fragment_functions.hh

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

#ifndef INCLUDED_protocols_forge_methods_fragment_functions_hh
#define INCLUDED_protocols_forge_methods_fragment_functions_hh

// type headers
#include <core/types.hh>

// project headers
#include <core/fragment/ConstantLengthFragSet.fwd.hh>
// AUTO-REMOVED #include <core/fragment/FrameIterator.hh>

#include <core/fragment/FrameIterator.fwd.hh>



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 = 1,
  bool const all_possible_smallmers = false
);


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


#endif /* INCLUDED_protocols_forge_methods_fragment_functions_HH */