ProfileScoreL1.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   protocols/frag_picker/scores/ProfileScore.hh
/// @brief  scores a fragment by L1 profile score
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_ProfileScoreL1_hh
#define INCLUDED_protocols_frag_picker_scores_ProfileScoreL1_hh

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


// package headers
#include <protocols/frag_picker/scores/CachingScoringMethod.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>
#include <protocols/frag_picker/scores/fragment_scoring_utilities.hh>

// AUTO-REMOVED #include <core/sequence/SequenceProfile.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

class ProfileScoreL1;
typedef utility::pointer::owning_ptr< ProfileScoreL1 > ProfileScoreL1OP;
typedef utility::pointer::owning_ptr< ProfileScoreL1 const > ProfileScoreL1COP;

/// @brief  a fragment candidate
class ProfileScoreL1: public CachingScoringMethod {
public:

  ProfileScoreL1(Size, Real , bool,
    sequence::SequenceProfileOP, utility::vector1<Size> &,Size);
  ~ProfileScoreL1();

  void do_caching_simple(VallChunkOP);
  void do_caching(VallChunkOP);
  void clean_up() {
  }
  bool score(FragmentCandidateOP, FragmentScoreMapOP);
  bool cached_score(FragmentCandidateOP, FragmentScoreMapOP);
  //bool describe_score(FragmentCandidateOP, FragmentScoreMapOP, std::ostream&);
protected:
  Matrix scores_;
  utility::vector1< Matrix > cache_;

private:
  sequence::SequenceProfileOP query_profile_;
  std::string cached_scores_id_;
  void clear();
};

class MakeProfileScoreL1: public MakeFragmentScoringMethod {
public:

  MakeProfileScoreL1() :
    MakeFragmentScoringMethod("ProfileScoreL1") {
  }

  FragmentScoringMethodOP make(Size, Real, bool, FragmentPickerOP, std::string);
};

} // scores
} // frag_picker
} // protocols


#endif /* INCLUDED_protocols_frag_picker_scores_ProfileScoreL1_HH */