MatrixScoringScheme.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 MatrixScoringScheme.hh
/// @brief class definition for a given scoring scheme for an alignment.
/// @detailed Simply based on comparing single characters from two protein
/// sequences, along 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_MatrixScoringScheme_hh
#define INCLUDED_core_sequence_MatrixScoringScheme_hh

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

#include <utility/io/izstream.fwd.hh>
#include <utility/file/FileName.fwd.hh>

#include <utility/vector1_bool.hh>


namespace core {
namespace sequence {

class MatrixScoringScheme : public ScoringScheme {

public:

  MatrixScoringScheme() {
    // gap open and gap extend set to default parameters
    // for NCBI BLASTP.
    gap_open  ( -11 );
    gap_extend( -1  );
    init_type();
  }

  /// @brief ctor
  MatrixScoringScheme(
    Real open,
    Real extend,
    utility::file::FileName const & fn
  )
  {
    read_from_file( fn );
    gap_open  ( open );
    gap_extend( extend );
    init_type();
  }

  MatrixScoringScheme(
    Real open,
    Real extend,
    utility::vector1< utility::vector1< core::Real > > matrix
  ) : scoring_matrix_( matrix ) {
    gap_open  ( open );
    gap_extend( extend );
    init_type();
  }

  /// @brief returns owning pointer to a new object with a deep copy of
  /// this object's values.
  ScoringSchemeOP clone() const {
    return new MatrixScoringScheme(
      gap_open(),
      gap_extend(),
      scoring_matrix()
    );
  }

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

  /// @brief Read an alignment matrix from the given database filename using the
  /// NCBI BLOSUM format for matrices.
  void read_from_database( std::string name="BLOSUM62" );
  /// @brief Read an alignment matrix from the given filename using the
  /// NCBI BLOSUM format for matrices.
  void read_from_file( utility::file::FileName const & fn );
  void read_data( utility::io::izstream & input );

  /// @brief Get the values for amino acid aa, in Rosetta aa order.
  utility::vector1< Real > values_for_aa( char aa );
  /// @brief Get the values for amino acid aa, in Rosetta aa order.
  utility::vector1< Real > values_for_aa( core::chemical::AA aa );
  utility::vector1< utility::vector1< Real > > scoring_matrix() const;

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

private:
  void init_type() {
    type( "Matrix" );
  }

  utility::vector1< utility::vector1< Real > > scoring_matrix_;
}; // class MatrixScoringScheme

} // sequence
} // core

#endif