#include <Job.hh>

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)

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...

virtual	~Job ()

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...

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	bad () const

void	set_completed (bool value=true)

void	set_bad (bool value=true)

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...

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::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
	)

Referenced by copy_without_output().

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

virtual

Member Function Documentation

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

add an output string

References long_strings_.

Referenced by protocols::anchored_design::AnchoredDesignMover::apply(), protocols::floppy_tail::create_extra_output(), protocols::features::JobDataFeatures::load_string_data(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb(), and protocols::simple_filters::RotamerBoltzmannWeight::write_to_pdb().

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_.

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_.

Referenced by protocols::simple_moves::AddJobPairData::apply(), protocols::ligand_docking::ComputeLigandRDF::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::motif_grafting::movers::MotifGraftMover::generate_match_pose(), protocols::features::JobDataFeatures::load_string_string_data(), protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck::operator()(), and protocols::surface_docking::FullatomRelaxMover::output_solution_state().

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

add output strings

adds output strings

References long_strings_.

Referenced by protocols::RotamerDump::RotamerDumpMover::apply(), and protocols::jd2::JobDistributor::go_main().

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

References inner_job_.

Referenced by to_do().

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_, Job(), and nstruct_index_.

Referenced by protocols::jd2::JobDistributor::clear_current_job_output(), and get_pose().

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_, protocols::jd2::JobDistributor::job_inputter(), and utility_exit_with_message.

Referenced by protocols::jd2::Parser::generate_mover_from_job().

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_, protocols::jd2::JobDistributor::job_inputter(), and utility_exit_with_message.

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

inline

References string_real_pairs_.

Referenced by protocols::ligand_docking::WriteLigandMolFile::apply().

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

inline

References string_string_pairs_.

Referenced by protocols::ligand_docking::WriteLigandMolFile::apply(), and protocols::ligand_docking::InterfaceScoreCalculator::apply().

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_.

Referenced by protocols::jd2::Parser::generate_mover_from_job(), and protocols::jd2::JobInputter::load_pose_into_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_.

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::hotspot_hashing::movers::PlaceProbeMover::apply(), and protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job().

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

References inner_job_.

Referenced by protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize().

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

References string_real_pairs_.

Referenced by protocols::jd2::AtomTreeDiffJobOutputter::final_pose(), and protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis().

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

References string_real_pairs_.

Referenced by protocols::jd2::AtomTreeDiffJobOutputter::final_pose(), and protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis().

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::set_bad ( bool value = true )

References inner_job_.

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

inline

References completed_.

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

inline

References status_prefix_.

Referenced by protocols::jd2::BOINCJobDistributor::job_failed().

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

virtual

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

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

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

inline

References status_prefix_.

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::completed_

private

container of evaluators

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

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(), get_strings(), protocols::jd2::operator==(), output_strings_begin(), output_strings_end(), and show().