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

- g -

• gap_ : bpp::SequenceWalker
• GenBank() : bpp::GenBank
• GENBANK_FORMAT : bpp::IoSequenceFactory
• generateCodonSiteWithoutRareVariant() : bpp::CodonSiteTools
• GeneticCode() : bpp::GeneticCode
• getAbbr() : bpp::ProteicAlphabet
• getAbbreviation() : bpp::ProteicAlphabetState
• getAlias() : bpp::ProteicAlphabet , bpp::RNA , bpp::AbstractAlphabet , bpp::RNY , bpp::AbstractAlphabet , bpp::WordAlphabet , bpp::Alphabet , bpp::DNA
• getAlignmentPosition() : bpp::SequenceWalker
• getAlignmentPositions() : bpp::SiteContainerTools
• getAlphabet() : bpp::AAIndex1Entry , bpp::AAIndex2Entry , bpp::AAMassIndex , bpp::AASEA1030Index , bpp::AASEAInf10Index , bpp::AASEASup30Index , bpp::AASurfaceIndex , bpp::AAVolumeIndex , bpp::AlphabetIndex1 , bpp::AlphabetIndex2 , bpp::BLOSUM50 , bpp::DefaultNucleotideScore , bpp::GranthamAAChemicalDistance , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::KleinAANetChargeIndex , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::SequenceApplicationTools , bpp::AlphabetException , bpp::AbstractSequenceContainer , bpp::SequenceContainer , bpp::AAChargeIndex , bpp::SymbolList , bpp::BasicSymbolList , bpp::AAChenGuHuangHydrophobicityIndex , bpp::EdSymbolList , bpp::AAChouFasmanAHelixIndex , bpp::AAChouFasmanBSheetIndex , bpp::AAChouFasmanTurnIndex
• getAlphabetCodingSize() : bpp::AlphabetTools
• getAlphabetFromSequence() : bpp::StringSequenceTools
• getAlphabetIndex1() : bpp::SimpleIndexDistance , bpp::SequenceApplicationTools
• getAlphabetIndex2() : bpp::SequenceApplicationTools
• getAlphabets() : bpp::AlphabetMismatchException
• getAlphabetType() : bpp::Alphabet , bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::CodonAlphabet , bpp::DefaultAlphabet , bpp::DNA , bpp::EchinodermMitochondrialCodonAlphabet , bpp::InvertebrateMitochondrialCodonAlphabet , bpp::ProteicAlphabet , bpp::RNA , bpp::RNY , bpp::StandardCodonAlphabet , bpp::VertebrateMitochondrialCodonAlphabet , bpp::WordAlphabet , bpp::YeastMitochondrialCodonAlphabet
• getAnnotation() : bpp::SequenceWithAnnotation
• getAnnotationTypes() : bpp::SequenceWithAnnotation
• getAvailableSequenceSelections() : bpp::MaseTools
• getAvailableSiteSelections() : bpp::MaseTools
• getBadChar() : bpp::BadCharException
• getBadInt() : bpp::BadIntException
• getBegin() : bpp::SymbolListSubstitutionEvent
• getBinaryCode() : bpp::NucleicAlphabetState
• getCDS() : bpp::SequenceTools
• getChar() : bpp::SequencePositionIterator , bpp::AbstractSequencePositionIterator , bpp::SymbolList , bpp::BasicSymbolList , bpp::EdSymbolList
• getCodingSequence() : bpp::GeneticCode
• getCodon() : bpp::CodonAlphabet , bpp::StopCodonException
• getCodonPosition() : bpp::SequenceContainerTools
• getColumnScores() : bpp::SiteContainerTools
• getComments() : bpp::AbstractSequenceContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::Sequence , bpp::BasicSequence , bpp::SequenceWithAnnotation
• getComplement() : bpp::SequenceTools
• getCompleteSites() : bpp::SiteContainerTools
• getConsensus() : bpp::SiteContainerTools
• getContainer() : bpp::EmptyContainerException
• getContent() : bpp::AbstractSequenceContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::SymbolList , bpp::BasicSymbolList , bpp::EdSymbolList
• getCounts() : bpp::SequenceContainerTools , bpp::SymbolListTools
• getDataType() : bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat , bpp::IOSequence , bpp::PhredPhd , bpp::PhredPoly , bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat
• getEnd() : bpp::SymbolListSubstitutionEvent
• getFirstPosition() : bpp::CodonAlphabet
• getFormatDescription() : bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat , bpp::Clustal , bpp::DCSE , bpp::Fasta , bpp::GenBank , bpp::Mase , bpp::NexusIOSequence , bpp::PhredPhd , bpp::PhredPoly , bpp::Phylip , bpp::Stockholm
• getFormatName() : bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat , bpp::Clustal , bpp::DCSE , bpp::Fasta , bpp::GenBank , bpp::Mase , bpp::NexusIOSequence , bpp::PhredPhd , bpp::PhredPoly , bpp::Phylip , bpp::Stockholm
• getFrequencies() : bpp::SequenceContainerTools , bpp::SymbolListTools
• getGapCharacterCode() : bpp::AbstractAlphabet , bpp::Alphabet
• getGCContent() : bpp::SymbolListTools
• getGCcontent() : bpp::StringSequenceTools
• getGeneralComments() : bpp::AbstractSequenceContainer , bpp::SequenceContainer
• getGeneric() : bpp::AbstractAlphabet , bpp::Alphabet , bpp::DNA , bpp::ProteicAlphabet , bpp::RNA , bpp::WordAlphabet
• getGeneticCode() : bpp::SequenceApplicationTools
• getIndex() : 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::AlphabetIndex1 , bpp::AlphabetIndex2 , bpp::BLOSUM50 , bpp::DefaultNucleotideScore , bpp::GranthamAAChemicalDistance , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::KleinAANetChargeIndex , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SimpleScore
• getIndexMatrix() : bpp::AAIndex2Entry , bpp::AlphabetIndex2 , bpp::BLOSUM50 , bpp::DefaultNucleotideScore , bpp::GranthamAAChemicalDistance , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SimpleScore
• getIndexVector() : bpp::AAIndex1Entry , bpp::AAMassIndex , bpp::AASEA1030Index , bpp::AASEAInf10Index , bpp::AASEASup30Index , bpp::AASurfaceIndex , bpp::AAVolumeIndex , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::KleinAANetChargeIndex , bpp::AlphabetIndex1 , bpp::AAChargeIndex , bpp::AAChenGuHuangHydrophobicityIndex , bpp::AAChouFasmanAHelixIndex , bpp::AAChouFasmanBSheetIndex , bpp::AAChouFasmanTurnIndex
• getInvert() : bpp::SequenceTools
• getKey() : bpp::MapSequenceContainer
• getKeys() : bpp::MapSequenceContainer
• getLength() : bpp::SymbolListInsertionEvent , bpp::SymbolListDeletionEvent , bpp::WordAlphabet
• getLetter() : bpp::AlphabetState
• getLetterAlphabet() : bpp::RNY
• getListener() : bpp::EdSymbolList
• getMask() : bpp::SequenceMask
• getMaskedEquivalentState() : bpp::CaseMaskedAlphabet
• getNAlphabet() : bpp::WordAlphabet
• getName() : bpp::AbstractAlphabet , bpp::Alphabet , bpp::AlphabetState , bpp::AbstractSequenceContainer , bpp::OrderedSequenceContainer , bpp::DistanceMatrix , bpp::Sequence , bpp::BasicSequence , bpp::BowkerTest , bpp::SequenceWithAnnotation , bpp::WordAlphabet , bpp::AbstractAlphabet
• getNameIndex() : bpp::DistanceMatrix
• getNames() : bpp::DistanceMatrix
• getNextCommand() : bpp::NexusTools
• getNextNonCommentLine() : bpp::NexusTools
• getNPosition() : bpp::WordAlphabet
• getNucleicAlphabet() : bpp::CodonAlphabet
• getNum() : bpp::AlphabetState
• getNumberOfChars() : bpp::Alphabet , bpp::AbstractAlphabet
• getNumberOfCompleteSites() : bpp::SequenceTools
• getNumberOfDistinctCharacters() : bpp::SiteTools
• getNumberOfDistinctPositions() : bpp::SymbolListTools
• getNumberOfListeners() : bpp::EdSymbolList
• getNumberOfPositionsWithoutGap() : bpp::SymbolListTools
• getNumberOfSequences() : bpp::CompressedVectorSiteContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::VectorSequenceContainer , bpp::Fasta::FileIndex , bpp::Phylip , bpp::SequenceFileIndex , bpp::VectorSiteContainer , bpp::MapSequenceContainer
• getNumberOfSequenceSelections() : bpp::MaseHeader
• getNumberOfSites() : bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::SiteContainer , bpp::VectorSiteContainer , bpp::SequenceTools
• getNumberOfSiteSelections() : bpp::MaseHeader
• getNumberOfTrees() : bpp::MaseHeader
• getNumberOfTypes() : bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::DefaultAlphabet , bpp::ProteicAlphabet , bpp::RNY , bpp::WordAlphabet , bpp::NucleicAlphabet , bpp::Alphabet
• getNumberOfUnresolvedSites() : bpp::SequenceTools
• getOverlap() : bpp::NucleicAlphabet
• getPartAnnotation() : bpp::SequenceAnnotation , bpp::SequenceQuality , bpp::SequenceMask
• getPercentIdentity() : bpp::SequenceTools
• getPhase() : bpp::MaseTools
• getPosition() : bpp::Site , bpp::SequencePositionIterator , bpp::SymbolListInsertionEvent , bpp::AbstractSequencePositionIterator , bpp::SymbolListDeletionEvent
• getPositions() : bpp::WordAlphabet
• getPutativeHaplotypes() : bpp::SequenceTools
• getPValue() : bpp::BowkerTest
• getQualities() : bpp::SequenceWithQuality
• getQuality() : bpp::SequenceWithQuality
• getRNY() : bpp::RNY
• getScores() : bpp::SequenceQuality
• getSecondPosition() : bpp::CodonAlphabet
• getSelectedSequences() : bpp::MaseTools , bpp::SequenceContainerTools
• getSelectedSites() : bpp::SiteContainerTools , bpp::MaseTools
• getSequence() : bpp::MapSequenceContainer , bpp::Fasta::FileIndex , bpp::CompressedVectorSiteContainer , bpp::SequenceContainer , bpp::CompressedVectorSiteContainer , bpp::OrderedSequenceContainer , bpp::VectorSequenceContainer , bpp::SequenceException , bpp::AbstractSequencePositionIterator , bpp::VectorSiteContainer , bpp::VectorSequenceContainer , bpp::MapSequenceContainer , bpp::VectorSiteContainer , bpp::SequencePositionIterator
• getSequence_() : bpp::MapSequenceContainer , bpp::VectorSequenceContainer
• getSequenceByKey() : bpp::MapSequenceContainer
• getSequenceContainer() : bpp::SequenceApplicationTools
• getSequenceId() : bpp::SequenceNotFoundException
• getSequencePosition() : bpp::CompressedVectorSiteContainer , bpp::VectorSequenceContainer , bpp::VectorSiteContainer , bpp::OrderedSequenceContainer , bpp::SequenceFileIndex , bpp::Fasta::FileIndex , bpp::SequenceWalker , bpp::MapSequenceContainer
• getSequencePositions() : bpp::SiteContainerTools
• getSequenceSelection() : bpp::MaseHeader
• getSequenceSelectionNames() : bpp::MaseHeader
• getSequenceSet() : bpp::MaseTools
• getSequencesNames() : bpp::MapSequenceContainer , bpp::OrderedSequenceContainer , bpp::SequenceContainer , bpp::VectorSiteContainer , bpp::CompressedVectorSiteContainer , bpp::VectorSequenceContainer
• getSequenceWithoutGaps() : bpp::SequenceTools
• getSequenceWithoutStops() : bpp::SequenceTools
• getSite() : bpp::CompressedVectorSiteContainer , bpp::SiteContainer , bpp::VectorSiteContainer , bpp::SiteException , bpp::AlignedSequenceContainer
• getSiteContainer() : bpp::SequenceApplicationTools
• getSiteId() : bpp::SiteNotFoundException
• getSiteIndex_() : bpp::CompressedVectorSiteContainer
• getSitePositions() : bpp::SiteContainer , bpp::AlignedSequenceContainer , bpp::CompressedVectorSiteContainer , bpp::VectorSiteContainer
• getSiteSelection() : bpp::MaseHeader
• getSiteSelectionNames() : bpp::MaseHeader
• getSiteSet() : bpp::MaseTools
• getSitesToAnalyse() : bpp::SequenceApplicationTools
• getSitesWithoutGaps() : bpp::SiteContainerTools
• getSize() : bpp::DefaultAlphabet , bpp::RNY , bpp::SequenceMask , bpp::SequenceQuality , bpp::BinaryAlphabet , bpp::ProteicAlphabet , bpp::NucleicAlphabet , bpp::CaseMaskedAlphabet , bpp::Alphabet , bpp::WordAlphabet
• getSizedNames() : bpp::Phylip
• getSourceAlphabet() : bpp::GeneticCode , bpp::DNAToRNA , bpp::Transliterator , bpp::NucleicAcidsReplication , bpp::AbstractReverseTransliterator
• getSplit() : bpp::Phylip
• getState() : bpp::Alphabet , bpp::NucleicAlphabet , bpp::AbstractAlphabet , bpp::Alphabet , bpp::NucleicAlphabet , bpp::ProteicAlphabet , bpp::AbstractAlphabet , bpp::ProteicAlphabet
• getStateAt() : bpp::NucleicAlphabet , bpp::ProteicAlphabet , bpp::AbstractAlphabet , bpp::NucleicAlphabet , bpp::AbstractAlphabet , bpp::ProteicAlphabet
• getStateByBinCode() : bpp::NucleicAlphabet
• getStateCodingSize() : bpp::Alphabet , bpp::AbstractAlphabet , bpp::WordAlphabet
• getStatistic() : bpp::BowkerTest
• getSumOfPairsScores() : bpp::SiteContainerTools
• getSupportedChars() : bpp::AbstractAlphabet , bpp::Alphabet
• getSupportedInts() : bpp::AbstractAlphabet , bpp::Alphabet
• getSymbolList() : bpp::SymbolListEditionEvent
• getSynonymous() : bpp::GeneticCode
• getTargetAlphabet() : bpp::DNAToRNA , bpp::Transliterator , bpp::GeneticCode , bpp::AbstractReverseTransliterator , bpp::NucleicAcidsReplication
• getThirdPosition() : bpp::CodonAlphabet
• getTree() : bpp::MaseHeader
• getTreeNames() : bpp::MaseHeader
• getType() : bpp::SequenceQuality , bpp::AlphabetTools , bpp::SequenceMask , bpp::SequenceAnnotation
• getUnknownCharacterCode() : bpp::NucleicAlphabet , bpp::ProteicAlphabet , bpp::DefaultAlphabet , bpp::RNY , bpp::Alphabet , bpp::WordAlphabet , bpp::CaseMaskedAlphabet , bpp::BinaryAlphabet
• getUnmaskedAlphabet() : bpp::CaseMaskedAlphabet
• getUnparsedArguments() : bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceWriterFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOAlignmentReaderFormat
• getValue() : bpp::SequencePositionIterator , bpp::AbstractSequencePositionIterator , bpp::BasicSymbolList , bpp::EdSymbolList , bpp::SymbolList
• getWord() : bpp::WordAlphabet
• GranthamAAChemicalDistance() : bpp::GranthamAAChemicalDistance
• GranthamAAPolarityIndex() : bpp::GranthamAAPolarityIndex
• GranthamAAVolumeIndex() : bpp::GranthamAAVolumeIndex