jabaws alignment marked as finished when job was cancelled or job failed due to invalid input

Submitting a job that causes an alignment binary to fail after generating lots of output (e.g. submitting an RNA sequence set to Muscle and specifying the BLOSUMN matrix which does not support 'U' characters) results in the job completing with a 'Success' status, but no alignment is displayed.

A related problem was that cancelling a job did not result in it being marked as cancelled. The problem seems to be that the job status is not being updated faithfully after the final call to cancelJob or parseResult.