X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;fp=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=806e4dc5c4b9c6a1953d61061c0c8ac6239b60f9;hb=de75573aa38c4b40686256d4332c3a069b6a98ca;hp=3bf09528fe842c2c515edf7acdd13f3c39392679;hpb=a6c05e6488b5acb43d0ad3aeced88c2dcbe83a4c;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 3bf0952..806e4dc 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -119,7 +119,7 @@ public class StockholmFileTest
               "Identify routine could not recognise output generated by '"
                       + ioformat + "' writer",
               ioformat.equals(identifyoutput));
-      testAlignmentEquivalence(al, al_input);
+      testAlignmentEquivalence(al, al_input, false);
       int numaliannot = 0, numsqswithali = 0;
       for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
       {
@@ -157,9 +157,11 @@ public class StockholmFileTest
    * @param al_input
    *          'secondary' or generated alignment from some datapreserving
    *          transformation
+   * @param ignoreFeatures
+   *          when true, differences in seuqence feature annotation are ignored.
    */
   public static void testAlignmentEquivalence(AlignmentI al,
-          AlignmentI al_input)
+          AlignmentI al_input, boolean ignoreFeatures)
   {
     assertNotNull("Original alignment was null", al);
     assertNotNull("Generated alignment was null", al_input);
@@ -261,8 +263,10 @@ public class StockholmFileTest
                   + " are not equal", ss_original.equals(ss_new));
 
           assertTrue(
-                  "Sequence Features were not equivalent",
-                  (seq_original[i].getSequenceFeatures() == null && seq_new[in]
+                  "Sequence Features were not equivalent"
+                          + (ignoreFeatures ? " ignoring." : ""),
+                  ignoreFeatures
+                          || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
                           .getSequenceFeatures() == null)
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));