export pictures of overview and via command-line

Hello,
I have two questions:

  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?

  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?

Thanks in advance,
Tim

hi, I am also interested in this feature! :slight_smile:

···

2010/4/1 Timothée Flutre <timothee.flutre@versailles.inra.fr>:

Hello,
I have two questions:

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?

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?

Thanks in advance,
Tim

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Hi Timothée !

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 :slight_smile: 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.

···

On 01/04/2010 12:24, Timothée Flutre wrote:

--
-------------------------------------------------------------------
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.

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@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.

  1. 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 :slight_smile: 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.