[Jalview-discuss] coloring by annotation

[Daron Standley]

Hi-

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? Also, I would like  
to ask the same question but in the cases where I use the "above  
threshold" option to color only high-scoring residue pairs.  (I am  
curious about this since Jalview seems to figure out the threshold  
based on the distribution of scores.)

Thanks in advance for your help.

Best wishes,

-Daron