public class CommandRunner extends Object
CLIMethod
annotation, to designate the relevant methods.GafCommandRunner
,
JsCommandRunner
,
SimCommandRunner
,
SolrCommandRunner
,
TaxonCommandRunner
Modifier and Type | Class and Description |
---|---|
class |
CommandRunner.OptionException |
Modifier and Type | Field and Description |
---|---|
boolean |
exitOnException |
OWLGraphWrapper |
g |
boolean |
isDisposeReasonerOnExit |
Set<org.semanticweb.owlapi.model.OWLObject> |
owlObjectCachedSet |
protected ParserWrapper |
pw |
org.semanticweb.owlapi.model.OWLOntology |
queryOntology |
org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
String |
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
|
protected void |
exit(int code) |
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.
|
protected OWLPrettyPrinter |
getPrettyPrinter() |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
void |
jsonLdToRdf(Opts opts) |
List<String> |
parseArgString(String str) |
void |
rdfToJsonLd(Opts opts) |
void |
removeRedundantInferredSuperClassAxioms(Opts opts) |
void |
removeSubsetEntities(Opts opts) |
org.semanticweb.owlapi.model.OWLClass |
resolveClass(String id) |
List<org.semanticweb.owlapi.model.OWLClass> |
resolveClassList(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(String id) |
Set<org.semanticweb.owlapi.model.OWLObject> |
resolveEntityList(Opts opts) |
org.semanticweb.owlapi.model.OWLObjectProperty |
resolveObjectProperty(String id) |
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyList(Opts opts) |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyListAsList(Opts opts) |
void |
run(Opts opts) |
void |
run(String[] args) |
void |
runDAGCheck(Opts opts) |
void |
runSingleIteration(Opts opts) |
void |
runSingleIteration(String[] args) |
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
void |
verifyChanges(Opts opts) |
public OWLGraphWrapper g
public org.semanticweb.owlapi.model.OWLOntology queryOntology
public boolean exitOnException
public boolean isDisposeReasonerOnExit
public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
public String reasonerName
public Set<org.semanticweb.owlapi.model.OWLObject> owlObjectCachedSet
protected ParserWrapper pw
protected void exit(int code)
public void createExternalMappings(Opts opts) throws Exception
Exception
public void assertInferredSubClassAxioms(Opts opts) throws Exception
Exception
public void createPartOfLinks(Opts opts) throws Exception
opts
- 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
protected OWLPrettyPrinter getPrettyPrinter()
public void summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyList(Opts opts)
public List<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyListAsList(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(String id)
public org.semanticweb.owlapi.model.OWLObjectProperty resolveObjectProperty(String id)
public org.semanticweb.owlapi.model.OWLClass resolveClass(String id)
public void help()
public void helpFooter()
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