[Jalview-discuss] Help with displaying a large number of alignments

Jim Procter jprocter at compbio.dundee.ac.uk
Mon Jan 21 08:21:33 GMT 2013

Hello Alvin,

On 18/01/2013 01:27, Yu Jin NG Alvin (IMCB) wrote:
> I was wondering if someone can tell me how to script/program jalview 
> so that I can display a large number of alignments (~1k) from a fasta 
> file and export it in a png (example attached) file with certain 
> display preferences.
> I require the alignment to be
> 1)Colored by percentage identity
> 2)Wrapped at around 50 residues
> 3)Not have any annotation
> 4)Have a scale above
> 5)Remove the left scale
> 6)Be species ordered
> 7)Exported to a png file
> I'm able to set preference for 1), 2), 3) for the first 100 I've done 
> so that it makes it a little faster for me.
> Any help/suggestions or a quick reference to the java functions? Would 
> be much appreciated.
We don't have a quick reference for the scripting api yet - I'm hoping 
that is something that will be put together in the next few months.

Are you using Jalview's command line mode for writing PNG files ? (I 
presume so - if not see 
http://www.jalview.org/help/html/features/clarguments.html ) - in which 
case, you can specify 1, 2 (sort of), 3, 4 and 5 via a properties file 
(see the format menu for the options).

The missing features as far as I can see is that there's no option for 
setting the number of columns in wrap mode, and species ordering is not 
something that Jalview can do automatically - but you could do it using 
a 'sort by annotation', 'sort by features' or 'sort by tree' operation 
after loading annotation onto the alignment, but there might be one or 
two snags that need straightening out.

Contact me off list with an example alignment and properties file and 
I'll take a look.

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