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

_DNA	bpp::SequenceTools	privatestatic
_DNARep	bpp::SequenceTools	privatestatic
_RNA	bpp::SequenceTools	privatestatic
_RNARep	bpp::SequenceTools	privatestatic
_RNY	bpp::SequenceTools	privatestatic
_transc	bpp::SequenceTools	privatestatic
bowkerTest(const Sequence &seq1, const Sequence &seq2)	bpp::SequenceTools	static
changeGapsToUnknownCharacters(SymbolList &l)	bpp::SymbolListTools	static
changeUnresolvedCharactersToGaps(SymbolList &l)	bpp::SymbolListTools	static
combineSequences(const Sequence &s1, const Sequence &s2)	bpp::SequenceTools	static
complement(Sequence &seq)	bpp::SequenceTools	static
concatenate(const Sequence &seq1, const Sequence &seq2)	bpp::SequenceTools	static
findFirstOf(const Sequence &seq, const Sequence &motif, bool strict=true)	bpp::SequenceTools	static
getCDS(Sequence &sequence, const GeneticCode &gCode, bool checkInit, bool checkStop, bool includeInit=true, bool includeStop=true)	bpp::SequenceTools	static
getComplement(const Sequence &sequence)	bpp::SequenceTools	static
getCounts(const SymbolList &list, std::map< int, size_t > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, size_t > > &counts)	bpp::SymbolListTools	inlinestatic
getCounts(const SymbolList &list, std::map< int, double > &counts, bool resolveUnknowns)	bpp::SymbolListTools	static
getCounts(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &counts, bool resolveUnknowns)	bpp::SymbolListTools	static
getFrequencies(const SymbolList &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getFrequencies(const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &frequencies, bool resolveUnknowns=false)	bpp::SymbolListTools	static
getGCContent(const SymbolList &list, bool ignoreUnresolved=true, bool ignoreGap=true)	bpp::SymbolListTools	static
getInvert(const Sequence &sequence)	bpp::SequenceTools	static
getNumberOfCompleteSites(const Sequence &seq)	bpp::SequenceTools	static
getNumberOfDistinctPositions(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
getNumberOfPositionsWithoutGap(const SymbolList &l1, const SymbolList &l2)	bpp::SymbolListTools	static
getNumberOfSites(const Sequence &seq)	bpp::SequenceTools	static
getNumberOfUnresolvedSites(const Sequence &seq)	bpp::SequenceTools	static
getPercentIdentity(const Sequence &seq1, const Sequence &seq2, bool ignoreGaps=false)	bpp::SequenceTools	static
getPutativeHaplotypes(const Sequence &seq, std::vector< Sequence *> &hap, unsigned int level=2)	bpp::SequenceTools	static
getRandomSequence(const Alphabet *alphabet, size_t length)	bpp::SequenceTools	static
getSequenceWithCompleteSites(const Sequence &seq)	bpp::SequenceTools	static
getSequenceWithoutGaps(const Sequence &seq)	bpp::SequenceTools	static
getSequenceWithoutStops(const Sequence &seq, const GeneticCode &gCode)	bpp::SequenceTools	static
invert(Sequence &seq)	bpp::SequenceTools	static
invertComplement(Sequence &seq)	bpp::SequenceTools	static
removeGaps(Sequence &seq)	bpp::SequenceTools	static
removeStops(Sequence &seq, const GeneticCode &gCode)	bpp::SequenceTools	static
replaceStopsWithGaps(Sequence &seq, const GeneticCode &gCode)	bpp::SequenceTools	static
reverseTranscript(const Sequence &sequence)	bpp::SequenceTools	static
RNYslice(const Sequence &sequence, int ph)	bpp::SequenceTools	static
RNYslice(const Sequence &sequence)	bpp::SequenceTools	static
SequenceTools()	bpp::SequenceTools	inline
subseq(const Sequence &sequence, size_t begin, size_t end)	bpp::SequenceTools	static
subtractHaplotype(const Sequence &s, const Sequence &h, std::string name="", unsigned int level=1)	bpp::SequenceTools	static
SymbolListTools()	bpp::SymbolListTools	inline
transcript(const Sequence &sequence)	bpp::SequenceTools	static
~SequenceTools()	bpp::SequenceTools	inlinevirtual
~SymbolListTools()	bpp::SymbolListTools	inlinevirtual