Bug in annotation file parser

Jalview Discussion
#1

Dear Jalview developers,

Thank you for programming this tool. I am not familiar with the
formalities of your bug reporting system, but I still want you to inform
about this issue.

There seems to be strange bug, if NO_GRAPH" secondary structure
annotations are parsed from an annotation file: If there is a lower case
representation of the used
secondary structure symbol ("H" or "E") present in the text label, the
visual result is an arrow that shows to left. Example...

H,phosphorylation site|

...results in a left directed arrow, while...

H,pxospxorylation site|

results in a bar.

If |E,phosphorylation site| and |E,phosphorylation sitx| are used, this
results in a left and right directed arrow, respectively. If three fields
are used, it is the third field (text label) that matters: |E,phosphorylation
site,phosphorylation sitx| results in right directed arrow, while

E,phosphorylation site,phosphorylation site| in a left directed one.

I use InstallAnywhere,Linux version that I downloaded a few days ago.

A little example is attached.

Best regards
Arne

my_alignment.fasta (186 Bytes)

my_annotation (167 Bytes)

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#2

Hello Arne,

Thanks for reporting this and providing such a clear example.

It does look like a bug, whose root cause is that the code is trying to interpret the display text of the annotation as if it were 'e' as in RNA secondary structure (E-e) base pair notation. (The bug also occurs with sequences that are unambiguously protein residues.)

I have raised a bug report for this
http://issues.jalview.org/browse/JAL-1813
and we'll fix it at the earliest opportunity.

Thanks and best regards,

Mungo

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

···

________________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Arne Sahm <asahm@fli-leibniz.de>
Sent: 14 July 2015 18:44
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Bug in annotation file parser

Dear Jalview developers,

Thank you for programming this tool. I am not familiar with the
formalities of your bug reporting system, but I still want you to inform
about this issue.

There seems to be strange bug, if NO_GRAPH" secondary structure
annotations are parsed from an annotation file: If there is a lower case
representation of the used
secondary structure symbol ("H" or "E") present in the text label, the
visual result is an arrow that shows to left. Example...

H,phosphorylation site|

...results in a left directed arrow, while...

H,pxospxorylation site|

results in a bar.

If |E,phosphorylation site| and |E,phosphorylation sitx| are used, this
results in a left and right directed arrow, respectively. If three fields
are used, it is the third field (text label) that matters: |E,phosphorylation
site,phosphorylation sitx| results in right directed arrow, while

E,phosphorylation site,phosphorylation site| in a left directed one.

I use InstallAnywhere,Linux version that I downloaded a few days ago.

A little example is attached.

Best regards
Arne

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   "Webmail for nuts!"
http://squirrelmail.org/

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http://squirrelmail.org/

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