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::StreamSequenceWithQualityIterator , bpp::StreamSequenceIterator
• sequence_ : bpp::SequenceException , bpp::AbstractSequencePositionIterator
• SequenceApplicationTools() : bpp::SequenceApplicationTools
• SequenceContainer() : bpp::SequenceContainer
• SequenceContainerTools() : bpp::SequenceContainerTools
• SequenceException() : bpp::SequenceException
• SequenceIterator() : bpp::SequenceIterator
• SequenceMask() : bpp::SequenceMask
• SequenceNotAlignedException() : bpp::SequenceNotAlignedException
• SequenceNotFoundException() : bpp::SequenceNotFoundException
• SequencePositionIterator() : bpp::SequencePositionIterator
• SequenceQuality() : bpp::SequenceQuality
• sequences_ : bpp::CompressedVectorSiteContainer , bpp::MapSequenceContainer , bpp::AbstractSequenceContainerIterator , bpp::VectorSequenceContainer , bpp::VectorSiteContainer
• sequenceSelections_ : bpp::MaseHeader
• sequencesHaveTheSameLength() : bpp::SequenceContainerTools
• SequenceTools() : bpp::SequenceTools
• SequenceWalker() : bpp::SequenceWalker
• SequenceWithAnnotation() : bpp::SequenceWithAnnotation
• SequenceWithGapException() : bpp::SequenceWithGapException
• SequenceWithQuality() : bpp::SequenceWithQuality
• SequenceWithQualityIterator() : bpp::SequenceWithQualityIterator
• sequential_ : bpp::Phylip
• setAbbreviation() : bpp::ProteicAlphabetState
• setBinaryCode() : bpp::NucleicAlphabetState
• setComments() : bpp::MapSequenceContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer , bpp::Sequence , bpp::BasicSequence , bpp::SequenceWithAnnotation , bpp::AbstractSequenceContainer , bpp::CompressedVectorSiteContainer
• setContent() : bpp::Sequence , bpp::BasicSequence , bpp::SequenceWithAnnotation , bpp::SymbolList , bpp::BasicSymbolList , bpp::EdSymbolList
• setElement() : bpp::SymbolList , bpp::BasicSymbolList , bpp::EdSymbolList
• setGeneralComments() : bpp::AbstractSequenceContainer , bpp::SequenceContainer
• setIndex() : bpp::UserAlphabetIndex1
• setLetter() : bpp::AlphabetState
• setMask() : bpp::SequenceMask
• setName() : bpp::AlphabetState , bpp::DistanceMatrix , bpp::Sequence , bpp::BasicSequence , bpp::SequenceWithAnnotation
• setNames() : bpp::DistanceMatrix
• setNum() : bpp::AlphabetState
• setPC1Sign() : bpp::GranthamAAChemicalDistance
• setPosition() : bpp::SequencePositionIterator , bpp::AbstractSequencePositionIterator , bpp::Site
• setPValue() : bpp::BowkerTest
• setQualities() : bpp::SequenceWithQuality
• setQuality() : bpp::SequenceWithQuality
• setScore() : bpp::SequenceQuality
• setScores() : bpp::SequenceQuality
• setSequence() : bpp::SequenceContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer , bpp::OrderedSequenceContainer , bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::MapSequenceContainer , bpp::OrderedSequenceContainer
• setSequenceByKey() : bpp::MapSequenceContainer
• setSequenceSelection() : bpp::MaseHeader
• setSequencesNames() : bpp::MapSequenceContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::VectorSiteContainer , bpp::CompressedVectorSiteContainer , bpp::VectorSequenceContainer
• setSite() : bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::VectorSiteContainer , bpp::SiteContainer
• setSiteSelection() : bpp::MaseHeader
• setSplit() : bpp::Phylip
• setState() : bpp::AbstractAlphabet , bpp::LetterAlphabet , bpp::NucleicAlphabet
• setStatistic() : bpp::BowkerTest
• setSymmetric() : bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::GranthamAAChemicalDistance
• setToSizeL() : bpp::Sequence , bpp::SequenceWithAnnotation , bpp::StringSequenceTools , bpp::BasicSequence
• setToSizeR() : bpp::Sequence , bpp::SequenceWithAnnotation , bpp::StringSequenceTools , bpp::BasicSequence
• setTree() : bpp::MaseHeader
• shuffle() : bpp::BasicSymbolList , bpp::EdSymbolList , bpp::SymbolList
• 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
• SimpleIndexDistance() : bpp::SimpleIndexDistance
• SimpleScore() : bpp::SimpleScore
• SimpleSequenceContainerIterator() : bpp::SimpleSequenceContainerIterator
• SimpleSequencePositionIterator() : bpp::SimpleSequencePositionIterator
• SimpleSiteContainerIterator() : bpp::SimpleSiteContainerIterator
• Site() : bpp::Site
• site_ : bpp::SiteException
• SiteContainer() : bpp::SiteContainer
• SiteContainerTools() : bpp::SiteContainerTools
• SiteException() : bpp::SiteException
• SiteIterator() : bpp::SiteIterator
• SiteNotFoundException() : bpp::SiteNotFoundException
• sites_ : bpp::VectorSiteContainer , bpp::CompressedVectorSiteContainer , bpp::AbstractSiteContainerIterator , bpp::AlignedSequenceContainer
• siteSelections_ : bpp::MaseHeader
• SiteTools() : bpp::SiteTools
• SiteWithGapException() : bpp::SiteWithGapException
• size() : bpp::BasicSymbolList , bpp::SymbolList , bpp::DistanceMatrix , bpp::EdSymbolList
• splitNameAndSequence() : bpp::Phylip
• splitNameAndSequence_() : bpp::NexusIOSequence
• StandardCodonAlphabet() : bpp::StandardCodonAlphabet
• StandardGeneticCode() : bpp::StandardGeneticCode
• stat_ : bpp::BowkerTest
• Stockholm() : bpp::Stockholm
• STOP : bpp::CodonAlphabet
• StopCodonException() : bpp::StopCodonException
• stopCodons() : bpp::CodonAlphabet
• stopCodons_ : bpp::CodonAlphabet
• stream_ : bpp::StreamSequenceWithQualityIterator , bpp::StreamSequenceIterator
• StreamSequenceIterator() : bpp::StreamSequenceIterator
• StreamSequenceWithQualityIterator() : bpp::StreamSequenceWithQualityIterator
• strictNames() : bpp::Fasta
• strictNames_ : bpp::Fasta
• StringSequenceTools() : bpp::StringSequenceTools
• subseq() : bpp::SequenceWithQualityTools , bpp::SequenceTools , bpp::StringSequenceTools
• subtract() : bpp::NucleicAlphabet
• subtractHaplotype() : bpp::SequenceTools
• surface_ : bpp::AASurfaceIndex
• sym_ : bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance
• SymbolListDeletionEvent() : bpp::SymbolListDeletionEvent
• SymbolListEditionEvent() : bpp::SymbolListEditionEvent
• SymbolListInsertionEvent() : bpp::SymbolListInsertionEvent
• SymbolListSubstitutionEvent() : bpp::SymbolListSubstitutionEvent
• SymbolListTools() : bpp::SymbolListTools