import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignViewportI;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
public class AlignViewportTest
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-nonews", "-props",
+ Jalview.main(new String[] {
+ //"-jabaws", "none",
+ "-nonews", "-props",
"test/jalview/testProps.jvprops" });
/*
* remove any sequence mappings left lying around by other tests
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
}
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
assertEquals(2, sequenceMappings.size());
assertTrue(sequenceMappings.contains(acf1));
@Test(groups = { "Functional" })
public void testDeregisterMapping_withNoReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave("SHOW_QUALITY",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+ Cache.setPropertyNoSave("SHOW_OCCUPANCY",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+ /*
+ * wait for Conservation thread to complete
+ */
+ AlignViewport viewport = af.getViewport();
+ waitForCalculations(viewport);
+ AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
assertTrue("No quality value in column 1", annotations[0].value > 10f);
}
+ /**
+ * Wait for consensus etc calculation threads to complete
+ *
+ * @param viewport
+ */
+ protected void waitForCalculations(AlignViewport viewport)
+ {
+ synchronized (this)
+ {
+ System.out.print("waiting...");
+ int n = 3;
+ while (--n >= 0 || viewport.getCalcManager().isWorking())
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ System.out.println("...done");
+ }
+ }
+
@Test(groups = { "Functional" })
public void testSetGlobalColourScheme()
{
/*
* test for JAL-2283: don't inadvertently turn on colour by conservation
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
ColourSchemeI cs = new PIDColourScheme();
- af.getViewport().setGlobalColourScheme(cs);
- assertFalse(af.getViewport().getResidueShading()
+ AlignViewport viewport = af.getViewport();
+ viewport.setGlobalColourScheme(cs);
+ assertFalse(viewport.getResidueShading()
.conservationApplied());
+
+ /*
+ * JAL-3201 groups have their own ColourSchemeI instances
+ */
+ AlignmentI aln = viewport.getAlignment();
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(aln.getSequenceAt(0), false);
+ sg1.addSequence(aln.getSequenceAt(2), false);
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(aln.getSequenceAt(1), false);
+ sg2.addSequence(aln.getSequenceAt(3), false);
+ aln.addGroup(sg1);
+ aln.addGroup(sg2);
+ viewport.setColourAppliesToAllGroups(true);
+ viewport.setGlobalColourScheme(new ClustalxColourScheme());
+ ColourSchemeI cs0 = viewport.getGlobalColourScheme();
+ ColourSchemeI cs1 = sg1.getColourScheme();
+ ColourSchemeI cs2 = sg2.getColourScheme();
+ assertTrue(cs0 instanceof ClustalxColourScheme);
+ assertTrue(cs1 instanceof ClustalxColourScheme);
+ assertTrue(cs2 instanceof ClustalxColourScheme);
+ assertNotSame(cs0, cs1);
+ assertNotSame(cs0, cs2);
+ assertNotSame(cs1, cs2);
}
@Test(groups = { "Functional" })
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewportI av = af.getViewport();
- Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
+ Assert.assertNull(av.getAlignmentGapAnnotation(),
+ "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getOccupancyAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getAlignmentGapAnnotation(),
+ "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
- null, av.getOccupancyAnnotation().label))
+ null, av.getAlignmentGapAnnotation().label))
{
c++;
}
String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
DataSourceType.PASTE);
- AlignmentViewport testme = af.getViewport();
+ AlignViewport testme = af.getViewport();
+ waitForCalculations(testme);
SequenceI cons = testme.getConsensusSeq();
- assertEquals("A-C", cons.getSequenceAsString());
+ String s = cons.getSequenceAsString();
+ System.out.println("s is " + s);
+
+ assertEquals("A-C", s);
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / blobdiff