[Jalview-discuss] Find command

Jim Procter jprocter at compbio.dundee.ac.uk
Thu Jan 3 10:45:56 GMT 2013


Hello Mark. Hope you had a good Christmas - despite your problems with 
Jalview's find dialog !

On 25/12/2012 18:45, Mark Saper wrote:
> I think in previous versions the Find command would also search sequence IDs and descriptions.
It actually only searches IDs. I've added a note on an existing 
improvement request about searching descriptions 
(http://issues.jalview.org/browse/JAL-347). This is the kind of feature 
that could be worked on during the Jalview hackathon 
(http://www.ebi.ac.uk/training/handson/course_130121_jalview).

>    It doesn't in the latest 2.8.  Could that be added back?
The find command functionality hasn't been changed in 2.8, but you may 
have had an active selection, in which case, Jalview will only search 
the currently selected range of sequence characters and IDs. Send me an 
example file if you're experiencing this problem without an active 
selection, and I'll see what I can do.
>    You could have some options in Find for where to look.  I have >200 sequences in my file and I want to find those correspoinding to one species.
Options are an excellent idea, and somewhat inevitable.  In addition to 
the description line, there are lots of other annotation and I'd like to 
have better support for species labelling in particular - Jalview 
doesn't do anything special with taxonomic terms (names or NCBI ids) 
currently, and there's lots of room for improvement. I just did some 
housekeeping on the issue tracker to collect some of the relevant 
bugs/feature requests together (see here: 
http://issues.jalview.org/browse/JAL/component/10480)

Jim.



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