[Jalview-discuss] rearranging sequences not working correctly

[Jim Procter]

Danny Rice wrote:
> When  I open a fasta file like:
>
> $JAVA -Djava.ext.dirs=$JALVIEW_HOME/lib -cp $JALVIEW_HOME/jalview.jar 
> jalview.bin.Jalview -open $file
>
> and click on the sequence name I can't move the sequence up or down with 
> the arrow keys.  If I go to Tools->Preferences and then Cancel I am then 
> able to move the sequence with the arrow keys.  I have noticed this on 
> all versions I have tried and also on the current version I just 
> installed yesterday.  I am using the Linux version and am using the jre 
> provided with Jalview.
>   
There may be a couple of issues here. Occasionally, the GoogleAnalytics
usage tracking dialog box and the Jalview splash screen 'interact' -
leaving the desktop window without input focus. I found that if you
respond to the prompt (rather than cancel it), and then quit (using the
dropdown menu) and restart Jalview, the Desktop window should behave
normally (ie. you can select seuqences and move them up/down). You could
also provide the -nousage option to prevent the dialog box launching.

If you find you get the same problem as me - and can't even click on the
menu items, then try starting Jalview via the -jar parameter:

$JAVA -Djava.ext.dirs=$JALVIEW_HOME/lib -jar $JALVIEW_HOME/jalview.jar 
-open $file

This really shouldn't make any difference, but for some reason it did in
my case (it may have been simply luck that the input focus race
condition described above didn't happen). let me know what
architecture/distro you are running if you are still having problems.

Jim.