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 SiteContainer &sites)	bpp::SiteContainerTools	static
changeGapsToUnknownCharacters(SiteContainer &sites)	bpp::SiteContainerTools	static
changeUnresolvedCharactersToGaps(SiteContainer &sites)	bpp::SiteContainerTools	static
computeSimilarity(const Sequence &seq1, const Sequence &seq2, bool dist=false, const std::string &gapOption=SIMILARITY_NODOUBLEGAP, bool unresolvedAsGap=true)	bpp::SiteContainerTools	static
computeSimilarityMatrix(const SiteContainer &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 SiteContainer &sites)	bpp::SiteContainerTools	static
getConsensus(const SiteContainer &sc, const std::string &name="consensus", bool ignoreGap=true, bool resolveUnknown=false)	bpp::SiteContainerTools	static
getSelectedPositions(const SiteContainer &sequences, const SiteSelection &selection)	bpp::SiteContainerTools	static
getSelectedSites(const SiteContainer &sequences, const SiteSelection &selection)	bpp::SiteContainerTools	static
getSequencePositions(const Sequence &seq)	bpp::SiteContainerTools	static
getSequencePositions(const SiteContainer &sites, Matrix< size_t > &positions)	bpp::SiteContainerTools	static
getSitesWithoutGaps(const SiteContainer &sites)	bpp::SiteContainerTools	static
getSumOfPairsScores(const Matrix< size_t > &positions1, const Matrix< size_t > &positions2, double na=0)	bpp::SiteContainerTools	static
merge(SiteContainer &seqCont1, const SiteContainer &seqCont2, bool leavePositionAsIs=false)	bpp::SiteContainerTools	static
removeGapOnlySites(const SiteContainer &sites)	bpp::SiteContainerTools	static
removeGapOnlySites(SiteContainer &sites)	bpp::SiteContainerTools	static
removeGapOrUnresolvedOnlySites(const SiteContainer &sites)	bpp::SiteContainerTools	static
removeGapOrUnresolvedOnlySites(SiteContainer &sites)	bpp::SiteContainerTools	static
removeGapSites(const SiteContainer &sites, double maxFreqGaps)	bpp::SiteContainerTools	static
removeGapSites(SiteContainer &sites, double maxFreqGaps)	bpp::SiteContainerTools	static
removeStopCodonSites(const SiteContainer &sites, const GeneticCode &gCode)	bpp::SiteContainerTools	static
resolveDottedAlignment(const SiteContainer &dottedAln, const Alphabet *resolvedAlphabet)	bpp::SiteContainerTools	static
sampleSites(const SiteContainer &sites, size_t nbSites, std::vector< size_t > *index=0)	bpp::SiteContainerTools	static
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 SiteContainer &sequences, size_t i1, size_t i2)	bpp::SiteContainerTools	static
~SiteContainerTools()	bpp::SiteContainerTools	inlinevirtual