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

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• AAChargeIndex() : bpp::AAChargeIndex
• AAChenGuHuangHydrophobicityIndex() : bpp::AAChenGuHuangHydrophobicityIndex
• AAChouFasmanAHelixIndex() : bpp::AAChouFasmanAHelixIndex
• AAChouFasmanBSheetIndex() : bpp::AAChouFasmanBSheetIndex
• AAChouFasmanTurnIndex() : bpp::AAChouFasmanTurnIndex
• AAIndex1Entry() : bpp::AAIndex1Entry
• AAIndex2Entry() : bpp::AAIndex2Entry
• AAMassIndex() : bpp::AAMassIndex
• AASEA1030Index() : bpp::AASEA1030Index
• AASEAInf10Index() : bpp::AASEAInf10Index
• AASEASup30Index() : bpp::AASEASup30Index
• AASurfaceIndex() : bpp::AASurfaceIndex
• AAVolumeIndex() : bpp::AAVolumeIndex
• abbr_ : bpp::ProteicAlphabetState
• AbstractAlphabet() : bpp::AbstractAlphabet
• AbstractCoreSequence() : bpp::AbstractCoreSequence
• AbstractCoreSite() : bpp::AbstractCoreSite
• AbstractIAlignment() : bpp::AbstractIAlignment
• AbstractIAlignment2() : bpp::AbstractIAlignment2
• AbstractIDistanceMatrix() : bpp::AbstractIDistanceMatrix
• AbstractIProbabilisticAlignment() : bpp::AbstractIProbabilisticAlignment
• AbstractIProbabilisticAlignment2() : bpp::AbstractIProbabilisticAlignment2
• AbstractIProbabilisticSequence() : bpp::AbstractIProbabilisticSequence
• AbstractISequence() : bpp::AbstractISequence
• AbstractOAlignment() : bpp::AbstractOAlignment
• AbstractODistanceMatrix() : bpp::AbstractODistanceMatrix
• AbstractOProbabilisticAlignment() : bpp::AbstractOProbabilisticAlignment
• AbstractOProbabilisticSequence() : bpp::AbstractOProbabilisticSequence
• AbstractOProbabilisticSequence2() : bpp::AbstractOProbabilisticSequence2
• AbstractOSequence() : bpp::AbstractOSequence
• AbstractOSequence2() : bpp::AbstractOSequence2
• AbstractReverseTransliterator() : bpp::AbstractReverseTransliterator
• AbstractSequencePositionIterator() : bpp::AbstractSequencePositionIterator
• AbstractTemplateEventDrivenSymbolList() : bpp::AbstractTemplateEventDrivenSymbolList< T >
• AbstractTemplateSequenceContainer() : bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >
• AbstractTemplateSiteContainerIterator() : bpp::AbstractTemplateSiteContainerIterator< SiteType, SequenceType, HashType >
• AbstractTemplateSymbolList() : bpp::AbstractTemplateSymbolList< T >
• AbstractTransliterator() : bpp::AbstractTransliterator
• addAnnotation() : bpp::SequenceWithAnnotation
• addCoreSymbolListListener() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• addElement() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::AbstractTemplateSymbolList< T > , bpp::EventDrivenIntSymbolList , bpp::IntSymbolList , bpp::IntSymbolListInterface , bpp::ProbabilisticSymbolList , bpp::Sequence , bpp::SequenceWithQuality , bpp::TemplateCoreSymbolListInterface< T >
• addIntSymbolListListener() : bpp::EventDrivenIntSymbolList
• addObject() : bpp::MappedNamedContainer< T > , bpp::PositionedNamedContainerInterface< T > , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T >
• addObject_() : bpp::MappedNamedContainer< T > , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T >
• addSequence() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSequenceContainerInterface< SequenceType, HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• addSite() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• afterSequenceChanged() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::CoreSymbolListListener< T > , bpp::EventDrivenIntSymbolList , bpp::SequenceMask , bpp::SequenceQuality , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• afterSequenceDeleted() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::CoreSymbolListListener< T > , bpp::EventDrivenIntSymbolList , bpp::SequenceMask , bpp::SequenceQuality , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• afterSequenceInserted() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::CoreSymbolListListener< T > , bpp::EventDrivenIntSymbolList , bpp::SequenceMask , bpp::SequenceQuality , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• afterSequenceSubstituted() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::CoreSymbolListListener< T > , bpp::EventDrivenIntSymbolList , bpp::SequenceMask , bpp::SequenceQuality , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• aHelix_ : bpp::AAChouFasmanAHelixIndex
• alignNW() : bpp::SiteContainerTools
• AllelicAlphabet() : bpp::AllelicAlphabet
• AllelicTransliterator() : bpp::AllelicAlphabet::AllelicTransliterator
• alnPos_ : bpp::SequenceWalker
• alph_ : bpp::AllelicAlphabet::AllelicTransliterator , bpp::AllelicAlphabet , bpp::UserAlphabetIndex1 , bpp::UserAlphabetIndex2
• alpha_ : bpp::CodonFromProteicAlphabetIndex1 , bpp::CodonFromProteicAlphabetIndex2 , bpp::DefaultNucleotideScore , bpp::ProteicAlphabetIndex1 , bpp::ProteicAlphabetIndex2
• alphabet() : bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > , bpp::AbstractTemplateSymbolList< T >
• Alphabet() : bpp::Alphabet
• alphabet() : bpp::AlphabetIndex1 , bpp::AlphabetIndex2 , bpp::CodonFromProteicAlphabetIndex1 , bpp::CodonFromProteicAlphabetIndex2 , bpp::CruxSymbolListInterface , bpp::DefaultNucleotideScore , bpp::ProbabilisticSymbolList , bpp::ProteicAlphabetIndex1 , bpp::ProteicAlphabetIndex2 , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::TemplateSequenceDataInterface< HashType > , bpp::UserAlphabetIndex1 , bpp::UserAlphabetIndex2
• alphabet1_ : bpp::AlphabetMismatchException
• alphabet2_ : bpp::AlphabetMismatchException
• alphabet_ : bpp::AbstractAlphabet , bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > , bpp::AbstractTemplateSymbolList< T > , bpp::AlphabetException , bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::ProbabilisticSymbolList , bpp::SimpleScore , bpp::TemplateStreamSequenceIterator< SequenceType >
• AlphabetException() : bpp::AlphabetException
• AlphabetIndex1() : bpp::AlphabetIndex1
• AlphabetIndex2() : bpp::AlphabetIndex2
• alphabetInheritsFrom() : bpp::AlphabetTools
• AlphabetMismatchException() : bpp::AlphabetMismatchException
• AlphabetNumericState() : bpp::AlphabetNumericState
• AlphabetState() : bpp::AlphabetState
• AlphabetTools() : bpp::AlphabetTools
• annotation() : bpp::SequenceWithAnnotation
• append() : bpp::Sequence , bpp::SequenceContainerTools , bpp::SequenceInterface , bpp::SequenceWithAnnotation , bpp::SequenceWithQuality
• appendAlignmentFromFile() : bpp::AbstractIAlignment , bpp::AbstractIProbabilisticAlignment
• appendAlignmentFromStream() : bpp::AbstractIAlignment , bpp::AbstractIProbabilisticAlignment , bpp::Clustal , bpp::DCSE , bpp::Fasta , bpp::Mase , bpp::NexusIOSequence , bpp::Pasta , bpp::Phylip
• appendObject() : bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T >
• appendSequencesFromFile() : bpp::AbstractIProbabilisticSequence , bpp::AbstractISequence
• appendSequencesFromStream() : bpp::AbstractIProbabilisticSequence , bpp::AbstractISequence , bpp::Fasta , bpp::GenBank , bpp::Mase
• areSequencesIdentical() : bpp::SequenceTools
• areSymbolListsIdentical() : bpp::SymbolListTools
• areSynonymous() : bpp::GeneticCode
• AscidianMitochondrialGeneticCode() : bpp::AscidianMitochondrialGeneticCode
• asMatrix() : bpp::DistanceMatrix