- 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