public class CommandRunner extends CommandRunnerBase
CLIMethod
annotation, to designate the relevant methods.GafCommandRunner
,
JsCommandRunner
,
SimCommandRunner
,
SolrCommandRunner
,
TaxonCommandRunner
CommandRunnerBase.OptionException
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
---|
CommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
assertAboxInferences(Opts opts) |
void |
assertInferredSubClassAxioms(Opts opts) |
void |
createBioChebi(Opts opts) |
void |
createExternalMappings(Opts opts) |
void |
createPartOfLinks(Opts opts)
GeneOntology specific function to create links between molecular
functions and their corresponding processes.
|
void |
createSlim(Opts opts) |
void |
createSubsetTags(Opts opts)
Simple helper to create a subset tag for matching entities, allows to specify exceptions
|
void |
extractAnnotationValue(Opts opts) |
void |
extractExtensionFile(Opts opts)
Extract all xps (
OWLEquivalentClassesAxiom ) from the loaded
ontology. |
void |
filterExtensionFile(Opts opts)
Retain only subclass of axioms and intersection of axioms if they contain
a class in it's signature of a given set of parent terms.
|
void |
removeRedundantInferredSuperClassAxioms(Opts opts) |
void |
removeRedundantInferredSVFs(Opts opts) |
void |
removeRedundantSubclasses(Opts opts) |
void |
removeRedundantSVFs(Opts opts) |
void |
removeSubsetEntities(Opts opts) |
void |
runDAGCheck(Opts opts) |
void |
runSingleIteration(Opts opts) |
void |
verifyChanges(Opts opts) |
exit, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, printVersion, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runSingleIteration, summarizeOntology
public void createExternalMappings(Opts opts) throws Exception
Exception
public void assertInferredSubClassAxioms(Opts opts) throws Exception
Exception
public void removeRedundantSubclasses(Opts opts) throws Exception
Exception
public void createPartOfLinks(Opts opts) throws Exception
opts
- Exception
public void removeRedundantInferredSVFs(Opts opts) throws Exception
Exception
public void removeRedundantInferredSuperClassAxioms(Opts opts) throws Exception
Exception
public void createSubsetTags(Opts opts) throws Exception
opts
- Exception
public void extractAnnotationValue(Opts opts) throws Exception
Exception
public void extractExtensionFile(Opts opts) throws Exception
OWLEquivalentClassesAxiom
) from the loaded
ontology. Requires a set of roots classes to restrict the set of
extracted xps.opts
- Exception
public void filterExtensionFile(Opts opts) throws Exception
opts
- Exception
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