Remove empty columns when running from command line

Jalview Discussion
1

Hi Jalview-ers,

I was wondering if it's possible to call Remove empty columns (Ctrl-E) from a script (Groovy or otherwise) when running from the command line?

Best wishes,

Tim

···

--
Dr Tim Nugent
Bioinformatics Group
Department of Computer Science
University College London
Gower Street
London WC1E 6BT
Tel: 020-7679-7981
t.nugent@cs.ucl.ac.uk
http://www.cs.ucl.ac.uk/staff/T.Nugent

2

This should do it :

currentAlFrame.removeGappedColumnMenuItem_actionPerformed(null);

However, it's not particularly future proof, since that function is the one called when you select the 'Remove Gapped Columns' menu item, which may change at a later date. Additionally, this will leave an action on the undo buffer which can't be easily cleared from a groovy script.

I've put in a feature request about adding an applet parameter and command line option to run this automatically when an alignment is loaded, as well as adding it as a function in the stable API (http://issues.jalview.org/browse/JAL-909).

Jim.

···

On 18/08/2011 15:06, Tim Nugent wrote:

Hi Jalview-ers,

I was wondering if it's possible to call Remove empty columns (Ctrl-E)
from a script (Groovy or otherwise) when running from the command line?

3

Thanks for the swift reply Jim, I'll give that a try.

Cheers,

Tim

···

On 18/08/2011 15:49, Jim Procter wrote:

On 18/08/2011 15:06, Tim Nugent wrote:

Hi Jalview-ers,

I was wondering if it's possible to call Remove empty columns (Ctrl-E)
from a script (Groovy or otherwise) when running from the command line?

This should do it :

currentAlFrame.removeGappedColumnMenuItem_actionPerformed(null);

However, it's not particularly future proof, since that function is the
one called when you select the 'Remove Gapped Columns' menu item, which
may change at a later date. Additionally, this will leave an action on
the undo buffer which can't be easily cleared from a groovy script.

I've put in a feature request about adding an applet parameter and
command line option to run this automatically when an alignment is
loaded, as well as adding it as a function in the stable API
(http://issues.jalview.org/browse/JAL-909).

Jim.

--
Dr Tim Nugent
Bioinformatics Group
Department of Computer Science
University College London
Gower Street
London WC1E 6BT
Tel: 020-7679-7981
t.nugent@cs.ucl.ac.uk
http://www.cs.ucl.ac.uk/staff/T.Nugent