SubstitutionModelSet.h

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//
// File: SubstitutionModelSet.h
// Created by: Bastien Boussau
//             Julien Dutheil
// Created on: Tue Aug 21 2007
//

/*
   Copyright or (c) or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data analysis.

   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
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _SUBSTITUTIONMODELSET_H_
#define _SUBSTITUTIONMODELSET_H_


#include "../Tree.h"
#include "SubstitutionModel.h"
#include "AbstractSubstitutionModel.h"
#include "FrequenciesSet/FrequenciesSet.h"

#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Random/RandomTools.h>
#include <Bpp/Numeric/VectorTools.h>

// From Seqlib:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>

// From the STL:
#include <vector>
#include <map>
#include <algorithm>
#include <memory>

namespace bpp
{
class SubstitutionModelSet :
  public AbstractParameterAliasable
{
protected:
  const Alphabet* alphabet_;

  size_t nbStates_;

  std::vector<SubstitutionModel*> modelSet_;

private:
  std::auto_ptr<FrequenciesSet> rootFrequencies_;

  mutable std::map<int, size_t> nodeToModel_;
  mutable std::map<size_t, std::vector<int> > modelToNodes_;

  std::vector<ParameterList> modelParameters_;

  bool stationarity_;

public:
  SubstitutionModelSet(const Alphabet* alpha):
    AbstractParameterAliasable(""),
    alphabet_(alpha),
    nbStates_(0),
    modelSet_(),
    rootFrequencies_(0),
    nodeToModel_(),
    modelToNodes_(),
    modelParameters_(),
    stationarity_(true)
  {
  }

  SubstitutionModelSet(const Alphabet* alpha, FrequenciesSet* rootFreqs):
    AbstractParameterAliasable(""),
    alphabet_(alpha),
    nbStates_(0),
    modelSet_(),
    rootFrequencies_(0),
    nodeToModel_(),
    modelToNodes_(),
    modelParameters_(),
    stationarity_(true)
  {
    setRootFrequencies(rootFreqs);
  }

  void clear();
  
  void setRootFrequencies(FrequenciesSet* rootFreqs);

  SubstitutionModelSet(const SubstitutionModelSet& set);

  SubstitutionModelSet& operator=(const SubstitutionModelSet& set);

  virtual ~SubstitutionModelSet()
  {
    for (size_t i = 0; i < modelSet_.size(); i++) { delete modelSet_[i]; }
  }

#ifndef NO_VIRTUAL_COV
  SubstitutionModelSet*
#else
  Clonable*
#endif
  clone() const { return new SubstitutionModelSet(*this); }

public:
  size_t getNumberOfStates() const throw (Exception)
  {
    return nbStates_;
  }

  virtual void fireParameterChanged(const ParameterList& parameters);

  size_t getNumberOfModels() const { return modelSet_.size(); }

  bool hasMixedSubstitutionModel() const;

  const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
  {
    if (i > modelSet_.size()) throw IndexOutOfBoundsException("SubstitutionModelSet::getNumberOfModels().", 0, modelSet_.size() - 1, i);
    return modelSet_[i];
  }

  SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
  {
    if (i > modelSet_.size()) throw IndexOutOfBoundsException("SubstitutionModelSet::getNumberOfModels().", 0, modelSet_.size() - 1, i);
    return modelSet_[i];
  }

  size_t getModelIndexForNode(int nodeId) const throw (Exception)
  {
   std::map<int, size_t>::iterator i = nodeToModel_.find(nodeId);
    if (i == nodeToModel_.end())
      throw Exception("SubstitutionModelSet::getModelIndexForNode(). No model associated to node with id " + TextTools::toString(nodeId));
    return i->second;
  }

  const SubstitutionModel* getModelForNode(int nodeId) const throw (Exception)
  {
   std::map<int, size_t>::const_iterator i = nodeToModel_.find(nodeId);
    if (i == nodeToModel_.end())
      throw Exception("SubstitutionModelSet::getModelForNode(). No model associated to node with id " + TextTools::toString(nodeId));
    return modelSet_[i->second];
  }
  SubstitutionModel* getModelForNode(int nodeId) throw (Exception)
  {
   std::map<int, size_t>::iterator i = nodeToModel_.find(nodeId);
    if (i == nodeToModel_.end())
      throw Exception("SubstitutionModelSet::getModelForNode(). No model associated to node with id " + TextTools::toString(nodeId));
    return modelSet_[i->second];
  }

  const std::vector<int>& getNodesWithModel(size_t i) const throw (IndexOutOfBoundsException)
  {
    if (i >= modelSet_.size()) throw IndexOutOfBoundsException("SubstitutionModelSet::getNodesWithModel().", i, 0, modelSet_.size());
    return modelToNodes_[i];
  }

  std::vector<int> getNodesWithParameter(const std::string& name) const throw (ParameterNotFoundException);

  void addModel(SubstitutionModel* model, const std::vector<int>& nodesId);//, const std::vector<std::string>& newParams) throw (Exception);

  void replaceModel(size_t modelIndex, SubstitutionModel* model) throw (Exception);

  void listModelNames(std::ostream& out = std::cout) const;

  const FrequenciesSet* getRootFrequenciesSet() const { return rootFrequencies_.get(); }

  std::vector<double> getRootFrequencies() const
  {
    if (stationarity_)
      return modelSet_[0]->getFrequencies();
    else
      return rootFrequencies_->getFrequencies();
  }

  ParameterList getRootFrequenciesParameters() const
  {
    if (stationarity_)
      return ParameterList();
    else
      return rootFrequencies_->getParameters();
  }

  ParameterList getNodeParameters() const
  {
    ParameterList pl;
    for (size_t i = stationarity_ ? 0 : rootFrequencies_->getNumberOfParameters();
        i < getNumberOfParameters(); i++)
    {
      pl.addParameter(getParameter_(i));
    }
    return pl;
  }

  ParameterList getModelParameters(size_t modelIndex) const;

  const Alphabet* getAlphabet() const { return alphabet_; }

  virtual const std::vector<int>& getAlphabetStates() const {
    return getModel(0)->getAlphabetStates();
  }

  virtual const StateMap& getStateMap() const {
    return getModel(0)->getStateMap();
  }

  virtual std::vector<size_t> getModelStates(int code) const {
    return getModel(0)->getModelStates(code);
  }

  virtual std::vector<size_t> getModelStates(const std::string& code) const {
    return getModel(0)->getModelStates(code);
  }

  virtual int getAlphabetStateAsInt(size_t index) const {
    return getModel(0)->getAlphabetStateAsInt(index);
  }
  
  virtual std::string getAlphabetStateAsChar(size_t index) const {
    return getModel(0)->getAlphabetStateAsChar(index);
  }

  bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw (Exception)
  {
    return checkOrphanModels(throwEx)
      //           && checkOrphanParameters(throwEx)
           && checkOrphanNodes(tree, throwEx)
           && checkUnknownNodes(tree, throwEx);
  }

protected:
  void updateRootFrequencies()
  {
    if (!stationarity_)
      rootFrequencies_->matchParametersValues(getParameters());
  }

  bool checkOrphanModels(bool throwEx) const throw (Exception);

  bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw (Exception);

  bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw (Exception);
};
} // end of namespace bpp.

#endif // _SUBSTITUTIONMODELSET_H_