PairScoringScheme.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
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/// @file PairScoringScheme.hh
/// @brief class definition for a given scoring scheme for an alignment.
/// @detailed Scoring scheme based on comparing sequence columns based on
/// the additive combination of several ScoringScheme objects.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_PairScoringScheme_hh
#define INCLUDED_core_sequence_PairScoringScheme_hh

#include <core/types.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/PairScoringScheme.fwd.hh>

// AUTO-REMOVED #include <utility/vector1.hh>

#include <utility/vector1_bool.hh>


namespace core {
namespace sequence {

class PairScoringScheme : public ScoringScheme {

public:
  PairScoringScheme() {
    gap_open  ( -4 );
    gap_extend( -1 );
    type("Pair");
  }

  /// @brief ctor
  PairScoringScheme(
    Real gap_open_in,
    Real gap_extend_in,
    utility::vector1< utility::vector1< core::Real > > pairs
  )
    : pairs_( pairs )
  {
    gap_open( gap_open_in );
    gap_extend( gap_extend_in );
    type("Pair");
  }

  ScoringSchemeOP clone() const {
    // maybe clone the scoring_schemes() if object re-use ever causes a weird
    // problem.
    return new PairScoringScheme(
      gap_open(),
      gap_extend(),
      pairs()
    );
  }

  utility::vector1< utility::vector1< core::Real > > pairs() const {
    return pairs_;
  }

  void add_scored_pair(
    core::Size const res1,
    core::Size const res2,
    core::Real const score
  ) {
    if ( pairs_.size() <= res1 ) {
      pairs_.resize( res1 );
    }

    if ( pairs_[res1].size() <= res2 ) {
      pairs_[res1].resize( res2 );
    }

    pairs_[res1][res2] = score;
  }

  /// @brief dtor
  virtual ~PairScoringScheme() {}

  virtual void read_from_file( utility::file::FileName const & fn );

  virtual Real score(
    SequenceOP seq1,
    SequenceOP seq2,
    core::Size pos1,
    core::Size pos2
  );

private:
  utility::vector1< utility::vector1< core::Real > > pairs_;
}; // class PairScoringScheme

} // sequence
} // core

#endif