#include <DatabaseJobOutputter.hh>

Inheritance diagram for protocols::features::DatabaseJobOutputter:

Public Types
typedef protocols::jd2::FileJobOutputter	parent

Public Types inherited from protocols::jd2::FileJobOutputter
typedef protocols::jd2::JobOutputter	parent

Public Member Functions
	DatabaseJobOutputter ()

	~DatabaseJobOutputter () override

void	load_options_from_option_system ()
	load options from option sytem More...

void	set_database_name (std::string const &database_name)
	Set database name. More...

std::string	get_database_name () const
	Get database name. More...

void	set_database_pq_schema (std::string const &database_pq_schema)
	Set database postgreSQL schema. More...

std::string	get_database_pq_schema () const
	Get database postgresQL schema. More...

void	flush () override
	see parent class for explanation More...

void	final_pose (protocols::jd2::JobOP job, core::pose::Pose const &pose, std::string const &tag) override
	this function outputs the final result of a job. More...

void	other_pose (protocols::jd2::JobOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false) override
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. More...

bool	job_has_completed (protocols::jd2::JobCOP job) override
	this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing. More...

std::string	output_name (protocols::jd2::JobCOP job) override
	this is the master function for determining the unique output identifier for a job More...

Public Member Functions inherited from protocols::jd2::FileJobOutputter
	FileJobOutputter ()

	~FileJobOutputter () override

void	set_defaults ()

void	file (JobCOP job, std::string const &data) override
	this function takes a string and writes it to disk (separately from Tracer output). More...

utility::file::FileName const &	scorefile_name ()

bool	write_scorefile () const

Public Member Functions inherited from protocols::jd2::JobOutputter
	JobOutputter ()
	constructor – reads cmd-line to initialize evaluators More...

	~JobOutputter () override

virtual void	starting_pose (core::pose::Pose const &)
	optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators More...

virtual std::string	filename (JobCOP) const

void	add_evaluation (evaluation::PoseEvaluatorOP)

void	set_evaluators (evaluation::PoseEvaluators const &)

void	clear_evaluators ()
	clear the list of evaluators More...

evaluation::PoseEvaluatorsCOP	evaluators () const

void	evaluate (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const

void	call_output_observers (core::pose::Pose const &pose, JobOP job) const
	call all output_observers More...

void	set_defaults ()
	clear the list of evaluators More...

Static Public Member Functions
static void	register_options ()

Private Attributes
protocols::features::ProteinSilentReportOP	protein_silent_report_

std::string	database_name_

std::string	database_pq_schema_

std::string	path_

Additional Inherited Members
Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void	scorefile (JobCOP job, core::pose::Pose const &pose, std::string prefix_tag="", std::string suffix_tag="", std::string scorefile="")
	this function will handle the scorefile. If you need to make it virtual do so. Latter two arguments are for redirecting the output to a different scorefile for "other_pose"s. Also adds StringReal job info to the score file. More...

Protected Member Functions inherited from protocols::jd2::JobOutputter
std::string	affixed_numbered_name (JobCOP job)
	this function generates the affixed, numbered name for the job as prefix + input + suffix + number (affixes from options system). This function is deliberately not virtual, this should be a common mechanism; your JobOutputter can not call it if it would like. More...

Detailed Description

this is a implementation of JobOutputter for database-based output.

Member Typedef Documentation

typedef protocols::jd2::FileJobOutputter protocols::features::DatabaseJobOutputter::parent

Constructor & Destructor Documentation

protocols::features::DatabaseJobOutputter::DatabaseJobOutputter ( )

References database_name_, database_pq_schema_, load_options_from_option_system(), path_, and protein_silent_report_.

protocols::features::DatabaseJobOutputter::~DatabaseJobOutputter ( )

override

Member Function Documentation

void protocols::features::DatabaseJobOutputter::final_pose	(	protocols::jd2::JobOP	job,
		core::pose::Pose const &	pose,
		std::string const &	tag
	)

overridevirtual

this function outputs the final result of a job.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), database_name_, database_pq_schema_, output_name(), path_, and protein_silent_report_.

void protocols::features::DatabaseJobOutputter::flush ( )

overridevirtual

see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

std::string protocols::features::DatabaseJobOutputter::get_database_name ( ) const

Get database name.

References database_name_.

string protocols::features::DatabaseJobOutputter::get_database_pq_schema ( ) const

Get database postgresQL schema.

References database_pq_schema_.

bool protocols::features::DatabaseJobOutputter::job_has_completed ( protocols::jd2::JobCOP job )

overridevirtual

this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing.

Implements protocols::jd2::FileJobOutputter.

References database_name_, database_pq_schema_, output_name(), path_, and protein_silent_report_.

void protocols::features::DatabaseJobOutputter::load_options_from_option_system ( )

load options from option sytem

References protocols::hybridization::path, path_, set_database_name(), and set_database_pq_schema().

Referenced by DatabaseJobOutputter().

void protocols::features::DatabaseJobOutputter::other_pose	(	protocols::jd2::JobOP	job,
		core::pose::Pose const &	pose,
		std::string const &	tag,
		int	copy_count = `-1`,
		bool	score_only = `false`
	)