DistanceMatrix.h

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//
// File: DistanceMatrix.h
// Created on: Wed jun 08 10:39 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 _DISTANCEMATRIX_H_
#define _DISTANCEMATRIX_H_

// From the STL:
#include <vector>
#include <string>
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/VectorExceptions.h> //DimensionException
#include <Bpp/Numeric/Matrix/Matrix.h>

namespace bpp
{

class DistanceMatrix:
  public virtual Clonable
{

  private:
    RowMatrix<double> distances_;
    std::vector<std::string> names_;

  public:

    DistanceMatrix(const std::vector<std::string>& names):
      distances_(names.size(), names.size()),
      names_(names)
    {
      reset();
    }

    DistanceMatrix(size_t n):
      distances_(n, n), names_(n)
    {
      resize(n);
    }

    virtual ~DistanceMatrix() {}

    DistanceMatrix(const DistanceMatrix& dist):
      distances_(dist.distances_),
      names_(dist.names_) {}

    DistanceMatrix& operator=(const DistanceMatrix& dist)
    {
      size_t n = dist.size();
      resize(n);
      for(size_t i = 0; i < n; ++i)
      {
        for(size_t j = 0; j < n; ++j)
        {
          distances_(i, j) = dist(i, j);
        }
      }
      names_ = dist.names_;
      return *this;
    }

    DistanceMatrix* clone() const { return new DistanceMatrix(*this); }
    
  public:

    void reset()
    {
      size_t n = size();
      for (size_t i = 0; i < n; ++i)
      {
        for (size_t j = 0; j < n; ++j)
        {
          distances_(i, j) = 0;
        }
      }
    }
    
    size_t size() const { return names_.size(); }

    const std::vector<std::string>& getNames() const { return names_; }

    const std::string& getName(size_t i) const throw (IndexOutOfBoundsException)
    { 
      if (i >= size()) throw IndexOutOfBoundsException("DistanceMatrix::getName. Invalid indice.", i, 0, size());
      return names_[i];
    }
    
    void setName(size_t i, const std::string& name) throw (IndexOutOfBoundsException)
    {
      if (i >= size()) throw IndexOutOfBoundsException("DistanceMatrix::setName. Invalid indice.", i, 0, size());
      names_[i] = name;
    }

    void setNames(const std::vector<std::string>& names) throw (DimensionException)
    {
      if (names.size() != names_.size()) throw DimensionException("DistanceMatrix::setNames. Invalid number of names.", names.size(), names_.size());
      names_ = names;
    }

    size_t getNameIndex(const std::string& name) const throw (Exception);

    void resize(size_t n) {
      //RowMatrix<double>::resize(n, n);
      distances_.resize(n, n);
      names_.resize(n);
      for (size_t i = 0; i < n; ++i)
        names_[i] = "Taxon " + TextTools::toString(i);
      reset();
    }

    virtual const double& operator()(const std::string& iName, const std::string& jName) const throw (Exception)
    {
      size_t i = getNameIndex(iName);
      size_t j = getNameIndex(jName);
      //return operator()(i,j);
      return distances_(i,j);
    }

    virtual double& operator()(const std::string& iName, const std::string& jName) throw (Exception)
    {
      size_t i = getNameIndex(iName);
      size_t j = getNameIndex(jName);
      //return operator()(i,j);
      return distances_(i,j);
    }

    virtual const double& operator()(size_t i, size_t j) const
    {
      //return RowMatrix<double>::operator()(i, j);
      return distances_(i, j);
    }
    virtual double& operator()(size_t i, size_t j)
    {
      //return RowMatrix<double>::operator()(i, j);
      return distances_(i, j);
    }

    virtual const Matrix<double>& asMatrix() const {
      return distances_;
    }
    
    virtual Matrix<double>& asMatrix() {
      return distances_;
    }
};

} //end of namespace bpp.

#endif //_DISTANCEMATRIX_H_