SequenceCoupling.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 SequenceCoupling.hh
/// @brief class definition for a sequence coupling profile that
//   represents a  probability distribution over the entire protein.
/// @author Hetu Kamisetty

#ifndef INCLUDED_core_sequence_SequenceCoupling_hh
#define INCLUDED_core_sequence_SequenceCoupling_hh

// Unit headers
#include <core/sequence/SequenceCoupling.fwd.hh>

// Project headers
#include <core/types.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>

// Utility headers
#include <utility/file/FileName.fwd.hh>

// C++ headers
#include <utility/vector1.hh>

namespace core {
namespace sequence {

class SequenceCoupling: public SequenceProfile{
  typedef std::string string;
  typedef utility::file::FileName FileName;
public:

  /// @brief ctors
  SequenceCoupling() : temp_( 1.0 ) {}
  /// @brief copy ctor
  SequenceCoupling( SequenceCoupling const & src ):
    SequenceProfile()
  {
    *this = src;
  }

  /*
  void profile(
    utility::vector1< utility::vector1< Real > > const & new_profile
  );
  utility::vector1< utility::vector1< Real > > const & profile() const;
  */

  /// @brief assignment operator.
  SequenceCoupling& operator = ( SequenceCoupling const & rhs ) {
    if ( this == &rhs ) return *this;

    id      ( rhs.id() );
    start   ( rhs.start()    );
    gap_char( rhs.gap_char() );
    sequence( rhs.sequence() );

    edgePots( rhs.edgePots() );
    edgeList( rhs.edgeList() );
    profile( rhs.profile() );
    //alphabet( rhs.alphabet() );
    temp    ( rhs.temp() );

    return *this;
  }

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

  /// @brief Read a SequenceCoupling model in GREMLIN format .
  virtual void read_from_file( FileName const & fn );

  std::string type() const {
    return "sequence_coupling";
  }

  /// @brief Print this SequenceCoupling object to the given std::ostream.
  /// Commenting out to fix PyRosetta build  friend std::ostream & operator<<( std::ostream & out, const SequenceCoupling & p );

  utility::vector1< utility::vector1< Size> > edgeList() const{
    return edgeList_;
  }

  utility::vector1< utility::vector1< utility::vector1< Real > > > edgePots() const{
    return edgePots_;
  }
  core::Real temp() const{
    return temp_;
  }
  Size npos() const{
    return numVerts_;
  }

  Size findEdgeId(Size vert1, Size vert2) const;

  utility::vector1< utility::vector1 < Real > > const & edgePotBetween(Size vert1, Size vert2) const;
  utility::vector1< utility::vector1 < Real > >  const & edgePotBetween(Size edgeId) const;

  void temp(core::Real const t){
    temp_ = t;
  }
  void edgeList(utility::vector1< utility::vector1< Size > > const & eList){
    edgeList_=eList;
  }
  void edgePots(utility::vector1< utility::vector1< utility::vector1< Real> > > const & ePots){
    edgePots_ = ePots;
  }


  ///virtual void generate_from_sequence( Sequence const & seq, std::string matrix="BLOSUM62" );
  //
  ///void rescale(core::Real factor=1);

  ///void convert_profile_to_probs();

  /// @brief Read profile matrix from the given filename using the NNMAKE
  /// .checkpoint format.
  ///void read_from_checkpoint( FileName const & fn );
  //
  virtual void insert_char( core::Size pos, char new_char );

  /// @brief Deletes the given position from the Sequence and shifts
  /// everything else back by one.
  virtual void delete_position( core::Size pos );

  ///Size width() const;

  ///virtual SequenceOP clone() const {
  /// SequenceOP new_seq_op( new SequenceProfile( *this ) );
  /// return new_seq_op;
  ///}
  //


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

private:
  // temp used to convert arbitrary scores to/from probabilities
  core::Real temp_;
  Size numVerts_, numEdges_;
  //utility::vector1< utility::vector1< Real > > vertexPots_;
  utility::vector1< utility::vector1< Size > > edgeList_;
  utility::vector1< utility::vector1< utility::vector1< Real> > > edgePots_;

}; // class SequenceCoupling

} // sequence
} // core

#endif