* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>BioJSON in Jalviwe</title>
+<title>BioJSON in Jalview</title>
</head>
<body>
<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>
+ 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>
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>
+
+ <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>
+ <p>BioJSON exports of an alignment view include the following
+ additional data:</p>
<ul>
<li>Alignment Annotations</li>
<li>Alignment Features</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>
+ <p>The following data are NOT currently preserved on export:</p>
<ul>
<li>Alignment Reference sequences</li>
<li>Representative sequence groups</li>