remove /start-end extention from output fasta files

Dear All,
Even if it is clearly written that it is possible to remove the /start-end extension added by Jalview* and just conserve the initial sequence id WITHOUT /start-end in an output fasta file format , THIS DOES NOT WORK FOLLOWING THE PROCEDURE * !
(i still have the start and end position after saving at fasta format).

I WOULD BE VERY GRATEFUL IF SOMEONE COULD HELP ME PLEASE

I have a MacOS Sierra 10.12.6 and Java v1.0 for Jalview

Many thanks in advance.

xavier

* In the “File Output” zone of the window (in Preferences), remove the checks from the boxes next to the names of the different formats available)

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Xavier Bailly

Functional Exploration in Marine Model Organisms

Head of Multicellular Marine Models Team (M3)

Station Biologique de Roscoff
Place Georges Teissier
CS 90074
29680 Roscoff Cedex
France

xavier.bailly@sb-roscoff.fr
http://www.sb-roscoff.fr
tel : + 33 2 98 29 23 29
tel : + 33 2 98 29 56 71 (lab)
ligne interne / internal line : 455 or 329

" If you think adventure is dangerous, try routine; it is lethal "

  • Paulo Coelho.

Hi Xavier

Even if it is clearly written that it is possible to remove the /start-end extension added by Jalview* and just conserve the initial sequence id WITHOUT /start-end in an output fasta file format , THIS DOES NOT WORK FOLLOWING THE PROCEDURE * !

This bug crept in a few releases ago. Thanks so much for spotting it !

We’ll release a patched version as soon as possible (
Right now, you can make the ouput work according to your user preferences by opening Jalview’s groovy console (via Tools menu) and pasting in this script:

**for (String format: jalview.io.FileFormats.getInstance().getWritableFormats(true)) {**
**  if ((pref = jalview.bin.Cache.getProperty(format.toUpperCase() + "_JVSUFFIX"))!=null) {**
**     jalview.bin.Cache.setProperty(format+"_JVSUFFIX",pref);**
<b>  }
}</b>

You’ll need to execute the script every time you change the output preferences.

Apologies for the inconvenience!

Jim.

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On 22/11/2017 13:53, xavier bailly wrote:

We’ll release a patched version as soon as possible (

Forgot to include a link to the bug report on our issue tracker: https://issues.jalview.org/browse/JAL-2849

As usual - log in and hit the ‘Watch’ button if you want email updates as we progress the bug…
Jim.

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On 22/11/2017 14:25, Jim Procter wrote: