L1ScoringScheme.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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file L1ScoringScheme.hh
/// @brief class definition for a profile-profile scoring scheme for
/// comparing two sequence profiles using the L1 city-block distance.
/// @detailed Simply based on comparing single profiles from two protein
/// sequences by computing the sum of P(A) - P(B) for all matching probabilities
/// in the profiles A and B. Also includes with affine gap penalties of the form
/// penalty = A + Bk, where A represents the penalty for starting a gap, and B
/// represents the penalty for extending a previously opened gap by k
/// characters.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_L1ScoringScheme_hh
#define INCLUDED_core_sequence_L1ScoringScheme_hh

#include <core/types.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/sequence/ScoringScheme.hh>

namespace core {
namespace sequence {

class L1ScoringScheme : public ScoringScheme {
public:

  /// @brief ctor
  L1ScoringScheme(
    Real open   = -4,
    Real extend = -1
  )
  {
    gap_open  ( open );
    gap_extend( extend );
    type("L1");
  }

  ScoringSchemeOP clone() const {
    return new L1ScoringScheme(
      gap_open(),
      gap_extend()
    );
  }

  /// @brief dtor
  virtual ~L1ScoringScheme() {}

  virtual Real score( SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2 );
}; // class L1ScoringScheme

} // sequence
} // core

#endif