ProfileScoreL1.cc

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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 && 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/scores/ProfileScore.cc
/// @brief  scores a fragment by an amino acid sequence identity
/// @author Dominik Gront (dgront@chem.uw.edu.pl)


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

#include <protocols/frag_picker/scores/ProfileScoreL1.hh>

// package headers
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/VallChunk.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.hh>

// mini headers
#include <core/sequence/SequenceProfile.hh>

// option key includes
#include <basic/options/keys/OptionKeys.hh>

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

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

using namespace basic::options;
using namespace basic::options::OptionKeys;

static basic::Tracer trProfScoreL1(
    "protocols.frag_picker.scores.ProfileScoreL1");

ProfileScoreL1::~ProfileScoreL1() {}

ProfileScoreL1::ProfileScoreL1(Size priority, Real lowest_acceptable_value, bool use_lowest,
      sequence::SequenceProfileOP query_profile, utility::vector1<Size> & frag_sizes,
      Size longest_vall_chunk) :
    CachingScoringMethod(priority, lowest_acceptable_value, use_lowest,
        "ProfileScoreL1") {
    query_profile_ = query_profile;

    for (Size i = 1; i <= query_profile->length(); ++i) {
      utility::vector1<Real> row(longest_vall_chunk);
      scores_.push_back(row);
    }
    create_cache(frag_sizes,query_profile->length(),longest_vall_chunk,cache_);
    if(trProfScoreL1.visible()) {
        trProfScoreL1 << "Created cache for fraglen:";
        for(Size i=1;i<=cache_.size();i++)
      if(cache_[i].size() > 0)
          trProfScoreL1 <<" "<<i;
        trProfScoreL1<<std::endl;
    }
}


void ProfileScoreL1::do_caching(VallChunkOP chunk) {

  std::string & tmp = chunk->chunk_key();
  if (tmp.compare(cached_scores_id_) == 0)
    return;
  cached_scores_id_ = tmp;

  do_caching_simple(chunk);
  for(Size fl=1;fl<=cache_.size();fl++) {
      if(cache_[fl].size() != 0) {
    trProfScoreL1.Trace << "caching profile score for " << chunk->get_pdb_id()
      << " of size " << chunk->size() << " for fragment size "<<fl<<std::endl;
    rolling_score(scores_,fl,cache_[fl]);
      }
  }
}


void ProfileScoreL1::do_caching_simple(VallChunkOP chunk) {

  Size size_q = query_profile_->length();

  trProfScoreL1.Debug << "caching profile score for " << chunk->get_pdb_id()
      << " of size " << chunk->size() << std::endl;
  for (Size i = 1; i <= size_q; ++i) {
    utility::vector1<Real> query_prof_row = query_profile_->prof_row(i);
    for (Size j = 1; j <= chunk->size(); ++j) {
      utility::vector1<Real> tmplt_prof_row = chunk->at(j)->profile();
      Real score = 0.0;
      for (Size k = 1; k <= 20; k++){
        score += std::abs(tmplt_prof_row[k] - query_prof_row[k]);
      }
      scores_[i][j] = score;
    }
  }

  trProfScoreL1.Debug << "precomputed matrix of L1 scores " << scores_.size()
      << "x" << chunk->size() << std::endl;
}

bool ProfileScoreL1::cached_score(FragmentCandidateOP f,
    FragmentScoreMapOP empty_map) {

  std::string tmp = f->get_chunk()->chunk_key();
  if (tmp.compare(cached_scores_id_) != 0)
    do_caching(f->get_chunk());

  Real totalScore = cache_[f->get_length()][f->get_first_index_in_query()][f->get_first_index_in_vall()];

  totalScore /= (Real) f->get_length();

  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}

bool ProfileScoreL1::score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {

  Real totalScore = 0.0;
  for (Size i = 1; i <= f->get_length(); i++) {
    utility::vector1<Real> query_prof_row = query_profile_->prof_row(f->get_first_index_in_query() + i - 1);
    VallChunkOP chunk = f->get_chunk();
    utility::vector1<Real> tmplt_prof_row = chunk->at(f->get_first_index_in_vall() + i - 1)->profile();
    for (Size k = 1; k <= 20; k++){
        totalScore += std::abs(tmplt_prof_row[k] - query_prof_row[k]);
    }
  }
  totalScore /= (Real) f->get_length();
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}


FragmentScoringMethodOP MakeProfileScoreL1::make(Size priority,
    Real lowest_acceptable_value, bool use_lowest, FragmentPickerOP picker, std::string) {

  Size len = picker->get_vall()->get_largest_chunk_size();
  trProfScoreL1 << "Profile scoring method is: L1" << std::endl;
  return (FragmentScoringMethodOP) new ProfileScoreL1(priority,
      lowest_acceptable_value, use_lowest, picker->get_query_seq(),
      picker->frag_sizes_,len);
}

} //scores
} // frag_picker
} // protocols

/*
bool ProfileScoreL1::cached_score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {

  std::string tmp = f->get_chunk()->chunk_key();
  if (tmp.compare(cached_scores_id_) != 0)
    do_caching(f->get_chunk());

  Real totalScore = 0.0;
  for (Size i = 1; i <= f->get_length(); i++) {
    assert(f->get_first_index_in_query() + i - 1 <= scores_.size());
    assert(f->get_first_index_in_vall()
        + i - 1<= scores_[1].size());
    totalScore
        += scores_[f->get_first_index_in_query() + i - 1][f->get_first_index_in_vall()
            + i - 1];
  }
  totalScore /= (Real) f->get_length();
  empty_map->set_score_component(totalScore, id_);
  if ((totalScore > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;
  return true;
}
*/