bpp-phyl3  3.0.0
bpp::PhylogeneticsApplicationTools Member List

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

addSubstitutionProcessCollectionMember(SubstitutionProcessCollection &SubProColl, size_t procNum, const std::map< std::string, std::string > &params, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
checkEstimatedParameters(const ParameterList &pl)bpp::PhylogeneticsApplicationToolsstatic
getBranchModel(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, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getBranchModels(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getFrequencySet(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::string &freqDescription, std::shared_ptr< const AlignmentDataInterface > data, std::map< std::string, std::string > &sharedParams, const std::vector< double > &rateFreqs, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsinlinestatic
getFrequencySet(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::string &freqDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, std::map< std::string, std::string > &sharedParams, const std::vector< double > &rateFreqs, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getModelPaths(const std::map< std::string, std::string > &params, const map< size_t, std::shared_ptr< BranchModelInterface >> &mModel, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getModelScenarios(const std::map< std::string, std::string > &params, const map< size_t, std::shared_ptr< ModelPath >> &mModelPath, const map< size_t, std::shared_ptr< BranchModelInterface >> &mModel, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getMultipleDistributionDefaultInstance(const std::string &distDescription, std::map< std::string, std::string > &unparsedParameterValues, bool verbose=true)bpp::PhylogeneticsApplicationToolsstatic
getPhyloLikelihoodContainer(Context &context, std::shared_ptr< SubstitutionProcessCollection > SPC, std::map< size_t, std::shared_ptr< SequenceEvolution >> &mSeqEvol, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getPhyloTrees(const std::map< std::string, std::string > &params, const std::map< size_t, std::shared_ptr< const 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::PhylogeneticsApplicationToolsstatic
getRateDistribution(const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true)bpp::PhylogeneticsApplicationToolsstatic
getRateDistributions(const std::map< std::string, std::string > &params, const string &suffix="", bool suffixIsOptional=true, bool verbose=true)bpp::PhylogeneticsApplicationToolsstatic
getRootFrequencySet(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &sharedparams, const std::vector< double > &rateFreqs, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getRootFrequencySet(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, std::map< std::string, std::string > &sharedparams, const std::vector< double > &rateFreqs, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsinlinestatic
getRootFrequencySets(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, const std::map< std::string, std::string > &params, std::map< std::string, std::string > &sharedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSequenceEvolutions(std::shared_ptr< SubstitutionProcessCollection > SPC, const std::map< std::string, std::string > &params, map< string, string > &unparsedParams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSubstitutionCount(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const SubstitutionModelInterface > model, const std::map< std::string, std::string > &params, string suffix="", bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSubstitutionModel(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, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSubstitutionProcess(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< const AlignmentDataInterface > data, const vector< std::shared_ptr< PhyloTree >> &vTree, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSubstitutionProcessCollection(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const map< size_t, std::shared_ptr< PhyloTree >> &mTree, const map< size_t, std::shared_ptr< BranchModelInterface >> &mMod, const map< size_t, std::shared_ptr< FrequencySetInterface >> &mRootFreq, const map< size_t, std::shared_ptr< DiscreteDistributionInterface >> &mDist, const map< size_t, std::shared_ptr< ModelScenario >> &mScen, const std::map< std::string, std::string > &params, map< string, string > &unparsedparams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
getSubstitutionRegister(const std::string &regTypeDesc, std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode, std::shared_ptr< AlphabetIndex2 > &weights, std::shared_ptr< AlphabetIndex2 > &distances, bool verbose=true)bpp::PhylogeneticsApplicationToolsstatic
getTree(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::PhylogeneticsApplicationToolsstatic
getTrees(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::PhylogeneticsApplicationToolsstatic
optimizeParameters(std::shared_ptr< PhyloLikelihoodInterface > lik, const std::map< std::string, std::string > &params, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
PhylogeneticsApplicationTools()bpp::PhylogeneticsApplicationTools
printAnalysisInformation(const PhyloLikelihoodContainer &phylocont, const std::string &infosFile, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printAnalysisInformation(const SingleDataPhyloLikelihoodInterface &phylolike, const std::string &infosFile, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printAnalysisInformation(const AlignedPhyloLikelihoodSetInterface &sOAP, const std::string &infosFile, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const BranchModelInterface &model, OutputStream &out, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const SubstitutionProcessInterface &process, OutputStream &out, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const SubstitutionProcessCollection &collection, OutputStream &out, int warn=1, bool withAlias=true)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const PhyloLikelihoodContainer &phylocont, OutputStream &out, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const SingleDataPhyloLikelihoodInterface &phylolike, OutputStream &out, size_t nPhylo=1, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const SequenceEvolution &evol, OutputStream &out, size_t nEvol=1, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
printParameters(const DiscreteDistributionInterface &rDist, OutputStream &out, bool withAlias=true)bpp::PhylogeneticsApplicationToolsstatic
uniqueToSharedMap(std::map< size_t, std::unique_ptr< T >> &mu)bpp::PhylogeneticsApplicationToolsinlinestatic
writePhyloTrees(const std::vector< const PhyloTree * > &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::PhylogeneticsApplicationToolsstatic
writePhyloTrees(const SubstitutionProcessCollection &spc, 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, bool withIds=false, int warn=1)bpp::PhylogeneticsApplicationToolsstatic
writeTree(const TreeTemplate< Node > &tree, 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::PhylogeneticsApplicationToolsstatic
~PhylogeneticsApplicationTools()bpp::PhylogeneticsApplicationToolsvirtual