- r -

• read() : bpp::BppOAlignmentReaderFormat , bpp::BppOAlignmentWriterFormat , bpp::BppOAlphabetIndex1Format , bpp::BppOAlphabetIndex2Format , bpp::BppOSequenceReaderFormat , bpp::BppOSequenceStreamReaderFormat , bpp::BppOSequenceWriterFormat , bpp::Fasta::FileIndex
• readAlignment() : bpp::AbstractIAlignment , bpp::AbstractIProbabilisticAlignment , bpp::IAlignment , bpp::IProbabilisticAlignment
• readAlignmentFromFile() : bpp::AbstractIAlignment , bpp::AbstractIProbabilisticAlignment
• readAlignmentFromStream() : bpp::AbstractIAlignment , bpp::AbstractIProbabilisticAlignment
• readDistanceMatrix() : bpp::AbstractIDistanceMatrix , bpp::IDistanceMatrix , bpp::PhylipDistanceMatrixFormat
• readHeader_() : bpp::Mase
• readInterleaved() : bpp::Phylip
• readMeta() : bpp::Mase
• readProbabilistic() : bpp::BppOAlignmentReaderFormat
• readSequences() : bpp::AbstractIAlignment2 , bpp::AbstractIProbabilisticAlignment2 , bpp::AbstractIProbabilisticSequence , bpp::AbstractISequence , bpp::Clustal , bpp::DCSE , bpp::IProbabilisticSequence , bpp::ISequence , bpp::Phylip
• readSequencesFromFile() : bpp::AbstractIProbabilisticSequence , bpp::AbstractISequence
• readSequencesFromStream() : bpp::AbstractIProbabilisticSequence , bpp::AbstractISequence
• readSequential() : bpp::Phylip
• realloc_() : bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• registerState() : bpp::AbstractAlphabet , bpp::LetterAlphabet , bpp::NucleicAlphabet , bpp::NumericAlphabet
• reindexSites() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateAlignmentDataInterface< HashType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• remap() : bpp::AbstractAlphabet , bpp::NumericAlphabet
• removeCoreSymbolListListener() : bpp::AbstractTemplateEventDrivenSymbolList< T > , bpp::TemplateEventDrivenCoreSymbolListInterface< T >
• removeGapOnlySites() : bpp::SiteContainerTools
• removeGapOrUnresolvedOnlySites() : bpp::SiteContainerTools
• removeGaps() : bpp::SequenceTools , bpp::SequenceWithQualityTools
• removeGapSites() : bpp::SiteContainerTools
• removeObject() : bpp::MappedNamedContainer< T > , bpp::NamedContainerInterface< T > , bpp::PositionedContainerInterface< T > , bpp::VectorMappedContainer< T > , bpp::VectorPositionedContainer< T >
• removeSequence() : bpp::CompressedVectorSiteContainer , bpp::TemplateSequenceContainerInterface< SequenceType, HashType > , bpp::TemplateVectorSequenceContainer< SequenceType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• removeSite() : bpp::CompressedVectorSiteContainer , bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType > , bpp::TemplateSiteContainerInterface< SiteType, SequenceType, HashType > , bpp::TemplateVectorSiteContainer< SiteType, SequenceType >
• removeSitesWithStopCodon() : bpp::SiteContainerTools
• removeStops() : bpp::SequenceTools
• replaceStopsWithGaps() : bpp::SequenceTools
• reset() : bpp::DistanceMatrix
• resize() : bpp::AbstractAlphabet , bpp::DistanceMatrix
• resolveDottedAlignment() : bpp::SiteContainerTools
• restrictSelectedSequencesByName() : bpp::SequenceApplicationTools
• reverse() : bpp::AbstractReverseTransliterator , bpp::CodonAlphabet , bpp::CoreWordAlphabet , bpp::DNAToRNA , bpp::NucleicAcidsReplication , bpp::ReverseTransliteratorInterface , bpp::StringSequenceTools , bpp::WordAlphabet
• reverseTranscript() : bpp::SequenceTools , bpp::SequenceWithQualityTools
• ReverseTransliteratorInterface() : bpp::ReverseTransliteratorInterface
• RNA() : bpp::RNA
• RNY() : bpp::RNY
• RNYslice() : bpp::SequenceTools