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 _