All Classes
AAindexFactory
AAIndexFileParser
AAIndexProvider
ABITrace
ABITracerCompoundSet
AboutDialog
AbstractAlignmentJmol
AbstractAnnotation
AbstractBean
AbstractCompound
AbstractCompoundSet
AbstractCompoundTranslator
AbstractFeature
AbstractLocation
AbstractMatrixAligner
AbstractNucleotideCompoundSet
AbstractPairwiseSequenceAligner
AbstractProfileProfileAligner
AbstractReference
AbstractScorer
AbstractScoresCache
AbstractSequence
AbstractSequence.AnnotationType
AbstractStructureAlignment
AbstractTerm
AbstractUserArgumentProcessor
AccesionedLocation
Accessioned
AccessionID
AFP
AFPAlignmentDisplay
AFPCalculator
AFPChain
AFPChainCoordManager
AFPChainer
AFPChainFlipper
AFPChainScorer
AfpChainWriter
AFPChainXMLConverter
AFPChainXMLParser
AFPFromFasta
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
AlignmentGuiDemo
AlignmentPositionListener
AlignmentProgressListener
AlignmentProgressListener
AlignmentResult
Alignments
Alignments.PairInProfileScorerType
Alignments.PairwiseSequenceAlignerType
Alignments.PairwiseSequenceScorerType
Alignments.ProfileProfileAlignerType
Alignments.RefinerType
AlignmentTextPanel
AlignmentTools
AlignmentTools.IdentityMap
AligNPE
AlignUtils
AligPanel
AligPanelMouseMotionListener
AligUIManager
AllChemCompProvider
AlreadyExistsException
AltAligComparator
AlternativeAlignment
AlternativeAlignmentFrame
AmbiguityDNACompoundSet
AmbiguityDNARNAHybridCompoundSet
AmbiguityRNACompoundSet
AminoAcid
AminoAcidComposition
AminoAcidCompositionTable
AminoAcidCompound
AminoAcidCompoundSet
AminoAcidImpl
AminoAcidProperties
AnchoredPairwiseSequenceAligner
AngleOrderDetectorPlus
AngleOutlier
Annotatable
Annotation
App
App
ArrayListProxySequenceReader
ArrayListSequenceReader
AsaCalculator
AssertionFailure
AssignmentXMLSerializer
Astral
Astral.AstralSet
Atom
AtomCache
AtomContact
AtomContactSet
AtomIdentifier
AtomImpl
AtomInfo
AtomInfoParser
AtomIterator
AtomPositionMap
AtomPositionMap.GroupMatcher
AtomSite
AtomSites
AuditAuthor
AugmentedResidueRange
Author
AutoSuggestProvider
AxisAligner
BasePairParameters
BasicSequence
BcifFileReader
BerkeleyScopInstallation
BetaBridge
BioAssemblyIdentifier
BioAssemblyInfo
BioAssemblyTools
BioJavaAADemo
BiojavaJmol
BioJavaStructureAlignment
BiologicalAssemblyBuilder
BiologicalAssemblyTransformation
BitSequenceReader
BitSequenceReader.BitArrayWorker
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
BoundingBox
BravaisLattice
BridgeType
BrowserOpener
BufferedReaderBytesRead
C2RotationSolver
CachedRemoteScopInstallation
CAConverter
Calc
CalcPoint
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
ChainImpl
ChainSignature
ChangeValue
ChargeAdder
ChemComp
ChemCompAtom
ChemCompBond
ChemCompConsumer
ChemCompDescriptor
ChemCompDistribution
ChemCompGroupFactory
ChemCompProvider
ChemCompTools
ChemicalComponentDictionary
ChiSq
Cholesky2
CholeskyDecomposition
ChooseDirAction
ChromosomeMappingTools
ChromosomeSequence
ChromPos
Chsolve2
CifFileConverter
CifFileReader
CIFLabel
Clash
ClasspathResource
ClinicalMetaDataOutcome
CliTools
ClusterAltAligs
ClusterDomains
CodonCompound
CollectionTools
ColorConverter
ColorInterpolator
ColorUtils
CommandPrompt
CommandPrompt.PropertyName
CompactCharSequence
Comparison
ComplementCompound
ComplementSequenceView
Component
ComponentXMLConverter
Compound
CompoundNotFoundException
CompoundSet
CompoundTranslator
ConcurrencyTools
ConfigPDBInstallPanel
ConfigStrucAligParams
ConfigurationException
ConfigXMLHandler
Constraints
Contact
ContinuousColorMapper
ContinuousColorMapperTransform
Convert2Charge
Convert2Hydrophobicity
Convert2NormalizedVanDerWaalsVolume
Convert2Polarity
Convert2Polarizability
Convert2SecondaryStructure
Convert2SolventAccessibility
Convertor
CookBook
CookbookMSA
CoordManager
CoreSuperimposer
CountProgressListener
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
DBRef
DBReferenceInfo
DBResultTable
DBSearchGUI
DefaultAAIndexProvider
DefaultAutoSuggestProvider
DefaultMatrixMapper
DefaultOps
DemoAlignmentFromFasta
DemoAlignProteins
DemoAsa
DemoAtomCache
DemoBerkeleyScop
DemoBioAssemblies
DemoCATH
DemoCE
DemoCeSymm
DemoChangeChemCompProvider
DemoCommandLineStartup
DemoContacts
DemoCrystalInterfaces
DemoDistanceTree
DemoDomainsplit
DemoFATCAT
DemoLoadSecStruc
DemoLoadStructure
DemoLoadSubstMax
DemoMMCIFReader
DemoMmcifToPdbConverter
DemoMmtfReader
DemoMmtfWriter
DemoMultipleMC
DemoNWALignment
DemoQsAlign
DemoQuatSymmetryJmol
DemoRotationAxis
DemoSCOP
DemoSecStrucCalc
DemoShowBiolAssembly
DemoShowCATHDomain
DemoShowLargeAssembly
DemoShowValidationResults
DemoSixFrameTranslation
DemoStructureFromFasta
DemoSW3DAligner
DemoSymmetry
DiscreteQuantizerInterface
DisplayAFP
DistanceBox
DistanceMatrixCalculator
DistanceTreeEvaluator
DNACompoundSet
DNASequence
DNASequence.DNAType
DNASequenceCreator
DNAToRNATranslator
Domain
DomainProvider
DomainProviderFactory
DotPlotPanel
DownloadChemCompProvider
DSSPParser
EcodDatabase
EcodDomain
EcodFactory
EcodInstallation
EcodInstallation.EcodParser
Edit
Edit.AbstractEdit
Edit.Delete
Edit.Insert
Edit.Substitute
EigenvalueDecomposition
Element
Element
ElementTable
ElementType
EmblId
EmblReader
EmblRecord
EmblReference
Entity
EntityFinder
EntityInfo
EntityPoly
EntityPolySeq
EntitySrcGen
EntitySrcNat
EntitySrcSyn
EntityType
Entry
Equals
ExonComparator
ExonSequence
ExperimentalTechnique
ExpressionFigure
Exptl
FarmJob
FarmJobParameters
FarmJobRunnable
FastaAFPChainConverter
FastaGeneWriter
FastaHeaderFormatInterface
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
FileProxyRNASequenceCreator
FlatFileCache
ForesterWrapper
FourBitSequenceReader
FourBitSequenceReader.FourBitArrayWorker
FractionalIdentityInProfileScorer
FractionalIdentityScorer
FractionalSimilarityInProfileScorer
FractionalSimilarityScorer
FragmentJoiner
FragmentPair
Frame
FuzzyPoint
GapArray
GapPenalty
GapPenalty.Type
GCStats
GenbankHeaderFormatInterface
GenbankProxySequenceReader
GenbankReader
GenbankReaderHelper
GenbankReference
GenbankSequenceParser
GenbankWriter
GenbankWriterHelper
GeneChromosomePosition
GeneChromosomePositionParser
GeneFeatureHelper
GeneIDGFF2Reader
GeneIDXMLReader
GeneMarkGTFReader
GeneName
GeneNamesParser
GenericFastaHeaderFormat
GenericFastaHeaderParser
GenericGenbankHeaderFormat
GenericGenbankHeaderParser
GenericInsdcHeaderFormat
GeneSequence
GetDistanceMatrix
GetRepresentatives
GFF3FromUniprotBlastHits
GFF3Reader
GFF3Writer
GOParser
Gotoh
GradientMapper
GradientPanel
GraphComponentOrderDetector
GraphComponentRefiner
Grid
GridCell
Group
GroupAsa
GroupContact
GroupContactSet
GroupIterator
GroupResults
GroupToSDF
GroupType
GuanUberbacher
GUIAlignmentProgressListener
GuideTree
GuideTreeNode
GUIFarmJobRunnable
GuiWrapper
Hashcoder
HasResultXMLConverter
HBond
HeaderInfo
HelicalRepeatUnit
Helix
HelixAxisAligner
HelixExtender
HelixLayers
HelixSolver
HelpDialog
HetatomImpl
HetatomImpl.PerformanceBehavior
HierarchicalClusterer
Hit
HmmerDemo
HmmerDomain
HmmerResult
HmmerScan
Hsp
HSVColorSpace
IcosahedralSampler
Icosahedron
IdxComparator
IgnoreField
IlluminaFastqReader
IlluminaFastqWriter
IndexPair
InputStreamProvider
InsdcLocations
InsdcLocations.BondLocation
InsdcLocations.GroupLocation
InsdcLocations.OneOfLocation
InsdcLocations.OrderLocation
InsdcParser
IntegerOntology
IntronSequence
InvalidTermException
IOUtils
IOUtils.ReaderProcessor
IPeptideProperties
IProfeatProperties
IProfeatProperties.ATTRIBUTE
IProfeatProperties.DISTRIBUTION
IProfeatProperties.GROUPING
IProfeatProperties.TRANSITION
Isotope
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
LightweightProfile
LightweightProfile.StringFormat
LinearColorInterpolator
LinearColorInterpolator.InterpolationDirection
ListStringWrapper
LocalPDBDirectory
LocalPDBDirectory.FetchBehavior
LocalPDBDirectory.ObsoleteBehavior
LocalProteinDomainParser
LocalScopDatabase
Location
Location
Location.Tools
LocationHelper
LocIterator
LogColorMapper
LUDecomposition
MapToStringTransformer
Maths
Matrices
Matrix
Matrix
MatrixAligner
MatrixListener
MeanModelComparator
MeanQuantizer
MemoryMonitor
MenuCreator
MenuCreator
MenuCreator.DotPlotListener
Messages
MetaDataInfo
MetalBondConsumer
MetalBondDistance
MetalBondParser
MismatchedBasePairParameters
MMcifConsumer
MMCIFFileReader
MMCIFFileTools
MMcifParser
MmtfActions
MMTFFileReader
MmtfStructureReader
MmtfStructureWriter
MmtfSummaryDataBean
MmtfUtils
Model
ModelledSubgroup
ModelLoader
ModelLoader.Model
ModelLoader.Threshold
ModificationCategory
ModificationCondition
ModificationConditionImpl
ModificationLinkage
ModificationOccurrenceType
ModifiedAminoAcidCompoundSet
ModifiedCompound
ModifiedCompoundImpl
ModifiedCompoundXMLConverter
MogAngleOutlier
MogBondOutlier
MomentsOfInertia
MomentsOfInertia.SymmetryClass
MultipleAlignment
MultipleAlignmentCalc
MultipleAlignmentCoordManager
MultipleAlignmentDisplay
MultipleAlignmentEnsemble
MultipleAlignmentEnsembleImpl
MultipleAlignmentGUI
MultipleAlignmentImpl
MultipleAlignmentJmol
MultipleAlignmentJmolDisplay
MultipleAlignmentScorer
MultipleAlignmentTools
MultipleAlignmentWriter
MultipleAlignmentXMLConverter
MultipleAlignmentXMLParser
MultipleAligPanel
MultipleAligPanelMouseMotionListener
MultipleMcMain
MultipleMcOptimizer
MultipleMcParameters
MultipleSequenceAlignment
MultipleStatusDisplay
MultipleStructureAligner
MultipleSuperimposer
MultiThreadedDBSearch
MutableAlignedSequence
MutableProfile
MutableProfilePair
MutableSequencePair
Mutator
MyAlignmentLoadListener
MyDistMaxListener
MyExportListener
MyJmolStatusListener
MyOpenPdbFileListener
MySaveFileListener
MyTableRowSorter
MyValidationEventHandler
Name2Count
NCBIQBlastAlignmentProperties
NCBIQBlastOutputProperties
NCBIQBlastService
NCBIQBlastServiceDemo
NeedlemanWunsch
NucleotideCompound
NucleotideImpl
NullOutputStream
NumbersAtRiskPanel
ObjectFactory
OboFileEventListener
OboFileHandler
OboFileParser
OboFileParser.SOPair
OboParser
Octahedron
Ontology
Ontology.Impl
OntologyException
OntologyFactory
OntologyOps
OntologyTerm
OntologyTerm.Impl
OntoTools
OperatorResolver
OptimalCECPMain
OptimalCECPParameters
OrderDetector
OrderedPair
ORonn
ORonnModel
OutputHitsGFF
Pair
PairInProfileScorer
PairwiseSequenceAligner
PairwiseSequenceScorer
ParameterGUI
ParseFastaFileDemo
ParseGO
ParseListener
ParserException
PartitionRefiner
PassthroughIdentifier
PDBBioAssemblyParser
PDBCrystallographicInfo
PDBDirPanel
PDBDomainProvider
PDBFileParser
PDBFileReader
PDBHeader
PdbIdLists
PdbPair
PdbPairsMessage
PdbPairXMLConverter
PDBParseException
PDBRecord
PDBServerPanel
PDBStatus
PDBStatus.Status
PDBTemporaryStorageUtils
PDBTemporaryStorageUtils.LinkRecord
PDBUploadPanel
PdbxAuditRevisionHistory
PdbxChemCompDescriptor
PdbxChemCompIdentifier
PdbxDatabaseStatus
PdbxEntityNonPoly
PdbxNonPolyScheme
PdbxPolySeqScheme
PdbxStructAssembly
PdbxStructAssemblyGen
PdbxStructAssemblyGenXMLContainer
PdbxStructAssemblyXMLContainer
PdbxStructOperList
PdbxStructOperListXMLContainer
PDPDistanceMatrix
PDPDomain
PDPParameters
PDPProvider
PeptideProperties
PeptideProperties.SingleLetterAACode
PeptidePropertiesImpl
PermutationGenerator
PermutationGroup
PlainFastaHeaderParser
Point
Point.Resolver
Polyhedron
PolymerType
PositionInQueueXMLConverter
PowerSet
PredictDisorder
PrettyXMLWriter
Prism
ProfeatProperties
ProfeatPropertiesImpl
Profile
Profile.StringFormat
ProfilePair
ProfileProfileAligner
ProfileProfileScorer
ProfileView
Program
Programs
ProteinComplexSignature
ProteinMappingTools
ProteinModification
ProteinModificationIdentifier
ProteinModificationImpl
ProteinModificationImpl.Builder
ProteinModificationRegistry
ProteinModificationXmlReader
ProteinSequence
ProteinSequenceCreator
ProxySequenceReader
QRDecomposition
QsAlign
QsAlignParameters
QsAlignResult
QsRelation
Qualifier
QualityFeature
QuantityFeature
QuatSuperpositionScorer
QuatSymmetryDetector
QuatSymmetryParameters
QuatSymmetryResults
QuatSymmetryScores
QuatSymmetrySolver
QuatSymmetrySubunits
RasmolCommandListener
RCSBDescription
RCSBDescriptionFactory
RCSBLigand
RCSBLigands
RCSBLigandsFactory
RCSBMacromolecule
RCSBPolymer
RCSBTaxonomy
RCSBUpdates
ReadUtils
RectangularPrism
ReducedChemCompProvider
ReferenceInterface
ReferenceSuperimposer
Refine
RefinerFailedException
RemoteDomainProvider
RemoteHmmerScan
RemotePairwiseAlignmentOutputProperties
RemotePairwiseAlignmentProperties
RemotePairwiseAlignmentService
RemotePDPProvider
RemoteScopInstallation
RemoteTerm
RemoteTerm.Impl
RenderStyle
RepresentativeXMLConverter
RescoreRefiner
ResidualsCoxph
ResidualsCoxph.Type
ResidueGroup
ResidueNumber
ResidueRange
ResidueRangeAndLength
ResidueType
ResourceManager
Result
ResultFactory
ReversedSequenceView
RiskInfo
RNACompoundSet
RNASequence
RNASequenceCreator
RnaSequenceView
RNAToAminoAcidTranslator
RonnConstraint
RonnConstraint.Threshold
Rotation
RotationAxis
RotationAxisAligner
RotationGroup
RotationSolver
SandboxStyleStructureProvider
SangerFastqReader
SangerFastqWriter
ScaleableMatrixPanel
ScaledSubstitutionMatrix
SchemaGenerator
SCOPAutoSuggestProvider
ScopCategory
ScopDatabase
ScopDescription
ScopDescriptions
ScopDomain
ScopDomains
ScopFactory
ScopInstallation
ScopInstallationInstance
ScopIOException
ScopMirror
ScopNode
ScopNodes
ScopSelectPanel
Scorer
ScoresCache
SearchIO
SecStrucCalc
SecStrucElement
SecStrucInfo
SecStrucState
SecStrucTools
SecStrucType
Segment
SegmentComparator
Selection
SelectionImpl
SelectMultiplePanel
SelectPDBPanel
SeqMisMatch
SeqMisMatchImpl
SeqRes2AtomAligner
Sequence
SequenceAsStringHelper
SequenceComparator
SequenceCreatorInterface
SequenceDisplay
SequenceFileProxyLoader
SequenceFunctionOrderDetector
SequenceFunctionRefiner
SequenceHeaderParserInterface
SequenceLocation
SequenceMixin
SequenceMixin.SequenceIterator
SequenceMouseListener
SequenceOptimizationHints
SequenceOptimizationHints.SequenceCollection
SequenceOptimizationHints.SequenceUsage
SequencePair
SequenceParserInterface
SequenceProxyView
SequenceReader
SequenceScalePanel
SequenceTools
SequenceUtil
SequenceView
SerializableCache
ShortSegmentRemover
ShowPDBIDListener
ShowStructureInJmol
SiftsChainEntry
SiftsChainToUniprotMapping
SiftsEntity
SiftsMappingProvider
SiftsResidue
SiftsSegment
SiftsXMLParser
SigEva
SimpleAlignedSequence
SimpleGapPenalty
SimpleLocation
SimpleMMcifConsumer
SimpleMMcifParser
SimplePoint
SimpleProfile
SimpleProfilePair
SimpleProfileProfileAligner
SimpleSequencePair
SimpleSubstitutionMatrix
SimpleTwoBitFileProvider
SingleCompoundSequenceReader
SingleLinkageClusterer
SingularValueDecomposition
Site
Site
SmallAnnotation
SmallMap
SmithWaterman
SmithWaterman3Daligner
SmithWaterman3DParameters
SmithWatermanUserArgumentProcessor
SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
SoftHashMap
SolexaFastqReader
SolexaFastqWriter
SpaceGroup
SpaceGroupMapElements
SpaceGroupMapRoot
SparseSquareMatrix
SparseVector
SphereSampler
SplitFasta
SqrtColorMapper
SSBondImpl
StainType
StandardAminoAcid
StandardRescoreRefiner
StartCodonSequence
StartupParameters
StaticMemberPlaceHolder
StatusDisplay
StdArrayIO
StockholmFileAnnotation
StockholmFileAnnotation.StockholmFileAnnotationReference
StockholmFileParser
StockholmStructure
StockholmStructure.DatabaseReference
Stoichiometry
Stoichiometry.StringOverflowStrategy
StopCodonSequence
Strand
StrataInfo
StrCompAlignment
StreamListener
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
Subunit
SubunitCluster
SubunitClusterer
SubunitClustererMethod
SubunitClustererParameters
SubunitExtractor
SuperPosition
SuperPositionAbstract
SuperPositionQCP
SuperPositionQuat
SuperPositions
SuperPositionSVD
SurvFitInfo
SurvFitKM
SurvFitKM.ConfLower
SurvFitKM.ConfType
SurvFitKM.Error
SurvFitKM.Method
SurvivalInfo
SurvivalInfoComparator
SurvivalInfoHelper
SurvivalInfoIndex
SurvivalInfoValueComparator
SymbolTable
SymmClash
Symmetry
SymmetryAxes
SymmetryAxes.Axis
SymmetryCalc
SymmetryDisplay
SymmetryGui
SymmetryListener
SymmetryPerceptionMethod
SymmetryRefiner
SymmetryTools
SymmOptimizer
SymoplibParser
SynchronizedOutFile
Synonym
SystematicSolver
SystemInfo
TabDelimParser
Table
Table.CaseInsensitiveTriplet
Table.Codon
TaxonomyID
Term
Term.Impl
TertiaryBasePairParameters
TestDNANeedlemanWunsch
Tetrahedron
TextFeature
Timer
TranscriptionEngine
TranscriptionEngine.Builder
TranscriptSequence
TransfAlgebraicAdapter
TransformType
TranslationException
TreeConstructor
TreeConstructorType
TreeMapSpaceGroupWrapper
TreeSetStringWrapper
TreeType
Triple
Triple.Impl
TwoBitFacade
TwoBitParser
TwoBitSequenceReader
TwoBitSequenceReader.TwoBitArrayWorker
UncompressInputStream
UniprotProxySequenceReader
UniprotToFasta
UnitCellBoundingBox
UnitQuaternions
URLConnectionTools
URLIdentifier
UserArgumentProcessor
UserConfiguration
Utils
Variable
Variable.Impl
WaldTest
WaldTestInfo
WeakValueHashMap
WebStartClientDemo
WebStartDBSearch
WebStartDBSearchResults
WebStartMain
WindowedSequence
WorkSheet
WrapLayout
WwPDBValidationInformation
XMLHelper
XMLUtil
XMLWriter
ZipChemCompProvider