Alteration of colours in Jalview

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

I forgot to attach a picture, which will be more explicit. Instead of brilliant blue (0000ff), it is a purple-like blue.

Thanks,
Romain

blue_pastel.png

···

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

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

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

···

From: Romain Studer rstuder@ebi.ac.uk
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 [<rstuder@ebi.ac.uk>](mailto:rstuder@ebi.ac.uk)
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: [jalview-discuss-bounces@jalview.org](mailto:jalview-discuss-bounces@jalview.org) [<jalview-discuss-bounces@jalview.org>](mailto:jalview-discuss-bounces@jalview.org) on behalf of Romain Studer [<rstuder@ebi.ac.uk>](mailto:rstuder@ebi.ac.uk)
Sent: 23 September 2015 17:21
To: [jalview-discuss@jalview.org](mailto: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

--
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 

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

Thanks! It works now.

Best regards,
Romain

···

On 25/09/2015 09:40, Mungo Carstairs (Staff) wrote:

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

--
Romain Studer
EMBL-EBI
Wellcome Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel: +44 (0)1223 492 547
Twitter: @RomainStuder