JAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 41538eb..34eaa60 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -34,7 +34,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -1435,7 +1436,7 @@ public class AlignmentUtils
       copyTo = copyTo.getDatasetSequence();
     }
 
-    SequenceOntology so = SequenceOntology.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     int count = 0;
     SequenceFeature[] sfs = fromSeq.getSequenceFeatures();
     if (sfs != null)