X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;fp=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=784229460e1320e576af3a657d800b5649336097;hb=4de7ee98ddea4e7aa9fbe71da003adb8bc19136a;hp=0d631e66ee3ed0c3124eb5f69f63d8a5f521f5f0;hpb=011b6facdd2bc4e179d95833613a39d0778b5681;p=jalview.git

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 0d631e6..7842294 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.so;
 
+import jalview.datamodel.ontology.OntologyBase;
 import jalview.io.gff.SequenceOntologyI;
 
 import java.io.BufferedInputStream;
@@ -48,7 +49,8 @@ import org.biojava.nbio.ontology.utils.Annotation;
  * 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
@@ -82,10 +84,10 @@ public class SequenceOntology implements SequenceOntologyI
    */
   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");
   }
@@ -404,7 +406,7 @@ public class SequenceOntology implements SequenceOntologyI
    */
   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();