Ah - no problem !
Your default jalview properties file lives in ~/.jalview_properties ..
since you aren't using the 'props' argument to provide a custom
properties file, jalview will use that one.
In your case, you can either append the lines to that file, or add the
settings via the GUI. For the ID width problem, simply open your Jalview
preferences, select the 'Output' tab, and then make sure the
'Automatically fit ID width' checkbox is checked. Right align is enabled
from the 'Visual' tab. Remember to press OK and close Jalview to update
your properties file afterwards.
For reproducibility's sake, once you've made the changes, I'd recommend
you copy your default file to somewhere where your script lives, and add
a -props argument to include it. That means your output will stay the
same even if you change your jalview preferences in the future.
Let me know how you get on !
Jim
On 09/06/2015 11:46, Alessandra Gastaldello wrote:
I am very sorry Jim but, however strange could sounds, I don't have a
properties file......
is It a text file? Where I could find it? or how create it?
I tried to understand what it was before to write to the discussion
forum to put it in my code, but I didn't understand how to do it. I am
new to this "world"....
I have attached my batch file and my code just to show you how they
look like. At the line 22 there is the code where I call for the batch.
Thank you very much.
Alessandra
2015-06-09 11:31 GMT+02:00 Jim Procter <[email protected]
<mailto:[email protected]>>:
Hi again, Alessandra.
Append the following lines to your jalview properties file:
FIGURE_AUTOIDWIDTH=true
RIGHT_ALIGN_IDS=false
(also make sure there's a return or blank line at the end of the
properties file).
This will tell jalview to automatically compute the margin to fit
in all sequence IDs, and also right align them so that the
start/end numbering appear in the same place each time.
Jim.
On 09/06/2015 09:53, Jim Procter wrote:
Hi Alessandra.
From your image, it looks like the ID width margin is not being
set automatically. There was a feature introduced to set the
margin automatically, or keep it as a fixed width for flipbook
style alignment browsing (where you don't want the margin to move
around).
We'll take a look at it and get back to you. Could you let me
know which version of Jalview you're running in your code ?
Jim
On 09/06/2015 09:24, Alessandra Gastaldello wrote:
Hello,
this is my problem:
I used a jalview batch to incorporate jalview into an alignment
program.
I put some parameters as -colour, and -png to safe the resulting
file as image.
All is ok except in the png files there is a superimposition of
some letters and numbers at the beginning of the images, as if
the images were not large enough to display correctly.
I can't find a way to set up some parameters to try to have
images with different dimensions.
To save in svg doesn't change the result.
If I use jalview desktop and I save the box as png image all is
ok, not superimposition, but i can't use it because I need to
include jalview into my code.
Any suggestion to set some parameters ?
I attached an image as example. As you can see numbers in the
left side are not display correctly.
Thanks.
Alessandra
_______________________________________________
Jalview-discuss mailing list
[email protected] <mailto:[email protected]>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
[email protected] <mailto:[email protected]>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
[email protected] <mailto:[email protected]>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
_______________________________________________
Jalview-discuss mailing list
[email protected]
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
