@Override
public void run()
{
- if (calcMan.isPending(this))
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ AlignmentAnnotation gap = getGapAnnotation();
+ if ((consensus == null && gap == null))
{
return;
}
- calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
- try
+ if (alignViewport.isClosed())
{
- AlignmentAnnotation consensus = getConsensusAnnotation();
- AlignmentAnnotation gap = getOccupancyAnnotation();
- if ((consensus == null && gap == null) || calcMan.isPending(this))
- {
- calcMan.workerComplete(this);
- return;
- }
- while (!calcMan.notifyWorking(this))
- {
- // System.err.println("Thread
- // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false, false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
- AlignmentI alignment = alignViewport.getAlignment();
+ abortAndDestroy();
+ return;
+ }
+ AlignmentI alignment = alignViewport.getAlignment();
- int aWidth = -1;
+ int aWidth = -1;
- if (alignment == null || (aWidth = alignment.getWidth()) < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
+ if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+ {
+ return;
+ }
- eraseConsensus(aWidth);
- computeConsensus(alignment);
- updateResultAnnotation(true);
+ eraseConsensus(aWidth);
+ computeConsensus(alignment);
+ updateResultAnnotation(true);
- if (ap != null)
- {
- ap.paintAlignment(true, true);
- }
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
- ap.raiseOOMWarning("calculating consensus", error);
- } finally
+ if (ap != null)
{
- /*
- * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
- * - alignment was edited at same time as calculation was running
- */
- calcMan.workerComplete(this);
+ ap.paintAlignment(true, true);
}
}
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- consensus.annotations = new Annotation[aWidth];
- AlignmentAnnotation gap = getOccupancyAnnotation();
+ if (consensus != null)
+ {
+ consensus.annotations = new Annotation[aWidth];
+ }
+ AlignmentAnnotation gap = getGapAnnotation();
if (gap != null)
{
gap.annotations = new Annotation[aWidth];
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
- alignViewport.setConsensusProfiles(hconsensus);
+ alignViewport.setSequenceConsensusHash(hconsensus);
setColourSchemeConsensus(hconsensus);
}
*
* @return
*/
- protected AlignmentAnnotation getOccupancyAnnotation()
+ protected AlignmentAnnotation getGapAnnotation()
{
- return alignViewport.getOccupancyAnnotation();
+ return alignViewport.getAlignmentGapAnnotation();
}
/**
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
- AlignmentAnnotation occupancy = getOccupancyAnnotation();
- if (occupancy != null)
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
{
- deriveOccupancy(occupancy, hconsensus);
+ deriveGap(gap, hconsensus);
}
}
}
* @param hconsensus
* the computed consensus data
*/
- protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
+ protected void deriveGap(AlignmentAnnotation gapAnnotation,
ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
+ AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
- return alignViewport.getConsensusProfiles();
+ return alignViewport.getSequenceConsensusHash();
}
}