CompositeSequence.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 CompositeSequence.hh
/// @brief class definition for a sequence profile that represents each
/// position in a sequence as a probability distribution over the allowed amino
/// acids at that position.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_CompositeSequence_hh
#define INCLUDED_core_sequence_CompositeSequence_hh

#include <core/sequence/CompositeSequence.fwd.hh>

#include <core/types.hh>
#include <core/sequence/Sequence.hh>
// AUTO-REMOVED #include <core/sequence/SequenceProfile.hh>

#include <utility/file/FileName.fwd.hh>
// AUTO-REMOVED #include <ObjexxFCL/string.functions.hh>

#include <utility/vector1.hh>

//Auto Headers
namespace core {
namespace sequence {

class CompositeSequence : public Sequence {
  typedef std::string string;

public:

  /// @brief ctors
  CompositeSequence() {}

  /// @brief copy ctor
  CompositeSequence( CompositeSequence const & src )
    : Sequence()
  {
    *this = src;
  }

  core::Size n_seqs() const;

  utility::vector1< SequenceOP > seqs() const;

  void add_sequence( SequenceOP seq );

  virtual Size length() const;

  virtual void delete_position( core::Size pos );

  virtual void insert_char( core::Size pos, char new_char );

  SequenceOP seq( core::Size idx ) const;

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

    seqs_.clear();
    for ( core::Size ii = 1; ii <= rhs.seqs().size(); ++ii ) {
      //seqs_.push_back( rhs.seq(ii)->clone() );
      add_sequence( rhs.seq(ii)->clone() );
    }

    id      ( rhs.id() );
    start   ( rhs.start() );
    gap_char( rhs.gap_char() );
    sequence( rhs.sequence() );
    return *this;
  }

  /// @brief dtor
  virtual ~CompositeSequence();

  /// @brief Returns an owning pointer to a new CompositeSequence object,
  /// with data that is a deep copy of the information in this object.
  virtual SequenceOP clone() const;

  virtual std::string to_string() const;

  virtual std::string type() const;

private:
  utility::vector1< SequenceOP > seqs_;
}; // class CompositeSequence

} // sequence
} // core

#endif