#include <JD2ResourceManagerJobInputter.hh>

Inheritance diagram for protocols::jd2::JD2ResourceManagerJobInputter:

Collaboration diagram for protocols::jd2::JD2ResourceManagerJobInputter:

Public Member Functions
	JD2ResourceManagerJobInputter ()

virtual	~JD2ResourceManagerJobInputter ()

virtual void	pose_from_job (core::pose::Pose &pose, JobOP job)
	this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. More...

virtual void	fill_jobs (Jobs &jobs)
	this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must". More...

virtual JobInputterInputSource::Enum	input_source () const
	return the type of input source that the JobInputter is currently using More...

void	fill_jobs_from_stream (std::istream &instream, Jobs &jobs)

Public Member Functions inherited from protocols::jd2::JobInputter
virtual	~JobInputter ()

Private Member Functions
virtual void	cleanup_after_job_completion (std::string const &job_tag)
	Delete the Resources associated with a job. More...

void	parse_jobs_tags (utility::tag::TagPtr tag, Jobs &jobs)

void	parse_job_tag (utility::tag::TagPtr jobs_tags, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)

void	parse_jobs_table_tag (utility::tag::TagPtr tag, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)

void	record_job (std::string const &job_name, std::map< std::string, std::string > const &resources_for_job, basic::resource_manager::JobOptionsOP job_options, Jobs &jobs)

void	read_Option_subtag_for_job (utility::tag::TagPtr options_tag, basic::resource_manager::JobOptionsOP job_options)

void	parse_options_name_and_value (std::string const &optname, std::string const &value, basic::resource_manager::JobOptionsOP job_options)

void	read_BooleanOption_subtag_for_job (basic::options::BooleanOptionKey const &boolopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_FileOption_subtag_for_job (basic::options::FileOptionKey const &fileopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_IntegerOption_subtag_for_job (basic::options::IntegerOptionKey const &intopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_PathOption_subtag_for_job (basic::options::PathOptionKey const &pathopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_RealOption_subtag_for_job (basic::options::RealOptionKey const &realopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_StringOption_subtag_for_job (basic::options::StringOptionKey const &stringopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_BooleanVectorOption_subtag_for_job (basic::options::BooleanVectorOptionKey const &boolvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_FileVectorOption_subtag_for_job (basic::options::FileVectorOptionKey const &filevectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_IntegerVectorOption_subtag_for_job (basic::options::IntegerVectorOptionKey const &intvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_PathVectorOption_subtag_for_job (basic::options::PathVectorOptionKey const &pathvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_RealVectorOption_subtag_for_job (basic::options::RealVectorOptionKey const &realvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_StringVectorOption_subtag_for_job (basic::options::StringVectorOptionKey const &strinvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_Data_for_subtag (utility::tag::TagPtr options_tag, std::string const &jobname, std::string &input_tag, std::map< std::string, std::string > &resources_for_job)

void	read_ResidueType_for_subtag (utility::tag::TagPtr options_tag, std::map< std::string, std::string > &resources_for_job)

void	check_each_job_has_startstruct (Jobs const &jobs) const

Private Attributes
std::string	last_input_tag_
	save the last input tag so the resources loaded for it can be unloaded when we see a new input tag More...

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobInputter
static std::string	job_inputter_input_source_to_string (JobInputterInputSource::Enum source)
	call this with input_source() to get the input source of a particular job inputter More...

Protected Member Functions inherited from protocols::jd2::JobInputter
void	load_pose_into_job (core::pose::Pose const &pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...

void	load_pose_into_job (core::pose::PoseCOP pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...

virtual core::Size	get_nstruct () const
	this code is here to restrict the use of inner_job_nonconst (this class is a friend class and can do it) More...

Constructor & Destructor Documentation

protocols::jd2::JD2ResourceManagerJobInputter::JD2ResourceManagerJobInputter ( )

protocols::jd2::JD2ResourceManagerJobInputter::~JD2ResourceManagerJobInputter ( )

virtual

Member Function Documentation

void protocols::jd2::JD2ResourceManagerJobInputter::check_each_job_has_startstruct ( Jobs const & jobs) const

private

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance().

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion ( std::string const & job_tag)

privatevirtual

Delete the Resources associated with a job.

References core::chemical::ChemicalManager::get_instance(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), core::chemical::ChemicalManager::nonconst_residue_type_set(), core::chemical::ResidueTypeSet::remove_residue_type(), and protocols::jd2::tr().

Referenced by pose_from_job().

void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs ( Jobs & jobs)

virtual

this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must".

Implements protocols::jd2::JobInputter.

References fill_jobs_from_stream(), and protocols::jd2::tr().

void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream	(	std::istream &	instream,
		Jobs &	jobs
	)

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), parse_jobs_tags(), protocols::jd2::JD2ResourceManager::read_resource_locators_tags(), protocols::jd2::JD2ResourceManager::read_resource_options_tags(), and protocols::jd2::JD2ResourceManager::read_resources_tags().

Referenced by fill_jobs().

JobInputterInputSource::Enum protocols::jd2::JD2ResourceManagerJobInputter::input_source ( ) const

virtual

return the type of input source that the JobInputter is currently using

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::RESOURCE_MANAGED_JOB.

void protocols::jd2::JD2ResourceManagerJobInputter::parse_job_tag	(	utility::tag::TagPtr	jobs_tags,
		std::map< std::string, std::string > const &	generic_resources_for_job,
		basic::resource_manager::JobOptions const &	generic_job_options,
		Jobs &	jobs
	)

private

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), parse_options_name_and_value(), read_Data_for_subtag(), read_Option_subtag_for_job(), read_ResidueType_for_subtag(), and record_job().

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_table_tag	(	utility::tag::TagPtr	tag,
		std::map< std::string, std::string > const &	generic_resources_for_job,
		basic::resource_manager::JobOptions const &	generic_job_options,
		Jobs &	jobs
	)

private

References parse_options_name_and_value(), record_job(), and protocols::jd2::tr().

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_tags	(	utility::tag::TagPtr	tag,
		Jobs &	jobs
	)

private

References check_each_job_has_startstruct(), parse_job_tag(), parse_jobs_table_tag(), read_Data_for_subtag(), and read_Option_subtag_for_job().

Referenced by fill_jobs_from_stream().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_options_name_and_value	(	std::string const &	optname,
		std::string const &	value,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

References read_BooleanOption_subtag_for_job(), read_BooleanVectorOption_subtag_for_job(), read_FileOption_subtag_for_job(), read_FileVectorOption_subtag_for_job(), read_IntegerOption_subtag_for_job(), read_IntegerVectorOption_subtag_for_job(), read_PathOption_subtag_for_job(), read_PathVectorOption_subtag_for_job(), read_RealOption_subtag_for_job(), read_RealVectorOption_subtag_for_job(), read_StringOption_subtag_for_job(), and read_StringVectorOption_subtag_for_job().

Referenced by parse_job_tag(), parse_jobs_table_tag(), and read_Option_subtag_for_job().

void protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job	(	core::pose::Pose &	pose,
		JobOP	job
	)

virtual

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

Implements protocols::jd2::JobInputter.

References core::chemical::ResidueTypeSet::add_residue_type(), cleanup_after_job_completion(), core::pose::Pose::clear(), core::chemical::ChemicalManager::get_instance(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), last_input_tag_, protocols::jd2::JobInputter::load_pose_into_job(), core::chemical::ChemicalManager::nonconst_residue_type_set(), core::chemical::ChemicalManager::residue_type_set(), and protocols::jd2::tr().

void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanOption_subtag_for_job	(	basic::options::BooleanOptionKey const &	boolopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanVectorOption_subtag_for_job	(	basic::options::BooleanVectorOptionKey const &	boolvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag	(	utility::tag::TagPtr	data_tag,
		std::string const &	jobname,
		std::string &	input_tag,
		std::map< std::string, std::string > &	resources_for_job
	)

private

Read the <Data> subtag of the <Job>

Form 1: <Data desc="resource_description" resource="resource_tag"> Precondition requirements: has_resource_configuration(resource_tag) Postcondition guarentees: resources_for_job["resource_description"] == "resource_tag"

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), and protocols::jd2::tr().

Referenced by parse_job_tag(), and parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::read_FileOption_subtag_for_job	(	basic::options::FileOptionKey const &	fileopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_FileVectorOption_subtag_for_job	(	basic::options::FileVectorOptionKey const &	filevectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerOption_subtag_for_job	(	basic::options::IntegerOptionKey const &	intopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerVectorOption_subtag_for_job	(	basic::options::IntegerVectorOptionKey const &	intvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_Option_subtag_for_job	(	utility::tag::TagPtr	options_tag,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

References parse_options_name_and_value().

Referenced by parse_job_tag(), and parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::read_PathOption_subtag_for_job	(	basic::options::PathOptionKey const &	pathopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_PathVectorOption_subtag_for_job	(	basic::options::PathVectorOptionKey const &	pathvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_RealOption_subtag_for_job	(	basic::options::RealOptionKey const &	realopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_RealVectorOption_subtag_for_job	(	basic::options::RealVectorOptionKey const &	realvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_ResidueType_for_subtag	(	utility::tag::TagPtr	options_tag,
		std::map< std::string, std::string > &	resources_for_job
	)

private

Referenced by parse_job_tag().

void protocols::jd2::JD2ResourceManagerJobInputter::read_StringOption_subtag_for_job	(	basic::options::StringOptionKey const &	stringopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_StringVectorOption_subtag_for_job	(	basic::options::StringVectorOptionKey const &	strinvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::record_job	(	std::string const &	job_name,
		std::map< std::string, std::string > const &	resources_for_job,
		basic::resource_manager::JobOptionsOP	job_options,
		Jobs &	jobs
	)

private

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance().

Referenced by parse_job_tag(), and parse_jobs_table_tag().

Member Data Documentation

std::string protocols::jd2::JD2ResourceManagerJobInputter::last_input_tag_

private

save the last input tag so the resources loaded for it can be unloaded when we see a new input tag

Referenced by pose_from_job().

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

src/protocols/jd2/JD2ResourceManagerJobInputter.hh
src/protocols/jd2/JD2ResourceManagerJobInputter.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation