* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>BioJSON-1.0</title>
+<title>BioJSON in Jalview</title>
</head>
<body>
- <h1>BioJSON 1.0</h1>
- BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of multiple sequence alignment data.
- The first version of the specification was developed in 2015 and implemented in Jalview 2.9. Find out more about BioJSON
- at <a href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
-
- <h2>Features supported</h2>
- Export and import of a single alignment along with it's properties listed below:
- <ul>
- <li>Alignment Annotations</li>
- <li>Alignment Features</li>
- <li>Alignment Sequences</li>
- <li>Color Scheme</li>
- <li>Hidden Columns</li>
- <li>Hidden Sequences</li>
- <li>Sequence Groups</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>
- <h2>Features not yet supported</h2>
- The following features are not supported in BioJSON-1.0:
- <ul>
- <li>Export and import of Reference sequence</li>
- <li>Export and import of Representative sequence</li>
- <li>Export and import of Trees</li>
- <li>Export and import of 3D Structures</li>
- </ul>
+ <p>
+ <strong>Jalview's Support for BioJSON v1.0</strong>
+ </p>
+ <p>BioJSON exports of an alignment view include the following
+ additional data:</p>
+ <ul>
+ <li>Alignment Annotations</li>
+ <li>Alignment Features</li>
+ <li>Alignment Sequences</li>
+ <li>Color Scheme</li>
+ <li>Hidden Columns</li>
+ <li>Hidden Sequences</li>
+ <li>Sequence Groups</li>
+ </ul>
+ <p>The following data are NOT currently preserved on export:</p>
+ <ul>
+ <li>Alignment Reference sequences</li>
+ <li>Representative sequence groups</li>
+ <li>Trees</li>
+ <li>3D Structures</li>
+ </ul>
</body>
</html>