[Jalview-discuss] export pictures of overview and via command-line

[Timothée Flutre]

Thanks for your answers!
I will use the "nodisplay" option from now on (instead of using tricks from
the Python "subprocess" module) and I am waiting for the next releases.
Tim


2010/4/2 Jim Procter <jprocter at compbio.dundee.ac.uk>

> Hi Timothée !
>
> On 01/04/2010 12:24, Timothée Flutre wrote:
>
>>
>> 1) I would like to export the overview of the MSA as a picture. Is it
>> possible within Jalview, ie without taking a screencast? If yes, is it
>> possible to do via the command-line?
>>
> Currently no. The best you could do at the moment is generate a png and
> then use a command line tool (PNGtools for instance) to rescale the image.
> However, Albert and I have a plan to enable Jalview to more easily generate
> overview images.
>
>
>  2) Similarly, when I export a picture of the MSA via the command-line, I
>> run this command:
>> $ java -Djava.ext.dirs=XXX/lib -cp XXX/jalview.jar jalview.bin.Jalview
>> -open myMsa.afa -png myPicture.png
>> But is it possible to do so without having Jalview opening the window?
>>
> Sure. This is one thing we did think of :) The nodisplay argument stops the
> GUI starting:
>
> java -Djava.ext.dirs=XXX/lib -cp XXX/jalview.jar jalview.bin.Jalview
> -nodisplay -open myMsa.afa -png myPicture.png
>
> Jim.
>
> ps. the -help argument will print all the command line arguments jalview
> understands.
> pps. there is a bug in the current 2.4.0b2 version which causes sequence
> features not to be rendered on the PNG images when Jalview is run from the
> command line. This is fixed in the development version and will appear in
> the next release.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
>
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