BioJSON support in Jalview

BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of multiple sequence alignment data.

Jalview 2.9 includes support for reading and writing BioJSON v1.0 data directly, or embedded in HTML documents. It can also generate HTML pages which employ the BioJS MSA viewer for interactive display of BioJSON data.

Finding out more about BioJSON

The BioJSON specification is published at http://jalview.github.io/biojson/.

Import of BioJSON data from HTML pages

When importing embedded data in an HTML document, Jalview searches for a hidden (usually) input or div element named "seqData":

        <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>

OR

        <input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>

Jalview can also import BioJSON data directly.

Jalview's Support for BioJSON v1.0

BioJSON exports of an alignment view include the following additional data:

- Alignment Annotations
- Alignment Features
- Alignment Sequences
- Color Scheme
- Hidden Columns
- Hidden Sequences
- Sequence Groups

The following data are NOT currently preserved on export:

- Alignment Reference sequences
- Representative sequence groups
- Trees
- 3D Structures