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
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
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.MSA_FORMAT
msa_compactor
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
pfam2go_extractor
pfam_go
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
WwPDBValidationInformation
XmlElement
XMLHelper
XMLUtil
XMLWriter
ZipChemCompProvider