a Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive More...

#include <ArchiveManager.hh>

Collaboration diagram for protocols::jd2::archive::Batch:

[legend]

Public Member Functions
	Batch (utility::options::OptionCollection const &options, bool intermediate_structs, bool has_silent_in, core::Size nstruct)

	Batch (core::Size id)
	c'stor More...

std::string	batch () const
	some useful file- and directory names More...

std::string	dir () const

std::string	silent_in () const

std::string	flag_file () const

std::string	broker_file () const

std::string	extra_broker_files () const

std::string	all_broker_files () const

std::string	silent_out () const

std::string	score_file () const

utility::options::OptionCollection const &	user_options () const

utility::options::OptionCollection &	user_options ()

bool	has_silent_in () const
	Getters. More...

bool	intermediate_structs () const
	writes out intermediate decoys More...

bool	has_finished () const
	batch has finished More...

bool	is_cancelled () const
	batch has finished More...

bool	allow_reading_cancelled_decoys () const
	batch has finished More...

core::Size &	nstruct ()
	nstruct ... More...

core::Size	nstruct () const

core::Size	id () const
	batch id More...

core::Size	decoys_returned () const
	how many structures have been processed by archive already More...

void	set_has_silent_in (bool setting=true)
	Setters. More...

void	set_intermediate_structs (bool setting=true)

void	mark_as_finished ()

void	mark_as_cancelled (bool allow_reading_of_decoys=true)

void	mark_as_invalid ()

bool	valid () const

void	set_id (core::Size id)

void	set_decoys_returned (core::Size setting)

void	show (std::ostream &, bool single_line=false) const

void	write_info_file () const
	read and write BATCH_INFO ( decoys_returned/ finished etc.. ) More...

void	read_info_file ()

Private Attributes
core::Size	batch_id_

core::Size	nstruct_

bool	intermediate_structs_

bool	has_silent_in_

bool	has_finished_

bool	is_cancelled_

bool	allow_reading_cancelled_decoys_

bool	invalid_

utility::options::OptionCollection	options_

core::Size	decoys_returned_to_archive_

Friends
std::ostream &	operator<< (std::ostream &, Batch const &)

std::istream &	operator>> (std::istream &, Batch &)

Detailed Description

a Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files the Batch-class helps to get the correct file- and directory names, and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive

Definition at line 54 of file ArchiveManager.hh.

Constructor & Destructor Documentation

protocols::jd2::archive::Batch::Batch	(	utility::options::OptionCollection const &	options,
		bool	intermediate_structs,
		bool	has_silent_in,
		core::Size	nstruct
	)

inline

Definition at line 58 of file ArchiveManager.hh.

protocols::jd2::archive::Batch::Batch ( core::Size id)

inline

c'stor

Definition at line 71 of file ArchiveManager.hh.

Member Function Documentation

std::string protocols::jd2::archive::Batch::all_broker_files ( ) const

inline

Definition at line 93 of file ArchiveManager.hh.

References broker_file(), and extra_broker_files().

Referenced by protocols::jd2::archive::ArchiveManager::finalize_batch(), and protocols::abinitio::IterativeBase::test_broker_settings().

bool protocols::jd2::archive::Batch::allow_reading_cancelled_decoys ( ) const

inline

batch has finished

Definition at line 119 of file ArchiveManager.hh.

References allow_reading_cancelled_decoys_.

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

std::string protocols::jd2::archive::Batch::batch ( ) const

some useful file- and directory names

Definition at line 119 of file ArchiveManager.cc.

std::string protocols::jd2::archive::Batch::broker_file ( ) const

Definition at line 146 of file ArchiveManager.cc.

core::Size protocols::jd2::archive::Batch::decoys_returned ( ) const

inline

how many structures have been processed by archive already

Definition at line 130 of file ArchiveManager.hh.

References decoys_returned_to_archive_.

Referenced by protocols::abinitio::HedgeArchive::add_evaluated_structure(), protocols::jd2::archive::ArchiveManager::jobs_completed(), and protocols::jd2::archive::ArchiveBase::read_structures().

std::string protocols::jd2::archive::Batch::dir ( ) const

Definition at line 123 of file ArchiveManager.cc.

std::string protocols::jd2::archive::Batch::extra_broker_files ( ) const

Definition at line 150 of file ArchiveManager.cc.

Referenced by all_broker_files().

std::string protocols::jd2::archive::Batch::flag_file ( ) const

Definition at line 142 of file ArchiveManager.cc.

bool protocols::jd2::archive::Batch::has_finished ( ) const

inline

batch has finished

Definition at line 113 of file ArchiveManager.hh.

References has_finished_.

Referenced by protocols::abinitio::HedgeArchive::add_evaluated_structure(), and protocols::jd2::archive::ArchiveManager::finalize_batch().

bool protocols::jd2::archive::Batch::has_silent_in ( ) const

inline

Getters.

has input decoys

Definition at line 107 of file ArchiveManager.hh.

References has_silent_in_.

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

core::Size protocols::jd2::archive::Batch::id ( ) const

inline

batch id

Definition at line 127 of file ArchiveManager.hh.

References batch_id_.

Referenced by protocols::abinitio::HedgeArchive::add_evaluated_structure(), protocols::abinitio::IterativeBase::add_fullatom_flags(), protocols::abinitio::IterativeBase::add_structure(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), protocols::abinitio::IterativeBase::reassign_noesy_data(), set_id(), and protocols::abinitio::IterativeBase::still_interested().

bool protocols::jd2::archive::Batch::intermediate_structs ( ) const

inline

writes out intermediate decoys

Definition at line 110 of file ArchiveManager.hh.

References intermediate_structs_.

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

bool protocols::jd2::archive::Batch::is_cancelled ( ) const

inline

batch has finished

Definition at line 116 of file ArchiveManager.hh.

References is_cancelled_.

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

void protocols::jd2::archive::Batch::mark_as_cancelled ( bool allow_reading_of_decoys = true)

inline

Definition at line 145 of file ArchiveManager.hh.

References allow_reading_cancelled_decoys_, and is_cancelled_.

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

void protocols::jd2::archive::Batch::mark_as_finished ( )

inline

Definition at line 141 of file ArchiveManager.hh.

References has_finished_.

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

void protocols::jd2::archive::Batch::mark_as_invalid ( )

inline

Definition at line 150 of file ArchiveManager.hh.

References invalid_.

core::Size& protocols::jd2::archive::Batch::nstruct ( )

inline

nstruct ...

Definition at line 122 of file ArchiveManager.hh.

References nstruct_.

Referenced by protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::abinitio::HedgeArchive::collect(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_stage2(), and protocols::jd2::archive::ArchiveManager::queue_batch().

core::Size protocols::jd2::archive::Batch::nstruct ( ) const

inline

Definition at line 124 of file ArchiveManager.hh.

References nstruct_.

void protocols::jd2::archive::Batch::read_info_file ( )

Definition at line 176 of file ArchiveManager.cc.

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

std::string protocols::jd2::archive::Batch::score_file ( ) const

Definition at line 138 of file ArchiveManager.cc.

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

void protocols::jd2::archive::Batch::set_decoys_returned ( core::Size setting)

inline

Definition at line 162 of file ArchiveManager.hh.

References decoys_returned_to_archive_.

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

void protocols::jd2::archive::Batch::set_has_silent_in ( bool setting = true)

inline

Setters.

Definition at line 133 of file ArchiveManager.hh.

References has_silent_in_.

Referenced by protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeFullatom::gen_resample_core(), and protocols::abinitio::IterativeBase::gen_resample_stage2().

void protocols::jd2::archive::Batch::set_id ( core::Size id)

inline

Definition at line 158 of file ArchiveManager.hh.

References batch_id_, and id().

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

void protocols::jd2::archive::Batch::set_intermediate_structs ( bool setting = true)

inline

Definition at line 137 of file ArchiveManager.hh.

References intermediate_structs_.

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

void protocols::jd2::archive::Batch::show	(	std::ostream &	out,
		bool	single_line = `false`
	)		const

Definition at line 154 of file ArchiveManager.cc.

Referenced by protocols::jd2::archive::operator<<().

std::string protocols::jd2::archive::Batch::silent_in ( ) const

Definition at line 131 of file ArchiveManager.cc.

Referenced by protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeFullatom::gen_resample_core(), and protocols::abinitio::IterativeBase::gen_resample_stage2().

std::string protocols::jd2::archive::Batch::silent_out ( ) const

Definition at line 127 of file ArchiveManager.cc.

Referenced by protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::jd2::archive::ArchiveManager::jobs_completed(), and protocols::jd2::archive::ArchiveBase::read_structures().

utility::options::OptionCollection const& protocols::jd2::archive::Batch::user_options ( ) const

inline

Definition at line 101 of file ArchiveManager.hh.

References options_.

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

utility::options::OptionCollection& protocols::jd2::archive::Batch::user_options ( )

inline

Definition at line 102 of file ArchiveManager.hh.

References options_.

bool protocols::jd2::archive::Batch::valid ( ) const

inline

Definition at line 154 of file ArchiveManager.hh.

References invalid_.

void protocols::jd2::archive::Batch::write_info_file ( ) const

read and write BATCH_INFO ( decoys_returned/ finished etc.. )

Definition at line 170 of file ArchiveManager.cc.

References protocols::jd2::tr().

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

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		Batch const &	batch
	)

friend

Definition at line 165 of file ArchiveManager.cc.

std::istream& operator>>	(	std::istream &	in,
		Batch &	batch
	)

friend

Definition at line 196 of file ArchiveManager.cc.

Member Data Documentation

bool protocols::jd2::archive::Batch::allow_reading_cancelled_decoys_

private

Definition at line 181 of file ArchiveManager.hh.

Referenced by allow_reading_cancelled_decoys(), and mark_as_cancelled().

core::Size protocols::jd2::archive::Batch::batch_id_

private

Definition at line 175 of file ArchiveManager.hh.

Referenced by id(), protocols::jd2::archive::operator>>(), and set_id().

core::Size protocols::jd2::archive::Batch::decoys_returned_to_archive_

private

Definition at line 184 of file ArchiveManager.hh.

Referenced by decoys_returned(), protocols::jd2::archive::operator>>(), and set_decoys_returned().

bool protocols::jd2::archive::Batch::has_finished_

private

Definition at line 179 of file ArchiveManager.hh.

Referenced by has_finished(), mark_as_finished(), and protocols::jd2::archive::operator>>().

bool protocols::jd2::archive::Batch::has_silent_in_

private

Definition at line 178 of file ArchiveManager.hh.

Referenced by has_silent_in(), protocols::jd2::archive::operator>>(), and set_has_silent_in().

bool protocols::jd2::archive::Batch::intermediate_structs_

private

Definition at line 177 of file ArchiveManager.hh.

Referenced by intermediate_structs(), and set_intermediate_structs().

bool protocols::jd2::archive::Batch::invalid_

private

Definition at line 182 of file ArchiveManager.hh.

Referenced by mark_as_invalid(), and valid().

bool protocols::jd2::archive::Batch::is_cancelled_

private

Definition at line 180 of file ArchiveManager.hh.

Referenced by is_cancelled(), mark_as_cancelled(), and protocols::jd2::archive::operator>>().

core::Size protocols::jd2::archive::Batch::nstruct_

private

Definition at line 176 of file ArchiveManager.hh.

Referenced by nstruct(), and protocols::jd2::archive::operator>>().

utility::options::OptionCollection protocols::jd2::archive::Batch::options_

private

Definition at line 183 of file ArchiveManager.hh.

Referenced by user_options().

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

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

Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation