Control the color of sequence text while using a user defined feature annotation

haim_ashkenazy · 28 January 2015 11:53

Dear JalView developers,

Thank you for developing and maintaining JalView. It is very useful for us!

We are using the JalView applet in our web-server. Specifically we use the option to annotate and color residues in the MSA using a feature file. You can find an example here: http://guidance.tau.ac.il/ver2/Gallery/MSA.MAFFT.Guidance2_JalView_test.html.

I wonder whether there is an option to control the color of the MSA text font. In the example above, color the residues in black instead of white, while keeping the background color according to the feature file.

Thanks in advance for your help.

Best regards,

Haim Ashkenazy

http://tau.ac.il/~haimash

g_m_carstairs · 28 January 2015 15:12

Hello Haim,

This looks like a variation on a known problem http://issues.jalview.org/browse/JAL-411.

The text colour should automatically change between black and white for maximum readability (as you can see if you move the Transparency slider in the Feature Settings dialog), however this does not always work as intended.

I will add a note on your problem to this issue and we will see whether it can be addressed. Unfortunately I don’t believe there is a workaround in the meantime.

Regards,

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Haim Ashkenazy haim.ashkenazy@gmail.com
Sent: 28 January 2015 11:53
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Control the color of sequence text while using a user defined feature annotation