bpp-seq  2.2.0
bpp::SequenceApplicationTools Member List

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

getAlphabet(std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool allowGeneric=false, int warn=1)bpp::SequenceApplicationToolsstatic
getAlphabetIndex1(const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true)bpp::SequenceApplicationToolsstatic
getAlphabetIndex2(const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true)bpp::SequenceApplicationToolsstatic
getGeneticCode(const NucleicAlphabet *alphabet, const std::string &description)bpp::SequenceApplicationToolsstatic
getSequenceContainer(const Alphabet *alpha, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::SequenceApplicationToolsstatic
getSiteContainer(const Alphabet *alpha, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::SequenceApplicationToolsstatic
getSitesToAnalyse(const SiteContainer &allSites, std::map< std::string, std::string > &params, std::string suffix="", bool suffixIsOptional=true, bool gapAsUnknown=true, bool verbose=true, int warn=1)bpp::SequenceApplicationToolsstatic
SequenceApplicationTools()bpp::SequenceApplicationToolsinline
writeAlignmentFile(const SiteContainer &sequences, std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)bpp::SequenceApplicationToolsstatic
writeSequenceFile(const SequenceContainer &sequences, std::map< std::string, std::string > &params, const std::string &suffix="", bool verbose=true, int warn=1)bpp::SequenceApplicationToolsstatic
~SequenceApplicationTools()bpp::SequenceApplicationToolsinlinevirtual