Awesome! Thanks so much for taking the time to work that out for me, Jim. I appreciate it. Looking forward to trying it out.
Dave On Mon, Sep 19, 2011 at 17:23, Jim Procter <[email protected]>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 > > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >
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