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Package Hierarchies:
org.biojava.bio.structure
,
org.biojava.bio.structure.align
,
org.biojava.bio.structure.align.ce
,
org.biojava.bio.structure.align.client
,
org.biojava.bio.structure.align.events
,
org.biojava.bio.structure.align.fatcat
,
org.biojava.bio.structure.align.fatcat.calc
,
org.biojava.bio.structure.align.gui
,
org.biojava.bio.structure.align.gui.aligpanel
,
org.biojava.bio.structure.align.gui.autosuggest
,
org.biojava.bio.structure.align.gui.jmol
,
org.biojava.bio.structure.align.helper
,
org.biojava.bio.structure.align.model
,
org.biojava.bio.structure.align.pairwise
,
org.biojava.bio.structure.align.seq
,
org.biojava.bio.structure.align.util
,
org.biojava.bio.structure.align.webstart
,
org.biojava.bio.structure.align.xml
,
org.biojava.bio.structure.domain
,
org.biojava.bio.structure.domain.pdp
,
org.biojava.bio.structure.gui
,
org.biojava.bio.structure.gui.events
,
org.biojava.bio.structure.gui.util
,
org.biojava.bio.structure.gui.util.color
,
org.biojava.bio.structure.io
,
org.biojava.bio.structure.io.mmcif
,
org.biojava.bio.structure.io.mmcif.chem
,
org.biojava.bio.structure.io.mmcif.model
,
org.biojava.bio.structure.io.sifts
,
org.biojava.bio.structure.io.util
,
org.biojava.bio.structure.jama
,
org.biojava.bio.structure.scop
,
org.biojava.bio.structure.scop.server
,
org.biojava.bio.structure.secstruc
,
org.biojava.bio.structure.server
,
org.biojava3.aaproperties
,
org.biojava3.aaproperties.profeat
,
org.biojava3.aaproperties.profeat.convertor
,
org.biojava3.aaproperties.xml
,
org.biojava3.alignment
,
org.biojava3.alignment.aaindex
,
org.biojava3.alignment.routines
,
org.biojava3.alignment.template
,
org.biojava3.core.exceptions
,
org.biojava3.core.sequence
,
org.biojava3.core.sequence.compound
,
org.biojava3.core.sequence.edits
,
org.biojava3.core.sequence.features
,
org.biojava3.core.sequence.io
,
org.biojava3.core.sequence.io.template
,
org.biojava3.core.sequence.io.util
,
org.biojava3.core.sequence.loader
,
org.biojava3.core.sequence.location
,
org.biojava3.core.sequence.location.template
,
org.biojava3.core.sequence.storage
,
org.biojava3.core.sequence.template
,
org.biojava3.core.sequence.transcription
,
org.biojava3.core.sequence.views
,
org.biojava3.core.util
,
org.biojava3.data.sequence
,
org.biojava3.genome
,
org.biojava3.genome.homology
,
org.biojava3.genome.parsers.geneid
,
org.biojava3.genome.parsers.gff
,
org.biojava3.genome.query
,
org.biojava3.genome.uniprot
,
org.biojava3.genome.util
,
org.biojava3.phylo
,
org.biojava3.protmod
,
org.biojava3.protmod.io
,
org.biojava3.protmod.structure
,
org.biojava3.ronn
,
org.biojava3.sequencing.io.fastq
,
org.biojava3.structure.gui
,
org.biojava3.ws.alignment
,
org.biojava3.ws.alignment.qblast
,
org.biojava3.ws.hmmer
,
org.forester.application
,
org.forester.archaeopteryx
,
org.forester.archaeopteryx.phylogeny.data
,
org.forester.archaeopteryx.webservices
,
org.forester.datastructures
,
org.forester.development
,
org.forester.go
,
org.forester.go.etc
,
org.forester.io.parsers
,
org.forester.io.parsers.nexus
,
org.forester.io.parsers.nhx
,
org.forester.io.parsers.phyloxml
,
org.forester.io.parsers.phyloxml.phylogenydata
,
org.forester.io.parsers.tol
,
org.forester.io.writers
,
org.forester.pccx
,
org.forester.phylogeny
,
org.forester.phylogeny.data
,
org.forester.phylogeny.factories
,
org.forester.phylogeny.iterators
,
org.forester.phylogenyinference
,
org.forester.sdi
,
org.forester.surfacing
,
org.forester.test
,
org.forester.tools
,
org.forester.util
Class Hierarchy
java.lang.
Object
org.biojava3.alignment.aaindex.
AAindexFactory
org.biojava3.alignment.aaindex.
AAIndexFileParser
org.biojava.bio.structure.align.gui.
AboutDialog
javax.swing.
AbstractAction
(implements javax.swing.
Action
, java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava.bio.structure.align.gui.
ChooseDirAction
org.biojava.bio.structure.io.mmcif.model.
AbstractBean
org.biojava.bio.structure.io.mmcif.model.
AtomSite
org.biojava.bio.structure.io.mmcif.model.
DatabasePDBremark
org.biojava.bio.structure.io.mmcif.model.
EntityPolySeq
org.biojava.bio.structure.io.mmcif.model.
Exptl
org.biojava.bio.structure.io.mmcif.model.
PdbxPolySeqScheme
org.biojava.bio.structure.io.mmcif.model.
StructAsym
org.biojava.bio.structure.io.mmcif.model.
StructRef
org.biojava.bio.structure.io.mmcif.model.
StructRefSeq
java.util.
AbstractCollection
<E> (implements java.util.
Collection
<E>)
java.util.
AbstractList
<E> (implements java.util.
List
<E>)
java.util.
ArrayList
<E> (implements java.lang.
Cloneable
, java.util.
List
<E>, java.util.
RandomAccess
, java.io.
Serializable
)
org.biojava3.genome.parsers.gff.
FeatureList
org.biojava3.core.sequence.template.
AbstractCompound
(implements org.biojava3.core.sequence.template.
Compound
)
org.biojava3.core.sequence.compound.
AminoAcidCompound
org.biojava3.core.sequence.compound.
CodonCompound
org.biojava3.core.sequence.compound.
NucleotideCompound
(implements org.biojava3.core.sequence.template.
ComplementCompound
)
org.biojava3.core.sequence.template.
AbstractCompoundSet
<C> (implements org.biojava3.core.sequence.template.
CompoundSet
<C>)
org.biojava3.core.sequence.template.
AbstractNucleotideCompoundSet
<C>
org.biojava3.core.sequence.compound.
DNACompoundSet
org.biojava3.core.sequence.compound.
AmbiguityDNACompoundSet
org.biojava3.core.sequence.compound.
RNACompoundSet
org.biojava3.core.sequence.compound.
AmbiguityRNACompoundSet
org.biojava3.core.sequence.template.
AbstractCompoundTranslator
<F,T> (implements org.biojava3.core.sequence.template.
CompoundTranslator
<F,T>)
org.biojava3.core.sequence.transcription.
DNAToRNATranslator
org.biojava3.core.sequence.transcription.
RNAToAminoAcidTranslator
org.biojava3.core.sequence.features.
AbstractFeature
<S,C> (implements org.biojava3.core.sequence.features.
FeatureInterface
<S,C>)
org.biojava3.core.sequence.features.
QualityFeature
<S,C>
org.biojava3.core.sequence.features.
QuantityFeature
<S,C>
org.biojava3.core.sequence.features.
TextFeature
<S,C>
org.biojava3.core.sequence.location.template.
AbstractLocation
(implements org.biojava3.core.sequence.location.template.
Location
)
org.biojava3.core.sequence.location.
InsdcLocations.BondLocation
org.biojava3.core.sequence.location.
InsdcLocations.OneOfLocation
org.biojava3.core.sequence.location.
SimpleLocation
org.biojava3.core.sequence.location.
InsdcLocations.GroupLocation
org.biojava3.core.sequence.location.
InsdcLocations.OrderLocation
org.biojava3.core.sequence.location.
SequenceLocation
<S,C>
java.util.
AbstractMap
<K,V> (implements java.util.
Map
<K,V>)
org.biojava.bio.structure.align.util.
AlignmentTools.IdentityMap
<K>
org.biojava3.core.util.
SoftHashMap
<K,V>
org.biojava3.alignment.template.
AbstractScorer
(implements org.biojava3.alignment.template.
Scorer
)
org.biojava3.alignment.template.
AbstractMatrixAligner
<S,C> (implements org.biojava3.alignment.template.
MatrixAligner
<S,C>)
org.biojava3.alignment.template.
AbstractPairwiseSequenceAligner
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceAligner
<S,C>)
org.biojava3.alignment.routines.
AnchoredPairwiseSequenceAligner
<S,C>
org.biojava3.alignment.routines.
GuanUberbacher
<S,C>
org.biojava3.alignment.
NeedlemanWunsch
<S,C>
org.biojava3.alignment.
SmithWaterman
<S,C>
org.biojava3.alignment.template.
AbstractProfileProfileAligner
<S,C> (implements org.biojava3.alignment.template.
ProfileProfileAligner
<S,C>)
org.biojava3.alignment.
SimpleProfileProfileAligner
<S,C>
org.biojava3.alignment.
FractionalIdentityScorer
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.
FractionalIdentityInProfileScorer
<S,C> (implements org.biojava3.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava3.alignment.
FractionalSimilarityScorer
<S,C> (implements org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.
FractionalSimilarityInProfileScorer
<S,C> (implements org.biojava3.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava3.alignment.
StandardRescoreRefiner
<S,C> (implements org.biojava3.alignment.template.
RescoreRefiner
<S,C>)
org.biojava3.core.sequence.template.
AbstractSequence
<C> (implements org.biojava3.core.sequence.template.
Sequence
<C>)
org.biojava3.core.sequence.
BasicSequence
<C>
org.biojava3.core.sequence.
DNASequence
org.biojava3.core.sequence.
CDSSequence
org.biojava3.core.sequence.
ChromosomeSequence
org.biojava3.core.sequence.
ExonSequence
org.biojava3.core.sequence.
GeneSequence
org.biojava3.core.sequence.
IntronSequence
org.biojava3.core.sequence.
StartCodonSequence
org.biojava3.core.sequence.
StopCodonSequence
org.biojava3.core.sequence.
TranscriptSequence
org.biojava3.core.sequence.
ProteinSequence
org.biojava3.core.sequence.
RNASequence
org.biojava.bio.structure.align.
AbstractStructureAlignment
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.ce.
CeMain
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.ce.
CeCPMain
org.biojava.bio.structure.align.ce.
CeSideChainMain
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.ce.
OptimalCECPMain
org.biojava.bio.structure.align.seq.
SmithWaterman3Daligner
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.ce.
AbstractUserArgumentProcessor
(implements org.biojava.bio.structure.align.ce.
UserArgumentProcessor
)
org.biojava.bio.structure.align.ce.
CeSideChainUserArgumentProcessor
org.biojava.bio.structure.align.ce.
CeUserArgumentProcessor
org.biojava.bio.structure.align.ce.
CeCPUserArgumentProcessor
org.biojava.bio.structure.align.fatcat.
FatCatUserArgumentProcessor
org.biojava.bio.structure.align.seq.
SmithWatermanUserArgumentProcessor
org.forester.phylogeny.data.
Accession
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.biojava3.core.sequence.
AccessionID
org.forester.io.parsers.phyloxml.phylogenydata.
AccessionParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.align.model.
AFP
(implements java.io.
Serializable
)
org.biojava.bio.structure.align.util.
AFPAlignmentDisplay
org.biojava.bio.structure.align.fatcat.calc.
AFPCalculator
org.biojava.bio.structure.align.model.
AFPChain
(implements java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava.bio.structure.align.gui.aligpanel.
AFPChainCoordManager
org.biojava.bio.structure.align.fatcat.calc.
AFPChainer
org.biojava.bio.structure.align.xml.
AFPChainFlipper
org.biojava.bio.structure.align.util.
AFPChainScorer
org.biojava.bio.structure.align.model.
AfpChainWriter
org.biojava.bio.structure.align.xml.
AFPChainXMLConverter
org.biojava.bio.structure.align.xml.
AFPChainXMLParser
org.biojava.bio.structure.align.fatcat.calc.
AFPOptimizer
org.biojava.bio.structure.align.fatcat.calc.
AFPPostProcessor
org.biojava.bio.structure.align.
AFPTwister
org.biojava.bio.structure.gui.util.
AlignedPosition
org.biojava3.alignment.routines.
AlignerHelper
org.biojava3.alignment.routines.
AlignerHelper.Cut
org.biojava.bio.structure.align.gui.
AlignmentCalc
(implements org.biojava.bio.structure.align.gui.
AlignmentCalculationRunnable
)
org.biojava.bio.structure.gui.util.
AlignmentCalc
(implements java.lang.
Runnable
)
org.biojava.bio.structure.align.gui.
AlignmentCalcDB
(implements org.biojava.bio.structure.align.gui.
AlignmentCalculationRunnable
)
org.biojava.bio.structure.align.pairwise.
AlignmentProgressListener
org.biojava.bio.structure.align.pairwise.
AlignmentResult
(implements java.io.
Serializable
)
org.biojava3.alignment.
Alignments
org.biojava.bio.structure.align.util.
AlignmentTools
org.biojava.bio.structure.align.pairwise.
AligNPE
org.biojava.bio.structure.align.helper.
AlignTools
org.biojava.bio.structure.align.gui.aligpanel.
AligPanelMouseMotionListener
(implements java.awt.event.
MouseListener
, java.awt.event.
MouseMotionListener
)
org.biojava.bio.structure.align.webstart.
AligUIManager
org.biojava.bio.structure.io.mmcif.
AllChemCompProvider
(implements org.biojava.bio.structure.io.mmcif.
ChemCompProvider
, java.lang.
Runnable
)
org.biojava.bio.structure.align.pairwise.
AltAligComparator
(implements java.util.
Comparator
<T>)
org.biojava.bio.structure.align.pairwise.
AlternativeAlignment
(implements java.io.
Serializable
)
org.forester.development.
AminoAcid
org.biojava3.aaproperties.xml.
AminoAcidComposition
org.biojava3.aaproperties.xml.
AminoAcidCompositionTable
org.biojava3.core.sequence.compound.
AminoAcidCompoundSet
(implements org.biojava3.core.sequence.template.
CompoundSet
<C>)
org.forester.development.
AminoAcidSequence
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.phylogeny.data.
Annotation
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
AnnotationParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava3.genome.
App
org.biojava3.phylo.
App
org.forester.archaeopteryx.
Archaeopteryx
org.biojava3.core.sequence.storage.
ArrayListSequenceReader
<C> (implements org.biojava3.core.sequence.template.
SequenceReader
<C>)
org.biojava3.core.sequence.loader.
ArrayListProxySequenceReader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.util.
AsciiHistogram
org.biojava.bio.structure.domain.
AssignmentXMLSerializer
org.biojava.bio.structure.align.util.
AtomCache
org.biojava.bio.structure.
AtomImpl
(implements org.biojava.bio.structure.
Atom
, org.biojava.bio.structure.
PDBRecord
, java.io.
Serializable
)
org.biojava.bio.structure.align.gui.jmol.
AtomInfo
org.biojava.bio.structure.align.gui.jmol.
AtomInfoParser
org.biojava.bio.structure.
AtomIterator
(implements java.util.
Iterator
<E>)
org.biojava.bio.structure.io.mmcif.model.
AuditAuthor
org.biojava.bio.structure.
Author
(implements java.io.
Serializable
)
org.forester.surfacing.
BasicBinaryDomainCombination
(implements org.forester.surfacing.
BinaryDomainCombination
)
org.forester.surfacing.
AdjactantDirectedBinaryDomainCombination
org.forester.surfacing.
DirectedBinaryDomainCombination
org.forester.phylogenyinference.
BasicCharacterStateMatrix
<S> (implements org.forester.phylogenyinference.
CharacterStateMatrix
<S>)
org.forester.surfacing.
BasicCombinableDomains
(implements org.forester.surfacing.
CombinableDomains
)
org.forester.surfacing.
AdjactantDirectedCombinableDomains
org.forester.surfacing.
DirectedCombinableDomains
org.forester.util.
BasicDescriptiveStatistics
(implements org.forester.util.
DescriptiveStatistics
)
org.forester.surfacing.
BasicDomain
(implements org.forester.surfacing.
Domain
)
org.forester.surfacing.
BasicDomainSimilarityCalculator
(implements org.forester.surfacing.
DomainSimilarityCalculator
)
org.forester.pccx.
BasicExternalNodeBasedCoverageExtender
(implements org.forester.pccx.
CoverageExtender
)
org.forester.surfacing.
BasicGenomeWideCombinableDomains
(implements org.forester.surfacing.
GenomeWideCombinableDomains
)
org.forester.go.
BasicGoRelationship
(implements org.forester.go.
GoRelationship
)
org.forester.go.
BasicGoSubset
(implements org.forester.go.
GoSubset
)
org.forester.go.
BasicGoTerm
(implements org.forester.go.
GoTerm
)
org.forester.go.
BasicGoXRef
(implements org.forester.go.
GoXRef
)
org.forester.development.
BasicMsa
(implements org.forester.development.
Msa
)
org.forester.archaeopteryx.webservices.
BasicPhylogeniesWebserviceClient
(implements org.forester.archaeopteryx.webservices.
PhylogeniesWebserviceClient
)
org.forester.phylogeny.factories.
BasicPhylogenyFactory
(implements org.forester.phylogeny.factories.
PhylogenyFactory
)
org.forester.phylogeny.factories.
ParserBasedPhylogenyFactory
org.forester.surfacing.
BasicProtein
(implements org.forester.surfacing.
Protein
)
org.forester.surfacing.
BasicSpecies
(implements org.forester.surfacing.
Species
)
org.forester.phylogenyinference.
BasicSymmetricalDistanceMatrix
(implements org.forester.phylogenyinference.
DistanceMatrix
)
org.forester.util.
BasicTable
<E>
org.forester.util.
BasicTableParser
org.biojava.bio.structure.secstruc.
BigSqrt
org.forester.phylogeny.data.
BinaryCharacters
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
BinaryCharactersParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.gui.
BiojavaJmol
org.biojava.bio.structure.align.
BioJavaStructureAlignment
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava3.core.sequence.storage.
BitSequenceReader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava3.core.sequence.storage.
FourBitSequenceReader
<C>
org.biojava3.core.sequence.storage.
TwoBitSequenceReader
<C>
org.biojava3.core.sequence.storage.
BitSequenceReader.BitArrayWorker
<C>
org.biojava3.core.sequence.storage.
FourBitSequenceReader.FourBitArrayWorker
<C>
org.biojava3.core.sequence.storage.
TwoBitSequenceReader.TwoBitArrayWorker
<C>
org.forester.archaeopteryx.
Blast
org.biojava3.genome.homology.
BlastHomologyHits
org.biojava3.ws.alignment.qblast.
BlastJob
org.biojava3.genome.query.
BlastXMLQuery
org.biojava.bio.structure.
Bond
org.forester.phylogeny.data.
BranchColor
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.pccx.
BranchCountingBasedScoringMethod
(implements org.forester.pccx.
ScoringMethodForExternalNode
)
org.forester.pccx.
BranchLengthBasedScoringMethod
org.forester.pccx.
LogBranchLengthBasedScoringMethod
org.forester.phylogeny.data.
BranchData
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.phylogeny.data.
BranchWidth
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
BranchWidthParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.align.webstart.
BrowserOpener
org.biojava.bio.structure.align.util.
CacheFactory
org.biojava.bio.structure.io.
CAConverter
org.biojava.bio.structure.
Calc
org.biojava3.alignment.template.
CallablePairwiseSequenceAligner
<S,C> (implements java.util.concurrent.
Callable
<V>)
org.biojava3.alignment.template.
CallablePairwiseSequenceScorer
<S,C> (implements java.util.concurrent.
Callable
<V>)
org.biojava3.alignment.template.
CallableProfileProfileAligner
<S,C> (implements java.util.concurrent.
Callable
<V>)
org.biojava.bio.structure.align.
CallableStructureAlignment
(implements java.util.concurrent.
Callable
<V>)
org.biojava3.aaproperties.xml.
CaseFreeAminoAcidCompoundSet
(implements org.biojava3.core.sequence.template.
CompoundSet
<C>)
org.biojava3.core.sequence.transcription.
CaseInsensitiveCompound
(implements org.biojava3.core.sequence.template.
Compound
)
org.biojava3.core.sequence.
CDSComparator
(implements java.util.
Comparator
<T>)
org.biojava.bio.structure.align.ce.
CECalculator
org.biojava.bio.structure.align.ce.
CeCalculatorEnhanced
org.biojava.bio.structure.align.ce.
CeCPMain.CPRange
org.biojava.bio.structure.align.ce.
CeParameters
(implements org.biojava.bio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava.bio.structure.align.ce.
OptimalCECPParameters
org.biojava.bio.structure.
ChainImpl
(implements org.biojava.bio.structure.
Chain
, java.io.
Serializable
)
org.biojava3.phylo.
CheckTreeAccuracy
org.forester.application.
CheckTreeAccuracy
org.biojava.bio.structure.io.mmcif.model.
ChemComp
(implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.biojava.bio.structure.io.mmcif.
ChemCompConsumer
(implements org.biojava.bio.structure.io.mmcif.
MMcifConsumer
)
org.biojava.bio.structure.io.mmcif.model.
ChemCompDescriptor
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.mmcif.
ChemCompGroupFactory
org.biojava.bio.structure.io.mmcif.chem.
ChemCompTools
org.biojava.bio.structure.io.mmcif.
ChemicalComponentDictionary
org.forester.phylogeny.iterators.
ChildNodeIteratorForward
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.biojava.bio.structure.jama.
CholeskyDecomposition
(implements java.io.
Serializable
)
org.biojava3.core.sequence.io.util.
ClasspathResource
org.biojava.bio.structure.align.util.
CliTools
org.biojava.bio.structure.align.
ClusterAltAligs
org.biojava.bio.structure.domain.pdp.
ClusterDomains
org.biojava.bio.structure.align.util.
CollectionTools
org.forester.io.parsers.phyloxml.phylogenydata.
ColorParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
java.awt.color.
ColorSpace
(implements java.io.
Serializable
)
org.biojava.bio.structure.gui.util.color.
HSVColorSpace
org.biojava.bio.structure.gui.util.color.
ColorUtils
org.forester.surfacing.
CombinationsBasedPairwiseDomainSimilarity
(implements org.forester.surfacing.
PairwiseDomainSimilarity
)
org.forester.surfacing.
CombinationsBasedPairwiseDomainSimilarityCalculator
(implements org.forester.surfacing.
PairwiseDomainSimilarityCalculator
)
org.forester.util.
CommandLineArguments
org.biojava3.aaproperties.
CommandPrompt
org.biojava3.phylo.
Comparison
java.awt.
Component
(implements java.awt.image.
ImageObserver
, java.awt.
MenuContainer
, java.io.
Serializable
)
java.awt.
Container
javax.swing.
JComponent
(implements java.io.
Serializable
)
javax.swing.
JPanel
(implements javax.accessibility.
Accessible
)
org.biojava.bio.structure.align.gui.
ConfigPDBInstallPanel
org.biojava.bio.structure.align.gui.
DBSearchGUI
org.biojava.bio.structure.gui.util.color.
GradientPanel
org.biojava.bio.structure.align.gui.
GUIAlignmentProgressListener
(implements java.awt.event.
ActionListener
, org.biojava.bio.structure.align.events.
AlignmentProgressListener
)
org.biojava.bio.structure.gui.
JMatrixPanel
org.biojava.bio.structure.align.gui.
JPrintPanel
(implements java.awt.event.
ActionListener
, java.awt.print.
Printable
)
org.biojava.bio.structure.align.gui.
AlignmentTextPanel
org.biojava.bio.structure.align.gui.aligpanel.
AligPanel
(implements java.awt.event.
ActionListener
, org.biojava.bio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.
WindowListener
)
org.biojava.bio.structure.align.gui.jmol.
JmolPanel
(implements java.awt.event.
ActionListener
)
org.forester.archaeopteryx.
MainPanel
(implements java.awt.event.
ComponentListener
)
org.biojava.bio.structure.gui.util.
PDBDirPanel
(implements org.biojava.bio.structure.gui.util.
StructurePairSelector
)
org.biojava.bio.structure.gui.util.
PDBServerPanel
(implements org.biojava.bio.structure.gui.util.
StructurePairSelector
)
org.biojava.bio.structure.gui.util.
PDBUploadPanel
(implements org.biojava.bio.structure.gui.util.
StructurePairSelector
)
org.biojava.bio.structure.gui.
ScaleableMatrixPanel
(implements java.awt.event.
ActionListener
, javax.swing.event.
ChangeListener
)
org.biojava.bio.structure.align.gui.
DotPlotPanel
org.biojava.bio.structure.gui.
ScaleableMatrixPanel.GradientRenderer
(implements javax.swing.
ListCellRenderer
)
org.biojava.bio.structure.gui.util.
ScopSelectPanel
(implements org.biojava.bio.structure.gui.util.
StructurePairSelector
)
org.biojava.bio.structure.align.gui.
SelectPDBPanel
(implements org.biojava.bio.structure.gui.util.
StructurePairSelector
)
org.biojava.bio.structure.gui.
SequenceDisplay
(implements javax.swing.event.
ChangeListener
)
org.biojava.bio.structure.gui.util.
SequenceScalePanel
org.forester.archaeopteryx.
TreePanel
(implements java.awt.event.
ActionListener
, java.awt.event.
MouseWheelListener
, java.awt.print.
Printable
)
javax.swing.text.
JTextComponent
(implements javax.accessibility.
Accessible
, javax.swing.
Scrollable
)
javax.swing.
JTextField
(implements javax.swing.
SwingConstants
)
org.biojava.bio.structure.align.gui.autosuggest.
JAutoSuggest
org.biojava.bio.structure.align.gui.aligpanel.
StatusDisplay
(implements org.biojava.bio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.
WindowListener
)
java.awt.
Panel
(implements javax.accessibility.
Accessible
)
java.applet.
Applet
javax.swing.
JApplet
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
)
org.forester.archaeopteryx.
ArchaeopteryxA
org.forester.archaeopteryx.
ArchaeopteryxE
(implements java.awt.event.
ActionListener
)
java.awt.
Window
(implements javax.accessibility.
Accessible
)
java.awt.
Dialog
javax.swing.
JDialog
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
, javax.swing.
WindowConstants
)
org.forester.archaeopteryx.
FontChooser
(implements java.awt.event.
ActionListener
, javax.swing.event.
ListSelectionListener
)
java.awt.
Frame
(implements java.awt.
MenuContainer
)
javax.swing.
JFrame
(implements javax.accessibility.
Accessible
, javax.swing.
RootPaneContainer
, javax.swing.
WindowConstants
)
org.biojava.bio.structure.align.gui.
AlignmentGui
org.biojava.bio.structure.gui.util.
AlternativeAlignmentFrame
org.forester.archaeopteryx.
MainFrame
(implements java.awt.event.
ActionListener
)
org.forester.archaeopteryx.
MainFrameApplet
org.forester.archaeopteryx.
MainFrameApplication
org.biojava.bio.structure.align.gui.
ParameterGUI
org.biojava3.protmod.
Component
org.biojava3.protmod.io.
ComponentXMLConverter
org.biojava.bio.structure.
Compound
(implements java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava3.core.util.
ConcurrencyTools
org.forester.application.
confadd
org.forester.phylogeny.data.
Confidence
(implements java.lang.
Comparable
<T>, org.forester.phylogeny.data.
PhylogenyData
)
org.forester.tools.
ConfidenceAssessor
org.forester.io.parsers.phyloxml.phylogenydata.
ConfidenceParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.archaeopteryx.
Constants
org.biojava3.aaproperties.
Constraints
org.biojava.bio.structure.gui.util.color.
ContinuousColorMapperTransform
(implements org.biojava.bio.structure.gui.util.color.
ContinuousColorMapper
)
org.biojava.bio.structure.gui.util.color.
LogColorMapper
org.biojava.bio.structure.gui.util.color.
SqrtColorMapper
org.biojava3.aaproperties.profeat.convertor.
Convertor
org.biojava3.aaproperties.profeat.convertor.
Convert2Charge
org.biojava3.aaproperties.profeat.convertor.
Convert2Hydrophobicity
org.biojava3.aaproperties.profeat.convertor.
Convert2NormalizedVanDerWaalsVolume
org.biojava3.aaproperties.profeat.convertor.
Convert2Polarity
org.biojava3.aaproperties.profeat.convertor.
Convert2Polarizability
org.biojava3.aaproperties.profeat.convertor.
Convert2SecondaryStructure
org.biojava3.aaproperties.profeat.convertor.
Convert2SolventAccessibility
org.biojava.bio.structure.gui.util.
CoordManager
org.forester.application.
count_support
org.biojava.bio.structure.align.client.
CountProgressListener
(implements org.biojava.bio.structure.align.events.
AlignmentProgressListener
)
org.forester.surfacing.
CountsBasedPairwiseDomainSimilarity
(implements org.forester.surfacing.
PairwiseDomainSimilarity
)
org.forester.pccx.
CoverageCalculator
org.biojava3.core.util.
CRC64Checksum
(implements java.util.zip.
Checksum
)
org.biojava.bio.structure.domain.pdp.
Cut
org.biojava.bio.structure.domain.pdp.
CutDomain
org.biojava.bio.structure.domain.pdp.
CutSites
org.biojava.bio.structure.domain.pdp.
CutValues
org.biojava.bio.structure.io.mmcif.model.
DatabasePDBrev
org.forester.phylogeny.data.
Date
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
DateParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.
DBRef
(implements org.biojava.bio.structure.
PDBRecord
, java.io.
Serializable
)
org.biojava3.core.sequence.features.
DBReferenceInfo
org.biojava.bio.structure.align.gui.
DBResultTable
(implements java.awt.event.
ActionListener
)
org.forester.application.
decorator
org.biojava3.alignment.aaindex.
DefaultAAIndexProvider
(implements org.biojava3.alignment.aaindex.
AAIndexProvider
)
org.biojava.bio.structure.align.gui.autosuggest.
DefaultAutoSuggestProvider
(implements org.biojava.bio.structure.align.gui.autosuggest.
AutoSuggestProvider
)
org.xml.sax.helpers.
DefaultHandler
(implements org.xml.sax.
ContentHandler
, org.xml.sax.
DTDHandler
, org.xml.sax.
EntityResolver
, org.xml.sax.
ErrorHandler
)
org.biojava.bio.structure.align.webstart.
ConfigXMLHandler
org.forester.io.parsers.phyloxml.
PhyloXmlHandler
org.forester.io.parsers.tol.
TolXmlHandler
org.biojava.bio.structure.gui.util.color.
DefaultMatrixMapper
(implements org.biojava.bio.structure.gui.util.color.
ContinuousColorMapper
)
org.forester.development.
DevelopmentTools
org.forester.phylogenyinference.
DiscreteState
(implements java.lang.
Comparable
<T>)
org.biojava.bio.structure.align.gui.
DisplayAFP
org.forester.sdi.
DistanceCalculator
org.biojava.bio.structure.secstruc.
DistEn
org.forester.phylogeny.data.
Distribution
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
DistributionParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava3.core.sequence.io.
DNASequenceCreator
(implements org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.forester.phylogenyinference.
DolloParsimony
org.biojava.bio.structure.domain.pdp.
Domain
(implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.forester.phylogeny.data.
DomainArchitecture
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.archaeopteryx.phylogeny.data.
RenderableDomainArchitecture
(implements org.forester.archaeopteryx.phylogeny.data.
RenderablePhylogenyData
)
org.forester.surfacing.
DomainArchitectureBasedGenomeSimilarityCalculator
org.forester.io.parsers.phyloxml.phylogenydata.
DomainArchitectureParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.surfacing.
DomainCountsBasedPairwiseSimilarityCalculator
(implements org.forester.surfacing.
PairwiseDomainSimilarityCalculator
)
org.forester.surfacing.
DomainCountsDifferenceUtil
org.forester.surfacing.
DomainId
(implements java.lang.
Comparable
<T>)
org.forester.surfacing.
DomainLengths
org.forester.surfacing.
DomainLengthsTable
org.forester.surfacing.
DomainParsimonyCalculator
org.biojava.bio.structure.domain.
DomainProviderFactory
org.biojava.bio.structure.io.mmcif.
DownloadChemCompProvider
(implements org.biojava.bio.structure.io.mmcif.
ChemCompProvider
)
org.biojava3.core.sequence.edits.
Edit.AbstractEdit
<C> (implements org.biojava3.core.sequence.edits.
Edit
<C>)
org.biojava3.core.sequence.edits.
Edit.Delete
<C>
org.biojava3.core.sequence.edits.
Edit.Insert
<C>
org.biojava3.core.sequence.edits.
Edit.Substitute
<C>
org.biojava.bio.structure.jama.
EigenvalueDecomposition
(implements java.io.
Serializable
)
org.biojava3.aaproperties.xml.
Element
org.biojava3.aaproperties.xml.
ElementTable
org.biojava.bio.structure.io.mmcif.model.
Entity
org.biojava3.core.util.
Equals
org.forester.phylogeny.data.
Event
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
EventParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava3.core.sequence.
ExonComparator
(implements java.util.
Comparator
<T>)
org.forester.phylogeny.iterators.
ExternalForwardIterator
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.forester.pccx.
ExternalNodeBasedCoverage
(implements org.forester.pccx.
Coverage
)
org.forester.pccx.
ExternalNodeBasedCoverageMethod
(implements org.forester.pccx.
CoverageCalculationMethod
)
org.forester.pccx.
ExternalNodeBasedCoverageMethodOptions
(implements org.forester.pccx.
CoverageCalculationOptions
)
org.biojava.bio.structure.align.
FarmJob
(implements java.lang.
Runnable
)
org.biojava.bio.structure.align.client.
FarmJobParameters
org.biojava.bio.structure.align.client.
FarmJobRunnable
(implements java.lang.
Runnable
)
org.biojava3.core.sequence.io.
FastaGeneWriter
org.biojava3.core.sequence.io.
FastaReader
<S,C>
org.biojava3.core.sequence.io.
FastaReaderHelper
org.biojava3.data.sequence.
FastaSequence
(implements java.lang.
Comparable
<T>)
org.biojava3.core.sequence.io.
FastaSequenceParser
(implements org.biojava3.core.sequence.io.template.
SequenceParserInterface
)
org.biojava.bio.structure.io.
FastaStructureParser
org.biojava3.core.sequence.io.
FastaWriter
<S,C>
org.biojava3.core.sequence.io.
FastaWriterHelper
org.biojava3.sequencing.io.fastq.
Fastq
org.biojava3.sequencing.io.fastq.
FastqBuilder
org.biojava3.sequencing.io.fastq.
FastqTools
org.biojava.bio.structure.align.fatcat.
FatCat
org.biojava.bio.structure.align.fatcat.
FatCatFlexible
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.fatcat.
FatCatRigid
(implements org.biojava.bio.structure.align.
StructureAlignment
)
org.biojava.bio.structure.align.fatcat.calc.
FatCatAligner
org.biojava.bio.structure.align.fatcat.calc.
FatCatParameters
(implements org.biojava.bio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava.bio.structure.align.fatcat.calc.
FCAlignHelper
org.biojava3.genome.parsers.gff.
Feature
(implements org.biojava3.genome.parsers.gff.
FeatureI
)
org.biojava3.genome.parsers.gff.
FeatureHelper
org.biojava.bio.structure.io.
FileConvert
org.biojava.bio.structure.io.util.
FileDownloadUtils
org.biojava.bio.structure.io.
FileParsingParameters
(implements java.io.
Serializable
)
org.biojava3.core.sequence.io.
FileProxyDNASequenceCreator
(implements org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava3.core.sequence.io.
FileProxyProteinSequenceCreator
(implements org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.forester.phylogenyinference.
FitchParsimony
<STATE_TYPE>
org.biojava3.core.util.
FlatFileCache
org.biojava.bio.structure.server.
FlatFileInstallation
(implements org.biojava.bio.structure.server.
PDBInstallation
)
org.forester.util.
ForesterConstants
org.forester.util.
ForesterUtil
org.biojava.bio.structure.align.pairwise.
FragmentJoiner
org.biojava.bio.structure.align.pairwise.
FragmentPair
org.biojava.bio.structure.align.helper.
GapArray
org.biojava3.genome.parsers.gff.
GCStats
org.biojava3.genome.
GeneFeatureHelper
org.biojava3.genome.parsers.gff.
GeneIDGFF2Reader
org.biojava3.genome.parsers.geneid.
GeneIDXMLReader
org.biojava3.genome.parsers.gff.
GeneMarkGTFReader
org.forester.util.
GeneralTable
<IDENTIFIER_TYPE,VALUE_TYPE>
org.biojava3.core.sequence.io.
GenericFastaHeaderFormat
<S,C> (implements org.biojava3.core.sequence.io.template.
FastaHeaderFormatInterface
<S,C>)
org.biojava3.core.sequence.io.
GenericFastaHeaderParser
<S,C> (implements org.biojava3.core.sequence.io.template.
FastaHeaderParserInterface
<S,C>)
org.forester.application.
get_distances
org.biojava.bio.structure.domain.pdp.
GetDistanceMatrix
org.biojava3.genome.homology.
GFF3FromUniprotBlastHits
org.biojava3.genome.parsers.gff.
GFF3Reader
org.biojava3.genome.parsers.gff.
GFF3Writer
org.forester.application.
goac
org.forester.go.
GoId
(implements java.lang.
Comparable
<T>)
org.forester.go.
GoNameSpace
org.biojava.bio.structure.align.pairwise.
Gotoh
org.forester.go.
GoUtils
org.biojava.bio.structure.gui.util.color.
GradientMapper
(implements org.biojava.bio.structure.gui.util.color.
ContinuousColorMapper
, java.util.
Map
<K,V>)
org.biojava.bio.structure.
GroupIterator
(implements java.util.
Iterator
<E>)
org.biojava.bio.structure.
GroupType
org.biojava3.alignment.
GuideTree
<S,C> (implements java.lang.
Iterable
<T>)
org.biojava3.alignment.
GuideTree.Node
(implements org.biojava3.alignment.template.
GuideTreeNode
<S,C>)
org.biojava.bio.structure.align.gui.
GUIFarmJobRunnable
(implements java.lang.
Runnable
)
org.biojava.bio.structure.align.ce.
GuiWrapper
org.biojava3.core.util.
Hashcoder
org.biojava.bio.structure.align.xml.
HasResultXMLConverter
org.biojava.bio.structure.secstruc.
HBond
org.biojava.bio.structure.align.gui.
HelpDialog
org.biojava.bio.structure.
HetatomImpl
(implements org.biojava.bio.structure.
Group
, java.io.
Serializable
)
org.biojava.bio.structure.
AminoAcidImpl
(implements org.biojava.bio.structure.
AminoAcid
, java.io.
Serializable
)
org.biojava.bio.structure.
NucleotideImpl
(implements org.biojava.bio.structure.
Group
, java.io.
Serializable
)
org.biojava.bio.structure.secstruc.
SecStrucGroup
(implements org.biojava.bio.structure.
Group
)
org.biojava3.ws.hmmer.
HmmerDomain
(implements java.lang.
Comparable
<T>)
org.biojava3.ws.hmmer.
HmmerResult
(implements java.lang.
Comparable
<T>)
org.forester.io.parsers.
HmmPfamOutputParser
org.forester.io.parsers.
HmmscanPerDomainTableParser
org.biojava.bio.structure.align.util.
HTTPConnectionTools
org.forester.phylogeny.data.
Identifier
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
IdentifierParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.align.helper.
IdxComparator
(implements java.util.
Comparator
<T>)
org.biojava3.sequencing.io.fastq.
IlluminaFastqReader
org.biojava3.sequencing.io.fastq.
IlluminaFastqWriter
org.biojava.bio.structure.align.helper.
IndexPair
(implements java.io.
Serializable
)
org.biojava.bio.structure.align.helper.
AligMatEl
java.io.
InputStream
(implements java.io.
Closeable
)
java.io.
FilterInputStream
org.biojava3.core.util.
UncompressInputStream
org.biojava3.core.util.
InputStreamProvider
org.biojava3.core.sequence.location.
InsdcLocations
org.biojava3.core.sequence.location.
InsdcParser
org.biojava3.core.sequence.io.util.
IOUtils
org.biojava3.aaproperties.xml.
Isotope
org.biojava3.core.sequence.io.
IUPACParser
org.biojava3.core.sequence.io.
IUPACParser.IUPACTable
(implements org.biojava3.core.sequence.transcription.
Table
)
org.biojava.bio.structure.align.client.
JFatCatClient
org.biojava.bio.structure.gui.events.
JmolAlignedPositionListener
(implements org.biojava.bio.structure.gui.events.
AlignmentPositionListener
)
org.biojava.bio.structure.align.gui.jmol.
JmolTools
org.biojava3.structure.gui.
JmolViewerImpl
(implements org.biojava3.structure.gui.
StructureViewer
)
org.biojava.bio.structure.align.webstart.
JNLPProxy
org.biojava3.core.sequence.storage.
JoiningSequenceReader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.bio.structure.align.helper.
JointFragments
org.biojava.bio.structure.
JournalArticle
(implements java.io.
Serializable
)
org.biojava3.ronn.
Jronn
org.biojava3.ronn.
Jronn.Range
java.awt.event.
KeyAdapter
(implements java.awt.event.
KeyListener
)
org.biojava.bio.structure.align.gui.jmol.
RasmolCommandListener
(implements java.awt.event.
ActionListener
, java.awt.event.
MouseListener
)
org.biojava.bio.structure.gui.
RasmolCommandListener
(implements java.awt.event.
ActionListener
, java.awt.event.
MouseListener
)
org.forester.phylogeny.iterators.
LevelOrderTreeIterator
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.biojava.bio.structure.gui.util.color.
LinearColorInterpolator
(implements org.biojava.bio.structure.gui.util.color.
ColorInterpolator
)
org.biojava.bio.structure.io.
LocalCacheStructureProvider
(implements org.biojava.bio.structure.io.
StructureProvider
)
org.biojava.bio.structure.domain.
LocalProteinDomainParser
org.biojava3.genome.parsers.gff.
Location
(implements java.lang.
Iterable
<T>)
org.biojava3.core.sequence.location.template.
Location.Tools
org.biojava3.core.sequence.location.
LocationHelper
org.biojava3.genome.parsers.gff.
LocIterator
(implements java.util.
Iterator
<E>)
org.biojava.bio.structure.jama.
LUDecomposition
(implements java.io.
Serializable
)
org.forester.surfacing.
MappingResults
org.biojava3.ws.alignment.qblast.
MapToStringTransformer
org.biojava.bio.structure.jama.
Maths
org.biojava.bio.structure.jama.
Matrix
(implements java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava.bio.structure.align.gui.
MenuCreator
org.biojava.bio.structure.gui.util.
MenuCreator
org.forester.application.
meta_ontologizer
org.forester.go.etc.
MetaOntologizer
org.biojava.bio.structure.server.
MMCIFFileInstallation
(implements org.biojava.bio.structure.server.
PDBInstallation
)
org.biojava.bio.structure.io.
MMCIFFileReader
(implements org.biojava.bio.structure.io.
StructureIOFile
)
org.forester.pccx.
ModelingUtils
org.biojava3.ronn.
ModelLoader
org.biojava3.ronn.
ModelLoader.Model
org.biojava3.ronn.
ModelLoader.Threshold
org.biojava3.protmod.
ModificationConditionImpl
(implements org.biojava3.protmod.
ModificationCondition
)
org.biojava3.protmod.
ModificationLinkage
org.biojava3.aaproperties.xml.
ModifiedAminoAcidCompoundSet
(implements org.biojava3.core.sequence.template.
CompoundSet
<C>)
org.biojava3.protmod.structure.
ModifiedCompoundImpl
(implements java.lang.
Comparable
<T>, org.biojava3.protmod.structure.
ModifiedCompound
, java.io.
Serializable
)
org.biojava3.protmod.io.
ModifiedCompoundXMLConverter
org.biojava3.core.sequence.
MultipleSequenceAlignment
<S,C> (implements org.biojava3.core.sequence.template.
LightweightProfile
<S,C>)
org.biojava.bio.structure.
Mutator
org.biojava.bio.structure.align.gui.
MyAlignmentLoadListener
(implements java.awt.event.
ActionListener
)
org.biojava.bio.structure.align.gui.
MyDistMaxListener
(implements java.awt.event.
ActionListener
)
org.biojava.bio.structure.align.gui.
MyExportListener
(implements java.awt.event.
ActionListener
)
org.biojava.bio.structure.align.gui.jmol.
MyJmolStatusListener
org.biojava.bio.structure.align.gui.
MyOpenPdbFileListener
(implements java.awt.event.
ActionListener
)
org.biojava.bio.structure.align.gui.
MySaveFileListener
(implements java.awt.event.
ActionListener
)
org.biojava3.aaproperties.xml.
MyValidationEventHandler
(implements javax.xml.bind.
ValidationEventHandler
)
org.biojava3.aaproperties.xml.
Name2Count
org.biojava3.ws.alignment.qblast.
NCBIQBlastAlignmentProperties
(implements org.biojava3.ws.alignment.
RemotePairwiseAlignmentProperties
)
org.biojava3.ws.alignment.qblast.
NCBIQBlastOutputProperties
(implements org.biojava3.ws.alignment.
RemotePairwiseAlignmentOutputProperties
)
org.biojava3.ws.alignment.qblast.
NCBIQBlastService
(implements org.biojava3.ws.alignment.
RemotePairwiseAlignmentService
)
org.forester.phylogenyinference.
NeighborJoining
org.forester.io.parsers.nexus.
NexusBinaryStatesMatrixParser
org.forester.io.parsers.nexus.
NexusCharactersParser
org.forester.io.parsers.nexus.
NexusConstants
org.forester.io.parsers.nexus.
NexusPhylogeniesParser
(implements org.forester.io.parsers.
PhylogenyParser
)
org.forester.application.
nhx_too
org.forester.io.parsers.nhx.
NHXParser
(implements org.forester.io.parsers.
PhylogenyParser
)
org.forester.io.parsers.nhx.
NHXtags
org.forester.application.
nj
org.forester.phylogeny.data.
NodeData
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.application.
obo_tool
org.forester.go.
OBOparser
org.forester.go.etc.
OntologizerResult
(implements java.lang.
Comparable
<T>)
org.forester.sdi.
ORcount
org.biojava3.ronn.
ORonn
(implements java.util.concurrent.
Callable
<V>)
org.biojava3.ronn.
ORonnModel
org.biojava3.genome.query.
OutputHitsGFF
java.io.
OutputStream
(implements java.io.
Closeable
, java.io.
Flushable
)
org.biojava3.ronn.
NullOutputStream
org.forester.surfacing.
PairwiseGenomeComparator
org.forester.io.parsers.
ParserUtils
org.forester.io.parsers.nexus.
PaupLogParser
org.forester.application.
pccx
org.biojava.bio.structure.
PDBCrystallographicInfo
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.
PDBFileParser
org.biojava.bio.structure.io.
PDBFileReader
(implements org.biojava.bio.structure.io.
StructureIOFile
)
org.biojava.bio.structure.
PDBHeader
(implements org.biojava.bio.structure.
PDBRecord
, java.io.
Serializable
)
org.biojava.bio.structure.align.client.
PdbPair
(implements java.lang.
Comparable
<T>)
org.biojava.bio.structure.align.xml.
PdbPairsMessage
org.biojava.bio.structure.align.xml.
PdbPairXMLConverter
org.biojava.bio.structure.io.
PDBSRSReader
(implements org.biojava.bio.structure.io.
StructureIO
)
org.biojava.bio.structure.
PDBStatus
org.biojava.bio.structure.io.mmcif.model.
PdbxEntityNonPoly
org.biojava.bio.structure.io.mmcif.model.
PdbxNonPolyScheme
org.biojava.bio.structure.domain.pdp.
PDPDistanceMatrix
org.biojava.bio.structure.domain.pdp.
PDPParameters
org.biojava3.aaproperties.
PeptideProperties
org.biojava3.aaproperties.
PeptidePropertiesImpl
(implements org.biojava3.aaproperties.
IPeptideProperties
)
org.forester.application.
perfume
org.biojava.bio.structure.align.webstart.
PersistentConfig
org.forester.application.
pfam_go
org.forester.application.
pfam2go_extractor
org.forester.go.
PfamToGoMapping
(implements org.forester.go.
Mapping
)
org.forester.go.
PfamToGoParser
org.forester.phylogeny.
Phylogeny
org.forester.phylogeny.
PhylogenyBranch
(implements org.forester.phylogeny.
Edge
)
org.forester.phylogeny.data.
PhylogenyDataUtil
org.forester.tools.
PhylogenyDecorator
org.forester.phylogeny.
PhylogenyMethods
org.forester.phylogeny.
PhylogenyNode
(implements java.lang.
Comparable
<T>, org.forester.phylogeny.
PhylogenyNodeI
)
org.forester.io.writers.
PhylogenyWriter
org.forester.application.
phyloxml_converter
org.forester.io.parsers.phyloxml.
PhyloXmlMapping
org.forester.io.writers.
PhyloXmlNodeWriter
org.forester.io.parsers.phyloxml.
PhyloXmlParser
(implements org.forester.io.parsers.
PhylogenyParser
)
org.forester.io.parsers.phyloxml.
PhyloXmlUtil
org.forester.phylogeny.data.
Point
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
PointParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.align.xml.
PositionInQueueXMLConverter
org.forester.phylogeny.iterators.
PostOrderStackObject
org.forester.phylogeny.iterators.
PostorderTreeIterator
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.forester.phylogeny.iterators.
PreorderTreeIterator
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.biojava.bio.structure.server.
PrepareIndexFile
org.biojava.bio.structure.server.
PrepareMMcifIndexFile
org.biojava3.core.util.
PrettyXMLWriter
(implements org.biojava3.core.util.
XMLWriter
)
org.forester.surfacing.
PrintableDomainSimilarity
(implements org.forester.surfacing.
DomainSimilarity
)
org.forester.application.
printAllSpecies
org.forester.application.
printSameOrder
org.biojava3.aaproperties.profeat.
ProfeatProperties
org.biojava3.aaproperties.profeat.
ProfeatPropertiesImpl
(implements org.biojava3.aaproperties.profeat.
IProfeatProperties
)
org.biojava3.phylo.
ProgessListenerStub
(implements org.biojava3.phylo.
NJTreeProgressListener
)
org.forester.phylogeny.data.
PropertiesMap
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.phylogeny.data.
Property
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
PropertyParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.surfacing.
ProteinCountsBasedPairwiseDomainSimilarityCalculator
(implements org.forester.surfacing.
PairwiseDomainSimilarityCalculator
)
org.forester.phylogeny.data.
ProteinDomain
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
ProteinDomainParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.surfacing.
ProteinId
(implements java.lang.
Comparable
<T>)
org.biojava3.protmod.structure.
ProteinModificationIdentifier
org.biojava3.protmod.
ProteinModificationImpl
(implements java.lang.
Comparable
<T>, org.biojava3.protmod.
ProteinModification
)
org.biojava3.protmod.
ProteinModificationImpl.Builder
org.biojava3.protmod.
ProteinModificationRegistry
org.biojava3.protmod.io.
ProteinModificationXmlReader
org.biojava3.core.sequence.io.
ProteinSequenceCreator
(implements org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava3.core.sequence.io.
CasePreservingProteinSequenceCreator
org.biojava.bio.structure.jama.
QRDecomposition
(implements java.io.
Serializable
)
org.forester.datastructures.
Queue
java.io.
Reader
(implements java.io.
Closeable
, java.lang.
Readable
)
org.biojava3.core.sequence.io.
BufferedReaderBytesRead
org.biojava.bio.structure.io.mmcif.
ReducedChemCompProvider
(implements org.biojava.bio.structure.io.mmcif.
ChemCompProvider
)
org.forester.phylogeny.data.
Reference
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
ReferenceParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava.bio.structure.io.mmcif.model.
Refine
org.biojava3.ws.hmmer.
RemoteHmmerScan
(implements org.biojava3.ws.hmmer.
HmmerScan
)
org.biojava.bio.structure.scop.
RemoteScopInstallation
(implements org.biojava.bio.structure.scop.
ScopDatabase
)
org.biojava.bio.structure.align.xml.
RepresentativeXMLConverter
org.biojava.bio.structure.
ResidueNumber
(implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.biojava3.phylo.
ResidueProperties
org.biojava.bio.structure.align.util.
ResourceManager
org.forester.application.
rio
org.forester.sdi.
RIO
org.forester.sdi.
RIOn
org.biojava3.core.sequence.io.
RNASequenceCreator
(implements org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava3.ronn.
RonnConstraint
javax.swing.
RowSorter
<M>
javax.swing.
DefaultRowSorter
<M,I>
javax.swing.table.
TableRowSorter
<M>
org.biojava.bio.structure.align.gui.
MyTableRowSorter
org.biojava.bio.structure.io.
SandboxStyleStructureProvider
(implements org.biojava.bio.structure.io.
StructureProvider
)
org.biojava3.sequencing.io.fastq.
SangerFastqReader
org.biojava3.sequencing.io.fastq.
SangerFastqWriter
org.forester.phylogenyinference.
SankoffParsimony
<STATE_TYPE>
org.biojava3.alignment.aaindex.
ScaledSubstitutionMatrix
(implements org.biojava3.alignment.template.
SubstitutionMatrix
<C>)
javax.xml.bind.
SchemaOutputResolver
org.biojava3.aaproperties.xml.
SchemaGenerator
org.biojava.bio.structure.align.gui.autosuggest.
SCOPAutoSuggestProvider
(implements org.biojava.bio.structure.align.gui.autosuggest.
AutoSuggestProvider
)
org.biojava.bio.structure.scop.
ScopDescription
(implements java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava.bio.structure.scop.server.
ScopDescriptions
(implements java.io.
Serializable
)
org.biojava.bio.structure.scop.
ScopDomain
(implements java.lang.
Cloneable
, java.io.
Serializable
)
org.biojava.bio.structure.scop.server.
ScopDomains
(implements java.io.
Serializable
)
org.biojava.bio.structure.scop.
ScopFactory
org.biojava.bio.structure.scop.
ScopInstallation
(implements org.biojava.bio.structure.scop.
ScopDatabase
)
org.biojava.bio.structure.scop.
BerkeleyScopInstallation
(implements org.biojava.bio.structure.scop.
ScopDatabase
)
org.biojava.bio.structure.gui.util.
ScopInstallationInstance
org.biojava.bio.structure.scop.
ScopNode
(implements java.io.
Serializable
)
org.biojava.bio.structure.scop.server.
ScopNodes
(implements java.io.
Serializable
)
org.biojava3.phylo.
ScoreMatrix
org.forester.application.
sdi
org.forester.sdi.
SDI
org.forester.sdi.
GSDI
org.forester.sdi.
SDIse
org.forester.sdi.
TaxonomyAssigner
org.forester.application.
sdi_r
org.forester.sdi.
SDIdirectory
org.forester.sdi.
SDIR
org.biojava.bio.structure.secstruc.
SecStruc
org.biojava.bio.structure.domain.pdp.
Segment
(implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.biojava.bio.structure.domain.pdp.
SegmentComparator
(implements java.util.
Comparator
<T>)
org.biojava3.structure.gui.
SelectionImpl
(implements org.biojava3.structure.gui.
Selection
)
org.biojava.bio.structure.io.
SeqRes2AtomAligner
org.forester.phylogeny.data.
Sequence
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.biojava3.core.sequence.storage.
SequenceAsStringHelper
<C>
org.biojava3.core.sequence.
SequenceComparator
(implements java.util.
Comparator
<T>)
org.biojava3.core.sequence.loader.
SequenceFileProxyLoader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava3.core.sequence.template.
SequenceMixin
org.biojava3.core.sequence.template.
SequenceMixin.SequenceIterator
<C> (implements java.util.
Iterator
<E>)
org.biojava.bio.structure.gui.util.
SequenceMouseListener
(implements java.awt.event.
MouseListener
, java.awt.event.
MouseMotionListener
)
org.biojava3.core.sequence.
SequenceOptimizationHints
org.forester.io.parsers.phyloxml.phylogenydata.
SequenceParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava3.core.sequence.template.
SequenceProxyView
<C> (implements org.biojava3.core.sequence.template.
SequenceView
<C>)
org.biojava3.core.sequence.views.
ComplementSequenceView
<C>
org.biojava3.core.sequence.views.
ReversedSequenceView
<C>
org.biojava3.core.sequence.views.
RnaSequenceView
(implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.phylogeny.data.
SequenceRelation
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
SequenceRelationParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.biojava3.core.util.
SequenceTools
org.biojava3.data.sequence.
SequenceUtil
org.biojava.bio.structure.domain.
SerializableCache
<K,V>
org.biojava.bio.structure.scop.
CachedRemoteScopInstallation
(implements org.biojava.bio.structure.scop.
ScopDatabase
)
org.biojava.bio.structure.domain.
RemoteDomainProvider
(implements org.biojava.bio.structure.domain.
DomainProvider
)
org.biojava.bio.structure.domain.
RemotePDPProvider
(implements org.biojava.bio.structure.domain.
PDPProvider
)
org.forester.application.
shin
org.forester.sdi.
Shin
org.biojava.bio.structure.domain.pdp.
ShortSegmentRemover
org.biojava.bio.structure.align.gui.
ShowPDBIDListener
(implements java.awt.event.
ActionListener
)
org.biojava.bio.structure.io.sifts.
SiftsEntity
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.sifts.
SiftsMappingProvider
org.biojava.bio.structure.io.sifts.
SiftsResidue
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.sifts.
SiftsSegment
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.sifts.
SiftsXMLParser
org.biojava.bio.structure.align.fatcat.calc.
SigEva
org.biojava3.alignment.
SimpleAlignedSequence
<S,C> (implements org.biojava3.alignment.template.
AlignedSequence
<S,C>)
org.forester.surfacing.
SimpleDomain
(implements org.forester.surfacing.
Domain
)
org.biojava3.alignment.
SimpleGapPenalty
(implements org.biojava3.alignment.template.
GapPenalty
)
org.biojava.bio.structure.io.mmcif.
SimpleMMcifConsumer
(implements org.biojava.bio.structure.io.mmcif.
MMcifConsumer
)
org.biojava.bio.structure.io.mmcif.
SimpleMMcifParser
(implements org.biojava.bio.structure.io.mmcif.
MMcifParser
)
org.forester.development.
SimpleMutableMsa
(implements org.forester.development.
Msa
)
org.biojava3.core.sequence.location.
SimplePoint
(implements org.biojava3.core.sequence.location.template.
Point
)
org.biojava3.core.sequence.location.
FuzzyPoint
org.biojava3.alignment.
SimpleProfile
<S,C> (implements org.biojava3.alignment.template.
Profile
<S,C>)
org.biojava3.alignment.
SimpleProfilePair
<S,C> (implements org.biojava3.alignment.template.
ProfilePair
<S,C>)
org.biojava3.alignment.
SimpleSequencePair
<S,C> (implements org.biojava3.alignment.template.
SequencePair
<S,C>)
org.biojava.bio.structure.server.
SimpleStructureServer
(implements org.biojava.bio.structure.server.
StructureListener
, org.biojava.bio.structure.server.
StructureServer
)
org.biojava3.alignment.
SimpleSubstitutionMatrix
<C> (implements org.biojava3.alignment.template.
SubstitutionMatrix
<C>)
org.biojava3.core.sequence.storage.
SingleCompoundSequenceReader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.bio.structure.jama.
SingularValueDecomposition
(implements java.io.
Serializable
)
org.biojava.bio.structure.
Site
(implements java.lang.
Comparable
<T>, org.biojava.bio.structure.
PDBRecord
, java.io.
Serializable
)
org.biojava.bio.structure.align.seq.
SmithWaterman3DParameters
(implements org.biojava.bio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava3.sequencing.io.fastq.
SolexaFastqReader
org.biojava3.sequencing.io.fastq.
SolexaFastqWriter
org.biojava3.genome.util.
SplitFasta
org.biojava.bio.structure.
SSBond
(implements org.biojava.bio.structure.
PDBRecord
, java.io.
Serializable
)
org.biojava.bio.structure.
StandardAminoAcid
org.biojava.bio.structure.align.ce.
StartupParameters
org.biojava.bio.structure.align.pairwise.
StrCompAlignment
(implements org.biojava.bio.structure.align.pairwise.
Alignable
)
org.biojava3.core.util.
StringManipulationHelper
org.biojava3.core.sequence.loader.
StringProxySequenceReader
<C> (implements org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.application.
strip
org.biojava.bio.structure.align.
StrucAligParameters
org.biojava.bio.structure.io.mmcif.model.
Struct
org.biojava.bio.structure.io.mmcif.model.
StructKeywords
org.biojava.bio.structure.align.gui.
StructureAlignmentDisplay
org.biojava.bio.structure.align.
StructureAlignmentFactory
org.biojava.bio.structure.align.gui.jmol.
StructureAlignmentJmol
(implements java.awt.event.
ActionListener
, java.awt.event.
MouseListener
, java.awt.event.
MouseMotionListener
, java.awt.event.
WindowListener
)
org.biojava.bio.structure.align.fatcat.calc.
StructureAlignmentOptimizer
org.biojava3.protmod.structure.
StructureAtom
org.biojava3.protmod.structure.
StructureAtomLinkage
org.biojava3.protmod.io.
StructureAtomXMLConverter
org.biojava.bio.structure.server.
StructureEventImpl
(implements org.biojava.bio.structure.server.
StructureEvent
)
org.biojava.bio.structure.server.
StructureFetcherRunnable
(implements java.lang.
Runnable
)
org.biojava3.protmod.structure.
StructureGroup
(implements java.lang.
Comparable
<T>)
org.biojava3.protmod.io.
StructureGroupXMLConverter
org.biojava.bio.structure.
StructureImpl
(implements java.io.
Serializable
, org.biojava.bio.structure.
Structure
)
org.biojava.bio.structure.align.client.
StructureName
(implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.biojava.bio.structure.align.
StructurePairAligner
org.biojava.bio.structure.io.
StructureSequenceMatcher
org.biojava.bio.structure.
StructureTools
org.biojava3.protmod.structure.
StructureUtil
org.biojava3.alignment.
SubstitutionMatrixHelper
org.forester.application.
support_statistics
org.forester.application.
support_transfer
org.forester.development.
SupportCount
org.forester.application.
surf_paup
org.forester.application.
surfacing
org.forester.application.
surfacing_old
org.forester.surfacing.
SurfacingConstants
org.forester.surfacing.
SurfacingUtil
org.biojava.bio.structure.
SVDSuperimposer
org.forester.phylogenyinference.
SymmetricalDistanceMatrixParser
(implements org.forester.phylogenyinference.
DistanceMatrixParser
)
org.biojava.bio.structure.align.util.
SynchronizedOutFile
org.biojava.bio.structure.align.gui.
SystemInfo
org.forester.application.
ta
org.biojava3.core.sequence.transcription.
Table.CaseInsensitiveTriplet
org.biojava3.core.sequence.transcription.
Table.Codon
(implements org.biojava3.core.sequence.template.
Compound
)
org.forester.phylogeny.data.
Taxonomy
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.biojava3.core.sequence.
TaxonomyID
org.forester.io.parsers.phyloxml.phylogenydata.
TaxonomyParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.development.
Test
org.forester.test.
Test
org.forester.go.
TestGo
org.forester.sdi.
TestGSDI
org.forester.pccx.
TestPccx
org.forester.phylogenyinference.
TestPhylogenyReconstruction
org.forester.surfacing.
TestSurfacing
java.lang.
Thread
(implements java.lang.
Runnable
)
org.biojava3.phylo.
TreeConstructor
<C,D>
java.lang.
Throwable
(implements java.io.
Serializable
)
java.lang.
Error
org.biojava3.core.exceptions.
CompoundNotFoundError
org.biojava3.core.exceptions.
FileAccessError
org.biojava3.core.exceptions.
HeaderParseException
org.biojava3.core.exceptions.
SequenceLengthError
java.lang.
Exception
org.biojava.bio.structure.align.util.
ConfigurationException
java.io.
IOException
org.forester.io.parsers.nexus.
NexusFormatException
org.forester.io.parsers.nhx.
NHXFormatException
org.forester.io.parsers.
PhylogenyParserException
org.biojava.bio.structure.align.client.
JobKillException
org.biojava.bio.structure.io.
PDBParseException
java.lang.
RuntimeException
org.biojava3.core.exceptions.
ParserException
org.forester.io.parsers.phyloxml.
PhyloXmlException
org.forester.io.parsers.phyloxml.
PhyloXmlDataFormatException
org.biojava3.core.exceptions.
TranslationException
org.biojava.bio.structure.
StructureException
org.biojava.bio.structure.
UnknownPdbAminoAcidException
org.biojava3.ronn.
Timer
org.forester.io.parsers.tol.
TolParser
(implements org.forester.io.parsers.
PhylogenyParser
)
org.forester.io.parsers.tol.
TolXmlMapping
org.biojava3.core.sequence.transcription.
TranscriptionEngine
org.biojava3.core.sequence.transcription.
TranscriptionEngine.Builder
org.forester.archaeopteryx.
TreeFontSet
org.biojava.bio.structure.scop.server.
TreeSetStringWrapper
(implements java.io.
Serializable
)
org.forester.tools.
TreeSplitMatrix
org.biojava3.core.sequence.loader.
UniprotProxySequenceReader
<C> (implements org.biojava3.core.sequence.features.
DatabaseReferenceInterface
, org.biojava3.core.sequence.features.
FeaturesKeyWordInterface
, org.biojava3.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava3.genome.uniprot.
UniprotToFasta
org.forester.phylogeny.data.
Uri
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.phylogenydata.
UriParser
(implements org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
)
org.forester.archaeopteryx.
UrlTreeReader
(implements java.lang.
Runnable
)
org.biojava.bio.structure.align.util.
UserConfiguration
org.biojava3.aaproperties.
Utils
org.forester.archaeopteryx.webservices.
WebservicesManager
org.forester.archaeopteryx.webservices.
WebserviceUtil
org.biojava.bio.structure.align.webstart.
WebStartDBSearch
org.biojava.bio.structure.align.webstart.
WebStartDBSearchResults
org.biojava.bio.structure.align.webstart.
WebStartMain
org.biojava3.core.sequence.views.
WindowedSequence
<C> (implements java.lang.
Iterable
<T>)
org.forester.util.
WindowsUtils
org.forester.io.parsers.phyloxml.
XmlElement
org.biojava3.core.util.
XMLHelper
org.biojava.bio.structure.scop.server.
XMLUtil
Interface Hierarchy
org.biojava3.alignment.aaindex.
AAIndexProvider
org.biojava3.core.sequence.template.
Accessioned
org.biojava3.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava3.core.sequence.location.template.
Location
)
org.biojava3.alignment.template.
AlignedSequence
<S,C>
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.core.sequence.location.template.
Location
(also extends java.lang.
Iterable
<T>)
org.biojava3.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava3.core.sequence.template.
Accessioned
)
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
Sequence
<C> (also extends java.lang.
Iterable
<T>)
org.biojava3.alignment.template.
AlignedSequence
<S,C>
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
SequenceReader
<C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
SequenceView
<C>
org.biojava3.core.sequence.template.
SequenceReader
<C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
SequenceView
<C>
org.biojava.bio.structure.align.pairwise.
Alignable
org.biojava.bio.structure.gui.events.
AlignmentPositionListener
org.biojava.bio.structure.align.events.
AlignmentProgressListener
org.biojava.bio.structure.align.gui.autosuggest.
AutoSuggestProvider
org.biojava.bio.structure.
Chain
org.forester.phylogenyinference.
CharacterStateMatrix
<S>
org.biojava.bio.structure.io.mmcif.
ChemCompProvider
java.lang.
Cloneable
org.biojava.bio.structure.
Atom
(also extends org.biojava.bio.structure.
PDBRecord
)
org.biojava.bio.structure.
Structure
org.biojava.bio.structure.gui.util.color.
ColorInterpolator
org.forester.surfacing.
CombinableDomains
java.lang.
Comparable
<T>
org.forester.surfacing.
BinaryDomainCombination
org.forester.surfacing.
Domain
org.forester.surfacing.
DomainSimilarity
org.forester.go.
GoRelationship
org.forester.go.
GoSubset
org.forester.go.
GoTerm
(also extends org.forester.phylogeny.data.
PhylogenyData
)
org.forester.go.
GoXRef
org.forester.go.
Mapping
org.biojava3.core.sequence.location.template.
Point
org.forester.surfacing.
Species
org.biojava3.core.sequence.template.
Compound
org.biojava3.core.sequence.template.
ComplementCompound
org.biojava3.core.sequence.template.
CompoundSet
<C>
org.biojava3.core.sequence.template.
CompoundTranslator
<F,T>
org.biojava.bio.structure.align.ce.
ConfigStrucAligParams
org.biojava.bio.structure.gui.util.color.
ContinuousColorMapper
org.forester.pccx.
Coverage
org.forester.pccx.
CoverageCalculationMethod
org.forester.pccx.
CoverageCalculationOptions
org.forester.pccx.
CoverageExtender
org.biojava3.core.sequence.features.
DatabaseReferenceInterface
org.forester.util.
DescriptiveStatistics
org.forester.phylogenyinference.
DistanceMatrix
org.forester.phylogenyinference.
DistanceMatrixParser
org.forester.phylogenyinference.
DistanceMethod
org.biojava.bio.structure.domain.
DomainProvider
org.forester.surfacing.
DomainSimilarityCalculator
org.forester.phylogeny.
Edge
org.biojava3.core.sequence.edits.
Edit
<C>
org.forester.development.
Factory
org.biojava3.core.sequence.io.template.
FastaHeaderFormatInterface
<S,C>
org.biojava3.core.sequence.io.template.
FastaHeaderParserInterface
<S,C>
org.biojava3.sequencing.io.fastq.
FastqReader
org.biojava3.sequencing.io.fastq.
FastqWriter
org.biojava3.genome.parsers.gff.
FeatureI
org.biojava3.core.sequence.features.
FeatureInterface
<S,C>
org.biojava3.core.sequence.features.
FeaturesKeyWordInterface
org.biojava3.alignment.template.
GapPenalty
org.forester.surfacing.
GenomeWideCombinableDomains
org.biojava.bio.structure.
Group
org.biojava.bio.structure.
AminoAcid
org.biojava3.alignment.template.
HierarchicalClusterer
<S,C>
org.biojava3.ws.hmmer.
HmmerScan
org.biojava3.core.sequence.io.util.
IOUtils.ReaderProcessor
org.biojava3.aaproperties.
IPeptideProperties
org.biojava3.aaproperties.profeat.
IProfeatProperties
java.lang.
Iterable
<T>
org.biojava3.core.sequence.location.template.
Location
(also extends org.biojava3.core.sequence.template.
Accessioned
)
org.biojava3.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava3.core.sequence.template.
Accessioned
)
org.biojava3.alignment.template.
Profile
<S,C>
org.biojava3.alignment.template.
MutableProfile
<S,C>
org.biojava3.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava3.alignment.template.
ProfilePair
<S,C>)
org.biojava3.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava3.alignment.template.
SequencePair
<S,C>)
org.biojava3.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava3.alignment.template.
MutableProfile
<S,C>, org.biojava3.alignment.template.
ProfilePair
<S,C>)
org.biojava3.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava3.alignment.template.
MutableProfile
<S,C>, org.biojava3.alignment.template.
SequencePair
<S,C>)
org.biojava3.alignment.template.
ProfilePair
<S,C>
org.biojava3.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava3.alignment.template.
MutableProfile
<S,C>)
org.biojava3.alignment.template.
ProfileView
<S,C>
org.biojava3.alignment.template.
SequencePair
<S,C>
org.biojava3.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava3.alignment.template.
MutableProfile
<S,C>)
org.biojava3.core.sequence.template.
Sequence
<C> (also extends org.biojava3.core.sequence.template.
Accessioned
)
org.biojava3.alignment.template.
AlignedSequence
<S,C>
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
SequenceReader
<C>
org.biojava3.core.sequence.template.
ProxySequenceReader
<C>
org.biojava3.core.sequence.template.
SequenceView
<C>
java.util.
Iterator
<E>
org.forester.phylogeny.iterators.
PhylogenyNodeIterator
org.biojava3.core.sequence.template.
LightweightProfile
<S,C>
org.biojava.bio.structure.align.ce.
MatrixListener
org.biojava.bio.structure.io.mmcif.
MMcifConsumer
org.biojava.bio.structure.io.mmcif.
MMcifParser
org.biojava3.protmod.
ModificationCondition
org.biojava3.protmod.structure.
ModifiedCompound
org.forester.development.
Msa
org.forester.development.
MsaFactory
org.forester.development.
StreamBasedMsaFactory
org.biojava3.phylo.
NJTreeProgressListener
org.forester.surfacing.
PairwiseDomainSimilarity
org.forester.surfacing.
PairwiseDomainSimilarityCalculator
org.biojava3.sequencing.io.fastq.
ParseListener
org.biojava.bio.structure.server.
PDBFilter
org.biojava.bio.structure.server.
PDBInstallation
org.biojava.bio.structure.
PDBRecord
org.biojava.bio.structure.
Atom
(also extends java.lang.
Cloneable
)
org.biojava.bio.structure.domain.
PDPProvider
org.forester.archaeopteryx.webservices.
PhylogeniesWebserviceClient
org.forester.phylogeny.data.
PhylogenyData
org.forester.go.
GoTerm
(also extends java.lang.
Comparable
<T>)
org.forester.archaeopteryx.phylogeny.data.
RenderablePhylogenyData
org.forester.io.parsers.phyloxml.phylogenydata.
PhylogenyDataPhyloXmlParser
org.forester.phylogeny.factories.
PhylogenyFactory
org.forester.phylogeny.
PhylogenyNodeI
org.forester.io.parsers.
PhylogenyParser
org.biojava3.core.sequence.location.template.
Point.Resolver
<T>
org.forester.surfacing.
Protein
org.biojava3.protmod.
ProteinModification
org.biojava3.ws.alignment.
RemotePairwiseAlignmentService
java.lang.
Runnable
org.biojava.bio.structure.align.gui.
AlignmentCalculationRunnable
org.biojava.bio.structure.scop.
ScopDatabase
org.biojava3.alignment.template.
Scorer
org.biojava3.alignment.template.
Aligner
<S,C>
org.biojava3.alignment.template.
MatrixAligner
<S,C>
org.biojava3.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava3.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava3.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava3.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava3.alignment.template.
RescoreRefiner
<S,C>
org.biojava3.alignment.template.
MatrixAligner
<S,C>
org.biojava3.alignment.template.
PairInProfileScorer
<S,C>
org.biojava3.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>, org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava3.alignment.template.
PairwiseSequenceScorer
<S,C>
org.biojava3.alignment.template.
PairInProfileScorer
<S,C>
org.biojava3.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>)
org.biojava3.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>, org.biojava3.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava3.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>, org.biojava3.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava3.alignment.template.
ProfileProfileScorer
<S,C>
org.biojava3.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>)
org.biojava3.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava3.alignment.template.
Aligner
<S,C>)
org.biojava3.alignment.template.
RescoreRefiner
<S,C>
org.forester.pccx.
ScoringMethodForExternalNode
org.biojava3.structure.gui.
Selection
org.forester.development.
Sequence
org.biojava3.core.sequence.io.template.
SequenceCreatorInterface
<C>
org.biojava3.core.sequence.io.template.
SequenceParserInterface
java.io.
Serializable
org.biojava3.ws.alignment.
RemotePairwiseAlignmentOutputProperties
org.biojava3.ws.alignment.
RemotePairwiseAlignmentProperties
org.biojava3.sequencing.io.fastq.
StreamListener
org.biojava.bio.structure.align.
StructureAlignment
org.biojava.bio.structure.server.
StructureEvent
org.biojava.bio.structure.io.
StructureIO
org.biojava.bio.structure.io.
StructureIOFile
org.biojava.bio.structure.server.
StructureListener
org.biojava.bio.structure.gui.util.
StructurePairSelector
org.biojava.bio.structure.io.
StructureProvider
org.biojava.bio.structure.server.
StructureServer
org.biojava3.structure.gui.
StructureViewer
org.biojava3.alignment.template.
SubstitutionMatrix
<C>
org.biojava3.core.sequence.transcription.
Table
javax.swing.tree.
TreeNode
org.biojava3.alignment.template.
GuideTreeNode
<S,C>
org.biojava.bio.structure.align.ce.
UserArgumentProcessor
org.biojava3.core.util.
XMLWriter
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
org.biojava.bio.structure.
Element
(implements java.io.
Serializable
)
org.biojava.bio.structure.
BondType
org.biojava.bio.structure.
PDBStatus.Status
org.biojava.bio.structure.
ElementType
(implements java.io.
Serializable
)
org.biojava.bio.structure.gui.util.color.
LinearColorInterpolator.InterpolationDirection
org.biojava.bio.structure.io.mmcif.chem.
PolymerType
(implements java.io.
Serializable
)
org.biojava.bio.structure.io.mmcif.chem.
ResidueType
(implements java.io.
Serializable
)
org.biojava.bio.structure.scop.
ScopCategory
(implements java.io.
Serializable
)
org.biojava3.aaproperties.
PeptideProperties.SingleLetterAACode
org.biojava3.aaproperties.
CommandPrompt.PropertyName
org.biojava3.aaproperties.profeat.
IProfeatProperties.ATTRIBUTE
org.biojava3.aaproperties.profeat.
IProfeatProperties.GROUPING
org.biojava3.aaproperties.profeat.
IProfeatProperties.TRANSITION
org.biojava3.aaproperties.profeat.
IProfeatProperties.DISTRIBUTION
org.biojava3.alignment.
Alignments.PairInProfileScorerType
org.biojava3.alignment.
Alignments.PairwiseSequenceAlignerType
org.biojava3.alignment.
Alignments.PairwiseSequenceScorerType
org.biojava3.alignment.
Alignments.ProfileProfileAlignerType
org.biojava3.alignment.
Alignments.RefinerType
org.biojava3.alignment.routines.
AlignerHelper.Last
org.biojava3.alignment.template.
GapPenalty.Type
org.biojava3.alignment.template.
AlignedSequence.Step
org.biojava3.alignment.template.
Profile.StringFormat
org.biojava3.core.sequence.
Strand
org.biojava3.core.sequence.
DataSource
org.biojava3.core.sequence.
DNASequence.DNAType
org.biojava3.core.sequence.
SequenceOptimizationHints.SequenceUsage
org.biojava3.core.sequence.
SequenceOptimizationHints.SequenceCollection
org.biojava3.core.sequence.template.
LightweightProfile.StringFormat
org.biojava3.core.sequence.template.
AbstractSequence.AnnotationType
org.biojava3.core.sequence.transcription.
Frame
org.biojava3.phylo.
TreeType
org.biojava3.phylo.
TreeConstructionAlgorithm
org.biojava3.protmod.
ModificationOccurrenceType
org.biojava3.protmod.
ModificationCategory
org.biojava3.ronn.
RonnConstraint.Threshold
org.biojava3.sequencing.io.fastq.
FastqVariant
org.biojava3.structure.gui.
RenderStyle
org.biojava3.ws.alignment.qblast.
BlastMatrixEnum
org.biojava3.ws.alignment.qblast.
BlastOutputParameterEnum
org.biojava3.ws.alignment.qblast.
BlastProgramEnum
org.biojava3.ws.alignment.qblast.
BlastOutputAlignmentFormatEnum
org.biojava3.ws.alignment.qblast.
BlastAlignmentParameterEnum
org.biojava3.ws.alignment.qblast.
BlastOutputFormatEnum
org.forester.archaeopteryx.webservices.
WebservicesManager.WsPhylogenyFormat
org.forester.go.
GoXRef.Type
org.forester.go.
GoSubset.Type
org.forester.go.
GoNameSpace.GoNamespaceType
org.forester.go.
GoRelationship.Type
org.forester.go.
OBOparser.ReturnType
org.forester.go.etc.
OntologizerResult.TYPE
org.forester.io.parsers.
HmmscanPerDomainTableParser.FilterType
org.forester.io.parsers.
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
org.forester.io.parsers.
HmmscanPerDomainTableParser.ReturnType
org.forester.io.parsers.
HmmPfamOutputParser.FilterType
org.forester.io.parsers.
HmmPfamOutputParser.ReturnType
org.forester.io.parsers.nhx.
NHXParser.TAXONOMY_EXTRACTION
org.forester.io.writers.
PhylogenyWriter.FORMAT
org.forester.phylogeny.data.
SequenceRelation.SEQUENCE_RELATION_TYPE
org.forester.phylogeny.data.
Property.AppliesTo
org.forester.phylogeny.data.
Event.EventType
org.forester.phylogenyinference.
DistanceMatrix.Format
org.forester.phylogenyinference.
CharacterStateMatrix.BinaryStates
org.forester.phylogenyinference.
CharacterStateMatrix.Format
org.forester.phylogenyinference.
CharacterStateMatrix.GainLossStates
org.forester.phylogenyinference.
CharacterStateMatrix.NucleotideStates
org.forester.phylogenyinference.
SymmetricalDistanceMatrixParser.InputMatrixType
org.forester.surfacing.
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
org.forester.surfacing.
PrintableDomainSimilarity.PRINT_OPTION
org.forester.surfacing.
DomainSimilarity.DomainSimilarityScoring
org.forester.surfacing.
DomainSimilarity.DomainSimilaritySortField
org.forester.surfacing.
DomainSimilarityCalculator.Detailedness
org.forester.surfacing.
DomainSimilarityCalculator.GoAnnotationOutput
org.forester.surfacing.
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
org.forester.surfacing.
BinaryDomainCombination.DomainCombinationType
org.forester.surfacing.
BinaryDomainCombination.OutputFormat
org.forester.tools.
PhylogenyDecorator.FIELD
org.forester.util.
ForesterUtil.PhylogenyNodeField
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