/*
* remove any sequence mappings left lying around by other tests
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance());
- ssm.resetAll();
+ Desktop.getStructureSelectionManager().resetAll();
}
@BeforeMethod(alwaysRun = true)
* Verify that creating the alignment for the new View has registered the
* mappings
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance());
- List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+ List<AlignedCodonFrame> sequenceMappings = Desktop.getInstance()
+ .getStructureSelectionManager().getSequenceMappings();
assertEquals(2, sequenceMappings.size());
assertTrue(sequenceMappings.contains(acf1));
assertTrue(sequenceMappings.contains(acf2));
{
Desktop d = Desktop.getInstance();
assertNotNull(d);
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance());
+ StructureSelectionManager ssm = Desktop.getInstance()
+ .getStructureSelectionManager();
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
{
Desktop d = Desktop.getInstance();
assertNotNull(d);
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance());
+ StructureSelectionManager ssm = Desktop.getInstance()
+ .getStructureSelectionManager();
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" }, timeOut=2000)
+ @Test(groups = { "Functional" }, timeOut = 2000)
public void testUpdateConservation_qualityOnly()
{
Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.setPropertyNoSave("SHOW_QUALITY",
+ Cache.setPropertyNoSave(Preferences.SHOW_QUALITY,
Boolean.TRUE.toString());
Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
AlignViewport viewport = af.getViewport();
synchronized (this)
{
+ // System.out.println("AVT consv: "
+ // + viewport.getAlignmentConservationAnnotation());
+ try
+ {
+ wait(250); // BH increased from 50 -- was getting Quality in column 1
+ // is null
+ } catch (InterruptedException e)
+ {
+ }
+ // System.out.println("AVT consv: "
+ // + viewport.getAlignmentConservationAnnotation());
while (viewport.getAlignmentConservationAnnotation() != null)
{
try
{
- wait(50);
+ wait(250); // BH increased from 50 -- was getting Quality in column 1
+ // is null
} catch (InterruptedException e)
{
}
}
}
+ af.paintImmediately(af.getBounds());
AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
{
c++;
}
- ;
Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
}
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);
+ synchronized (this)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ // af.paintImmediately(af.getBounds());
AlignViewport testme = af.getViewport();
SequenceI cons = testme.getConsensusSeq();
+ // System.out.println("AVT " + cons.getSequenceAsString());
assertEquals("A-C", cons.getSequenceAsString());
}