protocols::jd2::JobsContainer Class Reference

#include <JobsContainer.hh>

Inheritance diagram for protocols::jd2::JobsContainer:

Public Member Functions
	JobsContainer ()
	JobsContainer constructor. More...
	~JobsContainer () override
	JobsContainer destructor. More...
JobsContainerCOP	get_self_ptr () const
	Default (shallow copy) copy constructor/assignment operator is the desired behavior. More...
JobsContainerOP	get_self_ptr ()
	Get self owning pointers. More...
JobOP	operator[] (core::Size const index)
	Get a specific job, by number. More...
JobCOP	operator[] (core::Size const index) const
	Get a specific job, by number (const-access). More...
core::Size	size () const
	Get the total number of jobs. More...
void	push_back (JobOP new_job)
	Add a job to the list of jobs. More...
void	set_total_jobs (core::Size const total_jobs)
	Set the total number of jobs. More...
void	clear ()
	Clear the jobs list. More...
JobOP	back ()
	Access the last element. More...
void	shuffle ()
	Randomize the order of elements (the map keys) More...
void	erase (core::Size const index)
	Erase an element in the jobs list. More...
bool	has_job (core::Size const index) const
	Does the job with the given index exist in the currently-loaded list of jobs? More...
bool	can_be_deleted (core::Size const index) const
	Can the job with the given index be deleted? More...
core::Size	highest_job_index () const
	Return the index of the highest job currently loaded in memory. More...
void	set_job_inputter (JobInputterOP jobinputter)
	Set the job inputter. More...
void	get_loaded_job_indices (utility::vector1< core::Size > &output) const
	Get a list of job indices currently in memory. More...
void	set_all_current_jobs_as_deletable ()
	Mark all jobs currently in memory as deletable. More...
void	set_force_job_purging (bool const val=true)
	Set whether or not this JobsContainer forces job purging when higher-numbered jobs are requested. More...
bool	force_job_purging () const
	Get whether or not this JobsContainer forces job purging when higher-numbered jobs are requested. More...

Private Attributes
std::map< core::Size, JobOP >	joblist_
	The list of owning pointers to jobs, with the job number as the key. More...
core::Size	highest_job_index_
	The highest-index job in the joblist_ map. More...
core::Size	total_jobs_
	The total number of jobs. More...
bool	total_jobs_set_
	Has the total number of jobs been overridden? More...
JobInputterOP	job_inputter_
	The JobInputter that populated this object (or which is otherwise associated with it). More...
bool	force_job_purging_
	If true, and if a job inputter is used that limits the number of jobs in memory at any given time, then when a higher job index is requested than exists in memory, the JobsContainer will force job purging until that job exists in memory. If false (the default), then only deletable jobs will be purged, and the job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number is too high). More...

Detailed Description

The JobsContainer class contains a list of JobsOPs. It permits the list to be versatile – for example, if one wishes to load only a subset of jobs into memory at any given time.

Constructor & Destructor Documentation

protocols::jd2::JobsContainer::JobsContainer

(

)

JobsContainer constructor.

protocols::jd2::JobsContainer::~JobsContainer ( )

overridedefault

JobsContainer destructor.

Member Function Documentation

JobOP protocols::jd2::JobsContainer::back

(

)

Access the last element.

References highest_job_index_, and joblist_.

Referenced by protocols::comparative_modeling::ThreadingJobInputter::fill_jobs().

bool protocols::jd2::JobsContainer::can_be_deleted

(

core::Size const

index

)

const

Can the job with the given index be deleted?

References joblist_.

void protocols::jd2::JobsContainer::clear

(

)

Clear the jobs list.

References highest_job_index_, joblist_, total_jobs_, and total_jobs_set_.

Referenced by protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::SerializedPoseJobInputter::fill_jobs(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::comparative_modeling::GenericJobInputter::fill_jobs(), protocols::jd2::EmptyPoseJobInputter::fill_jobs(), protocols::make_rot_lib::MakeRotLibJobInputter::fill_jobs(), protocols::jd2::LargeNstructJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::EnsembleJobInputter::fill_jobs(), and protocols::features::DatabaseJobInputter::fill_jobs().

void protocols::jd2::JobsContainer::erase

(

core::Size const

index

)

Erase an element in the jobs list.

References joblist_.

bool protocols::jd2::JobsContainer::force_job_purging ( ) const

inline

Get whether or not this JobsContainer forces job purging when higher-numbered jobs are requested.

If true, and if a job inputter is used that limits the number of jobs in memory at any given time, then when a higher job index is requested than exists in memory, the JobsContainer will force job purging until that job exists in memory. If false (the default), then only deletable jobs will be purged, and the job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number is too high).

References force_job_purging_.

Referenced by operator[]().

void protocols::jd2::JobsContainer::get_loaded_job_indices

(

utility::vector1< core::Size > &

output

)

const

Get a list of job indices currently in memory.

The output vector is cleared and populated with the current job indices in memory.

References joblist_.

JobsContainerCOP protocols::jd2::JobsContainer::get_self_ptr ( ) const

inline

Default (shallow copy) copy constructor/assignment operator is the desired behavior.

Get self const owning pointers.

Referenced by operator[]().

JobsContainerOP protocols::jd2::JobsContainer::get_self_ptr ( )

inline

Get self owning pointers.

bool protocols::jd2::JobsContainer::has_job

(

core::Size const

index

)

const

Does the job with the given index exist in the currently-loaded list of jobs?

References joblist_.

Referenced by operator[](), and protocols::jd2::MPIWorkPoolJobDistributor::slave_get_new_job_id().

core::Size protocols::jd2::JobsContainer::highest_job_index ( ) const

inline

Return the index of the highest job currently loaded in memory.

References highest_job_index_.

Referenced by operator[](), and protocols::jd2::MPIWorkPoolJobDistributor::slave_get_new_job_id().

JobOP protocols::jd2::JobsContainer::operator[]

(

core::Size const

index

)

Get a specific job, by number.

Should work even if jobs have been deleted, since this uses a map instead of an array.

References force_job_purging(), get_self_ptr(), has_job(), highest_job_index(), job_inputter_, joblist_, size(), total_jobs_, and protocols::jd2::TR().

JobCOP protocols::jd2::JobsContainer::operator[]

(

core::Size const

index

)

const

Get a specific job, by number (const-access).

Should work even if jobs have been deleted, since this uses a map instead of an array.

References highest_job_index(), joblist_, and total_jobs_.

void protocols::jd2::JobsContainer::push_back

(

JobOP

new_job

)

Add a job to the list of jobs.

References highest_job_index_, joblist_, total_jobs_, and total_jobs_set_.

Referenced by protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::SerializedPoseJobInputter::fill_jobs(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::comparative_modeling::GenericJobInputter::fill_jobs(), protocols::jd2::EmptyPoseJobInputter::fill_jobs(), protocols::make_rot_lib::MakeRotLibJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::EnsembleJobInputter::fill_jobs(), protocols::features::DatabaseJobInputter::fill_jobs(), and protocols::jd2::LargeNstructJobInputter::populate_next_n_jobs().

void protocols::jd2::JobsContainer::set_all_current_jobs_as_deletable

(

)

Mark all jobs currently in memory as deletable.

This will result in all jobs being purged the next time a higher-index job is requeted.

void protocols::jd2::JobsContainer::set_force_job_purging ( bool const  val = true )

inline

Set whether or not this JobsContainer forces job purging when higher-numbered jobs are requested.

If true, and if a job inputter is used that limits the number of jobs in memory at any given time, then when a higher job index is requested than exists in memory, the JobsContainer will force job purging until that job exists in memory. If false (the default), then only deletable jobs will be purged, and the job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number is too high).

References force_job_purging_, and protocols::hybridization::val.

Referenced by protocols::jd2::MPIWorkPoolJobDistributor::MPIWorkPoolJobDistributor().

void protocols::jd2::JobsContainer::set_job_inputter ( JobInputterOP  jobinputter )

inline

Set the job inputter.

Needed if the job list is to be updated by the job inputter.

References job_inputter_.

Referenced by protocols::jd2::LargeNstructJobInputter::fill_jobs().

void protocols::jd2::JobsContainer::set_total_jobs

(

core::Size const

total_jobs

)

Set the total number of jobs.

This overrides whatever the length of the joblist_ is.

References highest_job_index_, total_jobs_, and total_jobs_set_.

Referenced by protocols::jd2::LargeNstructJobInputter::fill_jobs().

void protocols::jd2::JobsContainer::shuffle

(

)

Randomize the order of elements (the map keys)

References joblist_, and core::scoring::rg.

Referenced by protocols::jd2::ScreeningJobInputter::fill_jobs().

core::Size protocols::jd2::JobsContainer::size ( ) const

inline

Get the total number of jobs.

Might not be the number in the joblist_ map, if we're only holding a subset in memory at any given time.

References total_jobs_.

Referenced by protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::jd2::MPIWorkPartitionJobDistributor::get_new_job_id(), protocols::jd2::get_spanning_jobs(), protocols::jd2::BOINCJobDistributor::go(), protocols::jd2::VectorPoseJobDistributor::go_mpi(), protocols::jd2::VectorPoseJobDistributor::go_serial(), protocols::jd2::MPIFileBufJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::archive::MPIArchiveJobDistributor::notify_archive(), operator[](), and protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list().

Member Data Documentation

bool protocols::jd2::JobsContainer::force_job_purging_

private

If true, and if a job inputter is used that limits the number of jobs in memory at any given time, then when a higher job index is requested than exists in memory, the JobsContainer will force job purging until that job exists in memory. If false (the default), then only deletable jobs will be purged, and the job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number is too high).

Referenced by force_job_purging(), and set_force_job_purging().

core::Size protocols::jd2::JobsContainer::highest_job_index_

private

The highest-index job in the joblist_ map.

Starts at 0 and counts up as elements are added.

Referenced by back(), clear(), highest_job_index(), push_back(), and set_total_jobs().

JobInputterOP protocols::jd2::JobsContainer::job_inputter_

private

The JobInputter that populated this object (or which is otherwise associated with it).

Referenced by operator[](), and set_job_inputter().

std::map< core::Size, JobOP > protocols::jd2::JobsContainer::joblist_

private

The list of owning pointers to jobs, with the job number as the key.

Referenced by back(), can_be_deleted(), clear(), erase(), get_loaded_job_indices(), has_job(), operator[](), push_back(), and shuffle().

core::Size protocols::jd2::JobsContainer::total_jobs_

private

The total number of jobs.

By default, this will be the size of the joblist_, unless overridden.

Referenced by clear(), operator[](), push_back(), set_total_jobs(), and size().

bool protocols::jd2::JobsContainer::total_jobs_set_

private

Has the total number of jobs been overridden?

Default false.

Referenced by clear(), push_back(), and set_total_jobs().

---

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

• src/protocols/jd2/JobsContainer.hh
• src/protocols/jd2/JobsContainer.cc