JAL-1191 revert to using SequenceOntologyLite due to downstream

[jalview.git] / src / jalview / io / gff / InterProScanHelper.java

diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index 3323e27..68d5d4f 100644 (file)
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -89,10 +89,11 @@ public class InterProScanHelper extends Gff3Helper
    */
   public static boolean recognises(String[] columns)
   {
-    SequenceOntology so = SequenceOntology.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     String type = columns[TYPE_COL];
-    if (so.isProteinMatch(type)
-            || (".".equals(columns[SOURCE_COL]) && so.isPolypeptide(type)))
+    if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
+            || (".".equals(columns[SOURCE_COL]) && so.isA(type,
+                    SequenceOntologyI.POLYPEPTIDE)))
     {
       return true;
     }