alignment_handle.hh

Go to the documentation of this file.

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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