AbstractAgglomerativeDistanceMethod.h

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//
// File: AbstractAgglomerativeDistanceMethod.h
// Created by: Julien Dutheil
//             Vincent Ranwez
// Created on: Wed jun 22 10:00 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
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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 _ABSTRACTAGGLOMERATIVEDISTANCEMETHOD_H_
#define _ABSTRACTAGGLOMERATIVEDISTANCEMETHOD_H_

#include "DistanceMethod.h"
#include "../Node.h"
#include "../TreeTemplate.h"

// From the STL:
#include <map>

namespace bpp
{

class AbstractAgglomerativeDistanceMethod:
  public virtual AgglomerativeDistanceMethod
{
  protected:
    DistanceMatrix matrix_;
    Tree* tree_;

    std::map<size_t, Node*> currentNodes_;
    bool verbose_;
    bool rootTree_;
  
  public:
    //AbstractAgglomerativeDistanceMethod() :
    //  matrix_(0), tree_(0), currentNodes_(), verbose_(true), rootTree_(false) {}

    AbstractAgglomerativeDistanceMethod(bool verbose = true, bool rootTree = false) :
      matrix_(0), tree_(0), currentNodes_(), verbose_(verbose), rootTree_(rootTree) {}
    
    AbstractAgglomerativeDistanceMethod(const DistanceMatrix& matrix, bool verbose = true, bool rootTree = false) :
      matrix_(0), tree_(0), currentNodes_(), verbose_(verbose), rootTree_(rootTree)
    {
      setDistanceMatrix(matrix);
    }

    virtual ~AbstractAgglomerativeDistanceMethod()
    {
      if (tree_)
        delete tree_;
    }
    
    AbstractAgglomerativeDistanceMethod(const AbstractAgglomerativeDistanceMethod& a) :
      matrix_(a.matrix_), tree_(0), currentNodes_(), verbose_(a.verbose_), rootTree_(a.rootTree_)
    {
      // Hard copy of inner tree:
      if (a.tree_)
        tree_ = new TreeTemplate<Node>(* a.tree_);
    }

    AbstractAgglomerativeDistanceMethod& operator=(const AbstractAgglomerativeDistanceMethod& a)
    {
      matrix_ = a.matrix_;
      // Hard copy of inner tree:
      if (a.tree_)
        tree_ = new TreeTemplate<Node>(* a.tree_);
      else tree_ = 0;
      currentNodes_.clear();
      verbose_ = a.verbose_;
      rootTree_ = a.rootTree_;
      return *this;
    }

  public:
    virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw (Exception);

    virtual
#if defined(NO_VIRTUAL_COV)
    Tree *
#else
    TreeTemplate<Node> * 
#endif
    getTree() const
    {
      //Node * root = TreeTools::cloneSubtree<Node>(* dynamic_cast<TreeTemplate<Node> *>(tree_) -> getRootNode());
      //return new TreeTemplate<Node>(* root);
      return tree_ == 0 ? 0 : new TreeTemplate<Node>(*tree_);
    }
    
    virtual void computeTree() throw (Exception);

    void setVerbose(bool yn) { verbose_ = yn; }
    bool isVerbose() const { return verbose_; }

  protected:
    virtual std::vector<size_t> getBestPair() throw (Exception) = 0;
    
    virtual std::vector<double> computeBranchLengthsForPair(const std::vector<size_t> & pair) = 0;

    virtual double computeDistancesFromPair(const std::vector<size_t>& pair, const std::vector<double>& branchLengths, size_t pos) = 0;
    
    virtual void finalStep(int idRoot) = 0;

    virtual Node* getLeafNode(int id, const std::string& name);

    virtual Node* getParentNode(int id, Node * son1, Node * son2);
};

} //end of namespace bpp.

#endif //_ABSTRACTAGGLOMERATIVEDISTANCEMETHOD_H_