Dear Amyra.
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Dear Helene, and Amyra.
I was using the tool “Jalviw” to edit alignments for many weeks, but since this morning, after input an alignment, as soon as I load a features file, the tool stop runing, it deosn’t react anymore!! Could you please give me a solution.
I have worked out what the problem it and have updated the release version of Jalview with a workaround that should help you and your student. The issue is to do with the ‘Jalview java console’ which I added to version 2.5 - the console’s mutithreading is broken, and when lots of output is sent to the console (e.g. when you import a features file where lots of the features are not present in the alignement you are viewing, and jalview complains to StdOut), it becomes very slow and stops Jalview from responding.
The workaround I have implemented is to disable the console’s redirection when it is not displayed - this means that if the ‘Tools->Jalview Java Console’ entry of the desktop menu is not checked (or the console window is closed), then jalview should import your features quickly.
You can access the updated version via the ‘latest build of current release branch’ links on the versions page (http://www.jalview.org/versions.html), and the webstart link is here:
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp
Please note, this is a workaround, rather than a proper fix for the problem. I’ll hopefully have time to re-implement the console before the end of the summer!
Happy Jalviewing,
Jim.
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.