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Package Hierarchies:
org.biojava.nbio.aaproperties
,
org.biojava.nbio.aaproperties.profeat
,
org.biojava.nbio.aaproperties.profeat.convertor
,
org.biojava.nbio.aaproperties.xml
,
org.biojava.nbio.alignment
,
org.biojava.nbio.alignment.aaindex
,
org.biojava.nbio.alignment.io
,
org.biojava.nbio.alignment.routines
,
org.biojava.nbio.alignment.template
,
org.biojava.nbio.core.exceptions
,
org.biojava.nbio.core.sequence
,
org.biojava.nbio.core.sequence.compound
,
org.biojava.nbio.core.sequence.edits
,
org.biojava.nbio.core.sequence.features
,
org.biojava.nbio.core.sequence.io
,
org.biojava.nbio.core.sequence.io.template
,
org.biojava.nbio.core.sequence.io.util
,
org.biojava.nbio.core.sequence.loader
,
org.biojava.nbio.core.sequence.location
,
org.biojava.nbio.core.sequence.location.template
,
org.biojava.nbio.core.sequence.storage
,
org.biojava.nbio.core.sequence.template
,
org.biojava.nbio.core.sequence.transcription
,
org.biojava.nbio.core.sequence.views
,
org.biojava.nbio.core.util
,
org.biojava.nbio.data.sequence
,
org.biojava.nbio.genome
,
org.biojava.nbio.genome.homology
,
org.biojava.nbio.genome.parsers.cytoband
,
org.biojava.nbio.genome.parsers.geneid
,
org.biojava.nbio.genome.parsers.genename
,
org.biojava.nbio.genome.parsers.gff
,
org.biojava.nbio.genome.parsers.twobit
,
org.biojava.nbio.genome.query
,
org.biojava.nbio.genome.uniprot
,
org.biojava.nbio.genome.util
,
org.biojava.nbio.ontology
,
org.biojava.nbio.ontology.io
,
org.biojava.nbio.ontology.obo
,
org.biojava.nbio.ontology.utils
,
org.biojava.nbio.phosphosite
,
org.biojava.nbio.phylo
,
org.biojava.nbio.proteincomparisontool
,
org.biojava.nbio.protmod
,
org.biojava.nbio.protmod.io
,
org.biojava.nbio.protmod.structure
,
org.biojava.nbio.ronn
,
org.biojava.nbio.sequencing.io.fastq
,
org.biojava.nbio.structure
,
org.biojava.nbio.structure.align
,
org.biojava.nbio.structure.align.ce
,
org.biojava.nbio.structure.align.cemc
,
org.biojava.nbio.structure.align.client
,
org.biojava.nbio.structure.align.events
,
org.biojava.nbio.structure.align.fatcat
,
org.biojava.nbio.structure.align.fatcat.calc
,
org.biojava.nbio.structure.align.gui
,
org.biojava.nbio.structure.align.gui.aligpanel
,
org.biojava.nbio.structure.align.gui.autosuggest
,
org.biojava.nbio.structure.align.gui.jmol
,
org.biojava.nbio.structure.align.helper
,
org.biojava.nbio.structure.align.model
,
org.biojava.nbio.structure.align.multiple
,
org.biojava.nbio.structure.align.pairwise
,
org.biojava.nbio.structure.align.seq
,
org.biojava.nbio.structure.align.util
,
org.biojava.nbio.structure.align.webstart
,
org.biojava.nbio.structure.align.xml
,
org.biojava.nbio.structure.asa
,
org.biojava.nbio.structure.cath
,
org.biojava.nbio.structure.contact
,
org.biojava.nbio.structure.domain
,
org.biojava.nbio.structure.domain.pdp
,
org.biojava.nbio.structure.ecod
,
org.biojava.nbio.structure.gui
,
org.biojava.nbio.structure.gui.events
,
org.biojava.nbio.structure.gui.util
,
org.biojava.nbio.structure.gui.util.color
,
org.biojava.nbio.structure.io
,
org.biojava.nbio.structure.io.mmcif
,
org.biojava.nbio.structure.io.mmcif.chem
,
org.biojava.nbio.structure.io.mmcif.model
,
org.biojava.nbio.structure.io.sifts
,
org.biojava.nbio.structure.io.util
,
org.biojava.nbio.structure.jama
,
org.biojava.nbio.structure.math
,
org.biojava.nbio.structure.quaternary
,
org.biojava.nbio.structure.quaternary.io
,
org.biojava.nbio.structure.rcsb
,
org.biojava.nbio.structure.scop
,
org.biojava.nbio.structure.scop.server
,
org.biojava.nbio.structure.secstruc
,
org.biojava.nbio.structure.symmetry.analysis
,
org.biojava.nbio.structure.symmetry.core
,
org.biojava.nbio.structure.symmetry.geometry
,
org.biojava.nbio.structure.symmetry.jmolScript
,
org.biojava.nbio.structure.symmetry.misc
,
org.biojava.nbio.structure.symmetry.utils
,
org.biojava.nbio.structure.validation
,
org.biojava.nbio.structure.xtal
,
org.biojava.nbio.structure.xtal.io
,
org.biojava.nbio.survival.cox
,
org.biojava.nbio.survival.cox.comparators
,
org.biojava.nbio.survival.cox.matrix
,
org.biojava.nbio.survival.cox.stats
,
org.biojava.nbio.survival.data
,
org.biojava.nbio.survival.kaplanmeier.figure
,
org.biojava.nbio.survival.kaplanmeier.metadata
,
org.biojava.nbio.ws.alignment
,
org.biojava.nbio.ws.alignment.qblast
,
org.biojava.nbio.ws.hmmer
,
org.forester.analysis
,
org.forester.application
,
org.forester.archaeopteryx
,
org.forester.archaeopteryx.phylogeny.data
,
org.forester.archaeopteryx.tools
,
org.forester.archaeopteryx.webservices
,
org.forester.datastructures
,
org.forester.development
,
org.forester.evoinference
,
org.forester.evoinference.distance
,
org.forester.evoinference.matrix.character
,
org.forester.evoinference.matrix.distance
,
org.forester.evoinference.parsimony
,
org.forester.evoinference.tools
,
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.data
,
org.forester.io.parsers.tol
,
org.forester.io.parsers.util
,
org.forester.io.writers
,
org.forester.msa
,
org.forester.pccx
,
org.forester.phylogeny
,
org.forester.phylogeny.data
,
org.forester.phylogeny.factories
,
org.forester.phylogeny.iterators
,
org.forester.protein
,
org.forester.sdi
,
org.forester.sequence
,
org.forester.species
,
org.forester.surfacing
,
org.forester.test
,
org.forester.test.examples
,
org.forester.tools
,
org.forester.util
,
org.forester.ws.hmmer
,
org.forester.ws.seqdb
,
org.forester.ws.uniprot
,
org.forester.ws.wabi
,
org.jcolorbrewer
,
org.jcolorbrewer.ui
Class Hierarchy
java.lang.Object
org.biojava.nbio.alignment.aaindex.
AAindexFactory
org.biojava.nbio.alignment.aaindex.
AAIndexFileParser
org.biojava.nbio.structure.align.gui.
AboutDialog
javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.align.gui.
ChooseDirAction
org.biojava.nbio.structure.align.gui.jmol.
AbstractAlignmentJmol
(implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener)
org.biojava.nbio.structure.align.gui.jmol.
MultipleAlignmentJmol
org.biojava.nbio.structure.align.gui.jmol.
StructureAlignmentJmol
org.biojava.nbio.ontology.utils.
AbstractAnnotation
(implements org.biojava.nbio.ontology.utils.
Annotation
, java.io.Serializable)
org.biojava.nbio.ontology.utils.
SmallAnnotation
org.biojava.nbio.structure.io.mmcif.model.
AbstractBean
org.biojava.nbio.structure.io.mmcif.model.
AtomSite
org.biojava.nbio.structure.io.mmcif.model.
Cell
org.biojava.nbio.structure.io.mmcif.model.
DatabasePDBremark
org.biojava.nbio.structure.io.mmcif.model.
EntityPolySeq
org.biojava.nbio.structure.io.mmcif.model.
Exptl
org.biojava.nbio.structure.io.mmcif.model.
PdbxPolySeqScheme
org.biojava.nbio.structure.io.mmcif.model.
StructAsym
org.biojava.nbio.structure.io.mmcif.model.
StructNcsOper
org.biojava.nbio.structure.io.mmcif.model.
StructRef
org.biojava.nbio.structure.io.mmcif.model.
StructRefSeq
org.biojava.nbio.structure.io.mmcif.model.
Symmetry
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.biojava.nbio.genome.parsers.gff.
FeatureList
org.biojava.nbio.core.sequence.template.
AbstractCompound
(implements org.biojava.nbio.core.sequence.template.
Compound
)
org.biojava.nbio.core.sequence.compound.
AminoAcidCompound
org.biojava.nbio.core.sequence.compound.
CodonCompound
org.biojava.nbio.core.sequence.compound.
NucleotideCompound
(implements org.biojava.nbio.core.sequence.template.
ComplementCompound
)
org.biojava.nbio.core.sequence.template.
AbstractCompoundSet
<C> (implements org.biojava.nbio.core.sequence.template.
CompoundSet
<C>)
org.biojava.nbio.core.sequence.template.
AbstractNucleotideCompoundSet
<C>
org.biojava.nbio.core.sequence.compound.
DNACompoundSet
org.biojava.nbio.core.sequence.compound.
AmbiguityDNACompoundSet
org.biojava.nbio.core.sequence.compound.
RNACompoundSet
org.biojava.nbio.core.sequence.compound.
AmbiguityRNACompoundSet
org.biojava.nbio.core.sequence.template.
AbstractCompoundTranslator
<F,T> (implements org.biojava.nbio.core.sequence.template.
CompoundTranslator
<F,T>)
org.biojava.nbio.core.sequence.transcription.
DNAToRNATranslator
org.biojava.nbio.core.sequence.transcription.
RNAToAminoAcidTranslator
org.biojava.nbio.core.sequence.features.
AbstractFeature
<S,C> (implements org.biojava.nbio.core.sequence.features.
FeatureInterface
<S,C>)
org.biojava.nbio.core.sequence.features.
QualityFeature
<S,C>
org.biojava.nbio.core.sequence.features.
QuantityFeature
<S,C>
org.biojava.nbio.core.sequence.features.
TextFeature
<S,C>
org.biojava.nbio.core.sequence.location.template.
AbstractLocation
(implements org.biojava.nbio.core.sequence.location.template.
Location
)
org.biojava.nbio.core.sequence.location.
InsdcLocations.BondLocation
org.biojava.nbio.core.sequence.location.
InsdcLocations.OneOfLocation
org.biojava.nbio.core.sequence.location.
SimpleLocation
org.biojava.nbio.core.sequence.location.
InsdcLocations.GroupLocation
org.biojava.nbio.core.sequence.location.
InsdcLocations.OrderLocation
org.biojava.nbio.core.sequence.location.
SequenceLocation
<S,C>
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
org.biojava.nbio.structure.align.util.
AlignmentTools.IdentityMap
<K>
org.biojava.nbio.ontology.utils.
SmallMap
(implements java.io.Serializable)
org.biojava.nbio.core.util.
SoftHashMap
<K,V>
org.biojava.nbio.ontology.utils.
WeakValueHashMap
org.biojava.nbio.alignment.template.
AbstractScorer
(implements org.biojava.nbio.alignment.template.
Scorer
)
org.biojava.nbio.alignment.template.
AbstractMatrixAligner
<S,C> (implements org.biojava.nbio.alignment.template.
MatrixAligner
<S,C>)
org.biojava.nbio.alignment.template.
AbstractPairwiseSequenceAligner
<S,C> (implements org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C>)
org.biojava.nbio.alignment.routines.
AnchoredPairwiseSequenceAligner
<S,C>
org.biojava.nbio.alignment.routines.
GuanUberbacher
<S,C>
org.biojava.nbio.alignment.
NeedlemanWunsch
<S,C>
org.biojava.nbio.alignment.
SmithWaterman
<S,C>
org.biojava.nbio.alignment.template.
AbstractProfileProfileAligner
<S,C> (implements org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C>)
org.biojava.nbio.alignment.
SimpleProfileProfileAligner
<S,C>
org.biojava.nbio.alignment.
FractionalIdentityScorer
<S,C> (implements org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.alignment.
FractionalIdentityInProfileScorer
<S,C> (implements org.biojava.nbio.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava.nbio.alignment.
FractionalSimilarityScorer
<S,C> (implements org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.alignment.
FractionalSimilarityInProfileScorer
<S,C> (implements org.biojava.nbio.alignment.template.
PairInProfileScorer
<S,C>)
org.biojava.nbio.alignment.
StandardRescoreRefiner
<S,C> (implements org.biojava.nbio.alignment.template.
RescoreRefiner
<S,C>)
org.biojava.nbio.alignment.
SubstitutionMatrixScorer
<S,C> (implements org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.structure.align.multiple.
AbstractScoresCache
(implements org.biojava.nbio.structure.align.multiple.
ScoresCache
)
org.biojava.nbio.structure.align.multiple.
BlockImpl
(implements org.biojava.nbio.structure.align.multiple.
Block
, java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.align.multiple.
BlockSetImpl
(implements org.biojava.nbio.structure.align.multiple.
BlockSet
, java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentEnsembleImpl
(implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.
MultipleAlignmentEnsemble
, java.io.Serializable)
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentImpl
(implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.
MultipleAlignment
, java.io.Serializable)
org.biojava.nbio.core.sequence.template.
AbstractSequence
<C> (implements org.biojava.nbio.core.sequence.template.
Sequence
<C>)
org.biojava.nbio.core.sequence.
BasicSequence
<C>
org.biojava.nbio.core.sequence.
DNASequence
org.biojava.nbio.core.sequence.
CDSSequence
org.biojava.nbio.core.sequence.
ChromosomeSequence
org.biojava.nbio.core.sequence.
ExonSequence
org.biojava.nbio.core.sequence.
GeneSequence
org.biojava.nbio.core.sequence.
IntronSequence
org.biojava.nbio.core.sequence.
StartCodonSequence
org.biojava.nbio.core.sequence.
StopCodonSequence
org.biojava.nbio.core.sequence.
TranscriptSequence
org.biojava.nbio.core.sequence.
ProteinSequence
org.biojava.nbio.core.sequence.
RNASequence
org.biojava.nbio.structure.align.
AbstractStructureAlignment
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.align.ce.
CeMain
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.align.ce.
CeCPMain
org.biojava.nbio.structure.align.ce.
CeSideChainMain
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.align.ce.
OptimalCECPMain
org.biojava.nbio.structure.align.seq.
SmithWaterman3Daligner
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.ontology.
AbstractTerm
(implements org.biojava.nbio.ontology.
Term
)
org.biojava.nbio.ontology.
RemoteTerm.Impl
(implements org.biojava.nbio.ontology.
RemoteTerm
, java.io.Serializable)
org.biojava.nbio.ontology.
Term.Impl
(implements java.io.Serializable, org.biojava.nbio.ontology.
Term
)
org.biojava.nbio.ontology.
Variable.Impl
(implements org.biojava.nbio.ontology.
Variable
)
org.biojava.nbio.structure.align.ce.
AbstractUserArgumentProcessor
(implements org.biojava.nbio.structure.align.ce.
UserArgumentProcessor
)
org.biojava.nbio.structure.align.ce.
CeUserArgumentProcessor
org.biojava.nbio.structure.align.ce.
CeCPUserArgumentProcessor
org.biojava.nbio.structure.align.ce.
CeSideChainUserArgumentProcessor
org.biojava.nbio.structure.align.fatcat.
FatCatUserArgumentProcessor
org.biojava.nbio.structure.align.seq.
SmithWatermanUserArgumentProcessor
org.forester.phylogeny.data.
Accession
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.biojava.nbio.core.sequence.
AccessionID
org.forester.io.parsers.phyloxml.data.
AccessionParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.align.model.
AFP
(implements java.io.Serializable)
org.biojava.nbio.structure.align.util.
AFPAlignmentDisplay
org.biojava.nbio.structure.align.fatcat.calc.
AFPCalculator
org.biojava.nbio.structure.align.model.
AFPChain
(implements java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.align.gui.aligpanel.
AFPChainCoordManager
org.biojava.nbio.structure.align.fatcat.calc.
AFPChainer
org.biojava.nbio.structure.align.xml.
AFPChainFlipper
org.biojava.nbio.structure.align.util.
AFPChainScorer
org.biojava.nbio.structure.align.model.
AfpChainWriter
org.biojava.nbio.structure.align.xml.
AFPChainXMLConverter
org.biojava.nbio.structure.align.xml.
AFPChainXMLParser
org.biojava.nbio.structure.align.fatcat.calc.
AFPOptimizer
org.biojava.nbio.structure.align.fatcat.calc.
AFPPostProcessor
org.biojava.nbio.structure.align.
AFPTwister
org.biojava.nbio.survival.cox.stats.
AgScore
org.biojava.nbio.structure.gui.util.
AlignedPosition
org.biojava.nbio.alignment.routines.
AlignerHelper
org.biojava.nbio.alignment.routines.
AlignerHelper.Anchor
org.biojava.nbio.alignment.routines.
AlignerHelper.Anchor.QueryIndexComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.alignment.routines.
AlignerHelper.Cut
org.biojava.nbio.alignment.routines.
AlignerHelper.Subproblem
org.biojava.nbio.structure.align.gui.
AlignmentCalc
(implements org.biojava.nbio.structure.align.gui.
AlignmentCalculationRunnable
)
org.biojava.nbio.structure.gui.util.
AlignmentCalc
(implements java.lang.Runnable)
org.biojava.nbio.structure.align.gui.
AlignmentCalcDB
(implements org.biojava.nbio.structure.align.gui.
AlignmentCalculationRunnable
)
org.biojava.nbio.structure.align.pairwise.
AlignmentProgressListener
org.biojava.nbio.structure.align.pairwise.
AlignmentResult
(implements java.io.Serializable)
org.biojava.nbio.alignment.
Alignments
org.biojava.nbio.structure.align.util.
AlignmentTools
org.biojava.nbio.structure.align.pairwise.
AligNPE
org.biojava.nbio.structure.align.helper.
AlignTools
org.biojava.nbio.structure.align.gui.aligpanel.
AligPanelMouseMotionListener
(implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
org.biojava.nbio.structure.align.webstart.
AligUIManager
org.biojava.nbio.structure.io.mmcif.
AllChemCompProvider
(implements org.biojava.nbio.structure.io.mmcif.
ChemCompProvider
, java.lang.Runnable)
org.biojava.nbio.structure.align.pairwise.
AltAligComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.structure.align.pairwise.
AlternativeAlignment
(implements java.io.Serializable)
org.biojava.nbio.aaproperties.xml.
AminoAcidComposition
org.biojava.nbio.aaproperties.xml.
AminoAcidCompositionTable
org.biojava.nbio.core.sequence.compound.
AminoAcidCompoundSet
(implements org.biojava.nbio.core.sequence.template.
CompoundSet
<C>)
org.forester.analysis.
AncestralTaxonomyInference
org.biojava.nbio.structure.validation.
AngleOutlier
org.forester.phylogeny.data.
Annotation
(implements java.lang.Comparable<T>, org.forester.phylogeny.data.
MultipleUris
, org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
AnnotationParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.genome.
App
org.biojava.nbio.ontology.
App
org.forester.archaeopteryx.
AptxUtil
org.forester.archaeopteryx.
Archaeopteryx
org.biojava.nbio.core.sequence.storage.
ArrayListSequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
SequenceReader
<C>)
org.biojava.nbio.core.sequence.loader.
ArrayListProxySequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.nbio.structure.asa.
AsaCalculator
org.forester.util.
AsciiHistogram
org.biojava.nbio.structure.domain.
AssignmentXMLSerializer
org.biojava.nbio.structure.scop.
Astral
org.biojava.nbio.structure.align.util.
AtomCache
org.biojava.nbio.structure.contact.
AtomContact
org.biojava.nbio.structure.contact.
AtomContactSet
(implements java.lang.Iterable<T>)
org.biojava.nbio.structure.contact.
AtomIdentifier
org.biojava.nbio.structure.
AtomImpl
(implements org.biojava.nbio.structure.
Atom
, org.biojava.nbio.structure.
PDBRecord
, java.io.Serializable)
org.biojava.nbio.structure.align.gui.jmol.
AtomInfo
org.biojava.nbio.structure.align.gui.jmol.
AtomInfoParser
org.biojava.nbio.structure.
AtomIterator
(implements java.util.Iterator<E>)
org.biojava.nbio.structure.
AtomPositionMap
org.biojava.nbio.structure.io.mmcif.model.
AuditAuthor
org.biojava.nbio.structure.
Author
(implements java.io.Serializable)
org.biojava.nbio.structure.symmetry.core.
AxisAligner
org.biojava.nbio.structure.symmetry.core.
HelixAxisAligner
org.biojava.nbio.structure.symmetry.core.
RotationAxisAligner
org.forester.surfacing.
BasicBinaryDomainCombination
(implements org.forester.protein.
BinaryDomainCombination
)
org.forester.surfacing.
AdjactantDirectedBinaryDomainCombination
org.forester.surfacing.
DirectedBinaryDomainCombination
org.forester.evoinference.matrix.character.
BasicCharacterStateMatrix
<S> (implements org.forester.evoinference.matrix.character.
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.protein.
BasicDomain
(implements org.forester.protein.
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.msa.
BasicMsa
(implements org.forester.msa.
Msa
)
org.forester.msa.
ResampleableMsa
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.protein.
BasicProtein
(implements org.forester.protein.
Protein
)
org.forester.sequence.
BasicSequence
(implements org.forester.sequence.
Sequence
)
org.forester.species.
BasicSpecies
(implements org.forester.species.
Species
)
org.forester.evoinference.matrix.distance.
BasicSymmetricalDistanceMatrix
(implements org.forester.evoinference.matrix.distance.
DistanceMatrix
)
org.forester.util.
BasicTable
<E>
org.forester.util.
BasicTableParser
org.biojava.nbio.structure.secstruc.
BigSqrt
org.forester.phylogeny.data.
BinaryCharacters
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
BinaryCharactersParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.quaternary.
BioAssemblyInfo
org.biojava.nbio.structure.quaternary.
BioAssemblyTools
org.biojava.nbio.structure.gui.
BiojavaJmol
org.biojava.nbio.structure.align.
BioJavaStructureAlignment
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.quaternary.
BiologicalAssemblyBuilder
org.biojava.nbio.structure.quaternary.
BiologicalAssemblyTransformation
(implements java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.quaternary.io.
BioUnitDataProviderFactory
org.biojava.nbio.core.sequence.storage.
BitSequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.nbio.core.sequence.storage.
FourBitSequenceReader
<C>
org.biojava.nbio.core.sequence.storage.
TwoBitSequenceReader
<C>
org.biojava.nbio.core.sequence.storage.
BitSequenceReader.BitArrayWorker
<C>
org.biojava.nbio.core.sequence.storage.
FourBitSequenceReader.FourBitArrayWorker
<C>
org.biojava.nbio.core.sequence.storage.
TwoBitSequenceReader.TwoBitArrayWorker
<C>
org.forester.archaeopteryx.tools.
Blast
org.biojava.nbio.structure.symmetry.utils.
BlastClustReader
org.biojava.nbio.genome.homology.
BlastHomologyHits
org.biojava.nbio.ws.alignment.qblast.
BlastJob
org.biojava.nbio.genome.query.
BlastXMLQuery
org.biojava.nbio.structure.
Bond
(implements java.io.Serializable)
org.biojava.nbio.structure.io.
BondMaker
org.biojava.nbio.structure.validation.
BondOutlier
org.forester.evoinference.tools.
BootstrapResampler
org.biojava.nbio.structure.contact.
BoundingBox
(implements java.io.Serializable)
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.data.
BranchWidthParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.align.webstart.
BrowserOpener
org.biojava.nbio.structure.symmetry.core.
C2RotationSolver
(implements org.biojava.nbio.structure.symmetry.core.
QuatSymmetrySolver
)
org.biojava.nbio.structure.align.util.
CacheFactory
org.biojava.nbio.structure.io.
CAConverter
org.biojava.nbio.structure.
Calc
org.biojava.nbio.structure.symmetry.analysis.
CalcBioAssemblySymmetry
org.biojava.nbio.alignment.template.
CallablePairwiseSequenceAligner
<S,C> (implements java.util.concurrent.Callable<V>)
org.biojava.nbio.alignment.template.
CallablePairwiseSequenceScorer
<S,C> (implements java.util.concurrent.Callable<V>)
org.biojava.nbio.alignment.template.
CallableProfileProfileAligner
<S,C> (implements java.util.concurrent.Callable<V>)
org.biojava.nbio.structure.align.
CallableStructureAlignment
(implements java.util.concurrent.Callable<V>)
org.biojava.nbio.structure.quaternary.
CartesianProduct
<T>
org.biojava.nbio.aaproperties.xml.
CaseFreeAminoAcidCompoundSet
(implements org.biojava.nbio.core.sequence.template.
CompoundSet
<C>)
org.biojava.nbio.core.sequence.transcription.
CaseInsensitiveCompound
(implements org.biojava.nbio.core.sequence.template.
Compound
)
org.biojava.nbio.structure.cath.
CathDomain
(implements java.io.Serializable, org.biojava.nbio.structure.
StructureIdentifier
)
org.biojava.nbio.structure.cath.
CathFactory
org.biojava.nbio.structure.cath.
CathFragment
(implements java.io.Serializable)
org.biojava.nbio.structure.cath.
CathInstallation
(implements org.biojava.nbio.structure.cath.
CathDatabase
)
org.biojava.nbio.structure.cath.
CathNode
(implements java.io.Serializable)
org.biojava.nbio.structure.cath.
CathSegment
(implements java.io.Serializable)
org.biojava.nbio.core.sequence.
CDSComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.structure.align.ce.
CECalculator
org.biojava.nbio.structure.align.ce.
CeCalculatorEnhanced
org.biojava.nbio.structure.align.ce.
CeCPMain.CPRange
org.biojava.nbio.structure.align.cemc.
CeMcMain
(implements org.biojava.nbio.structure.align.
MultipleStructureAligner
)
org.biojava.nbio.structure.align.cemc.
CeMcOptimizer
(implements java.util.concurrent.Callable<V>)
org.biojava.nbio.survival.kaplanmeier.figure.
CensorStatus
(implements java.lang.Comparable<T>)
org.biojava.nbio.structure.align.ce.
CeParameters
(implements org.biojava.nbio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava.nbio.structure.align.ce.
CECPParameters
org.biojava.nbio.structure.align.cemc.
CeMcParameters
org.biojava.nbio.structure.align.ce.
OptimalCECPParameters
org.biojava.nbio.structure.symmetry.core.
ChainClusterer
org.biojava.nbio.structure.
ChainImpl
(implements org.biojava.nbio.structure.
Chain
, java.io.Serializable)
org.biojava.nbio.structure.symmetry.misc.
ChainSignature
(implements java.lang.Comparable<T>)
org.biojava.nbio.phylo.
CheckTreeAccuracy
org.biojava.nbio.structure.io.mmcif.model.
ChemComp
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.model.
ChemCompAtom
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.model.
ChemCompBond
org.biojava.nbio.structure.io.mmcif.
ChemCompConsumer
(implements org.biojava.nbio.structure.io.mmcif.
MMcifConsumer
)
org.biojava.nbio.structure.io.mmcif.model.
ChemCompDescriptor
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.
ChemCompGroupFactory
org.biojava.nbio.structure.io.mmcif.chem.
ChemCompTools
org.biojava.nbio.structure.io.mmcif.
ChemicalComponentDictionary
org.biojava.nbio.survival.cox.stats.
ChiSq
org.biojava.nbio.survival.cox.stats.
Cholesky2
org.biojava.nbio.structure.jama.
CholeskyDecomposition
(implements java.io.Serializable)
org.biojava.nbio.survival.cox.stats.
Chsolve2
org.biojava.nbio.structure.validation.
Clash
org.biojava.nbio.core.sequence.io.util.
ClasspathResource
org.biojava.nbio.survival.kaplanmeier.metadata.
ClinicalMetaDataOutcome
org.biojava.nbio.structure.align.util.
CliTools
org.biojava.nbio.structure.align.
ClusterAltAligs
org.biojava.nbio.structure.domain.pdp.
ClusterDomains
org.biojava.nbio.structure.symmetry.core.
ClusterMerger
org.biojava.nbio.structure.symmetry.core.
ClusterProteinChains
org.biojava.nbio.structure.align.util.
CollectionTools
org.biojava.nbio.structure.symmetry.jmolScript.
ColorConverter
org.forester.io.parsers.phyloxml.data.
ColorParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
java.awt.color.ColorSpace (implements java.io.Serializable)
org.biojava.nbio.structure.gui.util.color.
HSVColorSpace
org.biojava.nbio.structure.gui.util.color.
ColorUtils
org.biojava.nbio.structure.symmetry.utils.
CombinationGenerator
org.forester.surfacing.
CombinationsBasedPairwiseDomainSimilarity
(implements org.forester.surfacing.
PairwiseDomainSimilarity
)
org.forester.surfacing.
CombinationsBasedPairwiseDomainSimilarityCalculator
(implements org.forester.surfacing.
PairwiseDomainSimilarityCalculator
)
org.forester.util.
CommandLineArguments
org.forester.util.
CommandProcessBuilder
org.biojava.nbio.aaproperties.
CommandPrompt
org.biojava.nbio.survival.data.
CompactCharSequence
(implements java.lang.CharSequence, java.io.Serializable)
org.biojava.nbio.phylo.
Comparison
org.biojava.nbio.protmod.
Component
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
java.awt.Container
javax.swing.JComponent (implements java.io.Serializable)
org.forester.development.
AbstractRenderer
org.forester.development.
ResidueRenderer
javax.swing.JPanel (implements javax.accessibility.Accessible)
javax.swing.colorchooser.AbstractColorChooserPanel
org.jcolorbrewer.ui.
DivergingColorPalettePanel
(implements java.awt.event.ActionListener)
org.jcolorbrewer.ui.
QualitativeColorPalettePanel
(implements java.awt.event.ActionListener)
org.jcolorbrewer.ui.
SequentialColorPalettePanel
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.
ConfigPDBInstallPanel
org.biojava.nbio.structure.align.gui.
DBSearchGUI
org.biojava.nbio.survival.kaplanmeier.figure.
ExpressionFigure
org.biojava.nbio.structure.gui.util.color.
GradientPanel
org.biojava.nbio.structure.align.gui.
GUIAlignmentProgressListener
(implements java.awt.event.ActionListener, org.biojava.nbio.structure.align.events.
AlignmentProgressListener
)
org.biojava.nbio.structure.gui.
JMatrixPanel
org.biojava.nbio.structure.align.gui.
JPrintPanel
(implements java.awt.event.ActionListener, java.awt.print.Printable)
org.biojava.nbio.structure.align.gui.
AlignmentTextPanel
org.biojava.nbio.structure.align.gui.aligpanel.
AligPanel
(implements org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.WindowListener)
org.biojava.nbio.structure.align.gui.jmol.
JmolPanel
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.aligpanel.
MultipleAligPanel
(implements org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.WindowListener)
org.biojava.nbio.survival.kaplanmeier.figure.
KaplanMeierFigure
org.forester.archaeopteryx.
MainPanel
(implements java.awt.event.ComponentListener)
org.biojava.nbio.structure.align.gui.
MemoryMonitor
org.biojava.nbio.structure.align.gui.
MemoryMonitor.Surface
(implements java.lang.Runnable)
org.biojava.nbio.survival.kaplanmeier.figure.
NumbersAtRiskPanel
org.biojava.nbio.structure.gui.util.
PDBDirPanel
(implements org.biojava.nbio.structure.gui.util.
StructurePairSelector
)
org.biojava.nbio.structure.gui.util.
PDBServerPanel
(implements org.biojava.nbio.structure.gui.util.
StructurePairSelector
)
org.biojava.nbio.structure.gui.util.
PDBUploadPanel
(implements org.biojava.nbio.structure.gui.util.
StructurePairSelector
)
org.biojava.nbio.structure.gui.
ScaleableMatrixPanel
(implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
org.biojava.nbio.structure.align.gui.
DotPlotPanel
org.biojava.nbio.structure.gui.
ScaleableMatrixPanel.GradientRenderer
(implements javax.swing.ListCellRenderer<E>)
org.biojava.nbio.structure.gui.util.
ScopSelectPanel
(implements org.biojava.nbio.structure.gui.util.
StructurePairSelector
)
org.biojava.nbio.structure.align.gui.
SelectPDBPanel
(implements org.biojava.nbio.structure.gui.util.
StructurePairSelector
)
org.biojava.nbio.structure.gui.
SequenceDisplay
(implements javax.swing.event.ChangeListener)
org.biojava.nbio.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.nbio.structure.align.gui.autosuggest.
JAutoSuggest
org.biojava.nbio.structure.align.gui.aligpanel.
MultipleStatusDisplay
(implements org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.WindowListener)
org.biojava.nbio.structure.align.gui.aligpanel.
StatusDisplay
(implements org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
, java.awt.event.WindowListener)
org.forester.development.
MsaRenderer
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.jcolorbrewer.ui.
ColorPaletteChooserDialog
org.forester.archaeopteryx.
FontChooser
(implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
org.forester.archaeopteryx.tools.
PhyloInferenceDialog
(implements java.awt.event.ActionListener)
java.awt.Frame (implements java.awt.MenuContainer)
javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
org.biojava.nbio.structure.align.gui.
AlignmentGui
org.biojava.nbio.structure.gui.util.
AlternativeAlignmentFrame
org.forester.archaeopteryx.
MainFrame
(implements java.awt.event.ActionListener)
org.forester.archaeopteryx.
MainFrameApplet
org.forester.archaeopteryx.
MainFrameApplication
org.biojava.nbio.structure.align.gui.
ParameterGUI
org.biojava.nbio.structure.symmetry.utils.
ComponentFinder
<V>
org.biojava.nbio.protmod.io.
ComponentXMLConverter
org.biojava.nbio.structure.
Compound
(implements java.io.Serializable)
org.biojava.nbio.structure.io.
CompoundFinder
org.biojava.nbio.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.data.
ConfidenceParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.archaeopteryx.
Configuration
org.forester.archaeopteryx.
Constants
org.biojava.nbio.aaproperties.
Constraints
org.biojava.nbio.structure.gui.util.color.
ContinuousColorMapperTransform
(implements org.biojava.nbio.structure.gui.util.color.
ContinuousColorMapper
)
org.biojava.nbio.structure.gui.util.color.
LogColorMapper
org.biojava.nbio.structure.gui.util.color.
SqrtColorMapper
org.biojava.nbio.aaproperties.profeat.convertor.
Convertor
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2Charge
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2Hydrophobicity
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2NormalizedVanDerWaalsVolume
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2Polarity
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2Polarizability
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2SecondaryStructure
org.biojava.nbio.aaproperties.profeat.convertor.
Convert2SolventAccessibility
org.biojava.nbio.structure.gui.util.
CoordManager
org.forester.application.
count_support
org.biojava.nbio.structure.align.client.
CountProgressListener
(implements org.biojava.nbio.structure.align.events.
AlignmentProgressListener
)
org.forester.surfacing.
CountsBasedPairwiseDomainSimilarity
(implements org.forester.surfacing.
PairwiseDomainSimilarity
)
org.forester.pccx.
CoverageCalculator
org.biojava.nbio.survival.cox.
CoxCC
org.biojava.nbio.survival.cox.
CoxCoefficient
org.biojava.nbio.survival.cox.
CoxHelper
org.biojava.nbio.survival.cox.
CoxInfo
org.biojava.nbio.survival.cox.
CoxMart
org.biojava.nbio.survival.cox.
CoxR
org.biojava.nbio.survival.cox.
CoxScore
org.biojava.nbio.survival.cox.
CoxVariables
org.biojava.nbio.survival.cox.comparators.
CoxVariablesOverallModelFitComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.survival.cox.comparators.
CoxVariablesVariableComparator
(implements org.biojava.nbio.survival.cox.comparators.
CoxComparatorInterface
)
org.biojava.nbio.core.util.
CRC64Checksum
(implements java.util.zip.Checksum)
org.biojava.nbio.structure.xtal.
CrystalBuilder
org.biojava.nbio.structure.xtal.
CrystalCell
(implements java.io.Serializable)
org.biojava.nbio.structure.xtal.
CrystalTransform
(implements java.io.Serializable)
org.biojava.nbio.structure.domain.pdp.
Cut
org.biojava.nbio.structure.domain.pdp.
CutDomain
org.biojava.nbio.structure.domain.pdp.
CutSites
org.biojava.nbio.structure.domain.pdp.
CutValues
org.biojava.nbio.genome.parsers.cytoband.
Cytoband
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.genome.parsers.cytoband.
CytobandParser
org.biojava.nbio.structure.io.mmcif.model.
DatabasePDBrev
org.forester.ws.seqdb.
DatabaseTools
org.forester.ws.uniprot.
DatabaseTools
org.biojava.nbio.phosphosite.
Dataset
org.forester.phylogeny.data.
Date
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
DateParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.
DBRef
(implements org.biojava.nbio.structure.
PDBRecord
, java.io.Serializable)
org.biojava.nbio.structure.align.gui.
DBResultTable
(implements java.awt.event.ActionListener)
org.forester.application.
decorator
org.biojava.nbio.alignment.aaindex.
DefaultAAIndexProvider
(implements org.biojava.nbio.alignment.aaindex.
AAIndexProvider
)
org.biojava.nbio.structure.align.gui.autosuggest.
DefaultAutoSuggestProvider
(implements org.biojava.nbio.structure.align.gui.autosuggest.
AutoSuggestProvider
)
javax.swing.colorchooser.DefaultColorSelectionModel (implements javax.swing.colorchooser.ColorSelectionModel, java.io.Serializable)
org.jcolorbrewer.ui.
ColorPanelSelectionModel
org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
org.biojava.nbio.structure.align.webstart.
ConfigXMLHandler
org.forester.io.parsers.phyloxml.
PhyloXmlHandler
org.forester.io.parsers.tol.
TolXmlHandler
org.biojava.nbio.structure.gui.util.color.
DefaultMatrixMapper
(implements org.biojava.nbio.structure.gui.util.color.
ContinuousColorMapper
)
org.biojava.nbio.ontology.
DefaultOps
(implements org.biojava.nbio.ontology.
OntologyOps
, java.io.Serializable)
org.forester.development.
DevelopmentTools
org.forester.evoinference.matrix.character.
DiscreteState
(implements java.lang.Comparable<T>)
org.biojava.nbio.structure.align.gui.
DisplayAFP
org.biojava.nbio.structure.symmetry.geometry.
DistanceBox
<T>
org.forester.sdi.
DistanceCalculator
org.biojava.nbio.structure.secstruc.
DistEn
org.forester.phylogeny.data.
Distribution
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
DistributionParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.core.sequence.io.
DNASequenceCreator
(implements org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.forester.evoinference.parsimony.
DolloParsimony
org.biojava.nbio.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.data.
DomainArchitectureParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.surfacing.
DomainCountsBasedPairwiseSimilarityCalculator
(implements org.forester.surfacing.
PairwiseDomainSimilarityCalculator
)
org.forester.surfacing.
DomainCountsDifferenceUtil
org.forester.protein.
DomainId
(implements java.lang.Comparable<T>)
org.forester.surfacing.
DomainLengths
org.forester.surfacing.
DomainLengthsTable
org.forester.surfacing.
DomainParsimonyCalculator
org.biojava.nbio.structure.domain.
DomainProviderFactory
org.biojava.nbio.structure.io.mmcif.
DownloadChemCompProvider
(implements org.biojava.nbio.structure.io.mmcif.
ChemCompProvider
)
org.forester.ws.seqdb.
EbiDbEntry
(implements org.forester.ws.seqdb.
SequenceDatabaseEntry
)
org.forester.ws.uniprot.
EbiDbEntry
(implements org.forester.ws.uniprot.
SequenceDatabaseEntry
)
org.biojava.nbio.structure.ecod.
EcodDomain
(implements java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.ecod.
EcodFactory
org.biojava.nbio.structure.ecod.
EcodInstallation
(implements org.biojava.nbio.structure.ecod.
EcodDatabase
)
org.biojava.nbio.structure.ecod.
EcodInstallation.EcodParser
org.biojava.nbio.structure.symmetry.utils.
Edge
<V>
org.biojava.nbio.core.sequence.edits.
Edit.AbstractEdit
<C> (implements org.biojava.nbio.core.sequence.edits.
Edit
<C>)
org.biojava.nbio.core.sequence.edits.
Edit.Delete
<C>
org.biojava.nbio.core.sequence.edits.
Edit.Insert
<C>
org.biojava.nbio.core.sequence.edits.
Edit.Substitute
<C>
org.biojava.nbio.structure.jama.
EigenvalueDecomposition
(implements java.io.Serializable)
org.biojava.nbio.aaproperties.xml.
Element
org.biojava.nbio.aaproperties.xml.
ElementTable
org.biojava.nbio.structure.io.mmcif.model.
Entity
org.biojava.nbio.structure.io.mmcif.model.
EntitySrcGen
org.biojava.nbio.structure.io.mmcif.model.
EntitySrcNat
org.biojava.nbio.structure.io.mmcif.model.
EntitySrcSyn
org.biojava.nbio.structure.validation.
Entry
org.biojava.nbio.core.util.
Equals
org.forester.phylogeny.data.
Event
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
EventParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.test.examples.
Example1
org.forester.test.examples.
Example2
org.forester.test.examples.
Example3
org.forester.test.examples.
Example4
org.forester.test.examples.
Example5
org.biojava.nbio.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.forester.util.
ExternalProgram
org.biojava.nbio.structure.align.
FarmJob
(implements java.lang.Runnable)
org.biojava.nbio.structure.align.client.
FarmJobParameters
org.biojava.nbio.structure.align.client.
FarmJobRunnable
(implements java.lang.Runnable)
org.biojava.nbio.structure.io.
FastaAFPChainConverter
org.biojava.nbio.core.sequence.io.
FastaGeneWriter
org.forester.io.parsers.
FastaParser
org.biojava.nbio.core.sequence.io.
FastaReader
<S,C>
org.biojava.nbio.core.sequence.io.
FastaReaderHelper
org.biojava.nbio.data.sequence.
FastaSequence
(implements java.lang.Comparable<T>)
org.biojava.nbio.core.sequence.io.
FastaSequenceParser
(implements org.biojava.nbio.core.sequence.io.template.
SequenceParserInterface
)
org.biojava.nbio.structure.io.
FastaStructureParser
org.biojava.nbio.core.sequence.io.
FastaWriter
<S,C>
org.biojava.nbio.core.sequence.io.
FastaWriterHelper
org.biojava.nbio.sequencing.io.fastq.
Fastq
org.biojava.nbio.sequencing.io.fastq.
FastqBuilder
org.biojava.nbio.sequencing.io.fastq.
FastqTools
org.biojava.nbio.structure.align.fatcat.
FatCat
org.biojava.nbio.structure.align.fatcat.
FatCatFlexible
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.align.fatcat.
FatCatRigid
(implements org.biojava.nbio.structure.align.
StructureAlignment
)
org.biojava.nbio.structure.align.fatcat.calc.
FatCatAligner
org.biojava.nbio.structure.align.fatcat.calc.
FatCatParameters
(implements org.biojava.nbio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava.nbio.structure.align.fatcat.calc.
FCAlignHelper
org.biojava.nbio.genome.parsers.gff.
Feature
(implements org.biojava.nbio.genome.parsers.gff.
FeatureI
)
org.biojava.nbio.genome.parsers.gff.
FeatureHelper
org.biojava.nbio.structure.io.
FileConvert
org.biojava.nbio.structure.io.util.
FileDownloadUtils
org.biojava.nbio.structure.io.
FileParsingParameters
(implements java.io.Serializable)
org.biojava.nbio.core.sequence.io.
FileProxyDNASequenceCreator
(implements org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava.nbio.core.sequence.io.
FileProxyProteinSequenceCreator
(implements org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.forester.evoinference.parsimony.
FitchParsimony
<STATE_TYPE>
org.biojava.nbio.core.util.
FlatFileCache
org.forester.util.
ForesterConstants
org.forester.util.
ForesterUtil
org.biojava.nbio.structure.align.pairwise.
FragmentJoiner
org.biojava.nbio.structure.align.pairwise.
FragmentPair
org.biojava.nbio.structure.align.helper.
GapArray
org.biojava.nbio.genome.parsers.gff.
GCStats
org.biojava.nbio.core.sequence.io.
GenbankReader
<S,C>
org.biojava.nbio.core.sequence.io.
GenbankReaderHelper
org.biojava.nbio.core.sequence.io.
GenbankSequenceParser
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
SequenceParserInterface
)
org.biojava.nbio.core.sequence.io.
GenbankWriter
<S,C>
org.biojava.nbio.core.sequence.io.
GenbankWriterHelper
org.forester.application.
gene_tree_preprocess
org.biojava.nbio.genome.parsers.genename.
GeneChromosomePosition
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.genome.parsers.genename.
GeneChromosomePositionParser
org.biojava.nbio.genome.
GeneFeatureHelper
org.biojava.nbio.genome.parsers.gff.
GeneIDGFF2Reader
org.biojava.nbio.genome.parsers.geneid.
GeneIDXMLReader
org.biojava.nbio.genome.parsers.gff.
GeneMarkGTFReader
org.biojava.nbio.genome.parsers.genename.
GeneName
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.genome.parsers.genename.
GeneNamesParser
org.forester.io.parsers.
GeneralMsaParser
org.forester.util.
GeneralTable
<IDENTIFIER_TYPE,VALUE_TYPE>
org.biojava.nbio.core.sequence.io.
GenericFastaHeaderFormat
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
FastaHeaderFormatInterface
<S,C>)
org.biojava.nbio.core.sequence.io.
GenericFastaHeaderParser
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
SequenceHeaderParserInterface
<S,C>)
org.biojava.nbio.core.sequence.io.
GenericGenbankHeaderParser
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
SequenceHeaderParserInterface
<S,C>)
org.biojava.nbio.core.sequence.io.
GenericInsdcHeaderFormat
<S,C>
org.biojava.nbio.core.sequence.io.
GenericGenbankHeaderFormat
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
GenbankHeaderFormatInterface
<S,C>)
org.biojava.nbio.structure.domain.pdp.
GetDistanceMatrix
org.biojava.nbio.structure.rcsb.
GetRepresentatives
org.biojava.nbio.genome.homology.
GFF3FromUniprotBlastHits
org.biojava.nbio.genome.parsers.gff.
GFF3Reader
org.biojava.nbio.genome.parsers.gff.
GFF3Writer
org.forester.application.
goac
org.forester.go.
GoId
(implements java.lang.Comparable<T>)
org.forester.go.
GoNameSpace
org.biojava.nbio.ontology.io.
GOParser
org.biojava.nbio.structure.align.pairwise.
Gotoh
org.forester.go.
GoUtils
org.biojava.nbio.structure.gui.util.color.
GradientMapper
(implements org.biojava.nbio.structure.gui.util.color.
ContinuousColorMapper
, java.util.Map<K,V>)
org.biojava.nbio.structure.contact.
Grid
org.biojava.nbio.structure.contact.
GridCell
org.biojava.nbio.structure.asa.
GroupAsa
org.biojava.nbio.structure.contact.
GroupContact
org.biojava.nbio.structure.contact.
GroupContactSet
(implements java.lang.Iterable<T>)
org.biojava.nbio.structure.
GroupIterator
(implements java.util.Iterator<E>)
org.biojava.nbio.survival.kaplanmeier.figure.
GroupResults
org.forester.application.
gsdi
org.biojava.nbio.alignment.
GuideTree
<S,C> (implements java.lang.Iterable<T>)
org.biojava.nbio.alignment.
GuideTree.Node
(implements org.biojava.nbio.alignment.template.
GuideTreeNode
<S,C>)
org.biojava.nbio.structure.align.gui.
GUIFarmJobRunnable
(implements java.lang.Runnable)
org.biojava.nbio.structure.align.ce.
GuiWrapper
org.biojava.nbio.core.util.
Hashcoder
org.biojava.nbio.structure.align.xml.
HasResultXMLConverter
org.biojava.nbio.structure.secstruc.
HBond
org.biojava.nbio.survival.data.
HeaderInfo
org.biojava.nbio.structure.symmetry.core.
HelicalRepeatUnit
org.biojava.nbio.structure.symmetry.core.
Helix
org.biojava.nbio.structure.symmetry.core.
HelixExtender
org.biojava.nbio.structure.symmetry.core.
HelixLayers
org.biojava.nbio.structure.symmetry.core.
HelixSolver
org.forester.development.
Hello3d
org.biojava.nbio.structure.align.gui.
HelpDialog
org.biojava.nbio.structure.
HetatomImpl
(implements org.biojava.nbio.structure.
Group
, java.io.Serializable)
org.biojava.nbio.structure.
AminoAcidImpl
(implements org.biojava.nbio.structure.
AminoAcid
, java.io.Serializable)
org.biojava.nbio.structure.
NucleotideImpl
(implements java.lang.Cloneable, org.biojava.nbio.structure.
Group
, java.io.Serializable)
org.biojava.nbio.structure.secstruc.
SecStrucGroup
(implements org.biojava.nbio.structure.
Group
)
org.biojava.nbio.ws.hmmer.
HmmerDomain
(implements java.lang.Comparable<T>, java.io.Serializable)
org.forester.development.
HmmerRest
org.biojava.nbio.ws.hmmer.
HmmerResult
(implements java.lang.Comparable<T>, java.io.Serializable)
org.forester.io.parsers.
HmmPfamOutputParser
org.forester.io.parsers.
HmmscanPerDomainTableParser
org.biojava.nbio.structure.align.util.
HTTPConnectionTools
org.biojava.nbio.structure.symmetry.geometry.
IcosahedralSampler
org.biojava.nbio.structure.symmetry.geometry.
Icosahedron
(implements org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
)
org.biojava.nbio.structure.
Identifier
org.forester.phylogeny.data.
Identifier
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
IdentifierParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.align.helper.
IdxComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.sequencing.io.fastq.
IlluminaFastqReader
org.biojava.nbio.sequencing.io.fastq.
IlluminaFastqWriter
org.forester.archaeopteryx.tools.
ImageLoader
(implements java.lang.Runnable)
org.biojava.nbio.structure.align.helper.
IndexPair
(implements java.io.Serializable)
org.biojava.nbio.structure.align.helper.
AligMatEl
org.forester.archaeopteryx.tools.
InferenceManager
java.io.InputStream (implements java.io.Closeable)
java.io.FilterInputStream
org.biojava.nbio.core.util.
UncompressInputStream
org.biojava.nbio.genome.parsers.twobit.
TwoBitParser
org.biojava.nbio.core.util.
InputStreamProvider
org.biojava.nbio.core.sequence.location.
InsdcLocations
org.biojava.nbio.core.sequence.location.
InsdcParser
<S,C>
org.biojava.nbio.ontology.
IntegerOntology
(implements org.biojava.nbio.ontology.
Ontology
)
org.biojava.nbio.ontology.
IntegerOntology.IntTerm
(implements org.biojava.nbio.ontology.
Term
)
org.biojava.nbio.core.sequence.io.util.
IOUtils
org.biojava.nbio.aaproperties.xml.
Isotope
org.biojava.nbio.core.sequence.io.
IUPACParser
org.biojava.nbio.core.sequence.io.
IUPACParser.IUPACTable
(implements org.biojava.nbio.core.sequence.transcription.
Table
)
org.biojava.nbio.structure.align.client.
JFatCatClient
org.biojava.nbio.structure.gui.events.
JmolAlignedPositionListener
(implements org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
)
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGenerator
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorH
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorPointGroup
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorC1
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorCn
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorDn
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorI
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorO
org.biojava.nbio.structure.symmetry.jmolScript.
JmolSymmetryScriptGeneratorT
org.biojava.nbio.structure.align.gui.jmol.
JmolTools
org.biojava.nbio.structure.gui.
JmolViewerImpl
(implements org.biojava.nbio.structure.gui.
StructureViewer
)
org.biojava.nbio.structure.align.webstart.
JNLPProxy
org.biojava.nbio.core.sequence.storage.
JoiningSequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.nbio.structure.align.helper.
JointFragments
org.biojava.nbio.structure.
JournalArticle
(implements java.io.Serializable)
org.biojava.nbio.ronn.
Jronn
org.biojava.nbio.ronn.
Jronn.Range
java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
org.biojava.nbio.structure.align.gui.jmol.
RasmolCommandListener
(implements java.awt.event.ActionListener, java.awt.event.MouseListener)
org.biojava.nbio.structure.gui.
RasmolCommandListener
(implements java.awt.event.ActionListener, java.awt.event.MouseListener)
org.biojava.nbio.survival.kaplanmeier.figure.
KMFigureInfo
org.biojava.nbio.structure.secstruc.
Ladder
org.forester.phylogeny.iterators.
LevelOrderTreeIterator
(implements org.forester.phylogeny.iterators.
PhylogenyNodeIterator
)
org.biojava.nbio.structure.gui.util.color.
LinearColorInterpolator
(implements org.biojava.nbio.structure.gui.util.color.
ColorInterpolator
)
org.biojava.nbio.structure.scop.server.
ListStringWrapper
(implements java.io.Serializable)
org.biojava.nbio.structure.io.
LocalPDBDirectory
(implements org.biojava.nbio.structure.io.
StructureIOFile
)
org.biojava.nbio.structure.io.
MMCIFFileReader
org.biojava.nbio.structure.io.
PDBFileReader
org.biojava.nbio.structure.domain.
LocalProteinDomainParser
org.biojava.nbio.genome.parsers.gff.
Location
(implements java.lang.Iterable<T>)
org.biojava.nbio.core.sequence.location.template.
Location.Tools
org.biojava.nbio.core.sequence.location.
LocationHelper
org.biojava.nbio.genome.parsers.gff.
LocIterator
(implements java.util.Iterator<E>)
org.biojava.nbio.structure.jama.
LUDecomposition
(implements java.io.Serializable)
org.forester.msa.
Mafft
(implements org.forester.msa.
MsaInferrer
)
org.forester.msa.
MafftOLD
(implements org.forester.msa.
MsaInferrer
)
org.forester.surfacing.
MappingResults
org.biojava.nbio.ws.alignment.qblast.
MapToStringTransformer
org.biojava.nbio.structure.jama.
Maths
org.biojava.nbio.structure.jama.
Matrix
(implements java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.survival.cox.matrix.
Matrix
org.forester.application.
mcc
org.biojava.nbio.survival.cox.comparators.
MeanModelComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.survival.kaplanmeier.metadata.
MeanQuantizer
(implements org.biojava.nbio.survival.kaplanmeier.metadata.
DiscreteQuantizerInterface
)
org.biojava.nbio.structure.align.gui.
MenuCreator
org.biojava.nbio.structure.gui.util.
MenuCreator
org.biojava.nbio.structure.align.gui.
MenuCreator.DotPlotListener
(implements java.awt.event.ActionListener)
org.forester.application.
meta_ontologizer
org.biojava.nbio.survival.kaplanmeier.metadata.
MetaDataInfo
org.forester.go.etc.
MetaOntologizer
org.biojava.nbio.structure.quaternary.io.
MmCifBiolAssemblyProvider
(implements org.biojava.nbio.structure.quaternary.io.
BioUnitDataProvider
)
org.biojava.nbio.structure.io.mmcif.
MMCIFFileTools
org.biojava.nbio.structure.quaternary.io.
MmCifPDBBiolAssemblyProvider
(implements org.biojava.nbio.structure.quaternary.io.
RawBioUnitDataProvider
)
org.forester.pccx.
ModelingUtils
org.biojava.nbio.structure.validation.
ModelledSubgroup
org.biojava.nbio.ronn.
ModelLoader
org.biojava.nbio.ronn.
ModelLoader.Model
org.biojava.nbio.ronn.
ModelLoader.Threshold
org.biojava.nbio.protmod.
ModificationConditionImpl
(implements org.biojava.nbio.protmod.
ModificationCondition
)
org.biojava.nbio.protmod.
ModificationLinkage
org.biojava.nbio.aaproperties.xml.
ModifiedAminoAcidCompoundSet
(implements org.biojava.nbio.core.sequence.template.
CompoundSet
<C>)
org.biojava.nbio.protmod.structure.
ModifiedCompoundImpl
(implements java.lang.Comparable<T>, org.biojava.nbio.protmod.structure.
ModifiedCompound
, java.io.Serializable)
org.biojava.nbio.protmod.io.
ModifiedCompoundXMLConverter
org.biojava.nbio.structure.validation.
MogAngleOutlier
org.biojava.nbio.structure.validation.
MogBondOutlier
org.biojava.nbio.structure.symmetry.geometry.
MomentsOfInertia
org.forester.msa.
MsaMethods
org.biojava.nbio.structure.align.gui.aligpanel.
MultipleAlignmentCoordManager
org.biojava.nbio.structure.align.gui.
MultipleAlignmentDisplay
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentScorer
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentTools
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentWriter
org.biojava.nbio.structure.align.gui.aligpanel.
MultipleAligPanelMouseMotionListener
(implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
org.biojava.nbio.core.sequence.
MultipleSequenceAlignment
<S,C> (implements org.biojava.nbio.core.sequence.template.
LightweightProfile
<S,C>)
org.biojava.nbio.structure.align.
MultiThreadedDBSearch
org.biojava.nbio.structure.
Mutator
org.biojava.nbio.structure.align.gui.
MyAlignmentLoadListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.
MyDistMaxListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.
MyExportListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.jmol.
MyJmolStatusListener
org.biojava.nbio.structure.align.gui.
MyOpenPdbFileListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.align.gui.
MySaveFileListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.aaproperties.xml.
MyValidationEventHandler
(implements javax.xml.bind.ValidationEventHandler)
org.biojava.nbio.aaproperties.xml.
Name2Count
org.biojava.nbio.ws.alignment.qblast.
NCBIQBlastAlignmentProperties
(implements org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentProperties
)
org.biojava.nbio.ws.alignment.qblast.
NCBIQBlastOutputProperties
(implements org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentOutputProperties
)
org.biojava.nbio.ws.alignment.qblast.
NCBIQBlastService
(implements org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentService
)
org.forester.evoinference.distance.
NeighborJoining
org.forester.development.
neTest
org.forester.development.
neTest.DoublePointer
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.phylogeny.data.
NodeVisualization
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.biojava.nbio.structure.validation.
ObjectFactory
org.forester.application.
obo_tool
org.biojava.nbio.ontology.obo.
OboFileHandler
(implements org.biojava.nbio.ontology.obo.
OboFileEventListener
)
org.biojava.nbio.ontology.obo.
OboFileParser
org.biojava.nbio.ontology.obo.
OboFileParser.SOPair
org.biojava.nbio.ontology.io.
OboParser
org.forester.go.
OBOparser
org.biojava.nbio.structure.symmetry.geometry.
Octahedron
(implements org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
)
org.forester.go.etc.
OntologizerResult
(implements java.lang.Comparable<T>)
org.biojava.nbio.ontology.
Ontology.Impl
(implements org.biojava.nbio.ontology.
Ontology
, java.io.Serializable)
org.biojava.nbio.ontology.
OntologyTerm.Impl
(implements org.biojava.nbio.ontology.
OntologyTerm
, java.io.Serializable)
org.biojava.nbio.ontology.
OntoTools
org.biojava.nbio.structure.quaternary.
OperatorResolver
org.forester.archaeopteryx.
Options
org.forester.sdi.
ORcount
org.biojava.nbio.structure.quaternary.
OrderedPair
<T>
org.biojava.nbio.ronn.
ORonn
(implements java.util.concurrent.Callable<V>)
org.biojava.nbio.ronn.
ORonnModel
org.biojava.nbio.genome.query.
OutputHitsGFF
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
org.biojava.nbio.ronn.
NullOutputStream
org.biojava.nbio.structure.contact.
Pair
<T> (implements java.io.Serializable)
org.biojava.nbio.structure.symmetry.core.
PairwiseAlignment
org.forester.evoinference.distance.
PairwiseDistanceCalculator
org.forester.surfacing.
PairwiseGenomeComparator
org.jcolorbrewer.ui.
PaletteIcon
(implements javax.swing.Icon)
org.forester.io.parsers.util.
ParserUtils
org.forester.io.parsers.nexus.
PaupLogParser
org.forester.application.
pccx
org.biojava.nbio.structure.io.
PDBBioAssemblyParser
org.biojava.nbio.structure.quaternary.io.
PDBBioUnitDataProvider
(implements org.biojava.nbio.structure.quaternary.io.
BioUnitDataProvider
)
org.biojava.nbio.structure.
PDBCrystallographicInfo
(implements java.io.Serializable)
org.biojava.nbio.structure.domain.
PDBDomainProvider
(implements org.biojava.nbio.structure.domain.
DomainProvider
)
org.biojava.nbio.structure.io.
PDBFileParser
org.biojava.nbio.structure.
PDBHeader
(implements org.biojava.nbio.structure.
PDBRecord
, java.io.Serializable)
org.biojava.nbio.structure.align.client.
PdbPair
(implements java.lang.Comparable<T>)
org.biojava.nbio.structure.align.xml.
PdbPairsMessage
org.biojava.nbio.structure.align.xml.
PdbPairXMLConverter
org.biojava.nbio.structure.
PDBStatus
org.biojava.nbio.structure.io.util.
PDBTemporaryStorageUtils
org.biojava.nbio.structure.io.util.
PDBTemporaryStorageUtils.LinkRecord
org.biojava.nbio.structure.io.mmcif.model.
PdbxChemCompDescriptor
org.biojava.nbio.structure.io.mmcif.model.
PdbxChemCompIdentifier
org.biojava.nbio.structure.io.mmcif.model.
PdbxEntityNonPoly
org.biojava.nbio.structure.io.mmcif.model.
PdbxNonPolyScheme
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructAssembly
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructAssemblyGen
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructAssemblyGenXMLContainer
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructAssemblyXMLContainer
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructOperList
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.model.
PdbxStructOperListXMLContainer
org.biojava.nbio.structure.domain.pdp.
PDPDistanceMatrix
org.biojava.nbio.structure.domain.pdp.
PDPParameters
org.biojava.nbio.aaproperties.
PeptideProperties
org.biojava.nbio.aaproperties.
PeptidePropertiesImpl
(implements org.biojava.nbio.aaproperties.
IPeptideProperties
)
org.biojava.nbio.structure.symmetry.utils.
PermutationGenerator
org.biojava.nbio.structure.symmetry.core.
PermutationGroup
org.biojava.nbio.structure.align.webstart.
PersistentConfig
org.forester.application.
pfam_go
org.forester.application.
pfam2go_extractor
org.forester.application.
pfamacc2go
org.forester.application.
pfamacc2pfamid
org.forester.go.
PfamToGoMapping
(implements org.forester.go.
Mapping
)
org.forester.go.
PfamToGoParser
org.forester.archaeopteryx.tools.
PhylogeneticInferenceOptions
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.biojava.nbio.core.sequence.io.
PlainFastaHeaderParser
<S,C> (implements org.biojava.nbio.core.sequence.io.template.
SequenceHeaderParserInterface
<S,C>)
org.forester.phylogeny.data.
Point
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
PointParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.phylogeny.data.
Polygon
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
PolygonParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.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.nbio.core.util.
PrettyXMLWriter
(implements org.biojava.nbio.core.util.
XMLWriter
)
org.forester.surfacing.
PrintableDomainSimilarity
(implements org.forester.surfacing.
DomainSimilarity
)
org.forester.application.
printAllSpecies
org.forester.application.
printSameOrder
org.biojava.nbio.structure.symmetry.geometry.
Prism
(implements org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
)
org.forester.archaeopteryx.tools.
ProcessPool
org.forester.archaeopteryx.tools.
ProcessRunning
org.biojava.nbio.aaproperties.profeat.
ProfeatProperties
org.biojava.nbio.aaproperties.profeat.
ProfeatPropertiesImpl
(implements org.biojava.nbio.aaproperties.profeat.
IProfeatProperties
)
org.biojava.nbio.structure.validation.
Program
org.biojava.nbio.structure.validation.
Programs
org.biojava.nbio.phylo.
ProgressListenerStub
(implements org.biojava.nbio.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.data.
PropertyParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.symmetry.core.
ProteinChainExtractor
org.biojava.nbio.structure.symmetry.misc.
ProteinComplexSignature
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.data.
ProteinDomainParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.protein.
ProteinId
(implements java.lang.Comparable<T>)
org.biojava.nbio.protmod.structure.
ProteinModificationIdentifier
org.biojava.nbio.protmod.
ProteinModificationImpl
(implements java.lang.Comparable<T>, org.biojava.nbio.protmod.
ProteinModification
)
org.biojava.nbio.protmod.
ProteinModificationImpl.Builder
org.biojava.nbio.protmod.
ProteinModificationRegistry
org.biojava.nbio.protmod.io.
ProteinModificationXmlReader
org.biojava.nbio.structure.symmetry.core.
ProteinSequenceClusterer
org.biojava.nbio.core.sequence.io.
ProteinSequenceCreator
(implements org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava.nbio.core.sequence.io.
CasePreservingProteinSequenceCreator
org.biojava.nbio.structure.jama.
QRDecomposition
(implements java.io.Serializable)
org.biojava.nbio.core.sequence.features.
Qualifier
org.biojava.nbio.core.sequence.features.
DBReferenceInfo
org.biojava.nbio.core.sequence.features.
FeatureDbReferenceInfo
<S,C> (implements org.biojava.nbio.core.sequence.features.
FeatureInterface
<S,C>)
org.biojava.nbio.structure.symmetry.core.
QuatSuperpositionScorer
org.biojava.nbio.structure.symmetry.core.
QuatSymmetryDetector
org.biojava.nbio.structure.symmetry.core.
QuatSymmetryParameters
org.biojava.nbio.structure.symmetry.core.
QuatSymmetryResults
org.biojava.nbio.structure.symmetry.core.
QuatSymmetryScores
org.forester.datastructures.
Queue
org.forester.development.
RandomThing
org.biojava.nbio.structure.rcsb.
RCSBDescription
org.biojava.nbio.structure.rcsb.
RCSBDescriptionFactory
org.biojava.nbio.structure.rcsb.
RCSBLigand
org.biojava.nbio.structure.rcsb.
RCSBLigands
org.biojava.nbio.structure.rcsb.
RCSBLigandsFactory
org.biojava.nbio.structure.rcsb.
RCSBMacromolecule
org.biojava.nbio.structure.rcsb.
RCSBPolymer
org.biojava.nbio.structure.rcsb.
RCSBTaxonomy
java.io.Reader (implements java.io.Closeable, java.lang.Readable)
org.biojava.nbio.core.sequence.io.
BufferedReaderBytesRead
org.biojava.nbio.structure.rcsb.
ReadUtils
org.biojava.nbio.structure.symmetry.geometry.
RectangularPrism
(implements org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
)
org.biojava.nbio.structure.io.mmcif.
ReducedChemCompProvider
(implements org.biojava.nbio.structure.io.mmcif.
ChemCompProvider
)
java.lang.ref.Reference<T>
java.lang.ref.WeakReference<T>
org.biojava.nbio.ontology.utils.
KeyedWeakReference
org.forester.phylogeny.data.
Reference
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
ReferenceParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.structure.align.multiple.
ReferenceSuperimposer
(implements org.biojava.nbio.structure.align.multiple.
MultipleSuperimposer
)
org.biojava.nbio.structure.io.mmcif.model.
Refine
org.biojava.nbio.structure.quaternary.io.
RemoteBioUnitDataProvider
(implements org.biojava.nbio.structure.quaternary.io.
BioUnitDataProvider
)
org.biojava.nbio.ws.hmmer.
RemoteHmmerScan
(implements org.biojava.nbio.ws.hmmer.
HmmerScan
)
org.biojava.nbio.structure.quaternary.io.
RemoteRawBioUnitDataProvider
(implements org.biojava.nbio.structure.quaternary.io.
RawBioUnitDataProvider
)
org.biojava.nbio.structure.scop.
RemoteScopInstallation
(implements org.biojava.nbio.structure.scop.
ScopDatabase
)
org.forester.archaeopteryx.phylogeny.data.
RenderableVector
(implements org.forester.archaeopteryx.phylogeny.data.
RenderablePhylogenyData
)
org.biojava.nbio.structure.align.xml.
RepresentativeXMLConverter
org.biojava.nbio.survival.cox.
ResidualsCoxph
org.biojava.nbio.structure.
ResidueNumber
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.phylo.
ResidueProperties
org.biojava.nbio.structure.
ResidueRange
org.biojava.nbio.structure.
ResidueRangeAndLength
org.biojava.nbio.structure.
AugmentedResidueRange
org.biojava.nbio.structure.align.util.
ResourceManager
org.forester.ws.wabi.
RestUtil
org.forester.application.
rio
org.forester.sdi.
RIO
org.forester.sdi.
RIOn
org.biojava.nbio.survival.cox.
RiskInfo
org.biojava.nbio.core.sequence.io.
RNASequenceCreator
(implements org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>)
org.biojava.nbio.ronn.
RonnConstraint
org.biojava.nbio.structure.symmetry.core.
Rotation
org.biojava.nbio.structure.align.util.
RotationAxis
org.biojava.nbio.structure.symmetry.core.
RotationGroup
org.biojava.nbio.structure.symmetry.core.
RotationSolver
(implements org.biojava.nbio.structure.symmetry.core.
QuatSymmetrySolver
)
javax.swing.RowSorter<M>
javax.swing.DefaultRowSorter<M,I>
javax.swing.table.TableRowSorter<M>
org.biojava.nbio.structure.align.gui.
MyTableRowSorter
org.forester.archaeopteryx.tools.
RunnableProcess
(implements java.lang.Runnable)
org.forester.archaeopteryx.tools.
AncestralTaxonomyInferrer
org.forester.archaeopteryx.tools.
GoAnnotation
org.forester.archaeopteryx.tools.
PhylogeneticInferrer
org.forester.archaeopteryx.tools.
SequenceDataRetriver
org.forester.analysis.
TaxonomyDataManager
org.biojava.nbio.structure.io.
SandboxStyleStructureProvider
(implements org.biojava.nbio.structure.io.
StructureProvider
)
org.biojava.nbio.sequencing.io.fastq.
SangerFastqReader
org.biojava.nbio.sequencing.io.fastq.
SangerFastqWriter
org.forester.evoinference.parsimony.
SankoffParsimony
<STATE_TYPE>
org.biojava.nbio.alignment.aaindex.
ScaledSubstitutionMatrix
(implements org.biojava.nbio.alignment.template.
SubstitutionMatrix
<C>)
org.biojava.nbio.structure.symmetry.analysis.
ScanSymmetry
(implements java.lang.Runnable)
javax.xml.bind.SchemaOutputResolver
org.biojava.nbio.aaproperties.xml.
SchemaGenerator
org.biojava.nbio.structure.align.gui.autosuggest.
SCOPAutoSuggestProvider
(implements org.biojava.nbio.structure.align.gui.autosuggest.
AutoSuggestProvider
)
org.biojava.nbio.structure.scop.
ScopDescription
(implements java.lang.Cloneable, java.io.Serializable)
org.biojava.nbio.structure.scop.server.
ScopDescriptions
(implements java.io.Serializable)
org.biojava.nbio.structure.scop.
ScopDomain
(implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.
StructureIdentifier
)
org.biojava.nbio.structure.scop.server.
ScopDomains
(implements java.io.Serializable)
org.biojava.nbio.structure.scop.
ScopFactory
org.biojava.nbio.structure.scop.
ScopInstallation
(implements org.biojava.nbio.structure.scop.
LocalScopDatabase
)
org.biojava.nbio.structure.scop.
BerkeleyScopInstallation
org.biojava.nbio.structure.gui.util.
ScopInstallationInstance
org.biojava.nbio.structure.scop.
ScopMirror
org.biojava.nbio.structure.scop.
ScopNode
(implements java.io.Serializable)
org.biojava.nbio.structure.scop.server.
ScopNodes
(implements java.io.Serializable)
org.biojava.nbio.phylo.
ScoreMatrix
org.forester.sdi.
SDI
org.forester.sdi.
GSDI
org.forester.sdi.
SDIse
org.forester.application.
sdi_dir
org.forester.application.
sdi_r
org.forester.sdi.
SDIR
org.biojava.nbio.structure.secstruc.
SecStruc
org.biojava.nbio.structure.secstruc.
SecStrucState
org.biojava.nbio.structure.domain.pdp.
Segment
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.structure.domain.pdp.
SegmentComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.structure.gui.
SelectionImpl
(implements org.biojava.nbio.structure.gui.
Selection
)
org.biojava.nbio.structure.io.
SeqRes2AtomAligner
org.forester.phylogeny.data.
Sequence
(implements org.forester.phylogeny.data.
MultipleUris
, org.forester.phylogeny.data.
PhylogenyData
)
org.biojava.nbio.structure.symmetry.core.
SequenceAlignmentCluster
(implements java.lang.Cloneable)
org.biojava.nbio.core.sequence.storage.
SequenceAsStringHelper
<C>
org.biojava.nbio.core.sequence.
SequenceComparator
(implements java.util.Comparator<T>)
org.forester.ws.seqdb.
SequenceDbWsTools
org.forester.ws.uniprot.
SequenceDbWsTools
org.biojava.nbio.core.sequence.loader.
SequenceFileProxyLoader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.util.
SequenceIdParser
org.biojava.nbio.core.sequence.template.
SequenceMixin
org.biojava.nbio.core.sequence.template.
SequenceMixin.SequenceIterator
<C> (implements java.util.Iterator<E>)
org.biojava.nbio.structure.gui.util.
SequenceMouseListener
(implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
org.biojava.nbio.core.sequence.
SequenceOptimizationHints
org.forester.io.parsers.phyloxml.data.
SequenceParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.core.sequence.template.
SequenceProxyView
<C> (implements org.biojava.nbio.core.sequence.template.
SequenceView
<C>)
org.biojava.nbio.core.sequence.views.
ComplementSequenceView
<C>
org.biojava.nbio.core.sequence.views.
ReversedSequenceView
<C>
org.biojava.nbio.core.sequence.views.
RnaSequenceView
(implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.phylogeny.data.
SequenceRelation
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
SequenceRelationParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.biojava.nbio.core.util.
SequenceTools
org.biojava.nbio.data.sequence.
SequenceUtil
org.forester.io.writers.
SequenceWriter
org.biojava.nbio.structure.domain.
SerializableCache
<K,V>
org.biojava.nbio.structure.scop.
CachedRemoteScopInstallation
(implements org.biojava.nbio.structure.scop.
ScopDatabase
)
org.biojava.nbio.structure.domain.
RemoteDomainProvider
(implements org.biojava.nbio.structure.domain.
DomainProvider
)
org.biojava.nbio.structure.domain.
RemotePDPProvider
(implements org.biojava.nbio.structure.domain.
PDPProvider
)
org.biojava.nbio.structure.domain.pdp.
ShortSegmentRemover
org.biojava.nbio.structure.align.gui.
ShowPDBIDListener
(implements java.awt.event.ActionListener)
org.biojava.nbio.structure.io.sifts.
SiftsChainEntry
org.biojava.nbio.structure.io.sifts.
SiftsChainToUniprotMapping
org.biojava.nbio.structure.io.sifts.
SiftsEntity
(implements java.io.Serializable)
org.biojava.nbio.structure.io.sifts.
SiftsMappingProvider
org.biojava.nbio.structure.io.sifts.
SiftsResidue
(implements java.io.Serializable)
org.biojava.nbio.structure.io.sifts.
SiftsSegment
(implements java.io.Serializable)
org.biojava.nbio.structure.io.sifts.
SiftsXMLParser
org.biojava.nbio.structure.align.fatcat.calc.
SigEva
org.biojava.nbio.alignment.
SimpleAlignedSequence
<S,C> (implements org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>)
org.forester.surfacing.
SimpleDomain
(implements org.forester.protein.
Domain
)
org.biojava.nbio.alignment.
SimpleGapPenalty
(implements org.biojava.nbio.alignment.template.
GapPenalty
)
org.biojava.nbio.structure.symmetry.utils.
SimpleGraph
<V> (implements java.lang.Cloneable, org.biojava.nbio.structure.symmetry.utils.
Graph
<V>)
org.biojava.nbio.structure.io.mmcif.
SimpleMMcifConsumer
(implements org.biojava.nbio.structure.io.mmcif.
MMcifConsumer
)
org.biojava.nbio.structure.io.mmcif.
SimpleMMcifParser
(implements org.biojava.nbio.structure.io.mmcif.
MMcifParser
)
org.biojava.nbio.core.sequence.location.
SimplePoint
(implements org.biojava.nbio.core.sequence.location.template.
Point
)
org.biojava.nbio.core.sequence.location.
FuzzyPoint
org.biojava.nbio.alignment.
SimpleProfile
<S,C> (implements org.biojava.nbio.alignment.template.
Profile
<S,C>)
org.biojava.nbio.alignment.
SimpleProfilePair
<S,C> (implements org.biojava.nbio.alignment.template.
ProfilePair
<S,C>)
org.biojava.nbio.alignment.
SimpleSequencePair
<S,C> (implements org.biojava.nbio.alignment.template.
SequencePair
<S,C>)
org.biojava.nbio.alignment.
SimpleSubstitutionMatrix
<C> (implements org.biojava.nbio.alignment.template.
SubstitutionMatrix
<C>)
org.biojava.nbio.core.sequence.storage.
SingleCompoundSequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.nbio.core.util.
SingleLinkageClusterer
org.biojava.nbio.structure.jama.
SingularValueDecomposition
(implements java.io.Serializable)
org.biojava.nbio.phosphosite.
Site
org.biojava.nbio.structure.
Site
(implements java.lang.Comparable<T>, org.biojava.nbio.structure.
PDBRecord
, java.io.Serializable)
org.biojava.nbio.structure.align.seq.
SmithWaterman3DParameters
(implements org.biojava.nbio.structure.align.ce.
ConfigStrucAligParams
)
org.biojava.nbio.sequencing.io.fastq.
SolexaFastqReader
org.biojava.nbio.sequencing.io.fastq.
SolexaFastqWriter
org.biojava.nbio.structure.xtal.
SpaceGroup
(implements java.io.Serializable)
org.biojava.nbio.structure.xtal.io.
SpaceGroupMapElements
org.biojava.nbio.structure.xtal.io.
SpaceGroupMapRoot
org.biojava.nbio.structure.math.
SparseSquareMatrix
(implements java.io.Serializable)
org.biojava.nbio.structure.math.
SparseVector
(implements java.io.Serializable)
org.biojava.nbio.structure.symmetry.geometry.
SphereSampler
org.biojava.nbio.genome.util.
SplitFasta
org.biojava.nbio.structure.
SSBond
(implements java.lang.Cloneable, org.biojava.nbio.structure.
PDBRecord
, java.io.Serializable)
org.biojava.nbio.structure.
StandardAminoAcid
org.biojava.nbio.structure.align.ce.
StartupParameters
org.biojava.nbio.structure.align.ce.
CeUserArgumentProcessor.CeStartupParams
org.biojava.nbio.structure.align.ce.
CeCPUserArgumentProcessor.CeCPStartupParams
org.biojava.nbio.structure.align.fatcat.
FatCatUserArgumentProcessor.FatCatStartupParams
org.biojava.nbio.structure.align.seq.
SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
org.biojava.nbio.ontology.utils.
StaticMemberPlaceHolder
(implements java.io.Serializable)
org.biojava.nbio.survival.cox.matrix.
StdArrayIO
org.biojava.nbio.alignment.io.
StockholmFileAnnotation
org.biojava.nbio.alignment.io.
StockholmFileAnnotation.StockholmFileAnnotationReference
org.biojava.nbio.alignment.io.
StockholmFileParser
org.biojava.nbio.alignment.io.
StockholmStructure
org.biojava.nbio.alignment.io.
StockholmStructure.DatabaseReference
org.biojava.nbio.survival.cox.
StrataInfo
org.biojava.nbio.structure.align.pairwise.
StrCompAlignment
(implements org.biojava.nbio.structure.align.pairwise.
Alignable
)
org.biojava.nbio.core.util.
StringManipulationHelper
org.biojava.nbio.core.sequence.loader.
StringProxySequenceReader
<C> (implements org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.biojava.nbio.core.sequence.loader.
GenbankProxySequenceReader
<C> (implements org.biojava.nbio.core.sequence.features.
DatabaseReferenceInterface
, org.biojava.nbio.core.sequence.features.
FeatureRetriever
, org.biojava.nbio.core.sequence.features.
FeaturesKeyWordInterface
)
org.forester.application.
strip
org.biojava.nbio.structure.align.
StrucAligParameters
org.biojava.nbio.structure.io.mmcif.model.
Struct
org.biojava.nbio.structure.io.mmcif.model.
StructConn
org.biojava.nbio.structure.io.mmcif.model.
StructKeywords
org.biojava.nbio.structure.align.gui.
StructureAlignmentDisplay
org.biojava.nbio.structure.align.
StructureAlignmentFactory
org.biojava.nbio.structure.align.fatcat.calc.
StructureAlignmentOptimizer
org.biojava.nbio.protmod.structure.
StructureAtom
org.biojava.nbio.protmod.structure.
StructureAtomLinkage
org.biojava.nbio.protmod.io.
StructureAtomXMLConverter
org.biojava.nbio.protmod.structure.
StructureGroup
(implements java.lang.Comparable<T>)
org.biojava.nbio.protmod.io.
StructureGroupXMLConverter
org.biojava.nbio.structure.
StructureImpl
(implements java.io.Serializable, org.biojava.nbio.structure.
Structure
)
org.biojava.nbio.structure.contact.
StructureInterface
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.structure.contact.
StructureInterfaceCluster
(implements java.io.Serializable)
org.biojava.nbio.structure.contact.
StructureInterfaceList
(implements java.lang.Iterable<T>, java.io.Serializable)
org.biojava.nbio.structure.
StructureIO
org.biojava.nbio.structure.align.client.
StructureName
(implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.structure.align.
StructurePairAligner
org.biojava.nbio.structure.io.
StructureSequenceMatcher
org.biojava.nbio.structure.
StructureTools
org.biojava.nbio.protmod.structure.
StructureUtil
org.biojava.nbio.alignment.
SubstitutionMatrixHelper
org.biojava.nbio.structure.
SubstructureIdentifier
(implements org.biojava.nbio.structure.
StructureIdentifier
)
org.biojava.nbio.structure.symmetry.core.
SubunitGraph
org.biojava.nbio.structure.symmetry.core.
Subunits
org.biojava.nbio.structure.symmetry.geometry.
SuperPosition
org.biojava.nbio.structure.symmetry.geometry.
SuperPositionQCP
org.forester.application.
support_statistics
org.forester.application.
support_transfer
org.forester.tools.
SupportCount
org.forester.application.
surf_paup
org.forester.application.
surfacing
org.forester.surfacing.
SurfacingConstants
org.forester.surfacing.
SurfacingUtil
org.biojava.nbio.survival.cox.
SurvFitInfo
org.biojava.nbio.survival.kaplanmeier.figure.
SurvFitKM
org.biojava.nbio.survival.cox.
SurvivalInfo
(implements java.lang.Comparable<T>)
org.biojava.nbio.survival.cox.comparators.
SurvivalInfoComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.survival.cox.
SurvivalInfoHelper
org.biojava.nbio.survival.cox.
SurvivalInfoIndex
(implements java.lang.Comparable<T>)
org.biojava.nbio.survival.cox.comparators.
SurvivalInfoValueComparator
(implements java.util.Comparator<T>)
org.biojava.nbio.structure.
SVDSuperimposer
javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
org.biojava.nbio.structure.align.gui.
StructureLoaderThread
org.biojava.nbio.structure.math.
SymbolTable
<Key,Value> (implements java.lang.Iterable<T>, java.io.Serializable)
org.biojava.nbio.structure.validation.
SymmClash
org.forester.io.parsers.
SymmetricalDistanceMatrixParser
org.biojava.nbio.structure.xtal.
SymoplibParser
org.biojava.nbio.structure.align.util.
SynchronizedOutFile
org.biojava.nbio.ontology.
Synonym
(implements java.lang.Comparable<T>)
org.biojava.nbio.structure.symmetry.core.
SystematicSolver
(implements org.biojava.nbio.structure.symmetry.core.
QuatSymmetrySolver
)
org.forester.util.
SystemCommandExecutor
org.biojava.nbio.structure.align.gui.
SystemInfo
org.biojava.nbio.ontology.io.
TabDelimParser
org.biojava.nbio.core.sequence.transcription.
Table.CaseInsensitiveTriplet
org.biojava.nbio.core.sequence.transcription.
Table.Codon
(implements org.biojava.nbio.core.sequence.template.
Compound
)
org.forester.phylogeny.data.
Taxonomy
(implements java.lang.Comparable<T>, org.forester.phylogeny.data.
MultipleUris
, org.forester.phylogeny.data.
PhylogenyData
)
org.biojava.nbio.core.sequence.
TaxonomyID
org.forester.io.parsers.phyloxml.data.
TaxonomyParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.development.
Test
org.forester.test.
Test
org.forester.ws.hmmer.
Test
org.forester.go.
TestGo
org.forester.sdi.
TestGSDI
org.forester.pccx.
TestPccx
org.forester.evoinference.
TestPhylogenyReconstruction
org.forester.surfacing.
TestSurfacing
org.biojava.nbio.structure.symmetry.geometry.
Tetrahedron
(implements org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
)
java.lang.Thread (implements java.lang.Runnable)
org.biojava.nbio.phylo.
TreeConstructor
<C,D>
java.lang.Throwable (implements java.io.Serializable)
java.lang.Error
java.lang.AssertionError
org.biojava.nbio.ontology.utils.
AssertionFailure
java.lang.Exception
org.forester.analysis.
AncestralTaxonomyInferenceException
org.biojava.nbio.core.exceptions.
CompoundNotFoundException
org.biojava.nbio.structure.align.util.
ConfigurationException
java.io.IOException
org.forester.msa.
MsaFormatException
org.forester.io.parsers.nexus.
NexusFormatException
org.forester.io.parsers.nhx.
NHXFormatException
org.forester.io.parsers.util.
PhylogenyParserException
org.forester.io.parsers.phyloxml.
PhyloXmlDataFormatException
org.biojava.nbio.structure.align.client.
JobKillException
org.biojava.nbio.ontology.
OntologyException
org.biojava.nbio.ontology.
AlreadyExistsException
org.biojava.nbio.ontology.
InvalidTermException
org.biojava.nbio.structure.io.
PDBParseException
java.lang.RuntimeException
org.forester.util.
FailedConditionCheckException
java.lang.IllegalArgumentException
org.forester.util.
IllegalFormatUseException
org.biojava.nbio.core.exceptions.
ParserException
org.forester.io.parsers.phyloxml.
PhyloXmlException
org.biojava.nbio.structure.scop.
ScopIOException
org.biojava.nbio.core.exceptions.
TranslationException
org.forester.sdi.
SDIException
org.biojava.nbio.structure.
StructureException
org.forester.development.
Time
org.biojava.nbio.ronn.
Timer
org.forester.io.parsers.tol.
TolParser
(implements org.forester.io.parsers.
PhylogenyParser
)
org.forester.io.parsers.tol.
TolXmlMapping
org.biojava.nbio.core.sequence.transcription.
TranscriptionEngine
org.biojava.nbio.core.sequence.transcription.
TranscriptionEngine.Builder
org.forester.archaeopteryx.
TreeColorSet
org.forester.archaeopteryx.
TreeFontSet
org.biojava.nbio.structure.xtal.io.
TreeMapSpaceGroupWrapper
(implements java.io.Serializable)
org.biojava.nbio.structure.scop.server.
TreeSetStringWrapper
(implements java.io.Serializable)
org.forester.tools.
TreeSplitMatrix
org.biojava.nbio.ontology.
Triple.Impl
(implements java.io.Serializable, org.biojava.nbio.ontology.
Triple
)
org.forester.ws.wabi.
TxSearch
org.forester.ws.seqdb.
UniProtEntry
(implements org.forester.ws.seqdb.
SequenceDatabaseEntry
)
org.forester.ws.uniprot.
UniProtEntry
(implements org.forester.ws.uniprot.
SequenceDatabaseEntry
)
org.biojava.nbio.core.sequence.loader.
UniprotProxySequenceReader
<C> (implements org.biojava.nbio.core.sequence.features.
DatabaseReferenceInterface
, org.biojava.nbio.core.sequence.features.
FeaturesKeyWordInterface
, org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>)
org.forester.ws.seqdb.
UniProtTaxonomy
org.forester.ws.uniprot.
UniProtTaxonomy
org.biojava.nbio.genome.uniprot.
UniprotToFasta
org.biojava.nbio.structure.symmetry.core.
UniqueSequenceList
(implements java.lang.Cloneable)
org.biojava.nbio.structure.xtal.
UnitCellBoundingBox
org.forester.phylogeny.data.
Uri
(implements org.forester.phylogeny.data.
PhylogenyData
)
org.forester.io.parsers.phyloxml.data.
UriParser
(implements org.forester.io.parsers.phyloxml.data.
PhylogenyDataPhyloXmlParser
)
org.forester.archaeopteryx.
UrlTreeReader
(implements java.lang.Runnable)
org.biojava.nbio.structure.align.util.
UserConfiguration
org.biojava.nbio.aaproperties.
Utils
org.forester.ws.wabi.
WabiTools
org.biojava.nbio.survival.cox.
WaldTest
org.biojava.nbio.survival.cox.
WaldTestInfo
org.forester.archaeopteryx.webservices.
WebservicesManager
org.forester.archaeopteryx.webservices.
WebserviceUtil
org.biojava.nbio.structure.align.webstart.
WebStartDBSearch
org.biojava.nbio.structure.align.webstart.
WebStartDBSearchResults
org.biojava.nbio.structure.align.webstart.
WebStartMain
org.biojava.nbio.core.sequence.views.
WindowedSequence
<C> (implements java.lang.Iterable<T>)
org.forester.util.
WindowsUtils
org.biojava.nbio.survival.data.
WorkSheet
java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
java.io.BufferedWriter
org.forester.util.
EasyWriter
org.biojava.nbio.structure.validation.
WwPDBValidationInformation
javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
org.biojava.nbio.structure.xtal.io.
TransfAlgebraicAdapter
org.forester.io.parsers.phyloxml.
XmlElement
org.biojava.nbio.core.util.
XMLHelper
org.biojava.nbio.structure.scop.server.
XMLUtil
Interface Hierarchy
org.biojava.nbio.alignment.aaindex.
AAIndexProvider
org.biojava.nbio.core.sequence.template.
Accessioned
org.biojava.nbio.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava.nbio.core.sequence.location.template.
Location
)
org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.core.sequence.location.template.
Location
(also extends java.lang.Iterable<T>)
org.biojava.nbio.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava.nbio.core.sequence.template.
Accessioned
)
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
Sequence
<C> (also extends java.lang.Iterable<T>)
org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
SequenceReader
<C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
SequenceView
<C>
org.biojava.nbio.core.sequence.template.
SequenceReader
<C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
SequenceView
<C>
org.biojava.nbio.structure.align.pairwise.
Alignable
org.biojava.nbio.structure.gui.events.
AlignmentPositionListener
org.biojava.nbio.structure.align.events.
AlignmentProgressListener
org.biojava.nbio.ontology.utils.
Annotatable
org.biojava.nbio.ontology.
OntologyTerm
org.biojava.nbio.ontology.
RemoteTerm
org.biojava.nbio.ontology.
Term
org.biojava.nbio.ontology.
OntologyTerm
org.biojava.nbio.ontology.
RemoteTerm
org.biojava.nbio.ontology.
Triple
org.biojava.nbio.ontology.
Variable
org.biojava.nbio.ontology.
Triple
org.biojava.nbio.ontology.
Variable
org.biojava.nbio.ontology.utils.
Annotation
org.biojava.nbio.structure.
AtomPositionMap.GroupMatcher
org.biojava.nbio.structure.align.gui.autosuggest.
AutoSuggestProvider
org.biojava.nbio.structure.quaternary.io.
BioUnitDataProvider
org.biojava.nbio.structure.cath.
CathDatabase
org.biojava.nbio.survival.kaplanmeier.figure.
CensorStatusSelect
org.biojava.nbio.structure.
Chain
org.biojava.nbio.survival.data.
ChangeValue
org.forester.evoinference.matrix.character.
CharacterStateMatrix
<S>
org.biojava.nbio.structure.io.mmcif.
ChemCompProvider
java.lang.Cloneable
org.biojava.nbio.structure.
Atom
(also extends org.biojava.nbio.structure.
PDBRecord
)
org.biojava.nbio.structure.
Structure
(also extends org.biojava.nbio.structure.
StructureIdentifier
)
org.biojava.nbio.structure.gui.util.color.
ColorInterpolator
org.forester.surfacing.
CombinableDomains
java.lang.Comparable<T>
org.forester.protein.
BinaryDomainCombination
org.forester.protein.
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.biojava.nbio.core.sequence.location.template.
Point
org.forester.species.
Species
java.util.Comparator<T>
org.biojava.nbio.survival.cox.comparators.
CoxComparatorInterface
org.biojava.nbio.core.sequence.template.
Compound
org.biojava.nbio.core.sequence.template.
ComplementCompound
org.biojava.nbio.core.sequence.template.
CompoundSet
<C>
org.biojava.nbio.core.sequence.template.
CompoundTranslator
<F,T>
org.biojava.nbio.structure.align.ce.
ConfigStrucAligParams
org.biojava.nbio.structure.gui.util.color.
ContinuousColorMapper
org.forester.pccx.
Coverage
org.forester.pccx.
CoverageCalculationMethod
org.forester.pccx.
CoverageCalculationOptions
org.forester.pccx.
CoverageExtender
org.biojava.nbio.core.sequence.features.
DatabaseReferenceInterface
org.forester.util.
DescriptiveStatistics
org.biojava.nbio.survival.kaplanmeier.metadata.
DiscreteQuantizerInterface
org.forester.evoinference.matrix.distance.
DistanceMatrix
org.biojava.nbio.structure.domain.
DomainProvider
org.forester.surfacing.
DomainSimilarityCalculator
org.biojava.nbio.structure.ecod.
EcodDatabase
org.forester.phylogeny.
Edge
org.biojava.nbio.core.sequence.edits.
Edit
<C>
org.biojava.nbio.core.sequence.io.template.
FastaHeaderFormatInterface
<S,C>
org.biojava.nbio.sequencing.io.fastq.
FastqReader
org.biojava.nbio.sequencing.io.fastq.
FastqWriter
org.biojava.nbio.genome.parsers.gff.
FeatureI
org.biojava.nbio.core.sequence.features.
FeatureInterface
<S,C>
org.biojava.nbio.core.sequence.features.
FeatureRetriever
org.biojava.nbio.core.sequence.features.
FeaturesKeyWordInterface
org.biojava.nbio.alignment.template.
GapPenalty
org.biojava.nbio.core.sequence.io.template.
GenbankHeaderFormatInterface
<S,C>
org.forester.surfacing.
GenomeWideCombinableDomains
org.biojava.nbio.structure.symmetry.utils.
Graph
<V>
org.biojava.nbio.structure.
Group
org.biojava.nbio.structure.
AminoAcid
org.biojava.nbio.alignment.template.
HierarchicalClusterer
<S,C>
org.biojava.nbio.ws.hmmer.
HmmerScan
org.biojava.nbio.core.sequence.io.util.
IOUtils.ReaderProcessor
org.biojava.nbio.aaproperties.
IPeptideProperties
org.biojava.nbio.aaproperties.profeat.
IProfeatProperties
java.lang.Iterable<T>
org.biojava.nbio.core.sequence.location.template.
Location
(also extends org.biojava.nbio.core.sequence.template.
Accessioned
)
org.biojava.nbio.core.sequence.location.template.
AccesionedLocation
(also extends org.biojava.nbio.core.sequence.template.
Accessioned
)
org.biojava.nbio.alignment.template.
Profile
<S,C>
org.biojava.nbio.alignment.template.
MutableProfile
<S,C>
org.biojava.nbio.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfilePair
<S,C>)
org.biojava.nbio.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava.nbio.alignment.template.
SequencePair
<S,C>)
org.biojava.nbio.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>, org.biojava.nbio.alignment.template.
ProfilePair
<S,C>)
org.biojava.nbio.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>, org.biojava.nbio.alignment.template.
SequencePair
<S,C>)
org.biojava.nbio.alignment.template.
ProfilePair
<S,C>
org.biojava.nbio.alignment.template.
MutableProfilePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>)
org.biojava.nbio.alignment.template.
ProfileView
<S,C>
org.biojava.nbio.alignment.template.
SequencePair
<S,C>
org.biojava.nbio.alignment.template.
MutableSequencePair
<S,C> (also extends org.biojava.nbio.alignment.template.
MutableProfile
<S,C>)
org.biojava.nbio.core.sequence.template.
Sequence
<C> (also extends org.biojava.nbio.core.sequence.template.
Accessioned
)
org.biojava.nbio.alignment.template.
AlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.alignment.template.
MutableAlignedSequence
<S,C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
SequenceReader
<C>
org.biojava.nbio.core.sequence.template.
ProxySequenceReader
<C>
org.biojava.nbio.core.sequence.template.
SequenceView
<C>
java.util.Iterator<E>
org.forester.phylogeny.iterators.
PhylogenyNodeIterator
org.biojava.nbio.core.sequence.template.
LightweightProfile
<S,C>
org.biojava.nbio.structure.align.ce.
MatrixListener
org.biojava.nbio.structure.io.mmcif.
MMcifConsumer
org.biojava.nbio.structure.io.mmcif.
MMcifParser
org.biojava.nbio.protmod.
ModificationCondition
org.biojava.nbio.protmod.structure.
ModifiedCompound
org.forester.msa.
Msa
org.forester.msa.
MsaInferrer
org.biojava.nbio.structure.align.
MultipleStructureAligner
org.biojava.nbio.structure.align.multiple.
MultipleSuperimposer
org.forester.phylogeny.data.
MultipleUris
org.biojava.nbio.phylo.
NJTreeProgressListener
org.biojava.nbio.ontology.obo.
OboFileEventListener
org.biojava.nbio.ontology.
Ontology
org.biojava.nbio.ontology.
OntologyFactory
org.biojava.nbio.ontology.
OntologyOps
org.forester.surfacing.
PairwiseDomainSimilarity
org.forester.surfacing.
PairwiseDomainSimilarityCalculator
org.biojava.nbio.sequencing.io.fastq.
ParseListener
org.biojava.nbio.structure.
PDBRecord
org.biojava.nbio.structure.
Atom
(also extends java.lang.Cloneable)
org.biojava.nbio.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.data.
PhylogenyDataPhyloXmlParser
org.forester.phylogeny.factories.
PhylogenyFactory
org.forester.phylogeny.
PhylogenyNodeI
org.forester.io.parsers.
PhylogenyParser
org.biojava.nbio.core.sequence.location.template.
Point.Resolver
<T>
org.biojava.nbio.structure.symmetry.geometry.
Polyhedron
org.forester.protein.
Protein
org.biojava.nbio.protmod.
ProteinModification
org.biojava.nbio.structure.symmetry.core.
QuatSymmetrySolver
org.biojava.nbio.structure.quaternary.io.
RawBioUnitDataProvider
org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentService
java.lang.Runnable
org.biojava.nbio.structure.align.gui.
AlignmentCalculationRunnable
org.biojava.nbio.structure.scop.
ScopDatabase
org.biojava.nbio.structure.scop.
LocalScopDatabase
org.biojava.nbio.alignment.template.
Scorer
org.biojava.nbio.alignment.template.
Aligner
<S,C>
org.biojava.nbio.alignment.template.
MatrixAligner
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
RescoreRefiner
<S,C>
org.biojava.nbio.alignment.template.
MatrixAligner
<S,C>
org.biojava.nbio.alignment.template.
PairInProfileScorer
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>, org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>)
org.biojava.nbio.alignment.template.
PairwiseSequenceScorer
<S,C>
org.biojava.nbio.alignment.template.
PairInProfileScorer
<S,C>
org.biojava.nbio.alignment.template.
PairwiseSequenceAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>, org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>, org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileScorer
<S,C>
org.biojava.nbio.alignment.template.
PartitionRefiner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
ProfileProfileAligner
<S,C> (also extends org.biojava.nbio.alignment.template.
Aligner
<S,C>)
org.biojava.nbio.alignment.template.
RescoreRefiner
<S,C>
org.biojava.nbio.structure.align.multiple.
ScoresCache
org.biojava.nbio.structure.align.multiple.
Block
org.biojava.nbio.structure.align.multiple.
BlockSet
org.biojava.nbio.structure.align.multiple.
MultipleAlignment
org.biojava.nbio.structure.align.multiple.
MultipleAlignmentEnsemble
org.forester.pccx.
ScoringMethodForExternalNode
org.biojava.nbio.structure.gui.
Selection
org.forester.sequence.
Sequence
org.biojava.nbio.core.sequence.io.template.
SequenceCreatorInterface
<C>
org.forester.ws.seqdb.
SequenceDatabaseEntry
org.forester.ws.uniprot.
SequenceDatabaseEntry
org.biojava.nbio.core.sequence.io.template.
SequenceHeaderParserInterface
<S,C>
org.biojava.nbio.core.sequence.io.template.
SequenceParserInterface
java.io.Serializable
org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentOutputProperties
org.biojava.nbio.ws.alignment.
RemotePairwiseAlignmentProperties
org.biojava.nbio.sequencing.io.fastq.
StreamListener
org.biojava.nbio.structure.align.
StructureAlignment
org.biojava.nbio.structure.
StructureIdentifier
org.biojava.nbio.structure.
Structure
(also extends java.lang.Cloneable)
org.biojava.nbio.structure.gui.util.
StructurePairSelector
org.biojava.nbio.structure.io.
StructureProvider
org.biojava.nbio.structure.io.
StructureIOFile
org.biojava.nbio.structure.gui.
StructureViewer
org.biojava.nbio.alignment.template.
SubstitutionMatrix
<C>
org.biojava.nbio.core.sequence.transcription.
Table
javax.swing.tree.TreeNode
org.biojava.nbio.alignment.template.
GuideTreeNode
<S,C>
org.biojava.nbio.structure.align.ce.
UserArgumentProcessor
org.biojava.nbio.core.util.
XMLWriter
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.biojava.nbio.aaproperties.
PeptideProperties.SingleLetterAACode
org.biojava.nbio.aaproperties.
CommandPrompt.PropertyName
org.biojava.nbio.aaproperties.profeat.
IProfeatProperties.ATTRIBUTE
org.biojava.nbio.aaproperties.profeat.
IProfeatProperties.GROUPING
org.biojava.nbio.aaproperties.profeat.
IProfeatProperties.TRANSITION
org.biojava.nbio.aaproperties.profeat.
IProfeatProperties.DISTRIBUTION
org.biojava.nbio.alignment.
Alignments.PairInProfileScorerType
org.biojava.nbio.alignment.
Alignments.PairwiseSequenceAlignerType
org.biojava.nbio.alignment.
Alignments.PairwiseSequenceScorerType
org.biojava.nbio.alignment.
Alignments.ProfileProfileAlignerType
org.biojava.nbio.alignment.
Alignments.RefinerType
org.biojava.nbio.alignment.routines.
AlignerHelper.Last
org.biojava.nbio.alignment.template.
GapPenalty.Type
org.biojava.nbio.alignment.template.
Profile.StringFormat
org.biojava.nbio.alignment.template.
AlignedSequence.Step
org.biojava.nbio.core.sequence.
SequenceOptimizationHints.SequenceUsage
org.biojava.nbio.core.sequence.
SequenceOptimizationHints.SequenceCollection
org.biojava.nbio.core.sequence.
Strand
org.biojava.nbio.core.sequence.
DataSource
org.biojava.nbio.core.sequence.
DNASequence.DNAType
org.biojava.nbio.core.sequence.template.
LightweightProfile.StringFormat
org.biojava.nbio.core.sequence.template.
AbstractSequence.AnnotationType
org.biojava.nbio.core.sequence.transcription.
Frame
org.biojava.nbio.genome.parsers.cytoband.
StainType
(implements java.io.Serializable)
org.biojava.nbio.phylo.
TreeConstructionAlgorithm
org.biojava.nbio.phylo.
TreeType
org.biojava.nbio.protmod.
ModificationCategory
org.biojava.nbio.protmod.
ModificationOccurrenceType
org.biojava.nbio.ronn.
RonnConstraint.Threshold
org.biojava.nbio.sequencing.io.fastq.
FastqVariant
org.biojava.nbio.structure.
BondType
org.biojava.nbio.structure.
Element
(implements java.io.Serializable)
org.biojava.nbio.structure.
GroupType
org.biojava.nbio.structure.
ElementType
(implements java.io.Serializable)
org.biojava.nbio.structure.
ExperimentalTechnique
org.biojava.nbio.structure.
PDBStatus.Status
org.biojava.nbio.structure.align.ce.
CECPParameters.DuplicationHint
org.biojava.nbio.structure.align.ce.
CeParameters.ScoringStrategy
org.biojava.nbio.structure.cath.
CathCategory
org.biojava.nbio.structure.gui.
RenderStyle
org.biojava.nbio.structure.gui.util.color.
LinearColorInterpolator.InterpolationDirection
org.biojava.nbio.structure.io.
LocalPDBDirectory.ObsoleteBehavior
org.biojava.nbio.structure.io.
LocalPDBDirectory.FetchBehavior
org.biojava.nbio.structure.io.mmcif.chem.
ResidueType
(implements java.io.Serializable)
org.biojava.nbio.structure.io.mmcif.chem.
PolymerType
(implements java.io.Serializable)
org.biojava.nbio.structure.scop.
Astral.AstralSet
org.biojava.nbio.structure.scop.
ScopCategory
(implements java.io.Serializable)
org.biojava.nbio.structure.secstruc.
SecStrucType
(implements java.io.Serializable)
org.biojava.nbio.structure.secstruc.
BridgeType
(implements java.io.Serializable)
org.biojava.nbio.structure.symmetry.geometry.
MomentsOfInertia.SymmetryClass
org.biojava.nbio.structure.xtal.
TransformType
org.biojava.nbio.structure.xtal.
BravaisLattice
org.biojava.nbio.survival.cox.
ResidualsCoxph.Type
org.biojava.nbio.survival.cox.
CoxMethod
org.biojava.nbio.survival.kaplanmeier.figure.
SurvFitKM.Method
org.biojava.nbio.survival.kaplanmeier.figure.
SurvFitKM.Error
org.biojava.nbio.survival.kaplanmeier.figure.
SurvFitKM.ConfType
org.biojava.nbio.survival.kaplanmeier.figure.
SurvFitKM.ConfLower
org.biojava.nbio.ws.alignment.qblast.
BlastOutputAlignmentFormatEnum
org.biojava.nbio.ws.alignment.qblast.
BlastAlignmentParameterEnum
org.biojava.nbio.ws.alignment.qblast.
BlastOutputParameterEnum
org.biojava.nbio.ws.alignment.qblast.
BlastProgramEnum
org.biojava.nbio.ws.alignment.qblast.
BlastOutputFormatEnum
org.biojava.nbio.ws.alignment.qblast.
BlastMatrixEnum
org.forester.archaeopteryx.
Configuration.UI
org.forester.archaeopteryx.
AptxUtil.GraphicsExportType
org.forester.archaeopteryx.
Options.CLADOGRAM_TYPE
org.forester.archaeopteryx.
Options.NODE_LABEL_DIRECTION
org.forester.archaeopteryx.
Options.PHYLOGENY_GRAPHICS_TYPE
org.forester.archaeopteryx.webservices.
WebservicesManager.WsPhylogenyFormat
org.forester.evoinference.distance.
PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
org.forester.evoinference.matrix.character.
CharacterStateMatrix.BinaryStates
org.forester.evoinference.matrix.character.
CharacterStateMatrix.Format
org.forester.evoinference.matrix.character.
CharacterStateMatrix.GainLossStates
org.forester.evoinference.matrix.character.
CharacterStateMatrix.NucleotideStates
org.forester.evoinference.matrix.distance.
DistanceMatrix.Format
org.forester.go.
GoSubset.Type
org.forester.go.
GoXRef.Type
org.forester.go.
OBOparser.ReturnType
org.forester.go.
GoNameSpace.GoNamespaceType
org.forester.go.
GoRelationship.Type
org.forester.go.etc.
OntologizerResult.TYPE
org.forester.io.parsers.
HmmPfamOutputParser.FilterType
org.forester.io.parsers.
HmmPfamOutputParser.ReturnType
org.forester.io.parsers.
HmmscanPerDomainTableParser.FilterType
org.forester.io.parsers.
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
org.forester.io.parsers.
HmmscanPerDomainTableParser.ReturnType
org.forester.io.parsers.
SymmetricalDistanceMatrixParser.InputMatrixType
org.forester.io.writers.
PhylogenyWriter.FORMAT
org.forester.io.writers.
SequenceWriter.SEQ_FORMAT
org.forester.phylogeny.
PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE
org.forester.phylogeny.
PhylogenyMethods.PhylogenyNodeField
org.forester.phylogeny.
PhylogenyMethods.TAXONOMY_EXTRACTION
org.forester.phylogeny.
PhylogenyMethods.DESCENDANT_SORT_PRIORITY
org.forester.phylogeny.data.
Property.AppliesTo
org.forester.phylogeny.data.
NodeVisualization.NodeFill
org.forester.phylogeny.data.
NodeVisualization.NodeShape
org.forester.phylogeny.data.
SequenceRelation.SEQUENCE_RELATION_TYPE
org.forester.phylogeny.data.
Event.EventType
org.forester.protein.
BinaryDomainCombination.DomainCombinationType
org.forester.protein.
BinaryDomainCombination.OutputFormat
org.forester.sdi.
SDI.TaxonomyComparisonBase
org.forester.sequence.
Sequence.TYPE
org.forester.surfacing.
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
org.forester.surfacing.
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
org.forester.surfacing.
PrintableDomainSimilarity.PRINT_OPTION
org.forester.surfacing.
DomainSimilarityCalculator.Detailedness
org.forester.surfacing.
DomainSimilarityCalculator.GoAnnotationOutput
org.forester.surfacing.
DomainSimilarity.DomainSimilarityScoring
org.forester.surfacing.
DomainSimilarity.DomainSimilaritySortField
org.forester.tools.
PhylogenyDecorator.FIELD
org.forester.util.
ForesterConstants.PhylogeneticTreeFormats
org.forester.ws.seqdb.
SequenceDbWsTools.Db
org.forester.ws.uniprot.
SequenceDbWsTools.Db
org.forester.ws.wabi.
TxSearch.RANKS
org.forester.ws.wabi.
TxSearch.TAX_NAME_CLASS
org.forester.ws.wabi.
TxSearch.TAX_RANK
org.jcolorbrewer.
ColorBrewer
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