getting the sequence of edits done to MSA

Jalview Discussion
1

Hi all

Iam using applet version of Jalview(v2.4) in my website.

Currently, Iam able to edit the alignment and get the edited alignment into a text area of the webpage
using getAlignment() method and then save it in a databse.

Now I want to do the following: I want to to get the list of(or the sequence of) edits I did to the original
alignement to get my final edited alignment. That means if I give the original alignment and the list of edits done
by me on this original alignment, anybody should be able to get the final edited alignment by following the sequence of steps given in the list.

Can anybody tell me if there any way of getting this edit sequence list form Jalview

Thanks
Vani

2

Dear Vani.

Thanks for the interesting question !

Jalview does record the edits that you have made to the alignment - but it currently doesn’t have any serialization mechanism for this information - so there’s no ‘getEdits()’ method available at the moment.

Having said that - it would be possible to generate such a list… all that would be needed is to decide how each edit should be represented. Is this information something you are interested in analysing - or do you simply want to be able to import the edit list back into Jalview to replay the editing session ?

Jim.

··· 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
3

Dear Jim,

Thanks for your reply.

Having said that - it would be possible to generate such a list… all that would be needed is to decide how each edit should be >represented. Is this information something you are interested in analysing - or do you simply want to be able to import the edit >list back into Jalview to replay the editing session ?

I would say if both the options are possible it would be great!! When I edit an original alignment, if I can get the seqence of edits I did as a text file or a string, then the following can be done.

  1. Given the alignment and the text file of edits done, I can analyse the text file(edit list) and make any changes necessary
  2. Then I can Import the edit list into Jalview to perform the sequence of edits present in it on the original alignment .

Can you please tell me if any of these steps are possible currently

Thank you

Vani

···

On 26 April 2010 16:49, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Dear Vani.

Thanks for the interesting question !

Jalview does record the edits that you have made to the alignment - but it currently doesn’t have any serialization mechanism for this information - so there’s no ‘getEdits()’ methI wod available at the moment.

Having said that - it would be possible to generate such a list… all that would be needed is to decide how each edit should be represented. Is this information something you are interested in analysing - or do you simply want to be able to import the edit list back into Jalview to replay the editing session ?

Jim.

On 26/04/2010 04:14, subs subs wrote:

Hi all

Iam using applet version of Jalview(v2.4) in my website.

Currently, Iam able to edit the alignment and get the edited alignment into a text area of the webpage
using getAlignment() method and then save it in a databse.

Now I want to do the following: I want to to get the list of(or the sequence of) edits I did to the original
alignement to get my final edited alignment. That means if I give the original alignment and the list of edits done
by me on this original alignment, anybody should be able to get the final edited alignment by following the sequence of steps given in the list.

Can anybody tell me if there any way of getting this edit sequence list form Jalview

Thanks
Vani


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4

Hi Vani.

··· 
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-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
5

Ok Vani. What you ask is quite possible, so I will add it to the list of Jalview feature requests.

However, I have other features to implement currently, so I won’t be able to begin working on this until later on this year. If that’s a problem then I might be able to hack something together earlier (in a month, or so) - but I wouldn’t consider it of high enough quality to go into a production version of jalview.

Jim.

ps. I’d still like to have a more concrete idea of what kind of analysis you’d like to perform on the edit list - are there any human representations that you use already ?

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