Sequence IDs are cut off when generating PNG via the command line

Hi Sven.

Unfortunately there isn’t an option to make the label margins as wide as the longest id… and you’re right, that was a feature, but I’ve hit the problem you describe myself.

The simplest workaround is to enable the ‘right align ids’ option in Jalview’'s preferences (and merge the resulting new property file line with the properties your passing in on the command line). Then you will at least see the right hand part of all sequences, which is sometimes enough.

Let me know if that does the job!
Jim.

J. B. Procter Jalview/enfin Barton group

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-----Original Message-----
From: Sven-Eric Schelhorn pilgrim@gmx.ch
To: jalview-discuss@jalview.org
Sent: Tue, 08 Nov 2011 19:39
Subject: [Jalview-discuss] Sequence IDs are cut off when generating PNG via the command line

Dear Jalview Users,

when generating a PNG of a multifasta-alignment via the command-line option of Jalview, only the first 15 or so characters of the sequence IDs are correctly plotted to the image while the rest of the ID is cut off. Since the alignment itself is plotted just fine I suspect that this is a feature rather than a bug. However, I would like to see the full (30 characters or so long) sequence IDs in my PNG. Is there any option in the Jalview property file or elsewhere that enables plotting of the full, uncut sequence IDs?
Thank you very much for your support.

With regards,
Sven

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Dear Jim,

thanks for the reply. Yes, I also tried the right-aligned option, but it still does not cut it for me. I have 30 or so meaningful characters in the sequence ID and I need to see them all.

OK.

Any chance that the auto-sized label margins (or user-defined n characters wide margins) might be implemented in Jalview? Seems to be such a common and useful thing to have. Thanks!

I'm not sure how common it actually is - we've had a bug related to this in the database for a while, but I think most people who use Jalview don't generate lots of alignments in batch mode (and tend to use very short sequence ids, such as taxa shortnames).

That being said, it's a reasonably simple patch, and near code that I am working on at the moment, so I can probably get it done in the (very) near future. Certainly by next month, anyhow.

Jim.

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On 09/11/2011 09:46, Sven-Eric Schelhorn wrote:

Turns out it was a few hours to put together, and was easier to finish immediately than it was to file under 'todo'...
If you download the latest 2.7 branch build (http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/release/) then you'll find the 'Output' panel has a couple of new settings.. the one you want is 'Automatically set ID width'. You can also manually specify the ID width (in pixels), if you want a consistent margin when generating a large number of alignment figures.

Jim.

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On 09/11/2011 10:10, Jim Procter wrote:

That being said, it's a reasonably simple patch, and near code that I am working on at the moment, so I can probably get it done in the (very) near future.