Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

[jalview.git] / test / jalview / io / AnnotationFileIOTest.java

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index c3aa13e..05ce22d 100644 (file)
--- 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;
 
@@ -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();
@@ -115,7 +115,7 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      ColumnSelection cs = new ColumnSelection();
+      HiddenColumns cs = new HiddenColumns();
       assertTrue(
               "Test "
                       + testname
@@ -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)
     {