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protocols::jd2::JD2ResourceManagerJobInputter Class Reference

#include <JD2ResourceManagerJobInputter.hh>

Inheritance diagram for protocols::jd2::JD2ResourceManagerJobInputter:
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Collaboration diagram for protocols::jd2::JD2ResourceManagerJobInputter:
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Public Member Functions

 JD2ResourceManagerJobInputter ()
 
virtual ~JD2ResourceManagerJobInputter ()
 
virtual void pose_from_job (core::pose::Pose &pose, JobOP job)
 this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. More...
 
virtual void fill_jobs (Jobs &jobs)
 this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must". More...
 
virtual
JobInputterInputSource::Enum 
input_source () const
 return the type of input source that the JobInputter is currently using More...
 
void fill_jobs_from_stream (std::istream &instream, Jobs &jobs)
 
- Public Member Functions inherited from protocols::jd2::JobInputter
virtual ~JobInputter ()
 

Private Member Functions

virtual void cleanup_after_job_completion (std::string const &job_tag)
 Delete the Resources associated with a job. More...
 
void parse_jobs_tags (utility::tag::TagPtr tag, Jobs &jobs)
 
void parse_job_tag (utility::tag::TagPtr jobs_tags, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)
 
void parse_jobs_table_tag (utility::tag::TagPtr tag, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)
 
void record_job (std::string const &job_name, std::map< std::string, std::string > const &resources_for_job, basic::resource_manager::JobOptionsOP job_options, Jobs &jobs)
 
void read_Option_subtag_for_job (utility::tag::TagPtr options_tag, basic::resource_manager::JobOptionsOP job_options)
 
void parse_options_name_and_value (std::string const &optname, std::string const &value, basic::resource_manager::JobOptionsOP job_options)
 
void read_BooleanOption_subtag_for_job (basic::options::BooleanOptionKey const &boolopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_FileOption_subtag_for_job (basic::options::FileOptionKey const &fileopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_IntegerOption_subtag_for_job (basic::options::IntegerOptionKey const &intopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_PathOption_subtag_for_job (basic::options::PathOptionKey const &pathopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_RealOption_subtag_for_job (basic::options::RealOptionKey const &realopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_StringOption_subtag_for_job (basic::options::StringOptionKey const &stringopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)
 
void read_BooleanVectorOption_subtag_for_job (basic::options::BooleanVectorOptionKey const &boolvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_FileVectorOption_subtag_for_job (basic::options::FileVectorOptionKey const &filevectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_IntegerVectorOption_subtag_for_job (basic::options::IntegerVectorOptionKey const &intvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_PathVectorOption_subtag_for_job (basic::options::PathVectorOptionKey const &pathvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_RealVectorOption_subtag_for_job (basic::options::RealVectorOptionKey const &realvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_StringVectorOption_subtag_for_job (basic::options::StringVectorOptionKey const &strinvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)
 
void read_Data_for_subtag (utility::tag::TagPtr options_tag, std::string const &jobname, std::string &input_tag, std::map< std::string, std::string > &resources_for_job)
 
void read_ResidueType_for_subtag (utility::tag::TagPtr options_tag, std::map< std::string, std::string > &resources_for_job)
 
void check_each_job_has_startstruct (Jobs const &jobs) const
 

Private Attributes

std::string last_input_tag_
 save the last input tag so the resources loaded for it can be unloaded when we see a new input tag More...
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::jd2::JobInputter
static std::string job_inputter_input_source_to_string (JobInputterInputSource::Enum source)
 call this with input_source() to get the input source of a particular job inputter More...
 
- Protected Member Functions inherited from protocols::jd2::JobInputter
void load_pose_into_job (core::pose::Pose const &pose, JobOP job)
 this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
 
void load_pose_into_job (core::pose::PoseCOP pose, JobOP job)
 this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
 
virtual core::Size get_nstruct () const
 this code is here to restrict the use of inner_job_nonconst (this class is a friend class and can do it) More...
 

Constructor & Destructor Documentation

protocols::jd2::JD2ResourceManagerJobInputter::JD2ResourceManagerJobInputter ( )
protocols::jd2::JD2ResourceManagerJobInputter::~JD2ResourceManagerJobInputter ( )
virtual

Member Function Documentation

void protocols::jd2::JD2ResourceManagerJobInputter::check_each_job_has_startstruct ( Jobs const &  jobs) const
private
void protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion ( std::string const &  job_tag)
privatevirtual
void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs ( Jobs jobs)
virtual

this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must".

Implements protocols::jd2::JobInputter.

References fill_jobs_from_stream(), and protocols::jd2::tr().

void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream ( std::istream &  instream,
Jobs jobs 
)
JobInputterInputSource::Enum protocols::jd2::JD2ResourceManagerJobInputter::input_source ( ) const
virtual

return the type of input source that the JobInputter is currently using

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::RESOURCE_MANAGED_JOB.

void protocols::jd2::JD2ResourceManagerJobInputter::parse_job_tag ( utility::tag::TagPtr  jobs_tags,
std::map< std::string, std::string > const &  generic_resources_for_job,
basic::resource_manager::JobOptions const &  generic_job_options,
Jobs jobs 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_table_tag ( utility::tag::TagPtr  tag,
std::map< std::string, std::string > const &  generic_resources_for_job,
basic::resource_manager::JobOptions const &  generic_job_options,
Jobs jobs 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_tags ( utility::tag::TagPtr  tag,
Jobs jobs 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::parse_options_name_and_value ( std::string const &  optname,
std::string const &  value,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job ( core::pose::Pose pose,
JobOP  job 
)
virtual

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

Implements protocols::jd2::JobInputter.

References core::chemical::ResidueTypeSet::add_residue_type(), cleanup_after_job_completion(), core::pose::Pose::clear(), core::chemical::ChemicalManager::get_instance(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), last_input_tag_, protocols::jd2::JobInputter::load_pose_into_job(), core::chemical::ChemicalManager::nonconst_residue_type_set(), core::chemical::ChemicalManager::residue_type_set(), and protocols::jd2::tr().

void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanOption_subtag_for_job ( basic::options::BooleanOptionKey const &  boolopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanVectorOption_subtag_for_job ( basic::options::BooleanVectorOptionKey const &  boolvectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag ( utility::tag::TagPtr  data_tag,
std::string const &  jobname,
std::string &  input_tag,
std::map< std::string, std::string > &  resources_for_job 
)
private

Read the <Data> subtag of the <Job>

Form 1: <Data desc="resource_description" resource="resource_tag"> Precondition requirements: has_resource_configuration(resource_tag) Postcondition guarentees: resources_for_job["resource_description"] == "resource_tag"

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), and protocols::jd2::tr().

Referenced by parse_job_tag(), and parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::read_FileOption_subtag_for_job ( basic::options::FileOptionKey const &  fileopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_FileVectorOption_subtag_for_job ( basic::options::FileVectorOptionKey const &  filevectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerOption_subtag_for_job ( basic::options::IntegerOptionKey const &  intopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerVectorOption_subtag_for_job ( basic::options::IntegerVectorOptionKey const &  intvectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_Option_subtag_for_job ( utility::tag::TagPtr  options_tag,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_PathOption_subtag_for_job ( basic::options::PathOptionKey const &  pathopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_PathVectorOption_subtag_for_job ( basic::options::PathVectorOptionKey const &  pathvectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_RealOption_subtag_for_job ( basic::options::RealOptionKey const &  realopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_RealVectorOption_subtag_for_job ( basic::options::RealVectorOptionKey const &  realvectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_ResidueType_for_subtag ( utility::tag::TagPtr  options_tag,
std::map< std::string, std::string > &  resources_for_job 
)
private

Referenced by parse_job_tag().

void protocols::jd2::JD2ResourceManagerJobInputter::read_StringOption_subtag_for_job ( basic::options::StringOptionKey const &  stringopt,
std::string const &  optname,
std::string const &  val,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::read_StringVectorOption_subtag_for_job ( basic::options::StringVectorOptionKey const &  strinvectopt,
std::string const &  optname,
std::string const &  val,
utility::vector1< std::string > const &  vals,
basic::resource_manager::JobOptionsOP  job_options 
)
private
void protocols::jd2::JD2ResourceManagerJobInputter::record_job ( std::string const &  job_name,
std::map< std::string, std::string > const &  resources_for_job,
basic::resource_manager::JobOptionsOP  job_options,
Jobs jobs 
)
private

Member Data Documentation

std::string protocols::jd2::JD2ResourceManagerJobInputter::last_input_tag_
private

save the last input tag so the resources loaded for it can be unloaded when we see a new input tag

Referenced by pose_from_job().


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