Offline drawing using command line

[Yann Ponty]

Dear Yann Ponty,

I recently discovered your amazing RNA Drawing tool and I've to
congratulate you and your team for this very nice tool.

I really would like to use it to generate automatically some RNA
structures and I've been trying to use your API but you have only
documented the VARNAPanel class, is there any chance to get
documentation for the other classes? Or maybe some really simple
examples of how to load a structure, do basic annotations and save it
to JPG?

That would be a really big help for me!

Thanks again and congratulations,
Joao Guimaraes

[Yann Ponty]

Dear Joao,

To draw structures automatically, one doe not need to go into the
code, but should rather use the command line version of VARNA. For
instance:
java -cp VARNAv3-6.jar fr.orsay.lri.varna.applications.VARNAcmd -
sequenceDBN "CCCCAUAUAGGGG" -structureDBN "((((.....))))" -o out.jpg -
highlightRegion "5-9:fill=#bcffdd"
will do the following:
- Load an RNA having seq CCCCAUAUAGGGG and sec. str. ((((.....))))
(specified in the Dot Bracket Notation DBN, but files in BPSeq, CT,
RNAML... can also be loaded from disk through the "-i" option)
- Draw it according to the default algorithm (Overridden with option
"-algorithm")
- Highlight the 5-9 nucleotides with a greenish glow
- Export the resulting drawing to an "out.jpg" file (The type is
guessed automatically from the ".jpg" extension)
Notice that any applet option (documented in the "specifications tab"
of VARNA web site) is accepted as a valid command line option (through
appending a "-").
You can get an almost up-to-date list of options through the
"java -cp VARNAv3-6.jar fr.orsay.lri.varna.applications.VARNAcmd -x"
command.

Is that sufficient for you to start? I must shamefully admit that the
code itself was not very well commented... :(

Thanks for your interest in VARNA, and do not hesitate to contact me
if you have any further questions/problems.
Best,

Yann