FragSet.hh

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// (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
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/// @file   core/fragments/FragSet.hh
/// @brief  set of fragments
/// @author Oliver Lange ( olange@u.washington.edu)
/// @date   Wed Aug 22 12:08:31 2007
///

#ifndef INCLUDED_core_fragment_FragSet_HH
#define INCLUDED_core_fragment_FragSet_HH

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

// Package Headers
#include <core/types.hh>
#include <core/fragment/FragID.fwd.hh>
#include <core/fragment/Frame.fwd.hh>
// AUTO-REMOVED #include <core/fragment/FrameIterator.hh>
// AUTO-REMOVED #include <core/fragment/FrameList.hh>

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

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

#include <core/fragment/FrameIterator.fwd.hh>
#include <core/fragment/FrameList.fwd.hh>
#include <utility/vector1.hh>

#ifdef WIN32
  #include <core/fragment/FragID.hh>
#endif


// Package Headers

namespace core {
namespace fragment {

///@detail The FragSet: (Interface Definition -- Virtual BaseClass )
/*
   The FragSet is the basic interface to communicate with mover classes. Its main purpose is a fast access
   to fragments by seqpos. More functionality might be coming.

   To access fragments:

   by region: --> region( .. )
   all frames: FrameIterator it = fragset.begin() ... fragset.end()
   all fragments: FragID_Iterator it = fragset.begin() ... fragset.end()

   Two simple extensions are already provided:
    ConstantLengthFragSet: fragments are stored by their start-sequence position, only one frame per position
    OrderFragSet: fragments are stored by their start-sequence position, multiple frames per position
    what might be useful: a map from position to all fragments that overlap with that position

*/


class FragSet : public utility::pointer::ReferenceCount {

  //how to iterate over fragments that fit certain search criteria ?
public:
  FragSet() : min_pos_ ( 100000 ), max_pos_( 0 ), max_frag_length_( 0 )
  {}

  virtual ~FragSet() {}

  ///@brief clone and copy the pointer of all Frames (Frames will not be copied)
  virtual FragSetOP clone() const = 0;

  ///@brief create an empty clone
  virtual FragSetOP empty_clone() const = 0;


  ///@brief iterate over contents
  virtual FrameIterator begin() const = 0;
  virtual FrameIterator end() const = 0;

  ///@brief appends frames at sequence position pos to frames, returns nr of frames added
  virtual Size frames( core::Size pos, FrameList &frames ) const {
    return region_simple( pos, pos, frames);
  }

  ///@brief returns fragments that exactly span seq_pos start...end
  virtual Size region_simple( core::Size start, core::Size end, FrameList &frames ) const {
    // return region( start, end, end-start+1, end-start+1, frames );
    return region_all( start, end, end-start+1, end-start+1, frames );
  }

  ///@brief return a list of frames that all sample the specified region, assume all motions are allowed
  virtual Size region_all(
    core::Size start,
    core::Size end,
    core::Size min_overlap,
    core::Size min_length,
    FrameList &frames
  ) const;

  ///@brief the region thing has to be thought-over. How do we really want to sample fragments?
  /// for now, we ignore everything in this call and just return frags that have "start" as there specified start() entry.
  virtual Size region(
    kinematics::MoveMap const& move_map,
    core::Size start,
    core::Size end,
    core::Size min_overlap,
    core::Size min_length,
    FrameList &frames
  ) const = 0;

  ///@brief InsertMap and InsertSize gives quick overview which residues can be affected by fragments.
  /// insert_map --- list of start-positions, insert_size corresponding list of longest fragment at position x
  virtual void generate_insert_map( kinematics::MoveMap const& mm, InsertMap &insert_map, InsertSize &insert_size) const;

  ///@brief returns the maximal sequence position that can be affected by fragments in this set
  Size max_pos() const
  { return max_pos_; }

  ///@brief returns the first sequence position that can be affected by fragments in this set
  Size min_pos() const
  { return min_pos_; }

  ///@brief returns the longest fragment stored in this FragSet.
  Size max_frag_length() const
  { return max_frag_length_; }

  ///@brief add a single frame. if compatible frame is already in set the frames will be merged
  void add( FrameOP aFrame );

  ///@brief add all Frames in list
  void add( FrameList const& frames );

  ///@brief add all Frames in FragSet
  void add( FragSet const& frames );

  ///@brief add single fragment
  void add( FragID const& );

  // put all fragments in FragID_list into this FragSet.
  // this function has the following effect:
  //      fragments that belong to the same frame are copied into a new frame
  //      the frame gets added. If all fragments of a frame are in the list, the frame is just added as is
  //
  void add( FragID_List & list ) { //need to work on const-correctness to make this a const-add
    insert_fragID_list( list );
  }

  ///@brief add all fragments in FragID_List
  void insert_fragID_list( FragID_List & list );

  ///@brief returns total size--> counts together all frags in each frame
  Size size() const;

  ///@brief counts number of frames ( slow! - it really counts )
  Size nr_frames() const;

  virtual bool empty() const = 0;

  friend std::ostream & operator<<(std::ostream & out, FragSet const & frags );

protected:
  ///@brief setter for max_frag_length_
  void set_max_frag_length( Size setting ) {
    max_frag_length_ = setting;
  }

  void set_max_pos( Size pos ) { max_pos_=pos; }
  void set_min_pos( Size pos ) { min_pos_=pos; }

  /// @brief storage classes have to overload this one to add frames to their container
  virtual void add_( FrameOP aFrame ) = 0;

private:
  Size min_pos_;
  Size max_pos_;
  Size max_frag_length_;

}; // class FragSet



} /* core */
} /* fragment */

#endif