ProfileScore.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 an amino acid sequence identity
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_ProfileScore_hh
#define INCLUDED_protocols_frag_picker_scores_ProfileScore_hh

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

#include <protocols/frag_picker/scores/ProfileScore.fwd.hh>

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

#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/ScoringScheme.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

typedef utility::vector1<utility::vector1<Real> > Matrix;

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

  ProfileScore(Size priority, Real lowest_acceptable_value, bool use_lowest,
      sequence::SequenceProfileOP query_profile,
      sequence::ScoringSchemeOP profile_scoring, Size longest_vall_chunk) :
    CachingScoringMethod(priority, lowest_acceptable_value, use_lowest, "ProfileScore") {
    query_profile_ = query_profile;
    profile_scoring_ = profile_scoring;

    for (Size i = 1; i <= query_profile->length(); ++i) {
      utility::vector1<Real> row(longest_vall_chunk);
      scores_.push_back(row);
    }
  }

  ~ProfileScore();

  void do_caching(VallChunkOP);
  void clean_up() {
  }
  bool cached_score(FragmentCandidateOP, FragmentScoreMapOP);
  bool describe_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map,
      std::ostream& out);

protected:
  Matrix scores_;

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

class MakeProfileScore: public MakeFragmentScoringMethod {
public:

  MakeProfileScore() :
    MakeFragmentScoringMethod("ProfileScore") {
  }

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

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


#endif /* INCLUDED_protocols_frag_picker_scores_ProfileScore_HH */