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;
try
{
AlignmentI al = readAlignmentFile(f);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
assertTrue(
"Test "
+ testname
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(
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)
{