*/
package jalview.ext.so;
+import jalview.datamodel.ontology.OntologyBase;
import jalview.io.gff.SequenceOntologyI;
import java.io.BufferedInputStream;
* A wrapper class that parses the Sequence Ontology and exposes useful access
* methods. This version uses the BioJava parser.
*/
-public class SequenceOntology implements SequenceOntologyI
+public class SequenceOntology extends OntologyBase
+ implements SequenceOntologyI
{
/*
* the parsed Ontology data as modelled by BioJava
*/
public SequenceOntology()
{
- termsFound = new ArrayList<String>();
- termsNotFound = new ArrayList<String>();
- termsByDescription = new HashMap<String, Term>();
- termIsA = new HashMap<Term, List<Term>>();
+ termsFound = new ArrayList<>();
+ termsNotFound = new ArrayList<>();
+ termsByDescription = new HashMap<>();
+ termIsA = new HashMap<>();
loadOntologyZipFile("so-xp-simple.obo");
}
*/
protected synchronized void findParents(Term childTerm)
{
- List<Term> result = new ArrayList<Term>();
+ List<Term> result = new ArrayList<>();
for (Triple triple : ontology.getTriples(childTerm, null, isA))
{
Term parent = triple.getObject();