Bpp/Phyl/Simulation/MutationProcess.h

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//
// File: MutationProcess.h
// Created by: Julien Dutheil
// Created on: Wed Mar 12 16:11:44 2003
//

/*
Copyright or © 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 _MUTATIONPROCESS_H_
#define _MUTATIONPROCESS_H_

#include "../Model/SubstitutionModel.h"
#include "../Mapping/SubstitutionRegister.h"

#include <Bpp/Numeric/VectorTools.h>

namespace bpp
{

class MutationPath
{
  private:

    const Alphabet* alphabet_;

    std::vector<int> states_;

    std::vector<double> times_;
    
    int initialState_;

    double totalTime_;

  public:

    MutationPath(const Alphabet* alphabet, int initialState, double time) :
      alphabet_(alphabet), states_(), times_(), initialState_(initialState), totalTime_(time) {};
    
    MutationPath(const MutationPath& path) :
      alphabet_(path.alphabet_), states_(path.states_), times_(path.times_), initialState_(path.initialState_), totalTime_(path.totalTime_) {};

    MutationPath& operator=(const MutationPath& path) {
      alphabet_     = path.alphabet_;
      states_       = path.states_;
      times_        = path.times_;
      initialState_ = path.initialState_;
      totalTime_    = path.totalTime_;
      return *this;
    }

    virtual ~MutationPath() {};

  public:
  
    const Alphabet* getAlphabet() const { return alphabet_; }
    
    void addEvent(int state, double time) {
      states_.push_back(state);
      times_.push_back(time);
    }

    int getInitialState() const { return initialState_; }

    double getTotalTime() const { return totalTime_; }
    
    size_t getNumberOfEvents() const { return states_.size(); }

    template<class Scalar>
    void getEventCounts(Matrix<Scalar>& counts) const {
      if (counts.getNumberOfRows()    != alphabet_->getSize()
       || counts.getNumberOfColumns() != alphabet_->getSize())
        throw Exception("MutationPath::getEventCounts. Incorrect input matrix, does not match alphabet size.");
      int currentState = initialState_;
      for (size_t i = 0; i < states_.size(); ++i) {
        int newState = states_[i];
        counts(currentState, newState)++;
        currentState = newState;
      }
    }

    template<class Scalar>
    void getEventCounts(std::vector<Scalar>& counts, const SubstitutionRegister& reg) const {
      if (counts.size() != reg.getNumberOfSubstitutionTypes())
        throw Exception("MutationPath::getEventCounts. Incorrect input vector, does not match alphabet size.");
      int currentState = initialState_;
      for (size_t i = 0; i < states_.size(); ++i) {
        int newState = states_[i];
        size_t type = reg.getType(currentState, newState);
        if (type > 0) counts[type - 1]++;
        currentState = newState;
      }
    }

    int getFinalState() const {
      if (states_.size() == 0) return initialState_;
      else return states_[states_.size() - 1];
    }
};

class MutationProcess
{
  public:
    MutationProcess() {};
    virtual ~MutationProcess() {};
  
  public:
    
    virtual int mutate(int state) const = 0;

    virtual int mutate(int state, unsigned int n) const = 0;
  
    virtual double getTimeBeforeNextMutationEvent(int state) const = 0;
    
    virtual int evolve(int initialState, double time) const = 0;
  
    virtual MutationPath detailedEvolve(int initialState, double time) const = 0;

    virtual const SubstitutionModel* getSubstitutionModel() const = 0;
};

class AbstractMutationProcess :
  public virtual MutationProcess
{
  protected:
    
    const SubstitutionModel* model_;
  
    size_t size_;
  
    VVdouble repartition_;
  
  public:
    AbstractMutationProcess(const SubstitutionModel* model) :
      model_(model), size_(), repartition_()
    {}

    AbstractMutationProcess(const AbstractMutationProcess& amp) :
      model_(amp.model_), size_(amp.size_), repartition_(amp.repartition_)
    {}

    AbstractMutationProcess& operator=(const AbstractMutationProcess& amp)
    {
      model_       = amp.model_;
      size_        = amp.size_;
      repartition_ = amp.repartition_;
      return *this;
    }

    virtual ~AbstractMutationProcess() {}
  
  public:
    int mutate(int state) const;
    int mutate(int state, unsigned int n) const;
    double getTimeBeforeNextMutationEvent(int state) const;
    int evolve(int initialState, double time) const;
    MutationPath detailedEvolve(int initialState, double time) const;
    const SubstitutionModel* getSubstitutionModel() const { return model_; }
};

class SimpleMutationProcess : public AbstractMutationProcess
{
  public: // Constructor and destructor:
    
    SimpleMutationProcess(const SubstitutionModel* model);
  
    virtual ~SimpleMutationProcess();

    int evolve(int initialState, double time) const;
};

class SelfMutationProcess : public AbstractMutationProcess
{
    public:
      SelfMutationProcess(int alphabetSize);
  
      virtual ~SelfMutationProcess();
};

} //end of namespace bpp.

#endif  //_MUTATIONPROCESS_H_