- <h1>BioJson (version-1.0)</h1>
- BioJson is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data.
- BioJSon-1.0 schema/documentation is available <a href="http://www.jalview.org/builds/develop/examples/biojson-doc/">here</a>.
- You can keep up to date with BioJson development and latest news <a href="https://github.com/jalview/biojson/wiki">here</a>.
-
- <h2>Features supported</h2>
- Export/Import of the following alignment elements are supported in BioJson-1.0:
- <ul>
- <li>Alignment Sequences</li>
- <li>Alignment Features</li>
- <li>Alignment Annotations</li>
- <li>Sequence Groups</li>
- <li>Color Scheme</li>
- <li>Hidden Sequences</li>
- <li>Hidden Columns</li>
- </ul>
+ <p>
+ <strong>BioJSON support in Jalview</strong>
+ </p>
+ <p>BioJSON is a JavaScript Object Notation (JSON) specification
+ for the representation and exchange of multiple sequence alignment
+ data.</p>
+ <p>
+ 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 <a href="biojsmsa.html">BioJS MSA
+ viewer</a> for interactive display of BioJSON data.
+ </p>
+ <p>
+ <strong>Finding out more about BioJSON</strong>
+ </p>
+ <p>
+ The BioJSON specification is published at <a
+ href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
+ </p>
+ <p>
+ <em>Import of BioJSON data from HTML pages</em>
+ </p>
+ <p>When importing embedded data in an HTML document, Jalview
+ searches for a hidden (usually) input or div element named
+ "seqData":</p>
+ <pre>
+ <code><div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div></code>
+ </pre>
+ <strong>OR</strong>
+ <pre>
+ <code><input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/></code>
+ </pre>
+ <p>Jalview can also import BioJSON data directly.</p>