[Jalview-discuss] Delete non-gap sites in linked split frame view?

Povilus, Rebecca Ann rpovilus at fas.harvard.edu
Thu Jan 7 18:12:19 GMT 2016


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 at dundee.ac.uk]
Sent: Thursday, January 07, 2016 12:02 PM
To: Povilus, Rebecca Ann; jalview-discuss at 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


Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
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________________________________
From: jalview-discuss-bounces at jalview.org<mailto:jalview-discuss-bounces at jalview.org> <jalview-discuss-bounces at jalview.org<mailto:jalview-discuss-bounces at jalview.org>> on behalf of Povilus, Rebecca Ann <rpovilus at fas.harvard.edu<mailto:rpovilus at fas.harvard.edu>>
Sent: 07 January 2016 15:15
To: jalview-discuss at jalview.org<mailto:jalview-discuss at 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





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