[Jalview-discuss] about coloring text

[James Procter]

Hi Yanan - thanks for the email.

Yanan Jiang wrote:
> Can we insert gaps in a group using cursor model?
yes - hold control or shift together when pressing the space bar/delete 
to group insert/delete gaps.

> Is there a way to only color the nucleotides that are different from
> the consensus?
There is a new feature available in the latest CVS version of Jalview 
(see www.jalview.org/versions.html), which enables something like this. 
Once you have loaded your alignment, look for the 'show unconserved' 
setting under the format menu. You can also apply this to specific 
groups, to highlight the unconserved regions in a particlar area. 
However, the colourschemes will still be applied to the original residue 
(rather than only colouring the non-gap characters) - I've added this as 
a refinement to this new feature.

> Is there a way to color/highlight the whole text box instead of only
> coloring the text or the border?
I'm not quite sure what you mean here - for colouring with the applied 
colour scheme - the 'boxes' option colours the rectangle containing each 
sequence symbol, and the 'text' option controls whether the symbol is 
rendered or not.
> btw, can we make user defined shortcut keys? I found it's bothering to
> make several clicks every time I color a nucleotide.
no - shortcuts aren't configurable, and there isn't any macro function. 
Its a good idea, though - and has been suggested (even by me) but as yet 
no one has implemented it... that is something that may appear after the 
release of jalview version 3 (some time next year!).

happy jalviewing!
Jim.

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