BppPhylogeneticsApplication.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_APP_BPPPHYLOGENETICSAPPLICATION_H
#define BPP_PHYL_APP_BPPPHYLOGENETICSAPPLICATION_H
 
 
#include "../Likelihood/PhyloLikelihoods/PhyloLikelihoodContainer.h"
#include "../Likelihood/SequenceEvolution.h"
#include "../Likelihood/SubstitutionProcessCollection.h"
#include "../Tree/PhyloTree.h"
 
// From the STL:
#include <iostream>
#include <iomanip>
#include <limits>
 
using namespace std;
 
// From bpp-seq:
#include <Bpp/Seq/App/BppSequenceApplication.h>
 
namespace bpp
{
class BppPhylogeneticsApplication :
  public virtual BppSequenceApplication
{
public:
  BppPhylogeneticsApplication(int argc, char* argv[], const std::string& name) :
    BppApplication(argc, argv, name),
    BppSequenceApplication(argc, argv, name)
  {}
 
public:
  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;
 
  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;
 
  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;
 
  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;
 
 
  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;
 
  virtual void displayParameters(
      const PhyloLikelihoodInterface& tl,
      bool displaylL = true) const;
};
} // end of namespace bpp;
#endif // BPP_PHYL_APP_BPPPHYLOGENETICSAPPLICATION_H