Index (ODK ROBOT plugin 0.1.1-SNAPSHOT API)

B

BasePlugin - Class in org.incenp.obofoundry.odk: Helper base class for ROBOT commands.
BasePlugin(String, String, String) - Constructor for class org.incenp.obofoundry.odk.BasePlugin: Creates a new command.

COB_IRI - Static variable in class org.incenp.obofoundry.odk.Constants
Constants - Class in org.incenp.obofoundry.odk: Constant values used throughout the plugin.
Constants() - Constructor for class org.incenp.obofoundry.odk.Constants

excludePrefix(String) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Excludes classes within the given namespace when filling gaps.
execute(CommandState, String[]) - Method in class org.incenp.obofoundry.odk.BasePlugin

followProperty(IRI) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Adds an object property to follow when filling gaps.

getDescription() - Method in class org.incenp.obofoundry.odk.BasePlugin
getIRI(String, String) - Method in class org.incenp.obofoundry.odk.BasePlugin: Creates an IRI from a user-specified source.
getName() - Method in class org.incenp.obofoundry.odk.BasePlugin
getOptions() - Method in class org.incenp.obofoundry.odk.BasePlugin
getSubset(String) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Gets the list of classes that are marked as belonging to a given subset, where the subset is identified by a simple name.
getSubset(IRI) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Gets the list of classes that are marked as belonging to a given subset.
getSubset(IRI, OWLAnnotationProperty) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Gets the list of classes that are marked as belonging to a given subset.
getUsage() - Method in class org.incenp.obofoundry.odk.BasePlugin

HAS_SYNONYM_TYPE - Static variable in class org.incenp.obofoundry.odk.Constants

IN_SUBSET - Static variable in class org.incenp.obofoundry.odk.Constants
includeImports(boolean) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Includes or excludes axioms from imported ontologies.
includePrefix(String) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Only include classes within the given namespace when filling gaps.
injectDeclarations(OWLOntology, Set<String>, boolean, boolean) - Static method in class org.incenp.obofoundry.odk.NormalizeCommand: Inject SubAnnotationPropertyOf axioms for IRIs representing subsets or synonyms.
ioHelper - Variable in class org.incenp.obofoundry.odk.BasePlugin
isDangling(OWLOntology, OWLClass) - Static method in class org.incenp.obofoundry.odk.Util: Checks whether a class is dangling.
isObsolete(OWLOntology, OWLClass) - Static method in class org.incenp.obofoundry.odk.Util: Checks whether a class is marked as obsolete.

main(String[]) - Method in class org.incenp.obofoundry.odk.BasePlugin
main(String[]) - Static method in class org.incenp.obofoundry.odk.StandaloneRobot
makeSubset(Set<OWLClass>) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Creates a subset of the ontology.
mergeAxioms(OWLOntology) - Static method in class org.incenp.obofoundry.odk.NormalizeCommand: Merges all logically equivalent axioms in the given ontology.

NormalizeCommand - Class in org.incenp.obofoundry.odk: A command to perform various “normalisation” operations on an ontology.
NormalizeCommand() - Constructor for class org.incenp.obofoundry.odk.NormalizeCommand

performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.odk.BasePlugin: Performs whatever operation the command is supposed to do.
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.odk.NormalizeCommand
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.odk.SubsetCommand
performOperation(CommandState, CommandLine) - Method in class org.incenp.obofoundry.odk.ValidateCommand

readFile(String) - Method in class org.incenp.obofoundry.odk.BasePlugin: Reads a file and gets its contents as a set, one entry per line, excluding any blank line and lines starting with a '#' character.
readFileAsIRIs(String) - Method in class org.incenp.obofoundry.odk.BasePlugin: Reads a file and gets its contents as a set of IRIs, assuming one IRI per line, excluding any blank line and lines starting with a '#' character.

setExcludeDangling(boolean) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Enables or disables excluding dangling classes.
setFillGaps(boolean) - Method in class org.incenp.obofoundry.odk.SubsetExtractor: Enables or disables gap filling.
StandaloneRobot - Class in org.incenp.obofoundry.odk: This class provides a version of ROBOT that includes the commands from the ODK plugin as if they were built-in commands, prefixed with odk:.
StandaloneRobot() - Constructor for class org.incenp.obofoundry.odk.StandaloneRobot
SUBSET_PROPERTY - Static variable in class org.incenp.obofoundry.odk.Constants
SubsetCommand - Class in org.incenp.obofoundry.odk: A command to create an ontology subset.
SubsetCommand() - Constructor for class org.incenp.obofoundry.odk.SubsetCommand
SubsetExtractor - Class in org.incenp.obofoundry.odk: A helper class to extract subsets from an ontology.
SubsetExtractor(OWLOntology, OWLReasoner) - Constructor for class org.incenp.obofoundry.odk.SubsetExtractor: Creates a new instance.
SYNONYM_TYPE_PROPERTY - Static variable in class org.incenp.obofoundry.odk.Constants

Util - Class in org.incenp.obofoundry.odk: Helper methods used throughout the plugin.
Util() - Constructor for class org.incenp.obofoundry.odk.Util

ValidateCommand - Class in org.incenp.obofoundry.odk: A command to check the alignment of an ontology against another, upper-level ontology.
ValidateCommand() - Constructor for class org.incenp.obofoundry.odk.ValidateCommand