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;
import java.io.File;
import java.util.Hashtable;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String TestFiles[][] = {
{ "Test example annotation import/export", "examples/uniref50.fa",
"examples/testdata/example_annot_file.jva" },
}
}
- public static AlignmentI readAlignmentFile(File f)
+ AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
{
- al.getSequenceAt(i).setDatasetSequence(
- al.getSequenceAt(i).createDatasetSequence());
+ al.getSequenceAt(i).createDatasetSequence();
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
* - label for IO class used to write and read back in the data from
* f
*/
-
- // @Test(groups ={ "Functional" })
- public static void testAnnotationFileIO(String testname, File f,
+ void testAnnotationFileIO(String testname, File f,
File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
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)
{