How to modify writings on jalview images using jalview properties file?

Jalview Discussion
1

Hi,
I am using jalview to have svg image outputs for some protein alignment.
I have built-in into a program a script to do that so I am using jalview-properties file to specify features my svg images have to have.
Normally, in the image, protein ID is automatically followed by two numbers separated by a ‘-’ , indicating the start of the sequence (position 1) and its end (position 43 for example).
I would like to change this numbers by putting another interval or just a number indicating a single position.

Is it possible specifying some parameters to do that in the jalview-properties file or in an other manner?

Thanks!

Alessandra

2

Hello Alessandra

Normally, in the image, protein ID is automatically followed by two numbers separated by a '-' , indicating the start of the sequence (position 1) and its end (position 43 for example).

actually, you can configure the display of sequence limits via the 'Format' option, or the 'SHOW_JVSUFFIX' bookean property.

I would like to change this numbers by putting another interval or just a number indicating a single position.

Jalview honours the limits that are provided in the input file, and tries to deal sensibly with odd things like the sequence end being less than the sequence start, and when the sequence is longer or shorter than the limits suggest. If you only want a single number, then I'm afraid you'll need to encode that in the ID string - perhaps by putting a '-' symbol after the sequence ID.

Hope that helps !
Jim

···

On 09/09/2015 09:04, Alessandra Gastaldello wrote:

3

Thanks Jim!
I introduced ‘SHOW_JVSUFFIX’ and it works.
I didn’t try to modify my IDs because for my purposes is not ideal, but at the moment it is ok in this way1

Alessandra

···

2015-09-09 12:39 GMT+02:00 Jim Procter <jprocter@compbio.dundee.ac.uk>:

Hello Alessandra

On 09/09/2015 09:04, Alessandra Gastaldello wrote:

Normally, in the image, protein ID is automatically followed by two numbers separated by a ‘-’ , indicating the start of the sequence (position 1) and its end (position 43 for example).

actually, you can configure the display of sequence limits via the ‘Format’ option, or the ‘SHOW_JVSUFFIX’ bookean property.

I would like to change this numbers by putting another interval or just a number indicating a single position.

Jalview honours the limits that are provided in the input file, and tries to deal sensibly with odd things like the sequence end being less than the sequence start, and when the sequence is longer or shorter than the limits suggest. If you only want a single number, then I’m afraid you’ll need to encode that in the ID string - perhaps by putting a ‘-’ symbol after the sequence ID.

Hope that helps !
Jim