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!
J. B. Procter Jalview/enfin Barton group
From: Sven-Eric Schelhorn firstname.lastname@example.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.
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