L1ScoringScheme.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 L1ScoringScheme.cc
/// @brief method implementations for L1ScoringScheme class.
/// @author James Thompson

#include <core/types.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/L1ScoringScheme.hh>

#include <utility/exit.hh>
// AUTO-REMOVED #include <iostream>
#include <string>

#include <complex>

#include <utility/vector1.hh>



namespace core {
namespace sequence {

  Real L1ScoringScheme::score(
    SequenceOP seq1,
    SequenceOP seq2,
    Size pos1,
    Size pos2
  ) {
    SequenceProfileOP prof1 = SequenceProfileOP(
      static_cast < SequenceProfile * > ( seq1() )
    );
    SequenceProfileOP prof2 = SequenceProfileOP(
      static_cast < SequenceProfile * > ( seq2() )
    );

    runtime_assert( pos1 <= prof1->length() );
    runtime_assert( pos2 <= prof2->length() );
    runtime_assert( prof1->prof_row(pos1).size() == prof2->prof_row(pos2).size() );

    // compare the two profiles using L1 city-block distance
    Size n_aa( prof1->prof_row(pos1).size() );
    Real score( 0.0 );
    for ( Size i = 1; i <= n_aa; ++i ) {
      Real const & p1_num( prof1->prof_row(pos1)[i] );
      Real const & p2_num( prof2->prof_row(pos2)[i] );
      if ( is_good( p1_num ) && is_good( p2_num ) ) {
        //for ( Size jj = 1; jj < i; ++jj ) std::cout << " ";
        //std::cout << "comparing " << p1_num << " and " << p2_num << std::endl;
        score += std::abs( p1_num - p2_num );
      } else {
        score += 1.0;
      }
    }

    score *= -1;
    // make the score a positive number where bigger is better!
    //std::cout << "score(" << pos1 << "," << pos2 << ") = " << score
    //  << std::endl << std::endl;
    return score;

    // pseudocount a little to prevent score fom being 0.
    //Real const very_small_value( 1e-15 );
    //if ( score <= very_small_value ) score = very_small_value;
    //return std::exp( -1 * score );
  } // score

} // sequence
} // core