#include <FileJobOutputter.hh>

Inheritance diagram for protocols::jd2::FileJobOutputter:

Collaboration diagram for protocols::jd2::FileJobOutputter:

Public Types
typedef protocols::jd2::JobOutputter	parent

Public Member Functions
	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...

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 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. The base implementation looks for a pdb with the job's name already in existence. More...

virtual std::string	output_name (JobCOP job)=0
	this is the master function for determining the unique output identifier for a job More...

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

bool	write_scorefile () const

Public Member Functions inherited from protocols::jd2::JobOutputter
	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	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

Protected Member Functions
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 Attributes
bool	write_scorefile_
	this function will handle the scorefile for arbitrary poses. More...

utility::file::FileName	scorefile_name_

Detailed Description

this is a middle-layer implementation of JobOutputter for file-based output. It handles scorefile output, as scorefiles are common to file-outputting methods.

Member Typedef Documentation

typedef protocols::jd2::JobOutputter protocols::jd2::FileJobOutputter::parent

Constructor & Destructor Documentation

protocols::jd2::FileJobOutputter::FileJobOutputter ( )

References scorefile_name_, protocols::jd2::TR(), and write_scorefile_.

protocols::jd2::FileJobOutputter::~FileJobOutputter ( )

virtual

Member Function Documentation

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

virtual

this function takes a string and writes it to disk (separately from Tracer output).

this base class implementation will try to append whatever string it gets to a file named after the job, with a user-specified suffix.

Implements protocols::jd2::JobOutputter.

References output_name(), and protocols::jd2::TR().

Referenced by protocols::jd2::PDBJobOutputter::other_pose().

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

pure virtual

this function outputs the final result of a job.

Implements protocols::jd2::JobOutputter.

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

virtual bool protocols::jd2::FileJobOutputter::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. The base implementation looks for a pdb with the job's name already in existence.

Implements protocols::jd2::JobOutputter.

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

virtual void protocols::jd2::FileJobOutputter::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.

Implements protocols::jd2::JobOutputter.

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

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

pure virtual

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

Implements protocols::jd2::JobOutputter.

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

Referenced by file().

void protocols::jd2::FileJobOutputter::scorefile	(	JobCOP	job,
		core::pose::Pose const &	pose,
		std::string	tag = `""`,
		std::string	scorefile = `""`
	)

protectedvirtual

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.

Reimplemented in protocols::enzdes::EnzdesJobOutputter.

References core::sequence::end, protocols::jd2::ScoreMap::score_map_from_scored_pose(), protocols::jd2::TR(), and core::io::raw_data::ScoreFileData::write_pose().

Referenced by protocols::jd2::ScoreOnlyJobOutputter::final_pose(), protocols::jd2::PDBJobOutputter::final_pose(), protocols::jd2::ScoreOnlyJobOutputter::other_pose(), and protocols::jd2::PDBJobOutputter::other_pose().

utility::file::FileName const& protocols::jd2::FileJobOutputter::scorefile_name ( )

inline

References scorefile_name_.

Referenced by protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter(), protocols::jd2::SilentFileJobOutputter::final_pose(), protocols::jd2::SilentFileJobOutputter::other_pose(), protocols::jd2::ScoreOnlyJobOutputter::read_done_jobs(), and protocols::enzdes::EnzdesJobOutputter::scorefile().

bool protocols::jd2::FileJobOutputter::write_scorefile ( ) const

inline

References write_scorefile_.

Referenced by protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter(), and protocols::enzdes::EnzdesJobOutputter::scorefile().