X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=6a00cde06026f67122a8e062fe8ee8ceccd9ddf1;hb=613818a08b858e3fe0dd778c738a362b3a4a0882;hp=c3a1801377857729f76389f0333e3b94a03b526f;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index c3a1801..6a00cde 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -124,6 +124,7 @@ public class AnnotationFileIOTest
                       DataSourceType.FILE));
 
       AnnotationFile aff = new AnnotationFile();
+      // ViewDef is not used by Jalview
       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
               new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
@@ -152,7 +153,8 @@ public class AnnotationFileIOTest
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {