| add_option(utility::options::OptionKey const &key) | protocols::jd3::standard::StandardJobQueen | protected |
| add_options(utility::options::OptionKeyList const &opts) | protocols::jd3::standard::StandardJobQueen | protected |
| all_settings_to_defualt() | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| allow_pose_inputter(pose_inputters::PoseInputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
| allow_pose_outputter(pose_outputters::PoseOutputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
| append_common_tag_subelements(utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen) const override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
| append_job_tag_subelements(utility::tag::XMLSchemaDefinition &job_definition_xsd, utility::tag::XMLSchemaComplexTypeGenerator &job_ct_gen) const override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
| assign_output_index(jd3::LarvalJobCOP larval_job, jd3::ResultIndex result_index_for_job, core::Size n_results_for_job, jd3::JobOutputIndex &output_index) override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
| assign_output_index(jd3::GlobalJobID global_job_id, jd3::ResultIndex result_id, jd3::JobOutputIndex &output_index) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| build_output_index(protocols::jd3::LarvalJobCOP larval_job, ResultIndex result_index_for_job, core::Size n_results_for_job) | protocols::jd3::standard::StandardJobQueen | protected |
| checkpoints_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| cl_outputters_ | protocols::jd3::standard::StandardJobQueen | private |
| cluster(jd3::JobDAGNodeID stage_about_to_start) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| cluster_data_for_results_of_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| cluster_metric_tag_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| common_block_precedes_job_blocks_ | protocols::jd3::standard::StandardJobQueen | private |
| common_block_tags() const | protocols::jd3::standard::StandardJobQueen | protected |
| common_block_tags_ | protocols::jd3::standard::StandardJobQueen | private |
| complete_larval_job_maturation(jd3::LarvalJobCOP larval_job, utility::options::OptionCollectionCOP job_options, utility::vector1< jd3::JobResultCOP > const &input_job_results) override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
| completed_job_summary(jd3::GlobalJobID job_id, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) | protocols::multistage_rosetta_scripts::MRSJobQueen | |
| completed_job_summary(jd3::LarvalJobCOP job, jd3::ResultIndex result_index, jd3::JobSummaryOP summary) override | protocols::multistage_rosetta_scripts::MRSJobQueen | inlinevirtual |
| concatenate_all_options() const | protocols::jd3::standard::StandardJobQueen | private |
| create_and_init_inner_larval_job_from_preliminary(core::Size nstruct, PrelimJobNodeID prelim_job_node, JobDAGNodeID job_node) const | protocols::jd3::standard::StandardJobQueen | protected |
| create_and_set_initial_job_dag() | protocols::jd3::JobQueen | |
| create_and_store_output_specification_for_job_result(LarvalJobCOP job, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protected |
| create_and_store_output_specification_for_job_result(LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protected |
| create_initial_job_dag() override | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | virtual |
| create_inner_larval_job(core::Size nstruct, JobDAGNodeID job_node, PrelimJobNodeID preliminary_job_node) const | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| create_larval_job(InnerLarvalJobOP job, NStructIndex nstruct_index, core::Size larval_job_index) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| create_output_specification_for_job_result(LarvalJobCOP job, utility::options::OptionCollection const &job_options, ResultIndex result_index, core::Size nresults) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| curr_inner_larval_job_index_ | protocols::jd3::standard::StandardJobQueen | private |
| current_inner_larval_job_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| current_job_index() const | protocols::jd3::standard::StandardJobQueen | protected |
| deallocation_messages() override | protocols::jd3::standard::StandardJobQueen | virtual |
| default_outputter_creator_ | protocols::jd3::standard::StandardJobQueen | private |
| derived_process_deallocation_message(deallocation::DeallocationMessageOP message) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| determine_job_list(jd3::JobDAGNodeID job_dag_node_index, core::Size max_njobs) override | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | virtual |
| determine_job_list_and_track(JobDAGNodeID job_dag_node_index, core::Size max_njobs) | protocols::jd3::JobQueen | |
| determine_preliminary_job_list() | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| determine_preliminary_job_list_from_command_line() | protocols::jd3::standard::StandardJobQueen | private |
| determine_preliminary_job_list_from_xml_file(std::string const &job_def_string) | protocols::jd3::standard::StandardJobQueen | |
| determine_preliminary_job_list_from_xml_file(std::string const &job_def_string, std::string const &job_def_schema) | protocols::jd3::standard::StandardJobQueen | private |
| determine_validity_of_stage_tags() | protocols::multistage_rosetta_scripts::MRSJobQueen | |
| do_not_accept_all_pose_inputters_from_factory() | protocols::jd3::standard::StandardJobQueen | protected |
| do_not_accept_all_pose_outputters_from_factory() | protocols::jd3::standard::StandardJobQueen | protected |
| estimate_number_of_bytes_needed_for_archiving() | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | |
| expand_job_list(InnerLarvalJobOP inner_job, core::Size max_larval_jobs_to_create) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| fa_and_cen_sizes_for_archives(core::pose::PoseOP pose) | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | static |
| flush() override | protocols::jd3::standard::StandardJobQueen | virtual |
| get_job_graph() const | protocols::jd3::JobQueen | protected |
| get_job_tracker() | protocols::jd3::JobQueen | protected |
| get_job_tracker() const | protocols::jd3::JobQueen | protected |
| get_nth_job_for_initial_stage(jd3::LocalJobID local_job_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| get_nth_job_for_noninitial_stage(jd3::JobDAGNodeID stage, jd3::LocalJobID local_job_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| get_outputter_from_job_tag(utility::tag::TagCOP tag) const | protocols::jd3::standard::StandardJobQueen | private |
| get_prelim_larval_job_tracker() | protocols::jd3::standard::StandardJobQueen | protected |
| get_prelim_larval_job_tracker() const | protocols::jd3::standard::StandardJobQueen | protected |
| get_preliminary_larval_jobs() const | protocols::jd3::standard::StandardJobQueen | protected |
| get_preliminary_larval_jobs_determined() const | protocols::jd3::standard::StandardJobQueen | protected |
| has_been_initialized_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| has_job_previously_been_output(protocols::jd3::LarvalJobCOP job) override | protocols::jd3::standard::StandardJobQueen | virtual |
| inner_larval_jobs_for_curr_prelim_job_ | protocols::jd3::standard::StandardJobQueen | private |
| input_job_tags_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| input_pose_counter_ | protocols::jd3::standard::StandardJobQueen | private |
| input_pose_id_for_jobid(jd3::GlobalJobID global_jobid) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotected |
| input_pose_index_map_ | protocols::jd3::standard::StandardJobQueen | private |
| inputter_creator_list_ | protocols::jd3::standard::StandardJobQueen | private |
| inputter_creators_ | protocols::jd3::standard::StandardJobQueen | private |
| inputter_options_ | protocols::jd3::standard::StandardJobQueen | private |
| job_def_complex_type_name(std::string const &type) | protocols::jd3::standard::StandardJobQueen | static |
| job_definition_file_tags_ | protocols::jd3::standard::StandardJobQueen | private |
| job_definition_xsd() const override | protocols::jd3::standard::StandardJobQueen | virtual |
| job_genealogist_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| job_graph_ | protocols::jd3::JobQueen | private |
| job_results_have_been_discarded_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| job_results_that_should_be_discarded() override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
| job_subelement_mangler(std::string const &name) | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotectedstatic |
| job_tracker_ | protocols::jd3::JobQueen | private |
| JobQueen() | protocols::jd3::JobQueen | |
| jobs_that_should_be_output() override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
| load_job_definition_file(std::string const &job_def_string, std::string const &job_def_schema) | protocols::jd3::standard::StandardJobQueen | private |
| load_starting_poses_only_once_ | protocols::jd3::standard::StandardJobQueen | private |
| mature_larval_job(protocols::jd3::LarvalJobCOP job, utility::vector1< JobResultCOP > const &input_job_results) override | protocols::jd3::standard::StandardJobQueen | virtual |
| max_num_results_to_keep_per_input_struct_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| max_num_results_to_keep_per_instance_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| most_recent_cluster_results_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| most_recent_pose_id_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| MRSJobQueen() | protocols::multistage_rosetta_scripts::MRSJobQueen | |
| MRSJobQueenChecker() | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | |
| next_batch_of_larval_jobs_for_job_node(JobDAGNodeID job_dag_node_index, core::Size max_njobs) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| next_batch_of_larval_jobs_from_prelim(PrelimJobNodeID job_node_index, core::Size max_njobs) | protocols::jd3::standard::StandardJobQueen | private |
| njobs_made_for_curr_inner_larval_job_ | protocols::jd3::standard::StandardJobQueen | private |
| node_managers_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| note_job_completed(jd3::GlobalJobID job_id, jd3::JobStatus status, core::Size nresults, bool are_you_a_unit_test) | protocols::multistage_rosetta_scripts::MRSJobQueen | |
| note_job_completed(core::Size, jd3::JobStatus, core::Size) | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| note_job_completed(jd3::LarvalJobCOP job, jd3::JobStatus status, core::Size nresults) override | protocols::multistage_rosetta_scripts::MRSJobQueen | virtual |
| note_job_completed_and_track(LarvalJobCOP job, JobStatus status, core::Size nresults) | protocols::jd3::JobQueen | |
| note_job_result_discarded(LarvalJobCOP job, ResultIndex result_index) | protocols::jd3::standard::StandardJobQueen | private |
| note_preliminary_job_node_is_complete(PrelimJobNodeID pjn_index) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| num_input_structs() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| num_input_structs_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_jobs_per_input_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_results_to_keep_after_clustering_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_results_to_keep_for_stage(core::Size stage) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| num_results_to_keep_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_stages() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| num_stages_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_structs_output_for_input_job_tag_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| num_total_jobs_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| options_ | protocols::jd3::standard::StandardJobQueen | private |
| options_for_job(InnerLarvalJob const &inner_job) const | protocols::jd3::standard::StandardJobQueen | protected |
| options_from_tag(utility::tag::TagCOP job_options_tags) const | protocols::jd3::standard::StandardJobQueen | protected |
| outputter_creator_list_ | protocols::jd3::standard::StandardJobQueen | private |
| outputter_creators_ | protocols::jd3::standard::StandardJobQueen | private |
| outputter_options_ | protocols::jd3::standard::StandardJobQueen | private |
| outputters_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| override_default_outputter_ | protocols::jd3::standard::StandardJobQueen | private |
| parse_common_tag(utility::tag::TagCOP common_tag) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| parse_job_definition_tags(utility::tag::TagCOP common_block_tags, utility::vector1< jd3::standard::PreliminaryLarvalJob > const &) override | protocols::multistage_rosetta_scripts::MRSJobQueen | protectedvirtual |
| parse_single_job_tag(jd3::standard::PreliminaryLarvalJob const &prelim_larval_job, jd3::PrelimJobNodeID input_pose_id) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| parse_single_stage_tag(utility::tag::TagCOP subprotocol_tag) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| pose_for_inner_job(InnerLarvalJobCOP inner_job) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_for_inner_job(InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_for_inner_job_derived(jd3::InnerLarvalJobCOP inner_job, utility::options::OptionCollection const &options) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| pose_for_job(LarvalJobCOP job, utility::options::OptionCollection const &options) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_for_job_derived(jd3::LarvalJobCOP job, utility::options::OptionCollection const &options) | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| pose_inputter_for_job(InnerLarvalJob const &inner_job) const | protocols::jd3::standard::StandardJobQueen | protected |
| pose_output_specification_for_job_result_id_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| pose_outputter_for_job(InnerLarvalJob const &innerJob) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_outputter_for_job(InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_outputter_for_job(pose_outputters::PoseOutputSpecification const &spec) | protocols::jd3::standard::StandardJobQueen | protected |
| pose_outputter_map_ | protocols::jd3::standard::StandardJobQueen | private |
| pose_outputters_ | protocols::jd3::standard::StandardJobQueen | private |
| prelim_job_tracker_ | protocols::jd3::standard::StandardJobQueen | private |
| preliminary_larval_jobs_ | protocols::jd3::standard::StandardJobQueen | private |
| preliminary_larval_jobs_determined_ | protocols::jd3::standard::StandardJobQueen | private |
| print_job_lineage() const | protocols::multistage_rosetta_scripts::MRSJobQueen | protected |
| process_deallocation_message(deallocation::DeallocationMessageOP message) override | protocols::jd3::standard::StandardJobQueen | virtual |
| protocols_subelement_mangler(std::string const &name) | protocols::multistage_rosetta_scripts::MRSJobQueen | inlineprotectedstatic |
| read_input_poses_from_command_line() | protocols::jd3::standard::StandardJobQueen | private |
| recent_successes_ | protocols::jd3::standard::StandardJobQueen | private |
| refine_preliminary_job(PreliminaryLarvalJob const &prelim_job) | protocols::jd3::standard::StandardJobQueen | protectedvirtual |
| remove_default_input_element() | protocols::jd3::standard::StandardJobQueen | protected |
| representative_pose_outputter_map_ | protocols::jd3::standard::StandardJobQueen | private |
| representative_secondary_outputter_map_ | protocols::jd3::standard::StandardJobQueen | private |
| required_initialization_performed_ | protocols::jd3::standard::StandardJobQueen | private |
| resource_definition_xsd() const override | protocols::jd3::standard::StandardJobQueen | virtual |
| result_cutoffs_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| result_outputter(output::OutputSpecification const &spec) override | protocols::jd3::standard::StandardJobQueen | virtual |
| secondary_outputter_for_job(InnerLarvalJob const &inner_job, utility::options::OptionCollection const &job_options, std::string const &secondary_outputter_type, utility::tag::TagCOP outputter_tag) | protocols::jd3::standard::StandardJobQueen | private |
| secondary_outputter_for_job(pose_outputters::PoseOutputSpecification const &) | protocols::jd3::standard::StandardJobQueen | private |
| secondary_outputter_map_ | protocols::jd3::standard::StandardJobQueen | private |
| secondary_outputter_options_ | protocols::jd3::standard::StandardJobQueen | private |
| secondary_outputters_for_job(InnerLarvalJob const &innerJob, utility::options::OptionCollection const &job_options) | protocols::jd3::standard::StandardJobQueen | protected |
| set_common_block_precedes_job_blocks(bool setting) | protocols::jd3::standard::StandardJobQueen | inlineprotected |
| set_default_outputter(pose_outputters::PoseOutputterCreatorOP creator) | protocols::jd3::standard::StandardJobQueen | protected |
| sorter_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| stage_for_global_job_id(jd3::GlobalJobID global_job_id) const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| StandardJobQueen() | protocols::jd3::standard::StandardJobQueen | |
| tag_for_stage_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| tag_manager() const | protocols::multistage_rosetta_scripts::MRSJobQueen | inline |
| tag_manager_ | protocols::multistage_rosetta_scripts::MRSJobQueen | private |
| update_job_dag(JobDigraphUpdater &updater) override | protocols::jd3::standard::StandardJobQueen | virtual |
| use_factory_provided_pose_inputters_ | protocols::jd3::standard::StandardJobQueen | private |
| use_factory_provided_pose_outputters_ | protocols::jd3::standard::StandardJobQueen | private |
| ~JobQueen() override | protocols::jd3::JobQueen | |
| ~MRSJobQueen() override | protocols::multistage_rosetta_scripts::MRSJobQueen | |
| ~MRSJobQueenChecker() override | protocols::multistage_rosetta_scripts::MRSJobQueenChecker | |
| ~StandardJobQueen() override | protocols::jd3::standard::StandardJobQueen | |
