Here is a list of all class members with links to the classes they belong to:

- s -

• sampleSites() : bpp::SiteContainerTools
• sea1030_ : bpp::AASEA1030Index
• seaInf10_ : bpp::AASEAInf10Index
• seaSup30_ : bpp::AASEASup30Index
• seq_ : bpp::SequenceWalker
• seqPos_ : bpp::SequenceWalker
• seqStream_ : bpp::TemplateStreamSequenceIterator< SequenceType >
• sequence() : bpp::CompressedVectorSiteContainer
• Sequence() : bpp::Sequence
• sequence() : bpp::TemplateSequenceContainerInterface< SequenceType, HashType > , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• sequence_ : bpp::AbstractSequencePositionIterator , bpp::SequenceException , bpp::TemplateVectorSequenceContainer< SequenceType >
• SequenceApplicationTools() : bpp::SequenceApplicationTools
• sequenceComments_ : bpp::CompressedVectorSiteContainer , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• sequenceContainer_ : bpp::CompressedVectorSiteContainer , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• SequenceContainerTools() : bpp::SequenceContainerTools
• SequenceException() : bpp::SequenceException
• sequenceKey() : bpp::CompressedVectorSiteContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• SequenceMask() : bpp::SequenceMask
• sequenceNames_ : bpp::CompressedVectorSiteContainer , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• SequenceNotAlignedException() : bpp::SequenceNotAlignedException
• SequenceNotFoundException() : bpp::SequenceNotFoundException
• SequencePositionIterator() : bpp::SequencePositionIterator
• SequenceQuality() : bpp::SequenceQuality
• sequenceSelections_ : bpp::MaseHeader
• sequencesHaveTheSameLength() : bpp::SequenceContainerTools
• SequenceTools() : bpp::SequenceTools
• sequenceVectorMap_ : bpp::TemplateVectorSequenceContainer< SequenceType >
• SequenceWalker() : bpp::SequenceWalker
• SequenceWithAnnotation() : bpp::SequenceWithAnnotation
• SequenceWithGapException() : bpp::SequenceWithGapException
• SequenceWithQuality() : bpp::SequenceWithQuality
• sequential_ : bpp::Phylip
• setAbbreviation() : bpp::ProteicAlphabetState
• setBinaryCode() : bpp::NucleicAlphabetState
• setComments() : bpp::Commentable , bpp::SequencedValuesContainer , bpp::SimpleCommentable
• setContent() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::AbstractTemplateSymbolList< T > , bpp::EventDrivenIntSymbolList , bpp::IntSymbolList , bpp::IntSymbolListInterface , bpp::ProbabilisticSymbolList , bpp::ProbabilisticSymbolListInterface , bpp::Sequence , bpp::SequenceInterface , bpp::SequenceWithAnnotation , bpp::TemplateCoreSymbolListInterface< T >
• setCoordinate() : bpp::AbstractCoreSite , bpp::CoreSiteInterface
• setElement() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::AbstractTemplateSymbolList< T > , bpp::EventDrivenIntSymbolList , bpp::IntSymbolList , bpp::IntSymbolListInterface , bpp::ProbabilisticSymbolList , bpp::TemplateCoreSymbolListInterface< T >
• setGeneralComments() : bpp::SequencedValuesContainer
• setIndex() : bpp::UserAlphabetIndex1
• setIndexMatrix() : bpp::UserAlphabetIndex2
• setLetter() : bpp::AlphabetState
• setMask() : bpp::SequenceMask
• setName() : bpp::AbstractCoreSequence , bpp::AlphabetState , bpp::CoreSequenceInterface , bpp::DistanceMatrix
• setNames() : bpp::DistanceMatrix
• setNum() : bpp::AlphabetState
• setObjectName() : bpp::VectorMappedContainer< T >
• setObjectNames() : bpp::VectorMappedContainer< T >
• setPC1Sign() : bpp::GranthamAAChemicalDistance
• setPosition() : bpp::AbstractSequencePositionIterator , bpp::SequencePositionIterator
• setPValue() : bpp::BowkerTest
• setQualities() : bpp::SequenceWithQuality
• setQuality() : bpp::SequenceWithQuality
• setScore() : bpp::SequenceQuality
• setScores() : bpp::SequenceQuality
• setSequence() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSequenceContainerInterface< SequenceType, HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• setSequenceKeys() : bpp::CompressedVectorSiteContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• setSequenceNames() : bpp::CompressedVectorSiteContainer , bpp::SequencedValuesContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• setSequenceSelection() : bpp::MaseHeader
• setSite() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• setSiteCoordinates() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• setSiteSelection() : bpp::MaseHeader
• setSize() : bpp::PositionedContainerInterface< T > , bpp::VectorPositionedContainer< T >
• setSplit() : bpp::Phylip
• setState() : bpp::AbstractAlphabet , bpp::LetterAlphabet , bpp::NucleicAlphabet , bpp::NumericAlphabet
• setStatistic() : bpp::BowkerTest
• setSymmetric() : bpp::GranthamAAChemicalDistance , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance
• setToSizeL() : bpp::CoreSequenceInterface , bpp::ProbabilisticSequence , bpp::Sequence , bpp::SequenceWithAnnotation , bpp::StringSequenceTools
• setToSizeR() : bpp::CoreSequenceInterface , bpp::ProbabilisticSequence , bpp::Sequence , bpp::SequenceWithAnnotation , bpp::StringSequenceTools
• setTree() : bpp::MaseHeader
• setValue() : bpp::AlphabetNumericState
• shuffle() : bpp::AbstractTemplateSymbolList< T > , bpp::CruxSymbolListInterface , bpp::ProbabilisticSymbolList
• sign_ : bpp::GranthamAAChemicalDistance
• SIGN_ARBITRARY : bpp::GranthamAAChemicalDistance
• SIGN_NONE : bpp::GranthamAAChemicalDistance
• SIGN_PC1 : bpp::GranthamAAChemicalDistance
• signMatrix_ : bpp::GranthamAAChemicalDistance
• SIMILARITY_ALL : bpp::SiteContainerTools
• SIMILARITY_NODOUBLEGAP : bpp::SiteContainerTools
• SIMILARITY_NOFULLGAP : bpp::SiteContainerTools
• SIMILARITY_NOGAP : bpp::SiteContainerTools
• SimpleCommentable() : bpp::SimpleCommentable
• SimpleIndexDistance() : bpp::SimpleIndexDistance
• SimpleScore() : bpp::SimpleScore
• SimpleSequencePositionIterator() : bpp::SimpleSequencePositionIterator
• SimpleTemplateSiteContainerIterator() : bpp::SimpleTemplateSiteContainerIterator< SiteType, SequenceType, HashType >
• site() : bpp::CompressedVectorSiteContainer
• Site() : bpp::Site
• site() : bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• site_ : bpp::SiteException , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• siteContainer_ : bpp::CompressedVectorSiteContainer , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• SiteContainerTools() : bpp::SiteContainerTools
• SiteException() : bpp::SiteException
• SiteNotFoundException() : bpp::SiteNotFoundException
• sites_ : bpp::AbstractTemplateSiteContainerIterator< SiteType, SequenceType, HashType >
• siteSelections_ : bpp::MaseHeader
• SiteTools() : bpp::SiteTools
• siteVector_ : bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >
• SiteWithGapException() : bpp::SiteWithGapException
• size() : bpp::AbstractTemplateSymbolList< T > , bpp::CruxSymbolListInterface , bpp::DistanceMatrix , bpp::ProbabilisticSymbolList
• size_ : bpp::SimpleIndexDistance
• sourceAlphabet() : bpp::DNAToRNA , bpp::GeneticCode , bpp::NucleicAcidsReplication , bpp::TransliteratorInterface
• splitNameAndSequence() : bpp::Phylip
• splitNameAndSequence_() : bpp::NexusIOSequence
• StandardGeneticCode() : bpp::StandardGeneticCode
• stat_ : bpp::BowkerTest
• stateAlphabet() : bpp::AllelicAlphabet
• Stockholm() : bpp::Stockholm
• StopCodonException() : bpp::StopCodonException
• stream_ : bpp::TemplateStreamSequenceIterator< SequenceType >
• StreamSequenceIterator() : bpp::TemplateStreamSequenceIterator< SequenceType >
• strictNames() : bpp::Fasta
• strictNames_ : bpp::Fasta , bpp::Pasta
• StringSequenceTools() : bpp::StringSequenceTools
• subseq() : bpp::SequenceTools , bpp::SequenceWithQualityTools , bpp::StringSequenceTools
• subtract() : bpp::NucleicAlphabet
• subtractHaplotype() : bpp::SequenceTools
• surface_ : bpp::AASurfaceIndex
• SwitchDeleter() : bpp::SwitchDeleter< T >
• sym_ : bpp::AAIndex2Entry , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::UserAlphabetIndex2
• SymbolListTools() : bpp::SymbolListTools
• SymbolType : bpp::IntSymbolListInterface , bpp::ProbabilisticSymbolListInterface