QuotaCollector.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/frag_picker/quota/QuotaCollector.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_quota_QuotaCollector_hh
#define INCLUDED_protocols_frag_picker_quota_QuotaCollector_hh

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

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

#include <core/fragment/SecondaryStructure.fwd.hh>

#include <utility/vector1.hh>

namespace protocols {
namespace frag_picker {
namespace quota {

/// @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 QuotaCollector : public CandidatesCollector {
public:

  QuotaCollector(Size query_size, Size frag_size)  { storage_.resize(query_size-frag_size+1); frag_size_ = frag_size; }

  /// @brief  Insert a fragment candidate to the container
  bool add(std::pair<FragmentCandidateOP, scores::FragmentScoreMapOP>);

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

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

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

  /// @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.
  Size query_length() const { return storage_.size(); }

  //Undefined, commenting out to fix PyRosetta build  ScoredCandidatesVector1 const & get_candidates(Size position_in_query) const;
  ScoredCandidatesVector1 & get_candidates(Size position_in_query);

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

  /// @brief Inserts candidates from another QuotaCollector for a give position in the query
  /// Candidates may or may not get inserted depending on the candidate
  void insert(Size pos, CandidatesCollectorOP collector) {
    QuotaCollectorOP c = dynamic_cast<QuotaCollector*> (collector());
    if (c == 0)
      utility_exit_with_message("Cant' cast candidates' collector to QuotaCollector. Is quota set up correctly?");
    for(Size j=1;j<=storage_[pos].size();++j) {
      ScoredCandidatesVector1 & content = c->get_pool(pos, j)->get_candidates(0);
      for(Size l=1;l<=content.size();l++) storage_[pos][j]->push( content[l] );
    }
  }

  /// @brief list all registered pools with their capacity
  void list_pools(std::ostream & where) const;

  /// @brief prints the number of quota pools for a given positio in query
  Size count_pools(Size position) const {
      return storage_[position].size();
  }

  QuotaPoolCOP get_pool( Size position, Size pool_id ) const {
      return storage_[position][pool_id];
  }

  QuotaPoolOP get_pool( Size position, Size pool_id ) {
      return storage_[position][pool_id];
  }

  void add_pool(Size position,QuotaPoolOP the_pool) {
      if(position <= storage_.size())
    storage_[position].push_back(the_pool);
  }

  void renormalize_quota_pools();

  void attach_secondary_structure_pools(Real,core::fragment::SecondaryStructureOP,
        std::string, Size, utility::vector1<Size>,utility::vector1<Real>,Size);
private:
  Size frag_size_;
  ScoredCandidatesVector1 frags_for_pos_;
  utility::vector1< utility::vector1<QuotaPoolOP> > storage_;
};

} // quota
} // frag_picker
} // protocols

#endif /* INCLUDED_protocols_frag_picker_quota_QuotaCollector_HH */