Hello Romain,
This should be fixed in the next patch release of Jalview, expected soon.
You can try it out by running the WebStart Development Branch version from
http://www.jalview.org/development/development-builds
I have used this to correctly load a features file with modified feature group colouring.
Thanks for drawing this to our attention!
Logged as http://issues.jalview.org/browse/JAL-1904
Regards,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
________________________________________
From: Mungo Carstairs (Staff)
Sent: 24 September 2015 08:53
To: Romain Studer; Jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Alteration of colours in Jalview
Hi Romain,
Is it possible for you to send us your preferences (.jalview_properties), alignment and annotations file (by private email if you prefer)?
That would let us check for interactions such as transparency effects here.
Thanks,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School 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 Romain Studer <rstuder@ebi.ac.uk>
Sent: 23 September 2015 17:21
To: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Alteration of colours in Jalview
I forgot to attach a picture, which will be more explicit. Instead of
brilliant blue (0000ff), it is a purple-like blue.
Thanks,
Romain
On 23/09/2015 17:14, Romain Studer wrote:
Dear all,
I recently downloaded the last version of Jalview 2.9.
I developed a colour mapping for my alignment, which perfectly with 2.8.
But now the colours are altered. Instead of have a pure brilliant red, I
only get a pastel red. Same for blue or green.
This is the code I use in my annotations file:
1.0 YHR164C -1 91 91 red
I thought it was in the colour name, so I turned it to hex cod:
1.0 YHR164C -1 91 91 ff0000
But same result.
It might in the way of Jalview interpret the annotation file, because if
I load the Zappo colour scheme, I can have a brilliant red.
Any idea ? Is there a parameter for opacity ? Or a new coding?
Best regards,
Romain
--
Romain Studer
EMBL-EBI
Wellcome Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel: +44 (0)1223 492 547
Twitter: @RomainStuder
The University of Dundee is a registered Scottish Charity, No: SC015096