[Jalview-discuss] secondary structure annotation

[James Procter]

Hello Daron.

Daron Standley wrote:
> I thought I had all of this secondary structure stuff sorted out, but
> obviously not. Can someone tell me what I am doing wrong?
It looks like a bug to me. The score annotation is correctly associated
with the sequence, but the secondary structure annotation is not (you
can see this when you edit the alignment, or when you output the
annotation to a text box).  I'll have a look at the
jalview.io.AnnotationFile parser and see what its up to.

You can work around this by adding another SEQUENCE_REF entry before the
secondary structure row :

JALVIEW_ANNOTATION
SEQUENCE_REF	3bknmodA
BAR_GRAPH	Score	 0.06| 3.33| 1.68|-3.97|-1.44| 5.15| 0.97|-3.17|-3.01|
6.67|-3.19| 0.22| 5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86|
6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28| 0.09|-1.60|-1.56|
5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03| 6.65|-1.44|-3.19|
9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48| 1.83| 0.85|
0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91| 1.06|-2.37|-0.70|
5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98| 0.01| 8.89| 6.64|-0.76|
1.61|-3.17| 0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34|
0.94|-0.58|-3.01| 8.57|-1.53| 4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27|
0.22|-3.11|-2.37| 8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59|
1.55|-3.10|-1.57| 2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42|
9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50| 8.03|
7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0|0|0|0|0|0|
SEQUENCE_REF	3bknmodA
NO_GRAPH	Secondary Structure
H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||||||||||||||||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H||H|H|H|H|H|H|H|H||||||||

perseverence always wins out in the end !
Jim

-- 
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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.