-flat option in VARNA command line

[jcg]

I'm trying to draw the exterior loop flat and I'm using the command
line for that but it isn't working. The command used is the following:

java -cp VARNAv3-6.jar fr.orsay.lri.varna.applications.VARNAcmd -
sequenceDBN "TTCCCCAUAUAGGGGTT" -structureDBN "..((((.....)))).." -o
out.jpg -highlightRegion "5-9:fill=#bcffdd" -title "Test RNA" -flat 1

When I use the java applet interface, everything works fine, so
probably I'm not setting the correct options on the command line.

Can you please help with this?

Thanks,
Joao

[Yann Ponty]

Hi Joao,

This is due a glitch in the specs, already pointed out by Andrew at
http://groups.google.fr/group/varnarna/browse_thread/thread/476351d574c11c75
The flat command takes a "true"/"false" boolean as valid value.
I fixed it some time ago but forgot to re-upload the spec page.
Should be ok now...

Best,

Yann