BoundedCollector.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// 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/BoundedCollector.hh
/// @brief
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_BoundedCollector_hh
#define INCLUDED_protocols_frag_picker_BoundedCollector_hh

// package headers
#include <protocols/frag_picker/LazySortedVector1.hh>
// AUTO-REMOVED #include <protocols/frag_picker/BoundedPriorityQueue.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/BoundedCollector.fwd.hh>
#include <protocols/frag_picker/CandidatesCollector.hh>
#include <protocols/frag_picker/scores/FragmentScoreManager.hh>

#include <protocols/frag_picker/CommonFragmentComparators.hh>

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

// AUTO-REMOVED #include <basic/prof.hh>

/// ObjexxFCL headers
#include <ObjexxFCL/format.hh>

#include <iostream>

#include <utility/vector1.hh>

//Auto using namespaces
namespace std { } using namespace std; // AUTO USING NS
//Auto using namespaces end

//#include <algorithm>

namespace protocols {
namespace frag_picker {


/// @brief Keeps the N best fragments candidates for the final selection
/// @detailed The purpose of a collector is to keep the best fragment candidates to the end
/// of vall processing. In particular, the capacity of this collector may be larger than
/// the number of fragments one wants to get
template< class StrictWeakOrdering >
class BoundedCollector: public CandidatesCollector {
public:
  typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > > BoundedCollectorOP;
  typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > const> BoundedCollectorCOP;

public:

  /// @brief create a collector for a given size of a query sequence
  BoundedCollector(
    Size query_size,
    Size max_frags_per_pos,
    StrictWeakOrdering fragment_comparator,
    Size n_score_terms,
    Size buffer_factor = 5
  ) {

    FragmentCandidateOP worst_f = new FragmentCandidate(1,1,0,1);
    scores::FragmentScoreMapOP worst_s = new scores::FragmentScoreMap(n_score_terms);
    for(Size i=1;i<=n_score_terms;i++)
        worst_s->set_score_component(99999.9999,i);

    for (Size i = 1; i <= query_size; i++) {
      LazySortedVector1< std::pair< FragmentCandidateOP,
          scores::FragmentScoreMapOP >, StrictWeakOrdering > queue(
          fragment_comparator, max_frags_per_pos,max_frags_per_pos*buffer_factor);
      queue.set_worst( std::pair<FragmentCandidateOP,
                      scores::FragmentScoreMapOP>(worst_f,worst_s) );
      storage_.push_back(queue);
    }
  }

  /// @brief  Insert a fragment candidate to the container
  inline bool add( ScoredCandidate new_canditate) {

    return storage_[new_canditate.first->get_first_index_in_query()].push(
        new_canditate);
  }

  /// @brief  Check how many candidates have been already collected for a given position
  /// APL Note: you cannot have inlined virtual functions
  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
  /// APL Note: you cannot have inlined virtual functions
  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
  /// Candidates may or may not get inserted depending on the candidate
  void insert(Size pos, CandidatesCollectorOP collector) {
    BoundedCollectorOP c = dynamic_cast<BoundedCollector*> (collector());
    if (c == 0) {
      utility_exit_with_message("Cant' cast candidates' collector to BoundedCollector.");
    }
    ScoredCandidatesVector1 & content = c->get_candidates(pos);
    for(Size l=1;l<=content.size();l++) storage_.at(pos).push( content[l] );
  }

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

  inline void clear() {

      for (Size i_pos = 1; i_pos <= storage_.size(); ++i_pos)
    storage_[i_pos].clear();
  }

  /// @brief prints how many candidates have been collected for each position and how good they are
  void print_report(std::ostream& out, scores::FragmentScoreManagerOP scoring) const {
    using namespace ObjexxFCL::fmt;
    out
        << "\n pos  count   best     worst  | pos  count   best    worst   | pos  count    best    worst  |\n";
    Size cnt = 0;
    for (Size i_pos = 1; i_pos <= storage_.size(); ++i_pos) {

      if (storage_[i_pos].size() <= 1) {
        out << I(4, i_pos) << "      0                   |";
      } else {
        out << I(4, i_pos) << " " << I(6, storage_[i_pos].size())
            << " ";
        out << F(8, 2, scoring->total_score(
            storage_[i_pos].peek_front().second)) << " ";
        out << F(8, 2, scoring->total_score(
            storage_[i_pos].peek_back().second)) << " |";
      }
      ++cnt;
      if (cnt % 3 == 0)
        out << '\n';
    }
    out << std::endl;
  }

private:
  utility::vector1<LazySortedVector1<pair<FragmentCandidateOP,
      scores::FragmentScoreMapOP> , StrictWeakOrdering> > storage_;
};

// Concrete version for PyRosetta
class BoundedCollector_CompareTotalScore : public BoundedCollector<CompareTotalScore>
{
public:
  BoundedCollector_CompareTotalScore(Size query_size, Size max_frags_per_pos, CompareTotalScore fragment_comparator,Size n_score_terms,Size buffer_factor = 5)
   : BoundedCollector<CompareTotalScore>(query_size, max_frags_per_pos, fragment_comparator, n_score_terms, buffer_factor) {};
};

} // frag_picker
} // protocols


#endif /* INCLUDED_protocols_frag_picker_BoundedCollector_HH */