Hello Anne. On Wed Jun 20 17:41:03 2012, Ménard Anne wrote: > Good evening everyone, > I made good progress in the parser code RNAML this afternoon, so, I > did not ask questions by email: D ace :)
> I create a branch on the git my name but not the right place. I'll > take care of delete and recreate. This is not the right version > either, because I don't know how do to export a gitproject on eclipse . ok - these things are often done more easily from the command line, but Egit is catching up. You should be able do a fast-forward merge from 'develop' onto your branch to bring it up to date. You'll need to do this periodically to pull in changes as I update the development branch. It's also possible to do it from the command line (git checkout menard; git merge --no-ff develop). > However, I have a question. We discussed with Yann about the > possibility to predict the file rnamlfor two cases : > > 1) the user already has the sequence and he just wants to retrieve the > annotations in the rnaml file (open two files and then juxtapose the > information) > 2) the user doesn't have the sequence and so we recovered in the > rnamlfile ; the sequence and annotation. > > Is it possible ? essentially for the first case. both are possible. The second case is accomplished by supporting the basic jalview.io.AlignFile methods. The first case is accomplished by allowing RNAML files to be loaded via the 'Structure->Associate Structure with Sequence->From File' in the sequence ID popup menu (right click on an ID to get this). The action is implemented in the jalview.gui.PopupMenu class, and the logic implemented in the jalview.gui.AssociatePdbFileWithSeq class. The simplest approach is to modify this class to detect if the file is an RNAML file rather than a PDB file, and if so, read the file and transfer the RNA structure to the destination sequence. Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
