Hello Becky,
If you want to try it out, a version that correctly hides / shows columns in the split frame is available at
http://www.jalview.org/development/development-builds
- select the Development Branch (WebStart or InstallAnywhere version)
NB as the page says, this branch comes without guarantees, and do back up any valuable data before using!
All being well this should make it into the next official build of Jalview.
Regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
···
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: Povilus, Rebecca Ann rpovilus@fas.harvard.edu
Sent: 07 January 2016 18:12
To: Mungo Carstairs (Staff); jalview-discuss@jalview.org
Subject: RE: Delete non-gap sites in linked split frame view?
Hello Mungo,
I just doubled checked the help documentation, and since hidden columns won’t be used in subsequent analysis, I think that should work for my needs (I want to calculate trees from the edited nt alignment).
Thanks for checking and catching the buggy hide capability in split frame view. I’ll keep an eye out for updates on that.
Thanks!
-Becky
Becky Povilus
Ph.D. Candidate
Organismic and Evolutionary Biology
Harvard University
From: Mungo Carstairs (Staff) [mailto:g.m.carstairs@dundee.ac.uk]
Sent: Thursday, January 07, 2016 12:02 PM
To: Povilus, Rebecca Ann; jalview-discuss@jalview.org
Subject: Re: Delete non-gap sites in linked split frame view?
Hello Becky,
Rather than deleting columns, would it serve your purpose just to hide them?
This would be my preferred choice here (it’s simpler to change how the sequences look than what they are).
But having said that - I notice that ‘Hide Columns’ is buggy in the split frame view in a rather awkward way!
Hiding columns in one half doesn’t hide the equivalent columns in the other half.
Clicking on them in order to hide them as well - redisplays the ones you just hid. Ouch.
I will raise a task to fix this. Please let me know if that would meet your needs.
It’s great to have feedback on the split frame feature, as it is ‘new and experimental’. Any other comments or suggestions would be most welcome.
Best regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
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 Povilus, Rebecca Ann <rpovilus@fas.harvard.edu>
Sent: 07 January 2016 15:15
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Delete non-gap sites in linked split frame view?
Hello,
I’ve encountered an issue while working with the linked split frame view for looking simultaneously at the nucleotide and corresponding amino acid sequences of an alignment. What I would like to do is edit non-gap sites (specifically, delete entire columns) in the amino acid alignment and have the nucleotide alignment change/update accordingly.
If I understand it correctly, the current split frame view editing capability works with deleting and inserting gaps sites only (As stated in the jalview help documentation “Editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)”). It’s great that Jalview added this capability, but is it (or could it be) possible to delete non-gap sites as well?
Let me know additional information would be useful.
Thanks,
-Becky
Becky Povilus
Ph.D. Candidate
Organismic and Evolutionary Biology
Harvard University