[Jalview-discuss] Per-group annotation-based color schemes

[Gregory Jordan]

Hi all,

I'm trying to color an alignment on a per-group basis according to
numerical values coming from multiple annotation files.

For example, let's say I've got Groups A and B and numerical
annotation tracks X and Y. Would it be possible to color group A
according to X, and B according to Y?

I'm relatively new to the Jalview UI, but it appears that the Color ->
By Annotation panel only allows one to set the global color scheme.
And when I right-click on a group that I wish to color and select
Selection -> Group -> Group Color, I see a menu with various group
coloring options, but the "By Annotation" option is notably missing
from the list.

I'm up and running with the Jalview source code in Eclipse, so I'm
investigating how to approach this need either by (a) updating the UI
or (b) writing a script (Java or Groovy) to handle what I'm looking
for. Most likely, I'll pursue option B for the purposes of our current
project, with an eye towards option A for the sake of longevity. Has
anyone run into this issue before, or are there any tips on how to go
about implementing this?

Suggestions from more experienced users or developers would be much appreciated!

Cheers,
  Greg