protocols::jd3::LarvalJob, which is initialized by the JobQueen, during its intitialize_job_list method, is an immature form of the. It is matured into a Job that can be run by the JobQueen's mature_job method. A LarvalJob may be one of several LarvalJobs that have the same inputs, but differ in their random number seed (i.e. replicates); two jobs that share the same input are meant to point to the same "InnerLarvalJob" to avoid spending too much memory representing identical data. More...

#include <LarvalJob.hh>

Inheritance diagram for protocols::jd3::LarvalJob:

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Public Member Functions
	LarvalJob (InnerLarvalJobOP inner_job, NStructIndex nstruct_index, core::Size job_index)

	~LarvalJob () override

virtual bool	operator== (LarvalJob const &rhs) const
	Are these two jobs equivalent? (It does not ask if they are equal). Used for the sake of identifying bad jobs. This method ignores the nstruct_index_, which is unlikely to be equal, and should instead focus on the data that determines how a job would run. If the two jobs share identical input files and parameters (besides the random number seed), then they should be considered equivalent. Derived LarvalJob objects should invoke the base class's version of this function. More...

virtual bool	operator!= (LarvalJob const &rhs) const

virtual void	show (std::ostream &out) const

InnerLarvalJobCOP	inner_job () const
	read access to the inner-job More...

InnerLarvalJobOP	nonconst_inner_job () const
	write access to the inner-job; this should be reserved for the JobQueen only as she edits the inner job during its construction More...

std::string	input_tag () const
	The input tag (a short string, generally), is used to specify the input structure, but is not a complete description of the LarvalJob, and certainly not the identifier with which to identify output structures. More...

std::string	job_tag () const
	The job tag is a combination of the input tag and any other data that the JobQueen uses to describe the job, or that has been provided by the user in the job-definition XML file. More...

std::string	job_tag_with_index_suffix (JobOutputIndex const &output_index, core::Size const min_digits=4) const
	For output purposes, construct a string for a particular output of this job given a JobOutputIndex. More...

NStructIndex	nstruct_index () const
	The index used to identify which job this is out of many that have identical inputs but different random number seeds (controlled by the command-line flag "nstruct") More...

core::Size	nstruct_max () const
	The total number of jobs with the same inputs, but different random number seeds. More...

GlobalJobID	job_index () const
	The "global" index for this job among all jobs created by the JobQueen. More...

core::Size	job_node () const
	What is the Job Node for this LarvalJob? Returned from the InnerLarvalJob. More...

utility::vector1< JobResultID > const &	input_job_result_indices () const
	The list of the JobResults required to mature this LarvalJob, by global index of the already-executed (Lavral)Jobs and the result_index for that job. More...

void	set_status_prefix (std::string const &prefix)

void	set_status_suffix (std::string const &suffix)

std::string const &	status_prefix () const

std::string const &	status_suffix () const

bool	completed () const

bool	to_do () const

bool	bad () const

bool	defines_retry_limit () const

core::Size	retry_limit () const

void	completed (bool setting)

void	bad (bool setting)

void	retry_limit (core::Size setting)

Private Attributes
InnerLarvalJobOP	inner_job_
	a pointer to the "heavy" InnerLarvalJob which maintains the data in common with all of the LarvalJobs (that themselves differ only in their nstruct index). More...

NStructIndex	nstruct_index_
	which nstruct is this for the given InnerLarvalJob More...

GlobalJobID	job_index_
	What is the unique global index for this job? Every LarvalJob created by the JobQueen must be assigned a unique index. More...

std::string	status_prefix_
	string giving a brief indication for whether or not the job has failed (but for when the structure generated by this job should none the less be written as output). More...

std::string	status_suffix_
	string giving a brief indication for whether or not the job has failed (but for when the structure generated by this job should none the less be written as output). More...

bool	completed_

bool	bad_

bool	defines_retry_limit_

core::Size	retry_limit_

Detailed Description

protocols::jd3::LarvalJob, which is initialized by the JobQueen, during its intitialize_job_list method, is an immature form of the. It is matured into a Job that can be run by the JobQueen's mature_job method. A LarvalJob may be one of several LarvalJobs that have the same inputs, but differ in their random number seed (i.e. replicates); two jobs that share the same input are meant to point to the same "InnerLarvalJob" to avoid spending too much memory representing identical data.

Note that in JD2, the currently running Job was globally accessible. That is not the case in JD3. Any data that should be output by a running job must be tucked by a Mover inside the JobOutputData to be eventually retrieved by the JobQueen or by a JobDataOutputter at the end of execution.

Constructor & Destructor Documentation

protocols::jd3::LarvalJob::LarvalJob	(	InnerLarvalJobOP	inner_job,
		NStructIndex	nstruct_index,
		core::Size	job_index
	)

protocols::jd3::LarvalJob::~LarvalJob ( )

overridedefault

Member Function Documentation

bool protocols::jd3::LarvalJob::bad ( ) const

References bad_.

void protocols::jd3::LarvalJob::bad ( bool setting )

References bad_.

bool protocols::jd3::LarvalJob::completed ( ) const

References completed_.

void protocols::jd3::LarvalJob::completed ( bool setting )

References completed_.

bool protocols::jd3::LarvalJob::defines_retry_limit ( ) const

References defines_retry_limit_.

InnerLarvalJobCOP protocols::jd3::LarvalJob::inner_job ( ) const

read access to the inner-job

References inner_job_.

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputter::create_output_specification(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::create_output_specification(), and protocols::jd3::pose_outputters::PDBPoseOutputter::job_has_already_completed().

utility::vector1< JobResultID > const & protocols::jd3::LarvalJob::input_job_result_indices ( ) const

The list of the JobResults required to mature this LarvalJob, by global index of the already-executed (Lavral)Jobs and the result_index for that job.

References inner_job_.

std::string protocols::jd3::LarvalJob::input_tag ( ) const

The input tag (a short string, generally), is used to specify the input structure, but is not a complete description of the LarvalJob, and certainly not the identifier with which to identify output structures.

References inner_job_.

GlobalJobID protocols::jd3::LarvalJob::job_index ( ) const

The "global" index for this job among all jobs created by the JobQueen.

References job_index_.

Referenced by protocols::jd3::JobTracker::track_completed_job().

core::Size protocols::jd3::LarvalJob::job_node ( ) const

What is the Job Node for this LarvalJob? Returned from the InnerLarvalJob.

References inner_job_.

Referenced by protocols::jd3::JobTracker::track_completed_job().

std::string protocols::jd3::LarvalJob::job_tag ( ) const

The job tag is a combination of the input tag and any other data that the JobQueen uses to describe the job, or that has been provided by the user in the job-definition XML file.

References inner_job_.

std::string protocols::jd3::LarvalJob::job_tag_with_index_suffix	(	JobOutputIndex const &	output_index,
		core::Size const	min_digits = `4`
	)		const

For output purposes, construct a string for a particular output of this job given a JobOutputIndex.

The number of leading zeros is determined by the maximum number of jobs for the inner-job that this job points at. For 9999 nstruct, there should be 4 digits: 1 + int(log10( 9999 )) = 1 + int( 3.9999 ) = 4 For 10K nstruct, there should be 5 digits; 1 + int( log10( 10K )) = 5

References inner_job_, protocols::mean_field::max(), protocols::jd3::JobOutputIndex::n_primary_outputs, protocols::jd3::JobOutputIndex::n_secondary_outputs, protocols::jd3::JobOutputIndex::primary_output_index, and protocols::jd3::JobOutputIndex::secondary_output_index.

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputter::create_output_specification(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::create_output_specification(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::create_output_specification(), protocols::jd3::pose_outputters::mmTFPoseOutputter::output_name(), and protocols::jd3::pose_outputters::PDBPoseOutputter::output_name().

InnerLarvalJobOP protocols::jd3::LarvalJob::nonconst_inner_job ( ) const

write access to the inner-job; this should be reserved for the JobQueen only as she edits the inner job during its construction

References inner_job_.

NStructIndex protocols::jd3::LarvalJob::nstruct_index ( ) const

The index used to identify which job this is out of many that have identical inputs but different random number seeds (controlled by the command-line flag "nstruct")

References nstruct_index_.

Referenced by protocols::jd3::pose_outputters::PDBPoseOutputter::output_name().

core::Size protocols::jd3::LarvalJob::nstruct_max ( ) const

The total number of jobs with the same inputs, but different random number seeds.

References inner_job_.

Referenced by protocols::jd3::pose_outputters::PDBPoseOutputter::output_name().

bool protocols::jd3::LarvalJob::operator!= ( LarvalJob const & rhs ) const

virtual

bool protocols::jd3::LarvalJob::operator== ( LarvalJob const & rhs ) const

virtual

Are these two jobs equivalent? (It does not ask if they are equal). Used for the sake of identifying bad jobs. This method ignores the nstruct_index_, which is unlikely to be equal, and should instead focus on the data that determines how a job would run. If the two jobs share identical input files and parameters (besides the random number seed), then they should be considered equivalent. Derived LarvalJob objects should invoke the base class's version of this function.

Are two larval jobs equivalent? This ignores the data that describes the status of the job's execution. Intentionally ignored data members include: nstruct_index_, status_prefix_, completed_, and bad_

References inner_job_.

core::Size protocols::jd3::LarvalJob::retry_limit ( ) const

References retry_limit_.

void protocols::jd3::LarvalJob::retry_limit ( core::Size setting )

References defines_retry_limit_, and retry_limit_.

void protocols::jd3::LarvalJob::set_status_prefix ( std::string const & prefix )

References status_prefix_.

void protocols::jd3::LarvalJob::set_status_suffix ( std::string const & suffix )

References status_suffix_.

void protocols::jd3::LarvalJob::show ( std::ostream & out ) const

virtual

Referenced by protocols::jd3::operator<<().

std::string const & protocols::jd3::LarvalJob::status_prefix ( ) const

References status_prefix_.

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputter::create_output_specification(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::create_output_specification(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::create_output_specification(), protocols::jd3::pose_outputters::mmTFPoseOutputter::output_name(), and protocols::jd3::pose_outputters::PDBPoseOutputter::output_name().

std::string const & protocols::jd3::LarvalJob::status_suffix ( ) const

References status_suffix_.

Referenced by protocols::jd3::pose_outputters::ScoreFileOutputter::create_output_specification().

bool protocols::jd3::LarvalJob::to_do ( ) const

References bad_, and completed_.

Member Data Documentation

bool protocols::jd3::LarvalJob::bad_

private

Referenced by bad(), and to_do().

bool protocols::jd3::LarvalJob::completed_

private

Referenced by completed(), and to_do().

bool protocols::jd3::LarvalJob::defines_retry_limit_

private

Referenced by defines_retry_limit(), and retry_limit().

InnerLarvalJobOP protocols::jd3::LarvalJob::inner_job_

private

a pointer to the "heavy" InnerLarvalJob which maintains the data in common with all of the LarvalJobs (that themselves differ only in their nstruct index).

Referenced by inner_job(), input_job_result_indices(), input_tag(), job_node(), job_tag(), job_tag_with_index_suffix(), nonconst_inner_job(), nstruct_max(), and operator==().

GlobalJobID protocols::jd3::LarvalJob::job_index_

private

What is the unique global index for this job? Every LarvalJob created by the JobQueen must be assigned a unique index.

Referenced by job_index().

NStructIndex protocols::jd3::LarvalJob::nstruct_index_

private

which nstruct is this for the given InnerLarvalJob

Referenced by nstruct_index().

core::Size protocols::jd3::LarvalJob::retry_limit_

private

Referenced by retry_limit().

std::string protocols::jd3::LarvalJob::status_prefix_

private

string giving a brief indication for whether or not the job has failed (but for when the structure generated by this job should none the less be written as output).

Referenced by set_status_prefix(), and status_prefix().

std::string protocols::jd3::LarvalJob::status_suffix_

private

string giving a brief indication for whether or not the job has failed (but for when the structure generated by this job should none the less be written as output).

Referenced by set_status_suffix(), and status_suffix().

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

src/protocols/jd3/LarvalJob.hh
src/protocols/jd3/LarvalJob.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation