- Generated on Tue Jun 10 2025 12:12:10 for bpp-phyl3 by
1.9.4
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bpp-phyl3 3.0.0
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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 > ¶ms, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| checkEstimatedParameters(const ParameterList &pl) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| 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::PhylogeneticsApplicationTools | inlinestatic |
| 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::PhylogeneticsApplicationTools | static |
| getModelPaths(const std::map< std::string, std::string > ¶ms, const map< size_t, std::shared_ptr< BranchModelInterface > > &mModel, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getModelScenarios(const std::map< std::string, std::string > ¶ms, 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::PhylogeneticsApplicationTools | static |
| getMultipleDistributionDefaultInstance(const std::string &distDescription, std::map< std::string, std::string > &unparsedParameterValues, bool verbose=true) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getPhyloTrees(const std::map< std::string, std::string > ¶ms, 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::PhylogeneticsApplicationTools | static |
| getRateDistribution(const std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true) | bpp::PhylogeneticsApplicationTools | static |
| getRateDistributions(const std::map< std::string, std::string > ¶ms, const string &suffix="", bool suffixIsOptional=true, bool verbose=true) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, 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::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, 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::PhylogeneticsApplicationTools | inlinestatic |
| 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 > ¶ms, std::map< std::string, std::string > &sharedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getSequenceEvolutions(std::shared_ptr< SubstitutionProcessCollection > SPC, const std::map< std::string, std::string > ¶ms, map< string, string > &unparsedParams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getSubstitutionCount(std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const SubstitutionModelInterface > model, const std::map< std::string, std::string > ¶ms, string suffix="", bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, std::map< std::string, std::string > &unparsedparams, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| 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 > ¶ms, map< string, string > &unparsedparams, const string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getSubstitutionRegister(const std::string ®TypeDesc, 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::PhylogeneticsApplicationTools | static |
| getTree(const std::map< std::string, std::string > ¶ms, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| getTrees(const std::map< std::string, std::string > ¶ms, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| optimizeParameters(std::shared_ptr< PhyloLikelihoodInterface > lik, const std::map< std::string, std::string > ¶ms, const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| PhylogeneticsApplicationTools() | bpp::PhylogeneticsApplicationTools | |
| printAnalysisInformation(const PhyloLikelihoodContainer &phylocont, const std::string &infosFile, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printAnalysisInformation(const SingleDataPhyloLikelihoodInterface &phylolike, const std::string &infosFile, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printAnalysisInformation(const AlignedPhyloLikelihoodSetInterface &sOAP, const std::string &infosFile, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const BranchModelInterface &model, OutputStream &out, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const SubstitutionProcessInterface &process, OutputStream &out, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const SubstitutionProcessCollection &collection, OutputStream &out, int warn=1, bool withAlias=true) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const PhyloLikelihoodContainer &phylocont, OutputStream &out, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const SingleDataPhyloLikelihoodInterface &phylolike, OutputStream &out, size_t nPhylo=1, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const SequenceEvolution &evol, OutputStream &out, size_t nEvol=1, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| printParameters(const DiscreteDistributionInterface &rDist, OutputStream &out, bool withAlias=true) | bpp::PhylogeneticsApplicationTools | static |
| uniqueToSharedMap(std::map< size_t, std::unique_ptr< T > > &mu) | bpp::PhylogeneticsApplicationTools | inlinestatic |
| writePhyloTrees(const std::vector< const PhyloTree * > &trees, const std::map< std::string, std::string > ¶ms, const std::string &prefix="output.", const std::string &suffix="", bool suffixIsOptional=true, bool verbose=true, bool checkOnly=false, int warn=1) | bpp::PhylogeneticsApplicationTools | static |
| writePhyloTrees(const SubstitutionProcessCollection &spc, const std::map< std::string, std::string > ¶ms, 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::PhylogeneticsApplicationTools | static |
| writeTree(const TreeTemplate< Node > &tree, const std::map< std::string, std::string > ¶ms, 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 |
1.9.4