about coloring text

Hi James,

Can we insert gaps in a group using cursor model?
Is there a way to only color the nucleotides that are different from
the consensus?
Is there a way to color/highlight the whole text box instead of only
coloring the text or the border?
btw, can we make user defined shortcut keys? I found it's bothering to
make several clicks every time I color a nucleotide.

Thanks a lot!

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Yanan

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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