Hello Roisin Just to follow up here.. once you have run the script I'd recommend right-aligning the sequence IDs via the format menu so the species suffix is always visible.
Supporting species labels is a long standing goal that we will shortly start work on as part of our next major release, 2.12, so hopefully you'll only need to use this script for a few months! Jim. On Sat, 6 Jul 2019, 09:55 Mungo Carstairs (Staff), < [email protected]> wrote: > Hi Roisin, > > > When Jalview reads FASTA (and other format) sequence data, it splits the > sequence identifier into an id (everything before the first space) and > description (everything after the first space). > > > As this doesn't seem to be part of the FASTA specification, we could maybe > consider offering an option to treat the whole string as the id, but until > then there is no easy way in the application to 'recombine' them in the id. > > > What you could do as a workaround is to run this Groovy script (Tools | > Open Groovy Console): > > > al = jalview.bin.Jalview.currentAlignFrame.viewport.alignment > for (seq in al.sequences) > { > seq.name = seq.name + " " + seq.description > } > > And then click in the alignment to refresh the display. > > This should simply concatenate the description to the sequence name. > > > Best regards, > > > Mungo > [image: Email signature] > > [image: University of Dundee shield logo] <http://uod.ac.uk/sig-home> > > *Mungo Carstairs* > Jalview Computational Scientist > > The Barton Group > Division of Computational Biology > > School of Life Sciences > > University of Dundee, Dundee, Scotland, UK > > www.jalview.org > > www.compbio.dundee.ac.uk > [email protected] > [image: University of Dundee Facebook] <http://uod.ac.uk/sig-fb> [image: > University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [image: > University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [image: > University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [image: > University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [image: > University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> > *We're Scottish University of the Year again!* > <http://uod.ac.uk/sig-strapline> > The Times / Sunday Times Good University Guide 2016 and 2017 > ------------------------------ > *From:* roisin mcallister <[email protected]> > *Sent:* 05 July 2019 16:38:28 > *To:* Mungo Carstairs (Staff) > *Subject:* Re: [Jalview-discuss] how to see species names > > Hi Mungo > thanks for speedy reply! No error and I have pulled the panel out wider. I > attach so you can see what I mean. The species name is "there" if I point > to it with cursor....but I would like it displayed in name as well if poss. > Roisin > > On Fri, Jul 5, 2019 at 4:21 PM Mungo Carstairs (Staff) < > [email protected]> wrote: > > Hello Roisin, > > > Could you explain a bit more "I can't get JalView to allow me to see > them."? > > Is there an error happening, or is it just that the names are too long to > see? > > > If the latter, you can drag the name panel to be wider - put the cursor > just above the top sequence name until it changes to a 'drag cursor'. > > You can also change the font size from the Font menu (if that helps). > > > Best regards, > > > Mungo > > > [image: Email signature] > > [image: University of Dundee shield logo] <http://uod.ac.uk/sig-home> > > *Mungo Carstairs* > Jalview Computational Scientist > > The Barton Group > Division of Computational Biology > > School of Life Sciences > > University of Dundee, Dundee, Scotland, UK > > www.jalview.org > > www.compbio.dundee.ac.uk > [email protected] > [image: University of Dundee Facebook] <http://uod.ac.uk/sig-fb> [image: > University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [image: > University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [image: > University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [image: > University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [image: > University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> > *We're Scottish University of the Year again!* > <http://uod.ac.uk/sig-strapline> > The Times / Sunday Times Good University Guide 2016 and 2017 > ------------------------------ > *From:* [email protected] < > [email protected]> on behalf of roisin mcallister < > [email protected]> > *Sent:* 05 July 2019 16:16:33 > *To:* [email protected] > *Subject:* [Jalview-discuss] how to see species names > > Hi > I have a MSA (that has the species names included in the seq names) > I can't get JalView to allow me to see them. I can manually go in and edit > the name, but is there a better way? > Roisin > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >
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