GrabAllCollector.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file   protocols/frag_picker/GrabAllCollector.hh
/// @brief
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_GrabAllCollector_hh
#define INCLUDED_protocols_frag_picker_GrabAllCollector_hh

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

// utility headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/types.hh>

#include <utility/vector1.hh>



namespace protocols {
namespace frag_picker {

// Always always declare your OP typedefs if you're defining a polymorphic class.
// I shouldn't have to do this for you.
class GrabAllCollector;
typedef utility::pointer::owning_ptr< GrabAllCollector > GrabAllCollectorOP;
typedef utility::pointer::owning_ptr< GrabAllCollector const > GrabAllCollectorCOP;


/// @brief Keeps all fragments candidates for the final selection
/// @detailed The purpose of a collector is to keep fragment candidates to the end
/// of vall processing. This simple implementation keeps all candidates which might
/// use huge memory
class GrabAllCollector: public CandidatesCollector {
public:

  /// @brief create a collector for a given size of a query sequence
  GrabAllCollector(Size query_size)
  {
    storage_.resize(query_size);
    for (Size i = 1; i <= query_size; i++) {
      utility::vector1<std::pair<FragmentCandidateOP,
          scores::FragmentScoreMapOP> > vec;
      storage_[i] = vec;
    }
  }

  /// @brief  Insert a fragment candidate to the container
  inline bool add( ScoredCandidate new_canditate )
  {
    storage_[new_canditate.first->get_first_index_in_query()].push_back(
        new_canditate);
    return true;
  }

  inline void clear()
  {
      for(Size i=1;i<storage_.size();++i)
        storage_[i].clear();
  }

  /// @brief prints how many fragments have been collected for each position
  void print_report(
    std::ostream & output,
    scores::FragmentScoreManagerOP
  ) const {
    output << "\n pos  | count |  pos  | count | pos  | count |\n";
    for (Size i = 1; i <= storage_.size(); ++i) {
      output << I(5, i) << " |" << I(6, storage_[i].size()) << " |";
      if (i % 3 == 0)
        output << '\n';
    }
  }

  /// @brief  Check how many candidates have been already collected for a given position
  inline Size count_candidates(Size seq_pos) const {
    return storage_[seq_pos].size();
  }

  /// @brief  Check how many candidates have been already collected for all positions
  inline Size count_candidates() const {

    Size response = 0;
    for(Size i=1;i<=storage_.size();++i)
      response += storage_[i].size();
    return response;
  }

  /// @brief  Check the size of query sequence that this object knows.
  /// This is mainly to be able to check if it is the same as in the other parts of
  /// fragment picking machinery.
  inline Size query_length() const {
    return storage_.size();
  }

  /// @brief Inserts candidates from another Collector for a give position in the query
  inline void insert(Size pos, CandidatesCollectorOP collector) {
    GrabAllCollectorOP c = dynamic_cast<GrabAllCollector*> (collector());
    if (c == 0)
      utility_exit_with_message("Cant' cast candidates' collector to GrabAllCollector.");
    for(Size j=1;j<=storage_[pos].size();++j) {
      ScoredCandidatesVector1 & content = c->get_candidates(pos);
      for(Size l=1;l<=content.size();l++) storage_[pos].push_back( content[l] );
    }
  }

  /// @brief returns all stored fragment candidates that begins at a given position in a query
  inline virtual ScoredCandidatesVector1 & get_candidates(Size position_in_query) {
    return storage_.at(position_in_query);
  }

private:
  utility::vector1< ScoredCandidatesVector1 > storage_;
};

} // frag_picker
} // protocols


#endif /* INCLUDED_protocols_frag_picker_GrabAllCollector_HH */