________________________________
From: Romain Studer <[email protected]>
Sent: 24 September 2015 10:37
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] Alteration of colours in Jalview
Ok, thank you!
Not directly related, but I have to mention that, me and another colleague,
cannot install Jalview 2.9 on a Mac OSX 10.7.
We got this error:
/Applications/Jalview/Jalview.app/Contents/MacOS/Jalview
Invocation of this Java Application has caused an InvocationTargetException.
This application will now exit. (LAX)
Stack Trace:
java.lang.InternalError: java.lang.ClassNotFoundException:
ch.randelshofer.quaqua.subset.QuaquaLionFileChooserLAF
at
ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel(QuaquaManager.java:516)
at jalview.bin.Jalview.main(Jalview.java:188)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at com.zerog.lax.LAX.launch(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)
This Application has Unexpectedly Quit: Invocation of this Java Application has
caused an InvocationTargetException. This application will now exit. (LAX)
But we can install Javlview 2.8.
So may 2.9 is not any more supported on 10.7.
It might worth preventing the installation of 2.9 on Mac OSX 10.7 and older, or
at least give a warning.
Best regards,
Romain
On 24/09/2015 10:30, Mungo Carstairs (Staff) wrote:
Hi Romain,
Thanks for that. I am on the track of a bug in parsing the annotation file
colours.
We have a bug fix update for 2.9 due to go out next week and I'll try to ensure
this is included, will keep you posted.
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<http://www.jalview.org>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
________________________________________
From: Romain Studer <[email protected]><mailto:[email protected]>
Sent: 24 September 2015 10:05
To: Mungo Carstairs (Staff)
Subject: Re: [Jalview-discuss] Alteration of colours in Jalview
Hi Mungo,
Here is my files, FASTA and annotations => Columns 101 and 103 should
have some residues in red.
- I also tried with the Jalview 2.9 from a colleague, the problem is the
same. He has Mac OS X 10.10, I have 10.8.
- Downgrading to Jalview 2.8 solves the problem.
Thanks,
Romain
On 24/09/2015 08:53, Mungo Carstairs (Staff) wrote:
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<http://www.jalview.org>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
________________________________________
From:
[email protected]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
on behalf of Romain Studer <[email protected]><mailto:[email protected]>
Sent: 23 September 2015 17:21
To: [email protected]<mailto:[email protected]>
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
--
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
--
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
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