bioconda jalview : Headlessexception

[martin_raden]

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
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

[g_m_carstairs]

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

···

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

---

From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Martin Raden mmann@informatik.uni-freiburg.de
Sent: 18 February 2018 17:05:00
To: jalview-dev@jalview.org
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
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
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/

Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de

---

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