Dear Seb,
I am currently updating Jalview’s BioJS exporter templates to the latest BioJS
version. I noticed the following changes in the latest version of BioJS MSA:
* The ‘Features’ data model and renderer seems to have changed
* GFF parser is now completed and can also parse Jalview features
* GFF parser is favoured for adding features to BioJS MSA
Apart from ‘features’, every other thing seems to be working in the update. I
am wondering if the support for adding features programatically as shown below
is still supported, if so please could you point me to an updated
documentation/snippet.
var Feature = msa.model.feature;
var f1 = new Feature({xStart:7 ,xEnd: 20,text: "foo1", fillColor: "red"});
var f2 = new Feature({xStart:21,xEnd: 40,text: "foo2", fillColor: "blue"});
var f3 = new Feature({xStart:10,xEnd: 30,text: "foo3", fillColor: "green"});
m.seqs.at<http://m.seqs.at>(1).set("features", new
msa.model.featurecol([f1,f2,f3]));
Also, we developed BioJSON<http://jalview.github.io/biojson/> - a JSON format
for representing an alignment along with its meta-data (features, groups,
annotations, etc). This is actually what we embed into the exported BioJS file
and provide a converter code for transforming the data into BioJS MSA. It would
really be nice if BioJS MSA can support the BioJSON
format<http://jalview.github.io/biojson/>. Although this is still incubating,
we are hoping that this format will be wildly utilised and subsequently adopted
as a standard in the future.
Finally, I would like to follow BioJS MSA developments more closely, is there
any mailing list I can join for this purpose?
Thanks and regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
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