DnaChains.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file DnaChains.hh
/// @brief a descriptive but lightweight class to keep track of (usually basepaired) dna chains
/// @author ashworth

#ifndef INCLUDED_protocols_dna_DnaChains_hh
#define INCLUDED_protocols_dna_DnaChains_hh

#include <protocols/dna/DnaChains.fwd.hh>

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

#include <utility/pointer/ReferenceCount.hh>

#include <iosfwd>
#include <map>

#include <utility/vector1.hh>


namespace protocols {
namespace dna {

class DnaPosition {
///@brief Stores residue index/indices for a DNA position, which could be a basepair or a single-stranded position.  Accomplishes what std::pair<Size,Size> would, but is nicer to use
public: // constructors
  // default empty constructor
  DnaPosition() : top_(0), bottom_(0), paired_(false) {}
  // construct a single-stranded position
  DnaPosition( core::Size i ) : top_(i), bottom_(0), paired_(false) {}
  // construct a double-stranded position (a basepair)
  DnaPosition( core::Size i, core::Size j ) : top_(i), bottom_(j), paired_(true) {}
  ~DnaPosition(){}

public: // const methods
  core::Size top() const { return top_; }
  core::Size bottom() const { return bottom_; }
  bool paired() const { return paired_; }
  // there are no 'settors' -- just delete and reconstruct -- it is safer that way

private:
  core::Size top_;
  core::Size bottom_;
  bool paired_;
};

typedef std::map< core::Size, DnaPosition > DnaPositions;

class DnaChains : public utility::pointer::ReferenceCount {
// this class is a light wrapper for DnaPositions (a map which is typedefed above)
public: // constructors
  DnaChains();
  virtual ~DnaChains();
  DnaChains( DnaChains const & other );
  DnaChainsOP clone() const;

  void clear() { positions_.clear(); }
  bool empty() const { return positions_.empty(); }
  core::Size size() const { return positions_.size(); }

  DnaPosition & operator[] ( core::Size resindex ) { return positions_[ resindex ]; }
  DnaPosition const & operator[] ( core::Size resindex ) const
    { return ( *( positions_.find( resindex ))).second; }

  DnaPositions & positions() { return positions_; }
  DnaPositions const & positions() const { return positions_; }

  DnaPositions::iterator begin() { return positions_.begin(); }
  DnaPositions::iterator end() { return positions_.end(); }
  DnaPositions::const_iterator begin() const { return positions_.begin(); }
  DnaPositions::const_iterator end() const { return positions_.end(); }

  // top strand resid check (looks in map keys)
  bool is_top( core::Size index ) const
    { if ( positions_.count(index) != 0 ) return true; return false; }

  bool contains( core::Size index ) const;
  void print( core::pose::Pose const & pose, std::ostream & os ) const;

private:
  // map of DNA position info, keyed by Pose residue index
  DnaPositions positions_;
};

} // namespace dna
} // namespace protocols

#endif