#include <Job.hh>

Inheritance diagram for protocols::jd2::Job:

Public Types
typedef std::list< std::string >	Strings
	TODO these should be maps rather than lists. More...

typedef std::map< std::string, std::string >	StringStringPairs

typedef std::map< std::string, core::Real >	StringRealPairs

Public Member Functions
	Job (InnerJobOP inner_job, core::Size nstruct_index)

	Job (Job const &src)
	Copy constructor. More...

JobOP	copy_without_output () const
	returns a copy of this object whose "output fields" are zeroed out. Used by the JobDistributor in cases where the job fails and must be retried to prevent accumulation of Job state after a failure. This implementation was chosen over a clear_all_output function to prevent mover A from deleting mover B's hard work! You probably should not be trying to call this function. The exception: If you want an intermediate-output pose (not the final pose) to not have the aggregated accessory data in the "real" Job object. More...

JobOP	clone () const
	Return an owning pointer to a copy of this object. More...

	~Job () override

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

InnerJobCOP	inner_job () const
	access to inner-job ... use is discouraged - use sparingly! — DO NOT use my_job->inner_job()->get_pose() INSTEAD use my_job->get_pose() More...

std::string const &	input_tag () const
	return the input tag (a short string, generally) More...

InnerJobOP	inner_job_nonconst ()
	nonconst access is intended only for the JobInputter to load poses into the InnerJob, and the Parser to add constraints, and the JobDistributor to delete completed inputs (recycle memory) More...

core::pose::PoseCOP	get_pose () const
	get_pose : will return More...

void	get_pose (core::pose::Pose &) const
	in-place copy of input pose More...

core::Size	nstruct_index () const

core::Size	nstruct_max () const

void	add_string (std::string const &string_in)
	add an output string More...

void	add_strings (Strings const &)
	add output strings More...

void	add_string_string_pair (std::string const &string1, std::string const &string2)
	add a string/string pair More...

void	add_string_real_pair (std::string const &string_in, core::Real const real_in)
	add a string/real pair More...

void	clear_output ()
	Delete the output strings, string/string pairs, and string/real pairs. More...

Strings &	get_strings ()

StringStringPairs &	get_string_string_pairs ()

StringRealPairs &	get_string_real_pairs ()

Strings::const_iterator	output_strings_begin () const

Strings::const_iterator	output_strings_end () const

StringStringPairs::const_iterator	output_string_string_pairs_begin () const

StringStringPairs::const_iterator	output_string_string_pairs_end () const

StringRealPairs::const_iterator	output_string_real_pairs_begin () const

StringRealPairs::const_iterator	output_string_real_pairs_end () const

Strings	get_strings () const

StringStringPairs	get_string_string_pairs () const

StringRealPairs	get_string_real_pairs () const

void	set_status_prefix (std::string prefix)

std::string const &	status_prefix () const

bool	completed () const

bool	to_do () const

bool	can_be_deleted () const
	Returns true iff this job can be deleted to free up memory. More...

bool	bad () const

core::Size	start_time () const

core::Size	end_time () const

core::Size	elapsed_time () const

std::string	timestamp () const

void	set_completed (bool value=true)

void	set_can_be_deleted (bool value=true)
	Set whether this job can be deleted to free up memory. More...

void	set_bad (bool value=true)

void	start_timing ()

void	end_timing ()

void	add_output_observer (JobOutputterObserverAP an_observer)

void	remove_output_observer (JobOutputterObserverAP old_observer)

void	call_output_observers (core::pose::Pose const &pose)

Private Types
typedef std::set < JobOutputterObserverAP, utility::pointer::owner_less < JobOutputterObserverAP > >	JobOutputterObservers

Private Attributes
InnerJobOP	inner_job_
	a pointer to the "heavy" InnerJob which maintains the starting pose for the job (shared across nstruct) More...

core::Size const	nstruct_index_
	which nstruct is this? More...

std::string	status_prefix_

Strings	long_strings_
	the following block of data makes the Job class pretty heavy. If we create thousands of Jobs this can be a problem... More...

StringStringPairs	string_string_pairs_
	string-string pairs. Inserted into SCORE: lines in scorefiles/silentfiles. More...

StringRealPairs	string_real_pairs_
	string-real pairs (scoretype/score pairs). Inserted into SCORE: lines in scorefiles/silentfiles More...

bool	completed_
	container of evaluators More...

bool	can_be_deleted_
	Can the job be deleted? Used by the LargeNstructJobDistributor to determine which jobs can be removed to free up memory. More...

core::Size	start_time_

core::Size	end_time_

std::string	timestamp_

JobOutputterObservers	output_observers_

Friends
bool	operator== (Job const &a, Job const &b)
	Note: only compare if the pointers to the poses are to the same location. More...

bool	operator!= (Job const &a, Job const &b)

std::ostream &	operator<< (std::ostream &out, const Job &job)

Detailed Description

The Job class is directly used by the job distributor. It contains an index into nstruct and a lightweight pointer to an InnerJob (to share those heavier classes). It also directly contains job-associated output data. The idea here is that your scores, etc are associated with the job, not with a particular pose within that running job. Thus, the Job object is a better place to store them than the pose.

Member Typedef Documentation

typedef std::set< JobOutputterObserverAP, utility::pointer::owner_less< JobOutputterObserverAP > > protocols::jd2::Job::JobOutputterObservers

private

typedef std::map< std::string, core::Real > protocols::jd2::Job::StringRealPairs

typedef std::list< std::string > protocols::jd2::Job::Strings

TODO these should be maps rather than lists.

typedef std::map< std::string, std::string > protocols::jd2::Job::StringStringPairs

Constructor & Destructor Documentation

protocols::jd2::Job::Job	(	InnerJobOP	inner_job,
		core::Size	nstruct_index
	)

protocols::jd2::Job::Job ( Job const & src )

Copy constructor.

protocols::jd2::Job::~Job ( )

overridedefault

Member Function Documentation

void protocols::jd2::Job::add_output_observer ( JobOutputterObserverAP an_observer )

References output_observers_.

void protocols::jd2::Job::add_string ( std::string const & string_in )

add an output string

References long_strings_.

void protocols::jd2::Job::add_string_real_pair	(	std::string const &	string_in,
		core::Real const	real_in
	)

add a string/real pair

References string_real_pairs_.

Referenced by protocols::rosetta_scripts::ParsedProtocol::add_values_to_job(), and protocols::canonical_sampling::BiasEnergy::add_values_to_job().

void protocols::jd2::Job::add_string_string_pair	(	std::string const &	string1,
		std::string const &	string2
	)

add a string/string pair

References string_string_pairs_.

void protocols::jd2::Job::add_strings ( Strings const & strings )

add output strings

adds output strings

References long_strings_.

bool protocols::jd2::Job::bad ( ) const

References inner_job_.

Referenced by to_do().

void protocols::jd2::Job::call_output_observers ( core::pose::Pose const & pose )

References output_observers_.

bool protocols::jd2::Job::can_be_deleted ( ) const

inline

Returns true iff this job can be deleted to free up memory.

Should only be true if the job has completed, is bad, or has failed.

References can_be_deleted_.

void protocols::jd2::Job::clear_output ( )

Delete the output strings, string/string pairs, and string/real pairs.

References long_strings_, string_real_pairs_, and string_string_pairs_.

JobOP protocols::jd2::Job::clone ( ) const

Return an owning pointer to a copy of this object.

bool protocols::jd2::Job::completed ( ) const

inline

References completed_.

JobOP protocols::jd2::Job::copy_without_output ( ) const

returns a copy of this object whose "output fields" are zeroed out. Used by the JobDistributor in cases where the job fails and must be retried to prevent accumulation of Job state after a failure. This implementation was chosen over a clear_all_output function to prevent mover A from deleting mover B's hard work! You probably should not be trying to call this function. The exception: If you want an intermediate-output pose (not the final pose) to not have the aggregated accessory data in the "real" Job object.

returns a copy of this object whose "output fields" are zeroed out. Used by the JobDistributor in cases where the job fails and must be retried to prevent accumulation of Job state after a failure. This implementation was chosen over a clear_all_output function to prevent mover A from deleting mover B's hard work! You probably should not be trying to call this function.

References inner_job_, and nstruct_index_.

Referenced by get_pose().

core::Size protocols::jd2::Job::elapsed_time ( ) const

References end_time_, and start_time_.

core::Size protocols::jd2::Job::end_time ( ) const

References end_time_.

void protocols::jd2::Job::end_timing ( )

References end_time_, and start_time_.

core::pose::PoseCOP protocols::jd2::Job::get_pose ( ) const

get_pose : will return

return a COP to the input pose

References copy_without_output(), protocols::jd2::JobDistributor::get_instance(), inner_job_, and protocols::jd2::JobDistributor::job_inputter().

void protocols::jd2::Job::get_pose ( core::pose::Pose & pose ) const

in-place copy of input pose

References copy_without_output(), protocols::jd2::JobDistributor::get_instance(), inner_job_, and protocols::jd2::JobDistributor::job_inputter().

StringRealPairs& protocols::jd2::Job::get_string_real_pairs ( )

inline

References string_real_pairs_.

StringRealPairs protocols::jd2::Job::get_string_real_pairs ( ) const

inline

References string_real_pairs_.

StringStringPairs& protocols::jd2::Job::get_string_string_pairs ( )

inline

References string_string_pairs_.

StringStringPairs protocols::jd2::Job::get_string_string_pairs ( ) const

inline

References string_string_pairs_.

Strings& protocols::jd2::Job::get_strings ( )

inline

References long_strings_.

Strings protocols::jd2::Job::get_strings ( ) const

inline

References long_strings_.

InnerJobCOP protocols::jd2::Job::inner_job ( ) const

access to inner-job ... use is discouraged - use sparingly! — DO NOT use my_job->inner_job()->get_pose() INSTEAD use my_job->get_pose()

References inner_job_.

InnerJobOP protocols::jd2::Job::inner_job_nonconst ( )

nonconst access is intended only for the JobInputter to load poses into the InnerJob, and the Parser to add constraints, and the JobDistributor to delete completed inputs (recycle memory)

References inner_job_.

std::string const & protocols::jd2::Job::input_tag ( ) const

return the input tag (a short string, generally)

References inner_job_.

core::Size protocols::jd2::Job::nstruct_index ( ) const

References nstruct_index_.

core::Size protocols::jd2::Job::nstruct_max ( ) const

References inner_job_.

Job::StringRealPairs::const_iterator protocols::jd2::Job::output_string_real_pairs_begin ( ) const

References string_real_pairs_.

Job::StringRealPairs::const_iterator protocols::jd2::Job::output_string_real_pairs_end ( ) const

References string_real_pairs_.

Job::StringStringPairs::const_iterator protocols::jd2::Job::output_string_string_pairs_begin ( ) const

References string_string_pairs_.

Job::StringStringPairs::const_iterator protocols::jd2::Job::output_string_string_pairs_end ( ) const

References string_string_pairs_.

Job::Strings::const_iterator protocols::jd2::Job::output_strings_begin ( ) const

References long_strings_.

Job::Strings::const_iterator protocols::jd2::Job::output_strings_end ( ) const

References long_strings_.

void protocols::jd2::Job::remove_output_observer ( JobOutputterObserverAP old_observer )

References output_observers_.

void protocols::jd2::Job::set_bad ( bool value = true )

References can_be_deleted_, and inner_job_.

void protocols::jd2::Job::set_can_be_deleted ( bool value = true )

inline

Set whether this job can be deleted to free up memory.

References can_be_deleted_.

void protocols::jd2::Job::set_completed ( bool value = true )

inline

References can_be_deleted_, and completed_.

void protocols::jd2::Job::set_status_prefix ( std::string prefix )

inline

References status_prefix_.

void protocols::jd2::Job::show ( std::ostream & out ) const

virtual

References can_be_deleted_, completed_, inner_job_, long_strings_, nstruct_index_, status_prefix_, string_real_pairs_, and string_string_pairs_.

Referenced by protocols::jd2::operator<<().

core::Size protocols::jd2::Job::start_time ( ) const

References start_time_.

void protocols::jd2::Job::start_timing ( )

References end_time_, start_time_, and timestamp_.

std::string const& protocols::jd2::Job::status_prefix ( ) const

inline

References status_prefix_.

std::string protocols::jd2::Job::timestamp ( ) const

References timestamp_.

bool protocols::jd2::Job::to_do ( ) const

inline

References bad(), and completed_.

Friends And Related Function Documentation

bool operator!=	(	Job const &	a,
		Job const &	b
	)

friend

std::ostream& operator<<	(	std::ostream &	out,
		const Job &	job
	)

friend

bool operator==	(	Job const &	a,
		Job const &	b
	)

friend

Note: only compare if the pointers to the poses are to the same location.

Member Data Documentation

bool protocols::jd2::Job::can_be_deleted_

private

Can the job be deleted? Used by the LargeNstructJobDistributor to determine which jobs can be removed to free up memory.

False by default. True if the job has failed, is bad, or is completed.

Referenced by can_be_deleted(), protocols::jd2::operator==(), set_bad(), set_can_be_deleted(), set_completed(), and show().

bool protocols::jd2::Job::completed_

private

container of evaluators

Referenced by completed(), protocols::jd2::operator==(), set_completed(), show(), and to_do().

core::Size protocols::jd2::Job::end_time_

private

Referenced by elapsed_time(), end_time(), end_timing(), and start_timing().

InnerJobOP protocols::jd2::Job::inner_job_

private

a pointer to the "heavy" InnerJob which maintains the starting pose for the job (shared across nstruct)

Referenced by bad(), copy_without_output(), get_pose(), inner_job(), inner_job_nonconst(), input_tag(), nstruct_max(), protocols::jd2::operator==(), set_bad(), and show().

Strings protocols::jd2::Job::long_strings_

private

the following block of data makes the Job class pretty heavy. If we create thousands of Jobs this can be a problem...

used for arbitrary string data (stuff you've preformatted). Intended to be appended to the end of a PDB or dumped to a tracer if not in a PDB output mode.

Referenced by add_string(), add_strings(), clear_output(), get_strings(), protocols::jd2::operator==(), output_strings_begin(), output_strings_end(), and show().