Hi Alessandra. I'm glad you've got this working !
Regarding the SVG output - there's nothing in the current version of
Jalview that you can change to modify the borders on the SVG file. We're
working on a more flexible system for v2.9 - which is already in use on
the Jpred4 site (http://www.compbio.dundee.ac.uk/jpred4/), and I'll add
a feature request about allowing borders on the output. However, SVG
output is also very easy to manipulate, since it is simple XML, so it
might be easier to simply add in some additional commands to create a
white border around the alignment.
Jim
On 10/06/2015 11:04, Alessandra Gastaldello wrote:
Thank you Jim, It works!
Just a last question if I can.... Could I add some setting in the
properties file, to modify the pictures in a way I can have more blank
margins?
How you can see in the attached image It seems a little bit too 'cut'...
Thanks!
Alessandra
2015-06-09 14:02 GMT+02:00 Jim Procter <[email protected]
<mailto:[email protected]>>:
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
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