bpp::SiteContainerTools Member List

This is the complete list of members for bpp::SiteContainerTools, including all inherited members.

alignNW(const Sequence &seq1, const Sequence &seq2, const AlphabetIndex2 &s, double gap)	bpp::SiteContainerTools	static
alignNW(const Sequence &seq1, const Sequence &seq2, const AlphabetIndex2 &s, double opening, double extending)	bpp::SiteContainerTools	static
bootstrapSites(const TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites, TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &outputSites)	bpp::SiteContainerTools	inlinestatic
bootstrapSites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites)	bpp::SiteContainerTools	inlinestatic
changeGapsToUnknownCharacters(SiteContainerInterface &sites)	bpp::SiteContainerTools	static
changeGapsToUnknownCharacters(ProbabilisticSiteContainerInterface &sites)	bpp::SiteContainerTools	static
changeUnresolvedCharactersToGaps(SiteContainerInterface &sites)	bpp::SiteContainerTools	static
computeSimilarity(const SequenceInterface &seq1, const SequenceInterface &seq2, bool dist=false, const std::string &gapOption=SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap=true)	bpp::SiteContainerTools	static
computeSimilarityMatrix(const SiteContainerInterface &sites, bool dist=false, const std::string &gapOption=SIMILARITY_NOFULLGAP, bool unresolvedAsGap=true)	bpp::SiteContainerTools	static
getAlignmentPositions(const Sequence &seq)	bpp::SiteContainerTools	static
getColumnScores(const Matrix< size_t > &positions1, const Matrix< size_t > &positions2, int na=0)	bpp::SiteContainerTools	static
getCompleteSites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites)	bpp::SiteContainerTools	inlinestatic
getConsensus(const SiteContainerInterface &sc, const std::string &name="consensus", bool ignoreGap=true, bool resolveUnknown=false)	bpp::SiteContainerTools	static
getSelectedPositions(const TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites, const SiteSelection &selection, TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &outputSites)	bpp::SiteContainerTools	inlinestatic
getSelectedPositions(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites, const SiteSelection &selection)	bpp::SiteContainerTools	inlinestatic
getSelectedSites(const TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites, const SiteSelection &selection, TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &outputSites)	bpp::SiteContainerTools	inlinestatic
getSelectedSites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites, const SiteSelection &selection)	bpp::SiteContainerTools	inlinestatic
getSelectedSites(const AlignmentDataInterface &sites, const SiteSelection &selection)	bpp::SiteContainerTools	inlinestatic
getSequencePositions(const Sequence &seq)	bpp::SiteContainerTools	static
getSequencePositions(const SiteContainerInterface &sites, Matrix< size_t > &positions)	bpp::SiteContainerTools	static
getSitesWithoutGaps(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites)	bpp::SiteContainerTools	inlinestatic
getSitesWithoutStopCodon(const SiteContainerInterface &sites, const GeneticCode &gCode)	bpp::SiteContainerTools	inlinestatic
getSumOfPairsScores(const Matrix< size_t > &positions1, const Matrix< size_t > &positions2, double na=0)	bpp::SiteContainerTools	static
merge(TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &seqCont1, const TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &seqCont2, bool leavePositionAsIs=false)	bpp::SiteContainerTools	inlinestatic
removeGapOnlySites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites)	bpp::SiteContainerTools	inlinestatic
removeGapOnlySites(TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites)	bpp::SiteContainerTools	inlinestatic
removeGapOrUnresolvedOnlySites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites)	bpp::SiteContainerTools	inlinestatic
removeGapOrUnresolvedOnlySites(TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites)	bpp::SiteContainerTools	inlinestatic
removeGapSites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites, double maxFreqGaps)	bpp::SiteContainerTools	inlinestatic
removeGapSites(TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites, double maxFreqGaps)	bpp::SiteContainerTools	inlinestatic
removeSitesWithStopCodon(SiteContainerInterface &sites, const GeneticCode &gCode)	bpp::SiteContainerTools	inlinestatic
removeSitesWithStopCodon(ProbabilisticSiteContainerInterface &sites, const GeneticCode &gCode)	bpp::SiteContainerTools	inlinestatic
resolveDottedAlignment(const SiteContainerInterface &dottedAln, std::shared_ptr< const Alphabet > &resolvedAlphabet)	bpp::SiteContainerTools	static
sampleSites(const TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &sites, size_t nbSites, TemplateSiteContainerInterface< SiteType, SequenceType, HashType > &outSites, std::shared_ptr< std::vector< size_t >> index=nullptr)	bpp::SiteContainerTools	inlinestatic
sampleSites(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &sites, size_t nbSites, std::shared_ptr< std::vector< size_t >> index=nullptr)	bpp::SiteContainerTools	inlinestatic
SIMILARITY_ALL	bpp::SiteContainerTools	static
SIMILARITY_NODOUBLEGAP	bpp::SiteContainerTools	static
SIMILARITY_NOFULLGAP	bpp::SiteContainerTools	static
SIMILARITY_NOGAP	bpp::SiteContainerTools	static
SiteContainerTools()	bpp::SiteContainerTools	inline
translateAlignment(const Sequence &seq1, const Sequence &seq2)	bpp::SiteContainerTools	static
translateSequence(const SiteContainerInterface &sequences, size_t i1, size_t i2)	bpp::SiteContainerTools	static
~SiteContainerTools()	bpp::SiteContainerTools	inlinevirtual