*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.AlignmentViewport;
import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+@Test(singleThreaded = true)
public class Jalview2xmlTests
{
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
}
- public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+ int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
int numdsann = 0;
for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
}
+ /**
+ * Test save and reload of a project with a different representative sequence
+ * in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverReferenceSeqSettings() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ /*
+ * remember representative and hidden sequences marked
+ * on each panel
+ */
+ Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+
+ /*
+ * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+ * as reference sequence for itself and the preceding sequence
+ */
+ int n = 1;
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ int repIndex = n % alignment.getHeight();
+ SequenceI rep = alignment.getSequenceAt(repIndex);
+ refseqs.put(ap.getViewName(), rep);
+ List<String> hiddenNames = new ArrayList<String>();
+ hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+
+ /*
+ * hide rep sequence and the one before it
+ */
+ SequenceI seqToHide = alignment.getSequenceAt(repIndex);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqToHide, false);
+ SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+ sg.addSequence(precedingSeq, false);
+ av.setSelectionGroup(sg);
+ ((AlignmentViewport) av).hideSequences(seqToHide, true);
+
+ /*
+ * record names of hidden sequences
+ */
+ HiddenSequences hs = alignment.getHiddenSequences();
+ for (SequenceI seq : hs.hiddenSequences)
+ {
+ if (seq != null)
+ {
+ hiddenNames.add(seq.getName());
+ }
+ }
+ // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
+ // todo refactor this to an alignment view controller
+ av.setDisplayReferenceSeq(true);
+ av.setColourByReferenceSeq(true);
+ av.getAlignment().setSeqrep(rep);
+
+ n++;
+ }
+ File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ // check representative
+ AlignmentI alignment = ap.getAlignment();
+ SequenceI rep = alignment.getSeqrep();
+ Assert.assertNotNull(rep,
+ "Couldn't restore sequence representative from project");
+ // can't use a strong equals here, because by definition, the sequence IDs
+ // will be different.
+ // could set vamsas session save/restore flag to preserve IDs across
+ // load/saves.
+ Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
+ rep.toString(),
+ "Representative wasn't the same when recovered.");
+ Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
+ "Display reference sequence view setting not set.");
+ Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
+ "Colour By Reference Seq view setting not set.");
+
+ /*
+ * verify hidden sequences in restored panel
+ */
+ List<String> hidden = hiddenSeqNames.get(ap.getViewName());
+ HiddenSequences hs = alignment.getHiddenSequences();
+ assertEquals(
+ "wrong number of restored hidden sequences in "
+ + ap.getViewName(),
+ hidden.size(), hs.getSize());
+ }
+ }
+
@Test(groups = { "Functional" })
public void testIsVersionStringLaterThan()
{