#include <JobGenealogist.hh>

Inheritance diagram for protocols::jd3::JobGenealogist:

Classes
struct	JGJobNodeOP_hash

struct	JGResultNodeOP_hash

Public Member Functions
	JobGenealogist (core::Size num_job_dag_nodes, core::Size num_input_sources)

	~JobGenealogist () override

JGJobNodeOP	register_new_job (core::Size job_dag_node_id, core::Size global_job_id, core::Size input_source_id)
	register a new job that does not depend on a previous job result but rather takes a pose directly from an input source More...

JGJobNodeOP	register_new_job (core::Size job_dag_node_id, core::Size global_job_id, core::Size job_dag_node_id_of_parent, core::Size global_job_id_of_parent, core::Size result_id_of_parent)
	register a new job that depends on a single parent job result More...

JGJobNodeOP	register_new_job (core::Size job_dag_node_id, core::Size global_job_id, core::Size job_dag_node_id_of_parent, jd3::JobResultID const &id)
	register a new job that depends on a single parent job result More...

JGJobNodeOP	register_new_job (core::Size job_dag_node_id, core::Size global_job_id, JGResultNodeAP parent)
	register a new job that depends on a single parent job result More...

JGJobNodeOP	register_new_job (core::Size job_dag_node_id, core::Size global_job_id, utility::vector1< JGResultNodeAP > const &parents)
	register a new job that depends on multiple parent job results More...

void	note_job_completed (JGJobNodeAP job_node, core::Size nresults)
	Creates nresults new JGResultNodes for this job_node. More...

void	note_job_completed (core::Size dag_node_id, core::Size global_job_id, core::Size nresults)
	wrapper for the other overload. This one is designed to more closely match the argument provided to JobQueen::note_job_completed More...

void	discard_job_result (core::Size job_dag_node, core::Size global_job_id, core::Size result_id)
	At the end of job_results_that_should_be_discarded(), call this funciton for every JobResultID in the list. More...

void	discard_job_result (core::Size job_dag_node, jd3::JobResultID const &id)
	At the end of job_results_that_should_be_discarded(), call this funciton for every JobResultID in the list. More...

void	garbage_collection (core::Size job_dag_node, bool delete_downstream_job_if_it_has_no_results, std::list< jd3::JobResultID > &container_for_discarded_result_ids)
	return every job result id in this job_dag_node that does not have any jobs spawned after it. More...

void	all_job_results_for_node (core::Size job_dag_node, std::list< jd3::JobResultID > &container_for_output) const
	This method populates the list with every JobResultID for this job dag node. More...

std::string	newick_tree () const
	This returns the connectivity of the graph as a newick tree. If you graph is not a tree, this will have duplicate elements. More...

core::Size	input_source_for_job (core::Size job_dag_node, core::Size global_job_id) const

JGJobNodeCOP	get_const_job_node (core::Size job_dag_node, core::Size global_job_id) const

JGResultNodeCAP	get_const_result_node (core::Size node, core::Size global_job_id, core::Size result_id) const

void	print_all_nodes ()
	This is more for debugging than anything. Print the global_job_ids for every job dag node to the screen. More...

Protected Member Functions
JGJobNodeOP	get_job_node (core::Size job_dag_node, core::Size global_job_id)

JGResultNodeAP	get_result_node (core::Size node, core::Size global_job_id, core::Size result_id)

void	delete_node (JGJobNodeAP job_node, unsigned int job_dag_node, bool delete_from_vec=true)
	Are you all done with this JGJobNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN. More...

void	delete_node (JGJobNodeAP job_node, bool delete_from_vec=true)
	Are you all done with this JGJobNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN. More...

void	delete_node (JGResultNodeAP result_node)
	Are you all done with this JGResultNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN. More...

unsigned int	input_source_for_node (JGJobNodeCAP job_node) const
	This is currently just a wrapper for JGJobNode::input_source_id(). I am leaving it as a method because it may become more complicated in the future. More...

Private Member Functions
void	add_newick_tree_for_node (JGResultNodeCAP, std::stringstream &) const
	recursive utility function for std::string newick_tree(); More...

Private Attributes
core::Size	num_input_sources_

utility::vector1 < utility::vector1 < JGJobNodeOP > >	job_nodes_for_dag_node_

std::unordered_set < JGJobNodeOP, JGJobNodeOP_hash >	all_job_nodes_

std::unordered_set < JGResultNodeOP, JGResultNodeOP_hash >	all_result_nodes_

compare_job_nodes	sorter_

Constructor & Destructor Documentation

protocols::jd3::JobGenealogist::JobGenealogist	(	core::Size	num_job_dag_nodes,
		core::Size	num_input_sources
	)

References all_job_nodes_, all_result_nodes_, and job_nodes_for_dag_node_.

protocols::jd3::JobGenealogist::~JobGenealogist ( )

override

Member Function Documentation

void protocols::jd3::JobGenealogist::add_newick_tree_for_node	(	JGResultNodeCAP	result_node,
		std::stringstream &	ss
	)		const

private

recursive utility function for std::string newick_tree();

Referenced by newick_tree().

void protocols::jd3::JobGenealogist::all_job_results_for_node	(	core::Size	job_dag_node,
		std::list< jd3::JobResultID > &	container_for_output
	)		const

This method populates the list with every JobResultID for this job dag node.

Parameters

[out] container_for_output

References job_nodes_for_dag_node_.

void protocols::jd3::JobGenealogist::delete_node	(	JGJobNodeAP	job_node,
		unsigned int	job_dag_node,
		bool	delete_from_vec = `true`
	)

protected

Are you all done with this JGJobNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN.

References all_job_nodes_, core::sequence::end, protocols::jd3::JGJobNode::global_job_id(), job_nodes_for_dag_node_, and sorter_.

Referenced by delete_node(), discard_job_result(), and garbage_collection().

void protocols::jd3::JobGenealogist::delete_node	(	JGJobNodeAP	job_node,
		bool	delete_from_vec = `true`
	)

inlineprotected

Are you all done with this JGJobNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN.

References delete_node().

void protocols::jd3::JobGenealogist::delete_node ( JGResultNodeAP result_node )

inlineprotected

Are you all done with this JGResultNode? If so, this method deletes it and removes all traces of it. THIS DOES NOT DELETE ANY OF THE CHILDREN.

References all_result_nodes_.

void protocols::jd3::JobGenealogist::discard_job_result	(	core::Size	job_dag_node,
		core::Size	global_job_id,
		core::Size	result_id
	)

At the end of job_results_that_should_be_discarded(), call this funciton for every JobResultID in the list.

References delete_node(), and get_result_node().

Referenced by discard_job_result().

void protocols::jd3::JobGenealogist::discard_job_result	(	core::Size	job_dag_node,
		jd3::JobResultID const &	id
	)

inline

At the end of job_results_that_should_be_discarded(), call this funciton for every JobResultID in the list.

References discard_job_result().

void protocols::jd3::JobGenealogist::garbage_collection	(	core::Size	job_dag_node,
		bool	delete_downstream_job_if_it_has_no_results,
		std::list< jd3::JobResultID > &	container_for_discarded_result_ids
	)

return every job result id in this job_dag_node that does not have any jobs spawned after it.

Parameters

[out] container_for_discarded_result_ids

Consider the patter Job1 -> Result1 -> Job5 and Job5 has no children (results). Should Job1/Result1 be garbage collected? If so, set delete_downstream_job_if_it_has_no_results to true.

References protocols::cluster::calibur::aa, delete_node(), job_nodes_for_dag_node_, print_all_nodes(), core::id::swap(), and protocols::jd3::TR().

JGJobNodeCOP protocols::jd3::JobGenealogist::get_const_job_node	(	core::Size	job_dag_node,
		core::Size	global_job_id
	)		const

References core::sequence::end, protocols::jd3::JGJobNode::global_job_id(), job_nodes_for_dag_node_, and sorter_.

Referenced by get_const_result_node(), and input_source_for_job().

JGResultNodeCAP protocols::jd3::JobGenealogist::get_const_result_node	(	core::Size	node,
		core::Size	global_job_id,
		core::Size	result_id
	)		const

References get_const_job_node().

JGJobNodeOP protocols::jd3::JobGenealogist::get_job_node	(	core::Size	job_dag_node,
		core::Size	global_job_id
	)

protected

References core::sequence::end, protocols::jd3::JGJobNode::global_job_id(), job_nodes_for_dag_node_, and sorter_.

Referenced by get_result_node(), and note_job_completed().

JGResultNodeAP protocols::jd3::JobGenealogist::get_result_node	(	core::Size	node,
		core::Size	global_job_id,
		core::Size	result_id
	)

protected

References get_job_node().

Referenced by discard_job_result(), and register_new_job().

core::Size protocols::jd3::JobGenealogist::input_source_for_job	(	core::Size	job_dag_node,
		core::Size	global_job_id
	)		const

inline

References get_const_job_node(), and input_source_for_node().

unsigned int protocols::jd3::JobGenealogist::input_source_for_node ( JGJobNodeCAP job_node ) const

inlineprotected

This is currently just a wrapper for JGJobNode::input_source_id(). I am leaving it as a method because it may become more complicated in the future.

Referenced by input_source_for_job().

std::string protocols::jd3::JobGenealogist::newick_tree ( ) const

This returns the connectivity of the graph as a newick tree. If you graph is not a tree, this will have duplicate elements.

References add_newick_tree_for_node(), job_nodes_for_dag_node_, and num_input_sources_.

void protocols::jd3::JobGenealogist::note_job_completed	(	JGJobNodeAP	job_node,
		core::Size	nresults
	)

Creates nresults new JGResultNodes for this job_node.

References all_result_nodes_.

Referenced by note_job_completed().

void protocols::jd3::JobGenealogist::note_job_completed	(	core::Size	dag_node_id,
		core::Size	global_job_id,
		core::Size	nresults
	)

inline

wrapper for the other overload. This one is designed to more closely match the argument provided to JobQueen::note_job_completed

References get_job_node(), and note_job_completed().

void protocols::jd3::JobGenealogist::print_all_nodes ( )

This is more for debugging than anything. Print the global_job_ids for every job dag node to the screen.

References job_nodes_for_dag_node_, and protocols::jd3::TR().

Referenced by garbage_collection().

JGJobNodeOP protocols::jd3::JobGenealogist::register_new_job	(	core::Size	job_dag_node_id,
		core::Size	global_job_id,
		core::Size	input_source_id
	)

register a new job that does not depend on a previous job result but rather takes a pose directly from an input source

References all_job_nodes_, core::sequence::end, job_nodes_for_dag_node_, num_input_sources_, and sorter_.

Referenced by register_new_job().

JGJobNodeOP protocols::jd3::JobGenealogist::register_new_job	(	core::Size	job_dag_node_id,
		core::Size	global_job_id,
		core::Size	job_dag_node_id_of_parent,
		core::Size	global_job_id_of_parent,
		core::Size	result_id_of_parent
	)

register a new job that depends on a single parent job result

References all_job_nodes_, core::sequence::end, get_result_node(), job_nodes_for_dag_node_, and sorter_.

JGJobNodeOP protocols::jd3::JobGenealogist::register_new_job	(	core::Size	job_dag_node_id,
		core::Size	global_job_id,
		core::Size	job_dag_node_id_of_parent,
		jd3::JobResultID const &	id
	)

inline

register a new job that depends on a single parent job result

References register_new_job().

JGJobNodeOP protocols::jd3::JobGenealogist::register_new_job	(	core::Size	job_dag_node_id,
		core::Size	global_job_id,
		JGResultNodeAP	parent
	)

register a new job that depends on a single parent job result

References all_job_nodes_, core::sequence::end, job_nodes_for_dag_node_, and sorter_.

JGJobNodeOP protocols::jd3::JobGenealogist::register_new_job	(	core::Size	job_dag_node_id,
		core::Size	global_job_id,
		utility::vector1< JGResultNodeAP > const &	parents
	)