Thanks for getting back to us, Yann.
I'm unstacking my emails (was in deadline mode for the past couple of days), so my apologies for redundancies...
Sadly, the way we coded " Session export" is quick and dirty (serialization), and we couldn't maintain upward compatibility.
ah - that's what I thought. So its going to be important to preserve the version of VARNA used to create a particular snapshot.
Actually, if you guys have any experience/advice with this, I would be very much interested...
is there any way around this ? It would be really good if you could suggest a way of saving a VARNA annotated view so it will be compatible with future VARNA versions. Otherwise, we won't be able to store VARNA displays properly within Jalview projects, since they are always intended to be forwards-compatible (ie later versions of Jalview will always support projects from older versions).
I see, actually the best way would be to define a custom XML format for the full model (panel config+RNA), but I sadly cannot guarantee that anytime soon, as it needs to be done carefully, and I am a bit "underwater" at the moment.
know that feeling.
Of course, if anyone is willing to help with that, I can add him to the contributors of VARNA
Good point - I'll try and mention it to everyone I meet at BOSC & ISMB this year 
Meanwhile, Jan, Peter, and I will put our heads together to think of a stopgap for the purposes of Jan's project. Off the top of my head, there are two possibilities:
1. Use some standard export format that preserves most of the annotation.
2. Use VARNA's existing API methods for retrieving the visual attributes of the layout to populate an XML document, that can be used to reinstate the visualisation along with any buried annotation.
I've no idea if there is a standard export format for annotated RNA secondary structures that will hold all of the attributes that VARNA can control (text labels, box selections, sugar edges, colours, and more ?). If there is, but VARNA doesn't support its import/export then we are already into situation #2 - populating some new file format with the state of a VARNA view.
Does anyone else have any ideas about this ? (e.g., does rnaML provide the storage features we want ? and is it worth building an import/export class for this format that works with VARNA and Jalview ?).
Jim.
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On 04/07/2011 09:59, Yann Ponty wrote: