Changing text to black

Hello,

For my sequence features, they are lighter colors, and the text shows up in white. I can't figure out for the life of me how to change the text to black on a colored background.

Thanks,

Jordan

Hi Jordan - thanks for the email!

For my sequence features, they are lighter colors, and the text shows up in white. I can't figure out for the life of me how to change the text to black on a colored background.

Unfortunately, this is an outstanding problem that hasn't been fixed yet. If you like, you could register at issues.jalview.org and add yourself as a watcher to this bug:
http://issues.jalview.org/browse/JAL-411

I'm hoping we can address this one when we overhaul the sequence feature display functions in Jalview later this year. Before that, however, we have first got to finish extending the datamodel to support RNA secondary structure annotation and also cope with DAS 1.6 style hierarchical features - which should be done by the end of the summer!

Jim.

···

On 12/05/2011 01:49, Willis, Jordan R wrote:

Hi Jim,

when you update the sequence features would you consider introducing different font styles (e.g. italic, bold, underline etc.)? The reason I ask is that we in Tom Blundell's group like the JOY annotation (http://bioinformatics.oxfordjournals.org/content/14/7/617.short) for viewing structural changes within a sequence alignment.

-Will

···

On 12/05/11 11:17, Jim Procter wrote:

Hi Jordan - thanks for the email!

On 12/05/2011 01:49, Willis, Jordan R wrote:

For my sequence features, they are lighter colors, and the text shows up in white. I can't figure out for the life of me how to change the text to black on a colored background.

Unfortunately, this is an outstanding problem that hasn't been fixed
yet. If you like, you could register at issues.jalview.org and add
yourself as a watcher to this bug:
http://issues.jalview.org/browse/JAL-411

I'm hoping we can address this one when we overhaul the sequence feature
display functions in Jalview later this year. Before that, however, we
have first got to finish extending the datamodel to support RNA
secondary structure annotation and also cope with DAS 1.6 style
hierarchical features - which should be done by the end of the summer!

Jim.

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--
Dr Will Pitt
Visiting Research Associate
Cambridge University
Department of Biochemistry
80 Tennis Court Road
Cambridge
CB2 1GA
UK

44(0)1223 766028

Definitely. I'd really like Jalview to be able to display JOY annotation - IIRC there are some related issues on the bug tracker that I added regarding this when I thought about it last year. Its particularly important for multiple alignments, because there is usually no space for additional annotation tracks within the row occupied by a sequence.

Jim.

···

On 12/05/2011 11:48, Will Pitt wrote:

Hi Jim,

when you update the sequence features would you consider introducing
different font styles (e.g. italic, bold, underline etc.)? The reason I
ask is that we in Tom Blundell's group like the JOY annotation
(http://bioinformatics.oxfordjournals.org/content/14/7/617.short) for
viewing structural changes within a sequence alignment.

In the meantime, if you want to get more flexibility in colouring etc than is currently available in jalview, you might try our other program Alscript. Alscript is much harder to use, it is not interactive and requires you to set up a command file of instructions, but it is very flexible.

Geoff

···

On 12/05/2011 11:17, Jim Procter wrote:

Hi Jordan - thanks for the email!

On 12/05/2011 01:49, Willis, Jordan R wrote:

For my sequence features, they are lighter colors, and the text shows up in white. I can't figure out for the life of me how to change the text to black on a colored background.

Unfortunately, this is an outstanding problem that hasn't been fixed
yet. If you like, you could register at issues.jalview.org and add
yourself as a watcher to this bug:
http://issues.jalview.org/browse/JAL-411

I'm hoping we can address this one when we overhaul the sequence feature
display functions in Jalview later this year. Before that, however, we
have first got to finish extending the datamodel to support RNA
secondary structure annotation and also cope with DAS 1.6 style
hierarchical features - which should be done by the end of the summer!

Jim.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk

The University of Dundee is registered Scottish charity: No.SC015096