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1   /*
2    * The baseCode project
3    *
4    * Copyright (c) 2007-2019 University of British Columbia
5    *
6    * Licensed under the Apache License, Version 2.0 (the "License");
7    * you may not use this file except in compliance with the License.
8    * You may obtain a copy of the License at
9    *
10   *       http://www.apache.org/licenses/LICENSE-2.0
11   *
12   * Unless required by applicable law or agreed to in writing, software
13   * distributed under the License is distributed on an "AS IS" BASIS,
14   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15   * See the License for the specific language governing permissions and
16   * limitations under the License.
17   *
18   */
19  package ubic.basecode.ontology.jena;
20  
21  import com.hp.hpl.jena.enhanced.EnhGraph;
22  import com.hp.hpl.jena.enhanced.GraphPersonality;
23  import com.hp.hpl.jena.ontology.Individual;
24  import com.hp.hpl.jena.ontology.OntClass;
25  import com.hp.hpl.jena.ontology.Restriction;
26  import com.hp.hpl.jena.ontology.impl.OntClassImpl;
27  import com.hp.hpl.jena.rdf.model.Resource;
28  import ubic.basecode.ontology.model.OntologyIndividual;
29  import ubic.basecode.ontology.model.OntologyTerm;
30  
31  import java.util.Set;
32  
33  /**
34   * @author pavlidis
35   */
36  class OntologyIndividualImpl extends AbstractOntologyResource implements OntologyIndividual {
37  
38      private final Individual ind;
39      private final Set<Restriction> additionalRestrictions;
40  
41      public OntologyIndividualImpl( Individual ind, Set<Restriction> additionalRestrictions ) {
42          super( ind );
43          this.ind = ind;
44          this.additionalRestrictions = additionalRestrictions;
45      }
46  
47      public OntologyIndividualImpl( Individual ind, Set<Restriction> additionalRestrictions, double score ) {
48          super( ind, score );
49          this.ind = ind;
50          this.additionalRestrictions = additionalRestrictions;
51      }
52  
53      @Override
54      public OntologyTerm getInstanceOf() {
55          Resource type = ind.getRDFType();
56  
57          OntClass cl;
58          EnhGraph g = new EnhGraph( type.getModel().getGraph(), new GraphPersonality() );
59          if ( OntClassImpl.factory.canWrap( type.asNode(), g ) ) {
60              cl = new OntClassImpl( type.asNode(), g );
61          } else {
62              throw new IllegalStateException( "sorry, can't handle that of instance" );
63          }
64  
65          return new OntologyTermImpl( cl, additionalRestrictions );
66      }
67  }