Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

diff --combined test/jalview/io/AnnotationFileIOTest.java
index 105f6e4,62bd0b9..6a00cde
--- 1/test/jalview/io/AnnotationFileIOTest.java
--- 2/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@@ -24,7 -24,7 +24,7 @@@ import static org.testng.AssertJUnit.as
  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 +115,7 @@@ public class AnnotationFileIOTes
      try
      {
        AlignmentI al = readAlignmentFile(f);
 -      ColumnSelection cs = new ColumnSelection();
 +      HiddenColumns cs = new HiddenColumns();
        assertTrue(
                "Test "
                        + testname
@@@ -153,7 -153,8 +153,8 @@@
                        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)
      {