DRASDRTreeLikelihoodData.h

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//
// File: DRASDRTreeLikelihoodData.h
// Created by: Julien Dutheil
// Created on: Sat Dec 30 14:20 2006
// From file DRHomogeneousTreeLikelihood.h
//

/*
Copyright or © or Copr. CNRS, (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 _DRASDRHOMOGENEOUSTREELIKELIHOODDATA_H_
#define _DRASDRHOMOGENEOUSTREELIKELIHOODDATA_H_

#include "AbstractTreeLikelihoodData.h"
#include "../Model/SubstitutionModel.h"
#include "../PatternTools.h"
#include "../SitePatterns.h"

//From SeqLib:
#include <Bpp/Seq/Container/AlignedSequenceContainer.h>

// From the STL:
#include <map>

namespace bpp
{

class DRASDRTreeLikelihoodLeafData :
  public virtual TreeLikelihoodNodeData
{
  private:
    mutable VVdouble leafLikelihood_;
    const Node* leaf_;

  public:
    DRASDRTreeLikelihoodLeafData() : leafLikelihood_(), leaf_(0) {}

    DRASDRTreeLikelihoodLeafData(const DRASDRTreeLikelihoodLeafData& data) :
      leafLikelihood_(data.leafLikelihood_), leaf_(data.leaf_) {}
    
    DRASDRTreeLikelihoodLeafData& operator=(const DRASDRTreeLikelihoodLeafData& data)
    {
      leafLikelihood_ = data.leafLikelihood_;
      leaf_           = data.leaf_;
      return *this;
    }

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

  public:
    const Node* getNode() const { return leaf_; }
    void setNode(const Node* node) { leaf_ = node; }

    VVdouble& getLikelihoodArray()  { return leafLikelihood_;  }
};

class DRASDRTreeLikelihoodNodeData :
  public virtual TreeLikelihoodNodeData
{
  private:
    mutable std::map<int, VVVdouble> nodeLikelihoods_;
    mutable Vdouble nodeDLikelihoods_;
  
    mutable Vdouble nodeD2Likelihoods_;
    
    const Node* node_;

  public:
    DRASDRTreeLikelihoodNodeData() : nodeLikelihoods_(), nodeDLikelihoods_(), nodeD2Likelihoods_(), node_(0) {}
    
    DRASDRTreeLikelihoodNodeData(const DRASDRTreeLikelihoodNodeData& data) :
      nodeLikelihoods_(data.nodeLikelihoods_),
      nodeDLikelihoods_(data.nodeDLikelihoods_),
      nodeD2Likelihoods_(data.nodeD2Likelihoods_),
      node_(data.node_)
    {}
    
    DRASDRTreeLikelihoodNodeData& operator=(const DRASDRTreeLikelihoodNodeData& data)
    {
      nodeLikelihoods_   = data.nodeLikelihoods_;
      nodeDLikelihoods_  = data.nodeDLikelihoods_;
      nodeD2Likelihoods_ = data.nodeD2Likelihoods_;
      node_              = data.node_;
      return *this;
    }
 
    virtual ~DRASDRTreeLikelihoodNodeData() {}

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

  public:
    const Node* getNode() const { return node_; }
    
    void setNode(const Node* node) { node_ = node; }

    const std::map<int, VVVdouble>& getLikelihoodArrays() const { return nodeLikelihoods_; }
    
    std::map<int, VVVdouble>& getLikelihoodArrays() { return nodeLikelihoods_; }
    
    VVVdouble& getLikelihoodArrayForNeighbor(int neighborId)
    {
      return nodeLikelihoods_[neighborId];
    }
    
    const VVVdouble& getLikelihoodArrayForNeighbor(int neighborId) const
    {
      return nodeLikelihoods_[neighborId];
    }
    
    Vdouble& getDLikelihoodArray() { return nodeDLikelihoods_;  }
    
    const Vdouble& getDLikelihoodArray() const  {  return nodeDLikelihoods_;  }
    
    Vdouble& getD2LikelihoodArray()  {  return nodeD2Likelihoods_; }
    
    const Vdouble& getD2LikelihoodArrayForNeighbor() const  { return nodeD2Likelihoods_; }

    bool isNeighbor(int neighborId) const
    {
      return nodeLikelihoods_.find(neighborId) != nodeLikelihoods_.end();
    }

    void eraseNeighborArrays()
    {
      nodeLikelihoods_.erase(nodeLikelihoods_.begin(), nodeLikelihoods_.end());
      nodeDLikelihoods_.erase(nodeDLikelihoods_.begin(), nodeDLikelihoods_.end());
      nodeD2Likelihoods_.erase(nodeD2Likelihoods_.begin(), nodeD2Likelihoods_.end());
    }
};

class DRASDRTreeLikelihoodData :
  public virtual AbstractTreeLikelihoodData
{
  private:

    mutable std::map<int, DRASDRTreeLikelihoodNodeData> nodeData_;
    mutable std::map<int, DRASDRTreeLikelihoodLeafData> leafData_;
    mutable VVVdouble rootLikelihoods_;
    mutable VVdouble  rootLikelihoodsS_;
    mutable Vdouble   rootLikelihoodsSR_;

    SiteContainer* shrunkData_;
    size_t nbSites_; 
    size_t nbStates_;
    size_t nbClasses_;
    size_t nbDistinctSites_; 

  public:
    DRASDRTreeLikelihoodData(const TreeTemplate<Node>* tree, size_t nbClasses) :
      AbstractTreeLikelihoodData(tree),
      nodeData_(), leafData_(), rootLikelihoods_(), rootLikelihoodsS_(), rootLikelihoodsSR_(),
      shrunkData_(0), nbSites_(0), nbStates_(0), nbClasses_(nbClasses), nbDistinctSites_(0)
    {}

    DRASDRTreeLikelihoodData(const DRASDRTreeLikelihoodData& data):
      AbstractTreeLikelihoodData(data),
      nodeData_(data.nodeData_), leafData_(data.leafData_),
      rootLikelihoods_(data.rootLikelihoods_),
      rootLikelihoodsS_(data.rootLikelihoodsS_),
      rootLikelihoodsSR_(data.rootLikelihoodsSR_),
      shrunkData_(0),
      nbSites_(data.nbSites_), nbStates_(data.nbStates_),
      nbClasses_(data.nbClasses_), nbDistinctSites_(data.nbDistinctSites_)
    {
      if (data.shrunkData_)
        shrunkData_ = dynamic_cast<SiteContainer*>(data.shrunkData_->clone());
    }

    DRASDRTreeLikelihoodData& operator=(const DRASDRTreeLikelihoodData& data)
    {
      AbstractTreeLikelihoodData::operator=(data);
      nodeData_          = data.nodeData_;
      leafData_          = data.leafData_;
      rootLikelihoods_   = data.rootLikelihoods_;
      rootLikelihoodsS_  = data.rootLikelihoodsS_;
      rootLikelihoodsSR_ = data.rootLikelihoodsSR_;
      nbSites_           = data.nbSites_;
      nbStates_          = data.nbStates_;
      nbClasses_         = data.nbClasses_;
      nbDistinctSites_   = data.nbDistinctSites_;
      if (shrunkData_) delete shrunkData_;
      if (data.shrunkData_)
        shrunkData_      = dynamic_cast<SiteContainer *>(data.shrunkData_->clone());
      else
        shrunkData_      = 0;
      return *this;
    }

    virtual ~DRASDRTreeLikelihoodData() { delete shrunkData_; }

    DRASDRTreeLikelihoodData* clone() const { return new DRASDRTreeLikelihoodData(*this); }

  public:
    void setTree(const TreeTemplate<Node>* tree)
    { 
      tree_ = tree;
      for (std::map<int, DRASDRTreeLikelihoodNodeData>::iterator it = nodeData_.begin(); it != nodeData_.end(); it++)
      {
        int id = it->second.getNode()->getId();
        it->second.setNode(tree_->getNode(id));
      }
      for (std::map<int, DRASDRTreeLikelihoodLeafData>::iterator it = leafData_.begin(); it != leafData_.end(); it++)
      {
        int id = it->second.getNode()->getId();
        it->second.setNode(tree_->getNode(id));
      }
    }

    DRASDRTreeLikelihoodNodeData& getNodeData(int nodeId)
    { 
      return nodeData_[nodeId];
    }
    
    const DRASDRTreeLikelihoodNodeData& getNodeData(int nodeId) const
    { 
      return nodeData_[nodeId];
    }
    
    DRASDRTreeLikelihoodLeafData& getLeafData(int nodeId)
    { 
      return leafData_[nodeId];
    }
    
    const DRASDRTreeLikelihoodLeafData& getLeafData(int nodeId) const
    { 
      return leafData_[nodeId];
    }
    
    size_t getArrayPosition(int parentId, int sonId, size_t currentPosition) const
    {
      return currentPosition;
    }

    const std::map<int, VVVdouble>& getLikelihoodArrays(int nodeId) const 
    {
      return nodeData_[nodeId].getLikelihoodArrays();
    }
    
    std::map<int, VVVdouble>& getLikelihoodArrays(int nodeId)
    {
      return nodeData_[nodeId].getLikelihoodArrays();
    }

    VVVdouble& getLikelihoodArray(int parentId, int neighborId)
    {
      return nodeData_[parentId].getLikelihoodArrayForNeighbor(neighborId);
    }
    
    const VVVdouble& getLikelihoodArray(int parentId, int neighborId) const
    {
      return nodeData_[parentId].getLikelihoodArrayForNeighbor(neighborId);
    }
    
    Vdouble& getDLikelihoodArray(int nodeId)
    {
      return nodeData_[nodeId].getDLikelihoodArray();
    }
    
    const Vdouble& getDLikelihoodArray(int nodeId) const
    {
      return nodeData_[nodeId].getDLikelihoodArray();
    }
    
    Vdouble& getD2LikelihoodArray(int nodeId)
    {
      return nodeData_[nodeId].getD2LikelihoodArray();
    }

    const Vdouble& getD2LikelihoodArray(int nodeId) const
    {
      return nodeData_[nodeId].getD2LikelihoodArray();
    }

    VVdouble& getLeafLikelihoods(int nodeId)
    {
      return leafData_[nodeId].getLikelihoodArray();
    }
    
    const VVdouble& getLeafLikelihoods(int nodeId) const
    {
      return leafData_[nodeId].getLikelihoodArray();
    }
    
    VVVdouble& getRootLikelihoodArray() { return rootLikelihoods_; }
    const VVVdouble & getRootLikelihoodArray() const { return rootLikelihoods_; }
    
    VVdouble& getRootSiteLikelihoodArray() { return rootLikelihoodsS_; }
    const VVdouble& getRootSiteLikelihoodArray() const { return rootLikelihoodsS_; }
    
    Vdouble& getRootRateSiteLikelihoodArray() { return rootLikelihoodsSR_; }
    const Vdouble& getRootRateSiteLikelihoodArray() const { return rootLikelihoodsSR_; }

    size_t getNumberOfDistinctSites() const { return nbDistinctSites_; }
    
    size_t getNumberOfSites() const { return nbSites_; }
    
    size_t getNumberOfStates() const { return nbStates_; }
    
    size_t getNumberOfClasses() const { return nbClasses_; }

    const SiteContainer* getShrunkData() const { return shrunkData_; }
    
    void initLikelihoods(const SiteContainer& sites, const SubstitutionModel& model) throw (Exception);
    
    void reInit() throw (Exception);
    
    void reInit(const Node* node) throw (Exception);

  protected:
    void initLikelihoods(const Node* node, const SiteContainer& sites, const SubstitutionModel& model) throw (Exception);
    
};

} //end of namespace bpp.

#endif //_DRASDRHOMOGENEOUSTREELIKELIHOODDATA_H_