Hi. This is a known issue - please join issues.Jalview.org and check our bug tracker about this. Also, given that you plan to use a groovy script to achieve functionality to need, you can also modify the title directly from your script.
J. B. Procter Jalview/enfin Barton group
Is there a way with Jalview 2.6.1 to change the title of an alignment
window that displays sequence loaded from a URL?
We launch Jalview as a JWS app passing the URL as the value for the
“open” argument. The correct window is opened but the title has the
sequence URL which tends to be so long it can’t be completely
Please see attached screen shot for an example.
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy