NonHomogeneousSequenceSimulator.h

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//
// File: NonHomogeneousSequenceSimulator.h
// Created by: Julien Dutheil
//             Bastien Boussau
// Created on: Wed Aug  24 15:20 2005
//

/*
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 _NONHOMOGENEOUSSEQUENCESIMULATOR_H_
#define _NONHOMOGENEOUSSEQUENCESIMULATOR_H_

#include "DetailedSiteSimulator.h"
#include "SequenceSimulator.h"
#include "../TreeTemplate.h"
#include "../NodeTemplate.h"
#include "../Model/SubstitutionModel.h"

#include <Bpp/Numeric/Random/RandomTools.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>

// From SeqLib:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Site.h>
#include <Bpp/Seq/Container/SiteContainer.h>

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

#include "../Model/SubstitutionModelSet.h"

namespace bpp
{

class SimData
{
  public:
    size_t state;
    std::vector<size_t> states;
    VVVdouble cumpxy;
    const SubstitutionModel* model;

  public:
    SimData(): state(), states(), cumpxy(), model(0) {}
    SimData(const SimData& sd): state(sd.state), states(sd.states), cumpxy(), model(sd.model) {}
    SimData& operator=(const SimData& sd)
    {
      state  = sd.state;
      states = sd.states;
      cumpxy = sd.cumpxy;
      model  = sd.model;
      return *this;
    }
};

typedef NodeTemplate<SimData> SNode;

class NonHomogeneousSequenceSimulator:
  public DetailedSiteSimulator,
  public virtual SequenceSimulator
{
  private:
    const SubstitutionModelSet* modelSet_;
    const Alphabet            * alphabet_;
    std::vector<int>            supportedStates_;
    const DiscreteDistribution* rate_;
    const Tree                * templateTree_;
    mutable TreeTemplate<SNode> tree_;
    bool ownModelSet_;
  
    std::vector<SNode*> leaves_;
  
    std::vector<std::string> seqNames_;

    size_t nbNodes_;
    size_t nbClasses_;
    size_t nbStates_;

    bool continuousRates_;
  
  public:    
    NonHomogeneousSequenceSimulator(
      const SubstitutionModelSet* modelSet,
      const DiscreteDistribution* rate,
      const Tree* tree
    ) throw (Exception);

    NonHomogeneousSequenceSimulator(
      const SubstitutionModel* model,
      const DiscreteDistribution* rate,
      const Tree* tree
    );
      
    virtual ~NonHomogeneousSequenceSimulator()
    {
      if (ownModelSet_ && modelSet_) delete modelSet_;
    }

    NonHomogeneousSequenceSimulator(const NonHomogeneousSequenceSimulator& nhss) :
      modelSet_       (nhss.modelSet_),
      alphabet_       (nhss.alphabet_),
      supportedStates_(nhss.supportedStates_),
      rate_           (nhss.rate_),
      templateTree_   (nhss.templateTree_),
      tree_           (nhss.tree_),
      ownModelSet_    (nhss.ownModelSet_),
      leaves_         (nhss.leaves_),
      seqNames_       (nhss.seqNames_),
      nbNodes_        (nhss.nbNodes_),
      nbClasses_      (nhss.nbClasses_),
      nbStates_       (nhss.nbStates_),
      continuousRates_(nhss.continuousRates_)
    {}

    NonHomogeneousSequenceSimulator& operator=(const NonHomogeneousSequenceSimulator& nhss)
    {
      modelSet_        = nhss.modelSet_;
      alphabet_        = nhss.alphabet_;
      supportedStates_ = nhss.supportedStates_;
      rate_            = nhss.rate_;
      templateTree_    = nhss.templateTree_;
      tree_            = nhss.tree_;
      ownModelSet_     = nhss.ownModelSet_;
      leaves_          = nhss.leaves_;
      seqNames_        = nhss.seqNames_;
      nbNodes_         = nhss.nbNodes_;
      nbClasses_       = nhss.nbClasses_;
      nbStates_        = nhss.nbStates_;
      continuousRates_ = nhss.continuousRates_;
      return *this;
    }

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

  private:
    void init();

  public:
  
    Site* simulateSite() const;

    Site* simulateSite(size_t ancestralStateIndex) const;

    Site* simulateSite(size_t ancestralStateIndex, double rate) const;
    
    Site* simulateSite(double rate) const;

    std::vector<std::string> getSequencesNames() const { return seqNames_; }
    RASiteSimulationResult* dSimulateSite() const;
    
    RASiteSimulationResult* dSimulateSite(size_t ancestralStateIndex) const;
    
    RASiteSimulationResult* dSimulateSite(size_t ancestralStateIndex, double rate) const;
    
    RASiteSimulationResult* dSimulateSite(double rate) const;
    SiteContainer* simulate(size_t numberOfSites) const;
    const Alphabet* getAlphabet() const { return alphabet_; }
    virtual Site* simulateSite(size_t ancestralStateIndex, size_t rateClass) const;
    virtual RASiteSimulationResult* dSimulateSite(size_t ancestralStateIndex, size_t rateClass) const;
    const SubstitutionModelSet* getSubstitutionModelSet() const { return modelSet_; }
    
    const DiscreteDistribution* getRateDistribution() const { return rate_; }

    const Tree* getTree() const { return templateTree_; }

    void enableContinuousRates(bool yn) { continuousRates_ = yn; }
  
  protected:
    
    size_t evolve(const SNode* node, size_t initialStateIndex, size_t rateClass) const;
    
    size_t evolve(const SNode* node, size_t initialStateIndex, double rate) const;
    
    void multipleEvolve(
        const SNode* node,
        const std::vector<size_t>& initialStateIndices,
        const std::vector<size_t>& rateClasses,
        std::vector<size_t>& finalStates) const;
    SiteContainer* multipleEvolve(
        const std::vector<size_t>& initialStates,
        const std::vector<size_t>& rateClasses) const;
    
    void dEvolve(size_t initialState, double rate, RASiteSimulationResult& rassr) const;
    
    void evolveInternal(SNode* node, size_t rateClass) const;
    void evolveInternal(SNode* node, double rate) const;
     void multipleEvolveInternal(SNode* node, const std::vector<size_t>& rateClasses) const;

    void dEvolveInternal(SNode * node, double rate, RASiteSimulationResult & rassr) const;
};

} //end of namespace bpp.

#endif //_NONHOMOGENEOUSSEQUENCESIMULATOR_H_