bpp-seq
2.2.0
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This is the complete list of members for bpp::SequenceApplicationTools, including all inherited members.
getAlphabet(std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool allowGeneric=false, int warn=1) | bpp::SequenceApplicationTools | static |
getAlphabetIndex1(const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true) | bpp::SequenceApplicationTools | static |
getAlphabetIndex2(const Alphabet *alphabet, const std::string &description, const std::string &message="Alphabet distance:", bool verbose=true) | bpp::SequenceApplicationTools | static |
getGeneticCode(const NucleicAlphabet *alphabet, const std::string &description) | bpp::SequenceApplicationTools | static |
getSequenceContainer(const Alphabet *alpha, std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::SequenceApplicationTools | static |
getSiteContainer(const Alphabet *alpha, std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::SequenceApplicationTools | static |
getSitesToAnalyse(const SiteContainer &allSites, std::map< std::string, std::string > ¶ms, std::string suffix="", bool suffixIsOptional=true, bool gapAsUnknown=true, bool verbose=true, int warn=1) | bpp::SequenceApplicationTools | static |
SequenceApplicationTools() | bpp::SequenceApplicationTools | inline |
writeAlignmentFile(const SiteContainer &sequences, std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool verbose=true, int warn=1) | bpp::SequenceApplicationTools | static |
writeSequenceFile(const SequenceContainer &sequences, std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool verbose=true, int warn=1) | bpp::SequenceApplicationTools | static |
~SequenceApplicationTools() | bpp::SequenceApplicationTools | inlinevirtual |