[Jalview-discuss] open files from command line without spawning new Jalview instance?

Dave Messina David.Messina at sbc.su.se
Mon Sep 19 16:41:06 BST 2011

Awesome! Thanks so much for taking the time to work that out for me, Jim. I
appreciate it. Looking forward to trying it out.


On Mon, Sep 19, 2011 at 17:23, Jim Procter <jprocter at compbio.dundee.ac.uk>wrote:

> Hi Dave.
> On 19/09/2011 10:54, Dave Messina wrote:
> > When Jalview is already running, is it possible to open files in
> > Jalview from the command line?
> unfortunately, there isn't a really easy way of doing this, but after
> pondering the problem for a while, I came up with the following solution
> which I hope will work in your case.
> Firstly, enable groovy scripting in jalview by downloading the groovy
> binary distribution from groovy.codehouse.org. You then need to copy the
> 'groovy-all-1.X.jar' file from the 'embedded' directory into your
> jalview's lib directory.
> If this worked, then when you restart Jalview, you should see a new menu
> entry under the Tools menu: 'Groovy Console ...'. Select that option to
> open a groovy script execution window.
> Now cut'n'paste the line(s) below into the script input area (top half
> of the groovy console) :
> new groovy.ui.GroovySocketServer(
>          new GroovyShell(), false, "(new
> jalview.io.FileLoader()).LoadFileWaitTillLoaded(line,jalview.io.FormatAdapter.FILE);",
> true, 1962);
> Pressing 'Ctrl-R' will execute the script, and you should see something
> like 'groovy is listening on port 1962' appear in the output half of the
> console window. You now have a server set up that will try to use any
> text sent on port 1962 as a filename to open with the running Jalview.
> To test it out, try :
> echo <alignment filename> | nc localhost 1962
> If there are any problems, then you'll see errors written on Jalview's
> java console (opened using the Tools->Java Console' menu entry. If you
> use this regularly, I suggest you save the groovy script to a file, and
> pass it to Jalview on startup with the -groovy <scriptfile> argument.
> Have fun!
> Jim.
> ps. you can put in any bit of groovy scripting in the third argument to
> the GroovySocketServer constructor. For instance, you might want to tag
> on any additional commands, such as loading default features, etc. For
> full details, start with the javadoc for the groovy socket server here:
> http://groovy.codehaus.org/api/groovy/ui/GroovySocketServer.html
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