VallLibrary.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.
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// (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   core/fragment/picking_old/vall/VallLibrary.hh
/// @brief  Vall fragment library
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_VallLibrary_hh
#define INCLUDED_core_fragment_picking_old_vall_VallLibrary_hh

// unit headers
#include <core/fragment/picking_old/vall/VallLibrary.fwd.hh>

// package headers
#include <core/fragment/picking_old/concepts/Library.hh>
#include <core/fragment/picking_old/vall/VallSection.hh>

#include <utility/vector1.hh>


// utility headers


namespace core {
namespace fragment {
namespace picking_old {
namespace vall {


/// @brief Vall fragment library
class VallLibrary : public core::fragment::picking_old::concepts::Library< VallSections > {


private: // typedefs


  typedef core::fragment::picking_old::concepts::Library< VallSections > Super;


public: // typedefs


  typedef Super::Size Size;


public: // concept typedefs


  /// @brief typedef for Library concept
  typedef Super::BookConstIterator BookConstIterator;


  /// @brief typedef for Library concept
  typedef Super::BookIterator BookIterator;


public: // concept translation typedefs


  typedef BookConstIterator VallSectionConstIterator;
  typedef BookIterator VallSectionIterator;


public: // operators


  /// @brief access a specific VallSection within this section, 1-based indexing
  inline
  VallSection const & operator[]( Size const idx ) const {
    return sections()[ idx ];
  }


public: // section management


  /// brief add a section to the end of this library
  inline
  void add_section( VallSection const & section ) {
    sections().push_back( section );
    sections().back().index( sections().size() );
  }


  /// @brief access the last section in thie library
  inline
  VallSection const & last_section() const {
    return sections().back();
  }


  /// @brief access the last section in thie library
  inline
  VallSection & last_section() {
    return sections().back();
  }


  /// @brief total number of residues in the library
  inline
  Size n_residues() const {
    Size n = 0;
    for ( VallSectionConstIterator i = begin(), ie = end(); i != ie; ++i ) {
      n += i->size();
    }
    return n;
  }


  /// @brief re-index VallSections within this library so they number 1 .. n
  inline
  void reindex_sections() {
    Size count = 0;
    for ( VallSectionIterator i = begin(), ie = end(); i != ie; ++i ) {
      i->index( ++count );
    }
  }


public: // memory


  /// @brief ensure storage currently allocated for VallSections is at least the
  ///  given size
  inline
  void reserve( Size const n ) {
    sections().reserve( n );
  }


  /// @brief tighten memory usage
  /// @param sections_only if true, only tightens memory per-section and skips
  ///  the operation for the whole library
  /// @details Shrinks the capacity of the library by calling
  ///  <tt>VallSection::tighten_memory()</tt> for each section.  If 'sections_only' is
  ///  false, will additionally perform a swap of the library, effectively
  ///  requiring a similar amount of memory as the current library object.
  /// @warning The Vall libraries can be very large, so set 'sections_only'
  ///  false only if you won't be running on a constrained memory platform.
  inline
  void tighten_memory( bool const sections_only = true ) {
    for ( VallSectionIterator i = begin(), ie = end(); i != ie; ++i ) {
      i->tighten_memory();
    }

    // the following could require a lot of memory
    if ( !sections_only ) {
      VallSections( sections() ).swap( sections() );
    }
  }


private: // concept translation


  /// @brief return sections container
  inline
  VallSections const & sections() const {
    return books();
  }


  /// @brief return sections container
  inline
  VallSections & sections() {
    return books();
  }


};


} // vall
} // picking_old
} // fragment
} // core


#endif /* INCLUDED_core_fragment_picking_old_vall_VallLibrary_HH */