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
Hello Daron.
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
ยทยทยท
On Fri, 2 May 2008 13:43:25 +0900 Daron Standley <standley@protein.osaka-u.ac.jp> wrote:
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