stage/include/ost/seq/alignment_handle.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_ALIGNMENT_HANDLE_HH
#define OST_SEQ_ALIGNMENT_HANDLE_HH

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

#include <ost/seq/impl/sequence_list_impl_fw.hh>
#include <ost/seq/sequence_handle.hh>
#include <ost/seq/sequence_list.hh>

namespace ost { namespace seq {

class SequenceList;
class AlignedRegion;
class AlignedColumn;
class AlignedColumnIterator;

class DLLEXPORT_OST_SEQ AlignmentHandle {
public:

  typedef AlignedColumnIterator iterator;
  AlignmentHandle();

  int GetPos(int seq_index, int residue_index) const;

  int GetResidueIndex(int seq_index, int pos) const;

  mol::ResidueView GetResidue(int seq_index, int pos) const;

  char GetOneLetterCode(int seq_index, int pos) const;

  void AddSequence(const ConstSequenceHandle& sequence);

  ConstSequenceHandle GetSequence(int seq_id) const;
  
  void RemoveSequence(int seq_index);
  String ToString(int width=80) const;

  int GetLength() const;

  AlignmentHandle Copy() const;

  ConstSequenceHandle FindSequence(const String& name) const;
  
  int FindSequenceIndex(const String& name) const;
  
  void AttachView(int seq_index, const mol::EntityView& view);

  void AttachView(int seq_index, const mol::EntityView& view,
                  const String& chain_name);


  mol::EntityViewPair GetMatchingBackboneViews(int idx0=0, int idx1=1) const;
  void SetSequenceName(int seq_index, const String& name);

  void SetSequenceOffset(int seq_index, int offset); 
  int  GetSequenceOffset(int seq_index);
  ConstSequenceList GetSequences() const;

  AlignedRegion MakeRegion(int start, int n, int master=-1) const;

  int GetCount() const;

  bool operator==(const AlignmentHandle& rhs) const;
  bool operator!=(const AlignmentHandle& rhs) const;

  AlignedColumn operator[](int index) const;

  AlignmentHandle(const impl::SequenceListImplPtr& impl);

  void Cut(int start, int end);

  void Replace(const AlignedRegion& rhs, int start, int end);
  void ShiftRegion(int start, int end, int amount, int master=-1);

  iterator begin() const;
  iterator end() const;

  bool IsValid() const { return impl_.get()!=0; }
    
  Real GetCoverage(int seq_index) const;
  
  
  const String& GetSequenceRole(int seq_index);
  
  void SetSequenceRole(int seq_index, const String& role);
private:
  void CheckValidity() const;
  impl::SequenceListImplPtr impl_;
};

AlignmentHandle DLLEXPORT_OST_SEQ CreateAlignment();

AlignmentHandle DLLEXPORT_OST_SEQ
AlignmentFromSequenceList(const SequenceList& seq_list);

typedef std::vector<AlignmentHandle> AlignmentList;

}}

#endif

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