Hi,
I do use regularly user-defined colors (say, color cysteines red and tryptophans blue, etc) as I am investigating alignments, and I am having trouble using this function with 2.8.2.
When I select a few amino acids and their colors an hit Apply or OK in the "User defined colours" window (which used to work fine), I get a message saying "Please make a colour selection before to apply colour scheme". And it won't let me exit the "User defined colours" window, unless I cancel it. The funny thing is, the color scheme is applied on the alignment as I am defining the scheme; I can see, say my cysteines all turned red, but since I cannot exit the "User defined colours" window without canceling, my coloring scheme is deleted.
To test, I actually saved such a scheme as a .jc file, and loaded it, and it still gives me the same error, and won't let me exit the window without canceling the coloring scheme. It feels like a bug, but then there may be a hidden feature that I am not grasping here.
Any help with this would be deeply appreciated,
Engin
Hi Engin.
This sounds like a bug. Can you make sure the Jalview Java console is open and try to reproduce the problem ? Hopefully there'll be some error or warning message output.
I've created an issue under your name here:
http://issues.jalview.org/browse/JAL-1702
Jim
···
On 20/04/2015 17:29, Engin Özkan wrote:
Hi,
I do use regularly user-defined colors (say, color cysteines red and
tryptophans blue, etc) as I am investigating alignments, and I am having
trouble using this function with 2.8.2.
When I select a few amino acids and their colors an hit Apply or OK in
the "User defined colours" window (which used to work fine), I get a
message saying "Please make a colour selection before to apply colour
scheme". And it won't let me exit the "User defined colours" window,
unless I cancel it. The funny thing is, the color scheme is applied on
the alignment as I am defining the scheme; I can see, say my cysteines
all turned red, but since I cannot exit the "User defined colours"
window without canceling, my coloring scheme is deleted.
To test, I actually saved such a scheme as a .jc file, and loaded it,
and it still gives me the same error, and won't let me exit the window
without canceling the coloring scheme. It feels like a bug, but then
there may be a hidden feature that I am not grasping here.
Any help with this would be deeply appreciated,
Engin
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Hi Engin,
This is indeed a bug which we will fix in the next release.
Meanwhile a workaround is to select the 'Case Sensitive' option in the colour chooser dialog.
(There is no need to pick colours for lower case unless your sequences include lower case characters.)
Thanks,
Mungo
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 Jim Procter <jprocter@compbio.dundee.ac.uk>
Sent: 20 April 2015 19:04
To: Jalview-discuss@jalview.org; Engin Özkan
Subject: Re: [Jalview-discuss] Coloring error
Hi Engin.
This sounds like a bug. Can you make sure the Jalview Java console is
open and try to reproduce the problem ? Hopefully there'll be some
error or warning message output.
I've created an issue under your name here:
http://issues.jalview.org/browse/JAL-1702
Jim
On 20/04/2015 17:29, Engin Özkan wrote:
Hi,
I do use regularly user-defined colors (say, color cysteines red and
tryptophans blue, etc) as I am investigating alignments, and I am having
trouble using this function with 2.8.2.
When I select a few amino acids and their colors an hit Apply or OK in
the "User defined colours" window (which used to work fine), I get a
message saying "Please make a colour selection before to apply colour
scheme". And it won't let me exit the "User defined colours" window,
unless I cancel it. The funny thing is, the color scheme is applied on
the alignment as I am defining the scheme; I can see, say my cysteines
all turned red, but since I cannot exit the "User defined colours"
window without canceling, my coloring scheme is deleted.
To test, I actually saved such a scheme as a .jc file, and loaded it,
and it still gives me the same error, and won't let me exit the window
without canceling the coloring scheme. It feels like a bug, but then
there may be a hidden feature that I am not grasping here.
Any help with this would be deeply appreciated,
Engin
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
The University of Dundee is a registered Scottish Charity, No: SC015096
Thank you. The workaround works well.
I also just realized that I replied only to Jim (and not to the board) about the lack of error messages/warnings in the Java Console, but that's no longer important...
I am looking forward to the next release.
Engin
···
On 4/22/15 4:05 AM, Mungo Carstairs (Staff) wrote:
Hi Engin,
This is indeed a bug which we will fix in the next release.
Meanwhile a workaround is to select the 'Case Sensitive' option in the colour chooser dialog.
(There is no need to pick colours for lower case unless your sequences include lower case characters.)
Thanks,
Mungo
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 Jim Procter <jprocter@compbio.dundee.ac.uk>
Sent: 20 April 2015 19:04
To: Jalview-discuss@jalview.org; Engin Özkan
Subject: Re: [Jalview-discuss] Coloring error
Hi Engin.
This sounds like a bug. Can you make sure the Jalview Java console is
open and try to reproduce the problem ? Hopefully there'll be some
error or warning message output.
I've created an issue under your name here:
http://issues.jalview.org/browse/JAL-1702
Jim
On 20/04/2015 17:29, Engin Özkan wrote:
Hi,
I do use regularly user-defined colors (say, color cysteines red and
tryptophans blue, etc) as I am investigating alignments, and I am having
trouble using this function with 2.8.2.
When I select a few amino acids and their colors an hit Apply or OK in
the "User defined colours" window (which used to work fine), I get a
message saying "Please make a colour selection before to apply colour
scheme". And it won't let me exit the "User defined colours" window,
unless I cancel it. The funny thing is, the color scheme is applied on
the alignment as I am defining the scheme; I can see, say my cysteines
all turned red, but since I cannot exit the "User defined colours"
window without canceling, my coloring scheme is deleted.
To test, I actually saved such a scheme as a .jc file, and loaded it,
and it still gives me the same error, and won't let me exit the window
without canceling the coloring scheme. It feels like a bug, but then
there may be a hidden feature that I am not grasping here.
Any help with this would be deeply appreciated,
Engin
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
The University of Dundee is a registered Scottish Charity, No: SC015096
--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu