OrderedFragSet.hh

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/// @file   core/fragments/ConstantLengthFragSet.hh
/// @brief  yields a simple implementation of a fragset
/// @author Oliver Lange ( olange@u.washington.edu)
/// @date   Wed Aug 22 12:08:31 2007
///

#ifndef INCLUDED_core_fragment_OrderedFragSet_HH
#define INCLUDED_core_fragment_OrderedFragSet_HH

// Unit Headers
#include <core/fragment/OrderedFragSet.fwd.hh>

// Package Headers
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.fwd.hh>
#ifdef WIN32
#include <core/fragment/Frame.hh> // WIN32 INCLUDE
#endif

// Project Headers
#include <core/types.hh>
#include <core/kinematics/MoveMap.fwd.hh>

// std Headers
// AUTO-REMOVED #include <iterator>
#include <map>

#include <utility/vector1.hh>


namespace core {
namespace fragment {

/* classic 9mer Frags would be in one of those */
class OrderedFragSet : public FragSet {
public:
  typedef FragSet Parent;
  typedef std::map< Size, FrameList > FrameMap;

// ConstantLengthFragSet is a FragSet with only one frame per position!
public:

  OrderedFragSet();
  ~OrderedFragSet();

  virtual FragSetOP clone() const;
  virtual FragSetOP empty_clone() const;

  virtual Size region(
    kinematics::MoveMap const& mm,
    core::Size start,
    core::Size end, //not used
    core::Size , //min_overlap not used
    core::Size , //min_length not used
    FrameList &frames
  ) const;

  /// @brief Accessor for the Frame at the specified insertion position. Returns false if
  /// there is no frame at the specified position.
  virtual Size frames( Size pos, FrameList &frames ) const;

  virtual FrameIterator begin() const;

  virtual FrameIterator end() const;

  virtual bool empty() const;

protected:

  virtual void add_( FrameOP aframe );

private:
  FrameMap frames_;

};

}
}

#endif