CandidatesCollector.hh

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//
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/// @file   protocols/frag_picker/CandidatesCollector.hh
/// @brief  Pure virtual base class for a container holding fragment candidates
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_CandidatesCollector_hh
#define INCLUDED_protocols_frag_picker_CandidatesCollector_hh

// type headers
#include <utility/pointer/ReferenceCount.hh>

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

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


namespace protocols {
namespace frag_picker {

/// TODO write collector for mixed fragment lengths
/// @brief A base class for collecting fragments.
/// @detailed The purpose of a collector is to keep fragment candidates to the end
/// of vall processing. Then a selector will go through all the candidates stored
/// in a collector and select the final fragments
/// @see GrabAll collector for a possible implementation
class CandidatesCollector: public utility::pointer::ReferenceCount {
public:
  /// @brief  Insert a fragment candidate to the container
  virtual bool add( ScoredCandidate ) = 0;

  /// @brief removes all candidates from the container
  virtual void clear() = 0;

  /// @brief inserts candidates from another collector
  /// Candidates may or may not get inserted depending on the candidate and type of storage
  virtual void insert( Size, CandidatesCollectorOP ) = 0;

  /// @brief  Check how many candidates have been already collected for a given position
  virtual Size count_candidates(Size) const = 0;

  /// @brief  Check how many candidates have been already collected for all positions
  virtual Size count_candidates() const = 0;

  /// @brief  Check the size of query sequence that this object knows.
  /// This is mainly to be ale to check if it is the same as in the other parts of
  /// fragment picking machinery.
  virtual Size query_length() const =0;

  virtual ScoredCandidatesVector1 & get_candidates( Size position_in_query) = 0;

  /// @brief Describes what has been collected
  virtual void print_report(
    std::ostream & output,
    scores::FragmentScoreManagerOP scoring
  ) const = 0;
};

} // frag_picker
} // protocols

#endif /* INCLUDED_protocols_frag_picker_CandidatesCollector_HH */