fragment_scoring_utilities.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 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/scores/fragment_scoring_utilities.hh
/// @brief  functions and data types common for fragment scoring
/// @author Dominik Gront

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

#include <utility/vector1.hh>


namespace protocols {
namespace frag_picker {
namespace scores {

void create_cache(utility::vector1<Size> & frag_sizes,Size query_len,Size longest_vall_chunk,utility::vector1<Matrix> & cache) {

      std::sort(frag_sizes.begin(),frag_sizes.end());
      cache.resize(frag_sizes[frag_sizes.size()]);
      for(Size i=1;i<=frag_sizes.size();i++) {
    Matrix m;
    allocate_matrix(query_len,longest_vall_chunk,m);
    cache[frag_sizes[i]] = m;
      }
}

void allocate_matrix(Size i_size,Size j_size,Matrix & dst) {

      dst.clear();
      for(Size i = 1; i <= i_size;i++) {
    utility::vector1<Real> row(j_size);
    dst.push_back( row );
      }
}

void do_one_line(Size start_i,Size start_j,Matrix & small_scores,Size frag_len,Matrix & frag_scores) {

    Size stop_i = start_i + frag_len - 1;
    Size stop_j = start_j + frag_len - 1;
    Real last_score = small_scores[start_i][start_j];

    for(Size i=1;i<frag_len;i++) {
  last_score += small_scores[start_i+i][start_j+i];
    }
    frag_scores[start_i][start_j] = last_score;
    int max_steps = std::min((int) small_scores.size() - (int) start_i - (int) frag_len,
        (int) small_scores[1].size() - (int) start_j - (int) frag_len) + 1;
    int cnt = 1;
    while(cnt<=max_steps) {
  stop_i++;
  stop_j++;
  last_score += small_scores[stop_i][stop_j] - small_scores[start_i][start_j];
  start_i++;
  start_j++;
  frag_scores[start_i][start_j] = last_score;
  cnt++;
    }
}

void rolling_score(Matrix & small_scores,Size frag_len,Matrix & frag_scores) {

    do_one_line(1,1,small_scores,frag_len,frag_scores);
    for(Size i=2;i<=small_scores.size()-frag_len+1;i++)
  do_one_line(i,1,small_scores,frag_len,frag_scores);
    for(Size i=2;i<=small_scores[1].size()-frag_len+1;i++)
  do_one_line(1,i,small_scores,frag_len,frag_scores);
}


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