SequenceIdentity.hh

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//
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/// @file   protocols/frag_picker/scores/SequenceIdentity.hh
/// @brief  a base class for fragment scoring
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_scores_SequenceIdentity_hh
#define INCLUDED_protocols_frag_picker_scores_SequenceIdentity_hh

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

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

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

/// @brief  SequenceIdentity score counts identical residues
/// @detailed Resulting score is the number of identical residues
/// on corresponding positions in a vall fragment and a query sequence
class SequenceIdentity: public FragmentScoringMethod {
public:
  /// @brief will be added if the two residues are identical
  static const int REWARD = 0;
  /// @brief will be added if the two residues are NOT identical
  static const int PENALTY = 1;

  SequenceIdentity(Size priority, Real lowest_acceptable_value, bool use_lowest,
      std::string & fastaQuerySequence) :
    FragmentScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "SequenceIdentity"), query_(fastaQuerySequence) {
  }

  bool score(FragmentCandidateOP f, FragmentScoreMapOP empty_map);

  /// @brief prints a detailed explanation how a fragment score has been computed
  /// @detailed besides extensive output, the method should return the same result as score()
  bool describe_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map,
      std::ostream& out);

private:
  Real minScoreAllowed_;
  std::string& query_;
};

/// @brief  Maker class that produces a new SequenceIdentity object
class MakeSequenceIdentity: public MakeFragmentScoringMethod {
public:

  MakeSequenceIdentity() :
    MakeFragmentScoringMethod("SequenceIdentity") {
  }

  FragmentScoringMethodOP make(Size priority, Real lowest_acceptable_value, bool use_lowest,
      FragmentPickerOP picker, std::string) {
    return (FragmentScoringMethodOP) new SequenceIdentity(priority,
        lowest_acceptable_value, use_lowest, picker->get_query_seq_string());
  }
};

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


#endif /* INCLUDED_protocols_frag_picker_scores_SequenceIdentity_HH */