Hello Mungo. On 08/12/2016 09:18, Mungo Carstairs (Staff) wrote: > typo > > " there is NO associated colour action..." > What is it? Something that was included as prototype in 2.8.2:
http://issues.jalview.org/browse/JAL-1520 But has become broken since then. For the moment it may need to be disabled in any released version. For instance, see issue raised by Charles: http://issues.jalview.org/browse/JAL-1895 This should have been fixed back in 2015 for the 2.9 release, at the same time as you and I were trying to resolve the pseudoknot issue and linked VARNA display, but we backed off then because of other priorities. As you can see, nothing else was done. RNA interaction types are imported via RNAML filed derived from RNA 3D structures. Anne Menard implemented a prototype as part of her 'Jalview Summer of Code' in 2012, which encoded the sugar edge interactions as different RNA base pair symbols. Jalview renders these symbols as distinct colours already, making the 'RNA interaction colourscheme' redundant, but the implementation needs to be looked at again because it doesn't really fit the needs of an RNA alignment analyst. There's also a conflation in the data encoding, since alignment annotation glyph symbols are used for both sugar edge and pseudoknot pairings, when in fact these are not directly coupled. RNA interaction types should also passed to VARNA in order to display Leontis Westoff notation on each base pair. Does that help ? Jim. -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
