Hi Mungo On 25/10/2016 13:49, Mungo Carstairs (Staff) wrote: > If the consensus residue has a 'tie', would you expect all of the > tied residues to get coloured? Actually, yes - although neither would be coloured for 100% PID.
> Currently they don't, because the consensus is '+' and this doesn't match. argh. I'd bet that's been in since Jalview 1. > But it wouldn't be hard to change the behaviour so they do. We probably ought to provide an option for that so people can have the old behaviour if they prefer it. > I guess that could be confusing e.g. > > PR > > PR > > PS > > PS > > LF > > column 1 80% consensus with P = dark blue > > column 2 also has 80% of residues matching 'consensus' of [RS] - but is > this a PID of 80% or 40% or 0%? See comment above - the scale is quantitative, so R and S both receive 40 (the value calculated for them in the consensus block). > I also need to fix my branch so '+' is shown in the consensus sequence > and not multiple residues for this case! you do. TBH the consensus sequence shouldn't be referred to at all by this colourscheme. The same goes for the Blosum62 one, since formally, the average of costs to mutate each residue to the modal residues for the column should be used to compute the colour. Is there also a knock on for reference sequence shading ? I seem to remember making the 'get consensus sequence' method return the reference sequence when that was defined.... Jim _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
