PhylogeneticsApplicationTools.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_APP_PHYLOGENETICSAPPLICATIONTOOLS_H
#define BPP_PHYL_LEGACY_APP_PHYLOGENETICSAPPLICATIONTOOLS_H
 
#include <Bpp/Io/OutputStream.h>
#include <Bpp/Numeric/Function/Optimizer.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/Prob/MultipleDiscreteDistribution.h>
#include <Bpp/Text/TextTools.h>
 
#include "../../Model/MarkovModulatedSubstitutionModel.h"
#include "../../Model/SubstitutionModel.h"
#include "../../Tree/Tree.h"
#include "../Likelihood/HomogeneousTreeLikelihood.h"
#include "../Model/MixedSubstitutionModelSet.h"
#include "../Model/SubstitutionModelSet.h"
 
// From SeqLib:
#include <Bpp/Seq/Container/SiteContainer.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
#include <Bpp/Seq/Io/BppOAlphabetIndex2Format.h>
 
// From the STL:
#include <string>
#include <map>
#include <memory>
#include <vector>
 
 
namespace bpp
{
class LegacyPhylogeneticsApplicationTools
{
public:
  LegacyPhylogeneticsApplicationTools();
  virtual ~LegacyPhylogeneticsApplicationTools();
 
  static std::map<size_t, std::shared_ptr<Tree>> 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);
 
  static void 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);
 
  static std::unique_ptr<SubstitutionModelSet> 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);
 
 
  static void 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);
 
  static void 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);
 
  static std::shared_ptr<TreeLikelihoodInterface> 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);
 
 
  static void 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);
 
  static void 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);
 
  static void printParameters(
      const SubstitutionModelSet& modelSet,
      OutputStream& out,
      int warn = 1,
      bool withAlias = true);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_APP_PHYLOGENETICSAPPLICATIONTOOLS_H