SecondaryStructurePool.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/frag_picker/quota/SecondaryStructurePool.hh
/// @brief a quota pool based on secondary structure prediction
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_quota_SecondaryStructurePool_hh
#define INCLUDED_protocols_frag_picker_quota_SecondaryStructurePool_hh

#include <protocols/frag_picker/quota/SecondaryStructurePool.fwd.hh>
#include <protocols/frag_picker/quota/QuotaPool.hh>

// package headers
#include <protocols/frag_picker/LazySortedVector1.hh>
// #include <protocols/frag_picker/BoundedPriorityQueue.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>
#include <protocols/frag_picker/CommonFragmentComparators.hh>
// AUTO-REMOVED #include <core/fragment/SecondaryStructure.hh>

// utility headers
#include <core/types.hh>
#include <utility/vector1.hh>
#include <utility/pointer/owning_ptr.hh>

// C++ headers
#include <string>

namespace protocols {
namespace frag_picker {
namespace quota {

typedef LazySortedVector1<std::pair<FragmentCandidateOP,
                scores::FragmentScoreMapOP>, CompareByScoreCombination> BoundedQuotaContainer;
typedef utility::pointer::owning_ptr<BoundedQuotaContainer>
    BoundedQuotaContainerOP;

/// @brief represents a single pool used by quota selector
class SecondaryStructurePool : public QuotaPool {
public:
  /// @brief Creates a pool of a given size and name
  /// @param size - total number of fragments from all the pools at a given position
  /// @param name - name assigned to this pool. This in general may be any string that
  /// later allows one control pool's behavior from a flag file
  /// @param ss_type - what is the type of secondary structur this pool is accepting
  /// @param score_components_id - which scores will be used to sort this pool
  /// @param weights - weights for the scores that in general may be different than these used for fragment picking
  /// @param fraction - fraction of this pool in the entire population
  SecondaryStructurePool(Size,std::string,char,
      utility::vector1<Size>&,utility::vector1<Real>&,Real,Size,Size);

  char get_ss_type() const { return ss_type_; }

  virtual ~SecondaryStructurePool();

  /// @brief Says how many fragments (in total) may fit into this pool
  virtual Size total_size() const { return storage_->size(); }

  /// @brief Says how many fragments are currently in this pool
  virtual Size current_size() const { return storage_->count_inserted();}

  /// @brief Says how many fragments can still be inserted into this pool
  virtual Size size_left() const { return total_size() - current_size(); }

  virtual bool could_be_accepted(ScoredCandidate) const;

  /// @brief Push a fragment candidate into the container
  virtual void push(ScoredCandidate candidate) {
    storage_->push(candidate);
  }


// Stuff inherited from CandidatesCollector base
  /// @brief  Insert a fragment candidate to the container
  virtual bool add(ScoredCandidate);

  /// @brief removes all candidates from the container
  void clear() { storage_->clear(); }

  /// @brief  Check how many candidates have been already collected for a given position
  /// @detailed This is a very special case - collector will be used only for a given position.
  /// Thus it returns the total number of inserted candidates, as count_candidates() does
  Size count_candidates(Size) const { return current_size(); }

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

  /// @brief  Check the size of query sequence that this object knows.
  /// @detailed This is a very special case - collector will be used only for a given position and it does NOT
  /// know the tolal size. Thus it returns always 0
  Size query_length() const { return 0; }

  /// @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, CandidatesCollectorOP collector) {
    SecondaryStructurePoolOP c = dynamic_cast<SecondaryStructurePool*> (collector());
    if (c == 0)
      utility_exit_with_message("Cant' cast candidates' collector to SecondaryStructurePool.");
    ScoredCandidatesVector1 & content = c->get_candidates(0);
    for(Size l=1;l<=content.size();l++) storage_->push( content[l] );
  }

  /// @brief  Returns all the candidate in this pool
  ScoredCandidatesVector1 & get_candidates( Size //position_in_query
      ) {
      return storage_->expose_data();
  }

  void resize(Size new_size) {
      storage_->resize(new_size,new_size*buffer_factor_);
  }

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

  virtual void set_fraction(Real new_fraction) {
    QuotaPool::set_fraction(new_fraction);
    this_size_ = (Size)(total_size_*new_fraction);
    if ( this_size_ < 20 )
      this_size_ = 20;
    storage_->resize( this_size_,this_size_*buffer_factor_ );
  }

  virtual Real quota_score(ScoredCandidate candidate) const {
    Real t2(0);
    for(Size i=1;i<=components_.size();i++)
    t2 += candidate.second->at( components_[i] ) * weights_[i];
    return t2;
  }

private:
  Size total_size_;
  Size this_size_;
  char ss_type_;
  utility::vector1<Size> components_;
  utility::vector1<Real> weights_;
  BoundedQuotaContainerOP storage_;
  Size buffer_factor_;
};

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


#endif /* INCLUDED_protocols_frag_picker_quota_QuotaPool_HH */