[Jalview-discuss] coloring by annotation

[Jim Procter]

Hello Daron.

On Fri, 2 May 2008 13:43:25 +0900
Daron Standley <standley at protein.osaka-u.ac.jp> wrote:
> I am using Jalview to display pairwise alignments, with the residue  
> similarity score defined by me and plotted as a bar graph using an  
> external annotations file.
>  From the menu, I can color the alignment by the residue similarity:
> 
> color-> by annotation
> 
> Is there an easy way to make this coloring appear by default so that  
> the user doesn't have to use the pull-down menu?

actually, there isn't, without some kind of modification to the source. This goes for both the thresholded and the shaded colouring style. The best solution would be to extend the jalview annotation file format to allow the the 'by annotation' colouring style to be specified for the alignment, or for a particular group, along with the additional parameters (threshold mode, min/max colouring, threshold value).

> curious about this since Jalview seems to figure out the threshold  
> based on the distribution of scores.)
I don't think that it does anything too clever, here!

I'll have a think about the extensions to the annotations format and get back to you all on this. There are a few other things which can be added to the format, too (hidden column specification, view name/creation).

cheers.
Jim

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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