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Added a method to list all superclasses #15

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merged 1 commit into from Dec 10, 2015
Merged

Added a method to list all superclasses #15

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9 changes: 9 additions & 0 deletions plugins/net.bioclipse.owlapi/src/net/bioclipse/owlapi/business/IOWLAPIManager.java
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Expand Up @@ -14,6 +14,7 @@
import java.util.Collection;

import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IProgressMonitor;
import org.semanticweb.owlapi.model.OWLOntology;

import net.bioclipse.core.PublishedClass;
Expand Down Expand Up @@ -88,6 +89,14 @@ public Collection<String> getAnnotationProperties(OWLOntology ontology)
public Collection<String> getClasses(OWLOntology ontology)
throws IOException, BioclipseException, CoreException;

@Recorded
@PublishedMethod(
params = "OWLOntology ontology, String classIRI",
methodSummary = "Returns the (non-asserted) OWL super classes as a collection of String's."
)
public Collection<String> getSuperClasses(OWLOntology ontology, String classIRI)
throws IOException, BioclipseException, CoreException;

@Recorded
@PublishedMethod(
params = "OWLOntology ontology",
Expand Down
35 changes: 35 additions & 0 deletions plugins/net.bioclipse.owlapi/src/net/bioclipse/owlapi/business/OWLAPIManager.java
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Expand Up @@ -12,6 +12,7 @@
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
Expand All @@ -27,6 +28,7 @@
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
Expand All @@ -37,11 +39,13 @@
import org.semanticweb.owlapi.profiles.OWLProfileReport;
import org.semanticweb.owlapi.profiles.OWLProfileViolation;
import org.semanticweb.owlapi.search.EntitySearcher;
import org.semanticweb.owlapi.search.Searcher;
import org.semanticweb.owlapi.util.SimpleIRIMapper;

import net.bioclipse.business.BioclipsePlatformManager;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.managers.business.IBioclipseManager;
import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;

public class OWLAPIManager implements IBioclipseManager {

Expand Down Expand Up @@ -161,6 +165,37 @@ public Collection<String> getClasses(OWLOntology ontology, IProgressMonitor moni
return list;
}

public Collection<String> getSuperClasses(OWLOntology ontology, String clazz, IProgressMonitor monitor)
throws IOException, BioclipseException, CoreException {
if (monitor == null) monitor = new NullProgressMonitor();

Set<String> allSuperClasses = new HashSet<String>();
Set<OWLEntity> entities = ontology.getEntitiesInSignature(IRI.create(clazz));
if (entities.isEmpty()) {
// recurse, maybe it's there
for (OWLOntology importedOntology : ontology.getImports()) {
Collection<String> subList = getSuperClasses(importedOntology, clazz, monitor);
allSuperClasses.addAll(subList);
}
} else {
if (entities.size() > 1)
throw new BioclipseException("More than one entity found with this IRI.");
OWLEntity entity = entities.iterator().next(); // there is exactly one
if (!(entity instanceof OWLClass))
throw new BioclipseException("The IRI is not of an OWLClass in this ontology, but an " + entity.getEntityType());
OWLClass owlClazz = new OWLClassImpl(IRI.create(clazz));
Collection<OWLClassExpression> superClasses = Searcher.sup(ontology.getSubClassAxiomsForSubClass(owlClazz));
for (OWLClassExpression superClass : superClasses) {
OWLClass superOwlClass = superClass.asOWLClass();
String superIri = superOwlClass.getIRI().toString();
allSuperClasses.add(superIri);
// recurse
allSuperClasses.addAll(getSuperClasses(ontology, superIri, monitor));
}
}
return allSuperClasses;
}

public Collection<OWLAnnotationProperty> getAllAnnotationProperties(OWLOntology ontology, IProgressMonitor monitor)
throws IOException, BioclipseException, CoreException {
if (monitor == null) monitor = new NullProgressMonitor();
Expand Down