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

checkEstimatedParameters(const ParameterList &pl)	bpp::PhylogeneticsApplicationTools	static
completeMixedSubstitutionModelSet(MixedSubstitutionModelSet &mixedModelSet, const Alphabet alphabet, const SiteContainer data, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getFrequenciesSet(const Alphabet alphabet, const GeneticCode gCode, const std::string &freqDescription, const SiteContainer *data, const std::vector< double > &rateFreqs, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getMultipleDistributionDefaultInstance(const std::string &distDescription, std::map< std::string, std::string > &unparsedParameterValues, bool verbose=true)	bpp::PhylogeneticsApplicationTools	static
getRateDistribution(std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true)	bpp::PhylogeneticsApplicationTools	static
getRootFrequenciesSet(const Alphabet alphabet, const GeneticCode gCode, const SiteContainer *data, std::map< std::string, std::string > &params, const std::vector< double > &rateFreqs, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getSubstitutionCount(const Alphabet alphabet, const SubstitutionModel model, map< string, string > &params, string suffix="", bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getSubstitutionModel(const Alphabet alphabet, const GeneticCode gCode, const SiteContainer *data, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getSubstitutionModelSet(const Alphabet alphabet, const GeneticCode gcode, const SiteContainer *data, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
getTree(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::PhylogeneticsApplicationTools	static
getTrees(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::PhylogeneticsApplicationTools	static
optimizeParameters(TreeLikelihood *tl, const ParameterList &parameters, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
optimizeParameters(DiscreteRatesAcrossSitesClockTreeLikelihood *tl, const ParameterList &parameters, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
PhylogeneticsApplicationTools()	bpp::PhylogeneticsApplicationTools
printParameters(const SubstitutionModel *model, OutputStream &out, int warn=1)	bpp::PhylogeneticsApplicationTools	static
printParameters(const SubstitutionModelSet *modelSet, OutputStream &out, int warn=1)	bpp::PhylogeneticsApplicationTools	static
printParameters(const DiscreteDistribution *rDist, OutputStream &out)	bpp::PhylogeneticsApplicationTools	static
setSubstitutionModelParametersInitialValuesWithAliases(SubstitutionModel &model, std::map< std::string, std::string > &unparsedParameterValues, size_t modelNumber, const SiteContainer *data, std::map< std::string, double > &existingParams, std::map< std::string, std::string > &sharedParams, bool verbose)	bpp::PhylogeneticsApplicationTools	static
setSubstitutionModelSet(SubstitutionModelSet &modelSet, const Alphabet alphabet, const GeneticCode gcode, const SiteContainer *data, std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)	bpp::PhylogeneticsApplicationTools	static
writeTree(const TreeTemplate< Node > &tree, 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::PhylogeneticsApplicationTools	static
writeTrees(const std::vector< Tree *> &trees, 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::PhylogeneticsApplicationTools	static
~PhylogeneticsApplicationTools()	bpp::PhylogeneticsApplicationTools	virtual