fragment_functions.cc

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// vi: set ts=2 noet:
//
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/// @file protocols/forge/methods/fragment_functions.cc
/// @brief methods for manipulating fragments
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

// unit headers
#include <protocols/forge/methods/fragment_functions.hh>

// project headers
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FrameIteratorWorker_.hh>

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

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


namespace protocols {
namespace forge {
namespace methods {


/// @brief create small-mers from large-mers
/// @param[in] all_possible_smallmers Default false.  If true, grab all
///  possible smallmers using every possible starting position in a largemer
///  (you could end up with a *lot* of fragments per position).  If false,
///  grab smallmers using only the first position of a largemer as the starting
///  position.
core::fragment::ConstantLengthFragSetOP
smallmer_from_largemer(
  core::fragment::FrameIterator begin,
  core::fragment::FrameIterator end,
  core::Size const smallmer_size,
  bool const all_possible_smallmers
)
{
  using core::Size;
  using core::fragment::ConstantLengthFragSet;
  using core::fragment::ConstantLengthFragSetOP;
  using core::fragment::FrameIterator;

  assert( smallmer_size > 0 );

  ConstantLengthFragSetOP small = new ConstantLengthFragSet( smallmer_size );

  for ( FrameIterator f = begin; f != end; ++f ) {
    Size const ie = all_possible_smallmers ? f->length() - smallmer_size + 1 : 1;
    for ( Size i = 1; i <= ie; ++i ) {
      small->add( f->generate_sub_frame( smallmer_size, i ) );
    }
  }

  return small;
}


} // methods
} // forge
} // protocols