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(1).set(“features”, new msa.model.featurecol([f1,f2,f3]));
Also, we developed 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. 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
www.compbio.dundee.ac.uk
The University of Dundee is a registered Scottish Charity, No: SC015096