Hi Jean.
just experienced again th problem... after setting my preferences using the preferrence menu... it seems that if I do not check to check "Show Annotation" and at least one of the 3 option (did not check yet but displaying the quality it works then)
great. This was what I thought was going on - all my changes to 2.5 were very 'annotation oriented' - and I guess I just didn't think of testing it with no annotation being displayed at all. 
ok as I am testing now and updating this email, I have tried to navigate trhough the alignment the display seems to be deconnected... moving horizontally or vertically does not change the sequences shown only the top positions... but when cliking in the sequences panel then it goes to the right position... that is really weird...
That's exactly what I observed. What's happening is that the area of the display responsible for rendering the sequence alignment isn't being updated when the scroll bars move - because of something breaking when the window is created from the Jar file. The new view is created properly, so it works as you'd expect.
[Update]
loaded tha same alignment saved a couple of days ago in fasta format and scrolling is smooth... I have both .jar and .fasta opened in the same jalview installed (upadted Java and resintalled everything). Something seems weird using the .jar format.
yes. its a bug (sigh) - I know what's going on, but i wont have time to fix it till next week.
While you are looking at this issue that seems tricky, if one wants to use annotation is there any ways than using the .jar to save the annotations?
The sequence annotation can be exported as GFF or a Jalview specific features file (which also preserves the colours and display ordering). File -> export features will do this.
The annotation tracks below the alignment get saved as annotation files - again, look at the filemenu for this.
I stop now my complains
Thanks for being persistent! This is a serious bug -the whole point of the project file is it saves everything as you left it, and it should be compatible with all later versions. You've done a great job in isolating the problem!
Jim.
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On 26/05/2010 22:17, Jean Muller wrote:
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
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