jalview annotations

Best to send such questions to the Jalview Discuss list as Jim will then give you an authoritative answer.

I would think that you would need to specify your features in a feature group in the file. You can then control whether or not they are rendered in the features setting dialogue. As for removing them, I am not sure. The clunky way is to save before loading the features, and revert to the saved file if you don't like the features you have loaded.

Jim?

..d

···

--
David Martin PhD
College of Life Sciences
University of Dundee
01382 388704
The University of Dundee is a Scottish Registered Charity, No. SC015096.

************************************************************
Please consider the environment. Do you really need to print this email?>>> On 10/05/2010 at 17:45, in message
<C08D20B8-EFC7-4B5B-BADE-6D3A100786A7@mbi.uib.no>, Rein Aasland
<Aasland@mbi.uib.no> wrote:

    But for now: a quick one; - once I've loaded a set of (local)
annotations from a file, - is it possible to remove them again ?!
    (let's say, I didn't like it, and want to replase it with
something else)

Rein

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

Hello Rein, David is right here, both about the mailing list and the 'Undo'ability of features and annotation in jalview 2.5.

At the moment, nether features or annotations are covered by the undo system. Even worse, there are no group editing facities (not even a 'remove all' function!). This means that if you don't like the features or annotation that you just loaded on, then you need to either delete each one individually (double click to amend features, right click on the annotation track to remove the annotation row) or have saved the alignment beforehand (use the jalview project format if you have already got some annotations) so you can reload the un-tainted view using the 'Reload' function.

Jim.

···

On 10/05/2010 17:59, David Martin wrote:

Best to send such questions to the Jalview Discuss list as Jim will then give you an authoritative answer.

I would think that you would need to specify your features in a feature group in the file. You can then control whether or not they are rendered in the features setting dialogue. As for removing them, I am not sure. The clunky way is to save before loading the features, and revert to the saved file if you don't like the features you have loaded.

Jim?

..d

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Thanks for these tips, Jim and David,

and thanks for alerting me to the discussion list!

I shall also read the excellent documentation your have made before I start pestering the discussion forum. And I realise that, as I'm with a Mac laptop only (and can not get the right-click to work properly), I'll have to get a proper mouse and then see what I can do with the row/feature editing. I also got around with just reloding previous version of the .jar file!

Can I assume that I can also row-remove the alignment quality bar graph this way (which is nice when I want to make compact alignments for presentation)??

Thanks again!

Rein

···

On 11. mai 2010, at 10.10, Jim Procter wrote:

Hello Rein, David is right here, both about the mailing list and the
'Undo'ability of features and annotation in jalview 2.5.

At the moment, nether features or annotations are covered by the undo
system. Even worse, there are no group editing facities (not even a
'remove all' function!). This means that if you don't like the features
or annotation that you just loaded on, then you need to either delete
each one individually (double click to amend features, right click on
the annotation track to remove the annotation row) or have saved the
alignment beforehand (use the jalview project format if you have already
got some annotations) so you can reload the un-tainted view using the
'Reload' function.

Jim.

On 10/05/2010 17:59, David Martin wrote:

Best to send such questions to the Jalview Discuss list as Jim will then give you an authoritative answer.

I would think that you would need to specify your features in a feature group in the file. You can then control whether or not they are rendered in the features setting dialogue. As for removing them, I am not sure. The clunky way is to save before loading the features, and revert to the saved file if you don't like the features you have loaded.

Jim?

..d

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss