[Jalview-discuss] Hiding columns with many gaps

[Jim Procter]

On 18/04/2011 15:41, Jérôme Hénin wrote:
> Hi everyone,
>
> Sorry if this is something that has been discussed before, I looked
> for it and couldn't find any info.
>
> In large multiple alignments, it can be convenient to hide positions
> (columns) where more than a certain fraction of sequences have gaps.
> I've seen that option in other editors (e.g. MUST). Is there a way to
> do this in Jalview? If not, does anyone think it would be worthwhile
> to implement?
It's definitely worthwhile - and Jalview doesn't do it yet. 
Unfortunately, I've been distracted by other jalview development 
priorities. However, there's an entry (albeit rather terse) in our 
bug-tracker here: http://issues.jalview.org/browse/JAL-508

Essentially, the approach that would be taken is to have a dialog that 
allows the user to select and/or hide columns based on any annotation's 
threshold or label content, analogous to the colour by annotation dialog 
(you could even use the same dialog, and just put hide/select buttons 
there instead!).
> I'd offer to do it, but my knowledge of Java is pretty much zilch. I
> do know C++ though, so it might be easy to learn enough about Java to
> do the job, with pointers from people who know the code well.
It's not too hard to do. It would probably take someone experienced with 
the code a couple of days to do, in fact (including documentation and 
porting the feature to the java applet). In your case, it'd be more like 
a couple weeks work on & off (or maybe a week full-time), once I'd 
pointed you to the key classes/methods.

I've also been thinking of adding in GBLOCKS 
(http://molevol.cmima.csic.es/castresana/Gblocks.html) either as a 
service or as a built-in routine. This algorithm is one of a variety of 
methods that have been developed for automatically selecting the most 
informative/useful regions of an alignment prior to performing further 
analysis (e.g. tree building).

Let me know if you're interested in taking this further !  :)
Jim.