All Classes
AAindexFactory
AAIndexFileParser
AAIndexProvider
AboutDialog
AbstractBean
AbstractCompound
AbstractCompoundSet
AbstractCompoundTranslator
AbstractFeature
AbstractLocation
AbstractMatrixAligner
AbstractNucleotideCompoundSet
AbstractPairwiseSequenceAligner
AbstractProfileProfileAligner
AbstractScorer
AbstractSequence
AbstractSequence.AnnotationType
AbstractStructureAlignment
AbstractUserArgumentProcessor
AccesionedLocation
Accessioned
AccessionID
AFP
AFPAlignmentDisplay
AFPCalculator
AFPChain
AFPChainCoordManager
AFPChainer
AFPChainFlipper
AFPChainScorer
AfpChainWriter
AFPChainXMLConverter
AFPChainXMLParser
AFPOptimizer
AFPPostProcessor
AFPTwister
AligMatEl
Alignable
AlignedPosition
AlignedSequence
AlignedSequence.Step
Aligner
AlignerHelper
AlignerHelper.Cut
AlignerHelper.Last
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
AlignTools
AligPanel
AligPanelMouseMotionListener
AligUIManager
AllChemCompProvider
AltAligComparator
AlternativeAlignment
AlternativeAlignmentFrame
AmbiguityDNACompoundSet
AmbiguityRNACompoundSet
AminoAcid
AminoAcidComposition
AminoAcidCompositionTable
AminoAcidCompound
AminoAcidCompoundSet
AminoAcidImpl
AnchoredPairwiseSequenceAligner
App
App
ArrayListProxySequenceReader
ArrayListSequenceReader
AssignmentXMLSerializer
Atom
AtomCache
AtomImpl
AtomInfo
AtomInfoParser
AtomIterator
AtomSite
AuditAuthor
Author
AutoSuggestProvider
BasicSequence
BigSqrt
BiojavaJmol
BioJavaStructureAlignment
BitSequenceReader
BitSequenceReader.BitArrayWorker
BlastAlignmentParameterEnum
BlastHomologyHits
BlastJob
BlastMatrixEnum
BlastOutputAlignmentFormatEnum
BlastOutputFormatEnum
BlastOutputParameterEnum
BlastProgramEnum
BlastXMLQuery
Bond
BondType
BrowserOpener
BufferedReaderBytesRead
CachedRemoteScopInstallation
CacheFactory
CAConverter
Calc
CallablePairwiseSequenceAligner
CallablePairwiseSequenceScorer
CallableProfileProfileAligner
CallableStructureAlignment
CaseFreeAminoAcidCompoundSet
CaseInsensitiveCompound
CDSComparator
CDSSequence
CECalculator
CeCalculatorEnhanced
CeCPMain
CeCPMain.CPRange
CeMain
CeParameters
CeSideChainMain
CeSideChainUserArgumentProcessor
CeUserArgumentProcessor
Chain
ChainImpl
CheckTreeAccuracy
ChemComp
ChemCompConsumer
ChemCompDescriptor
ChemCompDistribution
ChemCompGroupFactory
ChemCompProvider
ChemCompTools
ChemicalComponentDictionary
CholeskyDecomposition
ChooseDirAction
ChromosomeSequence
ClasspathResource
CliTools
ClusterAltAligs
ClusterDomains
CodonCompound
CollectionTools
ColorInterpolator
ColorUtils
CommandPrompt
CommandPrompt.PropertyName
Comparison
ComplementCompound
ComplementSequenceView
Component
ComponentXMLConverter
Compound
Compound
CompoundNotFoundError
CompoundSet
CompoundTranslator
ConcurrencyTools
ConfigPDBInstallPanel
ConfigStrucAligParams
ConfigurationException
ConfigXMLHandler
Constraints
ContinuousColorMapper
ContinuousColorMapperTransform
Convert2Charge
Convert2Hydrophobicity
Convert2NormalizedVanDerWaalsVolume
Convert2Polarity
Convert2Polarizability
Convert2SecondaryStructure
Convert2SolventAccessibility
Convertor
CookBook
CoordManager
CountProgressListener
CRC64Checksum
Cut
CutDomain
CutSites
CutValues
DatabasePDBremark
DatabasePDBrev
DatabaseReferenceInterface
DataSource
DBRef
DBReferenceInfo
DBResultTable
DBSearchGUI
DefaultAAIndexProvider
DefaultAutoSuggestProvider
DefaultMatrixMapper
DemoAtomCache
DemoCE
DemoChangeChemCompProvider
DemoCommandLineStartup
DemoDomainsplit
DemoFATCAT
DemoLoadStructure
DemoMMCIFReader
DemoSCOP
DemoSW3DAligner
DisplayAFP
DistEn
DNACompoundSet
DNASequence
DNASequence.DNAType
DNASequenceCreator
DNAToRNATranslator
Domain
DomainProvider
DomainProviderFactory
DotPlotPanel
DownloadChemCompProvider
Edit
Edit.AbstractEdit
Edit.Delete
Edit.Insert
Edit.Substitute
EigenvalueDecomposition
Element
Element
ElementTable
ElementType
Entity
EntityPolySeq
Equals
ExonComparator
ExonSequence
Exptl
FarmJob
FarmJobParameters
FarmJobRunnable
FastaGeneWriter
FastaHeaderFormatInterface
FastaHeaderParserInterface
FastaReader
FastaReaderHelper
FastaSequence
FastaSequenceParser
FastaWriter
FastaWriterHelper
Fastq
FastqBuilder
FastqReader
FastqTools
FastqVariant
FastqWriter
FatCat
FatCatAligner
FatCatFlexible
FatCatParameters
FatCatRigid
FatCatUserArgumentProcessor
FCAlignHelper
Feature
FeatureHelper
FeatureI
FeatureInterface
FeatureList
FeaturesKeyWordInterface
FileAccessError
FileConvert
FileDownloadUtils
FileParsingParameters
FileProxyDNASequenceCreator
FileProxyProteinSequenceCreator
FlatFileCache
FlatFileInstallation
FourBitSequenceReader
FourBitSequenceReader.FourBitArrayWorker
FractionalIdentityInProfileScorer
FractionalIdentityScorer
FractionalSimilarityInProfileScorer
FractionalSimilarityScorer
FragmentJoiner
FragmentPair
Frame
FuzzyPoint
GapArray
GapPenalty
GapPenalty.Type
GCStats
GeneFeatureHelper
GeneIDGFF2Reader
GeneIDXMLReader
GeneMarkGTFReader
GenericFastaHeaderFormat
GenericFastaHeaderParser
GeneSequence
GetDistanceMatrix
GFF3FromUniprotBlastHits
GFF3Reader
GFF3Writer
Gotoh
GradientMapper
GradientPanel
Group
GroupIterator
GroupType
GuanUberbacher
GUIAlignmentProgressListener
GuideTree
GuideTreeNode
GUIFarmJobRunnable
GuiWrapper
Hashcoder
HasResultXMLConverter
HBond
HeaderParseException
HelpDialog
HetatomImpl
HierarchicalClusterer
HmmerDemo
HmmerDomain
HmmerResult
HmmerScan
HSVColorSpace
HTTPConnectionTools
IdxComparator
IlluminaFastqReader
IlluminaFastqWriter
IndexPair
InputStreamProvider
InsdcLocations
InsdcLocations.BondLocation
InsdcLocations.GroupLocation
InsdcLocations.OneOfLocation
InsdcLocations.OrderLocation
InsdcParser
IntronSequence
IOUtils
IOUtils.ReaderProcessor
IPeptideProperties
IProfeatProperties
IProfeatProperties.ATTRIBUTE
IProfeatProperties.DISTRIBUTION
IProfeatProperties.GROUPING
IProfeatProperties.TRANSITION
Isotope
IUPACParser
IUPACParser.IUPACTable
JAutoSuggest
JFatCatClient
JMatrixPanel
JmolAlignedPositionListener
JmolPanel
JmolTools
JmolViewerImpl
JNLPProxy
JobKillException
JoiningSequenceReader
JointFragments
JournalArticle
JPrintPanel
Jronn
Jronn.Range
LightweightProfile
LightweightProfile.StringFormat
LinearColorInterpolator
LinearColorInterpolator.InterpolationDirection
LocalCacheStructureProvider
LocalProteinDomainParser
Location
Location
Location.Tools
LocationHelper
LocIterator
LogColorMapper
LUDecomposition
MapToStringTransformer
Maths
Matrix
MatrixAligner
MatrixListener
MenuCreator
MenuCreator
MMcifConsumer
MMCIFFileInstallation
MMCIFFileReader
MMcifParser
ModelLoader
ModelLoader.Model
ModelLoader.Threshold
ModificationCategory
ModificationCondition
ModificationConditionImpl
ModificationLinkage
ModificationOccurrenceType
ModifiedAminoAcidCompoundSet
ModifiedCompound
ModifiedCompoundImpl
ModifiedCompoundXMLConverter
MultipleSequenceAlignment
MutableAlignedSequence
MutableProfile
MutableProfilePair
MutableSequencePair
Mutator
MyAlignmentLoadListener
MyDistMaxListener
MyExportListener
MyJmolStatusListener
MyOpenPdbFileListener
MySaveFileListener
MyTableRowSorter
MyValidationEventHandler
Name2Count
NCBIQBlastAlignmentProperties
NCBIQBlastOutputProperties
NCBIQBlastService
NCBIQBlastServiceDemo
NeedlemanWunsch
NJTreeProgressListener
NucleotideCompound
NucleotideImpl
NullOutputStream
OptimalCECPMain
OptimalCECPParameters
ORonn
ORonnModel
OutputHitsGFF
PairInProfileScorer
PairwiseSequenceAligner
PairwiseSequenceScorer
ParameterGUI
ParseListener
ParserException
PartitionRefiner
PDBDirPanel
PDBFileParser
PDBFileReader
PDBFilter
PDBHeader
PDBInstallation
PdbPair
PdbPairsMessage
PdbPairXMLConverter
PDBParseException
PDBRecord
PDBServerPanel
PDBSRSReader
PDBStatus
PDBStatus.Status
PDBUploadPanel
PdbxEntityNonPoly
PdbxNonPolyScheme
PdbxPolySeqScheme
PDPDistanceMatrix
PDPParameters
PeptideProperties
PeptideProperties.SingleLetterAACode
PeptidePropertiesImpl
PersistentConfig
Point
Point.Resolver
PolymerType
PositionInQueueXMLConverter
PrepareIndexFile
PrepareMMcifIndexFile
PrettyXMLWriter
ProfeatProperties
ProfeatPropertiesImpl
Profile
Profile.StringFormat
ProfilePair
ProfileProfileAligner
ProfileProfileScorer
ProfileView
ProgessListenerStub
ProteinModification
ProteinModificationIdentifier
ProteinModificationImpl
ProteinModificationImpl.Builder
ProteinModificationRegistry
ProteinModificationXmlReader
ProteinSequence
ProteinSequenceCreator
ProxySequenceReader
QRDecomposition
QualityFeature
QuantityFeature
RasmolCommandListener
RasmolCommandListener
ReducedChemCompProvider
Refine
RemoteDomainProvider
RemoteHmmerScan
RemotePairwiseAlignmentOutputProperties
RemotePairwiseAlignmentProperties
RemotePairwiseAlignmentService
RemotePDPProvider
RemoteScopInstallation
RenderStyle
RepresentativeXMLConverter
RescoreRefiner
ResidueNumber
ResidueProperties
ResidueType
ResourceManager
ReversedSequenceView
RNACompoundSet
RNASequence
RNASequenceCreator
RnaSequenceView
RNAToAminoAcidTranslator
RonnConstraint
RonnConstraint.Threshold
SandboxStyleStructureProvider
SangerFastqReader
SangerFastqWriter
ScaleableMatrixPanel
ScaledSubstitutionMatrix
SchemaGenerator
SCOPAutoSuggestProvider
ScopCategory
ScopDatabase
ScopDescription
ScopDescriptions
ScopDomain
ScopDomains
ScopFactory
ScopInstallation
ScopInstallationInstance
ScopNode
ScopNodes
ScopSelectPanel
ScoreMatrix
Scorer
SecStruc
SecStrucGroup
Segment
SegmentComparator
Selection
SelectionImpl
SelectPDBPanel
SeqRes2AtomAligner
Sequence
SequenceAsStringHelper
SequenceComparator
SequenceCreatorInterface
SequenceDisplay
SequenceFileProxyLoader
SequenceLengthError
SequenceLocation
SequenceMixin
SequenceMixin.SequenceIterator
SequenceMouseListener
SequenceOptimizationHints
SequenceOptimizationHints.SequenceCollection
SequenceOptimizationHints.SequenceUsage
SequencePair
SequenceParserInterface
SequenceProxyView
SequenceReader
SequenceScalePanel
SequenceTools
SequenceUtil
SequenceView
SerializableCache
ShortSegmentRemover
ShowPDBIDListener
ShowStructureInJmol
SiftsEntity
SiftsMappingProvider
SiftsResidue
SiftsSegment
SiftsXMLParser
SigEva
SimpleAlignedSequence
SimpleGapPenalty
SimpleLocation
SimpleMMcifConsumer
SimpleMMcifParser
SimplePoint
SimpleProfile
SimpleProfilePair
SimpleProfileProfileAligner
SimpleSequencePair
SimpleStructureServer
SimpleSubstitutionMatrix
SingleCompoundSequenceReader
SingularValueDecomposition
Site
SmithWaterman
SmithWaterman3Daligner
SmithWaterman3DParameters
SmithWatermanUserArgumentProcessor
SoftHashMap
SolexaFastqReader
SolexaFastqWriter
SplitFasta
SqrtColorMapper
SSBond
StandardAminoAcid
StandardRescoreRefiner
StartCodonSequence
StartupParameters
StatusDisplay
StopCodonSequence
Strand
StrCompAlignment
StreamListener
StringManipulationHelper
StringProxySequenceReader
StrucAligParameters
Struct
StructAsym
StructKeywords
StructRef
StructRefSeq
Structure
StructureAlignment
StructureAlignmentDisplay
StructureAlignmentFactory
StructureAlignmentJmol
StructureAlignmentOptimizer
StructureAtom
StructureAtomLinkage
StructureAtomXMLConverter
StructureEvent
StructureEventImpl
StructureException
StructureFetcherRunnable
StructureGroup
StructureGroupXMLConverter
StructureImpl
StructureIO
StructureIOFile
StructureListener
StructureName
StructurePairAligner
StructurePairSelector
StructureProvider
StructureServer
StructureTools
StructureUtil
StructureViewer
SubstitutionMatrix
SubstitutionMatrixHelper
SVDSuperimposer
SynchronizedOutFile
SystemInfo
Table
Table.CaseInsensitiveTriplet
Table.Codon
TaxonomyID
TextFeature
Timer
TranscriptionEngine
TranscriptionEngine.Builder
TranscriptSequence
TranslationException
TreeConstructionAlgorithm
TreeConstructor
TreeSetStringWrapper
TreeType
TwoBitSequenceReader
TwoBitSequenceReader.TwoBitArrayWorker
UncompressInputStream
UniprotProxySequenceReader
UniprotToFasta
UnknownPdbAminoAcidException
UserArgumentProcessor
UserConfiguration
Utils
WebStartClientDemo
WebStartDBSearch
WebStartDBSearchResults
WebStartMain
WindowedSequence
XMLHelper
XMLUtil
XMLWriter