[Jalview-discuss] Trouble adding gaps to a group of sequences

[Jim Procter]

Hi again, Felicia.
> Thanks so much for getting back to me!   It is really appreciated when 
> minor inquires like this get address.  I'm sorry to quibble, but I 
> have selected the region where I want to add the gap.  To select a 
> region I used  my left mouse button and dragged the mouse to the 
> bottom right corner of the region that I want (as it says in the 
> manual).  And I do get the dashed red box around the region I have 
> selected.  However, when I press the apple key (not control) I get the 
> Selection option - as if I have right clicked.  I know this is a minor 
> issue and does not detract from the all that Jalview can do, but I 
> thought I should be clear.  Maybe it is a bug with the OS I am using?  
> Or maybe it is just my machine....
no - its not your machine, its Jalview :)

What is happening is that Jalview isn't letting you insert gaps because 
you've selected a region within the alignment. When only a small section 
of the alignment is selected, the 'locked editing' function comes in to 
play - so you first need to add in some gaps so you have room to 
maneouver within the locked region. However, Jalview doesn't give you 
any feedback to indicate that this is what is stopping you editing the 
alignment.. so it feels like something is broken.

Instead of selecting the small region of the alignment, click on the 
seuqence IDs to select the whole row for each sequence you want to edit. 
Then, you should be able to freely insert gaps using CTRL+click + drag.

Hope this helps!
Jim.

>
> Thanks,
> Felicia
> ---------------------------------------------------------------
> Felicia Gomez
> Tishkoff Lab
> Department of Genetics
> University of Pennsylvania
> 430 Clinical Research Building
> 415 Curie Boulevard
> fgomez at mail.med.upenn.edu
> Lab Phone: 215-746-2683
>
> On Mar 18, 2010, at 7:22 AM, Jim Procter wrote:
>
>> On 17/03/2010 21:53, Felicia Gomez wrote:
>>> Hi,
>>> I have just  started using Jalview, so this may be a simple question,
>>> but I am not sure how to solve it.  I would like to add gaps to a
>>> group of sequences in an alignment, but I am having trouble doing
>>> so.   I have Jalview installed (I am not using the webstart version)
>>> on  a Mac running OS X 10.5.8.  I am able to add gaps to one sequence
>>> using the left  mouse button  and the  shift key, but when I  hold
>>> down the apple key (command key) and try to drag my sequences using
>>> the left mouse button it does not add gaps.
>> The control key + dragging within a selected group of sequences will
>> insert gaps into all the selected sequences. In the current version of
>> Jalview, you have to select sequences before you can insert gaps into a
>> group of them - I suspect you may not have done this. Try selecting a
>> few sequences and then inserting gaps.
>>
>> We plan to review the way that interactive editing works in Jalview -
>> thanks for highlighting this minor (but significant) issue !
>>
>> Thanks
>> Jim.
>>
>> -- 
>> -------------------------------------------------------------------
>> 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
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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
The University of Dundee is a Scottish Registered Charity, No. SC015096.