Rosetta Protocols: protocols::jd2::archive::BaseArchiveManager Class Reference

Rosetta Protocols 2014.35

ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys. More...

#include <ArchiveManager.hh>

Public Types
typedef utility::vector1< Batch >	BatchList

Public Member Functions
	BaseArchiveManager ()
	ctor is protected; singleton pattern More...

virtual	~BaseArchiveManager ()

virtual Batch &	start_new_batch ()

virtual void	finalize_batch (Batch &, bool reread=false)

virtual void	cancel_batches_previous_to (core::Size batch_id, bool allow_reading_of_decoys=true)

virtual void	save_archive ()=0

BatchList const &	batches () const

virtual bool	restore_archive ()=0

core::Size	last_batch_id () const

Protected Member Functions
virtual void	queue_batch (Batch const &batch)=0

virtual void	cancel_batch (Batch &batch, bool allow_reading_of_decoys=true)

void	set_archive (AbstractArchiveBaseOP)

AbstractArchiveBase &	the_archive ()

virtual void	unlock_file (Batch const &, bool)

void	read_returning_decoys (Batch &batch, bool final)

Protected Attributes
utility::vector1< Batch >	batches_

Static Protected Attributes
static bool	options_registered_

Private Attributes
AbstractArchiveBaseOP	theArchive_

Detailed Description

ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys.

he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY .

Member Typedef Documentation

typedef utility::vector1< Batch > protocols::jd2::archive::BaseArchiveManager::BatchList

Constructor & Destructor Documentation

protocols::jd2::archive::BaseArchiveManager::BaseArchiveManager ( )

inline

ctor is protected; singleton pattern

virtual protocols::jd2::archive::BaseArchiveManager::~BaseArchiveManager ( )

inlinevirtual

Member Function Documentation

BatchList const& protocols::jd2::archive::BaseArchiveManager::batches ( ) const

inline

References batches_.

Referenced by protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), and protocols::jd2::archive::ArchiveManager::unfinished_batches().

void protocols::jd2::archive::BaseArchiveManager::cancel_batch	(	Batch &	batch,
		bool	allow_reading_of_decoys = `true`
	)

protectedvirtual

Reimplemented in protocols::jd2::archive::ArchiveManager.

References protocols::jd2::archive::Batch::mark_as_cancelled().

Referenced by cancel_batches_previous_to().

void protocols::jd2::archive::BaseArchiveManager::cancel_batches_previous_to	(	core::Size	batch_id,
		bool	allow_reading_of_decoys = `true`
	)

virtual

References batches_, and cancel_batch().

Referenced by protocols::abinitio::IterativeBase::increment_stage(), and protocols::abinitio::IterativeBase::rescore_nonlocal_archive().

void protocols::jd2::archive::BaseArchiveManager::finalize_batch	(	Batch &	new_batch,
		bool	reread = `false`
	)

virtual

References add_all_rosetta_options(), utility::options::OptionCollection::add_built_in_options(), protocols::jd2::archive::Batch::all_broker_files(), protocols::jd2::archive::Batch::batch(), batches_, broker, protocols::jd2::archive::Batch::broker_file(), utility::file::file_exists(), file_exists(), protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::has_finished(), protocols::jd2::archive::Batch::has_silent_in(), protocols::jd2::archive::Batch::intermediate_structs(), run::intermediate_structures, protocols::jd2::archive::Batch::is_cancelled(), utility::options::OptionCollection::load_options_from_file_exception(), utility::options::OptionCollection::load_options_from_stream(), protocols::jd2::archive::Batch::mark_as_finished(), nstruct, out::nstruct, protocols::jd2::archive::Batch::nstruct(), queue_batch(), protocols::jd2::archive::Batch::read_info_file(), protocols::jd2::archive::report_batch_inconsistency(), protocols::jd2::archive::Batch::score_file(), out::file::scorefile, protocols::jd2::archive::Batch::set_decoys_returned(), broker::setup, utility::options::OptionCollection::show_inaccessed_user_options(), utility::options::OptionCollection::show_user(), out::file::silent, in::file::silent, protocols::jd2::archive::Batch::silent_in(), protocols::jd2::archive::Batch::silent_out(), protocols::jd2::archive::AbstractArchiveBase::still_interested(), the_archive(), protocols::jd2::tr, user, protocols::jd2::archive::Batch::user_options(), and protocols::jd2::archive::Batch::write_info_file().

Referenced by protocols::abinitio::IterativeBase::generate_batch(), and protocols::jd2::archive::ArchiveManager::read_existing_batches().

core::Size protocols::jd2::archive::BaseArchiveManager::last_batch_id ( ) const

inline

References batches_.

Referenced by protocols::abinitio::IterativeBase::increment_stage(), and start_new_batch().

virtual void protocols::jd2::archive::BaseArchiveManager::queue_batch ( Batch const & batch )

protectedpure virtual

Implemented in protocols::jd2::archive::ArchiveManager.

Referenced by finalize_batch(), and protocols::jd2::archive::ArchiveManager::send_stop_to_jobdistributor().

void protocols::jd2::archive::BaseArchiveManager::read_returning_decoys	(	Batch &	batch,
		bool	final
	)

protected

References protocols::jd2::archive::Batch::alternative_decoys_out(), basic::ARCHIVE_EVAL_DECOYS, basic::ARCHIVE_READ_DECOYS, protocols::jd2::archive::Batch::decoys_returned(), protocols::jd2::archive::Batch::intermediate_structs(), protocols::jd2::archive::Batch::mark_as_finished(), PROF_START, PROF_STOP, core::io::silent::SilentFileData::read_file(), protocols::jd2::archive::AbstractArchiveBase::read_structures(), runtime_assert, protocols::jd2::archive::Batch::set_decoys_returned(), protocols::jd2::archive::Batch::silent_out(), the_archive(), protocols::jd2::tr, and unlock_file().

Referenced by protocols::jd2::archive::ArchiveManager::jobs_completed().

virtual bool protocols::jd2::archive::BaseArchiveManager::restore_archive ( )

pure virtual

Implemented in protocols::jd2::archive::ArchiveManager.

virtual void protocols::jd2::archive::BaseArchiveManager::save_archive ( )

pure virtual

Implemented in protocols::jd2::archive::ArchiveManager.

Referenced by protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::abinitio::IterativeBase::reassign_noesy_data(), and protocols::jd2::archive::ArchiveManager::send_stop_to_jobdistributor().

void protocols::jd2::archive::BaseArchiveManager::set_archive ( AbstractArchiveBaseOP anArchive )

protected

Referenced by protocols::jd2::archive::ArchiveManager::go().

Batch & protocols::jd2::archive::BaseArchiveManager::start_new_batch ( )

virtual

References add_all_rosetta_options(), batches_, utility::file::create_directory(), utility::file::file_exists(), last_batch_id(), basic::options::OptionKeys::out::nstruct, basic::options::option, protocols::jd2::archive::Batch::set_id(), and protocols::jd2::tr.

Referenced by protocols::jd2::archive::ArchiveManager::read_existing_batches().

AbstractArchiveBase& protocols::jd2::archive::BaseArchiveManager::the_archive ( )

inlineprotected

References theArchive_.

Referenced by finalize_batch(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::archive::ArchiveManager::idle(), read_returning_decoys(), protocols::jd2::archive::ArchiveManager::restore_archive(), and protocols::jd2::archive::ArchiveManager::save_archive().

virtual void protocols::jd2::archive::BaseArchiveManager::unlock_file	(	Batch const &	,
		bool
	)

inlineprotectedvirtual

Reimplemented in protocols::jd2::archive::ArchiveManager.

Referenced by read_returning_decoys().

Member Data Documentation

utility::vector1< Batch > protocols::jd2::archive::BaseArchiveManager::batches_

protected

Referenced by batches(), cancel_batches_previous_to(), finalize_batch(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::archive::ArchiveManager::jobs_completed(), last_batch_id(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), and start_new_batch().

bool protocols::jd2::archive::BaseArchiveManager::options_registered_

staticprotected

AbstractArchiveBaseOP protocols::jd2::archive::BaseArchiveManager::theArchive_

private

Referenced by the_archive().

The documentation for this class was generated from the following files:

src/protocols/jd2/archive/ArchiveManager.hh
src/protocols/jd2/archive/ArchiveManager.cc