- // .updatingConservation = false;
- // AlignViewport.UPDATING_CONSERVATION = false;
-
- return;
- }
- consensus = alignViewport
- .getAlignmentConsensusAnnotation();
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
- hconsensus = new Hashtable[aWidth];
- try {
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hconsensus, true);
- } catch (ArrayIndexOutOfBoundsException x){
- // this happens due to a race condition -
- // alignment was edited at same time as calculation was running
- //
-// calcMan.workerCannotRun(this);
- calcMan.workerComplete(this);