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

- c -

• c_ : bpp::BadCharException
• CaseMaskedAlphabet() : bpp::CaseMaskedAlphabet
• caseSensitive_ : bpp::LetterAlphabet
• changeGapsToUnknownCharacters() : bpp::SiteContainerTools , bpp::SymbolListTools
• changeName() : bpp::MappedNamedContainer< T >
• changeUnresolvedCharactersToGaps() : bpp::SiteContainerTools , bpp::SymbolListTools
• charge_ : bpp::AAChargeIndex , bpp::KleinAANetChargeIndex
• charList_ : bpp::AbstractAlphabet
• chars_ : bpp::DefaultAlphabet
• charsByLine_ : bpp::Clustal , bpp::Fasta , bpp::Mase , bpp::NexusIOSequence , bpp::Pasta , bpp::Phylip
• CharStateNotSupportedException() : bpp::CharStateNotSupportedException
• charToInt() : bpp::AbstractAlphabet , bpp::AllelicAlphabet , bpp::Alphabet , bpp::CodonAlphabet , bpp::LetterAlphabet , bpp::RNY , bpp::WordAlphabet
• checkAlphabetCodingSize() : bpp::AlphabetTools
• checkNames() : bpp::Clustal , bpp::Fasta , bpp::Mase , bpp::NexusIOSequence , bpp::Stockholm
• checkNames_ : bpp::Clustal , bpp::Fasta , bpp::Mase , bpp::NexusIOSequence , bpp::Stockholm
• checkSize_() : bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >
• CiliateNuclearGeneticCode() : bpp::CiliateNuclearGeneticCode
• clear() : bpp::CompressedVectorSiteContainer , bpp::MappedNamedContainer< T > , bpp::NamedContainerInterface< T > , bpp::PositionedContainerInterface< T > , bpp::SequencedValuesContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType > , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T >
• clearComments() : bpp::Commentable , bpp::SimpleCommentable
• clone() : bpp::AAChargeIndex , bpp::AAChenGuHuangHydrophobicityIndex , bpp::AAChouFasmanAHelixIndex , bpp::AAChouFasmanBSheetIndex , bpp::AAChouFasmanTurnIndex , bpp::AAIndex1Entry , bpp::AAIndex2Entry , bpp::AAMassIndex , bpp::AASEA1030Index , bpp::AASEAInf10Index , bpp::AASEASup30Index , bpp::AASurfaceIndex , bpp::AAVolumeIndex , bpp::AbstractAlphabet , bpp::AbstractCoreSequence , bpp::AllelicAlphabet , bpp::Alphabet , bpp::AlphabetIndex1 , bpp::AlphabetIndex2 , bpp::AlphabetNumericState , bpp::AlphabetState , bpp::AscidianMitochondrialGeneticCode , bpp::BinaryAlphabet , bpp::BLOSUM50 , bpp::BowkerTest , bpp::CaseMaskedAlphabet , bpp::CiliateNuclearGeneticCode , bpp::CodonAlphabet , bpp::CodonFromProteicAlphabetIndex1 , bpp::CodonFromProteicAlphabetIndex2 , bpp::CompressedVectorSiteContainer , bpp::CoreSequenceInterface , bpp::CoreSiteInterface , bpp::CoreSymbolListListener< T > , bpp::CruxSymbolListInterface , bpp::DefaultAlphabet , bpp::DefaultNucleotideScore , bpp::DistanceMatrix , bpp::DNA , bpp::EchinodermMitochondrialGeneticCode , bpp::EventDrivenIntSymbolList , bpp::GeneticCode , bpp::GranthamAAChemicalDistance , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::IntegerAlphabet , bpp::IntSymbolList , bpp::InvertebrateMitochondrialGeneticCode , bpp::KD_AAHydropathyIndex , bpp::KleinAANetChargeIndex , bpp::LetterAlphabet , bpp::LexicalAlphabet , bpp::MappedNamedContainer< T > , bpp::MiyataAAChemicalDistance , bpp::MoldMitochondrialGeneticCode , bpp::NucleicAlphabet , bpp::NucleicAlphabetState , bpp::NumericAlphabet , bpp::PositionedNamedContainerInterface< T > , bpp::ProbabilisticSequence , bpp::ProbabilisticSequenceInterface , bpp::ProbabilisticSite , bpp::ProbabilisticSiteInterface , bpp::ProbabilisticSymbolList , bpp::ProteicAlphabet , bpp::ProteicAlphabetIndex1 , bpp::ProteicAlphabetIndex2 , bpp::ProteicAlphabetState , bpp::RNA , bpp::RNY , bpp::Sequence , bpp::SequenceAnnotation , bpp::SequenceInterface , bpp::SequenceMask , bpp::SequenceQuality , bpp::SequenceWithAnnotation , bpp::SequenceWithQuality , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::Site , bpp::SiteInterface , bpp::StandardGeneticCode , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateCoreSymbolListInterface< T > , bpp::TemplateEventDrivenCoreSymbolListInterface< T > , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType > , bpp::UserAlphabetIndex1 , bpp::UserAlphabetIndex2 , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T > , bpp::VertebrateMitochondrialGeneticCode , bpp::WordAlphabet , bpp::YeastMitochondrialGeneticCode
• Clustal() : bpp::Clustal
• CLUSTAL_FORMAT : bpp::IoSequenceFactory
• codeSequence() : bpp::StringSequenceTools
• codon_ : bpp::StopCodonException
• CodonAlphabet() : bpp::CodonAlphabet
• codonAlphabet() : bpp::GeneticCode
• codonAlphabet_ : bpp::GeneticCode
• CodonFromProteicAlphabetIndex1() : bpp::CodonFromProteicAlphabetIndex1
• CodonFromProteicAlphabetIndex2() : bpp::CodonFromProteicAlphabetIndex2
• CodonSiteTools() : bpp::CodonSiteTools
• combineSequences() : bpp::SequenceTools
• Commentable() : bpp::Commentable
• comments_ : bpp::SimpleCommentable
• complement() : bpp::SequenceTools , bpp::SequenceWithQualityTools , bpp::StringSequenceTools
• CompleteTemplateSiteContainerIterator() : bpp::CompleteTemplateSiteContainerIterator< SiteType, SequenceType, HashType >
• CompressedVectorSiteContainer() : bpp::CompressedVectorSiteContainer
• computeIndexMatrix_() : bpp::GranthamAAChemicalDistance , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance
• computeLikelihoods() : bpp::AllelicAlphabet
• computeSimilarity() : bpp::SiteContainerTools
• computeSimilarityMatrix() : bpp::SiteContainerTools
• concatenate() : bpp::SequenceTools , bpp::SequenceWithQualityTools
• container_ : bpp::EmptyContainerException
• containsGap() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::NumericAlphabet , bpp::RNY , bpp::WordAlphabet
• containsUnresolved() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::WordAlphabet
• content_ : bpp::AbstractTemplateSymbolList< T > , bpp::ProbabilisticSymbolList
• convertAlphabet() : bpp::SequenceContainerTools
• convertContainer() : bpp::SequenceContainerTools
• convertFromStateAlphabet() : bpp::AllelicAlphabet
• coordinate_ : bpp::AbstractCoreSite
• coordinates_ : bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >
• CoreSequenceInterface() : bpp::CoreSequenceInterface
• CoreSymbolListDeletionEvent() : bpp::CoreSymbolListDeletionEvent< T >
• CoreSymbolListEditionEvent() : bpp::CoreSymbolListEditionEvent< T >
• CoreSymbolListInsertionEvent() : bpp::CoreSymbolListInsertionEvent< T >
• CoreSymbolListSubstitutionEvent() : bpp::CoreSymbolListSubstitutionEvent< T >
• CoreWordAlphabet() : bpp::CoreWordAlphabet
• createAlignmentReader() : bpp::IoSequenceFactory
• createAlignmentWriter() : bpp::IoSequenceFactory
• createContainerOfSpecifiedSize() : bpp::SequenceContainerTools
• createContainerWithSequenceNames() : bpp::SequenceContainerTools
• createEmptyContainer() : bpp::CompressedVectorSiteContainer , bpp::SequencedValuesContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSequenceContainerInterface< SequenceType, HashType > , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• createMaskAnnotation() : bpp::SequenceWithAnnotationTools
• createReader() : bpp::IODistanceMatrixFactory , bpp::IoSequenceFactory
• createWriter() : bpp::IODistanceMatrixFactory , bpp::IoSequenceFactory
• currentPosition_ : bpp::AbstractSequencePositionIterator , bpp::AbstractTemplateSiteContainerIterator< SiteType, SequenceType, HashType >