Index

A

add_compound() (pathomx.db.databaseManager method) add_db_synonyms() (pathomx.db.databaseManager method) add_gene() (pathomx.db.databaseManager method) add_handler() (pathomx.config.ConfigManager method) add_handlers() (pathomx.config.ConfigManager method) add_identity() (pathomx.db.databaseManager method) add_input() (pathomx.data.DataManager method) add_output() (pathomx.data.DataManager method) add_pathway() (pathomx.db.databaseManager method) add_protein() (pathomx.db.databaseManager method) add_reaction() (pathomx.db.databaseManager method)

add_synonym() (pathomx.db.databaseManager method) add_synonyms() (pathomx.db.databaseManager method) annotations_from_XML() (pathomx.data.DataSet method) annotations_to_XML() (pathomx.data.DataSet method) appendChild() (pathomx.data.DataTreeItem method) as_class_groups() (pathomx.data.DataSet method) as_copy() (pathomx.data.DataSet method) as_csv() (pathomx.db.Compound method) (pathomx.db.Gene method) (pathomx.db.Pathway method) (pathomx.db.Protein method) (pathomx.db.Reaction method) as_filtered() (pathomx.data.DataSet method) as_summary() (pathomx.data.DataSet method) at_least_one_element_in_common() (in module pathomx.data)

B

build_dict_mapper() (in module pathomx.config)

build_tuple_mapper() (in module pathomx.config)

C

can_consume() (pathomx.data.DataDefinition method) (pathomx.data.DataManager method) can_consume_which_of() (pathomx.data.DataManager method) child() (pathomx.data.DataTreeItem method) childCount() (pathomx.data.DataTreeItem method) classes_l (pathomx.data.DataSet attribute) classes_n (pathomx.data.DataSet attribute) classes_t (pathomx.data.DataSet attribute) cmp_map (pathomx.data.DataDefinition attribute) columnCount() (pathomx.data.DataTreeItem method) (pathomx.data.DataTreeModel method) (pathomx.data.TableInterface method)

Compound (class in pathomx.db) compounds (pathomx.db.Reaction attribute) ConfigManager (class in pathomx.config) consume() (pathomx.data.DataManager method) consume_any_of() (pathomx.data.DataManager method) consume_with() (pathomx.data.DataManager method) consumed (pathomx.data.DataManager attribute) crop() (pathomx.data.DataSet method)

D

data() (pathomx.data.DataTreeItem method) (pathomx.data.DataTreeModel method) (pathomx.data.TableInterface method) databaseManager (class in pathomx.db) DataDefinition (class in pathomx.data) DataManager (class in pathomx.data)

DataSet (class in pathomx.data) DataTreeItem (class in pathomx.data) DataTreeModel (class in pathomx.data) dimensions (pathomx.data.DataSet attribute)

E

empty() (pathomx.data.DataSet method) entities_l (pathomx.data.DataSet attribute) entities_n (pathomx.data.DataSet attribute)

entities_t (pathomx.data.DataSet attribute) error (pathomx.threads.WorkerSignals attribute) extract_db_unification() (pathomx.db.databaseManager method)

F

finished (pathomx.threads.WorkerSignals attribute)

from_XML() (pathomx.data.DataSet method)

G

Gene (class in pathomx.db) get() (pathomx.config.ConfigManager method) (pathomx.data.DataManager method) get_cmp_fn() (pathomx.data.DataDefinition method) get_via_synonym() (pathomx.db.databaseManager method)

get_via_unification() (pathomx.db.databaseManager method) geto() (pathomx.data.DataManager method) getXMLConfig() (pathomx.config.ConfigManager method)

H

has_consumable() (pathomx.data.DataManager method)

headerData() (pathomx.data.DataTreeModel method) (pathomx.data.TableInterface method)

I

icon() (pathomx.data.DataTreeItem method) import_data() (pathomx.data.DataSet method) index() (pathomx.data.DataTreeModel method)

interfaces_changed (pathomx.data.DataManager attribute) is_empty (pathomx.data.DataSet attribute)

L

labels_l (pathomx.data.DataSet attribute) labels_n (pathomx.data.DataSet attribute) labels_t (pathomx.data.DataSet attribute) load_compounds() (pathomx.db.databaseManager method) load_genes() (pathomx.db.databaseManager method) load_gibbs() (pathomx.db.databaseManager method)

load_identities() (pathomx.db.databaseManager method) load_pathways() (pathomx.db.databaseManager method) load_proteins() (pathomx.db.databaseManager method) load_reactions() (pathomx.db.databaseManager method) load_synonyms() (pathomx.db.databaseManager method) load_xrefs() (pathomx.db.databaseManager method)

N

name (pathomx.db.ReactionIntermediate attribute)

notify_watchers() (pathomx.data.DataManager method)

P

parent() (pathomx.data.DataTreeItem method) (pathomx.data.DataTreeModel method) pathomx.config (module) pathomx.custom_exceptions (module) pathomx.data (module) pathomx.db (module) pathomx.qt (module) pathomx.threads (module) pathomx.translate (module) PathomxExternalResourceTimeoutException

PathomxExternalResourceUnavailableException PathomxIncorrectFileFormatException PathomxIncorrectFileStructureException Pathway (class in pathomx.db) process() (pathomx.threads.Worker method) Protein (class in pathomx.db) provide() (pathomx.data.DataManager method) put() (pathomx.data.DataManager method)

Q

QSettingsManager (class in pathomx.config)

R

Reaction (class in pathomx.db) ReactionIntermediate (class in pathomx.db) refresh() (pathomx.data.DataTreeModel method) (pathomx.data.TableInterface method) refresh_consumed_data() (pathomx.data.DataManager method) refresh_interfaces() (pathomx.data.DataSet method) register_interface() (pathomx.data.DataSet method) remove_handler() (pathomx.config.ConfigManager method) remove_input() (pathomx.data.DataManager method)

remove_invalid_data() (pathomx.data.DataSet method) remove_output() (pathomx.data.DataManager method) replace() (pathomx.config.ConfigManager method) reset() (pathomx.config.ConfigManager method) (pathomx.config.QSettingsManager method) (pathomx.data.DataManager method) result (pathomx.threads.WorkerSignals attribute) row() (pathomx.data.DataTreeItem method) rowCount() (pathomx.data.DataTreeModel method) (pathomx.data.TableInterface method) run (pathomx.threads.Worker attribute)

S

save_compounds() (pathomx.db.databaseManager method) save_genes() (pathomx.db.databaseManager method) save_pathways() (pathomx.db.databaseManager method) save_proteins() (pathomx.db.databaseManager method) save_reactions() (pathomx.db.databaseManager method) save_synonyms() (pathomx.db.databaseManager method) scales_n (pathomx.data.DataSet attribute) scales_r (pathomx.data.DataSet attribute) scales_t (pathomx.data.DataSet attribute) secondary_compounds (pathomx.db.Reaction attribute) set() (pathomx.config.ConfigManager method)

set_default() (pathomx.config.ConfigManager method) set_defaults() (pathomx.config.ConfigManager method) set_many() (pathomx.config.ConfigManager method) setupModelData() (pathomx.data.DataTreeModel method) setXMLConfig() (pathomx.config.ConfigManager method) shape (pathomx.data.DataSet attribute) sort() (pathomx.data.TableInterface method) source_updated (pathomx.data.DataManager attribute) status (pathomx.threads.WorkerSignals attribute) stop_consuming() (pathomx.data.DataManager method) stop_providing() (pathomx.data.DataManager method)

T

TableInterface (class in pathomx.data) to_XML() (pathomx.data.DataSet method) tr() (in module pathomx.translate)

type (pathomx.db.Compound attribute) (pathomx.db.Gene attribute) (pathomx.db.Pathway attribute) (pathomx.db.Protein attribute) (pathomx.db.Reaction attribute) (pathomx.db.ReactionIntermediate attribute) type_name (pathomx.db.Compound attribute) (pathomx.db.Gene attribute) (pathomx.db.Pathway attribute) (pathomx.db.Protein attribute) (pathomx.db.Reaction attribute) (pathomx.db.ReactionIntermediate attribute) types_MethodType() (in module pathomx.config)

U

unconsumed (pathomx.data.DataManager attribute) unget() (pathomx.data.DataManager method) unput() (pathomx.data.DataManager method)

updated (pathomx.config.ConfigManager attribute) url (pathomx.db.Compound attribute) (pathomx.db.Gene attribute) (pathomx.db.Pathway attribute) (pathomx.db.Protein attribute) (pathomx.db.Reaction attribute)

W

Worker (class in pathomx.threads)

WorkerSignals (class in pathomx.threads)