X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=6a00cde06026f67122a8e062fe8ee8ceccd9ddf1;hb=e3aa01ef27f11521dc4ff724055b5ab3d4ad1d25;hp=885c6736752b47ee51da89ad735855c90f04de0a;hpb=b0832234b2a89510d715951d94ae213e449ca6b2;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 885c673..6a00cde 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -24,7 +24,7 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile.ViewDef;
 
@@ -115,7 +115,7 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      ColumnSelection cs = new ColumnSelection();
+      HiddenColumns cs = new HiddenColumns();
       assertTrue(
               "Test "
                       + testname
@@ -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)
     {