cannot export visible columns of alignment with sequence associated annotation

Reported by Rodrigo Quiroga on jalview-discuss, April 13th 2009

rquiroga@fcq.unc.edu.ar wrote:
> > Greetings,
> >
> > I am having trouble saving only the visible columns of an alignment,
> > since no file is actually created (if I try output to textbox, and
> > select to only save visible columns I get an empty textbox).
> >
> > If I save all columns, everything works.
> >
> > The weird thing is that I have used Jalview to save only visible
> > columns before, and it used to work. I am sure it isn´t a problem with
> > my alignment file (an aligned FASTA file), have tried multiple inputs
> > with no success.
> >

****** ADDITIONAL INFORMATION ******

Fixed in 2.4 patch build on 14th April 2009. Additional workarounds also provided below:

Hello Rodrigo.

Thanks for your email - the error you posted unveiled a tiny but
annoying bug in jalview 2.4 that most often emerges when you have
sequence associated annotation in the alignment (say from a secondary
structure prediction). There are two solutions here:

 1. Enable 'Pad Gaps' in the edit menu of the alignment window - this
should avoid the situation where the bug occurs.
 2. Use the newly patched versions available from from the
(http://www.jalview.org/versions.html) web site.

happy jalviewing!
Jim.