* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>BioJson-1.0 A JSON File Format</title>
+<title>BioJSON in Jalviwe</title>
</head>
<body>
- <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>
-
- <h2>Features not yet supported</h2>
- Export/Import of the following alignment elements are not supported in BioJson-1.0:
- <ul>
- <li>Reference sequence</li>
- <li>Representative sequence</li>
- <li>Trees</li>
- <li>3D Structures</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 BioJS MSA viewer 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>
+ <strong>Jalview's Support for BioJSON v1.0</strong>
+ </p>
+ <p>It is currently possible to export an alignment view along with
+ 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>
+ <strong>Jalview data not supported in BioJSON v1.0</strong>
+ </p>
+ <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>
git://source.jalview.org / jalview.git / blobdiff