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

getAlphabet(const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool allowGeneric=false, int warn=1)	bpp::SequenceApplicationTools	static
getAlphabetIndex1(std::shared_ptr< const Alphabet > alphabet, const std::string &description, const std::string &message="Alphabet measure:", bool verbose=true)	bpp::SequenceApplicationTools	static
getAlphabetIndex1(std::shared_ptr< const CodonAlphabet > alphabet, std::shared_ptr< const GeneticCode > gencode, const std::string &description, const std::string &message="Alphabet measure:", bool verbose=true)	bpp::SequenceApplicationTools	static
getAlphabetIndex2(std::shared_ptr< const Alphabet > alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true)	bpp::SequenceApplicationTools	static
getAlphabetIndex2(std::shared_ptr< const CodonAlphabet > alphabet, std::shared_ptr< const GeneticCode > gencode, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true)	bpp::SequenceApplicationTools	static
getGeneticCode(std::shared_ptr< const NucleicAlphabet > alphabet, const std::string &description)	bpp::SequenceApplicationTools	static
getProbabilisticSiteContainer(std::shared_ptr< const Alphabet > alpha, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
getProbabilisticSiteContainers(std::shared_ptr< const Alphabet > alpha, const std::map< std::string, std::string > &params, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
getSequenceContainer(std::shared_ptr< const Alphabet > alpha, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
getSiteContainer(std::shared_ptr< const Alphabet > alpha, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
getSiteContainers(std::shared_ptr< const Alphabet > alpha, const std::map< std::string, std::string > &params, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
getSitesToAnalyse(const TemplateSiteContainerInterface< SiteType, SequenceType, std::string > &allSites, const std::map< std::string, std::string > &params, std::string suffix="", bool suffixIsOptional=true, bool gapAsUnknown=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	inlinestatic
restrictSelectedSequencesByName(SequenceContainerInterface &allSequences, const std::map< std::string, std::string > &params, std::string suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
SequenceApplicationTools()	bpp::SequenceApplicationTools	inline
writeAlignmentFile(const SiteContainerInterface &sequences, const std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
writeSequenceFile(const SequenceContainerInterface &sequences, const std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)	bpp::SequenceApplicationTools	static
~SequenceApplicationTools()	bpp::SequenceApplicationTools	inlinevirtual