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Package Hierarchies:
org.biojava.bibliography
,
org.biojava.bio
,
org.biojava.bio.alignment
,
org.biojava.bio.chromatogram
,
org.biojava.bio.chromatogram.graphic
,
org.biojava.bio.dist
,
org.biojava.bio.dp
,
org.biojava.bio.dp.onehead
,
org.biojava.bio.dp.twohead
,
org.biojava.bio.gui
,
org.biojava.bio.gui.sequence
,
org.biojava.bio.molbio
,
org.biojava.bio.program
,
org.biojava.bio.program.abi
,
org.biojava.bio.program.blast2html
,
org.biojava.bio.program.das
,
org.biojava.bio.program.gff
,
org.biojava.bio.program.hmmer
,
org.biojava.bio.program.indexdb
,
org.biojava.bio.program.phred
,
org.biojava.bio.program.sax
,
org.biojava.bio.program.sax.blastxml
,
org.biojava.bio.program.scf
,
org.biojava.bio.program.ssaha
,
org.biojava.bio.program.ssbind
,
org.biojava.bio.program.tagvalue
,
org.biojava.bio.program.unigene
,
org.biojava.bio.program.xff
,
org.biojava.bio.program.xml
,
org.biojava.bio.proteomics
,
org.biojava.bio.search
,
org.biojava.bio.seq
,
org.biojava.bio.seq.db
,
org.biojava.bio.seq.db.biofetch
,
org.biojava.bio.seq.db.biosql
,
org.biojava.bio.seq.db.emblcd
,
org.biojava.bio.seq.db.flat
,
org.biojava.bio.seq.distributed
,
org.biojava.bio.seq.homol
,
org.biojava.bio.seq.impl
,
org.biojava.bio.seq.io
,
org.biojava.bio.seq.io.agave
,
org.biojava.bio.seq.io.filterxml
,
org.biojava.bio.seq.io.game
,
org.biojava.bio.seq.io.game12
,
org.biojava.bio.seq.projection
,
org.biojava.bio.seq.ragbag
,
org.biojava.bio.symbol
,
org.biojava.bio.taxa
,
org.biojava.directory
,
org.biojava.stats.svm
,
org.biojava.stats.svm.tools
,
org.biojava.utils
,
org.biojava.utils.cache
,
org.biojava.utils.candy
,
org.biojava.utils.io
,
org.biojava.utils.lsid
,
org.biojava.utils.math
,
org.biojava.utils.net
,
org.biojava.utils.stax
,
org.biojava.utils.xml
Class Hierarchy
class java.lang.Object
class org.biojava.bio.program.abi.
ABIFParser
class org.biojava.bio.program.abi.
ABIFChromatogram.Parser
class org.biojava.bio.program.abi.
ABIFParser.TaggedDataRecord
class org.biojava.bio.program.abi.
ABITools
class org.biojava.bio.program.abi.
ABITrace
class org.biojava.bio.program.blast2html.
AbstractAlignmentStyler
(implements org.biojava.bio.program.blast2html.AlignmentStyler)
class org.biojava.bio.program.blast2html.
SimpleAlignmentStyler
class org.biojava.utils.
AbstractChangeable
(implements org.biojava.utils.
Changeable
)
class org.biojava.bio.gui.sequence.
AbiTraceRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.symbol.
AbstractAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
IntegerAlphabet.SubIntegerAlphabet
class org.biojava.bio.symbol.
SimpleAlphabet
(implements java.io.Serializable)
class org.biojava.bio.symbol.
SingletonAlphabet
(implements org.biojava.bio.symbol.
FiniteAlphabet
, java.io.Serializable)
class org.biojava.bio.
AbstractAnnotation
(implements org.biojava.bio.
Annotation
, java.io.Serializable)
class org.biojava.bio.
AnnotationChanger
class org.biojava.bio.
AnnotationRenamer
class org.biojava.bio.
BeanAsAnnotation
class org.biojava.bio.
SimpleAnnotation
class org.biojava.bio.
SmallAnnotation
class org.biojava.bio.gui.sequence.
AbstractBeadRenderer
(implements org.biojava.bio.gui.sequence.
BeadFeatureRenderer
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
EllipticalBeadRenderer
class org.biojava.bio.gui.sequence.
RectangularBeadRenderer
class org.biojava.bio.gui.sequence.
RoundRectangularBeadRenderer
class org.biojava.bio.dist.
AbstractDistribution
(implements org.biojava.bio.dist.
Distribution
, java.io.Serializable)
class org.biojava.bio.dist.
AbstractOrderNDistribution
(implements org.biojava.bio.dist.
OrderNDistribution
)
class org.biojava.bio.dist.
SimpleDistribution
(implements java.io.Serializable)
class org.biojava.bio.dist.
UntrainableDistribution
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.
ProjectedFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
, org.biojava.bio.seq.projection.
ProjectionContext
)
class org.biojava.bio.seq.
SimpleFeatureHolder
class org.biojava.bio.seq.db.
AbstractSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bio.seq.db.
AnnotatedSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.seq.distributed.
DistributedSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bio.seq.db.
DummySequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bio.seq.db.
HashSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.seq.db.
IndexedSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
, java.io.Serializable)
class org.biojava.bio.seq.db.
SequenceDBWrapper
(implements java.io.Serializable)
class org.biojava.bio.seq.db.
CachingSequenceDB
class org.biojava.bio.seq.db.
SubSequenceDB
class org.biojava.bio.seq.db.
ViewingSequenceDB
class org.biojava.bio.symbol.
AbstractSymbol
(implements org.biojava.bio.symbol.
Symbol
)
class org.biojava.bio.symbol.
FundamentalAtomicSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
, java.io.Serializable)
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.symbol.SimpleSymbol (implements java.io.Serializable, org.biojava.bio.symbol.
Symbol
)
class org.biojava.bio.symbol.SimpleBasisSymbol (implements org.biojava.bio.symbol.
BasisSymbol
)
class org.biojava.bio.symbol.
SimpleAtomicSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
)
class org.biojava.bio.symbol.
AbstractSymbolList
(implements org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bio.alignment.
AbstractULAlignment
(implements org.biojava.bio.alignment.
UnequalLengthAlignment
)
class org.biojava.bio.alignment.
FlexibleAlignment
(implements org.biojava.bio.alignment.
ARAlignment
, org.biojava.bio.alignment.
EditableAlignment
)
class org.biojava.bio.alignment.
AbstractULAlignment.SubULAlignment
(implements org.biojava.bio.alignment.
UnequalLengthAlignment
)
class org.biojava.bio.seq.impl.
AssembledSymbolList
class org.biojava.bio.symbol.
DummySymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
PackedDnaSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
PackedSymbolList
(implements java.io.Serializable)
class org.biojava.bio.symbol.
SimpleAlignment
(implements org.biojava.bio.symbol.
Alignment
, java.io.Serializable)
class org.biojava.bio.symbol.
SimpleGappedSymbolList
(implements org.biojava.bio.symbol.
GappedSymbolList
, java.io.Serializable)
class org.biojava.bio.seq.
SimpleGappedSequence
(implements org.biojava.bio.seq.
GappedSequence
)
class org.biojava.bio.symbol.
SimpleSymbolList
(implements org.biojava.utils.
ChangeListener
, java.io.Serializable)
class org.biojava.bio.taxa.
AbstractTaxon
(implements org.biojava.bio.taxa.
Taxon
)
class org.biojava.bio.taxa.
SimpleTaxon
class org.biojava.bio.taxa.
WeakTaxon
class org.biojava.bio.gui.sequence.
BasicFeatureRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
)
class org.biojava.bio.gui.sequence.
CrosshairRenderer
(implements org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer
)
class org.biojava.bio.program.das.
DAS
class org.biojava.bio.program.das.
DASSequence
(implements org.biojava.bio.program.das.DASSequenceI)
class org.biojava.bio.seq.
DummySequence
(implements org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.gui.sequence.
FeatureBlockSequenceRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.gui.sequence.
FeatureLabelRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
)
class org.biojava.bio.seq.
FeatureTypes.RepositoryImpl
(implements org.biojava.bio.seq.
FeatureTypes.Repository
)
class org.biojava.bio.dist.
IndexedCount
(implements org.biojava.bio.dist.
Count
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
LabelledSequenceRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.seq.
LazyFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
)
class org.biojava.bio.
MergeAnnotation
(implements org.biojava.bio.
Annotation
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
MultiLineRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
, java.io.Serializable)
class org.biojava.bio.
OverlayAnnotation
(implements org.biojava.bio.
Annotation
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
OverlayRendererWrapper
(implements org.biojava.bio.gui.sequence.
OverlayMarker
, org.biojava.bio.gui.sequence.
SequenceRenderer
, java.io.Serializable)
class org.biojava.bio.dist.
PairDistribution
(implements org.biojava.bio.dist.
Distribution
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
PairwiseDiagonalRenderer
(implements org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
PairwiseFilteringRenderer
(implements org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
PairwiseOverlayRenderer
(implements org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer
, java.io.Serializable)
class org.biojava.bio.search.
SequenceDBSearchHit
(implements org.biojava.bio.
Annotatable
, org.biojava.bio.search.
SeqSimilaritySearchHit
)
class org.biojava.bio.search.
SequenceDBSearchResult
(implements org.biojava.bio.
Annotatable
, org.biojava.bio.search.
SeqSimilaritySearchResult
)
class org.biojava.bio.search.
SequenceDBSearchSubHit
(implements org.biojava.bio.search.
SeqSimilaritySearchSubHit
)
class org.biojava.bio.gui.sequence.
SequenceRendererWrapper
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
AlignmentRenderer
class org.biojava.bio.gui.sequence.
BumpedRenderer
class org.biojava.bio.gui.sequence.
FilteringRenderer
class org.biojava.bio.gui.sequence.
PaddingRenderer
class org.biojava.bio.seq.
SimpleAssembly
(implements org.biojava.bio.seq.
RealizingFeatureHolder
, org.biojava.bio.seq.
Sequence
)
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.program.hmmer.
ProfileEmissionState
class org.biojava.bio.seq.impl.
SimpleFeature
(implements org.biojava.bio.seq.
Feature
, org.biojava.bio.seq.
RealizingFeatureHolder
, java.io.Serializable)
class org.biojava.bio.seq.impl.
SimpleStrandedFeature
(implements org.biojava.bio.seq.
StrandedFeature
)
class org.biojava.bio.seq.impl.
SimpleFramedFeature
(implements org.biojava.bio.seq.
Frame
, org.biojava.bio.seq.
FramedFeature
)
class org.biojava.bio.seq.impl.
SimpleHomologyFeature
(implements org.biojava.bio.seq.homol.
HomologyFeature
)
class org.biojava.bio.seq.impl.
SimpleRemoteFeature
(implements org.biojava.bio.seq.
RemoteFeature
, java.io.Serializable)
class org.biojava.bio.seq.impl.
SimpleRestrictionSite
(implements org.biojava.bio.molbio.
RestrictionSite
)
class org.biojava.bio.seq.impl.
SimpleSimilarityPairFeature
(implements org.biojava.bio.seq.homol.
SimilarityPairFeature
)
class org.biojava.bio.seq.homol.
SimpleHomology
(implements org.biojava.bio.seq.homol.
Homology
)
class org.biojava.bio.gui.sequence.
SimpleLabelRenderer
(implements org.biojava.bio.gui.sequence.
LabelRenderer
)
class org.biojava.bio.dp.
SimpleMarkovModel
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.bio.program.hmmer.
FullHmmerProfileHMM
class org.biojava.bio.dp.
ProfileHMM
class org.biojava.bio.program.hmmer.
HmmerProfileHMM
class org.biojava.bio.search.
SimpleSeqSimilaritySearchHit
(implements org.biojava.bio.search.
SeqSimilaritySearchHit
)
class org.biojava.bio.search.
SimpleSeqSimilaritySearchResult
(implements org.biojava.bio.search.
SeqSimilaritySearchResult
)
class org.biojava.bio.search.
SimpleSeqSimilaritySearchSubHit
(implements org.biojava.bio.search.
SeqSimilaritySearchSubHit
)
class org.biojava.bio.seq.impl.
SimpleSequence
(implements org.biojava.bio.seq.
RealizingFeatureHolder
, org.biojava.bio.seq.
Sequence
, java.io.Serializable)
class org.biojava.bio.program.phred.
PhredSequence
(implements org.biojava.bio.program.phred.
Qualitative
)
class org.biojava.bio.seq.impl.
RevCompSequence
class org.biojava.bio.gui.sequence.
SixFrameRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.gui.sequence.
SixFrameZiggyRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
StackedFeatureRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
)
class org.biojava.bio.gui.sequence.
TickFeatureRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
)
class org.biojava.bio.dist.
TranslatedDistribution
(implements org.biojava.bio.dist.
Distribution
, java.io.Serializable)
class org.biojava.bio.seq.db.
WebSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDBLite
)
class org.biojava.bio.seq.db.
NCBISequenceDB
class org.biojava.bio.dp.
WMAsMM
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
ZiggyFeatureRenderer
(implements org.biojava.bio.gui.sequence.
FeatureRenderer
, java.io.Serializable)
class org.biojava.bio.chromatogram.
AbstractChromatogram
(implements org.biojava.bio.chromatogram.
Chromatogram
)
class org.biojava.bio.program.abi.
ABIFChromatogram
class org.biojava.bio.program.scf.
SCF
class org.biojava.bio.chromatogram.
SimpleChromatogram
class java.util.AbstractCollection (implements java.util.Collection)
class java.util.AbstractList (implements java.util.List)
class org.biojava.utils.
FileAsList
(implements org.biojava.utils.
Commitable
)
class org.biojava.utils.
ListTools.Doublet
(implements java.io.Serializable)
class org.biojava.utils.
ListTools.Triplet
(implements java.io.Serializable)
class org.biojava.utils.
SingletonList
(implements java.io.Serializable)
class java.util.AbstractSet (implements java.util.Set)
class org.biojava.utils.
SmallSet
class org.biojava.bio.seq.io.AbstractGenEmblFileFormer
class org.biojava.bio.seq.io.
EmblFileFormer
(implements org.biojava.bio.seq.io.
SeqFileFormer
)
class org.biojava.bio.seq.io.
GenbankFileFormer
(implements org.biojava.bio.seq.io.
SeqFileFormer
)
class org.biojava.bio.seq.io.
ProteinRefSeqFileFormer
class org.biojava.bio.seq.io.
SwissprotFileFormer
(implements org.biojava.bio.seq.io.
SeqFileFormer
)
class org.biojava.bio.symbol.
AbstractLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.biojava.bio.symbol.
AbstractRangeLocation
class org.biojava.bio.symbol.
FuzzyLocation
(implements java.io.Serializable)
class org.biojava.bio.symbol.
PointLocation
(implements org.biojava.bio.symbol.
Location
, java.io.Serializable)
class org.biojava.bio.symbol.
RangeLocation
(implements java.io.Serializable)
class org.biojava.bio.symbol.
MergeLocation
class org.biojava.bio.symbol.
FuzzyPointLocation
class org.biojava.bio.symbol.
AbstractLocationDecorator
(implements org.biojava.bio.symbol.
Location
)
class org.biojava.bio.symbol.
BetweenLocation
class org.biojava.bio.symbol.
CircularLocation
class java.util.AbstractMap (implements java.util.Map)
class org.biojava.utils.
BeanAsMap
class org.biojava.utils.
OverlayMap
class org.biojava.utils.
SmallMap
(implements java.io.Serializable)
class org.biojava.utils.cache.
WeakValueHashMap
class org.biojava.bio.dp.twohead.
AbstractMatrixPairDPCursor
(implements org.biojava.bio.dp.twohead.
PairDPCursor
)
class org.biojava.bio.dp.twohead.
BackMatrixPairDPCursor
class org.biojava.bio.dp.twohead.
MatrixPairDPCursor
class org.biojava.bio.program.sax.AbstractNativeAppSAXParser (implements org.biojava.bio.program.sax.NamespaceConfigurationIF, org.xml.sax.XMLReader)
class org.biojava.bio.program.sax.
BlastLikeSAXParser
class org.biojava.bio.program.sax.
ClustalWAlignmentSAXParser
class org.biojava.bio.program.sax.
FastaSearchSAXParser
(implements org.biojava.bio.search.
SearchContentHandler
)
class org.biojava.bio.program.sax.
FastaSequenceSAXParser
class org.biojava.bio.program.sax.
PdbSAXParser
class org.biojava.bio.program.sax.
SequenceAlignmentSAXParser
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.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.biojava.bio.alignment.
AbstractULAlignment.LeftRightLocationComparator
(implements java.util.Comparator)
class org.biojava.bio.seq.io.agave.
AGAVEDbId
class org.biojava.bio.seq.io.agave.
AGAVEIdAlias
class org.biojava.bio.seq.io.agave.
AGAVEMapLocation
class org.biojava.bio.seq.io.agave.
AGAVEMapPosition
class org.biojava.bio.seq.io.agave.
AGAVEMatchRegion
class org.biojava.bio.seq.io.agave.
AGAVEProperty
class org.biojava.bio.seq.io.agave.
AGAVEQueryRegion
class org.biojava.bio.seq.io.agave.
AGAVERelatedAnnot
class org.biojava.bio.seq.io.agave.
AgaveWriter
class org.biojava.bio.seq.io.agave.
AgaveWriter.Indent
class org.biojava.bio.seq.io.agave.
AGAVEXref
class org.biojava.bio.seq.io.agave.
AGAVEXrefs
class org.biojava.bio.seq.io.
AlignIOConstants
class org.biojava.bio.symbol.
Alignment.SymbolListIterator
(implements java.util.Iterator)
class org.biojava.bio.program.blast2html.
AlignmentMarker
class org.biojava.bio.symbol.
AlphabetManager
class org.biojava.bio.program.ssbind.
AlphabetResolver
class org.biojava.bio.program.tagvalue.
AnnotationBuilder
(implements org.biojava.bio.program.tagvalue.
TagValueListener
)
class org.biojava.bio.program.ssbind.
AnnotationFactory
class org.biojava.bio.
AnnotationTools
class org.biojava.bio.
AnnotationType.Abstract
(implements org.biojava.bio.
AnnotationType
)
class org.biojava.bio.
AnnotationType.Impl
class org.biojava.utils.xml.
AppBeanRunner
class org.biojava.bio.dp.
BackPointer
class org.biojava.bio.gui.
BarLogoPainter
(implements org.biojava.bio.gui.
LogoPainter
)
class org.biojava.bio.program.xml.
BaseXMLWriter
class org.biojava.bio.program.xff.
BasicXFFHelper
(implements org.biojava.bio.program.xff.
XFFHelper
)
class org.biojava.bio.program.xff.
PropertyWriter
class org.biojava.bibliography.
BiblioCriterion
class org.biojava.bibliography.
BiblioDescription
class org.biojava.bibliography.
BiblioEntryStatus
class org.biojava.bibliography.
BiblioJournal
class org.biojava.bibliography.
BiblioProvider
class org.biojava.bibliography.
BiblioOrganisation
class org.biojava.bibliography.
BiblioPerson
class org.biojava.bibliography.
BiblioService
class org.biojava.bibliography.
BiblioScope
class org.biojava.bibliography.
BiblioSubject
class org.biojava.bibliography.
BibRef
class org.biojava.bibliography.
BiblioArticle
class org.biojava.bibliography.
BiblioBookArticle
class org.biojava.bibliography.
BiblioJournalArticle
class org.biojava.bibliography.
BiblioBook
class org.biojava.bibliography.
BiblioPatent
class org.biojava.bibliography.
BiblioProceeding
class org.biojava.bibliography.
BiblioTechReport
class org.biojava.bibliography.
BiblioThesis
class org.biojava.bibliography.
BiblioWebResource
class org.biojava.utils.math.
BinarySearch
class org.biojava.bio.seq.db.biofetch.
BioFetchSequenceDBProvider
(implements org.biojava.directory.
SequenceDBProvider
)
class org.biojava.bio.seq.db.
BioIndex
(implements org.biojava.bio.seq.db.
IndexStore
)
class org.biojava.bio.seq.db.biosql.
BioSQLSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bio.seq.db.biosql.
BioSQLSequenceDBProvider
(implements org.biojava.directory.
SequenceDBProvider
)
class org.biojava.bio.program.indexdb.
BioStore
(implements org.biojava.bio.program.indexdb.
IndexStore
)
class org.biojava.bio.program.indexdb.
BioStoreFactory
class org.biojava.bio.program.ssbind.
BlastLikeSearchBuilder
(implements org.biojava.bio.search.
SearchBuilder
)
class org.biojava.bio.program.
BlastLikeToXMLConverter
class org.biojava.utils.candy.
CandyEntry
class org.biojava.bio.
CardinalityConstraint
class org.biojava.bio.dp.twohead.
Cell
class org.biojava.utils.cache.
ChangeableCache
class org.biojava.utils.
ChangeAdapter
(implements org.biojava.utils.
ChangeListener
)
class org.biojava.utils.
ChangeForwarder
(implements org.biojava.utils.
ChangeListener
)
class org.biojava.bio.symbol.
AbstractSymbolList.EditScreener
class org.biojava.bio.symbol.
AbstractSymbolList.EditTranslater
class org.biojava.bio.
Annotatable.AnnotationForwarder
class org.biojava.bio.dist.
Distribution.NullModelForwarder
class org.biojava.bio.dp.
MarkovModel.DistributionForwarder
class org.biojava.bio.
MergeAnnotation.PropertyForwarder
class org.biojava.bio.
OverlayAnnotation.PropertyForwarder
class org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer.PairwiseRendererForwarder
class org.biojava.bio.seq.db.
SequenceDBWrapper.SequencesForwarder
class org.biojava.bio.gui.sequence.
SequenceRenderer.RendererForwarder
class org.biojava.utils.
ChangeListener.AlwaysVetoListener
(implements org.biojava.utils.
ChangeListener
)
class org.biojava.utils.
ChangeListener.LoggingListener
(implements org.biojava.utils.
ChangeListener
)
class org.biojava.utils.
ChangeSupport
class org.biojava.bio.program.tagvalue.
ChangeTable
class org.biojava.bio.program.tagvalue.
ChangeTable.ChainedChanger
(implements org.biojava.bio.program.tagvalue.
ChangeTable.Changer
)
class org.biojava.utils.
ChangeType
(implements java.io.Serializable)
class org.biojava.bio.chromatogram.
ChromatogramFactory
class org.biojava.bio.chromatogram.graphic.
ChromatogramGraphic
(implements java.lang.Cloneable)
class org.biojava.bio.chromatogram.graphic.
ChromatogramGraphic.Option
class org.biojava.bio.chromatogram.
ChromatogramTools
class org.biojava.bio.seq.io.
ChunkedSymbolListBuilder
class org.biojava.bio.seq.io.
ChunkedSymbolListFactory
class org.biojava.stats.svm.tools.
ClassifierExample
class org.biojava.stats.svm.tools.
Classify
class org.biojava.bio.
CollectionConstraint.AllValuesIn
(implements org.biojava.bio.
CollectionConstraint
)
class org.biojava.bio.
CollectionConstraint.And
(implements org.biojava.bio.
CollectionConstraint
)
class org.biojava.bio.
CollectionConstraint.Contains
(implements org.biojava.bio.
CollectionConstraint
)
class org.biojava.bio.
CollectionConstraint.Or
(implements org.biojava.bio.
CollectionConstraint
)
class org.biojava.bio.program.ssaha.
CompactedDataStore
(implements org.biojava.bio.program.ssaha.
DataStore
)
class org.biojava.bio.program.ssaha.
CompactedDataStoreFactory
(implements org.biojava.bio.program.ssaha.
DataStoreFactory
)
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 javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
class org.biojava.bio.gui.
FeatureTree
class org.biojava.bio.gui.sequence.
PairwiseSequencePanel
(implements org.biojava.utils.
Changeable
, org.biojava.bio.gui.sequence.
PairwiseRenderContext
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
SequencePanel
(implements org.biojava.utils.
Changeable
, org.biojava.bio.gui.sequence.
SequenceRenderContext
, javax.swing.SwingConstants)
class org.biojava.bio.gui.sequence.
SequencePoster
(implements org.biojava.utils.
Changeable
, org.biojava.bio.gui.sequence.
SequenceRenderContext
, javax.swing.SwingConstants)
class org.biojava.bio.gui.sequence.
TranslatedSequencePanel
(implements org.biojava.utils.
Changeable
, org.biojava.bio.gui.sequence.
SequenceRenderContext
)
class org.biojava.utils.
Constants
class org.biojava.bio.program.das.
DASLink
class org.biojava.bio.program.das.
DASSequenceDBProvider
(implements org.biojava.directory.
SequenceDBProvider
)
class org.biojava.bio.program.das.
DataSource
class org.biojava.bio.program.das.
ReferenceServer
(implements org.biojava.utils.
Changeable
)
class org.biojava.bio.seq.db.biosql.
DBHelper
class org.biojava.bio.seq.db.biosql.
MySQLDBHelper
class org.biojava.bio.seq.db.biosql.
PostgreSQLDBHelper
class org.biojava.bio.seq.db.biosql.
UnknownDBHelper
class org.biojava.bio.seq.db.biosql.
DBHelper.DeleteStyle
class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
class org.biojava.bio.program.blast2html.
Blast2HTMLHandler
class org.biojava.bio.program.xml.
SimpleXMLEmitter
class org.biojava.bio.dist.
XMLDistributionReader
class org.biojava.bio.program.blast2html.
DefaultURLGeneratorFactory
(implements org.biojava.bio.program.blast2html.
URLGeneratorFactory
)
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.proteomics.
Digest
class org.biojava.bio.dist.
DistributionFactory.DefaultDistributionFactory
(implements org.biojava.bio.dist.
DistributionFactory
, java.io.Serializable)
class org.biojava.bio.dist.
DistributionTools
class org.biojava.bio.symbol.
DNAAmbPack
(implements org.biojava.bio.symbol.
Packing
, java.io.Serializable)
class org.biojava.bio.symbol.
DNANoAmbPack
(implements org.biojava.bio.symbol.
Packing
, 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.dp.
DP
class org.biojava.bio.dp.twohead.
PairwiseDP
(implements java.io.Serializable)
class org.biojava.bio.dp.onehead.
SingleDP
(implements java.io.Serializable)
class org.biojava.bio.dp.
DP.ReverseIterator
(implements java.util.Iterator, java.io.Serializable)
class org.biojava.bio.dp.twohead.
DPCompiler
(implements org.biojava.bio.dp.twohead.
CellCalculatorFactoryMaker
)
class org.biojava.bio.dp.
DPFactory.DefaultFactory
(implements org.biojava.bio.dp.
DPFactory
)
class org.biojava.bio.dp.twohead.
DPInterpreter
(implements org.biojava.bio.dp.twohead.
CellCalculatorFactory
)
class org.biojava.bio.dp.twohead.
DPInterpreter.Maker
(implements org.biojava.bio.dp.twohead.
CellCalculatorFactoryMaker
)
class org.biojava.bio.seq.db.
DummySequenceDBInstallation
(implements org.biojava.bio.seq.db.
SequenceDBInstallation
)
class org.biojava.bio.program.blast2html.
EbiDatabaseURLGenerator
(implements org.biojava.bio.program.blast2html.
DatabaseURLGenerator
)
class org.biojava.bio.taxa.
EbiFormat
(implements org.biojava.bio.taxa.
TaxonParser
)
class org.biojava.bio.program.tagvalue.
Echo
(implements org.biojava.bio.program.tagvalue.
TagValueListener
)
class org.biojava.bio.symbol.
Edit
(implements java.io.Serializable)
class org.biojava.bio.program.xff.
ElementRecognizer.AllElementRecognizer
(implements org.biojava.bio.program.xff.
ElementRecognizer
)
class org.biojava.bio.seq.io.agave.
ElementRecognizer.AllElementRecognizer
(implements org.biojava.bio.seq.io.agave.
ElementRecognizer
)
class org.biojava.bio.seq.io.game.
ElementRecognizer.AllElementRecognizer
(implements org.biojava.bio.seq.io.game.
ElementRecognizer
)
class org.biojava.bio.program.xff.
ElementRecognizer.ByLocalName
(implements org.biojava.bio.program.xff.
ElementRecognizer
)
class org.biojava.bio.seq.io.agave.
ElementRecognizer.ByLocalName
(implements org.biojava.bio.seq.io.agave.
ElementRecognizer
)
class org.biojava.bio.seq.io.game.
ElementRecognizer.ByLocalName
(implements org.biojava.bio.seq.io.game.
ElementRecognizer
)
class org.biojava.bio.program.xff.
ElementRecognizer.ByNSName
(implements org.biojava.bio.program.xff.
ElementRecognizer
)
class org.biojava.bio.seq.io.agave.
ElementRecognizer.ByNSName
(implements org.biojava.bio.seq.io.agave.
ElementRecognizer
)
class org.biojava.bio.seq.io.game.
ElementRecognizer.ByNSName
(implements org.biojava.bio.seq.io.game.
ElementRecognizer
)
class org.biojava.bio.program.xff.
ElementRecognizer.HasAttribute
(implements org.biojava.bio.program.xff.
ElementRecognizer
)
class org.biojava.bio.seq.io.agave.
ElementRecognizer.HasAttribute
(implements org.biojava.bio.seq.io.agave.
ElementRecognizer
)
class org.biojava.bio.seq.io.game.
ElementRecognizer.HasAttribute
(implements org.biojava.bio.seq.io.game.
ElementRecognizer
)
class org.biojava.bio.seq.db.emblcd.
EmblCDROMIndexReader
class org.biojava.bio.seq.db.emblcd.
AcnumHitReader
class org.biojava.bio.seq.db.emblcd.
AcnumTrgReader
class org.biojava.bio.seq.db.emblcd.
DivisionLkpReader
class org.biojava.bio.seq.db.emblcd.
EntryNamIdxReader
class org.biojava.bio.seq.db.
EmblCDROMIndexStore
(implements org.biojava.bio.seq.db.
IndexStore
)
class org.biojava.bio.seq.db.emblcd.
EmblCDROMRandomAccess
class org.biojava.bio.seq.db.emblcd.
EntryNamRandomAccess
class org.biojava.bio.seq.io.
EmblLikeFormat
(implements org.biojava.utils.
ParseErrorListener
, org.biojava.utils.
ParseErrorSource
, org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.bio.seq.io.
EmblLikeLocationParser
class org.biojava.bio.seq.io.
EmblProcessor.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.dp.twohead.
EmissionCache
class java.util.EventObject (implements java.io.Serializable)
class org.biojava.utils.
ChangeEvent
class org.biojava.utils.
ParseErrorEvent
class org.biojava.bio.gui.sequence.
SequenceViewerEvent
class org.biojava.stats.svm.
TrainingEvent
class org.biojava.bio.seq.io.
FastaAlignmentFormat
(implements org.biojava.bio.seq.io.
AlignmentFormat
)
class org.biojava.bio.seq.io.
FastaDescriptionLineParser.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.seq.io.
FastaFormat
(implements org.biojava.utils.
ParseErrorListener
, org.biojava.utils.
ParseErrorSource
, org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.utils.xml.
FastXMLWriter
class org.biojava.bio.seq.
Feature.ByLocationComparator
(implements java.util.Comparator)
class org.biojava.bio.seq.
Feature.Template
(implements java.io.Serializable)
class org.biojava.bio.seq.
StrandedFeature.Template
class org.biojava.bio.seq.
ComponentFeature.Template
class org.biojava.bio.seq.
FramedFeature.Template
class org.biojava.bio.seq.homol.
HomologyFeature.Template
class org.biojava.bio.seq.
RemoteFeature.Template
class org.biojava.bio.molbio.
RestrictionSite.Template
class org.biojava.bio.seq.homol.
SimilarityPairFeature.Template
class org.biojava.bio.seq.
FeatureFilter.And
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByAncestor
(implements org.biojava.bio.seq.
OptimizableFilter
, org.biojava.bio.seq.Up)
class org.biojava.bio.seq.
FeatureFilter.ByAnnotationType
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.AnnotationContains
class org.biojava.bio.seq.
FeatureFilter.ByAnnotation
class org.biojava.bio.seq.
FeatureFilter.HasAnnotation
class org.biojava.bio.seq.
FeatureFilter.ByChild
(implements org.biojava.bio.seq.Down, org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByClass
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByComponentName
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByDescendant
(implements org.biojava.bio.seq.Down, org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByFeature
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByPairwiseScore
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByParent
(implements org.biojava.bio.seq.
OptimizableFilter
, org.biojava.bio.seq.Up)
class org.biojava.bio.seq.
FeatureFilter.BySequenceName
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.BySource
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ByType
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ContainedByLocation
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.FrameFilter
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.Not
(implements org.biojava.bio.seq.
FeatureFilter
)
class org.biojava.bio.seq.
FeatureFilter.OnlyChildren
(implements org.biojava.bio.seq.ByHierarchy, org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.OnlyDescendants
(implements org.biojava.bio.seq.ByHierarchy, org.biojava.bio.seq.
OptimizableFilter
)
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.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ShadowContainedByLocation
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.ShadowOverlapsLocation
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.
FeatureFilter.StrandFilter
(implements org.biojava.bio.seq.
OptimizableFilter
)
class org.biojava.bio.seq.impl.
FeatureImpl
class org.biojava.bio.gui.sequence.
FeatureLabelRenderer.AnnotationLabelMaker
(implements org.biojava.bio.gui.sequence.
FeatureLabelRenderer.LabelMaker
)
class org.biojava.bio.gui.sequence.
FeatureLabelRenderer.SourceLabelMaker
(implements org.biojava.bio.gui.sequence.
FeatureLabelRenderer.LabelMaker
)
class org.biojava.bio.gui.sequence.
FeatureLabelRenderer.TypeLabelMaker
(implements org.biojava.bio.gui.sequence.
FeatureLabelRenderer.LabelMaker
)
class org.biojava.bio.seq.io.
FeatureTableParser
class org.biojava.bio.seq.
FeatureTypes
class org.biojava.bio.seq.db.
FetchURL
class org.biojava.bio.seq.
FilterUtils
class org.biojava.bio.seq.
FilterUtils.DelegatingTransformer
(implements org.biojava.bio.seq.
FilterUtils.FilterTransformer
)
class org.biojava.utils.cache.
FixedSizeCache
(implements org.biojava.utils.cache.
Cache
)
class org.biojava.utils.cache.
FixedSizeMap
(implements org.biojava.utils.cache.
CacheMap
)
class org.biojava.bio.program.unigene.
FlatFileUnigeneFactory
(implements org.biojava.bio.program.unigene.
UnigeneFactory
)
class org.biojava.bio.seq.db.flat.
FlatSequenceDBProvider
(implements org.biojava.directory.
SequenceDBProvider
)
class org.biojava.bio.program.tagvalue.
Formats
class org.biojava.bio.seq.
FramedFeature.ReadingFrame
(implements org.biojava.bio.seq.
Frame
, java.io.Serializable)
class org.biojava.bio.seq.io.game.
GAMEDbxrefPropHandler.DbXrefElement
class org.biojava.bio.seq.io.
GAMEFormat
(implements org.biojava.bio.seq.io.
SequenceFormat
)
class org.biojava.bio.seq.io.
GenbankFormat
(implements org.biojava.utils.
ParseErrorListener
, org.biojava.utils.
ParseErrorSource
, org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.bio.seq.io.
GenbankProcessor.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.seq.db.
GenbankSequenceDB
class org.biojava.bio.seq.
GeneticCodes
class org.biojava.bio.seq.db.
GenpeptSequenceDB
class org.biojava.bio.seq.distributed.
GFFDataSource
(implements org.biojava.bio.seq.distributed.
DistDataSource
)
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.FrameFilter
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFRecordFilter.NotFilter
(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.
GFFRecordFilter.StrandFilter
(implements org.biojava.bio.program.gff.
GFFRecordFilter
)
class org.biojava.bio.program.gff.
GFFTools
class org.biojava.bio.program.gff.
GFFWriter
(implements org.biojava.bio.program.gff.
GFFDocumentHandler
)
class org.biojava.bio.gui.sequence.
HeadlessRenderContext
(implements org.biojava.bio.gui.sequence.
SequenceRenderContext
)
class org.biojava.bio.program.ssaha.
HitMerger
(implements org.biojava.bio.program.ssaha.
SearchListener
)
class org.biojava.bio.program.hmmer.
HmmerProfileParser
class org.biojava.bio.program.blast2html.
HTMLRenderer
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.gui.sequence.
ImageMap.ClientSide
(implements org.biojava.bio.gui.sequence.
ImageMap
, java.io.Serializable)
class org.biojava.bio.gui.sequence.
ImageMap.HotSpot
(implements java.io.Serializable)
class org.biojava.bio.gui.sequence.
ImageMap.ServerSide
(implements org.biojava.bio.gui.sequence.
ImageMap
, java.io.Serializable)
class org.biojava.bio.program.tagvalue.
Index2Model
class org.biojava.utils.
IndexedChangeHub
(implements org.biojava.utils.
ChangeHub
)
class org.biojava.utils.
IndexedChangeHub.ListenerMemento
class org.biojava.bio.program.tagvalue.
Indexer
(implements org.biojava.bio.program.tagvalue.
TagValueListener
)
class org.biojava.bio.program.tagvalue.
Indexer2
(implements org.biojava.bio.program.tagvalue.
TagValueListener
)
class org.biojava.bio.program.indexdb.
IndexTools
class java.io.InputStream
class org.biojava.utils.io.
CachingInputStream
(implements org.biojava.utils.io.
Seekable
)
class org.biojava.bio.proteomics.
IsoelectricPointCalc
class org.biojava.bio.proteomics.
IsoelectricPointCalc.ChargeCalculator
(implements org.biojava.utils.math.
ComputeObject
)
class org.biojava.utils.
JDBCConnectionPool
class org.biojava.bio.search.
KnuthMorrisPrattSearch
class org.biojava.bio.gui.sequence.
LabelRenderer.RenderNothing
(implements org.biojava.bio.gui.sequence.
LabelRenderer
)
class org.biojava.utils.io.
LargeBuffer
class org.biojava.bio.gui.sequence.
LayeredRenderer
class org.biojava.bio.seq.impl.
LazyFilterFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
)
class org.biojava.utils.lsid.
LifeScienceIdentifier
(implements java.io.Serializable)
class org.biojava.bio.dp.twohead.
LightPairDPCursor
(implements org.biojava.bio.dp.twohead.
PairDPCursor
)
class org.biojava.stats.svm.
LinearKernel
(implements java.io.Serializable, org.biojava.stats.svm.
SVMKernel
)
class org.biojava.bio.gui.sequence.
LineInfo
class org.biojava.bio.program.tagvalue.
LineSplitParser
(implements java.lang.Cloneable, org.biojava.bio.program.tagvalue.
TagValueParser
)
class org.biojava.utils.
ListTools
(implements java.io.Serializable)
class org.biojava.bio.symbol.
LocationTools
class org.biojava.bio.seq.db.
LocusLinkParser
class org.biojava.bio.program.ssaha.
MappedDataStoreFactory
(implements org.biojava.bio.program.ssaha.
DataStoreFactory
)
class org.biojava.bio.proteomics.
MassCalc
class org.biojava.bio.program.
Meme
class org.biojava.bio.symbol.
MotifTools
class org.biojava.bio.seq.io.
MSFAlignmentFormat
(implements org.biojava.bio.seq.io.
AlignmentFormat
)
class org.biojava.bio.program.blast2html.
NcbiDatabaseURLGenerator
(implements org.biojava.bio.program.blast2html.
DatabaseURLGenerator
)
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.biojava.bio.program.ssaha.
NIODataStoreFactory
(implements org.biojava.bio.program.ssaha.
DataStoreFactory
)
class org.biojava.bio.seq.
NucleotideTools
class org.biojava.directory.
OBDARegistryParser
class org.biojava.utils.
ObjectUtil
class org.biojava.bio.dist.
OrderNDistributionFactory
(implements org.biojava.bio.dist.
DistributionFactory
)
class org.biojava.bio.seq.io.
OrganismParser.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.symbol.
PackedSymbolListFactory
(implements org.biojava.bio.symbol.
SymbolListFactory
)
class org.biojava.bio.symbol.
PackingFactory
class org.biojava.bio.dp.twohead.
PairDPMatrix
(implements org.biojava.bio.dp.
DPMatrix
, java.io.Serializable)
class org.biojava.bio.program.tagvalue.
Parser
class org.biojava.bio.program.tagvalue.
ParserListener
class org.biojava.bio.program.
PdbToXMLConverter
class org.biojava.bio.program.phred.
PhredFormat
(implements org.biojava.bio.seq.io.
SequenceFormat
, java.io.Serializable)
class org.biojava.bio.program.phred.
PhredTools
class org.biojava.bio.gui.
PlainBlock
(implements org.biojava.bio.gui.
BlockPainter
)
class org.biojava.bio.gui.
PlainStyle
(implements org.biojava.bio.gui.
SymbolStyle
)
class org.biojava.utils.xml.
PrettyXMLWriter
(implements org.biojava.utils.xml.
XMLWriter
)
class org.biojava.bio.seq.projection.
ProjectedFeature
(implements org.biojava.bio.seq.
Feature
, org.biojava.bio.seq.projection.
Projection
)
class org.biojava.bio.seq.projection.
ProjectedStrandedFeature
(implements org.biojava.bio.seq.
StrandedFeature
)
class org.biojava.bio.seq.projection.
ProjectionEngine
class org.biojava.bio.seq.projection.
ProjectionEngine.InstantiatorImpl
(implements org.biojava.bio.seq.projection.
ProjectionEngine.Instantiator
)
class org.biojava.bio.seq.projection.
ProjectionUtils
class org.biojava.bio.
PropertyConstraint.And
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.
PropertyConstraint.ByAnnotationType
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.
PropertyConstraint.ByClass
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.
PropertyConstraint.Enumeration
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.
PropertyConstraint.ExactValue
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.
PropertyConstraint.Or
(implements org.biojava.bio.
PropertyConstraint
)
class org.biojava.bio.proteomics.
Protease
(implements java.io.Serializable)
class org.biojava.bio.proteomics.
ProteaseManager
class org.biojava.bio.seq.io.
ProteinRefSeqProcessor.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.seq.
ProteinTools
class org.biojava.bio.seq.ragbag.RagbagAbstractSequence (implements org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.seq.ragbag.
RagbagAssembly
class org.biojava.bio.seq.ragbag.
RagbagComponentDirectory.EmptyComponentDirectory
(implements org.biojava.bio.seq.ragbag.
RagbagComponentDirectory
)
class org.biojava.bio.seq.ragbag.
RagbagFeatureTypeCatcher
(implements org.biojava.bio.seq.ragbag.
RagbagFilterFactory
)
class org.biojava.bio.seq.ragbag.
RagbagFilteredCachedSeqFactory
(implements org.biojava.bio.seq.ragbag.
RagbagSequenceFactory
)
class org.biojava.bio.seq.ragbag.
RagbagFixedCacheSeqFactory
(implements org.biojava.bio.seq.ragbag.
RagbagSequenceFactory
)
class org.biojava.bio.seq.ragbag.
RagbagHashedComponentDirectory
(implements org.biojava.bio.seq.ragbag.
RagbagComponentDirectory
)
class org.biojava.bio.seq.ragbag.
RagbagIdleSequenceBuilder
(implements org.biojava.bio.seq.io.
SequenceBuilder
)
class org.biojava.bio.seq.ragbag.
RagbagMap.MapElement
class org.biojava.bio.seq.ragbag.
RagbagMap.MapEnum
(implements java.util.Enumeration)
class org.biojava.bio.seq.ragbag.
RagbagSoftRefSeqFactory
(implements org.biojava.bio.seq.ragbag.
RagbagSequenceFactory
)
class org.biojava.bio.seq.ragbag.
RagbagUncachedSeqFactory
(implements org.biojava.bio.seq.ragbag.
RagbagSequenceFactory
)
class java.io.RandomAccessFile (implements java.io.DataInput, java.io.DataOutput)
class org.biojava.utils.io.
RAF
class java.io.Reader
class java.io.BufferedReader
class org.biojava.utils.io.
CountedBufferedReader
class org.biojava.utils.io.
RandomAccessReader
class org.biojava.bio.program.indexdb.
Record.Impl
(implements org.biojava.bio.program.indexdb.
Record
)
class org.biojava.bio.gui.sequence.
RectangularImapRenderer
(implements org.biojava.bio.gui.sequence.
BeadFeatureRenderer
, org.biojava.bio.gui.sequence.
ImageMapRenderer
, java.io.Serializable)
class java.lang.ref.Reference
class java.lang.ref.WeakReference
class org.biojava.utils.cache.
KeyedWeakReference
class org.biojava.bio.program.tagvalue.
RegexChanger
(implements org.biojava.bio.program.tagvalue.
ChangeTable.Changer
)
class org.biojava.bio.program.tagvalue.
RegexParser
(implements org.biojava.bio.program.tagvalue.
TagValueParser
)
class org.biojava.bio.program.tagvalue.
RegexSplitter
(implements org.biojava.bio.program.tagvalue.
ChangeTable.Splitter
)
class org.biojava.directory.
Registry
class org.biojava.directory.
RegistryConfiguration.Composite
(implements org.biojava.directory.
RegistryConfiguration
)
class org.biojava.directory.
RegistryConfiguration.Impl
(implements org.biojava.directory.
RegistryConfiguration
)
class org.biojava.bio.seq.
RemoteFeature.Region
class org.biojava.utils.xml.
ResourceEntityResolver
(implements org.xml.sax.EntityResolver)
class org.biojava.bio.molbio.
RestrictionEnzyme
(implements java.io.Serializable)
class org.biojava.bio.molbio.
RestrictionEnzymeManager
class org.biojava.bio.molbio.
RestrictionMapper
(implements org.biojava.bio.seq.
SequenceAnnotator
)
class org.biojava.bio.seq.
RNATools
class org.biojava.bio.gui.sequence.
RulerRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.seq.io.agave.
SAX2StAXAdaptor
(implements org.xml.sax.ContentHandler)
class org.biojava.utils.stax.
SAX2StAXAdaptor
(implements org.xml.sax.ContentHandler)
class org.biojava.bio.dp.
ScoreType.NullModel
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.dp.
ScoreType.Odds
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.dp.
ScoreType.Probability
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.search.
SearchContentAdapter
(implements org.biojava.bio.search.
SearchContentHandler
)
class org.biojava.bio.search.
SearchContentFilter
(implements org.biojava.bio.search.
SearchContentHandler
)
class org.biojava.bio.seq.io.
SeqAlignReadWrite
class org.biojava.bio.seq.io.
SeqIOAdapter
(implements org.biojava.bio.seq.io.
SeqIOListener
)
class org.biojava.bio.seq.io.
SeqIOConstants
class org.biojava.bio.seq.io.
SeqIOFilter
(implements org.biojava.bio.seq.io.
SeqIOListener
)
class org.biojava.bio.seq.io.
SeqIOTools
class org.biojava.bio.program.ssbind.
SeqSimilarityAdapter
(implements org.xml.sax.ContentHandler)
class org.biojava.bio.search.
SeqSimilaritySearchHit.ByScoreComparator
(implements java.util.Comparator)
class org.biojava.bio.search.
SeqSimilaritySearchHit.BySubHitCountComparator
(implements java.util.Comparator)
class org.biojava.bio.search.
SeqSimilaritySearchSubHit.ByScoreComparator
(implements java.util.Comparator)
class org.biojava.bio.search.
SeqSimilaritySearchSubHit.BySubjectStartComparator
(implements java.util.Comparator)
class org.biojava.bio.seq.io.
SequenceBuilderBase
(implements org.biojava.bio.seq.io.
SequenceBuilder
)
class org.biojava.bio.seq.io.
SequenceDBSequenceBuilder
class org.biojava.bio.seq.io.
SimpleAssemblyBuilder
class org.biojava.bio.seq.io.
SimpleSequenceBuilder
class org.biojava.bio.seq.io.
SmartSequenceBuilder
class org.biojava.bio.seq.io.
SequenceBuilderFilter
(implements org.biojava.bio.seq.io.
SequenceBuilder
)
class org.biojava.bio.seq.io.
EmblProcessor
(implements org.biojava.utils.
ParseErrorSource
)
class org.biojava.bio.seq.io.
FastaDescriptionLineParser
class org.biojava.bio.seq.io.
GenbankProcessor
(implements org.biojava.utils.
ParseErrorSource
)
class org.biojava.bio.seq.io.
ProteinRefSeqProcessor
class org.biojava.bio.seq.io.
OrganismParser
class org.biojava.bio.seq.io.
SwissprotProcessor
(implements org.biojava.utils.
ParseErrorSource
)
class org.biojava.bio.seq.distributed.
SequenceDBDataSource
(implements org.biojava.bio.seq.distributed.
DistDataSource
)
class org.biojava.bio.gui.sequence.
SequencePanel.Border
(implements java.io.Serializable, javax.swing.SwingConstants)
class org.biojava.bio.gui.sequence.
SequencePoster.Border
(implements java.io.Serializable, javax.swing.SwingConstants)
class org.biojava.bio.gui.sequence.
SequenceRenderContext.Border
(implements java.io.Serializable, javax.swing.SwingConstants)
class org.biojava.bio.program.gff.
SequencesAsGFF
class org.biojava.bio.program.ssaha.
SequenceStreamer.FileStreamer
(implements org.biojava.bio.program.ssaha.
SequenceStreamer
)
class org.biojava.bio.program.ssaha.
SequenceStreamer.SequenceDBStreamer
(implements org.biojava.bio.program.ssaha.
SequenceStreamer
)
class org.biojava.bio.seq.
SequenceTools
class org.biojava.bio.gui.sequence.
SequenceViewerMotionSupport
class org.biojava.bio.gui.sequence.
SequenceViewerSupport
class org.biojava.utils.
Services
class org.biojava.stats.svm.
SigmoidKernel
(implements org.biojava.stats.svm.
SVMKernel
)
class org.biojava.bio.alignment.
SimpleAlignmentElement
(implements org.biojava.bio.alignment.
AlignmentElement
)
class org.biojava.bio.seq.io.agave.
SimpleAnnotFilter
(implements org.biojava.bio.seq.io.agave.
AGAVEAnnotFilter
)
class org.biojava.bio.seq.io.agave.
Agave2AgaveAnnotFilter
class org.biojava.bio.seq.io.agave.
Embl2AgaveAnnotFilter
class org.biojava.bio.dist.
SimpleDistribution.Trainer
(implements org.biojava.bio.dist.
DistributionTrainer
)
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.seq.
SimpleFeatureRealizer
(implements org.biojava.bio.seq.
FeatureRealizer
, java.io.Serializable)
class org.biojava.bio.symbol.
SimpleGappedSymbolList.Block
(implements java.io.Serializable)
class org.biojava.bio.program.gff.
SimpleGFFRecord
(implements org.biojava.bio.program.gff.
GFFRecord
)
class org.biojava.bio.seq.db.
SimpleIndex
(implements org.biojava.bio.seq.db.
Index
)
class org.biojava.stats.svm.
SimpleItemValue
(implements org.biojava.stats.svm.
ItemValue
)
class org.biojava.bio.seq.impl.
SimpleRemoteFeature.DBResolver
(implements org.biojava.bio.seq.
RemoteFeature.Resolver
)
class org.biojava.bio.seq.db.
SimpleSequenceDBInstallation
(implements org.biojava.bio.seq.db.
SequenceDBInstallation
)
class org.biojava.bio.seq.impl.
SimpleSequenceFactory
(implements org.biojava.bio.seq.
SequenceFactory
, java.io.Serializable)
class org.biojava.stats.svm.
SimpleSVMTarget
(implements org.biojava.stats.svm.
SVMTarget
)
class org.biojava.bio.symbol.
SimpleSymbolListFactory
(implements org.biojava.bio.symbol.
SymbolListFactory
)
class org.biojava.bio.symbol.
SimpleSymbolPropertyTable
(implements org.biojava.bio.symbol.
SymbolPropertyTable
)
class org.biojava.bio.gui.
SimpleSymbolStyle
(implements org.biojava.bio.gui.
SymbolStyle
)
class org.biojava.bio.taxa.
SimpleTaxonFactory
(implements org.biojava.bio.taxa.
TaxonFactory
)
class org.biojava.utils.
SimpleThreadPool
(implements org.biojava.utils.
ThreadPool
)
class org.biojava.bio.symbol.
SimpleTranslationTable
(implements java.io.Serializable, org.biojava.bio.symbol.
TranslationTable
)
class org.biojava.bio.symbol.
SimpleReversibleTranslationTable
(implements org.biojava.bio.symbol.
ReversibleTranslationTable
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleWeightMatrix
(implements java.io.Serializable, org.biojava.bio.dp.
WeightMatrix
)
class org.biojava.bio.dp.onehead.
SingleDPMatrix
(implements org.biojava.bio.dp.
DPMatrix
, java.io.Serializable)
class org.biojava.stats.svm.
SMORegressionTrainer
class org.biojava.stats.svm.
SMOTrainer
class org.biojava.utils.cache.
SoftReferenceCache
(implements org.biojava.utils.cache.
Cache
)
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.biojava.bio.program.unigene.
SQLUnigeneFactory
(implements org.biojava.bio.program.unigene.
UnigeneFactory
)
class org.biojava.bio.gui.
StackedLogoPainter
(implements org.biojava.bio.gui.
LogoPainter
)
class org.biojava.utils.
StaticMemberPlaceHolder
(implements java.io.Serializable)
class org.biojava.utils.stax.
StAXContentHandlerBase
(implements org.biojava.utils.stax.
StAXContentHandler
)
class org.biojava.utils.stax.
BooleanElementHandlerBase
class org.biojava.utils.stax.
ByteElementHandlerBase
class org.biojava.utils.stax.
CharElementHandlerBase
class org.biojava.utils.stax.
DoubleElementHandlerBase
class org.biojava.bio.program.xff.
FeatureHandler
class org.biojava.bio.program.xff.
StrandedFeatureHandler
class org.biojava.utils.stax.
FloatElementHandlerBase
class org.biojava.utils.stax.
IntElementHandlerBase
class org.biojava.bio.program.xff.
LocationHandlerBase
class org.biojava.utils.stax.
LongElementHandlerBase
class org.biojava.bio.seq.ragbag.
RagbagMap
class org.biojava.bio.program.ssbind.
SeqSimilarityStAXAdapter
class org.biojava.bio.program.ssbind.
SeqSimilarityStAXHandler
class org.biojava.bio.program.ssbind.
AlignmentStAXHandler
class org.biojava.bio.program.ssbind.
HeaderStAXHandler
class org.biojava.bio.program.ssbind.
HitStAXHandler
class org.biojava.bio.program.ssbind.
HSPStAXHandler
class org.biojava.bio.program.ssbind.
HSPSummaryStAXHandler
class org.biojava.bio.seq.io.game.
SequenceContentHandlerBase
class org.biojava.bio.seq.io.game.
GAMEResiduesPropHandler
class org.biojava.bio.program.sax.blastxml.StAXFeatureHandler
class org.biojava.bio.program.sax.blastxml.
BlastXMLParser
class org.biojava.bio.seq.io.game.
StAXFeatureHandler
class org.biojava.bio.seq.io.game.
GAMEAnnotationHandler
(implements org.biojava.bio.seq.io.game.
GAMEFeatureCallbackItf
)
class org.biojava.bio.seq.io.game.
GAMEFeatureSetHandler
(implements org.biojava.bio.seq.io.game.
GAMENameCallbackItf
, org.biojava.bio.seq.io.game.
GAMETranscriptCallbackItf
)
class org.biojava.bio.seq.io.game.
GAMEFeatureSpanHandler
class org.biojava.bio.seq.io.game.
GAMEHandler
class org.biojava.bio.seq.io.game12.
StAXFeatureHandler
class org.biojava.bio.seq.io.game12.
GAMEAnnotationHandler
class org.biojava.bio.seq.io.game12.
GAMEAspectHandler
class org.biojava.bio.seq.io.game12.
GAMEDbxrefHandler
class org.biojava.bio.seq.io.game12.
GAMEFeatureSetHandler
class org.biojava.bio.seq.io.game12.
GAMEFeatureSpanHandler
class org.biojava.bio.seq.io.game12.
GAMEGeneHandler
class org.biojava.bio.seq.io.game12.
GAMEHandler
class org.biojava.bio.seq.io.game12.
GAMEPropertyHandler
class org.biojava.bio.seq.io.game12.
GAMESeqHandler
class org.biojava.bio.seq.io.game12.
GAMESeqRelHandler
class org.biojava.bio.seq.io.game12.
GAMEFeatureSpanHandler.SeqRelHandler
class org.biojava.bio.seq.io.game12.
GAMESpanHandler
class org.biojava.bio.seq.io.game.
StAXPropertyHandler
class org.biojava.bio.seq.io.game.
GAMEAspectPropHandler
class org.biojava.bio.seq.io.game.
GAMEDbxrefPropHandler
class org.biojava.bio.seq.io.game.
GAMEFeatureSetPropHandler
class org.biojava.bio.seq.io.game.
GAMEGenePropHandler
(implements org.biojava.bio.seq.io.game.
GAMENameCallbackItf
)
class org.biojava.bio.seq.io.game.
GAMEMapPosPropHandler
class org.biojava.bio.seq.io.game.
GAMESeqPropHandler
(implements org.biojava.bio.seq.io.game.
GAMENameCallbackItf
)
class org.biojava.bio.seq.io.game.
GAMESeqRelPropHandler
class org.biojava.bio.seq.io.game.
GAMESpanPropHandler
class org.biojava.utils.stax.
StringElementHandlerBase
class org.biojava.bio.seq.io.game.
GAMEDescriptionPropHandler
class org.biojava.bio.seq.io.game.
GAMENamePropHandler
class org.biojava.bio.seq.io.game.
GAMETypePropHandler
class org.biojava.bio.program.xff.
PropDetailHandler
class org.biojava.bio.program.xff.
XFFFeatureSetHandler
class org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeHandler
class org.biojava.bio.seq.io.agave.
StAXContentHandlerBase
(implements org.biojava.bio.seq.io.agave.
StAXContentHandler
)
class org.biojava.bio.seq.io.agave.
StAXFeatureHandler
class org.biojava.bio.seq.io.agave.
AGAVEAssemblyHandler
(implements org.biojava.bio.seq.io.agave.
SequenceHandler
)
class org.biojava.bio.seq.io.agave.
AGAVEBioSeqHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEBioSeqCallbackItf
, org.biojava.bio.seq.io.agave.
SequenceHandler
)
class org.biojava.bio.seq.io.agave.
AGAVEBioSequenceHandler
class org.biojava.bio.seq.io.agave.
AGAVECdsHandler
class org.biojava.bio.seq.io.agave.
AGAVEChromosomeHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEChromosomeCallbackItf
, org.biojava.bio.seq.io.agave.
SequenceHandler
)
class org.biojava.bio.seq.io.agave.
AGAVEClassificationHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEIdAliasCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVECompResultHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEFeatureCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEComputationHandler
class org.biojava.bio.seq.io.agave.
AGAVEContigHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEContigCallbackItf
, org.biojava.bio.seq.io.agave.
SequenceHandler
)
class org.biojava.bio.seq.io.agave.
AGAVEEvidenceHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEEvidenceCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEFragmentOrderHandler
class org.biojava.bio.seq.io.agave.
AGAVEFragmentOrientationHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEFeatureCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEGeneHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEFeatureCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEHandler
(implements org.biojava.bio.seq.io.agave.
AGAVECallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEMrnaHandler
class org.biojava.bio.seq.io.agave.
AGAVEPredictedProteinHandler
class org.biojava.bio.seq.io.agave.
AGAVEQueryRegionPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEResultGroupHandler
class org.biojava.bio.seq.io.agave.
AGAVESeqFeatureHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEFeatureCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVESeqMapHandler
class org.biojava.bio.seq.io.agave.
AGAVETranscriptHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEEvidenceCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEUnorderedFragmentsHandler
class org.biojava.bio.seq.io.agave.
StAXPropertyHandler
class org.biojava.bio.seq.io.agave.
AGAVEAltIdsPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEAnnotationsHandler
class org.biojava.bio.seq.io.agave.
AGAVEDbIdPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEDescPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEElementIdPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEExonsPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEIdAliasPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEKeywordPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEMapLocationPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEMapPositionPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEMatchAlignPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEMatchDescPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEMatchRegionPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
, org.biojava.bio.seq.io.agave.
AGAVEEvidenceCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVENotePropHandler
class org.biojava.bio.seq.io.agave.
AGAVEQualifierPropHandler
class org.biojava.bio.seq.io.agave.
AGAVERelatedAnnotPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEEvidenceCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEResultPropertyPropHandler
class org.biojava.bio.seq.io.agave.
AGAVESciPropertyPropHandler
class org.biojava.bio.seq.io.agave.
AGAVESeqLocationPropHandler
class org.biojava.bio.seq.io.agave.
AGAVESeqPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEViewPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEXrefPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
, org.biojava.bio.seq.io.agave.
AGAVEDbIdPropCallbackItf
)
class org.biojava.bio.seq.io.agave.
AGAVEXrefPropPropHandler
class org.biojava.bio.seq.io.agave.
AGAVEXrefsPropHandler
(implements org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
, org.biojava.bio.seq.io.agave.
AGAVEXrefCallbackItf
)
class org.biojava.bio.program.ssbind.
StAXHandlerBinding
class org.biojava.bio.gui.sequence.
StopRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.seq.
StrandedFeature.Strand
(implements java.io.Serializable)
class org.biojava.bio.seq.
StrandParser
class org.biojava.bio.seq.io.
StreamReader
(implements org.biojava.utils.
ParseErrorListener
, org.biojava.bio.seq.
SequenceIterator
)
class org.biojava.bio.seq.io.
StreamWriter
class org.biojava.bio.proteomics.
StructureTools
class org.biojava.bio.gui.sequence.
SubPairwiseRenderContext
(implements org.biojava.bio.gui.sequence.
PairwiseRenderContext
)
class org.biojava.bio.seq.
SubSequence
(implements org.biojava.bio.seq.
Sequence
)
class org.biojava.bio.gui.sequence.
SubSequenceRenderContext
(implements org.biojava.bio.gui.sequence.
SequenceRenderContext
)
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.seq.io.
SwissprotProcessor.Factory
(implements org.biojava.bio.seq.io.
SequenceBuilderFactory
, java.io.Serializable)
class org.biojava.bio.seq.db.
SwissprotSequenceDB
class org.biojava.bio.seq.io.
SymbolListCharSequence
(implements java.lang.CharSequence)
class org.biojava.bio.symbol.
SymbolListViews
class org.biojava.bio.gui.sequence.
SymbolSequenceRenderer
(implements org.biojava.bio.gui.sequence.
SequenceRenderer
)
class org.biojava.bio.seq.io.
SymbolTokenization.TokenType
class org.biojava.directory.
SystemRegistry
class org.biojava.bio.seq.db.
TabIndexStore
(implements org.biojava.bio.seq.db.
IndexStore
, java.io.Serializable)
class org.biojava.bio.program.tagvalue.
TagMapper
class org.biojava.bio.program.tagvalue.
TagValue
class org.biojava.bio.program.tagvalue.
TagValueWrapper
(implements org.biojava.bio.program.tagvalue.
TagValueListener
)
class org.biojava.bio.program.tagvalue.
RegexFieldFinder
class org.biojava.bio.program.tagvalue.
TagDelegator
class org.biojava.bio.program.tagvalue.
TagDropper
class org.biojava.bio.program.tagvalue.
TagRenamer
class org.biojava.bio.program.tagvalue.
ValueChanger
class org.biojava.bio.gui.
TextBlock
(implements org.biojava.bio.gui.
BlockPainter
)
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.utils.
NestedError
class org.biojava.bio.
BioError
class java.lang.Exception
class org.biojava.utils.xml.
AppException
class org.biojava.bio.program.gff.
IgnoreRecordException
class org.biojava.utils.lsid.
LifeScienceIdentifierParseException
class org.biojava.utils.
NestedException
class org.biojava.bio.
BioException
class org.biojava.bio.taxa.
CircularReferenceException
class org.biojava.bio.symbol.
IllegalAlphabetException
class org.biojava.bio.seq.db.
IllegalIDException
class org.biojava.bio.symbol.
IllegalSymbolException
class org.biojava.bio.dp.
IllegalTransitionException
class org.biojava.bio.seq.io.
ParseException
class org.biojava.bio.chromatogram.
UnsupportedChromatogramFormatException
class org.biojava.utils.
ChangeVetoException
class org.biojava.utils.
ParserException
class org.biojava.directory.
RegistryException
class org.biojava.directory.
ProviderNotFoundException
class java.lang.RuntimeException
class org.biojava.utils.
NestedRuntimeException
class org.biojava.bio.
BioRuntimeException
class org.biojava.bio.alignment.
IllegalAlignmentEditException
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.biojava.bio.symbol.
UkkonenSuffixTree
class org.biojava.utils.
Unchangeable
(implements org.biojava.utils.
Changeable
)
class org.biojava.bio.seq.db.biofetch.
BioFetchSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDBLite
)
class org.biojava.bio.seq.io.
CharacterTokenization
(implements java.io.Serializable, org.biojava.bio.seq.io.
SymbolTokenization
)
class org.biojava.bio.program.das.
DASSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDB
)
class org.biojava.bio.symbol.
DoubleAlphabet
(implements org.biojava.bio.symbol.
Alphabet
, java.io.Serializable)
class org.biojava.bio.symbol.
DoubleAlphabet.DoubleRange
(implements org.biojava.bio.symbol.
BasisSymbol
, java.io.Serializable)
class org.biojava.bio.symbol.
DoubleAlphabet.DoubleSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
, java.io.Serializable)
class org.biojava.bio.symbol.
DoubleAlphabet.SubDoubleAlphabet
(implements org.biojava.bio.symbol.
Alphabet
, java.io.Serializable)
class org.biojava.bio.seq.
FeatureHolder.EmptyFeatureHolder
(implements org.biojava.bio.seq.
FeatureHolder
)
class org.biojava.bio.seq.db.flat.
FlatSequenceDB
(implements org.biojava.bio.seq.db.
SequenceDBLite
)
class org.biojava.bio.dist.
GapDistribution
(implements org.biojava.bio.dist.
Distribution
, 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.bio.symbol.
RelabeledAlignment
(implements org.biojava.bio.symbol.
Alignment
)
class org.biojava.bio.seq.homol.
SimilarityPairFeature.EmptyPairwiseAlignment
(implements org.biojava.bio.symbol.
Alignment
)
class org.biojava.bio.dp.
SimpleStatePath
(implements java.io.Serializable, org.biojava.bio.dp.
StatePath
)
class org.biojava.bio.symbol.
SymbolList.EmptySymbolList
(implements java.io.Serializable, org.biojava.bio.symbol.
SymbolList
)
class org.biojava.bio.seq.
ViewSequence
(implements org.biojava.bio.seq.
RealizingFeatureHolder
, org.biojava.bio.seq.
Sequence
, java.io.Serializable)
class org.biojava.bio.seq.
CircularView
class org.biojava.bio.seq.io.
WordTokenization
(implements java.io.Serializable, org.biojava.bio.seq.io.
SymbolTokenization
)
class org.biojava.bio.seq.io.
CrossProductTokenization
class org.biojava.bio.seq.io.
DoubleTokenization
class org.biojava.bio.seq.io.
IntegerTokenization
class org.biojava.bio.seq.io.
NameTokenization
class org.biojava.bio.program.unigene.
UnigeneTools
class org.biojava.bio.seq.io.agave.
UtilHelper
class org.biojava.bio.program.ssbind.
ViewSequenceFactory
class org.biojava.bio.program.ssbind.
BlastLikeHomologyBuilder
(implements org.biojava.bio.search.
SearchContentHandler
)
class org.biojava.bio.program.ssbind.
SimilarityPairBuilder
(implements org.biojava.bio.search.
SearchContentHandler
)
class org.biojava.utils.cache.
WeakCacheMap
(implements org.biojava.utils.cache.
CacheMap
)
class org.biojava.bio.taxa.
WeakTaxonFactory
(implements org.biojava.bio.taxa.
TaxonFactory
)
class org.biojava.bio.dp.
WeightMatrixAnnotator
(implements org.biojava.bio.seq.
SequenceAnnotator
, java.io.Serializable)
class org.biojava.bio.program.xff.
XFFTools
class org.biojava.bio.program.xff.
XFFWriter
class org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeWriter
class org.biojava.utils.xml.
XMLBeans
class org.biojava.utils.xml.
XMLDispatcher
(implements org.biojava.utils.xml.
XMLPeerFactory
)
class org.biojava.bio.dist.
XMLDistributionWriter
class org.biojava.bio.seq.io.filterxml.
XMLFilterHandler
class org.biojava.bio.seq.io.filterxml.
XMLFilterWriter
class org.biojava.bio.dp.
XmlMarkovModel
class org.biojava.utils.xml.
XMLPeerBuilder
(implements org.xml.sax.DocumentHandler)
class org.biojava.bio.gui.sequence.
ZiggyImapRenderer
(implements org.biojava.bio.gui.sequence.
ImageMapRenderer
, java.io.Serializable)
Interface Hierarchy
interface org.biojava.utils.
ActivityListener
interface org.biojava.bio.seq.io.agave.
AGAVEAnnotFilter
interface org.biojava.bio.seq.io.agave.
AGAVEAnnotFilterFactory
interface org.biojava.bio.seq.io.agave.
AGAVEBioSeqCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVECallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEChromosomeCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEContigCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEDbIdCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEDbIdPropCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEEvidenceCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEFeatureCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEIdAliasCallbackItf
interface org.biojava.bio.seq.io.agave.
AGAVEXrefCallbackItf
interface org.biojava.bio.alignment.
AlignmentElement
interface org.biojava.bio.seq.io.
AlignmentFormat
interface org.biojava.bio.
AnnotationType
interface org.biojava.utils.xml.
AppEntry
interface org.biojava.bibliography.
BibRefQuery
interface org.biojava.bibliography.
BibRefSupport
interface org.biojava.bio.gui.
BlockPainter
interface org.biojava.utils.cache.
Cache
interface org.biojava.utils.cache.
CacheMap
interface org.biojava.utils.cache.
CacheReference
interface org.biojava.bio.dp.twohead.
CellCalculator
interface org.biojava.bio.dp.twohead.
CellCalculatorFactory
interface org.biojava.bio.dp.twohead.
CellCalculatorFactoryMaker
interface org.biojava.utils.
Changeable
interface org.biojava.bio.symbol.
Alignment
interface org.biojava.bio.alignment.
ARAlignment
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.alignment.
UnequalLengthAlignment
interface org.biojava.bio.symbol.
Alphabet
interface org.biojava.bio.symbol.
FiniteAlphabet
interface org.biojava.bio.symbol.
AlphabetIndex
interface org.biojava.bio.
Annotatable
interface org.biojava.bio.symbol.
Alphabet
interface org.biojava.bio.symbol.
FiniteAlphabet
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.symbol.
BasisSymbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.seq.
Feature
(also extends org.biojava.bio.seq.
FeatureHolder
)
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
FeatureTypes.Repository
interface org.biojava.bio.seq.
FeatureTypes.Type
interface org.biojava.bio.symbol.
FiniteAlphabet
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
, org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.search.
SeqSimilaritySearchHit
interface org.biojava.bio.search.
SeqSimilaritySearchResult
interface org.biojava.bio.search.
SeqSimilaritySearchSubHit
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.seq.
FeatureHolder
, org.biojava.bio.symbol.
SymbolList
)
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
)
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.symbol.
Symbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.symbol.
BasisSymbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.seq.io.
SymbolTokenization
interface org.biojava.bio.taxa.
Taxon
interface org.biojava.bio.program.unigene.
UnigeneCluster
interface org.biojava.bio.
Annotation
interface org.biojava.bio.alignment.
ARAlignment
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.symbol.
BasisSymbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.dist.
Count
interface org.biojava.bio.dist.
Distribution
interface org.biojava.bio.dist.
OrderNDistribution
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.seq.
Feature
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.seq.
FeatureHolder
)
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
FeatureHolder
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
Feature
(also extends org.biojava.bio.
Annotatable
)
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
, org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RealizingFeatureHolder
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.symbol.
SymbolList
)
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
)
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.seq.
FeatureTypes.Repository
interface org.biojava.bio.seq.
FeatureTypes.Type
interface org.biojava.bio.symbol.
FiniteAlphabet
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
, org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.symbol.
GappedSymbolList
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.dp.
MarkovModel
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dist.
OrderNDistribution
interface org.biojava.bio.seq.
RealizingFeatureHolder
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.search.
SeqSimilaritySearchHit
interface org.biojava.bio.search.
SeqSimilaritySearchResult
interface org.biojava.bio.search.
SeqSimilaritySearchSubHit
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.seq.
FeatureHolder
, org.biojava.bio.symbol.
SymbolList
)
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
)
interface org.biojava.bio.seq.db.
SequenceDB
interface org.biojava.bio.seq.db.
SequenceDBLite
interface org.biojava.bio.seq.db.
SequenceDB
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.seq.
StrandedFeature
interface org.biojava.bio.seq.
ComponentFeature
interface org.biojava.bio.seq.
FramedFeature
interface org.biojava.bio.seq.homol.
HomologyFeature
interface org.biojava.bio.seq.
RemoteFeature
interface org.biojava.bio.molbio.
RestrictionSite
interface org.biojava.bio.seq.homol.
SimilarityPairFeature
interface org.biojava.bio.symbol.
Symbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.symbol.
BasisSymbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.symbol.
SymbolList
interface org.biojava.bio.symbol.
Alignment
interface org.biojava.bio.alignment.
ARAlignment
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.alignment.
UnequalLengthAlignment
interface org.biojava.bio.alignment.
ARAlignment
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
, org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.symbol.
GappedSymbolList
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.seq.
Sequence
)
interface org.biojava.bio.seq.
Sequence
(also extends org.biojava.bio.
Annotatable
, org.biojava.bio.seq.
FeatureHolder
)
interface org.biojava.bio.seq.
GappedSequence
(also extends org.biojava.bio.symbol.
GappedSymbolList
)
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.alignment.
UnequalLengthAlignment
interface org.biojava.bio.seq.io.
SymbolTokenization
interface org.biojava.bio.taxa.
Taxon
interface org.biojava.bio.alignment.
UnequalLengthAlignment
interface org.biojava.bio.program.unigene.
UnigeneCluster
interface org.biojava.bio.program.unigene.
UnigeneDB
interface org.biojava.utils.
ChangeHub
interface org.biojava.bio.program.tagvalue.
ChangeTable.Changer
interface org.biojava.bio.program.tagvalue.
ChangeTable.Splitter
interface org.biojava.bio.chromatogram.
Chromatogram
interface org.biojava.bio.
CollectionConstraint
interface org.biojava.bio.program.blast2html.
ColourCommand
interface org.biojava.utils.
Commitable
interface org.biojava.utils.math.
ComputeObject
interface org.biojava.bio.program.blast2html.
DatabaseURLGenerator
interface java.io.DataInput
interface org.biojava.bio.program.abi.
ABIFParser.DataAccess
(also extends org.biojava.utils.io.
Seekable
)
interface org.biojava.bio.program.ssaha.
DataStore
interface org.biojava.bio.program.ssaha.
DataStoreFactory
interface org.biojava.bio.seq.io.agave.
DelegationManager
interface org.biojava.utils.stax.
DelegationManager
interface org.biojava.bio.seq.distributed.
DistDataSource
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.
DPFactory
interface org.biojava.bio.dp.
DPMatrix
interface org.biojava.bio.alignment.
EditableAlignment
interface org.biojava.bio.program.xff.
ElementRecognizer
interface org.biojava.bio.seq.io.agave.
ElementRecognizer
interface org.biojava.bio.seq.io.game.
ElementRecognizer
interface java.util.EventListener
interface org.biojava.utils.candy.
CandyFinder
interface org.biojava.utils.candy.
CandyVocabulary
interface org.biojava.utils.
ChangeListener
interface org.biojava.utils.
ParseErrorListener
interface java.beans.PropertyChangeListener
interface org.biojava.utils.candy.
CandyFinder
interface org.biojava.utils.candy.
CandyVocabulary
interface org.biojava.bio.gui.sequence.
SequenceViewerListener
interface org.biojava.bio.gui.sequence.
SequenceViewerMotionListener
interface org.biojava.stats.svm.
TrainingListener
interface org.biojava.bio.gui.sequence.
FeatureLabelRenderer.LabelMaker
interface org.biojava.bio.seq.
FeatureRealizer
interface org.biojava.bio.gui.sequence.
FeatureRenderer
interface org.biojava.bio.gui.sequence.
BeadFeatureRenderer
interface org.biojava.bio.gui.sequence.
ImageMapRenderer
interface org.biojava.bio.seq.
FilterUtils.FilterTransformer
interface org.biojava.bio.seq.
Frame
interface org.biojava.bio.symbol.
FuzzyPointLocation.PointResolver
interface org.biojava.bio.seq.io.game.
GAMEFeatureCallbackItf
interface org.biojava.bio.seq.io.game.
GAMENameCallbackItf
interface org.biojava.bio.seq.io.game.
GAMETranscriptCallbackItf
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.homol.
Homology
interface org.biojava.bio.seq.homol.
HomologyDB
interface org.biojava.utils.lsid.
Identifiable
interface org.biojava.bio.seq.db.
IDMaker
interface org.biojava.bio.gui.sequence.
ImageMap
interface org.biojava.bio.seq.db.
Index
interface org.biojava.bio.program.indexdb.
IndexStore
interface org.biojava.bio.seq.db.
IndexStore
interface org.biojava.utils.xml.
Initializable
interface org.biojava.stats.svm.
ItemValue
interface org.biojava.bio.gui.sequence.
LabelRenderer
interface org.biojava.bio.symbol.
Location
interface org.biojava.bio.gui.
LogoContext
interface org.biojava.bio.gui.
LogoPainter
interface org.biojava.bio.gui.sequence.
OverlayMarker
interface org.biojava.bio.symbol.
Packing
interface org.biojava.bio.dp.twohead.
PairDPCursor
interface org.biojava.bio.gui.sequence.
PairwiseSequenceRenderer
interface org.biojava.utils.
ParseErrorSource
interface org.biojava.bio.seq.projection.
Projection
interface org.biojava.bio.seq.projection.
ProjectionContext
interface org.biojava.bio.seq.projection.
ProjectionEngine.Instantiator
interface org.biojava.bio.
PropertyConstraint
interface org.biojava.bio.program.phred.
Qualitative
interface org.biojava.bio.alignment.
QualitativeAlignment
interface org.biojava.bio.seq.ragbag.
RagbagComponentDirectory
interface org.biojava.bio.seq.ragbag.
RagbagFileParserFactory
interface org.biojava.bio.seq.ragbag.
RagbagFilterFactory
interface org.biojava.bio.seq.ragbag.
RagbagSequenceFactory
interface org.biojava.bio.program.indexdb.
Record
interface org.biojava.directory.
RegistryConfiguration
interface org.biojava.bio.seq.
RemoteFeature.Resolver
interface org.biojava.bio.dp.
ScoreType
interface org.biojava.bio.search.
SearchContentHandler
interface org.biojava.bio.search.
SearchBuilder
interface org.biojava.bio.program.ssaha.
SearchListener
interface org.biojava.utils.io.
Seekable
interface org.biojava.bio.program.abi.
ABIFParser.DataAccess
(also extends java.io.DataInput)
interface org.biojava.bio.seq.io.
SeqIOListener
interface org.biojava.bio.seq.io.
SeqFileFormer
interface org.biojava.bio.seq.io.
SequenceBuilder
interface org.biojava.bio.search.
SeqSimilaritySearcher
interface org.biojava.bio.seq.
SequenceAnnotator
interface org.biojava.bio.seq.io.
SequenceBuilderFactory
interface org.biojava.bio.seq.db.
SequenceDBInstallation
interface org.biojava.directory.
SequenceDBProvider
interface org.biojava.bio.seq.
SequenceFactory
interface org.biojava.bio.seq.io.
SequenceFormat
interface org.biojava.bio.seq.io.agave.
SequenceHandler
interface org.biojava.bio.seq.
SequenceIterator
interface org.biojava.bio.gui.sequence.
SequenceRenderer
interface org.biojava.bio.program.ssaha.
SequenceStreamer
interface java.io.Serializable
interface org.biojava.bio.seq.
FeatureFilter
interface org.biojava.bio.seq.
OptimizableFilter
interface org.biojava.bio.symbol.
FuzzyLocation.RangeResolver
interface org.biojava.bio.seq.
OptimizableFilter
interface org.biojava.bio.seq.io.agave.
StAXContentHandler
interface org.biojava.utils.stax.
StAXContentHandler
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeHandler.CollectionConstraintHandler
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeHandler.PropertyConstraintHandler
interface org.biojava.bio.seq.io.filterxml.
XMLFilterHandler.FilterHandler
interface org.biojava.bio.program.ssbind.
StAXHandlerFactory
interface org.biojava.bio.seq.io.agave.
StAXHandlerFactory
interface org.biojava.bio.seq.io.game.
StAXHandlerFactory
interface org.biojava.bio.seq.io.game12.
StAXHandlerFactory
interface org.biojava.bio.dp.
StoppingCriteria
interface org.biojava.bio.seq.io.
StreamParser
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 javax.swing.SwingConstants
interface org.biojava.bio.gui.sequence.
PairwiseRenderContext
interface org.biojava.bio.gui.sequence.
SequenceRenderContext
interface org.biojava.bio.gui.sequence.
PairwiseRenderContext
interface org.biojava.bio.symbol.
SymbolListFactory
interface org.biojava.bio.symbol.
SymbolPropertyTable
interface org.biojava.bio.seq.io.
SymbolReader
interface org.biojava.bio.gui.
SymbolStyle
interface org.biojava.bio.program.tagvalue.
TagValueContext
interface org.biojava.bio.program.tagvalue.
TagValueListener
interface org.biojava.bio.program.tagvalue.
TagValueParser
interface org.biojava.bio.taxa.
TaxonFactory
interface org.biojava.bio.taxa.
TaxonParser
interface org.biojava.utils.
ThreadPool
interface org.biojava.bio.dp.
Trainable
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
)
interface org.biojava.bio.dp.
TrainingAlgorithm
interface org.biojava.stats.svm.
TrainingContext
interface org.biojava.bio.dp.
TransitionTrainer
interface org.biojava.bio.symbol.
TranslationTable
interface org.biojava.bio.symbol.
ReversibleTranslationTable
interface org.biojava.bio.program.unigene.
UnigeneFactory
interface org.biojava.utils.net.
URLFactory
interface org.biojava.bio.program.blast2html.
URLGeneratorFactory
interface org.biojava.bio.dp.
WeightMatrix
interface org.biojava.bio.program.xff.
XFFHelper
interface org.biojava.bio.program.xff.
XFFPartHandlerFactory
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeWriter.XMLCollectionConstraintWriter
interface org.biojava.bio.seq.io.filterxml.
XMLAnnotationTypeWriter.XMLPropertyConstraintWriter
interface org.biojava.bio.seq.io.filterxml.
XMLFilterHandler.FilterHandlerFactory
interface org.biojava.bio.seq.io.filterxml.
XMLFilterWriter.FilterWriter
interface org.biojava.utils.xml.
XMLPeerFactory
interface org.biojava.utils.xml.
XMLWritable
interface org.biojava.utils.xml.
XMLWriter
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