DerivedSequenceMapping.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @brief
/// @author

#ifndef INCLUDED_core_sequence_DerivedSequenceMapping_hh
#define INCLUDED_core_sequence_DerivedSequenceMapping_hh

// Unit headers
#include <core/id/SequenceMapping.hh>
#include <core/id/SequenceMapping.fwd.hh>

// Project headers
#include <core/conformation/signals/LengthEvent.fwd.hh>
#include <core/types.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/exit.hh>

// C++ headers
// AUTO-REMOVED #include <iostream>
#include <string>

namespace core {
namespace sequence {

class DerivedSequenceMapping : public core::id::SequenceMapping {

public:
// constructors, destructors and assignment operator
  /// @brief ctor
  DerivedSequenceMapping() :
    core::id::SequenceMapping(),
    seq1_(""),
    seq2_(""),
    start_seq2_(0)
  {}

  /// @brief ctor
  DerivedSequenceMapping( Size s1, Size s2 ) :
    core::id::SequenceMapping(s1,s2)
  {}

  /// @brief dtor
  ~DerivedSequenceMapping();

  /// @brief copy constructor
  DerivedSequenceMapping( DerivedSequenceMapping const & src );

  DerivedSequenceMapping &
  operator=( DerivedSequenceMapping const & src );

public:

  std::string & seq1() {
    return seq1_;
  }

  std::string & seq2() {
    return seq2_;
  }

  std::string const & seq1() const {
    return seq1_;
  }

  std::string const & seq2() const {
    return seq2_;
  }

  Size const & start_seq2() const {
    return start_seq2_;
  }

  void seq1( std::string const & s ) {
    seq1_ = s;
  }

  void seq2( std::string const & s ) {
    seq2_ = s;
  }

  void start_seq2( Size s ) {
    start_seq2_ = s;
  }


private:
  std::string seq1_; //target=query sequence ... might be empty if not available
  std::string seq2_; //template sequence
  Size start_seq2_; // which is the first seq_pos of seq2_
}; // class SequenceMapping

} // sequence
} // core

#endif