X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=05ce22dad0f52ac78d33dd49e4d3999d4fe23fb1;hb=d603dfa09e451bde0b376798f68d60c2708dd2b8;hp=105f6e48ff58ebe609b4fdbf2c2fcd72f2022daf;hpb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 105f6e4..05ce22d 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -70,7 +70,7 @@ public class AnnotationFileIOTest
     }
   }
 
-  AlignmentI readAlignmentFile(File f)
+  protected AlignmentI readAlignmentFile(File f)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -153,7 +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)
     {