Hello Deepak - this is a great suggestion !
I've been meaning to introduce 'real' support for taxonomic names in
Jalview for some time, but there always seemed to be something else that
took higher priority. However - we will definitely have support for this
in the next major Jalview release, and I'll do what I can to introduce
basic support for this even sooner.
For the moment, you could consider running this groovy script (via the
groovy console under the tools menu) - which will do a search and
replace to put anything in parenthesis at the beginning of the sequence
name:
/// groovy script for inserting taxon name at beginning of sequence ID
import jalview.datamodel.*;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
// matches the species name in [parentheses]
def descpattern = ~/.*\[([^]]+)/;
def af = Jalview.getAlignframes();
// walk through all alignments, processing all sequences
for (ala in af)
{
def al = ala.viewport.alignment;
if (al!=null)
{
SequenceI[] seqs = al.getSequencesArray();
for (sq in seqs)
{
if (sq!=null) {
if (sq.getDatasetSequence()!=null)
{
// extract species from dataset sequence description
and place at beginning of ID string in alignment
def mtch =
sq.getDatasetSequence().getDescription().replaceAll(descpattern,'$1')
+"|"+sq.getDatasetSequence().getName();
sq.setName(mtch);
}
}
}
}
ala.repaint()
}
/// end of script - open Tools->Groovy console, copy and paste into
panel and hit the run button!
It's a bit rough and ready, but should do what you want for the moment.
hope that helps!
Jim.
On 18/07/2014 18:17, Deepak Barnabas wrote:
> Dear Jim,
>
> Jalview is indispensable to the vast majority of structural biologists
> including myself. Thanks for your good work with Jalview! We use it on an
> everyday basis. I have a small suggestion. You probably already have this
> option somewhere, and I am not looking hard enough. When visualising multiple
> alignments, it would be very helpful if the organism name is displayed
> instead of sequence name. Considering that a FASTA format download of
> multiple sequences following a BLAST from NCBI always results in the organism
> name being present in the sequence description within parentheses, would it
> not be easy (as an option) if Jalview extracted the string within these
> parentheses and displayed them instead of sequence name. Currently, one has
> to individually hover over each sequence name to display its description to
> look for the organism. Let me know, if I'm missing out on something.
>
> Thanks!
> Deepak
The University of Dundee is a registered Scottish Charity, No: SC015096
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