- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
- @Override
- public void run()
- {
- if (calcMan.isPending(this))
- {
- return;
- }
- calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
-
- List<AlignmentAnnotation> information = getInformationAnnotations();
- try
- {
- if ((information == null) || calcMan.isPending(this))
- {
- calcMan.workerComplete(this);
- return;
- }
- while (!calcMan.notifyWorking(this))
- {
- // System.err.println("Thread
- // (Information"+Thread.currentThread().getName()+") Waiting around.");
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
- AlignmentI alignment = alignViewport.getAlignment();
-
- int aWidth = -1;
-
- if (alignment == null || (aWidth = alignment.getWidth()) < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
-
- eraseInformation(aWidth);
- computeInformation(alignment);
- updateResultAnnotation(true);
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }