Hello Martin,
Thanks for pointing that out. I reproduced it and it led me to a line of code
with a comment against it:
// FIXME getDefaultToolkit throws an exception in Headless mode
which I added a year ago (blush).
As you say, I don't think it creates a functional problem here, but we can tidy
up the exception handling.
Mit freundlichen Grüßen.
Mungo
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The Barton Group
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________________________________
From: [email protected] <[email protected]> on
behalf of Martin Raden <[email protected]>
Sent: 18 February 2018 17:05:00
To: [email protected]
Subject: [Jalview-dev] bioconda jalview : Headlessexception
Hi all,
with the recent bioconda jalview installation I get for a call like this
jalview -nodisplay -open mRNA.fasta -feature mRNA_feature.txt
-annotation mRNA_annotation.txt -svg mRNA.svg
an output like that
#########################
Java version: 1.8.0_121
amd64 Linux 2.6.32-696.18.7.el6.x86_64
Jalview Version: 2.10.3-1 (bioconda git-commit: [])
CMD [-open mRNA.fasta] executed successfully!
File format identified as Fasta
Feb 18, 2018 5:55:40 PM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
java.awt.HeadlessException
CMD [-annotations mRNA_annotation.txt] executed successfully!
Written alignment in Fasta format to mRNA_feature.txt
Creating SVG image: mRNA.svg
#########################
I get the output I want but as far as I got the docu right, there
shouldnt be any HeadlessException in -nodisplay mode.. right?
Just to ping.. :)
Thanks and best,
Martin
--
Dr. Martin Raden, nee Mann, Postdoc
Bioinformatics - Prof. Dr. R. Backofen
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Forest Growth and Dendroecology
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