<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Split Frame View" target="splitframe" />
- <tocitem text="Fetching Sequences" target="seqfetch" />
- <tocitem text="BioJSON v1.0" target="biojson" />
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
<tocitem text="PDB Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
<tocitem text="Chimera Viewer" target="chimera" />
<tocitem text="Select columns by annotation" target="selectcolbyannot" />
<tocitem text="Annotations File Format" target="annotations.fileformat" />
+ <tocitem text="BioJSON v1.0" target="biojson" />
<tocitem text="Latest Release Notes" target="release"/>
</tocitem>
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>BioJSON-1.0</title>
+<title>BioJSON in Jalviwe</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>
-
- <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>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>
<title>Exporting alignments as artwork</title>
</head>
<body>
-<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>
-<p>The alignment view can be printed using
-<strong>File→Print</strong>, or exported in a number of ways via the
-<strong>File→Export</strong> menu:
-<ul>
-<li>HTML<br><em>for viewing in a web browser</em>
-</li>
-<li>PNG - a Portable Networks Graphics image<br><em>For low quality
-diagrams and powerpoint presentations</em>
-</li>
-<li>EPS - an Encapsulated Postscript Document<br><em>For high quality
-diagrams and publications.</em>
-<li>SVG - a Scalable Vector Graphics document<br><em>For high quality
-diagrams in publications and on the web.</em>
-</li>
-<li>BioJS - A JavaScript based multiple sequence alignment visualiser. <br><em>For viewing in a web browser. Get more info about BioJS at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a></em>
-</li>
-
-</ul>
-
-<p>From Jalview 2.9, the HTML exporting system was re-implemented to use SVG rendering. Also, optional embedding of <a href="../features/bioJsonFormat.html">BioJSON</a> data to the generated HTML file was introduced.
-This is achieved using a hidden input or div element which MUST be named "seqData" as seen in the examples below:
-<pre><code> <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>
- OR
- <input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/></pre></code>
-HTML file embedded with BioJSON can be imported back to Jalview at a later date. During the import operation, Jalview uses an API called JSoup to traverse through the HTML file and extract the embedded BioJSON data from the target div or input element named <b>'seqData'</b>. The extracted data is then parsed as a BioJSON format.
-
+ <p>
+ <strong>Exporting alignments as graphics and lineart<a
+ name="export"></a></strong>
+ </p>
+ <p>
+ The alignment view can be printed using <strong>File→Print</strong>,
+ or exported in a number of ways via the <strong>File→Export</strong>
+ menu:
+
+ <ul>
+ <li>HTML<br>
+ <em>for viewing in a web browser</em>
+ </li>
+ <li>PNG - a Portable Networks Graphics image<br>
+ <em>For low quality diagrams and powerpoint presentations</em>
+ </li>
+ <li>EPS - an Encapsulated Postscript Document<br>
+ <em>For high quality diagrams and publications.</em>
+ <li>SVG - a Scalable Vector Graphics document<br>
+ <em>For high quality diagrams in publications and on the web.</em>
+ </li>
+ <li>BioJS MSA - A JavaScript based multiple sequence alignment
+ viewer. <br> <em>For interactive alignment data
+ visualisation in a web browser.<br />Get more info about the
+ BioJS MSA viewer at a
+ href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+ </em>
+ </li>
+ </ul>
+ <a name="htmlexport" />
+ <p>
+ <strong>Exporting alignments as Web Pages</strong>
+ <p>
+ In Jalview 2.9, new HTML exporting options were introduced. The
+ standard HTML export option displays alignments as SVG documents
+ embedded as scollable panes. Exported pages can optionally also
+ include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
+ which allows Jalview to extract the original data used to create the
+ page. Jalview can also generate HTML pages which embed BioJSON data
+ and the BioJS MSA viewer, a pure javascript alignment viewer that
+ provides a range of interactive analysis capabiltiies.
+ </p>
+ <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 input or div element named "seqData":
+ <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>
+ Jalview can also import JSON data directly if it conforms to the BioJSON specification.
+</p>
<p><em>Tips for working with EPS Files</em></p>
<li>The EPS file generated by Jalview contains vector graphics which are directly
editable in graphics applications such as Adobe Illustrator.</li>
including the loss of pseudoknots when RNA secondary structure is
shown VARNA.</li>
<li><strong>Protein Secondary Structure predictions
- with JPred4</strong>Jalview includes a number of new features for working
+ with JPred4</strong><br/>Jalview includes a number of new features for working
with secondary structure predictions from the JPred4 server. These
include the ability to automatically hide insertions and highlight
mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new scrollable SVG HTML export mode was also
+ Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable SVG HTML export</a> was also
developed specifically for the JPred4 server.</li>
</ul>
git://source.jalview.org / jalview.git / commitdiff