#include <JobOutputter.hh>

Inheritance diagram for protocols::jd2::JobOutputter:

Collaboration diagram for protocols::jd2::JobOutputter:

Public Member Functions
	JobOutputter ()

virtual	~JobOutputter ()

virtual void	flush ()
	this function is meant to be redefined in child classes to allow for flushing of memory buffers. More...

virtual void	file (JobCOP job, std::string const &data)=0
	this function takes a string and writes it to disk (separately from Tracer output). use some sort of extention option system - default .dat? .data? More...

virtual void	final_pose (JobCOP job, core::pose::Pose const &pose)=0
	this function outputs the final result of a job. More...

virtual void	other_pose (JobCOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false)=0
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. More...

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 bool	job_has_completed (JobCOP job)=0
	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 (JobCOP job)=0
	this is the master function for determining the unique output identifier for a job - should this be defined in the base class? 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

Protected Member Functions
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...

Private Member Functions
JobOutputter &	operator= (JobOutputter const &rhs)
	operator= defined for the sake of the remove-headers-in-headers initiative. As of this writing, there is no reason to actually call this function, so it is declared but UNIMPLEMENTED to force compiler errors if you try to do this (instead of allowing the compiler to autogenerate the code). If you have a valid need for this function, feel free to implement it properly and make it a public function. More...

	JobOutputter (JobOutputter const &cpy)
	copy ctor defined for the sake of the remove-headers-in-headers initiative. As of this writing, there is no reason to actually call this function, so it is declared but UNIMPLEMENTED to force compiler errors if you try to do this (instead of allowing the compiler to autogenerate the code). If you have a valid need for this function, feel free to implement it properly and make it a public function. More...

Private Attributes
evaluation::PoseEvaluatorsOP	evaluators_

Detailed Description

the JobOutputter class is responsible for dealing with output, as well as determining what jobs have already been output and what sort of name is associated with a job. Derived classes will be responsible for output such as PDBS, PDBS.tar.gz and silent files.

Definition at line 45 of file JobOutputter.hh.

Constructor & Destructor Documentation

protocols::jd2::JobOutputter::JobOutputter ( )

Definition at line 51 of file JobOutputter.cc.

References protocols::evaluation::EvaluatorFactory::add_all_evaluators(), evaluators_, and protocols::evaluation::EvaluatorFactory::get_instance().

protocols::jd2::JobOutputter::~JobOutputter ( )

virtual

Definition at line 56 of file JobOutputter.cc.

protocols::jd2::JobOutputter::JobOutputter ( JobOutputter const & cpy)

private

copy ctor defined for the sake of the remove-headers-in-headers initiative. As of this writing, there is no reason to actually call this function, so it is declared but UNIMPLEMENTED to force compiler errors if you try to do this (instead of allowing the compiler to autogenerate the code). If you have a valid need for this function, feel free to implement it properly and make it a public function.

Member Function Documentation

void protocols::jd2::JobOutputter::add_evaluation ( evaluation::PoseEvaluatorOP ev_in)

add another PoseEvaluator to the list of evaluations

Definition at line 132 of file JobOutputter.cc.

References evaluators_.

std::string protocols::jd2::JobOutputter::affixed_numbered_name ( JobCOP job)

protected

this function provides the extended name, not just the output name. e.g output_name returns 1UBQ_0001, this returns 1UBQ_0001.pdb

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.

this is copied from protocols/jobdist/Jobs.cc, r24761 Checks the current JobInputter input source from the singleton instance of JobDistributor. If a PDB_FILE, it will deliberately discard any path information in the input tag as well as any file name extension (since input tags are usually file names). Otherwise, it will keep the entire input tag as-is.

Definition at line 67 of file JobOutputter.cc.

References protocols::vip::base_name(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobInputterInputSource::PDB_FILE, and core::io::pdb::split().

Referenced by protocols::jd2::NoOutputJobOutputter::output_name(), protocols::jd2::ScoreOnlyJobOutputter::output_name(), protocols::jd2::AtomTreeDiffJobOutputter::output_name(), protocols::jd2::PDBJobOutputter::output_name(), protocols::jd2::SilentFileJobOutputter::output_name(), and protocols::features::DatabaseJobOutputter::output_name().

void protocols::jd2::JobOutputter::clear_evaluators ( )

clear the list of evaluators

Definition at line 144 of file JobOutputter.cc.

References evaluators_.

void protocols::jd2::JobOutputter::evaluate	(	core::pose::Pose &	pose,
		std::string	tag,
		core::io::silent::SilentStruct &	pss
	)		const

run the PoseEvaluators on the pose evaluation creates string value pairs which end up in the SilentStruct energy object instead of filling things into a SilentStruct we could provide a different interface... wait until Steven has finished his string/value pair output

Definition at line 118 of file JobOutputter.cc.

References evaluators(), and core::io::serialization::size().

Referenced by protocols::jd2::SilentFileJobOutputter::dump_pose().

evaluation::PoseEvaluatorsCOP protocols::jd2::JobOutputter::evaluators ( ) const

return the list of PoseEvaluators

Definition at line 149 of file JobOutputter.cc.

References evaluators_.

Referenced by evaluate().

virtual void protocols::jd2::JobOutputter::file	(	JobCOP	job,
		std::string const &	data
	)

pure virtual

this function takes a string and writes it to disk (separately from Tracer output). use some sort of extention option system - default .dat? .data?

Implemented in protocols::jd2::FileJobOutputter, and protocols::jd2::NoOutputJobOutputter.

virtual std::string protocols::jd2::JobOutputter::filename ( JobCOP ) const

inlinevirtual

Reimplemented in protocols::jd2::SilentFileJobOutputter.

Definition at line 94 of file JobOutputter.hh.

virtual void protocols::jd2::JobOutputter::final_pose	(	JobCOP	job,
		core::pose::Pose const &	pose
	)

pure virtual

this function outputs the final result of a job.

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::FileJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::dna::PDBOutput, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, protocols::jd2::NoOutputJobOutputter, and protocols::enzdes::EnzdesJobOutputter.

void protocols::jd2::JobOutputter::flush ( )

virtual

this function is meant to be redefined in child classes to allow for flushing of memory buffers.

base implementation does nothing

Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that the output would be flushed at end of runtime. The original implementation was to A) bend over backward to ensure that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed because it's static) and B) flush the buffers in the destructor. This caused a problem because the buffer-flushing tried to use the Tracers, which had already been destructed...boom crash.

New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush function to force this stuff out. So here it is:

Reimplemented in protocols::features::DatabaseJobOutputter, and protocols::jd2::SilentFileJobOutputter.

Definition at line 59 of file JobOutputter.cc.

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

pure 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.

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::FileJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::NoOutputJobOutputter, and protocols::enzdes::EnzdesJobOutputter.

JobOutputter& protocols::jd2::JobOutputter::operator= ( JobOutputter const & rhs)

private

operator= defined for the sake of the remove-headers-in-headers initiative. As of this writing, there is no reason to actually call this function, so it is declared but UNIMPLEMENTED to force compiler errors if you try to do this (instead of allowing the compiler to autogenerate the code). If you have a valid need for this function, feel free to implement it properly and make it a public function.

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

pure virtual

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

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::FileJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::jd2::NoOutputJobOutputter.

virtual std::string protocols::jd2::JobOutputter::output_name ( JobCOP job)

pure virtual

this is the master function for determining the unique output identifier for a job - should this be defined in the base class?

Implemented in protocols::features::DatabaseJobOutputter, protocols::jd2::SilentFileJobOutputter, protocols::jd2::PDBJobOutputter, protocols::jd2::FileJobOutputter, protocols::jd2::AtomTreeDiffJobOutputter, protocols::jd2::ScoreOnlyJobOutputter, and protocols::jd2::NoOutputJobOutputter.

void protocols::jd2::JobOutputter::set_evaluators ( evaluation::PoseEvaluators const & ev_in)

set a list of Evaluations ( the list will be copied, the evaluations are OPs )

Definition at line 139 of file JobOutputter.cc.

References evaluators_.

void protocols::jd2::JobOutputter::starting_pose ( core::pose::Pose const & )

virtual

optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators

optionally pass a starting (reference) pose to a JobOutputter for comparison purposes and/or as interface for initializing evaluators. (Currently does nothing in this base class.)

Reimplemented in protocols::dna::PDBOutput.

Definition at line 129 of file JobOutputter.cc.

Member Data Documentation

evaluation::PoseEvaluatorsOP protocols::jd2::JobOutputter::evaluators_

private

Definition at line 112 of file JobOutputter.hh.

Referenced by add_evaluation(), clear_evaluators(), evaluators(), JobOutputter(), and set_evaluators().

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

src/protocols/jd2/JobOutputter.hh
src/protocols/jd2/JobOutputter.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation