VallLibrarian.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   core/fragment/picking_old/vall/VallLibrarian.hh
/// @brief  Librarian that picks fragments from the Vall
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_core_fragment_picking_old_vall_VallLibrarian_hh
#define INCLUDED_core_fragment_picking_old_vall_VallLibrarian_hh

// AUTO-REMOVED #include <time.h>

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

// type headers
#include <core/types.hh>

// package headers
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/FragData.fwd.hh>
#include <core/fragment/picking_old/concepts/Librarian.hh>
// AUTO-REMOVED #include <core/fragment/picking_old/vall/util.hh>
#include <core/fragment/picking_old/vall/VallLibrary.hh>
#include <core/fragment/picking_old/vall/VallResidue.hh>
#include <core/fragment/picking_old/vall/eval/VallFragmentEval.hh>
#include <core/fragment/picking_old/vall/gen/VallFragmentGen.hh>

// project headers
#include <basic/Tracer.hh>

// utility headers
#include <utility/pointer/owning_ptr.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

// C++ headers
#include <functional>

#include <utility/vector1.hh>

#ifdef WIN32
  #include <ctime>
#endif


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


/// @brief Librarian that picks fragments from the Vall
class VallLibrarian : public core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary > {


private: // typedefs


  typedef core::fragment::picking_old::concepts::Librarian< scores::VallFragmentScore, eval::VallFragmentEval, gen::VallFragmentGen, VallLibrary > Super;


public: // typedefs


  typedef core::Size Size;

  typedef core::fragment::FragDataList FragDataList;
  typedef core::fragment::FragData FragData;
  typedef core::fragment::FragDataOP FragDataOP;

  typedef eval::VallFragmentEval VallFragmentEval;
  typedef scores::VallFragmentScore VallFragmentScore;


public: // concept typedefs


  typedef Super::BookIterator BookIterator;
  typedef Super::BookConstIterator BookConstIterator;
  typedef Super::PageConstIterator PageConstIterator;
  typedef Super::PageIterator PageIterator;
  typedef Super::ExtentEvalOP ExtentEvalOP;
  typedef Super::ExtentEvalCOP ExtentEvalCOP;
  typedef Super::ExtentGenOP ExtentGenOP;
  typedef Super::ExtentGenCOP ExtentGenCOP;
  typedef Super::Bookmarks Bookmarks;
  typedef Super::BookmarkConstIterator BookmarkConstIterator;
  typedef Super::BookmarkIterator BookmarkIterator;

  typedef Super::ExtentGenOPs ExtentGenOPs;
  typedef Super::ExtentEvalOPs ExtentEvalOPs;


public: // concept translation typedefs


  typedef ExtentEvalOP VallFragmentEvalOP;
  typedef ExtentEvalCOP VallFragmentEvalCOP;
  typedef ExtentGenOP VallFragmentGenOP;
  typedef ExtentGenCOP VallFragmentGenCOP;
  typedef Bookmarks Scores;
  typedef BookmarkConstIterator ScoreConstIterator;
  typedef BookmarkIterator ScoreIterator;


protected: // concept translation typedefs


  typedef BookConstIterator VallSectionConstIterator;
  typedef BookIterator VallSectionIterator;
  typedef PageConstIterator VallResidueConstIterator;
  typedef PageIterator VallResidueIterator;
  typedef ExtentGenOPs VallFragmentGenOPs;
  typedef ExtentEvalOPs VallFragmentEvalOPs;


public: // construct/destruct


  /// @brief default constructor
  VallLibrarian();


  /// @brief default destructor
  virtual
  ~VallLibrarian();


private: // disallow copy


  /// @brief disallow copy constructor
  // NOTE: If implementing copy in the future, remember to clone OPs.
  VallLibrarian( VallLibrarian const & rval );


  /// @brief disallow copy assignment
  // NOTE: If implementing copy in the future, remember to clone OPs.
  VallLibrarian & operator =( VallLibrarian const & rval );


public: // accessors


  /// @brief preallocate scores container prior to catalog() to attempt
  ///  speedup?, default true
  inline
  bool preallocate() const {
    return preallocate_;
  }


public: // mutators


  /// @brief set flag to preallocate scores container prior to catalog() to
  ///  attempt speedup
  inline
  void preallocate( bool const flag ) {
    preallocate_ = flag;
  }


public: // generator management


  /// @brief add a fragment generator (aka extent generator)
  inline
  void add_fragment_gen( VallFragmentGenCOP const & gen ) {
    Super::add_extent_gen( gen );
  }


  /// @brief clear list of generators
  inline
  void clear_fragment_gen() {
    Super::clear_extent_gen();
  }


  /// @brief the number of currently defined fragment generators
  inline
  Size n_fragment_gen() const {
    return Super::extent_gen().size();
  }


public: // evaluator management


  /// @brief add a fragment evaluator (aka extent evaluator)
  inline
  void add_fragment_eval( VallFragmentEvalCOP eval ) {
    Super::add_extent_eval( eval );
  }


  /// @brief clear list of evaluators
  inline
  void clear_fragment_eval() {
    Super::clear_extent_eval();
  }


  /// @brief the number of currently defined fragment evaluators
  inline
  Size n_fragment_eval() const {
    return Super::extent_eval().size();
  }


public: // library operations


  /// @brief create sorted list corresponding to fragments in Library
  /// @details uses Score's '<' for evaluation
  /// @return true if creation successful, false otherwise (e.g. no VallFragmentEval or VallFragmentGen found)
  bool catalog( VallLibrary const & library ) {
    return catalog( library, std::less< VallFragmentScore >() );
  }


  /// @brief create sorted list corresponding to fragments in Library
  /// @tparam LessThan predicate <tt> Pr( left, right ) </tt> evaluating <tt> left < right <tt> for Scores (aka Bookmarks)
  /// @return true if creation successful, false otherwise (e.g. no VallFragmentEval or VallFragmentGen found)
  template< typename LessThan >
  bool catalog( VallLibrary const & library, LessThan const & lt ) {
    pre_catalog_ops( library );

    TR_.Debug << "Cataloging " << library.size() << " residues in fragment library..." << std::endl;

    time_t time_start = time( NULL );
    bool const status = Super::catalog( library, lt );
    time_t time_end = time( NULL );

    TR_.Debug << "... done.  " << scores().size() << " scores filed.  Time elapsed: " << ( time_end - time_start ) << " seconds." << std::endl;

    post_catalog_ops( library );

    return status;
  }


  /// @brief number of scores currently filed
  inline
  Size n_scores() const {
    return scores().size();
  }


public: // fragment extraction


  /// @brief get top 'N' fragments from prior catalog()
  /// @param n The number of fragments to get.
  /// @param srfd_type The BBTorsionSRFD type to use.
  FragDataList top_fragments(
    Size const n,
    BBTorsionSRFD const & srfd_type = BBTorsionSRFD()
  ) const;


  /// @brief get fragments from prior catalog() [from, to]
  /// @param from index of the first fragment in the list, indexing starts from '1'
  /// @param to index of the last fragment in the list (inclusive)
  /// @param srfd_type The BBTorsionSRFD type to use.
  /// @return filled FragDataList if sort() was called successfully, otherwise empty FragDataList
  FragDataList fragments(
    Size from,
    Size to,
    BBTorsionSRFD const & srfd_type = BBTorsionSRFD()
  ) const;


public: // concept translation


  /// @brief return scores container
  inline
  Scores const & scores() const {
    return Super::bookmarks();
  }


  /// @brief return scores container
  inline
  Scores & scores() {
    return Super::bookmarks();
  }


private: // additional catalog methods


  /// @brief this function runs before main routine in catalog() starts
  void pre_catalog_ops( VallLibrary const & library );


  /// @brief this function runs after main routine catalog() finishes
  void post_catalog_ops( VallLibrary const & library );


private: // data


  /// @brief flag controls preallocation of score container, default true
  bool preallocate_;


  /// @brief static Tracer instance for this class
  static basic::Tracer TR_;


};


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


#endif /* INCLUDED_core_fragment_picking_old_vall_VallLibrarian_HH */