#include <DatabaseJobOutputter.hh>

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::JobOP job, core::pose::Pose const &pose, std::string const &tag)
	this function outputs the final result of a job. More...

virtual void	other_pose (protocols::jd2::JobOP 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 ()

void	set_defaults ()

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

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

void	add_output_observer (JobOutputterObserverAP an_observer)

void	remove_output_observer (JobOutputterObserverAP old_observer)

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_

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 provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb 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_, get_db_session(), jd2, load_options_from_option_system(), and protein_silent_report_.

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

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

virtual

Member Function Documentation

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

virtual

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_, get_db_session(), output_name(), and protein_silent_report_.

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

virtual

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_, and utility_exit_with_message.

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 )

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.

References database_name_, database_pq_schema_, get_db_session(), option, output_name(), protein_silent_report_, out::resume_batch, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and user.

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

load options from option sytem

References inout::dbms::database_name, utility::options::OptionCollection::has(), option, inout::dbms::pq_schema, 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`
	)

virtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.

Implements protocols::jd2::FileJobOutputter.

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

std::string protocols::features::DatabaseJobOutputter::output_name ( protocols::jd2::JobCOP job )

virtual

this is the master function for determining the unique output identifier for a job

Database tags should preserve the FULL NAME such that we don't end up with duplicate tags. This will cause problems on BOINC if changed.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::affixed_numbered_name().

Referenced by final_pose(), and job_has_completed().

void protocols::features::DatabaseJobOutputter::register_options ( )

static

References utility::options::OptionCollection::add_relevant(), inout::dbms::database_name, inout::dbms::host, option, inout::dbms::password, inout::dbms::port, inout::dbms::pq_schema, out::resume_batch, inout::dbms::separate_db_per_mpi_process, and inout::dbms::user.

void protocols::features::DatabaseJobOutputter::set_database_name ( std::string const & database_name )

Set database name.

References database_name_.

Referenced by load_options_from_option_system().

void protocols::features::DatabaseJobOutputter::set_database_pq_schema ( std::string const & database_pq_schema )

Set database postgreSQL schema.

References database_name_.

Referenced by load_options_from_option_system().

Member Data Documentation

std::string protocols::features::DatabaseJobOutputter::database_name_

private

Referenced by DatabaseJobOutputter(), final_pose(), get_database_name(), job_has_completed(), other_pose(), set_database_name(), and set_database_pq_schema().

std::string protocols::features::DatabaseJobOutputter::database_pq_schema_

private

Referenced by DatabaseJobOutputter(), final_pose(), get_database_pq_schema(), job_has_completed(), and other_pose().

protocols::features::ProteinSilentReportOP protocols::features::DatabaseJobOutputter::protein_silent_report_

private

Referenced by DatabaseJobOutputter(), final_pose(), job_has_completed(), and other_pose().

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

src/protocols/features/DatabaseJobOutputter.hh
src/protocols/features/DatabaseJobOutputter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation