Find command

I think in previous versions the Find command would also search sequence IDs and descriptions. It doesn't in the latest 2.8. Could that be added back? 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.

Thanks, Mark

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Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

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

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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On 25/12/2012 18:45, Mark Saper wrote: