#include <DatabaseJobOutputter.hh>

Inheritance diagram for protocols::features::DatabaseJobOutputter:

Collaboration 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 ()

virtual	~DatabaseJobOutputter ()

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...

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

virtual void	final_pose (protocols::jd2::JobCOP job, core::pose::Pose const &pose)
	this function outputs the final result of a job. More...

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

virtual bool	job_has_completed (protocols::jd2::JobCOP job)
	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...

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

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

virtual	~FileJobOutputter ()

virtual void	file (JobCOP job, std::string const &data)
	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 ()

virtual	~JobOutputter ()

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

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_

Additional Inherited Members
Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void	scorefile (JobCOP job, core::pose::Pose const &pose, std::string 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...

Detailed Description

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

Definition at line 43 of file DatabaseJobOutputter.hh.

Member Typedef Documentation

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

Definition at line 47 of file DatabaseJobOutputter.hh.

Constructor & Destructor Documentation

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

Definition at line 63 of file DatabaseJobOutputter.cc.

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

Referenced by protocols::features::DatabaseJobOutputterCreator::create_JobOutputter().

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

virtual

Definition at line 76 of file DatabaseJobOutputter.cc.

Member Function Documentation

void protocols::features::DatabaseJobOutputter::final_pose	(	protocols::jd2::JobCOP	job,
		core::pose::Pose const &	pose
	)

virtual

this function outputs the final result of a job.

Implements protocols::jd2::FileJobOutputter.

Definition at line 146 of file DatabaseJobOutputter.cc.

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

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

virtual

see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

Definition at line 143 of file DatabaseJobOutputter.cc.

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

Get database name.

Definition at line 132 of file DatabaseJobOutputter.cc.

References database_name_.

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

Get database postgresQL schema.

Definition at line 120 of file DatabaseJobOutputter.cc.

References database_pq_schema_.

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

virtual

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.

Definition at line 174 of file DatabaseJobOutputter.cc.

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

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

load options from option sytem

Definition at line 81 of file DatabaseJobOutputter.cc.

References set_database_name(), and set_database_pq_schema().

Referenced by DatabaseJobOutputter().

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