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Hierarchy For All Packages
Package Hierarchies:
GNOME
,
org.acedb
,
org.acedb.seq
,
org.acedb.socket
,
org.acedb.staticobj
,
org.Biocorba.Seqcore
,
org.biojava.bio
,
org.biojava.bio.dist
,
org.biojava.bio.dp
,
org.biojava.bio.gui
,
org.biojava.bio.gui.sequence
,
org.biojava.bio.program
,
org.biojava.bio.program.gff
,
org.biojava.bio.search
,
org.biojava.bio.seq
,
org.biojava.bio.seq.db
,
org.biojava.bio.seq.io
,
org.biojava.bio.symbol
,
org.biojava.bridge.Biocorba.Seqcore
,
org.biojava.bridge.GNOME
,
org.biojava.stats.svm
,
org.biojava.stats.svm.tools
,
org.biojava.utils
,
org.biojava.utils.contract
,
org.biojava.utils.xml
Class Hierarchy
class java.lang.Object
class org.biojava.bio.symbol.
AbstractAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
)
class org.biojava.bio.symbol.
SimpleAlphabet
(implements java.io.Serializable)
class org.biojava.bio.dist.
AbstractDistribution
(implements org.biojava.bio.dist.
Distribution
)
class org.biojava.bio.dist.
DNADistribution
(implements java.io.Serializable)
class org.biojava.bio.dist.
PairDistribution
(implements java.io.Serializable)
class org.biojava.bio.dist.
SimpleDistribution
(implements java.io.Serializable)
class org.biojava.bio.dist.
UniformDistribution
(implements java.io.Serializable)
class org.biojava.bio.seq.
AbstractFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
)
class org.biojava.bio.seq.
MergeFeatureHolder
class org.biojava.bio.seq.
SimpleFeatureHolder
class org.biojava.stats.svm.
AbstractSVMClassifierModel
(implements org.biojava.stats.svm.
SVMClassifierModel
)
class org.biojava.stats.svm.
SimpleSVMClassifierModel
class org.biojava.stats.svm.
AbstractSVMTarget
(implements org.biojava.stats.svm.
SVMTarget
)
class org.biojava.bio.symbol.
AbstractSymbolList
(implements org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bio.symbol.
GappedSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
OrderNSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
ReverseSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
SimpleAlignment
(implements org.biojava.bio.symbol.
Alignment
, java.io.Serializable)
class org.biojava.bio.symbol.
SimpleSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
TranslatedSymbolList
(implements org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bio.symbol.
WindowedSymbolList
(implements java.io.Serializable)
class org.biojava.bio.dp.
AbstractTrainer
(implements org.biojava.bio.dp.
TrainingAlgorithm
)
class org.biojava.bio.dp.
BaumWelchSampler
(implements java.io.Serializable)
class org.biojava.bio.dp.
BaumWelchTrainer
(implements java.io.Serializable)
class org.acedb.
Ace
class org.acedb.seq.
AceAnnotation
(implements org.biojava.bio.
Annotation
)
class org.acedb.
AcePerlParser
class org.acedb.seq.
AceSequence
(implements org.biojava.bio.seq.
Sequence
)
class org.acedb.seq.
AceSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.acedb.
AceURL
class org.acedb.
AceUtils
class org.biojava.bio.symbol.
AllTokensAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
Alphabet.EmptyAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
AlphabetManager
class org.biojava.bio.symbol.
AlphabetManager.ListWrapper
class org.biojava.bio.seq.db.
AnnotatedSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.
Annotation.EmptyAnnotation
(implements org.biojava.bio.
Annotation
, java.io.Serializable)
class org.Biocorba.Seqcore.
AnonymousSeqHelper
class org.Biocorba.Seqcore.
AnonymousSeqHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bio.gui.
BarLogoPainter
(implements org.biojava.bio.gui.
LogoPainter
)
class org.biojava.bio.gui.sequence.
BasicFeatureRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
)
class org.biojava.bio.seq.db.
CachingSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.stats.svm.tools.
ClassifierExample
class org.biojava.stats.svm.tools.
Classify
class org.biojava.bio.dist.
ComplementaryDistribution
(implements org.biojava.bio.dist.
Distribution
, java.io.Serializable)
class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
class java.awt.Container
class javax.swing.JComponent (implements java.io.Serializable)
class org.biojava.stats.svm.tools.
ClassifierExample.PointClassifier
class org.biojava.bio.gui.
DistributionLogo
class org.biojava.bio.gui.
SequencePanel
(implements javax.swing.SwingConstants)
class org.biojava.bio.symbol.
CompoundLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.biojava.utils.contract.
Contract
class org.biojava.bio.symbol.
CrossProductSymbolNameParser
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolParser
)
class org.biojava.bio.seq.io.
DefaultDescriptionReader
(implements org.biojava.bio.seq.io.
FastaDescriptionReader
, java.io.Serializable)
class java.util.Dictionary
class java.util.Hashtable (implements java.lang.Cloneable, java.util.Map, java.io.Serializable)
class java.util.Properties
class org.biojava.utils.
TypedProperties
class org.biojava.bio.dist.
DistributionFactory.DefaultDistributionFactory
(implements org.biojava.bio.dist.
DistributionFactory
, java.io.Serializable)
class org.biojava.bio.gui.
DNAStyle
(implements org.biojava.bio.gui.
SymbolStyle
)
class org.biojava.bio.seq.
DNATools
class org.biojava.bio.symbol.
DoubleAlphabet
(implements org.biojava.bio.symbol.
Alphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
DoubleAlphabet.DoubleSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
, java.io.Serializable)
class org.biojava.bio.dp.
DP
class org.biojava.bio.dp.
PairwiseDP
(implements java.io.Serializable)
class org.biojava.bio.dp.
DP.ReverseIterator
(implements java.util.Iterator, java.io.Serializable)
class org.biojava.bio.dp.
DPFactory
class org.biojava.bio.seq.io.
EmblFormat
(implements org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.Biocorba.Seqcore.
EndOfStreamHelper
class org.Biocorba.Seqcore.
EndOfStreamHolder
(implements org.omg.CORBA.portable.Streamable)
class java.util.EventObject (implements java.io.Serializable)
class org.biojava.bio.dp.
ModelChangeEvent
class org.biojava.bio.dp.
TransitionEvent
class org.biojava.stats.svm.
TrainingEvent
class org.biojava.bio.seq.io.
FastaFormat
(implements org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.bio.seq.
Feature.Template
(implements java.io.Serializable)
class org.biojava.bio.seq.
StrandedFeature.Template
class org.biojava.bridge.Biocorba.Seqcore.
FeatureAdapter
(implements org.biojava.bio.seq.
Feature
)
class org.biojava.bio.gui.sequence.
FeatureBlockSequenceRenderer
(implements java.beans.PropertyChangeListener, org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.seq.
FeatureFilter.AcceptAllFilter
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.And
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.BySource
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByType
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.ContainedByLocation
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.Not
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.Or
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.OverlapsLocation
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureHolder.EmptyFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
)
class org.biojava.bio.symbol.
FixedWidthParser
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolParser
)
class org.biojava.bio.dist.
GapDistribution
(implements org.biojava.bio.dist.
Distribution
)
class org.biojava.bio.seq.io.
GenbankFormat
(implements org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.bio.seq.
GeneticCode
class org.biojava.bio.program.gff.
GFFEntrySet
class org.biojava.bio.program.gff.
GFFErrorHandler.AbortErrorHandler
(implements org.biojava.bio.program.gff.
GFFErrorHandler
)
class org.biojava.bio.program.gff.
GFFErrorHandler.SkipRecordErrorHandler
(implements org.biojava.bio.program.gff.
GFFErrorHandler
)
class org.biojava.bio.program.gff.
GFFFilterer
(implements org.biojava.bio.program.gff.
GFFDocumentHandler
)
class org.biojava.bio.program.gff.
GFFParser
class org.biojava.bio.program.gff.
GFFRecordFilter.AcceptAll
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFRecordFilter.FeatureFilter
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFRecordFilter.SequenceFilter
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFRecordFilter.SourceFilter
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFWriter
(implements org.biojava.bio.program.gff.
GFFDocumentHandler
)
class org.biojava.bio.seq.db.
HashSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.seq.db.
IDMaker.ByName
(implements org.biojava.bio.seq.db.
IDMaker
, java.io.Serializable)
class org.biojava.bio.seq.db.
IDMaker.ByURN
(implements org.biojava.bio.seq.db.
IDMaker
, java.io.Serializable)
class org.biojava.bio.dist.
IgnoreCountsTrainer
(implements org.biojava.bio.dist.
DistributionTrainer
)
class org.biojava.bio.seq.db.
IndexedSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.symbol.
IntegerAlphabet
(implements org.biojava.bio.symbol.
Alphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
IntegerAlphabet.IntegerSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
, java.io.Serializable)
class org.biojava.stats.svm.
LinearKernel
(implements java.io.Serializable, org.biojava.stats.svm.
SVMKernel
)
class org.biojava.bio.symbol.
Location.EmptyLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.biojava.bio.symbol.
Location.LocationComparator
(implements java.util.Comparator, java.io.Serializable)
class org.biojava.bio.program.
Meme
class org.biojava.bio.dp.
ModelView
(implements org.biojava.bio.dp.
MarkovModel
)
class org.biojava.bio.dp.
ModelView.ViewTransitionTrainer
(implements java.io.Serializable, org.biojava.bio.dp.
TransitionTrainer
)
class org.biojava.bio.symbol.
NameParser
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolParser
)
class org.Biocorba.Seqcore.
NameValueSet
(implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
NameValueSetHelper
class org.Biocorba.Seqcore.
NameValueSetHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
NameValueSetListHelper
class org.Biocorba.Seqcore.
NameValueSetListHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.stats.svm.
NestedKernel
(implements java.io.Serializable, org.biojava.stats.svm.
SVMKernel
)
class org.biojava.stats.svm.
CachingKernel
class org.biojava.stats.svm.
DiagonalAddKernel
class org.biojava.stats.svm.
DiagonalCachingKernel
class org.biojava.stats.svm.
ListSumKernel
class org.biojava.stats.svm.
NormalizingKernel
class org.biojava.stats.svm.
PolynomialKernel
class org.biojava.stats.svm.
RadialBaseKernel
class org.omg.CORBA.portable.ObjectImpl (implements org.omg.CORBA.Object)
class org.Biocorba.Seqcore.
_AnonymousSeqStub
(implements org.Biocorba.Seqcore.
AnonymousSeq
)
class org.Biocorba.Seqcore.
_PrimarySeqDBStub
(implements org.Biocorba.Seqcore.
PrimarySeqDB
)
class org.Biocorba.Seqcore.
_PrimarySeqIteratorStub
(implements org.Biocorba.Seqcore.
PrimarySeqIterator
)
class org.Biocorba.Seqcore.
_PrimarySeqStub
(implements org.Biocorba.Seqcore.
PrimarySeq
)
class org.Biocorba.Seqcore.
_SeqDBStub
(implements org.Biocorba.Seqcore.
SeqDB
)
class org.Biocorba.Seqcore.
_SeqFeatureIteratorStub
(implements org.Biocorba.Seqcore.
SeqFeatureIterator
)
class org.Biocorba.Seqcore.
_SeqFeatureStub
(implements org.Biocorba.Seqcore.
SeqFeature
)
class org.Biocorba.Seqcore.
_SeqStub
(implements org.Biocorba.Seqcore.
Seq
)
class GNOME.
_UnknownStub
(implements GNOME.
Unknown
)
class org.omg.CORBA.DynamicImplementation
class org.Biocorba.Seqcore.
_AnonymousSeqImplBase
(implements org.Biocorba.Seqcore.
AnonymousSeq
)
class org.Biocorba.Seqcore.
_AnonymousSeq_Tie
class org.Biocorba.Seqcore.
_PrimarySeqDBImplBase
(implements org.Biocorba.Seqcore.
PrimarySeqDB
)
class org.Biocorba.Seqcore.
_PrimarySeqDB_Tie
class org.Biocorba.Seqcore.
_PrimarySeqImplBase
(implements org.Biocorba.Seqcore.
PrimarySeq
)
class org.Biocorba.Seqcore.
_PrimarySeq_Tie
class org.Biocorba.Seqcore.
_PrimarySeqIteratorImplBase
(implements org.Biocorba.Seqcore.
PrimarySeqIterator
)
class org.Biocorba.Seqcore.
_PrimarySeqIterator_Tie
class org.Biocorba.Seqcore.
_SeqDBImplBase
(implements org.Biocorba.Seqcore.
SeqDB
)
class org.Biocorba.Seqcore.
_SeqDB_Tie
class org.Biocorba.Seqcore.
_SeqFeatureImplBase
(implements org.Biocorba.Seqcore.
SeqFeature
)
class org.Biocorba.Seqcore.
_SeqFeature_Tie
class org.Biocorba.Seqcore.
_SeqFeatureIteratorImplBase
(implements org.Biocorba.Seqcore.
SeqFeatureIterator
)
class org.Biocorba.Seqcore.
_SeqFeatureIterator_Tie
class org.Biocorba.Seqcore.
_SeqImplBase
(implements org.Biocorba.Seqcore.
Seq
)
class org.Biocorba.Seqcore.
_Seq_Tie
class GNOME.
_UnknownImplBase
(implements GNOME.
Unknown
)
class GNOME.
_Unknown_Tie
class org.biojava.utils.
ObjectUtil
class org.Biocorba.Seqcore.
OutOfRangeHelper
class org.Biocorba.Seqcore.
OutOfRangeHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bio.
OverlayAnnotation
(implements org.biojava.bio.
Annotation
)
class org.biojava.bio.dp.
PairDPMatrix
(implements org.biojava.bio.dp.
DPMatrix
, java.io.Serializable)
class org.biojava.bio.gui.
PlainStyle
(implements org.biojava.bio.gui.
SymbolStyle
)
class org.biojava.bio.symbol.
PointLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.Biocorba.Seqcore.
primaryidListHelper
class org.Biocorba.Seqcore.
primaryidListHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
PrimarySeqDBHelper
class org.Biocorba.Seqcore.
PrimarySeqDBHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
PrimarySeqHelper
class org.Biocorba.Seqcore.
PrimarySeqHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
PrimarySeqIteratorHelper
class org.Biocorba.Seqcore.
PrimarySeqIteratorHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bio.seq.
ProteinTools
class org.biojava.bio.symbol.
RangeLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.Biocorba.Seqcore.
RequestTooLargeHelper
class org.Biocorba.Seqcore.
RequestTooLargeHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqDBHelper
class org.Biocorba.Seqcore.
SeqDBHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqFeatureHelper
class org.Biocorba.Seqcore.
SeqFeatureHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqFeatureIteratorHelper
class org.Biocorba.Seqcore.
SeqFeatureIteratorHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqFeatureListHelper
class org.Biocorba.Seqcore.
SeqFeatureListHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqHelper
class org.Biocorba.Seqcore.
SeqHolder
(implements org.omg.CORBA.portable.Streamable)
class org.Biocorba.Seqcore.
SeqType
(implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
SeqTypeHelper
class org.Biocorba.Seqcore.
SeqTypeHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bridge.Biocorba.Seqcore.
SequenceDBAdapter
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bridge.Biocorba.Seqcore.
SequenceIteratorAdapter
(implements org.biojava.bio.seq.
SequenceIterator
)
class org.biojava.bio.gui.
SequencePanel.Border
(implements java.io.Serializable, javax.swing.SwingConstants)
class org.biojava.bio.program.gff.
SequencesAsGFF
class org.biojava.stats.svm.
SigmoidKernel
(implements org.biojava.stats.svm.
SVMKernel
)
class org.biojava.bio.
SimpleAnnotation
(implements org.biojava.bio.
Annotation
, java.io.Serializable)
class org.biojava.bio.symbol.
SimpleAtomicSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
)
class org.biojava.bio.dp.
SimpleDotState
(implements org.biojava.bio.dp.
DotState
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleModelInState
(implements org.biojava.bio.dp.
ModelInState
)
class org.biojava.bio.dist.
SimpleDistributionTrainer
(implements org.biojava.bio.dist.
DistributionTrainer
, java.io.Serializable)
class org.biojava.bio.dist.
SimpleDistributionTrainerContext
(implements org.biojava.bio.dist.
DistributionTrainerContext
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleModelTrainer
(implements org.biojava.bio.dp.
ModelTrainer
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleEmissionState
(implements org.biojava.bio.dp.
EmissionState
, java.io.Serializable)
class org.biojava.bio.dp.
MagicalState
class org.biojava.bio.seq.io.
SimpleFeatureBuilder
(implements org.biojava.bio.seq.io.
FeatureBuilder
, java.io.Serializable)
class org.biojava.bio.seq.
SimpleFeatureRealizer
(implements org.biojava.bio.seq.
FeatureRealizer
, java.io.Serializable)
class org.biojava.bio.program.gff.
SimpleGFFRecord
(implements org.biojava.bio.program.gff.
GFFRecord
)
class org.biojava.stats.svm.
SimpleItemValue
(implements org.biojava.stats.svm.
ItemValue
)
class org.biojava.bio.dp.
SimpleMarkovModel
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.bio.dp.
ProfileHMM
class org.biojava.bio.search.
SimpleSeqSimilaritySearchHit
(implements java.lang.Cloneable, org.biojava.bio.search.
SeqSimilaritySearchHit
)
class org.biojava.bio.search.
SimpleSeqSimilaritySearchResult
(implements java.lang.Cloneable, org.biojava.bio.search.
SeqSimilaritySearchResult
)
class org.biojava.bio.search.
SimpleSeqSimilaritySearchSubHit
(implements java.lang.Cloneable, org.biojava.bio.search.
SeqSimilaritySearchSubHit
)
class org.biojava.bio.seq.
SimpleSequence
(implements org.biojava.bio.seq.
RealizingFeatureHolder
, org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.seq.db.
SimpleSequenceDBInstallation
(implements org.biojava.bio.seq.db.
SequenceDBInstallation
)
class org.biojava.bio.seq.
SimpleSequenceFactory
(implements org.biojava.bio.seq.
SequenceFactory
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleStatePath
(implements java.io.Serializable, org.biojava.bio.dp.
StatePath
)
class org.biojava.stats.svm.
SimpleSVMTarget
(implements org.biojava.stats.svm.
SVMTarget
)
class org.biojava.bio.symbol.
SimpleSymbol
(implements java.io.Serializable, org.biojava.bio.symbol.
Symbol
)
class org.biojava.bio.gui.
SimpleSymbolStyle
(implements org.biojava.bio.gui.
SymbolStyle
)
class org.biojava.bio.dp.
SimpleTransitionTrainer
(implements java.io.Serializable, org.biojava.bio.dp.
TransitionTrainer
)
class org.biojava.bio.symbol.
SimpleTranslationTable
(implements java.io.Serializable, org.biojava.bio.symbol.
TranslationTable
)
class org.biojava.bio.dp.
SimpleWeightMatrix
(implements java.io.Serializable, org.biojava.bio.dp.
WeightMatrix
)
class org.biojava.bio.symbol.
SingletonAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
, java.io.Serializable)
class org.biojava.stats.svm.
SMORegressionTrainer
class org.biojava.stats.svm.
SMOTrainer
class org.acedb.socket.
SocketDriver
(implements org.acedb.
Driver
)
class org.acedb.socket.
SocketResultSet
(implements org.acedb.
AceSet
)
class org.biojava.stats.svm.
SparseVector
(implements java.io.Serializable)
class org.biojava.stats.svm.
SparseVector.NormalizingKernel
(implements java.io.Serializable, org.biojava.stats.svm.
SVMKernel
)
class org.acedb.staticobj.
StaticAceNode
(implements org.acedb.
AceNode
)
class org.acedb.staticobj.
StaticAceObject
(implements org.acedb.
AceObject
)
class org.acedb.staticobj.
StaticDateValue
(implements org.acedb.
DateValue
)
class org.acedb.staticobj.
StaticFloatValue
(implements org.acedb.
FloatValue
)
class org.acedb.staticobj.
StaticIntValue
(implements org.acedb.
IntValue
)
class org.acedb.staticobj.
StaticModelNode
(implements org.acedb.
ModelNode
)
class org.acedb.staticobj.
StaticModelInclude
(implements org.acedb.
ModelInclude
)
class org.acedb.staticobj.
StaticModelReference
(implements org.acedb.
ModelReference
)
class org.acedb.staticobj.
StaticModelType
(implements org.acedb.
ModelType
)
class org.acedb.staticobj.
StaticReference
(implements org.acedb.
Reference
)
class org.acedb.staticobj.
StaticStringValue
(implements org.acedb.
StringValue
)
class org.acedb.staticobj.
StaticAceSet
(implements org.acedb.
AceSet
)
class org.biojava.utils.
StaticMemberPlaceHolder
(implements java.io.Serializable)
class org.biojava.bio.seq.
StrandedFeature.Strand
(implements java.io.Serializable)
class org.biojava.bio.seq.io.
StreamReader
(implements org.biojava.bio.seq.
SequenceIterator
)
class org.biojava.bio.seq.io.
StreamReader.Context
class org.biojava.bio.seq.io.
StreamWriter
class org.Biocorba.Seqcore.
stringListHelper
class org.Biocorba.Seqcore.
stringListHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bio.symbol.
SuffixTree
(implements java.io.Serializable)
class org.biojava.bio.symbol.
SuffixTree.SuffixNode
(implements java.io.Serializable)
class org.biojava.stats.svm.tools.
SuffixTreeKernel
(implements java.io.Serializable, org.biojava.stats.svm.
SVMKernel
)
class org.biojava.stats.svm.tools.
SuffixTreeKernel.MultipleScalar
(implements java.io.Serializable, org.biojava.stats.svm.tools.
SuffixTreeKernel.DepthScaler
)
class org.biojava.stats.svm.tools.
SuffixTreeKernel.NullModelScaler
(implements java.io.Serializable, org.biojava.stats.svm.tools.
SuffixTreeKernel.DepthScaler
)
class org.biojava.stats.svm.tools.
SuffixTreeKernel.SelectionScalar
(implements java.io.Serializable, org.biojava.stats.svm.tools.
SuffixTreeKernel.DepthScaler
)
class org.biojava.stats.svm.tools.
SuffixTreeKernel.UniformScaler
(implements java.io.Serializable, org.biojava.stats.svm.tools.
SuffixTreeKernel.DepthScaler
)
class org.biojava.stats.svm.tools.
SVM_Light
class org.biojava.stats.svm.tools.
SVM_Light.LabelledVector
class org.biojava.stats.svm.
SVMRegressionModel
class org.biojava.bio.symbol.
SymbolList.EmptySymbolList
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bridge.Biocorba.Seqcore.
SymbolListAdapter
(implements org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bridge.Biocorba.Seqcore.
SequenceAdapter
(implements org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.gui.sequence.
SymbolSequenceRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.gui.
TextLogoPainter
(implements org.biojava.bio.gui.
LogoPainter
)
class java.lang.Throwable (implements java.io.Serializable)
class java.lang.Error
class org.biojava.bio.
BioError
class org.acedb.
AceError
class java.lang.Exception
class org.biojava.bio.
BioException
class org.acedb.
AceException
class org.acedb.
AceURLException
class org.biojava.bio.symbol.
IllegalAlphabetException
class org.biojava.bio.symbol.
IllegalSymbolException
class org.biojava.bio.dp.
IllegalTransitionException
class org.biojava.bio.program.gff.
IgnoreRecordException
class org.biojava.bio.dp.
ModelVetoException
class org.biojava.utils.
ParserException
class java.lang.RuntimeException
class org.biojava.utils.contract.
AssertionFailedException
class java.lang.IllegalArgumentException
class org.biojava.utils.contract.
PreconditionNotMetException
class org.biojava.utils.contract.
PostconditionNotMetException
class org.omg.CORBA.UserException (implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
EndOfStream
(implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
OutOfRange
(implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
RequestTooLarge
(implements org.omg.CORBA.portable.IDLEntity)
class org.Biocorba.Seqcore.
UnableToProcess
(implements org.omg.CORBA.portable.IDLEntity)
class org.biojava.bio.symbol.
TokenParser
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolParser
)
class org.biojava.stats.svm.tools.
Train
class org.biojava.bio.dp.
TrainerTransition
(implements java.io.Serializable)
class org.biojava.stats.svm.tools.
TrainRegression
class org.biojava.bio.dp.
Transition
(implements java.io.Serializable)
class org.Biocorba.Seqcore.
UnableToProcessHelper
class org.Biocorba.Seqcore.
UnableToProcessHolder
(implements org.omg.CORBA.portable.Streamable)
class GNOME.
UnknownHelper
class GNOME.
UnknownHolder
(implements org.omg.CORBA.portable.Streamable)
class org.biojava.bridge.GNOME.
UnknownImpl
(implements GNOME.
_Unknown_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
AnonymousSeqImpl
(implements org.Biocorba.Seqcore.
_AnonymousSeq_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
PrimarySeqImpl
(implements org.Biocorba.Seqcore.
_PrimarySeq_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
SeqImpl
(implements org.Biocorba.Seqcore.
_Seq_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
PrimarySeqDBImpl
(implements org.Biocorba.Seqcore.
_PrimarySeqDB_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
SeqDBImpl
(implements org.Biocorba.Seqcore.
_SeqDB_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
PrimarySeqIteratorImpl
(implements org.Biocorba.Seqcore.
_PrimarySeqIterator_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
SeqFeatureImpl
(implements org.Biocorba.Seqcore.
_SeqFeature_Operations
)
class org.biojava.bridge.Biocorba.Seqcore.
SeqFeatureIteratorImpl
(implements org.Biocorba.Seqcore.
_SeqFeatureIterator_Operations
)
class java.net.URLStreamHandler
class org.acedb.
Handler
class org.biojava.bio.seq.
ViewSequence
(implements org.biojava.bio.seq.
RealizingFeatureHolder
, org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.dp.
WeightMatrixAnnotator
(implements org.biojava.bio.seq.
SequenceAnnotator
, java.io.Serializable)
class org.biojava.bio.dp.
WMAsMM
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.utils.xml.
XMLDispatcher
(implements org.biojava.utils.xml.
XMLPeerFactory
)
class org.biojava.bio.dp.
XmlMarkovModel
class org.biojava.utils.xml.
XMLPeerBuilder
(implements org.xml.sax.DocumentHandler)
Interface Hierarchy
interface GNOME.
_Unknown_Operations
interface org.Biocorba.Seqcore.
_AnonymousSeq_Operations
interface org.Biocorba.Seqcore.
_PrimarySeq_Operations
interface org.Biocorba.Seqcore.
_Seq_Operations
interface org.Biocorba.Seqcore.
_PrimarySeqDB_Operations
interface org.Biocorba.Seqcore.
_SeqDB_Operations
interface org.Biocorba.Seqcore.
_PrimarySeqIterator_Operations
interface org.Biocorba.Seqcore.
_SeqFeature_Operations
interface org.Biocorba.Seqcore.
_SeqFeatureIterator_Operations
interface org.acedb.
AceSet
interface org.acedb.
AceNode
interface org.acedb.
AceElement
interface org.acedb.
AceObject
interface org.acedb.
AceValue
interface org.acedb.
DateValue
interface org.acedb.
FloatValue
interface org.acedb.
IntValue
interface org.acedb.
ModelNode
interface org.acedb.
ModelInclude
interface org.acedb.
ModelReference
interface org.acedb.
ModelType
interface org.acedb.
Reference
interface org.acedb.
StringValue
interface org.biojava.bio.seq.io.
AlignmentFormat
interface org.biojava.bio.
Annotatable
interface org.biojava.bio.symbol.
Alphabet
interface org.biojava.bio.symbol.
CrossProductAlphabet
interface org.biojava.bio.symbol.
FiniteAlphabet
interface org.biojava.bio.seq.
Feature
(also extends org.biojava.bio.seq.
FeatureHolder
)
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.seq.
FeatureHolder
, org.biojava.bio.symbol.
SymbolList
)
interface org.biojava.bio.symbol.
Symbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
(also extends org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.symbol.
CrossProductSymbol
interface org.biojava.bio.
Annotation
interface java.lang.Cloneable
interface org.biojava.bio.search.
SeqSimilaritySearcher
interface org.biojava.bio.search.
SeqSimilaritySearchHit
interface org.biojava.bio.search.
SeqSimilaritySearchResult
interface org.biojava.bio.search.
SeqSimilaritySearchSubHit
interface org.acedb.
Connection
interface org.acedb.
Database
interface org.biojava.bio.dist.
Distribution
interface org.biojava.bio.dist.
DistributionFactory
interface org.biojava.bio.dist.
DistributionTrainer
interface org.biojava.bio.dist.
DistributionTrainerContext
interface org.biojava.bio.dp.
ModelTrainer
interface org.biojava.bio.dp.
DPMatrix
interface org.acedb.
Driver
interface java.util.EventListener
interface org.biojava.stats.svm.
TrainingListener
interface org.biojava.bio.seq.io.
FastaDescriptionReader
interface org.biojava.bio.seq.io.
FeatureBuilder
interface org.biojava.bio.seq.
FeatureHolder
interface org.biojava.bio.seq.
Feature
(also extends org.biojava.bio.
Annotatable
)
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
RealizingFeatureHolder
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.symbol.
SymbolList
)
interface org.biojava.bio.seq.
FeatureRealizer
interface org.biojava.bio.gui.sequence.
FeatureRenderer
interface org.biojava.bio.program.gff.
GFFDocumentHandler
interface org.biojava.bio.program.gff.
GFFErrorHandler
interface org.biojava.bio.program.gff.
GFFRecord
interface org.biojava.bio.program.gff.
GFFRecordFilter
interface org.biojava.bio.seq.db.
IDMaker
interface org.biojava.stats.svm.
ItemValue
interface org.biojava.bio.symbol.
Location
interface org.biojava.bio.gui.
LogoPainter
interface org.omg.CORBA.Object
interface org.Biocorba.Seqcore.
AnonymousSeq
(also extends org.omg.CORBA.portable.IDLEntity, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.Biocorba.Seqcore.
AnonymousSeq
, org.omg.CORBA.portable.IDLEntity)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqDB
(also extends org.omg.CORBA.portable.IDLEntity, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqIterator
(also extends org.omg.CORBA.portable.IDLEntity, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.Biocorba.Seqcore.
PrimarySeq
)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.Biocorba.Seqcore.
PrimarySeqDB
)
interface org.Biocorba.Seqcore.
SeqFeature
(also extends org.omg.CORBA.portable.IDLEntity, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
SeqFeatureIterator
(also extends org.omg.CORBA.portable.IDLEntity, GNOME.
Unknown
)
interface GNOME.
Unknown
(also extends org.omg.CORBA.portable.IDLEntity)
interface org.Biocorba.Seqcore.
AnonymousSeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqIterator
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqFeature
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqFeatureIterator
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.biojava.bio.seq.
SequenceAnnotator
interface org.biojava.bio.seq.db.
SequenceDB
interface org.biojava.bio.seq.db.
SequenceDBInstallation
interface org.biojava.bio.seq.
SequenceFactory
interface org.biojava.bio.seq.io.
SequenceFormat
interface org.biojava.bio.seq.
SequenceIterator
interface org.biojava.bio.gui.sequence.
SequenceRenderer
interface java.io.Serializable
interface org.biojava.bio.seq.
FeatureFilter
interface org.omg.CORBA.portable.IDLEntity
interface org.Biocorba.Seqcore.
AnonymousSeq
(also extends org.omg.CORBA.Object, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.Biocorba.Seqcore.
AnonymousSeq
, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqDB
(also extends org.omg.CORBA.Object, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqIterator
(also extends org.omg.CORBA.Object, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.Object, org.Biocorba.Seqcore.
PrimarySeq
)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.Object, org.Biocorba.Seqcore.
PrimarySeqDB
)
interface org.Biocorba.Seqcore.
SeqFeature
(also extends org.omg.CORBA.Object, GNOME.
Unknown
)
interface org.Biocorba.Seqcore.
SeqFeatureIterator
(also extends org.omg.CORBA.Object, GNOME.
Unknown
)
interface GNOME.
Unknown
(also extends org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
AnonymousSeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
Seq
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqDB
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
PrimarySeqIterator
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqFeature
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.Biocorba.Seqcore.
SeqFeatureIterator
(also extends org.omg.CORBA.portable.IDLEntity, org.omg.CORBA.Object)
interface org.biojava.bio.dp.
StoppingCriteria
interface org.biojava.stats.svm.tools.
SuffixTreeKernel.DepthScaler
interface org.biojava.stats.svm.
SVMClassifierModel
interface org.biojava.stats.svm.
SVMKernel
interface org.biojava.stats.svm.
SVMTarget
interface org.biojava.bio.symbol.
SymbolList
interface org.biojava.bio.symbol.
Alignment
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.seq.
FeatureHolder
)
interface org.biojava.bio.symbol.
SymbolParser
interface org.biojava.bio.gui.
SymbolStyle
interface org.biojava.bio.dp.
Trainable
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.bio.dp.
State
)
interface org.biojava.bio.dp.
MarkovModel
interface org.biojava.bio.dp.
ModelInState
(also extends org.biojava.bio.dp.
State
)
interface org.biojava.bio.dp.
TrainingAlgorithm
interface org.biojava.stats.svm.
TrainingContext
interface org.biojava.bio.dp.
TransitionListener
interface org.biojava.bio.dp.
TransitionTrainer
interface org.biojava.bio.symbol.
TranslationTable
interface org.biojava.bio.dp.
WeightMatrix
interface org.biojava.utils.xml.
XMLPeerFactory
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