aligned_region.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_SEQ_ALIGNED_REGION_HH
#define OST_SEQ_ALIGNED_REGION_HH

/*
  Author: Marco Biasini
 */
#include <ost/seq/module_config.hh>
#include <ost/seq/alignment_handle.hh>
#include <ost/seq/aligned_column_iterator.hh>

namespace ost { namespace seq {


class DLLEXPORT_OST_SEQ AlignedRegion {
public:
  typedef AlignedColumnIterator iterator;
  AlignedRegion(const AlignmentHandle& aln, 
                int start, int end, int master=-1);
  
  int GetEnd() const;
  int GetStart() const;
  int GetMaster() const;
  void SetMaster(int master);
  void Delete();
  void Replace(const AlignedRegion& aln_r);
  
  void ShiftLeft(int n);
  
  void ShiftRight(int n);
  
  int GetLength() const;
  
  AlignmentHandle GetAlignmentHandle() const;

  AlignedColumn operator[](int index) const;
  
  AlignedColumnIterator begin();
  AlignedColumnIterator end();
  
  bool operator==(const AlignedRegion& rhs) const;
  bool operator!=(const AlignedRegion& rhs) const;  
private:
  AlignmentHandle aln_;
  int             start_;
  int             end_ ;
  int             master_;
};

typedef std::vector<AlignedRegion> AlignedRegionList;

}}

#endif