#include <Bpp/Phyl/App/BppPhylogeneticsApplication.h>
Inheritance diagram for bpp::BppPhylogeneticsApplication:
Collaboration diagram for bpp::BppPhylogeneticsApplication:
Public Member Functions | |
| BppPhylogeneticsApplication (int argc, char *argv[], const std::string &name) | |
| virtual void | fixLikelihood (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, std::shared_ptr< PhyloLikelihoodInterface > phylolik, const std::string &suffix="", bool suffixIsOptional=true) const |
| Method to have a clean likelihood (ie not saturated, nor infinite). More... | |
| virtual void | displayParameters (const PhyloLikelihoodInterface &tl, bool displaylL=true) const |
| Display parameter values. More... | |
| virtual std::shared_ptr< Alphabet > | getAlphabet (const string &suffix="", bool suffixIsOptional=true, bool allowGeneric=false) const |
| virtual std::shared_ptr< GeneticCode > | getGeneticCode (std::shared_ptr< const Alphabet > &alphabet, const string &suffix="", bool suffixIsOptional=true) const |
| virtual std::map< size_t, std::unique_ptr< AlignmentDataInterface > > | getAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const |
| virtual std::map< size_t, std::unique_ptr< const AlignmentDataInterface > > | getConstAlignmentsMap (std::shared_ptr< const Alphabet > &alphabet, bool changeGapsToUnknownCharacters=true, bool optionalData=false, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const |
| virtual void | startTimer () |
| virtual void | done () |
| virtual const std::map< std::string, std::string > & | getParams () const |
| virtual std::map< std::string, std::string > & | getParams () |
| virtual const std::string & | getParam (const std::string &name) const |
| virtual std::string & | getParam (const std::string &name) |
| virtual bool | isVerbose () const |
| virtual int | getWarningLevel () const |
| virtual void | help (const std::string &program) const |
| virtual std::map< size_t, std::shared_ptr< PhyloTree > > | getPhyloTreesMap (const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const |
| Methods to build objects. More... | |
| virtual std::unique_ptr< SubstitutionProcessCollection > | getCollection (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, const std::map< size_t, std::shared_ptr< PhyloTree > > &mpTree, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const |
| get the collection of objects necessary to build substitution processes. More... | |
| virtual std::unique_ptr< SubstitutionProcessCollection > | getCollection (std::shared_ptr< const Alphabet > alphabet, std::shared_ptr< const GeneticCode > gCode, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, std::map< std::string, std::string > &unparsedParams, const std::string &prefix="input.", const std::string &suffix="", bool suffixIsOptional=true) const |
| virtual std::map< size_t, std::unique_ptr< SequenceEvolution > > | getProcesses (std::shared_ptr< SubstitutionProcessCollection > collection, std::map< std::string, std::string > &unparsedParams, const std::string &suffix="", bool suffixIsOptional=true) const |
| get the substitution processes. More... | |
| virtual std::shared_ptr< PhyloLikelihoodContainer > | getPhyloLikelihoods (Context &context, std::map< size_t, std::shared_ptr< SequenceEvolution > > mSeqEvol, std::shared_ptr< SubstitutionProcessCollection > collection, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface > > &mSites, const std::string &suffix="", bool suffixIsOptional=true) const |
| get the phylolikelihoods. More... | |
Protected Attributes | |
| std::string | appName_ |
| std::map< std::string, std::string > | params_ |
| bool | timerStarted_ |
| bool | verbose_ |
| int | warn_ |
Detailed Description
Definition at line 26 of file BppPhylogeneticsApplication.h.
Constructor & Destructor Documentation
◆ BppPhylogeneticsApplication()
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inline |
Definition at line 30 of file BppPhylogeneticsApplication.h.
Member Function Documentation
◆ displayParameters()
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virtual |
Display parameter values.
- Parameters
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tl the phylolikelihood displaylL if log-likelihood is displayed (default: true)
Definition at line 286 of file BppPhylogeneticsApplication.cpp.
References bpp::ParameterList::deleteParameters(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::PhyloLikelihoodInterface::getBranchLengthParameters(), bpp::SecondOrderDerivable::getNumberOfParameters(), bpp::ParameterList::getParameterNames(), bpp::SecondOrderDerivable::getParameters(), bpp::SecondOrderDerivable::getValue(), bpp::ParameterList::size(), and bpp::TextTools::toString().
◆ fixLikelihood()
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virtual |
Method to have a clean likelihood (ie not saturated, nor infinite).
Definition at line 111 of file BppPhylogeneticsApplication.cpp.
References bpp::ApplicationTools::displayBooleanResult(), bpp::ApplicationTools::displayError(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayWarning(), bpp::ApplicationTools::error, bpp::ApplicationTools::getBooleanParameter(), bpp::ProbabilisticSite::getCoordinate(), bpp::Site::getCoordinate(), bpp::SiteContainerTools::getSelectedSites(), bpp::ProbabilisticSite::getStateValueAt(), bpp::Site::getValue(), bpp::AlphabetTools::isCodonAlphabet(), bpp::ParameterList::matchParametersValues(), bpp::BppApplication::params_, bpp::ParameterList::size(), bpp::ProbabilisticSite::size(), bpp::Site::size(), bpp::TextTools::toString(), and bpp::BppApplication::warn_.
◆ getCollection() [1/2]
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virtual |
get the collection of objects necessary to build substitution processes.
Definition at line 61 of file BppPhylogeneticsApplication.cpp.
References bpp::PhylogeneticsApplicationTools::getBranchModels(), bpp::PhylogeneticsApplicationTools::getModelPaths(), bpp::PhylogeneticsApplicationTools::getModelScenarios(), bpp::PhylogeneticsApplicationTools::getRateDistributions(), bpp::PhylogeneticsApplicationTools::getRootFrequencySets(), bpp::PhylogeneticsApplicationTools::getSubstitutionProcessCollection(), bpp::BppApplication::params_, bpp::BppApplication::verbose_, and bpp::BppApplication::warn_.
Referenced by getCollection().
◆ getCollection() [2/2]
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virtual |
Definition at line 47 of file BppPhylogeneticsApplication.cpp.
References getCollection(), and getPhyloTreesMap().
◆ getPhyloLikelihoods()
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virtual |
get the phylolikelihoods.
Definition at line 98 of file BppPhylogeneticsApplication.cpp.
References bpp::PhylogeneticsApplicationTools::getPhyloLikelihoodContainer(), bpp::BppApplication::params_, bpp::BppApplication::verbose_, and bpp::BppApplication::warn_.
◆ getPhyloTreesMap()
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virtual |
Methods to build objects.
Get the std::map of initial phylo trees
Definition at line 19 of file BppPhylogeneticsApplication.cpp.
References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::getDoubleParameter(), bpp::PhylogeneticsApplicationTools::getPhyloTrees(), bpp::BppApplication::params_, bpp::BppApplication::verbose_, and bpp::BppApplication::warn_.
Referenced by getCollection().
◆ getProcesses()
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virtual |
get the substitution processes.
Definition at line 87 of file BppPhylogeneticsApplication.cpp.
References bpp::PhylogeneticsApplicationTools::getSequenceEvolutions(), bpp::BppApplication::params_, bpp::BppApplication::verbose_, and bpp::BppApplication::warn_.
The documentation for this class was generated from the following files:
- Bpp/Phyl/App/BppPhylogeneticsApplication.h
- Bpp/Phyl/App/BppPhylogeneticsApplication.cpp
