* 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) // BH removed 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);
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());
}