FragSetCollection.cc

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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.cc
/// @brief  set of fragments for a certain alignment frame
/// @author Oliver Lange (olange@u.washington.edu)
/// @author James Thompson (tex@u.washington.edu)
/// @date   Wed Oct 20 12:08:31 2007
///

// Unit Headers
#include <core/fragment/FragSetCollection.hh>
#ifdef WIN32
#include <core/fragment/Frame.hh>
#endif

// Package Headers
#include <core/fragment/FragSet.hh>
#include <core/fragment/FrameIteratorWorker_.hh>

// Project Headers
#include <core/types.hh>

// Utility headers
#include <utility/vector1.fwd.hh>
#include <utility/exit.hh>

//#include <basic/Tracer.hh>

// AUTO-REMOVED #include <ostream>
// AUTO-REMOVED #include <set>

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


namespace core {
namespace fragment {

//static basic::Tracer tr("core.fragment");
using namespace kinematics;

FragSetCollection::FragSetCollection() {}
FragSetCollection::~FragSetCollection() {}
FragSetCollection::FragSetCollection( FragSetCollection const & src ) :
  Parent( src ),
  fragset_list_( src.fragset_list_ )
{}

FragSetOP FragSetCollection::clone() const {
  return new FragSetCollection( *this );
}
FragSetOP FragSetCollection::empty_clone() const {
  return new FragSetCollection();
}


Size
FragSetCollection::region(
  MoveMap const& move_map,
  Size start,
  Size end,
  Size min_overlap,
  Size min_length,
  FrameList &frames
) const {
  Size count ( 0 );
  for ( FragSetList::const_iterator it = fragset_list_.begin(), eit = fragset_list_.end();
        it != eit; ++it ) {
    count += (*it)->region(  move_map, start, end, min_overlap, min_length, frames );
  }
  return count;
}

void FragSetCollection::add_fragset( FragSetOP fragset ) {
  if ( fragset->max_frag_length() > max_frag_length() ) set_max_frag_length( fragset->max_frag_length() );
  if ( fragset->min_pos() < min_pos() ) set_min_pos( fragset->min_pos() );
  if ( fragset->max_pos() > max_pos() ) set_max_pos( fragset->max_pos() );
  fragset_list_.push_back( fragset );
}

FrameIterator FragSetCollection::begin() const {
  std::cout << "iterator of FragSetCollection has stubbed out " << std::endl;
  assert( 0 );
  utility_exit_with_message( "iterator of FragSetCollection has stubbed out " );
  return FrameIterator(); //too make compiler happy
}

FrameIterator FragSetCollection::end() const {
  std::cout << "iterator of FragSetCollection has stubbed out " << std::endl;
  assert( 0 );
  utility_exit_with_message( "iterator of FragSetCollection has stubbed out " );
  return FrameIterator(); //too make compiler happy
}

bool FragSetCollection::empty() const {
  for ( FragSetList::const_iterator it = fragset_list_.begin(); it != fragset_list_.end(); ++it ) {
    if ( !(*it)->empty() ) return false;
  }
  return true;
}

void FragSetCollection::add_( FrameOP ) {
  //tricky which FragSet should it add the frame to? needs a way to determine this
  std::cout << "add Frame to FragSetCollection has stubbed out " << std::endl;
  assert( 0 );
  utility_exit_with_message( "add Frame to FragSetCollection has stubbed out " );
}


} //fragment
} //core