import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
-import jalview.api.AlignCalcManagerI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.util.MessageManager;
import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
*/
assertFalse(alignFrame.hideFeatureColumns("exon", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy()
- .isEmpty());
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
assertFalse(alignFrame.hideFeatureColumns("exon", false));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy()
- .isEmpty());
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
/*
* hiding a feature in all columns does nothing
*/
assertFalse(alignFrame.hideFeatureColumns("Metal", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- List<int[]> hidden = alignFrame.getViewport().getAlignment()
- .getHiddenColumns()
- .getHiddenColumnsCopy();
- assertTrue(hidden.isEmpty());
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
/*
* hide a feature present in some columns
* [1-3], [6-8] base zero
*/
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
- hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy();
- assertEquals(hidden.size(), 2);
- assertEquals(hidden.get(0)[0], 1);
- assertEquals(hidden.get(0)[1], 3);
- assertEquals(hidden.get(1)[0], 6);
- assertEquals(hidden.get(1)[1], 8);
+ Iterator<int[]> regions = alignFrame.getViewport().getAlignment()
+ .getHiddenColumns().iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 2);
+ int[] next = regions.next();
+ assertEquals(next[0], 1);
+ assertEquals(next[1], 3);
+ next = regions.next();
+ assertEquals(next[0], 6);
+ assertEquals(next[1], 8);
}
@BeforeClass(alwaysRun = true)
new String[] { "Background" }));
/*
- * make a new View, wait for Conservation thread to complete,
- * verify alignment and group colour schemes
+ * make a new View, verify alignment and group colour schemes
*/
af.newView_actionPerformed(null);
assertEquals(af.alignPanel.getViewName(), "View 1");
AlignViewport av2 = af.getViewport();
assertNotSame(av, av2);
assertSame(av2, af.alignPanel.av);
- AlignCalcManagerI calcManager = av2.getCalcManager();
- do
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException x)
- {
- }
- } while (calcManager.isWorking());
rs = av2.getResidueShading();
assertNotSame(av.getResidueShading(), rs);
assertEquals(rs.getThreshold(), 10);