- g -

• GenBank() : bpp::GenBank
• generateCodonSiteWithoutRareVariant() : bpp::CodonSiteTools
• GeneticCode() : bpp::GeneticCode
• getAbbr() : bpp::ProteicAlphabet
• getAbbreviation() : bpp::ProteicAlphabetState
• getAlias() : bpp::AbstractAlphabet , bpp::AllelicAlphabet , bpp::Alphabet , bpp::BinaryAlphabet , bpp::CodonAlphabet , bpp::DNA , bpp::NumericAlphabet , bpp::ProteicAlphabet , bpp::RNA , bpp::RNY , bpp::WordAlphabet
• getAlignmentPosition() : bpp::SequenceWalker
• getAlignmentPositions() : bpp::SiteContainerTools
• getAlignmentsMap() : bpp::BppSequenceApplication
• getAlphabet() : bpp::AbstractTemplateSequenceContainer< SequenceType, HashType > , bpp::AbstractTemplateSymbolList< T > , bpp::AlphabetException , bpp::AlphabetIndex1 , bpp::AlphabetIndex2 , bpp::BppSequenceApplication , bpp::CodonFromProteicAlphabetIndex1 , bpp::CodonFromProteicAlphabetIndex2 , bpp::CruxSymbolListInterface , bpp::DefaultNucleotideScore , bpp::ProbabilisticSymbolList , bpp::ProteicAlphabetIndex1 , bpp::ProteicAlphabetIndex2 , bpp::SequenceApplicationTools , bpp::SequencedValuesContainer , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::TemplateSequenceDataInterface< HashType > , bpp::UserAlphabetIndex1 , bpp::UserAlphabetIndex2
• getAlphabetCodingSize() : bpp::AlphabetTools
• getAlphabetFromSequence() : bpp::StringSequenceTools
• getAlphabetIndex1() : bpp::SequenceApplicationTools , bpp::SimpleIndexDistance
• getAlphabetIndex2() : bpp::SequenceApplicationTools
• getAlphabetType() : bpp::AllelicAlphabet , bpp::Alphabet , bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::CodonAlphabet , bpp::DefaultAlphabet , bpp::DNA , bpp::IntegerAlphabet , bpp::LexicalAlphabet , bpp::NumericAlphabet , bpp::ProteicAlphabet , bpp::RNA , bpp::RNY , bpp::WordAlphabet
• getAnnotationTypes() : bpp::SequenceWithAnnotation
• getAvailableSequenceSelections() : bpp::MaseTools
• getAvailableSiteSelections() : bpp::MaseTools
• getBadChar() : bpp::BadCharException
• getBadInt() : bpp::BadIntException
• getBegin() : bpp::CoreSymbolListSubstitutionEvent< T >
• getBinaryCode() : bpp::NucleicAlphabetState
• getCDS() : bpp::SequenceTools
• getChar() : bpp::AbstractSequencePositionIterator , bpp::EventDrivenIntSymbolList , bpp::IntSymbolList , bpp::IntSymbolListInterface , bpp::Sequence , bpp::SequencePositionIterator
• getCharCodeAt() : bpp::AbstractAlphabet , bpp::Alphabet
• getCodingSequence() : bpp::GeneticCode
• getCodon() : bpp::CodonAlphabet , bpp::StopCodonException
• getCodonAlphabet() : bpp::GeneticCode
• getCodonPosition() : bpp::SequenceContainerTools
• getColumnScores() : bpp::SiteContainerTools
• getComments() : bpp::Commentable , bpp::SequencedValuesContainer , bpp::SimpleCommentable
• getComplement() : bpp::SequenceTools
• getCompleteSites() : bpp::SiteContainerTools
• getConsensus() : bpp::SiteContainerTools
• getConstAlignmentsMap() : bpp::BppSequenceApplication
• getContainer() : bpp::EmptyContainerException
• getContent() : bpp::AbstractTemplateSymbolList< T > , bpp::ProbabilisticSymbolList , bpp::TemplateCoreSymbolListInterface< T >
• getCoordinate() : bpp::AbstractCoreSite , bpp::CoreSiteInterface
• getCoreSymbolList() : bpp::CoreSymbolListEditionEvent< T >
• getCounts() : bpp::SequenceContainerTools , bpp::SymbolListTools
• getCountsResolveUnknowns() : bpp::SymbolListTools
• getDataType() : bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat , bpp::IODistanceMatrix , bpp::IOProbabilisticSequence , bpp::IOSequence , bpp::Pasta , bpp::PhredPhd , bpp::PhredPoly
• getDelta() : bpp::NumericAlphabet
• getElement() : bpp::AbstractTemplateSymbolList< T > , bpp::ProbabilisticSymbolList , bpp::TemplateCoreSymbolListInterface< T >
• getEnd() : bpp::CoreSymbolListSubstitutionEvent< T >
• getFirstAlphabet() : bpp::AlphabetMismatchException
• 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::Pasta , bpp::PhredPhd , bpp::PhredPoly , bpp::Phylip , bpp::PhylipDistanceMatrixFormat , 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::Pasta , bpp::PhredPhd , bpp::PhredPoly , bpp::Phylip , bpp::PhylipDistanceMatrixFormat , bpp::Stockholm
• getFrequencies() : bpp::SequenceContainerTools , bpp::SymbolListTools
• getGapCharacterCode() : bpp::AbstractAlphabet , bpp::Alphabet
• getGCcontent() : bpp::StringSequenceTools
• getGCContent() : bpp::SymbolListTools
• getGCinCodon() : bpp::CodonAlphabet
• getGeneralComments() : bpp::SequencedValuesContainer
• getGeneric() : bpp::AbstractAlphabet , bpp::AllelicAlphabet , bpp::Alphabet , bpp::CodonAlphabet , bpp::DNA , bpp::ProteicAlphabet , bpp::RNA , bpp::WordAlphabet
• getGeneticCode() : bpp::BppSequenceApplication , 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::CodonFromProteicAlphabetIndex1 , bpp::CodonFromProteicAlphabetIndex2 , bpp::DefaultNucleotideScore , bpp::GranthamAAChemicalDistance , bpp::GranthamAAPolarityIndex , bpp::GranthamAAVolumeIndex , bpp::KD_AAHydropathyIndex , bpp::KleinAANetChargeIndex , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::UserAlphabetIndex1 , bpp::UserAlphabetIndex2
• getIndexMatrix() : bpp::AAIndex2Entry , bpp::AlphabetIndex2 , bpp::BLOSUM50 , bpp::CodonFromProteicAlphabetIndex2 , bpp::DefaultNucleotideScore , bpp::GranthamAAChemicalDistance , bpp::MiyataAAChemicalDistance , bpp::SimpleIndexDistance , bpp::SimpleScore , bpp::UserAlphabetIndex2
• getIntCodeAt() : bpp::AbstractAlphabet , bpp::Alphabet
• getInvert() : bpp::SequenceTools
• getLength() : bpp::CodonAlphabet , bpp::CoreSymbolListDeletionEvent< T > , bpp::CoreSymbolListInsertionEvent< T > , bpp::CoreWordAlphabet , bpp::WordAlphabet
• getLetter() : bpp::AlphabetState
• getLetterAlphabet() : bpp::RNY
• getListener() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• getMajorAllele() : bpp::SymbolListTools
• getMajorAlleleFrequency() : bpp::SymbolListTools
• getMask() : bpp::SequenceMask
• getMaskedEquivalentState() : bpp::CaseMaskedAlphabet
• getMinorAllele() : bpp::SymbolListTools
• getMinorAlleleFrequency() : bpp::SymbolListTools
• getNAlphabet() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::WordAlphabet
• getName() : bpp::AbstractAlphabet , bpp::AbstractCoreSequence , bpp::Alphabet , bpp::AlphabetState , bpp::BowkerTest , bpp::CoreSequenceInterface , bpp::DistanceMatrix , bpp::WordAlphabet
• getNameIndex() : bpp::DistanceMatrix
• getNames() : bpp::DistanceMatrix
• getNbAlleles() : bpp::AllelicAlphabet
• getNextCommand() : bpp::NexusTools
• getNextNonCommentLine() : bpp::NexusTools
• getNPosition() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::WordAlphabet
• getNucleicAlphabet() : bpp::CodonAlphabet
• getNum() : bpp::AlphabetState
• getNumberOfChars() : bpp::AbstractAlphabet , bpp::Alphabet
• getNumberOfCompleteSites() : bpp::SequenceTools
• getNumberOfDistinctCharacters() : bpp::SymbolListTools
• getNumberOfDistinctPositions() : bpp::SymbolListTools
• getNumberOfListeners() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• getNumberOfObjects() : bpp::VectorMappedContainer< T >
• getNumberOfPositionsWithoutGap() : bpp::SymbolListTools
• getNumberOfSequences() : bpp::CompressedVectorSiteContainer , bpp::Fasta::FileIndex , bpp::Phylip , bpp::SequencedValuesContainer , bpp::SequenceFileIndex , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getNumberOfSequenceSelections() : bpp::MaseHeader
• getNumberOfSites() : bpp::CompressedVectorSiteContainer , bpp::SequenceTools , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getNumberOfSiteSelections() : bpp::MaseHeader
• getNumberOfStates() : bpp::AbstractAlphabet , bpp::Alphabet
• getNumberOfStopCodons() : bpp::AscidianMitochondrialGeneticCode , bpp::CiliateNuclearGeneticCode , bpp::EchinodermMitochondrialGeneticCode , bpp::GeneticCode , bpp::InvertebrateMitochondrialGeneticCode , bpp::MoldMitochondrialGeneticCode , bpp::StandardGeneticCode , bpp::VertebrateMitochondrialGeneticCode , bpp::YeastMitochondrialGeneticCode
• getNumberOfTrees() : bpp::MaseHeader
• getNumberOfTypes() : bpp::AllelicAlphabet , bpp::Alphabet , bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::CodonAlphabet , bpp::DefaultAlphabet , bpp::IntegerAlphabet , bpp::LexicalAlphabet , bpp::NucleicAlphabet , bpp::NumericAlphabet , bpp::ProteicAlphabet , bpp::RNY , bpp::WordAlphabet
• getNumberOfUniqueSites() : bpp::CompressedVectorSiteContainer
• getNumberOfUnresolvedSites() : bpp::SequenceTools
• getObject() : bpp::MappedNamedContainer< T > , bpp::NamedContainerInterface< T > , bpp::PositionedContainerInterface< T > , bpp::VectorPositionedContainer< T >
• getObject_() : bpp::VectorPositionedContainer< T >
• getObjectName() : bpp::PositionedNamedContainerInterface< T > , bpp::VectorMappedContainer< T >
• getObjectNames() : bpp::MappedNamedContainer< T > , bpp::NamedContainerInterface< T > , bpp::VectorMappedContainer< T >
• getObjectPosition() : bpp::PositionedNamedContainerInterface< T > , bpp::VectorMappedContainer< T >
• getOverlap() : bpp::NucleicAlphabet
• getPartAnnotation() : bpp::SequenceAnnotation , bpp::SequenceMask , bpp::SequenceQuality
• getPercentIdentity() : bpp::SequenceTools
• getPhase() : bpp::MaseTools
• getPosition() : bpp::AbstractSequencePositionIterator , bpp::CoreSymbolListDeletionEvent< T > , bpp::CoreSymbolListInsertionEvent< T > , bpp::SequencePositionIterator
• getPositions() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::WordAlphabet
• getProbabilisticSiteContainer() : bpp::SequenceApplicationTools
• getProbabilisticSiteContainers() : bpp::SequenceApplicationTools
• getProteicAlphabet() : bpp::GeneticCode
• getPutativeHaplotypes() : bpp::SequenceTools
• getPValue() : bpp::BowkerTest
• getQualities() : bpp::SequenceWithQuality
• getQuality() : bpp::SequenceWithQuality
• getRandomSequence() : bpp::SequenceTools
• getResolvedChars() : bpp::AbstractAlphabet , bpp::Alphabet
• getRNY() : bpp::RNY
• getScores() : bpp::SequenceQuality
• getSecondAlphabet() : bpp::AlphabetMismatchException
• getSecondPosition() : bpp::CodonAlphabet
• getSelectedPositions() : bpp::SiteContainerTools
• getSelectedSequences() : bpp::MaseTools , bpp::SequenceContainerTools
• getSelectedSites() : bpp::MaseTools , bpp::SiteContainerTools
• getSequence() : bpp::AbstractSequencePositionIterator , bpp::Fasta::FileIndex , bpp::SequenceException , bpp::SequencePositionIterator
• getSequenceComments() : bpp::CompressedVectorSiteContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getSequenceContainer() : bpp::SequenceApplicationTools
• getSequenceId() : bpp::SequenceNotFoundException
• getSequenceKeys() : bpp::CompressedVectorSiteContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getSequenceNames() : bpp::CompressedVectorSiteContainer , bpp::SequencedValuesContainer , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getSequencePosition() : bpp::CompressedVectorSiteContainer , bpp::Fasta::FileIndex , bpp::SequenceFileIndex , bpp::SequenceWalker , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getSequencePositions() : bpp::SiteContainerTools
• getSequenceSelection() : bpp::MaseHeader
• getSequenceSelectionNames() : bpp::MaseHeader
• getSequenceSet() : bpp::MaseTools
• getSequenceWithCompleteSites() : bpp::SequenceTools
• getSequenceWithoutGaps() : bpp::SequenceTools
• getSequenceWithoutStops() : bpp::SequenceTools
• getSite() : bpp::SiteException
• getSite_() : bpp::CompressedVectorSiteContainer
• getSiteContainer() : bpp::SequenceApplicationTools
• getSiteContainers() : bpp::SequenceApplicationTools
• getSiteCoordinates() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getSiteId() : bpp::SiteNotFoundException
• getSiteIndex_() : bpp::CompressedVectorSiteContainer
• getSiteSelection() : bpp::MaseHeader
• getSiteSelectionNames() : bpp::MaseHeader
• getSiteSet() : bpp::MaseTools
• getSitesToAnalyse() : bpp::SequenceApplicationTools
• getSitesWithoutGaps() : bpp::SiteContainerTools
• getSitesWithoutStopCodon() : bpp::SiteContainerTools
• getSize() : bpp::AllelicAlphabet , bpp::Alphabet , bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::DefaultAlphabet , bpp::IntegerAlphabet , bpp::LexicalAlphabet , bpp::MappedNamedContainer< T > , bpp::NamedContainerInterface< T > , bpp::NucleicAlphabet , bpp::NumericAlphabet , bpp::PositionedContainerInterface< T > , bpp::ProteicAlphabet , bpp::RNY , bpp::SequenceMask , bpp::SequenceQuality , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T > , bpp::WordAlphabet
• getSizedNames() : bpp::Phylip
• getSourceAlphabet() : bpp::AllelicAlphabet::AllelicTransliterator , bpp::DNAToRNA , bpp::GeneticCode , bpp::NucleicAcidsReplication , bpp::TransliteratorInterface
• getSplit() : bpp::Phylip
• getState() : bpp::AbstractAlphabet , bpp::Alphabet , bpp::NucleicAlphabet , bpp::ProteicAlphabet
• getStateAlphabet() : bpp::AllelicAlphabet
• getStateAt() : bpp::AbstractAlphabet , bpp::Alphabet , bpp::NucleicAlphabet , bpp::NumericAlphabet , bpp::ProteicAlphabet
• getStateByBinCode() : bpp::NucleicAlphabet
• getStateCodingSize() : bpp::AbstractAlphabet , bpp::AllelicAlphabet , bpp::Alphabet , bpp::CodonAlphabet , bpp::WordAlphabet
• getStateIndex() : bpp::AbstractAlphabet , bpp::Alphabet
• getStateValueAt() : bpp::CompressedVectorSiteContainer , bpp::CoreSiteInterface , bpp::CruxSymbolListInterface , bpp::IntSymbolList , bpp::ProbabilisticSequence , bpp::ProbabilisticSite , bpp::ProbabilisticSymbolList , bpp::Sequence , bpp::SequencedValuesContainer , bpp::Site , bpp::TemplateSequenceDataInterface< HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• getStatistic() : bpp::BowkerTest
• getStopCodonsAsChar() : bpp::AscidianMitochondrialGeneticCode , bpp::CiliateNuclearGeneticCode , bpp::EchinodermMitochondrialGeneticCode , bpp::GeneticCode , bpp::InvertebrateMitochondrialGeneticCode , bpp::MoldMitochondrialGeneticCode , bpp::StandardGeneticCode , bpp::VertebrateMitochondrialGeneticCode , bpp::YeastMitochondrialGeneticCode
• getStopCodonsAsInt() : bpp::AscidianMitochondrialGeneticCode , bpp::CiliateNuclearGeneticCode , bpp::EchinodermMitochondrialGeneticCode , bpp::GeneticCode , bpp::InvertebrateMitochondrialGeneticCode , bpp::MoldMitochondrialGeneticCode , bpp::StandardGeneticCode , bpp::VertebrateMitochondrialGeneticCode , bpp::YeastMitochondrialGeneticCode
• getSumOfPairsScores() : bpp::SiteContainerTools
• getSupportedChars() : bpp::AbstractAlphabet , bpp::Alphabet
• getSupportedInts() : bpp::AbstractAlphabet , bpp::Alphabet
• getSynonymous() : bpp::GeneticCode
• getTable() : bpp::ProbabilisticSymbolList , bpp::ProbabilisticSymbolListInterface
• getTargetAlphabet() : bpp::AllelicAlphabet::AllelicTransliterator , bpp::DNAToRNA , bpp::GeneticCode , bpp::NucleicAcidsReplication , bpp::TransliteratorInterface
• getThirdPosition() : bpp::CodonAlphabet
• getTree() : bpp::MaseHeader
• getTreeNames() : bpp::MaseHeader
• getType() : bpp::AlphabetTools , bpp::SequenceAnnotation , bpp::SequenceMask , bpp::SequenceQuality
• getUnknownCharacterCode() : bpp::AllelicAlphabet , bpp::Alphabet , bpp::BinaryAlphabet , bpp::CaseMaskedAlphabet , bpp::CodonAlphabet , bpp::DefaultAlphabet , bpp::IntegerAlphabet , bpp::LexicalAlphabet , bpp::NucleicAlphabet , bpp::NumericAlphabet , bpp::ProteicAlphabet , bpp::RNY , bpp::WordAlphabet
• getUnmaskedAlphabet() : bpp::CaseMaskedAlphabet
• getUnparsedArguments() : bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat
• getValue() : bpp::AbstractSequencePositionIterator , bpp::AbstractTemplateSymbolList< T > , bpp::AlphabetNumericState , bpp::ProbabilisticSymbolList , bpp::SequencePositionIterator , bpp::TemplateCoreSymbolListInterface< T >
• getValueIndex() : bpp::NumericAlphabet
• getWord() : bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::WordAlphabet
• GranthamAAChemicalDistance() : bpp::GranthamAAChemicalDistance
• GranthamAAPolarityIndex() : bpp::GranthamAAPolarityIndex
• GranthamAAVolumeIndex() : bpp::GranthamAAVolumeIndex