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
• changeUnresolvedCharactersToGaps() : bpp::SymbolListTools , bpp::SiteContainerTools
• charge_ : bpp::AAChargeIndex , bpp::KleinAANetChargeIndex
• charList_ : bpp::AbstractAlphabet
• chars_ : bpp::DefaultAlphabet
• charsByLine_ : bpp::NexusIOSequence , bpp::Phylip , bpp::Clustal , bpp::Fasta , bpp::Mase
• CharStateNotSupportedException() : bpp::CharStateNotSupportedException
• charToInt() : bpp::AbstractAlphabet , bpp::Alphabet , bpp::LetterAlphabet , bpp::RNY , bpp::WordAlphabet
• checkAlphabetCodingSize() : bpp::AlphabetTools
• checkNames() : bpp::NexusIOSequence , bpp::Phylip , bpp::Stockholm , bpp::Clustal , bpp::Fasta , bpp::Mase
• checkNames_ : bpp::Clustal , bpp::Fasta , bpp::Mase , bpp::NexusIOSequence , bpp::Phylip , bpp::Stockholm
• checkSize_() : bpp::AlignedSequenceContainer
• clear() : bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::MapSequenceContainer , bpp::SequenceContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer
• clone() : bpp::AASEASup30Index , bpp::AASurfaceIndex , bpp::AAVolumeIndex , bpp::BLOSUM50 , bpp::DefaultNucleotideScore , bpp::EdSymbolList , bpp::GranthamAAChemicalDistance , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::Site , bpp::KleinAANetChargeIndex , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SequenceWithAnnotation , bpp::SimpleScore , bpp::UserAlphabetIndex1 , bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::MapSequenceContainer , bpp::SiteContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer , bpp::Sequence , bpp::BasicSequence , bpp::BowkerTest , bpp::SequenceAnnotation , bpp::SequenceMask , bpp::SequenceQuality , bpp::SequenceWithQuality , bpp::SymbolList , bpp::BasicSymbolList , bpp::SymbolListListener , bpp::AlphabetState , bpp::NucleicAlphabetState , bpp::ProteicAlphabetState , bpp::AAChargeIndex , bpp::AAChenGuHuangHydrophobicityIndex , bpp::AASEAInf10Index , bpp::AAChouFasmanAHelixIndex , bpp::AAChouFasmanBSheetIndex , bpp::AAChouFasmanTurnIndex , bpp::AAIndex1Entry , bpp::AAIndex2Entry , bpp::AAMassIndex , bpp::AASEA1030Index
• Clustal() : bpp::Clustal
• CLUSTAL_FORMAT : bpp::IoSequenceFactory
• codeSequence() : bpp::StringSequenceTools
• codon_ : bpp::StopCodonException
• CodonAlphabet() : bpp::CodonAlphabet
• codonAlphabet_ : bpp::GeneticCode
• CodonSiteTools() : bpp::CodonSiteTools
• combineSequences() : bpp::SequenceTools
• comments_ : bpp::CompressedVectorSiteContainer , bpp::BasicSequence , bpp::VectorSiteContainer , bpp::AbstractSequenceContainer , bpp::SequenceWithAnnotation
• complement() : bpp::StringSequenceTools , bpp::SequenceWithQualityTools , bpp::SequenceTools
• CompleteSiteContainerIterator() : bpp::CompleteSiteContainerIterator
• CompressedVectorSiteContainer() : bpp::CompressedVectorSiteContainer
• computeSimilarity() : bpp::SiteContainerTools
• computeSimilarityMatrix() : bpp::SiteContainerTools
• concatenate() : bpp::SequenceTools , bpp::SequenceWithQualityTools
• ConstSequenceIterator() : bpp::ConstSequenceIterator
• ConstSequenceWithQualityIterator() : bpp::ConstSequenceWithQualityIterator
• ConstSiteIterator() : bpp::ConstSiteIterator
• container_ : bpp::EmptyContainerException
• containsGap() : bpp::WordAlphabet , bpp::RNY
• containsUnresolved() : bpp::WordAlphabet
• content_ : bpp::BasicSymbolList , bpp::EdSymbolList
• convertAlphabet() : bpp::SequenceContainerTools
• convertContainer() : bpp::SequenceContainerTools
• createAlignmentReader() : bpp::IoSequenceFactory
• createAlignmentWriter() : bpp::IoSequenceFactory
• createContainerOfSpecifiedSize() : bpp::SequenceContainerTools
• createContainerWithSequenceNames() : bpp::SequenceContainerTools
• createEmptyContainer() : bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer , bpp::MapSequenceContainer , bpp::SequenceContainer
• createMaskAnnotation() : bpp::SequenceWithAnnotationTools
• createReader() : bpp::IoSequenceFactory
• createWriter() : bpp::IoSequenceFactory
• currentPosition_ : bpp::AbstractSequenceContainerIterator , bpp::AbstractSequencePositionIterator , bpp::AbstractSiteContainerIterator