All Classes

  • aa
  • aaa
  • AAindexFactory
  • AAIndexFileParser
  • AAIndexProvider
  • AboutDialog
  • AbstractAlignmentJmol
  • AbstractAnnotation
  • AbstractBean
  • AbstractCompound
  • AbstractCompoundSet
  • AbstractCompoundTranslator
  • AbstractFeature
  • AbstractLocation
  • AbstractMatrixAligner
  • AbstractNucleotideCompoundSet
  • AbstractPairwiseSequenceAligner
  • AbstractProfileProfileAligner
  • AbstractRenderer
  • AbstractScorer
  • AbstractScoresCache
  • AbstractSequence
  • AbstractSequence.AnnotationType
  • AbstractStructureAlignment
  • AbstractTerm
  • AbstractUserArgumentProcessor
  • AccesionedLocation
  • Accession
  • Accession.Source
  • Accessioned
  • AccessionID
  • AccessionParser
  • AdjactantDirectedBinaryDomainCombination
  • AdjactantDirectedCombinableDomains
  • AFP
  • AFPAlignmentDisplay
  • AFPCalculator
  • AFPChain
  • AFPChainCoordManager
  • AFPChainer
  • AFPChainFlipper
  • AFPChainScorer
  • AfpChainWriter
  • AFPChainXMLConverter
  • AFPChainXMLParser
  • AFPOptimizer
  • AFPPostProcessor
  • AFPTwister
  • AgScore
  • AligMatEl
  • Alignable
  • AlignedPosition
  • AlignedSequence
  • AlignedSequence.Step
  • Aligner
  • AlignerHelper
  • AlignerHelper.Anchor
  • AlignerHelper.Anchor.QueryIndexComparator
  • AlignerHelper.Cut
  • AlignerHelper.Last
  • AlignerHelper.Subproblem
  • AlignmentCalc
  • AlignmentCalc
  • AlignmentCalcDB
  • AlignmentCalculationRunnable
  • AlignmentGui
  • AlignmentPositionListener
  • AlignmentProgressListener
  • AlignmentProgressListener
  • AlignmentResult
  • Alignments
  • Alignments.PairInProfileScorerType
  • Alignments.PairwiseSequenceAlignerType
  • Alignments.PairwiseSequenceScorerType
  • Alignments.ProfileProfileAlignerType
  • Alignments.RefinerType
  • AlignmentTextPanel
  • AlignmentTools
  • AlignmentTools.IdentityMap
  • AligNPE
  • AlignTools
  • AligPanel
  • AligPanelMouseMotionListener
  • AligUIManager
  • AllChemCompProvider
  • AlreadyExistsException
  • AltAligComparator
  • AlternativeAlignment
  • AlternativeAlignmentFrame
  • AmbiguityDNACompoundSet
  • AmbiguityDNARNAHybridCompoundSet
  • AmbiguityRNACompoundSet
  • AminoAcid
  • AminoAcidComposition
  • AminoAcidCompositionTable
  • AminoAcidCompound
  • AminoAcidCompoundSet
  • AminoAcidImpl
  • AncestralTaxonomyInference
  • AncestralTaxonomyInferenceException
  • AncestralTaxonomyInferrer
  • AnchoredPairwiseSequenceAligner
  • AngleOrderDetectorPlus
  • AngleOutlier
  • Annotatable
  • Annotation
  • Annotation
  • AnnotationParser
  • annotator
  • App
  • App
  • AptxUtil
  • AptxUtil.GraphicsExportType
  • Archaeopteryx
  • ArchaeopteryxA
  • ArchaeopteryxE
  • ArrayListProxySequenceReader
  • ArrayListSequenceReader
  • AsaCalculator
  • AsciiHistogram
  • AssertionFailure
  • AssignmentXMLSerializer
  • Astral
  • Astral.AstralSet
  • Atom
  • AtomCache
  • AtomContact
  • AtomContactSet
  • AtomIdentifier
  • AtomImpl
  • AtomInfo
  • AtomInfoParser
  • AtomIterator
  • AtomPositionMap
  • AtomPositionMap.GroupMatcher
  • AtomSite
  • AtomSites
  • AuditAuthor
  • AugmentedResidueRange
  • Author
  • AutoSuggestProvider
  • AxisAligner
  • BasicBinaryDomainCombination
  • BasicCharacterStateMatrix
  • BasicCombinableDomains
  • BasicDescriptiveStatistics
  • BasicDomain
  • BasicDomainSimilarityCalculator
  • BasicExternalNodeBasedCoverageExtender
  • BasicGenomeWideCombinableDomains
  • BasicGoRelationship
  • BasicGoSubset
  • BasicGoTerm
  • BasicGoXRef
  • BasicMsa
  • BasicPhylogeniesWebserviceClient
  • BasicProtein
  • BasicSequence
  • BasicSequence
  • BasicSpecies
  • BasicSymmetricalDistanceMatrix
  • BasicTable
  • BasicTableParser
  • BerkeleyScopInstallation
  • BetaBridge
  • BinaryCharacters
  • BinaryCharactersParser
  • BinaryDomainCombination
  • BinaryDomainCombination.DomainCombinationType
  • BinaryDomainCombination.OutputFormat
  • BioAssemblyIdentifier
  • BioAssemblyInfo
  • BioAssemblyTools
  • BiojavaJmol
  • BioJavaStructureAlignment
  • BiologicalAssemblyBuilder
  • BiologicalAssemblyTransformation
  • BioUnitDataProvider
  • BioUnitDataProviderFactory
  • BitSequenceReader
  • BitSequenceReader.BitArrayWorker
  • Blast
  • BlastAlignmentParameterEnum
  • BlastClustReader
  • BlastHitBuilder
  • BlastHomologyHits
  • BlastHspBuilder
  • BlastJob
  • BlastMatrixEnum
  • BlastOutputAlignmentFormatEnum
  • BlastOutputFormatEnum
  • BlastOutputParameterEnum
  • BlastProgramEnum
  • BlastResult
  • BlastResultBuilder
  • BlastTabularParser
  • BlastXMLParser
  • BlastXMLQuery
  • Block
  • BlockImpl
  • BlockSet
  • BlockSetImpl
  • Bond
  • BondImpl
  • BondMaker
  • BondOutlier
  • BondType
  • BootstrapResampler
  • BoundingBox
  • BranchColor
  • BranchCountingBasedScoringMethod
  • BranchData
  • BranchLengthBasedScoringMethod
  • BranchWidth
  • BranchWidthParser
  • BravaisLattice
  • BridgeType
  • BrowserOpener
  • BufferedReaderBytesRead
  • C2RotationSolver
  • CachedRemoteScopInstallation
  • CacheFactory
  • CAConverter
  • Calc
  • CalcBioAssemblySymmetry
  • CallablePairwiseSequenceAligner
  • CallablePairwiseSequenceScorer
  • CallableProfileProfileAligner
  • CallableStructureAlignment
  • CartesianProduct
  • CaseFreeAminoAcidCompoundSet
  • CaseInsensitiveCompound
  • CasePreservingProteinSequenceCreator
  • CathCategory
  • CathDatabase
  • CathDomain
  • CathFactory
  • CathFragment
  • CathInstallation
  • CathNode
  • CathSegment
  • CDSComparator
  • CDSSequence
  • CECalculator
  • CeCalculatorEnhanced
  • CeCPMain
  • CeCPMain.CPRange
  • CECPParameters
  • CECPParameters.DuplicationHint
  • CeCPUserArgumentProcessor
  • Cell
  • CeMain
  • CensorStatus
  • CensorStatusSelect
  • CeParameters
  • CeParameters.ScoringStrategy
  • CeSideChainMain
  • CeSideChainUserArgumentProcessor
  • CeSymm
  • CeSymmIterative
  • CESymmParameters
  • CESymmParameters.OrderDetectorMethod
  • CESymmParameters.RefineMethod
  • CESymmParameters.SymmetryType
  • CeSymmResult
  • CeUserArgumentProcessor
  • CeUserArgumentProcessor.CeStartupParams
  • Chain
  • ChainClusterer
  • ChainImpl
  • ChainSignature
  • ChangeValue
  • CharacterStateMatrix
  • CharacterStateMatrix.BinaryStates
  • CharacterStateMatrix.Format
  • CharacterStateMatrix.GainLossStates
  • CharacterStateMatrix.NucleotideStates
  • ChargeAdder
  • Chart
  • check_fasta
  • ChemComp
  • ChemCompAtom
  • ChemCompBond
  • ChemCompConsumer
  • ChemCompDescriptor
  • ChemCompGroupFactory
  • ChemCompProvider
  • ChemCompTools
  • ChemicalComponentDictionary
  • ChiSq
  • Cholesky2
  • CholeskyDecomposition
  • ChooseDirAction
  • ChromosomeMappingTools
  • ChromosomeSequence
  • ChromPos
  • Chsolve2
  • CIFLabel
  • Clash
  • ClasspathResource
  • ClinicalMetaDataOutcome
  • CliTools
  • ClustalOmega
  • ClusterAltAligs
  • ClusterDomains
  • ClusterMerger
  • ClusterProteinChains
  • CodonCompound
  • CollectionTools
  • ColorBrewer
  • ColorConverter
  • ColorInterpolator
  • ColorPaletteChooserDialog
  • ColorPanelSelectionModel
  • ColorParser
  • ColorUtils
  • CombinableDomains
  • CombinationGenerator
  • CombinationsBasedPairwiseDomainSimilarity
  • CombinationsBasedPairwiseDomainSimilarityCalculator
  • CommandLineArguments
  • CommandProcessBuilder
  • CommandPrompt
  • CommandPrompt.PropertyName
  • CompactCharSequence
  • Comparison
  • ComplementCompound
  • ComplementSequenceView
  • Component
  • ComponentXMLConverter
  • Compound
  • Compound
  • CompoundFinder
  • CompoundNotFoundException
  • CompoundSet
  • CompoundTranslator
  • ConcurrencyTools
  • confadd
  • Confidence
  • ConfidenceAssessor
  • ConfidenceParser
  • ConfigPDBInstallPanel
  • ConfigStrucAligParams
  • Configuration
  • Configuration.EXT_NODE_DATA_RETURN_ON
  • Configuration.UI
  • ConfigurationException
  • ConfigXMLHandler
  • Constants
  • Constraints
  • ContinuousColorMapper
  • ContinuousColorMapperTransform
  • Convert2Charge
  • Convert2Hydrophobicity
  • Convert2NormalizedVanDerWaalsVolume
  • Convert2Polarity
  • Convert2Polarizability
  • Convert2SecondaryStructure
  • Convert2SolventAccessibility
  • Convertor
  • CoordManager
  • core_chars
  • CoreSuperimposer
  • count_support
  • CountProgressListener
  • CountsBasedPairwiseDomainSimilarity
  • Coverage
  • CoverageCalculationMethod
  • CoverageCalculationOptions
  • CoverageCalculator
  • CoverageExtender
  • CoxCC
  • CoxCoefficient
  • CoxComparatorInterface
  • CoxHelper
  • CoxInfo
  • CoxMart
  • CoxMethod
  • CoxR
  • CoxScore
  • CoxVariables
  • CoxVariablesOverallModelFitComparator
  • CoxVariablesVariableComparator
  • CRC64Checksum
  • CrystalBuilder
  • CrystalCell
  • CrystalTransform
  • Cut
  • CutDomain
  • CutSites
  • CutValues
  • Cytoband
  • CytobandParser
  • DatabasePDBremark
  • DatabasePDBrev
  • DatabasePdbrevRecord
  • DatabaseReferenceInterface
  • Dataset
  • DataSource
  • Date
  • DateParser
  • DBRef
  • DBReferenceInfo
  • DBResultTable
  • DBSearchGUI
  • decorator
  • decoratorX
  • DefaultAAIndexProvider
  • DefaultAutoSuggestProvider
  • DefaultMatrixMapper
  • DefaultOps
  • DeleteableMsa
  • DescriptiveStatistics
  • DevelopmentTools
  • DirectedBinaryDomainCombination
  • DirectedCombinableDomains
  • DiscreteQuantizerInterface
  • DisplayAFP
  • DistanceBox
  • DistanceMatrix
  • DistanceMatrix.Format
  • DistanceMatrixCalculator
  • DistanceTreeEvaluator
  • Distribution
  • DistributionParser
  • DivergingColorPalettePanel
  • DNACompoundSet
  • DNASequence
  • DNASequence.DNAType
  • DNASequenceCreator
  • DNAToRNATranslator
  • DolloParsimony
  • dom_dup
  • Domain
  • Domain
  • DomainArchitecture
  • DomainArchitectureBasedGenomeSimilarityCalculator
  • DomainArchitectureParser
  • DomainCountsBasedPairwiseSimilarityCalculator
  • DomainCountsDifferenceUtil
  • DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
  • DomainLengths
  • DomainLengthsTable
  • domainloss_replacement
  • DomainParsimonyCalculator
  • DomainProvider
  • DomainProviderFactory
  • DomainSimilarity
  • DomainSimilarity.DomainSimilarityScoring
  • DomainSimilarity.DomainSimilaritySortField
  • DomainSimilarity.PRINT_OPTION
  • DomainSimilarityCalculator
  • DomainSimilarityCalculator.Detailedness
  • DomainSimilarityCalculator.GoAnnotationOutput
  • DotPlotPanel
  • DownloadChemCompProvider
  • DSSPParser
  • EasyWriter
  • EbiDbEntry
  • EcodDatabase
  • EcodDomain
  • EcodFactory
  • EcodInstallation
  • EcodInstallation.EcodParser
  • Edit
  • Edit.AbstractEdit
  • Edit.Delete
  • Edit.Insert
  • Edit.Substitute
  • EigenvalueDecomposition
  • Element
  • Element
  • ElementTable
  • ElementType
  • Entity
  • EntityPolySeq
  • EntitySrcGen
  • EntitySrcNat
  • EntitySrcSyn
  • Entry
  • Equals
  • Event
  • Event.EventType
  • EventParser
  • Example1
  • Example2
  • Example3
  • Example4
  • Example5
  • ExonComparator
  • ExonSequence
  • ExperimentalTechnique
  • ExpressionFigure
  • Exptl
  • ExternalForwardIterator
  • ExternalNodeBasedCoverage
  • ExternalNodeBasedCoverageMethod
  • ExternalNodeBasedCoverageMethodOptions
  • ExternalProgram
  • FailedConditionCheckException
  • FarmJob
  • FarmJobParameters
  • FarmJobRunnable
  • fasta_split
  • FastaAFPChainConverter
  • FastaGeneWriter
  • FastaHeaderFormatInterface
  • FastaParser
  • FastaReader
  • FastaReaderHelper
  • FastaSequence
  • FastaSequenceParser
  • FastaStructureParser
  • FastaWriter
  • FastaWriterHelper
  • Fastq
  • FastqBuilder
  • FastqReader
  • FastqTools
  • FastqVariant
  • FastqWriter
  • FatCat
  • FatCatAligner
  • FatCatFlexible
  • FatCatParameters
  • FatCatRigid
  • FatCatUserArgumentProcessor
  • FCAlignHelper
  • Feature
  • FeatureDbReferenceInfo
  • FeatureHelper
  • FeatureI
  • FeatureInterface
  • FeatureList
  • FeatureRetriever
  • FeaturesKeyWordInterface
  • FileConvert
  • FileDownloadUtils
  • FileParsingParameters
  • FileProxyDNASequenceCreator
  • FileProxyProteinSequenceCreator
  • FitchParsimony
  • FlatFileCache
  • FontChooser
  • ForesterConstants
  • ForesterConstants.PhylogeneticTreeFormats
  • ForesterUtil
  • ForesterWrapper
  • FourBitSequenceReader
  • FourBitSequenceReader.FourBitArrayWorker
  • FractionalIdentityInProfileScorer
  • FractionalIdentityScorer
  • FractionalSimilarityInProfileScorer
  • FractionalSimilarityScorer
  • FragmentJoiner
  • FragmentPair
  • Frame
  • FuzzyPoint
  • GapArray
  • GapContribution
  • GapPenalty
  • GapPenalty.Type
  • GCStats
  • GenbankHeaderFormatInterface
  • GenbankProxySequenceReader
  • GenbankReader
  • GenbankReaderHelper
  • GenbankSequenceParser
  • GenbankWriter
  • GenbankWriterHelper
  • gene_tree_preprocess
  • GeneChromosomePosition
  • GeneChromosomePositionParser
  • GeneFeatureHelper
  • GeneIDGFF2Reader
  • GeneIDXMLReader
  • GeneMarkGTFReader
  • GeneName
  • GeneNamesParser
  • GeneralMsaParser
  • GeneralTable
  • GenericFastaHeaderFormat
  • GenericFastaHeaderParser
  • GenericGenbankHeaderFormat
  • GenericGenbankHeaderParser
  • GenericInsdcHeaderFormat
  • GeneSequence
  • genome_counts_for_once_appearing_dcs
  • GenomeWideCombinableDomains
  • GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
  • get_distances
  • get_genome_counts_per_char
  • get_loss_nodes
  • get_shared_chars
  • get_subtree_specific_chars
  • GetDistanceMatrix
  • GetRepresentatives
  • GFF3FromUniprotBlastHits
  • GFF3Reader
  • GFF3Writer
  • goac
  • GoId
  • GoNameSpace
  • GoNameSpace.GoNamespaceType
  • GOParser
  • GoRelationship
  • GoRelationship.Type
  • GoSubset
  • GoSubset.Type
  • GoTerm
  • Gotoh
  • GoUtils
  • GoXRef
  • GoXRef.Type
  • GradientMapper
  • GradientPanel
  • GraphComponentOrderDetector
  • GraphComponentRefiner
  • Grid
  • GridCell
  • Group
  • GroupAsa
  • GroupContact
  • GroupContactSet
  • GroupIterator
  • GroupResults
  • GroupToSDF
  • GroupType
  • gsdi
  • GSDI
  • GSDII
  • GSDIR
  • GuanUberbacher
  • GUIAlignmentProgressListener
  • GuideTree
  • GuideTreeNode
  • GUIFarmJobRunnable
  • GuiWrapper
  • Hashcoder
  • HasResultXMLConverter
  • HBond
  • HeaderInfo
  • HelicalRepeatUnit
  • Helix
  • HelixAxisAligner
  • HelixExtender
  • HelixLayers
  • HelixSolver
  • Hello3d
  • HelpDialog
  • HetatomImpl
  • HetatomImpl.PerformanceBehavior
  • HierarchicalClusterer
  • Hit
  • HmmerDomain
  • HmmerRest
  • HmmerResult
  • HmmerScan
  • HmmPfamOutputParser
  • HmmPfamOutputParser.FilterType
  • HmmPfamOutputParser.ReturnType
  • HmmscanPerDomainTableParser
  • HmmscanPerDomainTableParser.FilterType
  • HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
  • HmmscanPerDomainTableParser.ReturnType
  • Hsp
  • HSVColorSpace
  • HTTPConnectionTools
  • IcosahedralSampler
  • Icosahedron
  • Identifier
  • Identifier
  • IdentifierParser
  • IdxComparator
  • IgnoreField
  • IllegalFormatUseException
  • IlluminaFastqReader
  • IlluminaFastqWriter
  • ImageLoader
  • IndexPair
  • InferenceManager
  • InputStreamProvider
  • InsdcLocations
  • InsdcLocations.BondLocation
  • InsdcLocations.GroupLocation
  • InsdcLocations.OneOfLocation
  • InsdcLocations.OrderLocation
  • InsdcParser
  • IntegerOntology
  • IntMatrix
  • IntronSequence
  • InvalidTermException
  • inverted_dcs
  • IOUtils
  • IOUtils.ReaderProcessor
  • IPeptideProperties
  • IProfeatProperties
  • IProfeatProperties.ATTRIBUTE
  • IProfeatProperties.DISTRIBUTION
  • IProfeatProperties.GROUPING
  • IProfeatProperties.TRANSITION
  • Isotope
  • IteratingPhylogenyParser
  • IUPACParser
  • IUPACParser.IUPACTable
  • JAutoSuggest
  • JFatCatClient
  • JMatrixPanel
  • JmolAlignedPositionListener
  • JmolPanel
  • JmolPanel.JmolLoggerAdapter
  • JmolSymmetryScriptGenerator
  • JmolSymmetryScriptGeneratorC1
  • JmolSymmetryScriptGeneratorCn
  • JmolSymmetryScriptGeneratorDn
  • JmolSymmetryScriptGeneratorH
  • JmolSymmetryScriptGeneratorI
  • JmolSymmetryScriptGeneratorO
  • JmolSymmetryScriptGeneratorPointGroup
  • JmolSymmetryScriptGeneratorT
  • JmolTools
  • JmolViewerImpl
  • JNLPProxy
  • JobKillException
  • JoiningSequenceReader
  • JointFragments
  • JournalArticle
  • JPrintPanel
  • Jronn
  • Jronn.Range
  • KaplanMeierFigure
  • KeyedWeakReference
  • KMFigureInfo
  • Ladder
  • LevelOrderTreeIterator
  • LightweightProfile
  • LightweightProfile.StringFormat
  • LinearColorInterpolator
  • LinearColorInterpolator.InterpolationDirection
  • ListStringWrapper
  • LocalPDBDirectory
  • LocalPDBDirectory.FetchBehavior
  • LocalPDBDirectory.ObsoleteBehavior
  • LocalProteinDomainParser
  • LocalScopDatabase
  • Location
  • Location
  • Location.Tools
  • LocationHelper
  • LocIterator
  • LogBranchLengthBasedScoringMethod
  • LogColorMapper
  • LUDecomposition
  • Mafft
  • MainFrame
  • MainFrameApplet
  • MainFrameApplication
  • MainPanel
  • map_lengths
  • Mapping
  • MappingResults
  • MapToStringTransformer
  • Maths
  • Matrix
  • Matrix
  • MatrixAligner
  • MatrixListener
  • mcc
  • MeanModelComparator
  • MeanQuantizer
  • MemoryMonitor
  • MenuCreator
  • MenuCreator
  • MenuCreator.DotPlotListener
  • Messages
  • meta_ontologizer
  • MetaDataInfo
  • MetalBondConsumer
  • MetalBondDistance
  • MetalBondParser
  • MetaOntologizer
  • MmCifBiolAssemblyProvider
  • MMcifConsumer
  • MMCIFFileReader
  • MMCIFFileTools
  • MMcifParser
  • MmCifPDBBiolAssemblyProvider
  • ModelingUtils
  • ModelledSubgroup
  • ModelLoader
  • ModelLoader.Model
  • ModelLoader.Threshold
  • ModificationCategory
  • ModificationCondition
  • ModificationConditionImpl
  • ModificationLinkage
  • ModificationOccurrenceType
  • ModifiedAminoAcidCompoundSet
  • ModifiedCompound
  • ModifiedCompoundImpl
  • ModifiedCompoundXMLConverter
  • MogAngleOutlier
  • MogBondOutlier
  • MolecularSequence
  • MolecularSequence.TYPE
  • MomentsOfInertia
  • MomentsOfInertia.SymmetryClass
  • Msa
  • msa_compactor
  • Msa.MSA_FORMAT
  • MsaCompactor
  • MsaFormatException
  • MsaInferrer
  • MsaMethods
  • MsaProperties
  • MsaRenderer
  • MultipleAlignment
  • MultipleAlignmentCalc
  • MultipleAlignmentCoordManager
  • MultipleAlignmentDisplay
  • MultipleAlignmentEnsemble
  • MultipleAlignmentEnsembleImpl
  • MultipleAlignmentGUI
  • MultipleAlignmentImpl
  • MultipleAlignmentJmol
  • MultipleAlignmentJmolDisplay
  • MultipleAlignmentScorer
  • MultipleAlignmentTools
  • MultipleAlignmentWriter
  • MultipleAlignmentXMLConverter
  • MultipleAlignmentXMLParser
  • MultipleAligPanel
  • MultipleAligPanelMouseMotionListener
  • MultipleMcMain
  • MultipleMcOptimizer
  • MultipleMcParameters
  • MultipleSequenceAlignment
  • MultipleStatusDisplay
  • MultipleStructureAligner
  • MultipleSuperimposer
  • MultipleUris
  • MultiThreadedDBSearch
  • MutableAlignedSequence
  • MutableProfile
  • MutableProfilePair
  • MutableSequencePair
  • Mutator
  • MyAlignmentLoadListener
  • MyDistMaxListener
  • MyExportListener
  • MyJmolStatusListener
  • MyOpenPdbFileListener
  • MySaveFileListener
  • MyTableRowSorter
  • MyValidationEventHandler
  • Name2Count
  • NCBIQBlastAlignmentProperties
  • NCBIQBlastOutputProperties
  • NCBIQBlastService
  • NeedlemanWunsch
  • NeighborJoining
  • NeighborJoiningF
  • NeighborJoiningR
  • neTest
  • NexusBinaryStatesMatrixParser
  • NexusCharactersParser
  • NexusConstants
  • NexusFormatException
  • NexusPhylogeniesParser
  • NHXFormatException
  • NHXParser
  • NHXParser.TAXONOMY_EXTRACTION
  • NHXtags
  • nj
  • NodeData
  • NodeDataField
  • NodeVisualData
  • NodeVisualData.FontType
  • NodeVisualData.NodeFill
  • NodeVisualData.NodeShape
  • NucleotideCompound
  • NucleotideImpl
  • NullOutputStream
  • NumbersAtRiskPanel
  • ObjectFactory
  • obo_tool
  • OboFileEventListener
  • OboFileHandler
  • OboFileParser
  • OboFileParser.SOPair
  • OboParser
  • OBOparser
  • OBOparser.ReturnType
  • Octahedron
  • OntologizerResult
  • OntologizerResult.TYPE
  • Ontology
  • Ontology.Impl
  • OntologyException
  • OntologyFactory
  • OntologyOps
  • OntologyTerm
  • OntologyTerm.Impl
  • OntoTools
  • OperatorResolver
  • OptimalCECPMain
  • OptimalCECPParameters
  • Options
  • Options.CLADOGRAM_TYPE
  • Options.NODE_LABEL_DIRECTION
  • Options.PHYLOGENY_GRAPHICS_TYPE
  • OrderDetector
  • OrderedPair
  • ORonn
  • ORonnModel
  • OutputHitsGFF
  • Pair
  • PairInProfileScorer
  • PairwiseAlignment
  • PairwiseDistanceCalculator
  • PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
  • PairwiseDomainSimilarity
  • PairwiseDomainSimilarityCalculator
  • PairwiseGenomeComparator
  • PairwiseSequenceAligner
  • PairwiseSequenceScorer
  • PaletteIcon
  • ParameterGUI
  • ParseListener
  • ParserBasedPhylogenyFactory
  • ParserException
  • ParserUtils
  • PartitionRefiner
  • PassthroughIdentifier
  • PaupLogParser
  • pccx
  • PDBBioAssemblyParser
  • PDBBioUnitDataProvider
  • PDBCrystallographicInfo
  • PDBDirPanel
  • PDBDomainProvider
  • PDBFileParser
  • PDBFileReader
  • PDBHeader
  • PdbIdLists
  • PdbPair
  • PdbPairsMessage
  • PdbPairXMLConverter
  • PDBParseException
  • PDBRecord
  • PDBServerPanel
  • PDBStatus
  • PDBStatus.Status
  • PDBTemporaryStorageUtils
  • PDBTemporaryStorageUtils.LinkRecord
  • PDBUploadPanel
  • PdbxChemCompDescriptor
  • PdbxChemCompIdentifier
  • PdbxEntityNonPoly
  • PdbxNonPolyScheme
  • PdbxPolySeqScheme
  • PdbxStructAssembly
  • PdbxStructAssemblyGen
  • PdbxStructAssemblyGenXMLContainer
  • PdbxStructAssemblyXMLContainer
  • PdbxStructOperList
  • PdbxStructOperListXMLContainer
  • PDPDistanceMatrix
  • PDPDomain
  • PDPParameters
  • PDPProvider
  • PeptideProperties
  • PeptideProperties.SingleLetterAACode
  • PeptidePropertiesImpl
  • PermutationGenerator
  • PermutationGroup
  • pfam_go
  • pfam2go_extractor
  • pfamacc2go
  • pfamacc2pfamid
  • PfamToGoMapping
  • PfamToGoParser
  • phylo2coloredgraphics
  • phylo2graphics
  • PhylogeneticInferenceOptions
  • PhylogeneticInferrer
  • PhylogeneticInferrer.MSA_PRG
  • PhylogeniesWebserviceClient
  • Phylogeny
  • PhylogenyBranch
  • PhylogenyData
  • PhylogenyDataPhyloXmlParser
  • PhylogenyDataUtil
  • PhylogenyDecorator
  • PhylogenyDecorator.FIELD
  • PhylogenyFactory
  • PhylogenyMethods
  • PhylogenyMethods.DESCENDANT_SORT_PRIORITY
  • PhylogenyMethods.PhylogenyNodeField
  • PhylogenyNode
  • PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE
  • PhylogenyNodeIterator
  • PhylogenyParser
  • PhylogenyParserException
  • PhylogenyWriter
  • PhylogenyWriter.FORMAT
  • PhyloInferenceDialog
  • phylostrip
  • phyloxml_converter
  • PhyloXmlDataFormatException
  • PhyloXmlException
  • PhyloXmlHandler
  • PhyloXmlMapping
  • PhyloXmlNodeWriter
  • PhyloXmlParser
  • PhyloXmlUtil
  • PlainFastaHeaderParser
  • Point
  • Point
  • Point.Resolver
  • PointParser
  • Polygon
  • PolygonParser
  • Polyhedron
  • PolymerType
  • PositionInQueueXMLConverter
  • PostOrderStackObject
  • PostorderTreeIterator
  • PreorderTreeIterator
  • PrettyXMLWriter
  • Prism
  • ProcessPool
  • ProcessRunning
  • ProfeatProperties
  • ProfeatPropertiesImpl
  • Profile
  • Profile.StringFormat
  • ProfilePair
  • ProfileProfileAligner
  • ProfileProfileScorer
  • ProfileView
  • Program
  • Programs
  • PropertiesMap
  • Property
  • Property.AppliesTo
  • PropertyParser
  • Protein
  • ProteinChainExtractor
  • ProteinComplexSignature
  • ProteinCountsBasedPairwiseDomainSimilarityCalculator
  • ProteinDomain
  • ProteinDomainParser
  • ProteinId
  • ProteinModification
  • ProteinModificationIdentifier
  • ProteinModificationImpl
  • ProteinModificationImpl.Builder
  • ProteinModificationRegistry
  • ProteinModificationXmlReader
  • ProteinSequence
  • ProteinSequenceClusterer
  • ProteinSequenceCreator
  • ProxySequenceReader
  • QRDecomposition
  • Qualifier
  • QualitativeColorPalettePanel
  • QualityFeature
  • QuantityFeature
  • QuatSuperpositionScorer
  • QuatSymmetryDetector
  • QuatSymmetryParameters
  • QuatSymmetryResults
  • QuatSymmetryScores
  • QuatSymmetrySolver
  • Queue
  • RandomThing
  • RasmolCommandListener
  • RasmolCommandListener
  • RawBioUnitDataProvider
  • RCSBDescription
  • RCSBDescriptionFactory
  • RCSBLigand
  • RCSBLigands
  • RCSBLigandsFactory
  • RCSBMacromolecule
  • RCSBPolymer
  • RCSBTaxonomy
  • RCSBUpdates
  • ReadUtils
  • RectangularPrism
  • ReducedChemCompProvider
  • Reference
  • ReferenceParser
  • ReferenceSuperimposer
  • Refine
  • RefinerFailedException
  • reinv_count
  • RemoteBioUnitDataProvider
  • RemoteDomainProvider
  • RemoteHmmerScan
  • RemotePairwiseAlignmentOutputProperties
  • RemotePairwiseAlignmentProperties
  • RemotePairwiseAlignmentService
  • RemotePDPProvider
  • RemoteRawBioUnitDataProvider
  • RemoteScopInstallation
  • RemoteTerm
  • RemoteTerm.Impl
  • RenderableDomainArchitecture
  • RenderableMsaSequence
  • RenderablePhylogenyData
  • RenderableVector
  • RenderStyle
  • RepresentativeXMLConverter
  • ResampleableMsa
  • RescoreRefiner
  • ResidualsCoxph
  • ResidualsCoxph.Type
  • ResidueGroup
  • ResidueNumber
  • ResidueRange
  • ResidueRangeAndLength
  • ResidueRenderer
  • ResidueType
  • ResourceManager
  • RestUtil
  • Result
  • ResultFactory
  • ReversedSequenceView
  • rio
  • RIO
  • RIO.REROOTING
  • RIOException
  • RiskInfo
  • RNACompoundSet
  • RNASequence
  • RNASequenceCreator
  • RnaSequenceView
  • RNAToAminoAcidTranslator
  • RonnConstraint
  • RonnConstraint.Threshold
  • Rotation
  • RotationAxis
  • RotationAxisAligner
  • RotationGroup
  • RotationSolver
  • RunnableProcess
  • SandboxStyleStructureProvider
  • SangerFastqReader
  • SangerFastqWriter
  • SankoffParsimony
  • Sarray
  • ScaleableMatrixPanel
  • ScaledSubstitutionMatrix
  • ScanSymmetry
  • SchemaGenerator
  • SCOPAutoSuggestProvider
  • ScopCategory
  • ScopDatabase
  • ScopDescription
  • ScopDescriptions
  • ScopDomain
  • ScopDomains
  • ScopFactory
  • ScopInstallation
  • ScopInstallationInstance
  • ScopIOException
  • ScopMirror
  • ScopNode
  • ScopNodes
  • ScopSelectPanel
  • Scorer
  • ScoresCache
  • ScoringMethodForExternalNode
  • SDI
  • SDIException
  • SDIR
  • SDIutil
  • SDIutil.ALGORITHM
  • SDIutil.TaxonomyComparisonBase
  • SearchIO
  • SecStrucCalc
  • SecStrucElement
  • SecStrucInfo
  • SecStrucState
  • SecStrucTools
  • SecStrucType
  • Segment
  • SegmentComparator
  • Selection
  • SelectionImpl
  • SelectMultiplePanel
  • SelectPDBPanel
  • SeqMisMatch
  • SeqMisMatchImpl
  • SeqRes2AtomAligner
  • Sequence
  • Sequence
  • SequenceAccessionTools
  • SequenceAlignmentCluster
  • SequenceAsStringHelper
  • SequenceComparator
  • SequenceCreatorInterface
  • SequenceDatabaseEntry
  • SequenceDataRetriver
  • SequenceDbWsTools
  • SequenceDisplay
  • SequenceFileProxyLoader
  • SequenceFunctionOrderDetector
  • SequenceFunctionRefiner
  • SequenceHeaderParserInterface
  • SequenceLocation
  • SequenceMixin
  • SequenceMixin.SequenceIterator
  • SequenceMouseListener
  • SequenceOptimizationHints
  • SequenceOptimizationHints.SequenceCollection
  • SequenceOptimizationHints.SequenceUsage
  • SequencePair
  • SequenceParser
  • SequenceParserInterface
  • SequenceProxyView
  • SequenceReader
  • SequenceRelation
  • SequenceRelation.SEQUENCE_RELATION_TYPE
  • SequenceRelationParser
  • SequenceScalePanel
  • SequenceTools
  • SequenceUtil
  • SequenceView
  • SequenceWriter
  • SequenceWriter.SEQ_FORMAT
  • SequentialColorPalettePanel
  • SerializableCache
  • set_comparator
  • shared_chars_in_ext_nodes
  • ShortSegmentRemover
  • ShowPDBIDListener
  • SiftsChainEntry
  • SiftsChainToUniprotMapping
  • SiftsEntity
  • SiftsMappingProvider
  • SiftsResidue
  • SiftsSegment
  • SiftsXMLParser
  • SigEva
  • simple_node_processor
  • SimpleAlignedSequence
  • SimpleDomain
  • SimpleGapPenalty
  • SimpleLocation
  • SimpleMMcifConsumer
  • SimpleMMcifParser
  • SimplePoint
  • SimpleProfile
  • SimpleProfilePair
  • SimpleProfileProfileAligner
  • SimpleSequencePair
  • SimpleSubstitutionMatrix
  • SingleCompoundSequenceReader
  • SingleLinkageClusterer
  • SingularValueDecomposition
  • Site
  • Site
  • SmallAnnotation
  • SmallMap
  • SmithWaterman
  • SmithWaterman3Daligner
  • SmithWaterman3DParameters
  • SmithWatermanUserArgumentProcessor
  • SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
  • SoftHashMap
  • SolexaFastqReader
  • SolexaFastqWriter
  • SpaceGroup
  • SpaceGroupMapElements
  • SpaceGroupMapRoot
  • SparseSquareMatrix
  • SparseVector
  • Species
  • SphereSampler
  • SplitFasta
  • SqrtColorMapper
  • SSBondImpl
  • Sset
  • StainType
  • StandardAminoAcid
  • StandardRescoreRefiner
  • StartCodonSequence
  • StartupParameters
  • StaticMemberPlaceHolder
  • StatusDisplay
  • StdArrayIO
  • StockholmFileAnnotation
  • StockholmFileAnnotation.StockholmFileAnnotationReference
  • StockholmFileParser
  • StockholmStructure
  • StockholmStructure.DatabaseReference
  • StopCodonSequence
  • Strand
  • StrataInfo
  • StrCompAlignment
  • StreamListener
  • StringInt
  • StringInt.DescendingIntComparator
  • StringManipulationHelper
  • StringProxySequenceReader
  • StrucAligParameters
  • Struct
  • StructAsym
  • StructConn
  • StructKeywords
  • StructNcsOper
  • StructRef
  • StructRefSeq
  • StructRefSeqDif
  • StructSite
  • StructSiteGen
  • Structure
  • StructureAlignment
  • StructureAlignmentDisplay
  • StructureAlignmentFactory
  • StructureAlignmentJmol
  • StructureAlignmentOptimizer
  • StructureAtom
  • StructureAtomLinkage
  • StructureAtomXMLConverter
  • StructureException
  • StructureGroup
  • StructureGroupXMLConverter
  • StructureIdentifier
  • StructureImpl
  • StructureInterface
  • StructureInterfaceCluster
  • StructureInterfaceList
  • StructureIO
  • StructureIO.StructureFiletype
  • StructureIOFile
  • StructureLoaderThread
  • StructureName
  • StructureName.Source
  • StructurePairAligner
  • StructurePairSelector
  • StructureProvider
  • StructureSequenceMatcher
  • StructureTools
  • StructureUtil
  • StructureViewer
  • SubstitutionMatrix
  • SubstitutionMatrixHelper
  • SubstitutionMatrixScorer
  • SubstructureIdentifier
  • subtree_feature_count
  • SubunitGraph
  • Subunits
  • SuperPosition
  • SuperPositionQCP
  • support_statistics
  • support_transfer
  • SupportCount
  • surfacing
  • SurfacingConstants
  • SurfacingUtil
  • SurvFitInfo
  • SurvFitKM
  • SurvFitKM.ConfLower
  • SurvFitKM.ConfType
  • SurvFitKM.Error
  • SurvFitKM.Method
  • SurvivalInfo
  • SurvivalInfoComparator
  • SurvivalInfoHelper
  • SurvivalInfoIndex
  • SurvivalInfoValueComparator
  • SVDSuperimposer
  • SymbolTable
  • SymmClash
  • SymmetricalDistanceMatrixParser
  • SymmetricalDistanceMatrixParser.InputMatrixType
  • Symmetry
  • SymmetryAxes
  • SymmetryAxes.Axis
  • SymmetryCalc
  • SymmetryDisplay
  • SymmetryGui
  • SymmetryListener
  • SymmetryRefiner
  • SymmetryTools
  • SymmOptimizer
  • SymoplibParser
  • SynchronizedOutFile
  • Synonym
  • SystematicSolver
  • SystemCommandExecutor
  • SystemInfo
  • TabDelimParser
  • Table
  • Table.CaseInsensitiveTriplet
  • Table.Codon
  • table2fasta
  • tax_code_cleaner
  • Taxonomy
  • TaxonomyColors
  • TaxonomyDataManager
  • TaxonomyID
  • TaxonomyParser
  • TaxonomyUtil
  • Term
  • Term.Impl
  • Test
  • Test
  • Test
  • TestGo
  • TestGSDI
  • TestPccx
  • TestPhylogenyReconstruction
  • TestRIO
  • TestSurfacing
  • Tetrahedron
  • TextFeature
  • Time
  • Timer
  • TolParser
  • TolXmlHandler
  • TolXmlMapping
  • TranscriptionEngine
  • TranscriptionEngine.Builder
  • TranscriptSequence
  • TransfAlgebraicAdapter
  • TransformType
  • TranslationException
  • TreeColorSet
  • TreeConstructor
  • TreeConstructorType
  • TreeFontSet
  • TreeMapSpaceGroupWrapper
  • TreePanel
  • TreePanelUtil
  • TreeSetStringWrapper
  • TreeSplitMatrix
  • TreeType
  • Triple
  • Triple.Impl
  • TwoBitParser
  • TwoBitSequenceReader
  • TwoBitSequenceReader.TwoBitArrayWorker
  • TxSearch
  • TxSearch.RANKS
  • TxSearch.TAX_NAME_CLASS
  • TxSearch.TAX_RANK
  • UncompressInputStream
  • UniProtEntry
  • UniprotProxySequenceReader
  • UniProtTaxonomy
  • UniprotToFasta
  • UniqueSequenceList
  • UnitCellBoundingBox
  • Uri
  • UriParser
  • URLIdentifier
  • UrlTreeReader
  • UserArgumentProcessor
  • UserConfiguration
  • Utils
  • Variable
  • Variable.Impl
  • WabiTools
  • WaldTest
  • WaldTestInfo
  • WeakValueHashMap
  • WebservicesManager
  • WebservicesManager.WsPhylogenyFormat
  • WebserviceUtil
  • WebStartDBSearch
  • WebStartDBSearchResults
  • WebStartMain
  • wiki_examples
  • WindowedSequence
  • WindowsUtils
  • WorkSheet
  • WrapLayout
  • WwPDBValidationInformation
  • XmlElement
  • XMLHelper
  • XMLUtil
  • XMLWriter
  • ZipChemCompProvider