diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java index 7823293..cebdfb0 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java @@ -1,10 +1,12 @@ package org.monarchinitiative.owlsim.kb.impl; -import java.time.Duration; -import java.time.Instant; -import java.util.*; -import java.util.stream.Collectors; - +import com.google.common.base.Preconditions; +import com.googlecode.javaewah.EWAHCompressedBitmap; +import com.hp.hpl.jena.query.*; +import com.hp.hpl.jena.rdf.model.Literal; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.RDFNode; +import com.hp.hpl.jena.rdf.model.Resource; import org.apache.log4j.Logger; import org.monarchinitiative.owlsim.io.OWLLoader; import org.monarchinitiative.owlsim.io.Ontology; @@ -16,49 +18,16 @@ import org.monarchinitiative.owlsim.model.kb.Entity; import org.monarchinitiative.owlsim.model.kb.KBMetadata; import org.prefixcommons.CurieUtil; -import org.semanticweb.owlapi.model.AxiomType; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLAnnotation; -import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; -import org.semanticweb.owlapi.model.OWLAnnotationProperty; -import org.semanticweb.owlapi.model.OWLAnnotationValue; -import org.semanticweb.owlapi.model.OWLClass; -import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLDataProperty; -import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom; -import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom; -import org.semanticweb.owlapi.model.OWLIndividual; -import org.semanticweb.owlapi.model.OWLIndividualAxiom; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLNamedIndividual; -import org.semanticweb.owlapi.model.OWLNamedObject; -import org.semanticweb.owlapi.model.OWLObjectComplementOf; -import org.semanticweb.owlapi.model.OWLObjectProperty; -import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; -import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLPropertyAssertionAxiom; -import org.semanticweb.owlapi.model.OWLPropertyAssertionObject; -import org.semanticweb.owlapi.model.OWLPropertyExpression; +import org.semanticweb.owlapi.model.*; import org.semanticweb.owlapi.reasoner.Node; import org.semanticweb.owlapi.reasoner.NodeSet; import org.semanticweb.owlapi.reasoner.OWLReasoner; import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; -import com.google.common.base.Preconditions; -import com.googlecode.javaewah.EWAHCompressedBitmap; -import com.hp.hpl.jena.query.Query; -import com.hp.hpl.jena.query.QueryExecution; -import com.hp.hpl.jena.query.QueryExecutionFactory; -import com.hp.hpl.jena.query.QueryFactory; -import com.hp.hpl.jena.query.QuerySolution; -import com.hp.hpl.jena.query.ResultSet; -import com.hp.hpl.jena.rdf.model.Literal; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.RDFNode; -import com.hp.hpl.jena.rdf.model.Resource; +import java.time.Duration; +import java.time.Instant; +import java.util.*; +import java.util.stream.Collectors; /** * Implementation of {@link BMKnowledgeBase} that uses the OWLAPI. @@ -435,7 +404,7 @@ private void addOpposingClassPairAsym(OWLClass c, OWLClassExpression d) { } private void storeInferences() { - + LOG.info("Storing inferences..."); // Note: if there are any nodes containing >1 class or individual, then // the store method is called redundantly. This is unlikely to affect performance, // and the semantics are unchanged @@ -1065,7 +1034,7 @@ private OWLNamedIndividual getOWLNamedIndividual(IRI iri) { * CURIE-style * @return OWLAPI Class object */ - public OWLNamedIndividual getOWLNamedIndividual(String id) { + private OWLNamedIndividual getOWLNamedIndividual(String id) { Preconditions.checkNotNull(id); //TODO: check - this is redundant code simply return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id))); will suffice if (curieUtil.getCurieMap().isEmpty()) {