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

completeMixedSubstitutionModelSet(MixedSubstitutionModelSet &mixedModelSet, std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
getSubstitutionModelSet(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gcode, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
getTrees(const std::map< std::string, std::string > &params, const std::map< size_t, std::shared_ptr< AlignmentDataInterface > > &mSeq, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
LegacyPhylogeneticsApplicationTools()	bpp::LegacyPhylogeneticsApplicationTools
optimizeParameters(std::shared_ptr< TreeLikelihoodInterface > tl, const ParameterList &parameters, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
printParameters(const SubstitutionModelSet &modelSet, OutputStream &out, int warn=1, bool withAlias=true)	bpp::LegacyPhylogeneticsApplicationTools	static
setSubstitutionModelParametersInitialValuesWithAliases(BranchModelInterface &model, std::map< std::string, std::string > &unparsedParameterValues, size_t modelNumber, std::shared_ptr< const AlignmentDataInterface > data, std::map< std::string, std::string > &sharedParams, bool verbose)	bpp::LegacyPhylogeneticsApplicationTools	static
setSubstitutionModelSet(SubstitutionModelSet &modelSet, std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gcode, std::shared_ptr< const AlignmentDataInterface > data, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
writeTrees(const std::vector< const Tree * > &trees, const std::map< std::string, std::string > &params, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
writeTrees(const std::vector< const TreeTemplate< Node > * > &trees, const std::map< std::string, std::string > &params, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, int warn=1)	bpp::LegacyPhylogeneticsApplicationTools	static
~LegacyPhylogeneticsApplicationTools()	bpp::LegacyPhylogeneticsApplicationTools	virtual