AbstractPhylogenyReconstructionMafIterator.h

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//
// File: AbstractPhylogenyReconstructionMafIterators.h
// Created by: Julien Dutheil
// Created on: Jul 24 2012
//

/*
Copyright or © or Copr. Bio++ Development Team

This software is a computer program whose purpose is to test the
homogeneity of the substitution process of a given alignment.

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
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In this respect, the user's attention is drawn to the risks associated
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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
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*/

#ifndef _ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_
#define _ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_

#include <Bpp/Seq/Io/Maf/MafIterator.h>
#include <Bpp/Phyl/Tree.h>

namespace bpp {

class AbstractPhylogenyReconstructionMafIterator:
  public AbstractFilterMafIterator
{
  public:
    AbstractPhylogenyReconstructionMafIterator(MafIterator* iterator):
      AbstractFilterMafIterator(iterator)
    {}

  virtual ~AbstractPhylogenyReconstructionMafIterator() {}

  private:
    MafBlock* analyseCurrentBlock_() throw (Exception)
    {
      MafBlock* block = iterator_->nextBlock();
      if (!block) return 0;
      Tree* tree = buildTreeForBlock(*block);
      block->setProperty(getPropertyName(), tree);
      return block;
    }

  public:
    virtual std::string getPropertyName() const = 0;
    virtual Tree* buildTreeForBlock(const MafBlock& block) = 0;

};

} //end of namespace

#endif //_ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_