - Static method in class org.biojava.utils.ObjectUtil
 
HashSequenceDB - class org.biojava.bio.seq.db.HashSequenceDB.
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
HashSequenceDB() - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashSequenceDB(IDMaker) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashSequenceDB(IDMaker, String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
HashSequenceDB(String) - Constructor for class org.biojava.bio.seq.db.HashSequenceDB
Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name.
hasListeners(String) - Method in class org.biojava.bio.gui.TextLogoPainter
 
hasNext() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
hasNext() - Method in class org.biojava.bio.seq.io.StreamReader
 
hasNext() - Method in interface org.biojava.bio.seq.SequenceIterator
Returns whether there are more sequences to iterate over.
hasNext() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter
 
heads() - Method in class org.biojava.bio.dp.WMAsMM
 
heads() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
heads() - Method in interface org.biojava.bio.dp.MarkovModel
The number of heads on this model.

I

id() - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
id() - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
id() - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
id() - Static method in class org.Biocorba.Seqcore.SeqHelper
 
id() - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
id() - Static method in class org.Biocorba.Seqcore.stringListHelper
 
id() - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
id() - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
id() - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
id() - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
id() - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
id() - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
id() - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
id() - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
id() - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
id() - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
id() - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
id() - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
id() - Static method in class GNOME.UnknownHelper
 
IDMaker - interface org.biojava.bio.seq.db.IDMaker.
Interface for objects that define how to make an ID for a sequence.
IDMaker.ByName - class org.biojava.bio.seq.db.IDMaker.ByName.
 
IDMaker.ByName() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByName
 
IDMaker.ByURN - class org.biojava.bio.seq.db.IDMaker.ByURN.
 
IDMaker.ByURN() - Constructor for class org.biojava.bio.seq.db.IDMaker.ByURN
 
ids() - Method in class org.acedb.seq.AceSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
ids() - Method in interface org.biojava.bio.seq.db.SequenceDB
Get an imutable set of all of the IDs in the database.
ids() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
ids() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
ids() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
ignorableWhitespace(char[], int, int) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
IgnoreCountsTrainer - class org.biojava.bio.dist.IgnoreCountsTrainer.
A distribution trainer that just ignores all counts.
IgnoreCountsTrainer() - Constructor for class org.biojava.bio.dist.IgnoreCountsTrainer
 
IgnoreRecordException - exception org.biojava.bio.program.gff.IgnoreRecordException.
Ignore this record in the stream.
IgnoreRecordException() - Constructor for class org.biojava.bio.program.gff.IgnoreRecordException
 
IllegalAlphabetException - exception org.biojava.bio.symbol.IllegalAlphabetException.
The exception to indicate that an invalid aphabet has been used.
IllegalAlphabetException() - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
Just make the exception.
IllegalAlphabetException(String) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
Make the exception with a message.
IllegalAlphabetException(Throwable) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalAlphabetException(Throwable, String) - Constructor for class org.biojava.bio.symbol.IllegalAlphabetException
 
IllegalSymbolException - exception org.biojava.bio.symbol.IllegalSymbolException.
The exception to indicate that a symbol is not valid within a context.
IllegalSymbolException(String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
Make the exception with a message.
IllegalSymbolException(Symbol, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
Make the exception with a message and a symbol.
IllegalSymbolException(Throwable, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
 
IllegalSymbolException(Throwable, Symbol, String) - Constructor for class org.biojava.bio.symbol.IllegalSymbolException
 
IllegalTransitionException - exception org.biojava.bio.dp.IllegalTransitionException.
This exception indicates that there is no transition between two states.
IllegalTransitionException() - Constructor for class org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State) - Constructor for class org.biojava.bio.dp.IllegalTransitionException
 
IllegalTransitionException(State, State, String) - Constructor for class org.biojava.bio.dp.IllegalTransitionException
 
incCounts(int, int) - Method in class org.biojava.bio.symbol.SuffixTree
 
index(State) - Method in class org.biojava.bio.dp.WMAsMM
 
index(Symbol) - Static method in class org.biojava.bio.seq.DNATools
Return an integer index for a symbol - compatible with forIndex.
IndexedSequenceDB - class org.biojava.bio.seq.db.IndexedSequenceDB.
This class reads in a file or a set of files containing sequence data.
indexForSymbol(Symbol) - Method in class org.biojava.bio.symbol.SuffixTree
Return an internal index number corresponding to the given Symbol.
insert(Any, AnonymousSeq) - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
insert(Any, EndOfStream) - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
insert(Any, NameValueSet) - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
insert(Any, NameValueSet[]) - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
insert(Any, OutOfRange) - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
insert(Any, PrimarySeq) - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
insert(Any, PrimarySeqDB) - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
insert(Any, PrimarySeqIterator) - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
insert(Any, RequestTooLarge) - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
insert(Any, Seq) - Static method in class org.Biocorba.Seqcore.SeqHelper
 
insert(Any, SeqDB) - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
insert(Any, SeqFeature) - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
insert(Any, SeqFeature[]) - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
insert(Any, SeqFeatureIterator) - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
insert(Any, SeqType) - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
insert(Any, String[]) - Static method in class org.Biocorba.Seqcore.stringListHelper
 
insert(Any, String[]) - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
insert(Any, UnableToProcess) - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
insert(Any, Unknown) - Static method in class GNOME.UnknownHelper
 
instance() - Static method in class org.biojava.bio.symbol.AlphabetManager
Deprecated. all AlphabetManager methods have become static
IntegerAlphabet - class org.biojava.bio.symbol.IntegerAlphabet.
An efficient implementation of an Alphabet over the infinite set of integer values.
IntegerAlphabet.IntegerSymbol - class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol.
A single int value.
IntegerAlphabet.IntegerSymbol(int) - Constructor for class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
IntegerAlphabet() - Constructor for class org.biojava.bio.symbol.IntegerAlphabet
 
internalClassify(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
intersection(Location) - Method in class org.biojava.bio.symbol.PointLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.RangeLocation
 
intersection(Location) - Method in class org.biojava.bio.symbol.CompoundLocation
 
intersection(Location) - Method in interface org.biojava.bio.symbol.Location
Returns a Location that contains all points common to both ranges.
intersection(Location) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
IntValue - interface org.acedb.IntValue.
An int value.
intValue() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
 
invalidEnd(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `end' field of the GFF entry was not a valid value.
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidEnd(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidEnd(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidFrame(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `frame' field of the GFF entry was not a valid value.
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidFrame(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidFrame(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidScore(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `score' field of the GFF entry was not a valid value.
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidScore(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidScore(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStart(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `start' field of the GFF entry was not a valid value.
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStart(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invalidStart(String, NumberFormatException) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
invalidStrand(String) - Method in interface org.biojava.bio.program.gff.GFFErrorHandler
The `strand' field of the GFF entry was not a valid value.
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
 
invalidStrand(String) - Method in class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._SeqImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._PrimarySeqDBImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._PrimarySeqImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._SeqDBImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._SeqFeatureImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._AnonymousSeqImplBase
 
invoke(ServerRequest) - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase
 
invoke(ServerRequest) - Method in class GNOME._UnknownImplBase
 
isContiguous() - Method in class org.biojava.bio.symbol.PointLocation
 
isContiguous() - Method in class org.biojava.bio.symbol.RangeLocation
 
isContiguous() - Method in class org.biojava.bio.symbol.CompoundLocation
 
isContiguous() - Method in interface org.biojava.bio.symbol.Location
Determine if a Location is contiguous.
isContiguous() - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
isRecoverable() - Method in class org.acedb.AceException
 
isStreamEmpty() - Method in class org.biojava.bio.seq.io.StreamReader.Context
Check if the stream is empty.
isTerminal() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Determine is this node is terminal (has no children).
isTrainingComplete(TrainingAlgorithm) - Method in interface org.biojava.bio.dp.StoppingCriteria
 
itemAlphas() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
itemAlphas() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
items() - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
items() - Method in interface org.biojava.stats.svm.SVMTarget
 
items() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
items() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
itemTargets() - Method in interface org.biojava.stats.svm.SVMTarget
 
itemTargets() - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
ItemValue - interface org.biojava.stats.svm.ItemValue.
A simple Object-double tuple.
iterator() - Method in class org.acedb.seq.AceSequence
 
iterator() - Method in class org.acedb.staticobj.StaticAceNode
 
iterator() - Method in class org.acedb.staticobj.StaticAceSet
 
iterator() - Method in class org.acedb.socket.SocketResultSet
 
iterator() - Method in interface org.acedb.AceSet
An iterator over every thing in this set.
iterator() - Method in class org.biojava.bio.dp.SimpleStatePath
 
iterator() - Method in class org.biojava.bio.seq.ViewSequence
 
iterator() - Method in class org.biojava.bio.seq.SimpleSequence
 
iterator() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
iterator() - Method in interface org.biojava.bio.symbol.SymbolList
An Iterator over all Symbols in this SymbolList.
iterator() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
iterator() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
iterator() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
Retrieve an Iterator over the Symbols in this FiniteAlphabet.
iterator() - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
iterator() - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
iterator() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 

K

kernel - Static variable in class org.biojava.stats.svm.SparseVector
 
keys() - Method in class org.acedb.seq.AceAnnotation
 
keys() - Method in interface org.biojava.bio.Annotation
Get a set of key objects.
keys() - Method in class org.biojava.bio.Annotation.EmptyAnnotation
 
keys() - Method in class org.biojava.bio.OverlayAnnotation
Return a Set containing all key objects visible in this annotation.
keys() - Method in class org.biojava.bio.SimpleAnnotation
 

L

lastNonGap() - Method in class org.biojava.bio.symbol.GappedSymbolList
Return the index of the last Symbol that is not a Gap character.
length() - Method in class org.acedb.seq.AceSequence
 
length() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
length() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
length() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
length() - Method in interface org.Biocorba.Seqcore.AnonymousSeq
 
length() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
length() - Method in class org.Biocorba.Seqcore._SeqStub
 
length() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
length() - Method in class org.biojava.bio.dp.SimpleStatePath
 
length() - Method in class org.biojava.bio.seq.ViewSequence
 
length() - Method in class org.biojava.bio.seq.SimpleSequence
 
length() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
length() - Method in class org.biojava.bio.symbol.GappedSymbolList
 
length() - Method in interface org.biojava.bio.symbol.SymbolList
The number of symbols in this SymbolList.
length() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
length() - Method in class org.biojava.bio.symbol.ReverseSymbolList
 
length() - Method in class org.biojava.bio.symbol.SimpleSymbolList
Get the length of this SymbolList.
length() - Method in class org.biojava.bio.symbol.TranslatedSymbolList
 
length() - Method in class org.biojava.bio.symbol.WindowedSymbolList
 
length() - Method in class org.biojava.bio.symbol.OrderNSymbolList
 
length() - Method in class org.biojava.bio.symbol.SimpleAlignment
 
length() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
length(ObjectImpl) - Method in interface org.Biocorba.Seqcore._AnonymousSeq_Operations
 
length(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
LinearKernel - class org.biojava.stats.svm.LinearKernel.
Deprecated. Just use SparseVector.kernel instead...
LinearKernel() - Constructor for class org.biojava.stats.svm.LinearKernel
Deprecated.  
lineIterator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Loop over all lines in the set.
ListSumKernel - class org.biojava.stats.svm.ListSumKernel.
This kernel computes the sum of the dot products between items of two lists at corresponding indexes.
ListSumKernel() - Constructor for class org.biojava.stats.svm.ListSumKernel
 
load(Class, String) - Method in class org.biojava.utils.TypedProperties
Reads a property list (key and element pairs) from the given file which is interpreted as a resource of the given class.
load(String) - Method in class org.biojava.utils.TypedProperties
Reads a property list (key and element pairs) from the file with the given file name.
location - Variable in class org.biojava.bio.seq.Feature.Template
 
Location - interface org.biojava.bio.symbol.Location.
A biological location.
Location.EmptyLocation - class org.biojava.bio.symbol.Location.EmptyLocation.
The implementation of Location that contains no positions at all.
Location.EmptyLocation() - Constructor for class org.biojava.bio.symbol.Location.EmptyLocation
 
Location.LocationComparator - class org.biojava.bio.symbol.Location.LocationComparator.
 
Location.LocationComparator() - Constructor for class org.biojava.bio.symbol.Location.LocationComparator
 
lockModel() - Method in class org.biojava.bio.dp.DP
 
LogoPainter - interface org.biojava.bio.gui.LogoPainter.
The interface for something that will draw the sequence logo for a state.

M

MagicalState - class org.biojava.bio.dp.MagicalState.
Start/end state for HMMs.
magicalState() - Method in class org.biojava.bio.dp.WMAsMM
 
magicalState() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
magicalState() - Method in interface org.biojava.bio.dp.MarkovModel
The MagicalState for this model.
main(String[]) - Static method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
test this class
main(String[]) - Static method in class org.biojava.stats.svm.tools.TrainRegression
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.Classify
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.Train
 
main(String[]) - Static method in class org.biojava.stats.svm.tools.ClassifierExample
Entry point for the application.
make_PrimarySeqIterator() - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
make_PrimarySeqIterator() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
make_PrimarySeqIterator() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
make_PrimarySeqIterator() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
make_PrimarySeqIterator() - Method in interface org.Biocorba.Seqcore.PrimarySeqDB
 
make_PrimarySeqIterator(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeqDB_Operations
 
make_PrimarySeqIterator(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
mapTag(String, XMLPeerFactory) - Method in class org.biojava.utils.xml.XMLDispatcher
Add an XMLPeerFactory which constructs objects corresponding to a specific XML tag.
MarkovModel - interface org.biojava.bio.dp.MarkovModel.
A markov model.
max_feature_request() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
max_feature_request() - Method in class org.Biocorba.Seqcore._SeqStub
 
max_feature_request() - Method in interface org.Biocorba.Seqcore.Seq
 
max_feature_request(ObjectImpl) - Method in interface org.Biocorba.Seqcore._Seq_Operations
 
max_feature_request(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
max_request_length() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
max_request_length() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
max_request_length() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
max_request_length() - Method in interface org.Biocorba.Seqcore.AnonymousSeq
 
max_request_length() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
max_request_length() - Method in class org.Biocorba.Seqcore._SeqStub
 
max_request_length() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
max_request_length(ObjectImpl) - Method in interface org.Biocorba.Seqcore._AnonymousSeq_Operations
 
max_request_length(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
maxIndex() - Method in class org.biojava.stats.svm.SparseVector
 
maxLength() - Method in class org.biojava.bio.symbol.SuffixTree
Return the length of the longest motif represented in this SuffixTree
Meme - class org.biojava.bio.program.Meme.
The results of a meme run.
Meme(InputStream, SymbolParser) - Constructor for class org.biojava.bio.program.Meme
 
MergeFeatureHolder - class org.biojava.bio.seq.MergeFeatureHolder.
FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
MergeFeatureHolder() - Constructor for class org.biojava.bio.seq.MergeFeatureHolder
 
model() - Method in interface org.biojava.bio.dp.DPMatrix
 
model() - Method in class org.biojava.bio.dp.PairDPMatrix
 
ModelChangeEvent - class org.biojava.bio.dp.ModelChangeEvent.
 
ModelChangeEvent(MarkovModel) - Constructor for class org.biojava.bio.dp.ModelChangeEvent
 
ModelInclude - interface org.acedb.ModelInclude.
A node in an AceDB model structure.
ModelInState - interface org.biojava.bio.dp.ModelInState.
A state that contains an entire sub-model.
ModelNode - interface org.acedb.ModelNode.
A node in an AceDB model structure.
ModelReference - interface org.acedb.ModelReference.
A node in an AceDB model structure.
ModelTrainer - interface org.biojava.bio.dp.ModelTrainer.
Encapsulates the training of an entire model.
ModelType - interface org.acedb.ModelType.
A node in an AceDB model structure.
ModelVetoException - exception org.biojava.bio.dp.ModelVetoException.
 
ModelVetoException(String, ModelChangeEvent) - Constructor for class org.biojava.bio.dp.ModelVetoException
 
ModelView - class org.biojava.bio.dp.ModelView.
A model that exposes some translated view of another model.
ModelView.ViewTransitionTrainer - class org.biojava.bio.dp.ModelView.ViewTransitionTrainer.
 
ModelView.ViewTransitionTrainer(ModelView) - Constructor for class org.biojava.bio.dp.ModelView.ViewTransitionTrainer
 
ModelView() - Constructor for class org.biojava.bio.dp.ModelView
 

N

name - Variable in class org.Biocorba.Seqcore.NameValueSet
 
nameIterator() - Method in class org.acedb.staticobj.StaticAceNode
 
nameIterator() - Method in class org.acedb.staticobj.StaticAceSet
 
nameIterator() - Method in class org.acedb.socket.SocketResultSet
 
nameIterator() - Method in interface org.acedb.AceSet
An iterator over the names associated with each thing in the set.
NameParser - class org.biojava.bio.symbol.NameParser.
This uses Symbol names to parse characters into symbols.
NameParser(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.NameParser
 
NameParser(Map) - Constructor for class org.biojava.bio.symbol.NameParser
 
NameValueSet - class org.Biocorba.Seqcore.NameValueSet.
 
NameValueSet() - Constructor for class org.Biocorba.Seqcore.NameValueSet
 
NameValueSet(String, String[]) - Constructor for class org.Biocorba.Seqcore.NameValueSet
 
NameValueSetHelper - class org.Biocorba.Seqcore.NameValueSetHelper.
 
NameValueSetHolder - class org.Biocorba.Seqcore.NameValueSetHolder.
 
NameValueSetHolder() - Constructor for class org.Biocorba.Seqcore.NameValueSetHolder
 
NameValueSetHolder(NameValueSet) - Constructor for class org.Biocorba.Seqcore.NameValueSetHolder
 
NameValueSetListHelper - class org.Biocorba.Seqcore.NameValueSetListHelper.
 
NameValueSetListHolder - class org.Biocorba.Seqcore.NameValueSetListHolder.
 
NameValueSetListHolder() - Constructor for class org.Biocorba.Seqcore.NameValueSetListHolder
 
NameValueSetListHolder(NameValueSet[]) - Constructor for class org.Biocorba.Seqcore.NameValueSetListHolder
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.SeqHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
narrow(Object) - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
narrow(Object) - Static method in class GNOME.UnknownHelper
 
naturalOrder - Static variable in interface org.biojava.bio.symbol.Location
 
NEGATIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
flag to indicate that a feature is on the negative strand.
NestedKernel - class org.biojava.stats.svm.NestedKernel.
Encapsulates a kernel that wraps another kernel up.
NestedKernel() - Constructor for class org.biojava.stats.svm.NestedKernel
Create a new NestedKernel.
NestedKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NestedKernel
Create a new NestedKernel that wraps k.
next() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
next() - Method in interface org.Biocorba.Seqcore.SeqFeatureIterator
 
next() - Method in interface org.Biocorba.Seqcore.PrimarySeqIterator
 
next() - Method in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
next() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
next() - Method in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
next() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
next(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeatureIterator_Operations
 
next(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeqIterator_Operations
 
next(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqIteratorImpl
 
next(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl
 
nextSequence() - Method in class org.biojava.bio.seq.io.StreamReader
Pull the next sequence out of the stream.
nextSequence() - Method in interface org.biojava.bio.seq.SequenceIterator
Returns the next sequence in the iterator.
nextSequence() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter
 
NO_FRAME - Static variable in interface org.biojava.bio.program.gff.GFFRecord
Flag to indicate that there is no frame info.
NO_SCORE - Static variable in interface org.biojava.bio.program.gff.GFFRecord
Flag to indicate that there is no score info.
node - Variable in class org.acedb.seq.AceAnnotation
 
NormalizingKernel - class org.biojava.stats.svm.NormalizingKernel.
Performs a normalization on the results of a nested kernel.
NormalizingKernel() - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
NormalizingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.NormalizingKernel
 
normalLengthVector(SparseVector, double) - Static method in class org.biojava.stats.svm.SparseVector
 

O

ObjectUtil - class org.biojava.utils.ObjectUtil.
utility methods for implementing the equals() and hashCode() methods of Objects.
ObjectUtil() - Constructor for class org.biojava.utils.ObjectUtil
 
openConnection(URL) - Method in class org.acedb.Handler
 
openDB(File) - Static method in class org.biojava.bio.seq.db.IndexedSequenceDB
Open an index at indexFile.
OrderNSymbolList - class org.biojava.bio.symbol.OrderNSymbolList.
An n-th order view of another SymbolList.
OrderNSymbolList(SymbolList, int) - Constructor for class org.biojava.bio.symbol.OrderNSymbolList
Create an order n OrderNSymbolList from source.
org.acedb - package org.acedb
Bindings to ACeDB.
org.acedb.seq - package org.acedb.seq
The bridge from AceDB objects to biojava implementations.
org.acedb.socket - package org.acedb.socket
An implementation of an ACeDB database for use with the ACeDB socket server.
org.acedb.staticobj - package org.acedb.staticobj
Implementations of the ACeDB data nodes which are vanilla java.
org.Biocorba.Seqcore - package org.Biocorba.Seqcore
 
org.biojava.bio - package org.biojava.bio
The core classes that will be used throughout the bio packages.
org.biojava.bio.dist - package org.biojava.bio.dist
Probability distributions over Alphabets.
org.biojava.bio.dp - package org.biojava.bio.dp
HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui - package org.biojava.bio.gui
Graphical interfaces for biojava objects.
org.biojava.bio.gui.sequence - package org.biojava.bio.gui.sequence
Graphical displays of biological sequences and associated annotations (highly experimental).
org.biojava.bio.program - package org.biojava.bio.program
Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.gff - package org.biojava.bio.program.gff
GFF manipulation.
org.biojava.bio.search - package org.biojava.bio.search
 
org.biojava.bio.seq - package org.biojava.bio.seq
Classes and Interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db - package org.biojava.bio.seq.db
Collections of biological sequence data.
org.biojava.bio.seq.io - package org.biojava.bio.seq.io
Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.symbol - package org.biojava.bio.symbol
Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bridge.Biocorba.Seqcore - package org.biojava.bridge.Biocorba.Seqcore
 
org.biojava.bridge.GNOME - package org.biojava.bridge.GNOME
 
org.biojava.stats.svm - package org.biojava.stats.svm
Support Vector Machine classification and regression.
org.biojava.stats.svm.tools - package org.biojava.stats.svm.tools
Tools for use of the SVM package.
org.biojava.utils - package org.biojava.utils
Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.contract - package org.biojava.utils.contract
 
org.biojava.utils.xml - package org.biojava.utils.xml
This package contains a number of utilities for processing XML documents.
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.DNAStyle
 
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.PlainStyle
 
outlinePaint(Symbol) - Method in interface org.biojava.bio.gui.SymbolStyle
Return the outline paint for a symbol.
outlinePaint(Symbol) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
OutOfRange - exception org.Biocorba.Seqcore.OutOfRange.
 
OutOfRange() - Constructor for class org.Biocorba.Seqcore.OutOfRange
 
OutOfRange(String) - Constructor for class org.Biocorba.Seqcore.OutOfRange
 
OutOfRangeHelper - class org.Biocorba.Seqcore.OutOfRangeHelper.
 
OutOfRangeHolder - class org.Biocorba.Seqcore.OutOfRangeHolder.
 
OutOfRangeHolder() - Constructor for class org.Biocorba.Seqcore.OutOfRangeHolder
 
OutOfRangeHolder(OutOfRange) - Constructor for class org.Biocorba.Seqcore.OutOfRangeHolder
 
overlaps(Location) - Method in class org.biojava.bio.symbol.PointLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.RangeLocation
 
overlaps(Location) - Method in class org.biojava.bio.symbol.CompoundLocation
 
overlaps(Location) - Method in interface org.biojava.bio.symbol.Location
Checks if these two locations overlap, using this locations's concept of overlaping.
overlaps(Location) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
OverlayAnnotation - class org.biojava.bio.OverlayAnnotation.
Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
OverlayAnnotation(Annotation) - Constructor for class org.biojava.bio.OverlayAnnotation
Construct an annotation which can overlay new key-value pairs onto an underlying annotation.

P

paint(Graphics2D, SequencePanel, Rectangle2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
Render a portion (possibly all) of the information for sp to g, displaying all of the data that would fall within seqBox.
paint(Graphics2D, SequencePanel, Rectangle2D) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
paint(Graphics2D, SequencePanel, Rectangle2D) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
paintComponent(Graphics) - Method in class org.biojava.bio.gui.DistributionLogo
Transforms the graphics context so that it is in bits space, and then requests the logo painter to fill the area.
paintComponent(Graphics) - Method in class org.biojava.bio.gui.SequencePanel
 
paintComponent(Graphics) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Renders this component to display the points, and if present, the support vector machine.
paintLogo(Graphics, DistributionLogo) - Method in class org.biojava.bio.gui.TextLogoPainter
 
paintLogo(Graphics, DistributionLogo) - Method in interface org.biojava.bio.gui.LogoPainter
Render the state from sl onto the graphics object g.
paintLogo(Graphics, DistributionLogo) - Method in class org.biojava.bio.gui.BarLogoPainter
 
PairDistribution - class org.biojava.bio.dist.PairDistribution.
Class for pairing up two unique distributions.
PairDistribution(Distribution, Distribution) - Constructor for class org.biojava.bio.dist.PairDistribution
 
PairDPMatrix - class org.biojava.bio.dp.PairDPMatrix.
Storage structure for intermediate values from a pairwise dynamic programming run.
PairDPMatrix(DP, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.PairDPMatrix
 
PairwiseDP - class org.biojava.bio.dp.PairwiseDP.
Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
PairwiseDP(MarkovModel) - Constructor for class org.biojava.bio.dp.PairwiseDP
 
parse(BufferedReader, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFParser
Informs handler of each line of gff read from bReader.
parse(BufferedReader, GFFDocumentHandler, String) - Method in class org.biojava.bio.program.gff.GFFParser
Informs handler of each line of gff read from bReader
parse(String) - Method in class org.biojava.bio.symbol.CrossProductSymbolNameParser
 
parse(String) - Method in class org.biojava.bio.symbol.FixedWidthParser
 
parse(String) - Method in class org.biojava.bio.symbol.TokenParser
 
parse(String) - Method in interface org.biojava.bio.symbol.SymbolParser
Parse an entire string into a SymbolList.
parse(String) - Method in class org.biojava.bio.symbol.NameParser
 
parseAnnotation(String, Annotation) - Method in interface org.biojava.bio.seq.io.FastaDescriptionReader
Add any annotation to this annotation bundle that can be extracted from the description.
parseAnnotation(String, Annotation) - Method in class org.biojava.bio.seq.io.DefaultDescriptionReader
Parses annotation out from the description line.
parseAttribute(String) - Method in class org.biojava.bio.program.gff.GFFParser
Parse attValList into a Map of attributes and value lists.
parseExample(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
parseObject(String) - Method in class org.acedb.AcePerlParser
 
ParserException - exception org.biojava.utils.ParserException.
Exception thrown when an error occurs in document parsing.
ParserException(String) - Constructor for class org.biojava.utils.ParserException
 
ParserException(String, String) - Constructor for class org.biojava.utils.ParserException
 
ParserException(String, String, int) - Constructor for class org.biojava.utils.ParserException
 
ParserException(String, String, int, String) - Constructor for class org.biojava.utils.ParserException
 
ParserException(String, String, int, String, int) - Constructor for class org.biojava.utils.ParserException
 
parseToken(String) - Method in class org.biojava.bio.symbol.CrossProductSymbolNameParser
 
parseToken(String) - Method in class org.biojava.bio.symbol.FixedWidthParser
 
parseToken(String) - Method in class org.biojava.bio.symbol.TokenParser
 
parseToken(String) - Method in interface org.biojava.bio.symbol.SymbolParser
Returns the symbol for a single token.
parseToken(String) - Method in class org.biojava.bio.symbol.NameParser
 
parseURNName(String) - Method in interface org.biojava.bio.seq.io.FastaDescriptionReader
Parse out the name and urn from the description line.
parseURNName(String) - Method in class org.biojava.bio.seq.io.DefaultDescriptionReader
Parses the description line, extracting the names for the URI and name fields.
pcs - Variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
pcs - Variable in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
pcs - Variable in class org.biojava.bio.gui.SequencePanel.Border
 
pick(AceSet) - Static method in class org.acedb.AceUtils
 
PlainStyle - class org.biojava.bio.gui.PlainStyle.
A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling.
PlainStyle() - Constructor for class org.biojava.bio.gui.PlainStyle
 
PlainStyle(Paint, Paint) - Constructor for class org.biojava.bio.gui.PlainStyle
 
PointLocation - class org.biojava.bio.symbol.PointLocation.
A single symbol.
PointLocation(int) - Constructor for class org.biojava.bio.symbol.PointLocation
 
polyKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
PolynomialKernel - class org.biojava.stats.svm.PolynomialKernel.
This kernel computes all possible products of order features in feature space.
PolynomialKernel() - Constructor for class org.biojava.stats.svm.PolynomialKernel
 
POSITIVE - Static variable in interface org.biojava.bio.seq.StrandedFeature
flag to indicate that a feature is on the positive strand.
post(boolean, String) - Static method in class org.biojava.utils.contract.Contract
check if postcondition is met and throw an exception if not.
postChangeTransitionScore(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
PostconditionNotMetException - exception org.biojava.utils.contract.PostconditionNotMetException.
Exception class that is thrown if a postcondition of a method is not met.
PostconditionNotMetException() - Constructor for class org.biojava.utils.contract.PostconditionNotMetException
construct with no particular message
PostconditionNotMetException(String) - Constructor for class org.biojava.utils.contract.PostconditionNotMetException
construct with the given message
postCreateTransition(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
postDestroyTransition(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
pre(boolean, String) - Static method in class org.biojava.utils.contract.Contract
check if precondition is met and throw an exception if not.
preChangeTransitionScore(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
PreconditionNotMetException - exception org.biojava.utils.contract.PreconditionNotMetException.
Exception class that is thrown if a precondition of a method is not met.
PreconditionNotMetException() - Constructor for class org.biojava.utils.contract.PreconditionNotMetException
construct with no particular message
PreconditionNotMetException(String) - Constructor for class org.biojava.utils.contract.PreconditionNotMetException
construct with the given message
preCreateTransition(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
preDestroyTransition(TransitionEvent) - Method in interface org.biojava.bio.dp.TransitionListener
 
primary_id() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
primary_id() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
primary_id() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
primary_id() - Method in interface org.Biocorba.Seqcore.PrimarySeq
 
primary_id() - Method in class org.Biocorba.Seqcore._SeqStub
 
primary_id(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeq_Operations
 
primary_id(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
primaryidListHelper - class org.Biocorba.Seqcore.primaryidListHelper.
 
primaryidListHolder - class org.Biocorba.Seqcore.primaryidListHolder.
 
primaryidListHolder() - Constructor for class org.Biocorba.Seqcore.primaryidListHolder
 
primaryidListHolder(String[]) - Constructor for class org.Biocorba.Seqcore.primaryidListHolder
 
PrimarySeq - interface org.Biocorba.Seqcore.PrimarySeq.
 
PrimarySeq_is_available() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
PrimarySeq_is_available() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
PrimarySeq_is_available() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
PrimarySeq_is_available(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
PrimarySeq_is_available(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
PrimarySeqDB - interface org.Biocorba.Seqcore.PrimarySeqDB.
 
PrimarySeqDBHelper - class org.Biocorba.Seqcore.PrimarySeqDBHelper.
 
PrimarySeqDBHolder - class org.Biocorba.Seqcore.PrimarySeqDBHolder.
 
PrimarySeqDBHolder() - Constructor for class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
PrimarySeqDBHolder(PrimarySeqDB) - Constructor for class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
PrimarySeqDBImpl - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl.
 
PrimarySeqDBImpl(SequenceDB) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqDBImpl
 
PrimarySeqHelper - class org.Biocorba.Seqcore.PrimarySeqHelper.
 
PrimarySeqHolder - class org.Biocorba.Seqcore.PrimarySeqHolder.
 
PrimarySeqHolder() - Constructor for class org.Biocorba.Seqcore.PrimarySeqHolder
 
PrimarySeqHolder(PrimarySeq) - Constructor for class org.Biocorba.Seqcore.PrimarySeqHolder
 
PrimarySeqImpl - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl.
Implements a CORBA PrimarySeq object by adapting a biojava SymbolList.
PrimarySeqImpl(SymbolList) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
PrimarySeqImpl(SymbolList, String) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
PrimarySeqImpl(SymbolList, String, String, String) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
PrimarySeqIterator - interface org.Biocorba.Seqcore.PrimarySeqIterator.
 
PrimarySeqIteratorHelper - class org.Biocorba.Seqcore.PrimarySeqIteratorHelper.
 
PrimarySeqIteratorHolder - class org.Biocorba.Seqcore.PrimarySeqIteratorHolder.
 
PrimarySeqIteratorHolder() - Constructor for class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
PrimarySeqIteratorHolder(PrimarySeqIterator) - Constructor for class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
PrimarySeqIteratorImpl - class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqIteratorImpl.
 
PrimarySeqIteratorImpl(SequenceIterator) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqIteratorImpl
 
PRIME - Static variable in class org.biojava.utils.ObjectUtil
the current hashCode is always first multiplied with this prime before the hashCode value for a particular field is added.
printStackTrace() - Method in class org.biojava.bio.BioException
 
printStackTrace() - Method in class org.biojava.bio.BioError
 
printStackTrace(PrintStream) - Method in class org.biojava.bio.BioException
 
printStackTrace(PrintStream) - Method in class org.biojava.bio.BioError
 
printStackTrace(PrintWriter) - Method in class org.biojava.bio.BioException
 
printStackTrace(PrintWriter) - Method in class org.biojava.bio.BioError
 
processDB(SequenceDB, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Process all Sequences within a SequenceDB, informing handler of any suitable features.
processingInstruction(String, String) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
processSequence(Sequence, GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Process an individual Sequence, informing handler of any suitable features.
ProfileHMM - class org.biojava.bio.dp.ProfileHMM.
 
ProfileHMM(Alphabet, int, DistributionFactory, DistributionFactory) - Constructor for class org.biojava.bio.dp.ProfileHMM
Create a new ProfileHMM.
propertiesAllocated() - Method in class org.biojava.bio.SimpleAnnotation
A convenience method to see if we have allocated the properties map yet.
propertyChange(PropertyChangeEvent) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
PROTEIN - Static variable in class org.Biocorba.Seqcore.SeqType
 
ProteinTools - class org.biojava.bio.seq.ProteinTools.
The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
ProteinTools() - Constructor for class org.biojava.bio.seq.ProteinTools
 
put(int, double) - Method in class org.biojava.stats.svm.SparseVector
Set the value at a particular dimension.
putParser(String, SymbolParser) - Method in class org.biojava.bio.symbol.AbstractAlphabet
Assigns a symbol parser to a string object.

Q

qualifiers() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
qualifiers() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
qualifiers() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
qualifiers(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
qualifiers(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
query_interface(ObjectImpl, String) - Method in class org.biojava.bridge.GNOME.UnknownImpl
 
query_interface(ObjectImpl, String) - Method in interface GNOME._Unknown_Operations
 
query_interface(String) - Method in class org.Biocorba.Seqcore._Seq_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqDBStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._SeqStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
query_interface(String) - Method in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
query_interface(String) - Method in interface GNOME.Unknown
 
query_interface(String) - Method in class GNOME._UnknownStub
 
query_interface(String) - Method in class GNOME._Unknown_Tie
 
QUERY_LABEL - Static variable in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
this object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence

R

RadialBaseKernel - class org.biojava.stats.svm.RadialBaseKernel.
This kernel computes the radial base kernel that corresponds to a gausian distribution.
RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel
 
RangeLocation - class org.biojava.bio.symbol.RangeLocation.
A simple implementation of Location that contains all points between getMin and getMax inclusive.
RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation
 
rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat
Read in an alignment from a buffered reader object
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.stringListHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
read(InputStream) - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
read(InputStream) - Static method in class GNOME.UnknownHelper
 
readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder
 
readSequence(StreamReader.Context, SymbolParser, SequenceFactory) - Method in interface org.biojava.bio.seq.io.SequenceFormat
Read in a single sequence.
readSequence(StreamReader.Context, SymbolParser, SequenceFactory) - Method in class org.biojava.bio.seq.io.EmblFormat
 
readSequence(StreamReader.Context, SymbolParser, SequenceFactory) - Method in class org.biojava.bio.seq.io.GenbankFormat
 
readSequence(StreamReader.Context, SymbolParser, SequenceFactory) - Method in class org.biojava.bio.seq.io.FastaFormat
 
realizeFeature(Feature.Template) - Method in class org.acedb.seq.AceSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.ViewSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleSequence
 
realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder
Realize a feature template.
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer
Install a feature on the specified sequence.
realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
 
RealizingFeatureHolder - interface org.biojava.bio.seq.RealizingFeatureHolder.
Interface for FeatureHolder objects which know how to instantiate new child Features.
reason - Variable in class org.Biocorba.Seqcore.OutOfRange
 
reason - Variable in class org.Biocorba.Seqcore.RequestTooLarge
 
reason - Variable in class org.Biocorba.Seqcore.UnableToProcess
 
recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
A record line has been encountered.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer
Only forward the GFFRecords that match a filter.
recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter
Prints record to the PrintWriter.
ref() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
ref() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
ref() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
ref() - Method in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
ref() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
ref() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
ref() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
ref() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
ref() - Method in class org.Biocorba.Seqcore._SeqStub
 
ref() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
ref() - Method in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
ref() - Method in interface GNOME.Unknown
 
ref() - Method in class GNOME._UnknownStub
 
ref() - Method in class GNOME._Unknown_Tie
 
ref(ObjectImpl) - Method in class org.biojava.bridge.GNOME.UnknownImpl
 
ref(ObjectImpl) - Method in interface GNOME._Unknown_Operations
 
Reference - interface org.acedb.Reference.
Encapsulates a reference to another object within an ACeDB database.
registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
Register an alphabet by name.
registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Register a distribution object
registerDistributionTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
registerDistributionTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Register a distribution and an associated distributiontrainer object
registerDriver(Driver) - Static method in class org.acedb.Ace
Register a driver with the manager.
registerTrainerForModel(MarkovModel, TransitionTrainer) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
registerTrainerForModel(MarkovModel, TransitionTrainer) - Method in interface org.biojava.bio.dp.ModelTrainer
Register a trainer as being for a model.
registerTrainerForTransition(State, State, TransitionTrainer, State, State) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
registerTrainerForTransition(State, State, TransitionTrainer, State, State) - Method in interface org.biojava.bio.dp.ModelTrainer
Register a TransitionTrainer, a source and a destination state with a pair of states.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.ComplementaryDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution
Register this distribution with a training context.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution
Register an IgnoreCountsTrainer instance as the trainer for this distribution.
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.DNADistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution
 
registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution
Register a simple trainer for this distribution.
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.ModelView
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleModelInState
 
registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable
Perform any registration that is necisary with mt.
registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution
Register this paired distribution with a model trainer.
relativeURL(String) - Method in class org.acedb.AceURL
 
remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
 
removeFeature(Feature) - Method in class org.acedb.seq.AceSequence
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.ViewSequence
Remove a feature from this sequence.
removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
 
removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
Remove a feature from this FeatureHolder.
removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
 
removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleSequence
Remove a feature attached to this sequence.
removeFeature(Feature) - Method in class org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
 
removeFeature(Feature) - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
removeFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
Remove a file from the database
removeGap(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Remove a single gap at position pos in this GappedSymbolList.
removeGaps(int, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Remove some gaps at position pos in this GappedSymbolList.
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.SequencePanel.Border
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
 
removeState(State) - Method in class org.biojava.bio.dp.WMAsMM
 
removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel
Remove a state from the model.
removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
Remove a symbol from this alphabet.
removeTransitionListener(TransitionListener) - Method in class org.biojava.bio.dp.WMAsMM
 
removeTransitionListener(TransitionListener) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
removeTransitionListener(TransitionListener) - Method in interface org.biojava.bio.dp.MarkovModel
Unregister a TransitionListener with the model.
renderFeature(Graphics2D, Feature, Rectangle2D, SequencePanel) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
 
renderFeature(Graphics2D, Feature, Rectangle2D, SequencePanel) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
renumber(int, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Renumber the view indexes from block, adding delta to each offset.
RequestTooLarge - exception org.Biocorba.Seqcore.RequestTooLarge.
 
RequestTooLarge() - Constructor for class org.Biocorba.Seqcore.RequestTooLarge
 
RequestTooLarge(String, int) - Constructor for class org.Biocorba.Seqcore.RequestTooLarge
 
RequestTooLargeHelper - class org.Biocorba.Seqcore.RequestTooLargeHelper.
 
RequestTooLargeHolder - class org.Biocorba.Seqcore.RequestTooLargeHolder.
 
RequestTooLargeHolder() - Constructor for class org.Biocorba.Seqcore.RequestTooLargeHolder
 
RequestTooLargeHolder(RequestTooLarge) - Constructor for class org.Biocorba.Seqcore.RequestTooLargeHolder
 
resizeAndValidate() - Method in class org.biojava.bio.gui.SequencePanel
 
resList() - Method in interface org.biojava.bio.dp.DPMatrix
 
resList() - Method in class org.biojava.bio.dp.PairDPMatrix
 
retrieve(AceSet, List) - Static method in class org.acedb.AceUtils
 
retrieve(AceSet, String) - Static method in class org.acedb.AceUtils
 
retrieve(String) - Method in class org.acedb.staticobj.StaticAceNode
 
retrieve(String) - Method in class org.acedb.staticobj.StaticAceSet
 
retrieve(String) - Method in class org.acedb.socket.SocketResultSet
 
retrieve(String) - Method in interface org.acedb.AceSet
Retrieve a memeber by name.
reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
Retrieve a reverse-complement view of list.
ReverseSymbolList - class org.biojava.bio.symbol.ReverseSymbolList.
An reverse view of another SymbolList.
ReverseSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.ReverseSymbolList
Create a reverse view of source.
RNA - Static variable in class org.Biocorba.Seqcore.SeqType
 
rootURL(AceURL) - Static method in class org.acedb.AceUtils
Get the root URL for a database.

S

sampleSymbol() - Method in class org.biojava.bio.dist.ComplementaryDistribution
 
sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution
Sample a symbol from this state's probability distribution.
sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution
 
sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution
 
sampleTransition(State) - Method in class org.biojava.bio.dp.WMAsMM
 
sampleTransition(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
sampleTransition(State) - Method in class org.biojava.bio.dp.ModelView
 
sampleTransition(State) - Method in interface org.biojava.bio.dp.MarkovModel
Sample a transition from the distribution of transitions.
SCORES - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the likelyhood at each step.
scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
using this sequence similarity searcher, search with the given sequence against the given sequence database.
Seq - interface org.Biocorba.Seqcore.Seq.
 
seq_primary_id() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
seq_primary_id() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
seq_primary_id() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
seq_primary_id(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
seq_primary_id(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
SeqDB - interface org.Biocorba.Seqcore.SeqDB.
 
SeqDBHelper - class org.Biocorba.Seqcore.SeqDBHelper.
 
SeqDBHolder - class org.Biocorba.Seqcore.SeqDBHolder.
 
SeqDBHolder() - Constructor for class org.Biocorba.Seqcore.SeqDBHolder
 
SeqDBHolder(SeqDB) - Constructor for class org.Biocorba.Seqcore.SeqDBHolder
 
SeqDBImpl - class org.biojava.bridge.Biocorba.Seqcore.SeqDBImpl.
 
SeqDBImpl(SequenceDB) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqDBImpl
 
SeqFeature - interface org.Biocorba.Seqcore.SeqFeature.
 
SeqFeatureHelper - class org.Biocorba.Seqcore.SeqFeatureHelper.
 
SeqFeatureHolder - class org.Biocorba.Seqcore.SeqFeatureHolder.
 
SeqFeatureHolder() - Constructor for class org.Biocorba.Seqcore.SeqFeatureHolder
 
SeqFeatureHolder(SeqFeature) - Constructor for class org.Biocorba.Seqcore.SeqFeatureHolder
 
SeqFeatureImpl - class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl.
 
SeqFeatureImpl(Seq, Feature) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
SeqFeatureIterator - interface org.Biocorba.Seqcore.SeqFeatureIterator.
 
SeqFeatureIteratorHelper - class org.Biocorba.Seqcore.SeqFeatureIteratorHelper.
 
SeqFeatureIteratorHolder - class org.Biocorba.Seqcore.SeqFeatureIteratorHolder.
 
SeqFeatureIteratorHolder() - Constructor for class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
SeqFeatureIteratorHolder(SeqFeatureIterator) - Constructor for class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
SeqFeatureIteratorImpl - class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl.
 
SeqFeatureIteratorImpl(Seq, Iterator) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureIteratorImpl
 
SeqFeatureListHelper - class org.Biocorba.Seqcore.SeqFeatureListHelper.
 
SeqFeatureListHolder - class org.Biocorba.Seqcore.SeqFeatureListHolder.
 
SeqFeatureListHolder() - Constructor for class org.Biocorba.Seqcore.SeqFeatureListHolder
 
SeqFeatureListHolder(SeqFeature[]) - Constructor for class org.Biocorba.Seqcore.SeqFeatureListHolder
 
SeqHelper - class org.Biocorba.Seqcore.SeqHelper.
 
SeqHolder - class org.Biocorba.Seqcore.SeqHolder.
 
SeqHolder() - Constructor for class org.Biocorba.Seqcore.SeqHolder
 
SeqHolder(Seq) - Constructor for class org.Biocorba.Seqcore.SeqHolder
 
SeqImpl - class org.biojava.bridge.Biocorba.Seqcore.SeqImpl.
 
SeqImpl(Sequence) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
SeqImpl(Sequence, String) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
SeqImpl(Sequence, String, String, String) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SeqImpl
 
seqObj - Variable in class org.acedb.seq.AceSequence
 
seqSet - Variable in class org.acedb.seq.AceSequenceDB
 
SeqSimilaritySearcher - interface org.biojava.bio.search.SeqSimilaritySearcher.
objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilaritySearchHit - interface org.biojava.bio.search.SeqSimilaritySearchHit.
objects of this type represent one particular hit (i.e.
SeqSimilaritySearchResult - interface org.biojava.bio.search.SeqSimilaritySearchResult.
objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit - interface org.biojava.bio.search.SeqSimilaritySearchSubHit.
objects of this type represent one particular sub-hit (i.e.
seqString() - Method in class org.acedb.seq.AceSequence
 
seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
 
seqString() - Method in class org.biojava.bio.seq.ViewSequence
 
seqString() - Method in class org.biojava.bio.seq.SimpleSequence
 
seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
seqString() - Method in interface org.biojava.bio.symbol.SymbolList
Stringify this symbol list.
seqString() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
seqString() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
SeqType - class org.Biocorba.Seqcore.SeqType.
 
SeqTypeHelper - class org.Biocorba.Seqcore.SeqTypeHelper.
 
SeqTypeHolder - class org.Biocorba.Seqcore.SeqTypeHolder.
 
SeqTypeHolder() - Constructor for class org.Biocorba.Seqcore.SeqTypeHolder
 
SeqTypeHolder(SeqType) - Constructor for class org.Biocorba.Seqcore.SeqTypeHolder
 
Sequence - interface org.biojava.bio.seq.Sequence.
A sequence.
SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the emitted sequence.
SequenceAdapter - class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter.
 
SequenceAdapter(PrimarySeq) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter
 
SequenceAnnotator - interface org.biojava.bio.seq.SequenceAnnotator.
An object which adds some additional information to a Sequence.
SequenceDB - interface org.biojava.bio.seq.db.SequenceDB.
A database of sequences.
SequenceDBAdapter - class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter.
 
SequenceDBAdapter(PrimarySeqDB) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
SequenceDBInstallation - interface org.biojava.bio.seq.db.SequenceDBInstallation.
A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.
SequenceFactory - interface org.biojava.bio.seq.SequenceFactory.
The interface for objects that will manufacture sequences.
SequenceFormat - interface org.biojava.bio.seq.io.SequenceFormat.
Defines what a sequence format does.
SequenceIterator - interface org.biojava.bio.seq.SequenceIterator.
An iterator over a bag of sequences.
sequenceIterator() - Method in class org.acedb.seq.AceSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
 
sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB
Returns a SequenceTterator over all sequences in the database.
sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
 
sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB
 
sequenceIterator() - Method in class org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter
 
SequenceIteratorAdapter - class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter.
 
SequenceIteratorAdapter(PrimarySeqIterator) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SequenceIteratorAdapter
 
SequencePanel - class org.biojava.bio.gui.SequencePanel.
A panel that visualy displays a Sequence.
SequencePanel.Border - class org.biojava.bio.gui.SequencePanel.Border.
 
SequencePanel() - Constructor for class org.biojava.bio.gui.SequencePanel
 
SequenceRenderer - interface org.biojava.bio.gui.sequence.SequenceRenderer.
The interface for things that can render a line of information about a sequence.
SequencesAsGFF - class org.biojava.bio.program.gff.SequencesAsGFF.
Turns a sequence database into a GFF event stream.
SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
 
sequenceToGraphics(int) - Method in class org.biojava.bio.gui.SequencePanel
 
servant - Variable in class org.Biocorba.Seqcore._Seq_Tie
 
servant - Variable in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
servant - Variable in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
servant - Variable in class org.Biocorba.Seqcore._SeqDB_Tie
 
servant - Variable in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
servant - Variable in class org.Biocorba.Seqcore._SeqFeature_Tie
 
servant - Variable in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
servant - Variable in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
servant - Variable in class GNOME._Unknown_Tie
 
setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set a flag so that newly added points will be in the positive class or negative class, depending on wether addPos is true or false respectively.
setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setAlignment(int) - Method in class org.biojava.bio.gui.SequencePanel.Border
 
setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setArrowScoop(float) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setArrowSize(float) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setC(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the comment to comment.
setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setDepth(double) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
Change the current DepthScaler to depthScaler.
setDescriptionReader(FastaDescriptionReader) - Method in class org.biojava.bio.seq.io.FastaFormat
Set the descripiton reader.
setDirection(int) - Method in class org.biojava.bio.gui.SequencePanel
 
setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState
Set the Distribution associated with this state.
setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo
Set the dist to render.
setDocumentLocator(Locator) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the end coordinate to end.
setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer
 
setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser
Set the error handler used by this parser.
setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the feature type to type.
setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
Set the feature to feature.
setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Replace the current FeatureFilter with filter.
setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.SimpleSequenceFactory
Set the FeatureRealizer used by new sequences created by this factory.
setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
 
setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the frame to frame.
setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Replace the group-attribute Map with ga.
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the kernel used for classification.
setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setLabel(String) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
 
setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel
Set the scale factor.
setLines(int) - Method in class org.biojava.bio.gui.SequencePanel
 
setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat
Set the line width.
setList(List) - Method in class org.biojava.bio.symbol.AlphabetManager.ListWrapper
Assigns a list of objects to a different list of objects.
setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter
Set the current logo font.
setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo
Set the logo painter.
setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
 
setName(String) - Method in class org.biojava.bio.seq.SimpleSequence
Assign a name to this sequence
setName(String) - Method in class org.biojava.bio.symbol.SimpleSymbol
Assign a name to the symbol
setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet
Assign a name to the alphabet
setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the Shape to represent the negative points.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel
Set the SVMKernel to nest to k.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
Set the kernel to nest.
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
 
setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
Set the normalizing vector.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
Assign a background distribution
setNullModel(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution
Assign a background distribution
setNullModel(Distribution) - Method in class org.biojava.bio.dist.DNADistribution
Assign a background probability distribution to the DNA distribution.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution
Assign a distribution to be the background null model.
setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution
Set a null background distribution.
setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
Assign a weight to the background distribution
setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
Set the number associated with this node.
setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel
 
setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
 
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
 
setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
 
setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
Set the Shape to represent the positive points.
setProperty(Object, Object) - Method in class org.acedb.seq.AceAnnotation
 
setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation
Set the value of a property.
setProperty(Object, Object) - Method in class org.biojava.bio.Annotation.EmptyAnnotation
 
setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
 
setProperty(Object, Object) - Method in class org.biojava.bio.SimpleAnnotation
 
setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
Set whether features will be filtered recursively to recurse.
setScale(double) - Method in class org.biojava.bio.gui.SequencePanel
 
setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the score to score.
setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the sequence name to seqName.
setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
Set the sequence name to seqName.
setSequence(Sequence) - Method in class org.biojava.bio.gui.SequencePanel
 
setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the feature source to source.
setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
Set the source to source.
setSpacer(int) - Method in class org.biojava.bio.gui.SequencePanel
 
setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the start coordinate to start.
setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
Set the strand to strand.
setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo
Set the symbol style.
setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
 
setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
 
setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
 
setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
 
setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
 
setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
 
setTransitionScore(State, State, double) - Method in class org.biojava.bio.dp.WMAsMM
 
setTransitionScore(State, State, double) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
setTransitionScore(State, State, double) - Method in interface org.biojava.bio.dp.MarkovModel
Set the transition score associated with a transition.
setTranslation(Symbol, Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
Alter the translation mapping.
setURN(String) - Method in class org.biojava.bio.seq.SimpleSequence
Provide the URN for this sequence
setValue(double) - Method in interface org.biojava.stats.svm.ItemValue
 
setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.ComplementaryDistribution
 
setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution
Set the probability or odds that Symbol s is emited by this state.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
Set the weight of a given symbol in this distribution.
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.DNADistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution
 
setWeight(Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution
Set the weight associated with the specified symbol in this distribution.
setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
 
setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel
 
SigmoidKernel - class org.biojava.stats.svm.SigmoidKernel.
This kernel implements a three layer neural net.
SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
 
sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
 
SimpleAlignment - class org.biojava.bio.symbol.SimpleAlignment.
A simple implementation of an Alignment.
SimpleAlignment(Map) - Constructor for class org.biojava.bio.symbol.SimpleAlignment
Generate an alignment from a list of SymbolLists.
SimpleAlphabet - class org.biojava.bio.symbol.SimpleAlphabet.
A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
 
SimpleAnnotation - class org.biojava.bio.SimpleAnnotation.
A no-frills implementation of Annotation that is just a wrapper around a Map.
SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation
 
SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation
 
SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation
 
SimpleAtomicSymbol - class org.biojava.bio.symbol.SimpleAtomicSymbol.
A no-frills implementation of AtomicSymbol.
SimpleAtomicSymbol(char, String, Annotation) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
 
SimpleDistribution - class org.biojava.bio.dist.SimpleDistribution.
A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution
 
SimpleDistributionTrainer - class org.biojava.bio.dist.SimpleDistributionTrainer.
An implemenation of a simple distribution trainer
SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer
 
SimpleDistributionTrainerContext - class org.biojava.bio.dist.SimpleDistributionTrainerContext.
A no-frills implementation of DistributionTrainerContext.
SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
SimpleDotState - class org.biojava.bio.dp.SimpleDotState.
A Dot state that you can make and use.
SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
 
SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
 
SimpleEmissionState - class org.biojava.bio.dp.SimpleEmissionState.
 
SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
 
SimpleFeatureBuilder - class org.biojava.bio.seq.io.SimpleFeatureBuilder.
Simple FeatureBuilder implementation.
SimpleFeatureBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleFeatureBuilder
 
SimpleFeatureHolder - class org.biojava.bio.seq.SimpleFeatureHolder.
A no-frills implementation of FeatureHolder.
SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
 
SimpleFeatureRealizer - class org.biojava.bio.seq.SimpleFeatureRealizer.
FeatureRealizer which uses a lookup table to map template classes to implementations.
SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
 
SimpleGFFRecord - class org.biojava.bio.program.gff.SimpleGFFRecord.
A no-frills implementation of a GFFRecord.
SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
 
SimpleItemValue - class org.biojava.stats.svm.SimpleItemValue.
A no-frills implementation of ItemValue.
SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
 
SimpleMarkovModel - class org.biojava.bio.dp.SimpleMarkovModel.
 
SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
 
SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
 
SimpleModelInState - class org.biojava.bio.dp.SimpleModelInState.
 
SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
 
SimpleModelTrainer - class org.biojava.bio.dp.SimpleModelTrainer.
 
SimpleModelTrainer(MarkovModel, Distribution, double, double, double) - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
Create a model trainer for a particular model.
SimpleSeqSimilaritySearchHit - class org.biojava.bio.search.SimpleSeqSimilaritySearchHit.
a simple implementation of interface SeqSimilaritySearchHit that takes care of all the housekeeping.
SimpleSeqSimilaritySearchHit(SeqSimilaritySearchResult, double, double, double, String, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
construct an immutable object from the values of all properties.
SimpleSeqSimilaritySearchResult - class org.biojava.bio.search.SimpleSeqSimilaritySearchResult.
an class that implements the trivial (housekeeping) responsibilities of interface SeqSimilaritySearchResult.
SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher, SymbolList, SequenceDB, Map, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
construct an immutable object by giving all its properties.
SimpleSeqSimilaritySearchSubHit - class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit.
a simple implementation of interface SeqSimilaritySearchSubHit that takes care of all the house-keeping.
SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit, double, double, double, Alignment) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
construct an immutable object of this class by providing all properties.
SimpleSequence - class org.biojava.bio.seq.SimpleSequence.
A basic implementation of the Sequence interface.
SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.SimpleSequence
Create a SimpleSequence with the symbols and alphabet of res, and the sequence properties listed.
SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleSequence
Create a SimpleSequence using a specified FeatureRealizer.
SimpleSequenceDBInstallation - class org.biojava.bio.seq.db.SimpleSequenceDBInstallation.
this class is an implementation of interface SequenceDBInstallation that manages a set of HashSequenceDB objects.
SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
create an initially empty SimpleSequenceDBInstallation
SimpleSequenceFactory - class org.biojava.bio.seq.SimpleSequenceFactory.
A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.SimpleSequenceFactory
 
SimpleStatePath - class org.biojava.bio.dp.SimpleStatePath.
A no-frills implementation of StatePath.
SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
 
SimpleSVMClassifierModel - class org.biojava.stats.svm.SimpleSVMClassifierModel.
A no-frills implementation of an SVM classifier model.
SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
 
SimpleSVMTarget - class org.biojava.stats.svm.SimpleSVMTarget.
No-frills implementation of SVMTarget.
SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
 
SimpleSymbol - class org.biojava.bio.symbol.SimpleSymbol.
A no-frills implementation of a symbol.
SimpleSymbol(char, String, Alphabet, Annotation) - Constructor for class org.biojava.bio.symbol.SimpleSymbol
Create a new SimpleSymbol.
SimpleSymbolList - class org.biojava.bio.symbol.SimpleSymbolList.
Basic implementation of SymbolList.
SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct an empty SimpleSymbolList.
SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a SymbolList containing the symbols in the specified list.
SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
Construct a copy of an existing SymbolList.
SimpleSymbolStyle - class org.biojava.bio.gui.SimpleSymbolStyle.
A no-frills implementation of SymbolStyle.
SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle
 
SimpleTransitionTrainer - class org.biojava.bio.dp.SimpleTransitionTrainer.
A simple implementation of a TransitionTrainer.
SimpleTransitionTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleTransitionTrainer
 
SimpleTranslationTable - class org.biojava.bio.symbol.SimpleTranslationTable.
A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
Create a new translation table that will translate symbols from source to target.
SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
Create a new translation table that will translate symbols from source to target.
SimpleWeightMatrix - class org.biojava.bio.dp.SimpleWeightMatrix.
 
SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer
 
singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler
 
SingletonAlphabet - class org.biojava.bio.symbol.SingletonAlphabet.
An alphabet that contains a single atomic symbol.
SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
 
size() - Method in class org.acedb.staticobj.StaticAceNode
 
size() - Method in class org.acedb.staticobj.StaticAceSet
 
size() - Method in class org.acedb.socket.SocketResultSet
 
size() - Method in interface org.acedb.AceSet
The number of items in this AceSet.
size() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
The number of symbols in the alphabet.
size() - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
size() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
size() - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
size() - Method in class org.biojava.bio.program.gff.GFFEntrySet
Return how many lines are in this set.
size() - Method in class org.biojava.stats.svm.SparseVector
The number of used dimensions.
size() - Method in class org.biojava.stats.svm.SVMRegressionModel
 
SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
 
SMORegressionTrainer - class org.biojava.stats.svm.SMORegressionTrainer.
Train a regression support vector machine using the Sequential Minimal Optimization algorithm.
SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
 
SMOTrainer - class org.biojava.stats.svm.SMOTrainer.
Train a support vector machine using the Sequential Minimal Optimization algorithm.
SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
 
SocketDriver - class org.acedb.socket.SocketDriver.
 
SocketDriver() - Constructor for class org.acedb.socket.SocketDriver
 
SocketResultSet - class org.acedb.socket.SocketResultSet.
 
SocketResultSet(SocketDatabase, AceSet, List, AceURL) - Constructor for class org.acedb.socket.SocketResultSet
 
source - Variable in class org.biojava.bio.seq.Feature.Template
 
source() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
source() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
source() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
source(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
source(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
sourceToView(GappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from source to view.
sourceToView(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from source to view.
SparseVector - class org.biojava.stats.svm.SparseVector.
An implementation of a sparse vector.
SparseVector.NormalizingKernel - class org.biojava.stats.svm.SparseVector.NormalizingKernel.
A version of the standard dot-product kernel that scales each column independantly.
SparseVector.NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
Generate a normalizing kernel defined by the SparseVectors in vectors.
SparseVector.NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
Generate a normalizing kernel with the normalizing vector s.
SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector
 
SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector
 
start() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
start() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
start() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
start(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
start(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
startDocument() - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
Indicates that a new GFF document has been started.
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
 
startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter
 
startElement(String, AttributeList) - Method in class org.biojava.utils.xml.XMLPeerBuilder
 
State - interface org.biojava.bio.dp.State.
A state in a markov process.
stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
 
stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
FiniteAlphabet of the states.
stateList(MarkovModel) - Static method in class org.biojava.bio.dp.DP
 
StatePath - interface org.biojava.bio.dp.StatePath.
Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelyhoods.
STATES - Static variable in interface org.biojava.bio.dp.StatePath
Alignment label for the state path.
states() - Method in interface org.biojava.bio.dp.DPMatrix
 
states() - Method in class org.biojava.bio.dp.PairDPMatrix
 
StaticAceNode - class org.acedb.staticobj.StaticAceNode.
 
StaticAceNode(String, AceSet) - Constructor for class org.acedb.staticobj.StaticAceNode
 
StaticAceNode(String, Map, AceSet) - Constructor for class org.acedb.staticobj.StaticAceNode
 
StaticAceObject - class org.acedb.staticobj.StaticAceObject.
 
StaticAceObject(String, AceSet, String) - Constructor for class org.acedb.staticobj.StaticAceObject
 
StaticAceSet - class org.acedb.staticobj.StaticAceSet.
 
StaticAceSet(AceSet, AceURL, String) - Constructor for class org.acedb.staticobj.StaticAceSet
 
StaticDateValue - class org.acedb.staticobj.StaticDateValue.
 
StaticDateValue(Date, AceNode) - Constructor for class org.acedb.staticobj.StaticDateValue
 
StaticFloatValue - class org.acedb.staticobj.StaticFloatValue.
 
StaticFloatValue(float, AceNode) - Constructor for class org.acedb.staticobj.StaticFloatValue
 
StaticIntValue - class org.acedb.staticobj.StaticIntValue.
 
StaticIntValue(int, AceNode) - Constructor for class org.acedb.staticobj.StaticIntValue
 
StaticMemberPlaceHolder - class org.biojava.utils.StaticMemberPlaceHolder.
 
StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
 
StaticModelInclude - class org.acedb.staticobj.StaticModelInclude.
 
StaticModelInclude(String, AceNode) - Constructor for class org.acedb.staticobj.StaticModelInclude
 
StaticModelNode - class org.acedb.staticobj.StaticModelNode.
 
StaticModelNode(String, AceNode) - Constructor for class org.acedb.staticobj.StaticModelNode
 
StaticModelReference - class org.acedb.staticobj.StaticModelReference.
 
StaticModelReference(String, AceNode) - Constructor for class org.acedb.staticobj.StaticModelReference
 
StaticModelType - class org.acedb.staticobj.StaticModelType.
 
StaticModelType(String, AceNode) - Constructor for class org.acedb.staticobj.StaticModelType
 
StaticReference - class org.acedb.staticobj.StaticReference.
 
StaticReference(String, AceNode, AceURL) - Constructor for class org.acedb.staticobj.StaticReference
 
StaticStringValue - class org.acedb.staticobj.StaticStringValue.
 
StaticStringValue(String, AceNode) - Constructor for class org.acedb.staticobj.StaticStringValue
 
StoppingCriteria - interface org.biojava.bio.dp.StoppingCriteria.
 
strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
 
strand() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
strand() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
strand() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
strand(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
strand(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
StrandedFeature - interface org.biojava.bio.seq.StrandedFeature.
Adds the concept of 'strand' to features.
StrandedFeature.Strand - class org.biojava.bio.seq.StrandedFeature.Strand.
Class to represent the 'strandedness' of a feature.
StrandedFeature.Template - class org.biojava.bio.seq.StrandedFeature.Template.
Template class for parameterizing the creation of a new StrandedFeature.
StrandedFeature.Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
 
streamEmpty() - Method in class org.biojava.bio.seq.io.StreamReader.Context
Signal that the stream contains no more sequence data.
StreamReader - class org.biojava.bio.seq.io.StreamReader.
Parses a stream into sequences.
StreamReader.Context - class org.biojava.bio.seq.io.StreamReader.Context.
Encapsulate a stream for reading sequence data.
StreamReader.Context(BufferedReader) - Constructor for class org.biojava.bio.seq.io.StreamReader.Context
 
StreamReader.Context(InputStream) - Constructor for class org.biojava.bio.seq.io.StreamReader.Context
 
StreamReader(BufferedReader, SequenceFormat, SymbolParser, SequenceFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
StreamReader(InputStream, SequenceFormat, SymbolParser, SequenceFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
 
StreamWriter - class org.biojava.bio.seq.io.StreamWriter.
Writes all of the sequences from a SequenceIterator to a stream with a particular format.
StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter
Generate a new StreamWriter to the stream os and using format.
stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord
Create a String representation of attMap.
stringListHelper - class org.Biocorba.Seqcore.stringListHelper.
 
stringListHolder - class org.Biocorba.Seqcore.stringListHolder.
 
stringListHolder() - Constructor for class org.Biocorba.Seqcore.stringListHolder
 
stringListHolder(String[]) - Constructor for class org.Biocorba.Seqcore.stringListHolder
 
StringValue - interface org.acedb.StringValue.
A string value.
subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subAlignment(Set, Location) - Method in interface org.biojava.bio.symbol.Alignment
Make a view onto this alignment.
subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.SimpleAlignment
 
subList(int, int) - Method in class org.acedb.seq.AceSequence
 
subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subList(int, int) - Method in class org.biojava.bio.seq.ViewSequence
 
subList(int, int) - Method in class org.biojava.bio.seq.SimpleSequence
 
subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
Return a new SymbolList for the symbols start to end inclusive.
subList(int, int) - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
subList(int, int) - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
subStr(int, int) - Method in class org.acedb.seq.AceSequence
 
subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
subStr(int, int) - Method in class org.biojava.bio.seq.ViewSequence
 
subStr(int, int) - Method in class org.biojava.bio.seq.SimpleSequence
 
subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
Return a region of this symbol list as a String.
subStr(int, int) - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
subStr(int, int) - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
SuffixTree - class org.biojava.bio.symbol.SuffixTree.
Suffix tree implementation.
SuffixTree.SuffixNode - class org.biojava.bio.symbol.SuffixTree.SuffixNode.
A node in the suffix tree.
SuffixTree.SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
 
SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree
Construct a new SuffixTree to contain motifs over the specified alphabet.
SuffixTreeKernel - class org.biojava.stats.svm.tools.SuffixTreeKernel.
Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.
SuffixTreeKernel.DepthScaler - interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler.
Encapsulates the scale factor to apply at a given depth.
SuffixTreeKernel.MultipleScalar - class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar.
Scale using a multiple of two DepthScalers.
SuffixTreeKernel.MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
 
SuffixTreeKernel.NullModelScaler - class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler.
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
SuffixTreeKernel.NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
 
SuffixTreeKernel.SelectionScalar - class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar.
Scale using a BitSet to allow/dissalow depths.
SuffixTreeKernel.SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
Make a new SelectionScalar that masks in different depths.
SuffixTreeKernel.UniformScaler - class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler.
Scale all depths by 1.0
SuffixTreeKernel.UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
 
SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel
 
suggested_size - Variable in class org.Biocorba.Seqcore.RequestTooLarge
 
SVM_Light - class org.biojava.stats.svm.tools.SVM_Light.
 
SVM_Light.LabelledVector - class org.biojava.stats.svm.tools.SVM_Light.LabelledVector.
 
SVM_Light.LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
SVM_Light.LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
 
SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
 
SVMClassifierModel - interface org.biojava.stats.svm.SVMClassifierModel.
An SVM classifier model.
SVMKernel - interface org.biojava.stats.svm.SVMKernel.
Kernel for support vector machines and related methods.
SVMRegressionModel - class org.biojava.stats.svm.SVMRegressionModel.
 
SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
 
SVMTarget - interface org.biojava.stats.svm.SVMTarget.
An SVM classifier model.
Symbol - interface org.biojava.bio.symbol.Symbol.
A single symbol.
symbolAt(int) - Method in class org.acedb.seq.AceSequence
 
symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(int) - Method in class org.biojava.bio.seq.ViewSequence
 
symbolAt(int) - Method in class org.biojava.bio.seq.SimpleSequence
 
symbolAt(int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
 
symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList
Return the symbol at index, counting from 1.
symbolAt(int) - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.ReverseSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
Find a symbol at a specified offset in the SymbolList.
symbolAt(int) - Method in class org.biojava.bio.symbol.TranslatedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.WindowedSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.OrderNSymbolList
 
symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleAlignment
 
symbolAt(int) - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
symbolAt(Object, int) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolAt(Object, int) - Method in interface org.biojava.bio.symbol.Alignment
Retrieve a symbol by label and column.
symbolAt(Object, int) - Method in class org.biojava.bio.symbol.SimpleAlignment
 
symbolForIndex(int) - Method in class org.biojava.bio.symbol.SuffixTree
Return the Symbol corresponding to a specified index number.
symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
Retrieve the symbol represented a String object
SymbolList - interface org.biojava.bio.symbol.SymbolList.
A sequence of symbols that belong to an alphabet.
SymbolList.EmptySymbolList - class org.biojava.bio.symbol.SymbolList.EmptySymbolList.
The empty immutable implementation.
SymbolList.EmptySymbolList() - Constructor for class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
SymbolListAdapter - class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter.
 
SymbolListAdapter(AnonymousSeq) - Constructor for class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
symbolListForLabel(Object) - Method in class org.biojava.bio.dp.SimpleStatePath
 
symbolListForLabel(Object) - Method in interface org.biojava.bio.symbol.Alignment
Retrieve a single row of the alignment by label.
symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.SimpleAlignment
 
SymbolParser - interface org.biojava.bio.symbol.SymbolParser.
These objects are responsible for converting strings into Symbols and SymbolLists.
symbols() - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
symbols() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
A list of symbols that make up this alphabet.
symbols() - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
symbols() - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
symbols() - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.PointLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.RangeLocation
 
symbols(SymbolList) - Method in class org.biojava.bio.symbol.CompoundLocation
 
symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location
Return the symbols in a sequence that fall within this range.
symbols(SymbolList) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
SymbolSequenceRenderer - class org.biojava.bio.gui.sequence.SymbolSequenceRenderer.
 
SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
 
SymbolStyle - interface org.biojava.bio.gui.SymbolStyle.
The interface for things that say how to paint a symbol.

T

t() - Static method in class org.biojava.bio.seq.DNATools
 
tanh(double) - Method in class org.biojava.stats.svm.SigmoidKernel
 
TextLogoPainter - class org.biojava.bio.gui.TextLogoPainter.
A logo painter that paints in stacked letters.
TextLogoPainter() - Constructor for class org.biojava.bio.gui.TextLogoPainter
 
to - Variable in class org.biojava.bio.dp.TrainerTransition
 
to - Variable in class org.biojava.bio.dp.Transition
 
toDate() - Method in class org.acedb.staticobj.StaticDateValue
 
toDate() - Method in interface org.acedb.DateValue
Get the value as a Java date.
toFloat() - Method in class org.acedb.staticobj.StaticFloatValue
 
toFloat() - Method in interface org.acedb.FloatValue
 
toInt() - Method in class org.acedb.staticobj.StaticIntValue
 
toInt() - Method in interface org.acedb.IntValue
 
TokenParser - class org.biojava.bio.symbol.TokenParser.
This uses symbol token to parse characters into Symbols.
TokenParser(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.TokenParser
Generate a new TokenParser for an alphabet.
toList() - Method in class org.acedb.seq.AceSequence
 
toList() - Method in class org.biojava.bio.dp.SimpleStatePath
 
toList() - Method in class org.biojava.bio.seq.ViewSequence
 
toList() - Method in class org.biojava.bio.seq.SimpleSequence
 
toList() - Method in class org.biojava.bio.symbol.AbstractSymbolList
 
toList() - Method in interface org.biojava.bio.symbol.SymbolList
Returns a List of symbols.
toList() - Method in class org.biojava.bio.symbol.SymbolList.EmptySymbolList
 
toList() - Method in class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
 
toList(String) - Static method in class org.acedb.AceUtils
 
toString() - Method in class org.acedb.staticobj.StaticStringValue
 
toString() - Method in class org.acedb.AceURL
 
toString() - Method in interface org.acedb.StringValue
 
toString() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
 
toString() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
 
toString() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
 
toString() - Method in class org.biojava.bio.symbol.SimpleSymbol
 
toString() - Method in class org.biojava.bio.symbol.RangeLocation
 
toString() - Method in class org.biojava.bio.symbol.CompoundLocation
 
toString() - Method in class org.biojava.bio.SimpleAnnotation
 
toString() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
 
toString() - Method in class org.biojava.stats.svm.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalCachingKernel
 
toString() - Method in class org.biojava.stats.svm.DiagonalAddKernel
 
toString() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
 
toString() - Method in class org.biojava.stats.svm.CachingKernel
 
toString() - Method in class org.biojava.stats.svm.PolynomialKernel
 
toString() - Method in class org.biojava.stats.svm.RadialBaseKernel
 
toString() - Method in class org.biojava.stats.svm.ListSumKernel
 
toString() - Method in class org.biojava.stats.svm.SigmoidKernel
 
toString() - Method in class org.biojava.utils.ParserException
Represent this exception as a string.
toString() - Method in class org.biojava.utils.TypedProperties
 
totalBits() - Method in class org.biojava.bio.gui.DistributionLogo
Retrieve the maximal number of bits possible for this type of dist.
totalInformation() - Method in class org.biojava.bio.gui.DistributionLogo
Calculates the total information of the dist in bits.
toURL() - Method in class org.acedb.staticobj.StaticAceNode
 
toURL() - Method in class org.acedb.staticobj.StaticAceSet
 
toURL() - Method in class org.acedb.socket.SocketResultSet
 
toURL() - Method in interface org.acedb.Database
Returns the url to the database.
toURL() - Method in interface org.acedb.AceSet
A URL that can be used to retrieve this set (assuming that the server will still be there when you try).
Train - class org.biojava.stats.svm.tools.Train.
 
train() - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
train() - Method in interface org.biojava.bio.dp.ModelTrainer
Trains up the transitions in this model with the counts so far.
Train() - Constructor for class org.biojava.stats.svm.tools.Train
 
train(Distribution, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
 
train(Distribution, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
 
train(Distribution, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
Trains the Distribution, given a null model.
train(double, double) - Method in class org.biojava.bio.dp.ModelView.ViewTransitionTrainer
 
train(double, double) - Method in class org.biojava.bio.dp.SimpleTransitionTrainer
 
train(double, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
Trains the transition, given an expected probability, and a weight for that probability.
train(SequenceDB, Distribution, double, StoppingCriteria) - Method in interface org.biojava.bio.dp.TrainingAlgorithm
Trains the sequences in db untill stopper says to finnish.
train(SequenceDB, Distribution, double, StoppingCriteria) - Method in class org.biojava.bio.dp.AbstractTrainer
Trains the sequences in db until stopper says to finnish.
Trainable - interface org.biojava.bio.dp.Trainable.
Flags an object as being able to register itself with a model trainer.
trainDistributions() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
 
trainDistributions() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
Trains the Distribution, given a null model.
trainer - Variable in class org.biojava.bio.dp.TrainerTransition
 
trainer - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
 
trainersForTransition(State, State) - Method in class org.biojava.bio.dp.SimpleModelTrainer
 
trainersForTransition(State, State) - Method in interface org.biojava.bio.dp.ModelTrainer
Retrieves a Set of TransitionTrainers associated with a transition between a pair of states.
TrainerTransition - class org.biojava.bio.dp.TrainerTransition.
This is a small and ugly class for storing a trainer and a transition.
TrainerTransition(TransitionTrainer, State, State) - Constructor for class org.biojava.bio.dp.TrainerTransition
 
TrainingAlgorithm - interface org.biojava.bio.dp.TrainingAlgorithm.
 
trainingComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingContext - interface org.biojava.stats.svm.TrainingContext.
 
trainingCycleComplete(TrainingEvent) - Method in interface org.biojava.stats.svm.TrainingListener
 
TrainingEvent - class org.biojava.stats.svm.TrainingEvent.
 
TrainingEvent(TrainingContext) - Constructor for class org.biojava.stats.svm.TrainingEvent
 
TrainingListener - interface org.biojava.stats.svm.TrainingListener.
 
trainModel(SVMRegressionModel, double[]) - Method in class org.biojava.stats.svm.SMORegressionTrainer
 
trainModel(SVMTarget, SVMKernel, TrainingListener) - Method in class org.biojava.stats.svm.SMOTrainer
 
TrainRegression - class org.biojava.stats.svm.tools.TrainRegression.
 
TrainRegression() - Constructor for class org.biojava.stats.svm.tools.TrainRegression
 
transact(String) - Method in interface org.acedb.Connection
Execute a command on an ACeDB database.
Transition - class org.biojava.bio.dp.Transition.
This is a small and ugly class for storing a transition.
Transition(State, State) - Constructor for class org.biojava.bio.dp.Transition
 
TransitionEvent - class org.biojava.bio.dp.TransitionEvent.
 
TransitionEvent(MarkovModel, State, State) - Constructor for class org.biojava.bio.dp.TransitionEvent
 
TransitionEvent(MarkovModel, State, State, double, double) - Constructor for class org.biojava.bio.dp.TransitionEvent
 
TransitionListener - interface org.biojava.bio.dp.TransitionListener.
 
transitionsFrom(State) - Method in class org.biojava.bio.dp.WMAsMM
 
transitionsFrom(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsFrom(State) - Method in class org.biojava.bio.dp.ModelView
 
transitionsFrom(State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns a Set of all legal transitions from a state.
transitionsTo(State) - Method in class org.biojava.bio.dp.WMAsMM
 
transitionsTo(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
 
transitionsTo(State) - Method in class org.biojava.bio.dp.ModelView
 
transitionsTo(State) - Method in interface org.biojava.bio.dp.MarkovModel
Returns a Set of all legal transitions to a state.
TransitionTrainer - interface org.biojava.bio.dp.TransitionTrainer.
An object that can be used to train the transitions within a MarkovModel.
translate(int) - Method in class org.biojava.bio.symbol.PointLocation
 
translate(int) - Method in class org.biojava.bio.symbol.RangeLocation
 
translate(int) - Method in class org.biojava.bio.symbol.CompoundLocation
 
translate(int) - Method in interface org.biojava.bio.symbol.Location
Create a location that is a translation of this location.
translate(int) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
Translate a single symbol from source alphabet to the target alphabet.
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
 
TranslatedSymbolList - class org.biojava.bio.symbol.TranslatedSymbolList.
Provides a 'translated' view of an underlying SymbolList.
TranslatedSymbolList(SymbolList, TranslationTable) - Constructor for class org.biojava.bio.symbol.TranslatedSymbolList
 
TranslationTable - interface org.biojava.bio.symbol.TranslationTable.
Encapsulates the mapping from a source to a destination alphabet.
type - Variable in class org.biojava.bio.seq.Feature.Template
 
type() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
type() - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
type() - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
type() - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
type() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
type() - Method in interface org.Biocorba.Seqcore.SeqFeature
 
type() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
type() - Static method in class org.Biocorba.Seqcore.SeqHelper
 
type() - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
type() - Static method in class org.Biocorba.Seqcore.stringListHelper
 
type() - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
type() - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
type() - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
type() - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
type() - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
type() - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
type() - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
type() - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
type() - Method in interface org.Biocorba.Seqcore.AnonymousSeq
 
type() - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
type() - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
type() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
type() - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
type() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
type() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
type() - Method in class org.Biocorba.Seqcore._SeqStub
 
type() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
type() - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
type() - Static method in class GNOME.UnknownHelper
 
type(ObjectImpl) - Method in interface org.Biocorba.Seqcore._SeqFeature_Operations
 
type(ObjectImpl) - Method in interface org.Biocorba.Seqcore._AnonymousSeq_Operations
 
type(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
 
type(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.SeqFeatureImpl
 
TypedProperties - class org.biojava.utils.TypedProperties.
a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an objcet of type XXX.
TypedProperties() - Constructor for class org.biojava.utils.TypedProperties
Creates an empty property list with no default values.
TypedProperties(Properties) - Constructor for class org.biojava.utils.TypedProperties
Creates an empty property list with the specified defaults.

U

UnableToProcess - exception org.Biocorba.Seqcore.UnableToProcess.
 
UnableToProcess() - Constructor for class org.Biocorba.Seqcore.UnableToProcess
 
UnableToProcess(String) - Constructor for class org.Biocorba.Seqcore.UnableToProcess
 
UnableToProcessHelper - class org.Biocorba.Seqcore.UnableToProcessHelper.
 
UnableToProcessHolder - class org.Biocorba.Seqcore.UnableToProcessHolder.
 
UnableToProcessHolder() - Constructor for class org.Biocorba.Seqcore.UnableToProcessHolder
 
UnableToProcessHolder(UnableToProcess) - Constructor for class org.Biocorba.Seqcore.UnableToProcessHolder
 
UniformDistribution - class org.biojava.bio.dist.UniformDistribution.
An implementation of an uniform distribution
UniformDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.UniformDistribution
 
union(Location) - Method in class org.biojava.bio.symbol.PointLocation
 
union(Location) - Method in class org.biojava.bio.symbol.RangeLocation
 
union(Location) - Method in class org.biojava.bio.symbol.CompoundLocation
 
union(Location) - Method in interface org.biojava.bio.symbol.Location
Return a Loctaion containing all points in either ranges.
union(Location) - Method in class org.biojava.bio.symbol.Location.EmptyLocation
 
UNIVERSAL - Static variable in class org.biojava.bio.seq.GeneticCode
The UNIVERSAL genetic code - used by most organisms for their primary genome.
Unknown - interface GNOME.Unknown.
 
UNKNOWN - Static variable in interface org.biojava.bio.seq.StrandedFeature
flag to indicate that a feature has an unknown strand.
UnknownHelper - class GNOME.UnknownHelper.
 
UnknownHolder - class GNOME.UnknownHolder.
 
UnknownHolder() - Constructor for class GNOME.UnknownHolder
 
UnknownHolder(Unknown) - Constructor for class GNOME.UnknownHolder
 
UnknownImpl - class org.biojava.bridge.GNOME.UnknownImpl.
 
UnknownImpl() - Constructor for class org.biojava.bridge.GNOME.UnknownImpl
 
unlockModel() - Method in class org.biojava.bio.dp.DP
 
unref() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
unref() - Method in class org.Biocorba.Seqcore._SeqDB_Tie
 
unref() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
unref() - Method in class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
unref() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
unref() - Method in class org.Biocorba.Seqcore._SeqFeature_Tie
 
unref() - Method in class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
unref() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
unref() - Method in class org.Biocorba.Seqcore._SeqStub
 
unref() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
unref() - Method in class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
unref() - Method in interface GNOME.Unknown
 
unref() - Method in class GNOME._UnknownStub
 
unref() - Method in class GNOME._Unknown_Tie
 
unref(ObjectImpl) - Method in class org.biojava.bridge.GNOME.UnknownImpl
I think that this should release the object from the server when no clients are referencing it.
unref(ObjectImpl) - Method in interface GNOME._Unknown_Operations
 
updateTransitions() - Method in class org.biojava.bio.dp.DP
 
updateTransitions() - Method in class org.biojava.bio.dp.PairwiseDP
 

V

validate(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
 
validate(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet.
validate(Symbol) - Method in class org.biojava.bio.symbol.Alphabet.EmptyAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
 
validate(Symbol) - Method in class org.biojava.bio.symbol.AllTokensAlphabet
 
value - Variable in class org.Biocorba.Seqcore.UnableToProcessHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
value - Variable in class org.Biocorba.Seqcore.EndOfStreamHolder
 
value - Variable in class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
value - Variable in class org.Biocorba.Seqcore.AnonymousSeqHolder
 
value - Variable in class org.Biocorba.Seqcore.primaryidListHolder
 
value - Variable in class org.Biocorba.Seqcore.PrimarySeqHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqFeatureListHolder
 
value - Variable in class org.Biocorba.Seqcore.RequestTooLargeHolder
 
value - Variable in class org.Biocorba.Seqcore.NameValueSetHolder
 
value - Variable in class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqTypeHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqDBHolder
 
value - Variable in class org.Biocorba.Seqcore.OutOfRangeHolder
 
value - Variable in class org.Biocorba.Seqcore.SeqFeatureHolder
 
value - Variable in class org.Biocorba.Seqcore.stringListHolder
 
value - Variable in class org.Biocorba.Seqcore.NameValueSetListHolder
 
value - Variable in class GNOME.UnknownHolder
 
value() - Method in class org.Biocorba.Seqcore.SeqType
 
values - Variable in class org.Biocorba.Seqcore.NameValueSet
 
vectorToString(SparseVector) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
version() - Method in class org.Biocorba.Seqcore._Seq_Tie
 
version() - Method in class org.Biocorba.Seqcore._PrimarySeq_Tie
 
version() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
version() - Method in interface org.Biocorba.Seqcore.PrimarySeq
 
version() - Method in class org.Biocorba.Seqcore._SeqStub
 
version(ObjectImpl) - Method in interface org.Biocorba.Seqcore._PrimarySeq_Operations
 
version(ObjectImpl) - Method in class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
 
ViewSequence - class org.biojava.bio.seq.ViewSequence.
A view onto another Sequence object.
ViewSequence(Sequence) - Constructor for class org.biojava.bio.seq.ViewSequence
Construct a view onto an existing sequence.
ViewSequence(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.ViewSequence
Construct a view onto a sequence, using a specific FeatureRealizer
viewToSource(GappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from view to source.
viewToSource(int) - Method in class org.biojava.bio.symbol.GappedSymbolList
Coordinate conversion from view to source.
viterbi(SymbolList[]) - Method in class org.biojava.bio.dp.DP
 
viterbi(SymbolList[]) - Method in class org.biojava.bio.dp.PairwiseDP
 

W

WeightMatrix - interface org.biojava.bio.dp.WeightMatrix.
A log odds weight matrix.
WeightMatrixAnnotator - class org.biojava.bio.dp.WeightMatrixAnnotator.
Annotates a sequence with hits to a weight-matrix.
WeightMatrixAnnotator(WeightMatrix, double) - Constructor for class org.biojava.bio.dp.WeightMatrixAnnotator
 
WindowedSymbolList - class org.biojava.bio.symbol.WindowedSymbolList.
A view of windows onto another SymbolList.
WindowedSymbolList(SymbolList, int) - Constructor for class org.biojava.bio.symbol.WindowedSymbolList
Create a WindowedSymbolList with the given window width.
WMAsMM - class org.biojava.bio.dp.WMAsMM.
Wraps a weight matrix up so that it appears to be a very simple hmm.
WMAsMM(WeightMatrix) - Constructor for class org.biojava.bio.dp.WMAsMM
 
write(OutputStream, AnonymousSeq) - Static method in class org.Biocorba.Seqcore.AnonymousSeqHelper
 
write(OutputStream, EndOfStream) - Static method in class org.Biocorba.Seqcore.EndOfStreamHelper
 
write(OutputStream, NameValueSet) - Static method in class org.Biocorba.Seqcore.NameValueSetHelper
 
write(OutputStream, NameValueSet[]) - Static method in class org.Biocorba.Seqcore.NameValueSetListHelper
 
write(OutputStream, OutOfRange) - Static method in class org.Biocorba.Seqcore.OutOfRangeHelper
 
write(OutputStream, PrimarySeq) - Static method in class org.Biocorba.Seqcore.PrimarySeqHelper
 
write(OutputStream, PrimarySeqDB) - Static method in class org.Biocorba.Seqcore.PrimarySeqDBHelper
 
write(OutputStream, PrimarySeqIterator) - Static method in class org.Biocorba.Seqcore.PrimarySeqIteratorHelper
 
write(OutputStream, RequestTooLarge) - Static method in class org.Biocorba.Seqcore.RequestTooLargeHelper
 
write(OutputStream, Seq) - Static method in class org.Biocorba.Seqcore.SeqHelper
 
write(OutputStream, SeqDB) - Static method in class org.Biocorba.Seqcore.SeqDBHelper
 
write(OutputStream, SeqFeature) - Static method in class org.Biocorba.Seqcore.SeqFeatureHelper
 
write(OutputStream, SeqFeature[]) - Static method in class org.Biocorba.Seqcore.SeqFeatureListHelper
 
write(OutputStream, SeqFeatureIterator) - Static method in class org.Biocorba.Seqcore.SeqFeatureIteratorHelper
 
write(OutputStream, SeqType) - Static method in class org.Biocorba.Seqcore.SeqTypeHelper
 
write(OutputStream, String[]) - Static method in class org.Biocorba.Seqcore.stringListHelper
 
write(OutputStream, String[]) - Static method in class org.Biocorba.Seqcore.primaryidListHelper
 
write(OutputStream, UnableToProcess) - Static method in class org.Biocorba.Seqcore.UnableToProcessHelper
 
write(OutputStream, Unknown) - Static method in class GNOME.UnknownHelper
 
writeDescription(Sequence) - Method in interface org.biojava.bio.seq.io.FastaDescriptionReader
Write the description for a sequence.
writeDescription(Sequence) - Method in class org.biojava.bio.seq.io.DefaultDescriptionReader
 
writeMatrix(WeightMatrix, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModel(MarkovModel, PrintStream) - Static method in class org.biojava.bio.dp.XmlMarkovModel
 
writeModelFile(SVMClassifierModel, String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
 
writeSequence(Sequence, PrintStream) - Method in interface org.biojava.bio.seq.io.SequenceFormat
Write out a sequence to the specified printstream
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.EmblFormat
This is not implemented.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFormat
This is not implemented.
writeSequence(Sequence, PrintStream) - Method in class org.biojava.bio.seq.io.FastaFormat
 
writeStream(SequenceIterator) - Method in class org.biojava.bio.seq.io.StreamWriter
Write each of the sequences in ss to the stream in the given format.

X

XMLDispatcher - class org.biojava.utils.xml.XMLDispatcher.
Simple implemntation of XMLPeerFactory which delegates object- construction on the basis of tag name.
XMLDispatcher() - Constructor for class org.biojava.utils.xml.XMLDispatcher
Construct a new XMLDispatcher which does not know about any tag names.
XmlMarkovModel - class org.biojava.bio.dp.XmlMarkovModel.
 
XmlMarkovModel() - Constructor for class org.biojava.bio.dp.XmlMarkovModel
 
XMLPeerBuilder - class org.biojava.utils.xml.XMLPeerBuilder.
SAX DocumentHandler which uses an XMLPeerFactory to construct Java objects reflecting an XML document.
XMLPeerBuilder(XMLPeerFactory) - Constructor for class org.biojava.utils.xml.XMLPeerBuilder
Construct a new XMLPeerBuilder, using the specified XMLPeerFactory
XMLPeerFactory - interface org.biojava.utils.xml.XMLPeerFactory.
Interface to an factory which produces Java objects which reflect element in an XML document.

_

_AnonymousSeq_Operations - interface org.Biocorba.Seqcore._AnonymousSeq_Operations.
 
_AnonymousSeq_Tie - class org.Biocorba.Seqcore._AnonymousSeq_Tie.
 
_AnonymousSeq_Tie(_AnonymousSeq_Operations) - Constructor for class org.Biocorba.Seqcore._AnonymousSeq_Tie
 
_AnonymousSeqImplBase - class org.Biocorba.Seqcore._AnonymousSeqImplBase.
 
_AnonymousSeqImplBase() - Constructor for class org.Biocorba.Seqcore._AnonymousSeqImplBase
 
_AnonymousSeqStub - class org.Biocorba.Seqcore._AnonymousSeqStub.
 
_AnonymousSeqStub(Delegate) - Constructor for class org.Biocorba.Seqcore._AnonymousSeqStub
 
_DNA - Static variable in class org.Biocorba.Seqcore.SeqType
 
_ids() - Method in class org.Biocorba.Seqcore._SeqImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqDBImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqDBStub
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqStub
 
_ids() - Method in class org.Biocorba.Seqcore._SeqDBImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._SeqDBStub
 
_ids() - Method in class org.Biocorba.Seqcore._SeqFeatureImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._AnonymousSeqImplBase
 
_ids() - Method in class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
_ids() - Method in class org.Biocorba.Seqcore._SeqFeatureStub
 
_ids() - Method in class org.Biocorba.Seqcore._SeqStub
 
_ids() - Method in class org.Biocorba.Seqcore._AnonymousSeqStub
 
_ids() - Method in class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase
 
_ids() - Method in class GNOME._UnknownStub
 
_ids() - Method in class GNOME._UnknownImplBase
 
_PrimarySeq_Operations - interface org.Biocorba.Seqcore._PrimarySeq_Operations.
 
_PrimarySeq_Tie - class org.Biocorba.Seqcore._PrimarySeq_Tie.
 
_PrimarySeq_Tie(_PrimarySeq_Operations) - Constructor for class org.Biocorba.Seqcore._PrimarySeq_Tie
 
_PrimarySeqDB_Operations - interface org.Biocorba.Seqcore._PrimarySeqDB_Operations.
 
_PrimarySeqDB_Tie - class org.Biocorba.Seqcore._PrimarySeqDB_Tie.
 
_PrimarySeqDB_Tie(_PrimarySeqDB_Operations) - Constructor for class org.Biocorba.Seqcore._PrimarySeqDB_Tie
 
_PrimarySeqDBImplBase - class org.Biocorba.Seqcore._PrimarySeqDBImplBase.
 
_PrimarySeqDBImplBase() - Constructor for class org.Biocorba.Seqcore._PrimarySeqDBImplBase
 
_PrimarySeqDBStub - class org.Biocorba.Seqcore._PrimarySeqDBStub.
 
_PrimarySeqDBStub(Delegate) - Constructor for class org.Biocorba.Seqcore._PrimarySeqDBStub
 
_PrimarySeqImplBase - class org.Biocorba.Seqcore._PrimarySeqImplBase.
 
_PrimarySeqImplBase() - Constructor for class org.Biocorba.Seqcore._PrimarySeqImplBase
 
_PrimarySeqIterator_Operations - interface org.Biocorba.Seqcore._PrimarySeqIterator_Operations.
 
_PrimarySeqIterator_Tie - class org.Biocorba.Seqcore._PrimarySeqIterator_Tie.
 
_PrimarySeqIterator_Tie(_PrimarySeqIterator_Operations) - Constructor for class org.Biocorba.Seqcore._PrimarySeqIterator_Tie
 
_PrimarySeqIteratorImplBase - class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase.
 
_PrimarySeqIteratorImplBase() - Constructor for class org.Biocorba.Seqcore._PrimarySeqIteratorImplBase
 
_PrimarySeqIteratorStub - class org.Biocorba.Seqcore._PrimarySeqIteratorStub.
 
_PrimarySeqIteratorStub(Delegate) - Constructor for class org.Biocorba.Seqcore._PrimarySeqIteratorStub
 
_PrimarySeqStub - class org.Biocorba.Seqcore._PrimarySeqStub.
 
_PrimarySeqStub(Delegate) - Constructor for class org.Biocorba.Seqcore._PrimarySeqStub
 
_PROTEIN - Static variable in class org.Biocorba.Seqcore.SeqType
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.UnableToProcessHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.EndOfStreamHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.AnonymousSeqHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.primaryidListHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureListHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.RequestTooLargeHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.NameValueSetHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqTypeHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqDBHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.OutOfRangeHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.stringListHolder
 
_read(InputStream) - Method in class org.Biocorba.Seqcore.NameValueSetListHolder
 
_read(InputStream) - Method in class GNOME.UnknownHolder
 
_RNA - Static variable in class org.Biocorba.Seqcore.SeqType
 
_Seq_Operations - interface org.Biocorba.Seqcore._Seq_Operations.
 
_Seq_Tie - class org.Biocorba.Seqcore._Seq_Tie.
 
_Seq_Tie(_Seq_Operations) - Constructor for class org.Biocorba.Seqcore._Seq_Tie
 
_SeqDB_Operations - interface org.Biocorba.Seqcore._SeqDB_Operations.
 
_SeqDB_Tie - class org.Biocorba.Seqcore._SeqDB_Tie.
 
_SeqDB_Tie(_SeqDB_Operations) - Constructor for class org.Biocorba.Seqcore._SeqDB_Tie
 
_SeqDBImplBase - class org.Biocorba.Seqcore._SeqDBImplBase.
 
_SeqDBImplBase() - Constructor for class org.Biocorba.Seqcore._SeqDBImplBase
 
_SeqDBStub - class org.Biocorba.Seqcore._SeqDBStub.
 
_SeqDBStub(Delegate) - Constructor for class org.Biocorba.Seqcore._SeqDBStub
 
_SeqFeature_Operations - interface org.Biocorba.Seqcore._SeqFeature_Operations.
 
_SeqFeature_Tie - class org.Biocorba.Seqcore._SeqFeature_Tie.
 
_SeqFeature_Tie(_SeqFeature_Operations) - Constructor for class org.Biocorba.Seqcore._SeqFeature_Tie
 
_SeqFeatureImplBase - class org.Biocorba.Seqcore._SeqFeatureImplBase.
 
_SeqFeatureImplBase() - Constructor for class org.Biocorba.Seqcore._SeqFeatureImplBase
 
_SeqFeatureIterator_Operations - interface org.Biocorba.Seqcore._SeqFeatureIterator_Operations.
 
_SeqFeatureIterator_Tie - class org.Biocorba.Seqcore._SeqFeatureIterator_Tie.
 
_SeqFeatureIterator_Tie(_SeqFeatureIterator_Operations) - Constructor for class org.Biocorba.Seqcore._SeqFeatureIterator_Tie
 
_SeqFeatureIteratorImplBase - class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase.
 
_SeqFeatureIteratorImplBase() - Constructor for class org.Biocorba.Seqcore._SeqFeatureIteratorImplBase
 
_SeqFeatureIteratorStub - class org.Biocorba.Seqcore._SeqFeatureIteratorStub.
 
_SeqFeatureIteratorStub(Delegate) - Constructor for class org.Biocorba.Seqcore._SeqFeatureIteratorStub
 
_SeqFeatureStub - class org.Biocorba.Seqcore._SeqFeatureStub.
 
_SeqFeatureStub(Delegate) - Constructor for class org.Biocorba.Seqcore._SeqFeatureStub
 
_SeqImplBase - class org.Biocorba.Seqcore._SeqImplBase.
 
_SeqImplBase() - Constructor for class org.Biocorba.Seqcore._SeqImplBase
 
_SeqStub - class org.Biocorba.Seqcore._SeqStub.
 
_SeqStub(Delegate) - Constructor for class org.Biocorba.Seqcore._SeqStub
 
_type() - Method in class org.Biocorba.Seqcore.UnableToProcessHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
_type() - Method in class org.Biocorba.Seqcore.EndOfStreamHolder
 
_type() - Method in class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
_type() - Method in class org.Biocorba.Seqcore.AnonymousSeqHolder
 
_type() - Method in class org.Biocorba.Seqcore.primaryidListHolder
 
_type() - Method in class org.Biocorba.Seqcore.PrimarySeqHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqFeatureListHolder
 
_type() - Method in class org.Biocorba.Seqcore.RequestTooLargeHolder
 
_type() - Method in class org.Biocorba.Seqcore.NameValueSetHolder
 
_type() - Method in class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqTypeHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqDBHolder
 
_type() - Method in class org.Biocorba.Seqcore.OutOfRangeHolder
 
_type() - Method in class org.Biocorba.Seqcore.SeqFeatureHolder
 
_type() - Method in class org.Biocorba.Seqcore.stringListHolder
 
_type() - Method in class org.Biocorba.Seqcore.NameValueSetListHolder
 
_type() - Method in class GNOME.UnknownHolder
 
_Unknown_Operations - interface GNOME._Unknown_Operations.
 
_Unknown_Tie - class GNOME._Unknown_Tie.
 
_Unknown_Tie(_Unknown_Operations) - Constructor for class GNOME._Unknown_Tie
 
_UnknownImplBase - class GNOME._UnknownImplBase.
 
_UnknownImplBase() - Constructor for class GNOME._UnknownImplBase
 
_UnknownStub - class GNOME._UnknownStub.
 
_UnknownStub(Delegate) - Constructor for class GNOME._UnknownStub
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.UnableToProcessHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureIteratorHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.EndOfStreamHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqDBHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.AnonymousSeqHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.primaryidListHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureListHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.RequestTooLargeHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.NameValueSetHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.PrimarySeqIteratorHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqTypeHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqDBHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.OutOfRangeHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.SeqFeatureHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.stringListHolder
 
_write(OutputStream) - Method in class org.Biocorba.Seqcore.NameValueSetListHolder
 
_write(OutputStream) - Method in class GNOME.UnknownHolder
 

A B C D E F G H I K L M N O P Q R S T U V W X _