#include <SilentFileJobOutputter.hh>

Inheritance diagram for protocols::jd2::SilentFileJobOutputter:

Collaboration diagram for protocols::jd2::SilentFileJobOutputter:

Public Types
typedef protocols::jd2::FileJobOutputter	parent

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

Public Member Functions
	SilentFileJobOutputter ()

virtual	~SilentFileJobOutputter ()

virtual void	flush ()
	this function flushes any internal buffers - see parent class for explanation More...

virtual void	final_pose (JobCOP job, core::pose::Pose const &pose)
	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)
	this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. —>these go to file silent_filename+tag More...

virtual bool	job_has_completed (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 (JobCOP job)
	this is the master function for determining the unique output identifier for a job More...

virtual std::string	filename (JobCOP) const

void	set_silent_file_name (utility::file::FileName name)

void	set_write_separate_scorefile (bool write_separate_scorefile)

void	set_write_no_structures (bool value=true)

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...

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
core::io::silent::SilentStructOP	dump_pose (utility::file::FileName const &filename, JobCOP job, core::pose::Pose const &pose, bool bWriteScoreOnly, int copy_count=-1)

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...

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...

Private Member Functions
void	add_silent_struct (core::io::silent::SilentStructOP ss, utility::file::FileName const &fn)

void	set_defaults ()
	called by the constructor to set filename and options More...

void	read_done_jobs ()

void	write_all_structs ()
	this function is called at the end of job distribution to flush the buffers More...

Private Attributes
bool	bWriteIntermediateFiles_

bool	bWriteIntermediateStructures_

bool	bWriteNoStructures_
	toggle to switch off writing of structures More...

bool	write_separate_scorefile_
	whether to write a separate scorefile that contains the scorelines from the silent file More...

utility::file::FileName	silent_file_

utility::vector1< std::string >	silent_file_tags_

core::Size	n_to_buffer_

core::Real	random_flush_frequency_

utility::vector1< std::pair < core::io::silent::SilentStructOP, utility::file::FileName > >	saved_structs_

Detailed Description

this is a implementation of JobOutputter for silent-file-based output.

Definition at line 42 of file SilentFileJobOutputter.hh.

Member Typedef Documentation

typedef protocols::jd2::FileJobOutputter protocols::jd2::SilentFileJobOutputter::parent

Definition at line 46 of file SilentFileJobOutputter.hh.

Constructor & Destructor Documentation

protocols::jd2::SilentFileJobOutputter::SilentFileJobOutputter ( )

Definition at line 57 of file SilentFileJobOutputter.cc.

References read_done_jobs(), and set_defaults().

Referenced by protocols::jd2::SilentFileJobOutputterCreator::create_JobOutputter().

protocols::jd2::SilentFileJobOutputter::~SilentFileJobOutputter ( )

virtual

Definition at line 62 of file SilentFileJobOutputter.cc.

Member Function Documentation

void protocols::jd2::SilentFileJobOutputter::add_silent_struct	(	core::io::silent::SilentStructOP	ss,
		utility::file::FileName const &	fn
	)

private

Definition at line 272 of file SilentFileJobOutputter.cc.

References saved_structs_.

Referenced by dump_pose().

core::io::silent::SilentStructOP protocols::jd2::SilentFileJobOutputter::dump_pose	(	utility::file::FileName const &	filename,
		JobCOP	job,
		core::pose::Pose const &	pose,
		bool	bWriteScoreOnly,
		int	copy_count = `-1`
	)

protected

Definition at line 223 of file SilentFileJobOutputter.cc.

References protocols::jd2::add_job_data_to_ss(), add_silent_struct(), protocols::jd2::current_replica(), protocols::jd2::JobOutputter::evaluate(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), n_to_buffer_, output_name(), random_flush_frequency_, protocols::RG(), saved_structs_, protocols::jd2::tr(), and write_all_structs().

Referenced by final_pose(), and other_pose().

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

inlinevirtual

Reimplemented from protocols::jd2::JobOutputter.

Definition at line 85 of file SilentFileJobOutputter.hh.

References silent_file_.

Referenced by other_pose().

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

virtual

this function outputs the final result of a job.

creating output functions/////////////////////////////////////////

Implements protocols::jd2::FileJobOutputter.

Definition at line 171 of file SilentFileJobOutputter.cc.

References bWriteNoStructures_, dump_pose(), protocols::jd2::FileJobOutputter::scorefile_name(), silent_file_, write_separate_scorefile_, and core::io::silent::SilentFileData::write_silent_struct().

void protocols::jd2::SilentFileJobOutputter::flush ( )

virtual

this function flushes any internal buffers - see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

Definition at line 66 of file SilentFileJobOutputter.cc.

References write_all_structs().

bool protocols::jd2::SilentFileJobOutputter::job_has_completed ( 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 280 of file SilentFileJobOutputter.cc.

References core::sequence::end, output_name(), core::scoring::pair, read_done_jobs(), saved_structs_, and silent_file_tags_.

void protocols::jd2::SilentFileJobOutputter::other_pose	(	JobCOP	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. —>these go to file silent_filename+tag

Implements protocols::jd2::FileJobOutputter.

Definition at line 197 of file SilentFileJobOutputter.cc.

References bWriteIntermediateFiles_, bWriteIntermediateStructures_, dump_pose(), filename(), protocols::jd2::FileJobOutputter::scorefile_name(), silent_file_, write_separate_scorefile_, and core::io::silent::SilentFileData::write_silent_struct().