Merge branch 'Jalview-JS/develop' into merge_js_develop

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index fd8800f..11f8b7b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -732,7 +732,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * for sequence_variant on reverse strand, have to convert the allele
        * values to their complements
        */
-      if (!forwardStrand && SequenceOntologyFactory.getInstance()
+      if (!forwardStrand && SequenceOntologyFactory.getSequenceOntology()
               .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
       {
         reverseComplementAlleles(copy);
@@ -966,7 +966,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   public static boolean isTranscript(String featureType)
   {
     return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
-            || SequenceOntologyFactory.getInstance().isA(featureType,
+            || SequenceOntologyFactory.getSequenceOntology().isA(featureType,
                     SequenceOntologyI.TRANSCRIPT);
   }
 }