MaximumLikelihoodModelFitMafStatistics.h

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//
// File: MaximumLikelihoodModelFitMafStatistics.h
// Created by: Julien Dutheil
// Created on: Mar 25 2014
//

/*
Copyright or © or Copr. Bio++ Development Team

This software is a computer program whose purpose is to test the
homogeneity of the substitution process of a given alignment.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
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encouraged to load and test the software's suitability as regards their
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same conditions as regards security. 

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*/

#ifndef _MAXIMUMLIKELIHOODMODELFITMAFSTATISTICS_H_
#define _MAXIMUMLIKELIHOODMODELFITMAFSTATISTICS_H_

#include <Bpp/Seq/Io/Maf/MafStatistics.h>
#include <Bpp/Seq/Container/SiteContainer.h>

//From bpp-phyl:
#include <Bpp/Phyl/Model/SubstitutionModel.h>
#include <Bpp/Phyl/Model/SubstitutionModelSetTools.h>
#include <Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h>
#include <Bpp/Phyl/Tree.h>
#include <Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h>

//From bpp-core
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>

namespace bpp {

class MaximumLikelihoodModelFitMafStatistics:
  public AbstractMafStatistics
{

  private:
    std::auto_ptr<SubstitutionModel> model_;
    std::auto_ptr<SubstitutionModelSet> modelSet_; //Only used in case of non-stationary model.
    std::auto_ptr<DiscreteDistribution> rDist_;
    std::auto_ptr<NucleotideFrequenciesSet> rootFreqs_;
    std::string treePropertyIn_;
    std::auto_ptr<const Tree> tree_;
    std::vector<std::string> parametersOut_;
    bool reestimateBrLen_;
    double propGapsToKeep_; //Exclude sites with too many gaps
    bool gapsAsUnresolved_;  //For most models, should be yes as they do not allow for gap characters
    ParameterList initParameters_;
    ParameterList fixedParameters_;

  public:
    MaximumLikelihoodModelFitMafStatistics(
        SubstitutionModel* model,
        DiscreteDistribution* rDist,
        NucleotideFrequenciesSet* rootFreqs,
        const std::string& treePropertyIn,
        const std::vector<std::string>& parametersOut,
        const ParameterList& fixedParameters,
        bool reestimateBrLen = true,
        double propGapsToKeep = 0,
        bool gapsAsUnresolved = true):
      AbstractMafStatistics(),
      model_(model), modelSet_(0), rDist_(rDist), rootFreqs_(rootFreqs),
      treePropertyIn_(treePropertyIn), tree_(0), parametersOut_(parametersOut),
      reestimateBrLen_(reestimateBrLen), propGapsToKeep_(propGapsToKeep), gapsAsUnresolved_(gapsAsUnresolved),
      initParameters_(), fixedParameters_(fixedParameters)
    {
      if (!rootFreqs)
        init_();
      //Otherwise we do not initialize parameters as the tree might change for each block.
      //We therefore have to initialize once for each block.
    }

    MaximumLikelihoodModelFitMafStatistics(
        SubstitutionModel* model,
        DiscreteDistribution* rDist,
        NucleotideFrequenciesSet* rootFreqs,
        const Tree* tree,
        const std::vector<std::string>& parametersOut,
        const ParameterList& fixedParameters,
        bool reestimateBrLen = true,
        double propGapsToKeep = 0,
        bool gapsAsUnresolved = true):
      AbstractMafStatistics(),
      model_(model), modelSet_(0), rDist_(rDist), rootFreqs_(rootFreqs),
      treePropertyIn_(NO_PROPERTY), tree_(0), parametersOut_(parametersOut),
      reestimateBrLen_(reestimateBrLen), propGapsToKeep_(propGapsToKeep), gapsAsUnresolved_(gapsAsUnresolved),
      initParameters_(), fixedParameters_(fixedParameters)
    {
      if (rootFreqs)
        modelSet_.reset(SubstitutionModelSetTools::createHomogeneousModelSet(model->clone(), rootFreqs->clone(), tree));
      init_();
    }

  private:
    MaximumLikelihoodModelFitMafStatistics(const MaximumLikelihoodModelFitMafStatistics& mafstat):
      AbstractMafStatistics(),
      model_(0), modelSet_(0), rDist_(0), rootFreqs_(0),
      treePropertyIn_(mafstat.treePropertyIn_), tree_(0), parametersOut_(mafstat.parametersOut_),
      reestimateBrLen_(mafstat.reestimateBrLen_), propGapsToKeep_(mafstat.propGapsToKeep_), gapsAsUnresolved_(mafstat.gapsAsUnresolved_),
      initParameters_(mafstat.initParameters_), fixedParameters_(mafstat.fixedParameters_)
    {}
    
    MaximumLikelihoodModelFitMafStatistics& operator=(const MaximumLikelihoodModelFitMafStatistics& mafstat)
    {
      model_.reset();
      modelSet_.reset();
      rDist_.reset();
      rootFreqs_.reset();
      treePropertyIn_ = mafstat.treePropertyIn_;
      tree_.reset();
      parametersOut_ = mafstat.parametersOut_;
      reestimateBrLen_ = mafstat.reestimateBrLen_;
      propGapsToKeep_ = mafstat.propGapsToKeep_;
      gapsAsUnresolved_ = mafstat.gapsAsUnresolved_;
      initParameters_ = mafstat.initParameters_;
      fixedParameters_ = mafstat.fixedParameters_;
      return *this;
    }
     
  public:
    std::string getShortName() const { return "MLModelFit"; }
    std::string getFullName() const { return "Maximum Likelihood Model Fitting"; }
    void compute(const MafBlock& block);
    std::vector<std::string> getSupportedTags() const { 
      std::vector<std::string> tags;
      tags.push_back("NbIterations");
      tags.insert(tags.end(), parametersOut_.begin(), parametersOut_.end());
      return tags;
    }

    static const std::string NO_PROPERTY;
  
  private:
    void init_();
};

} //end of namespace bpp.

#endif //_MAXIMUMLIKELIHOODDISTANCEESTIMATIONMAFSTATISTICS_H_