Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2

[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..e1334e1 100644 (file)
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignmentI;
@@ -89,10 +109,11 @@ 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;
     }