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+ *Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+<title>The BioJS MSA Templating System</title>
+<body>
+ <h2>BioJS MSA Templates</h2>
+ <p>The Jalview Desktop uses a template file to embed data when
+ exporting an alignment as a BioJS MSA HTML page. This means it is
+ possible to update Jalview's template with different versions of the
+ BioJS MSA viewer, or even customise the page for your own needs.</p>
+ <p>NOTE: This is an experimental feature new in jalview 2.9 -
+ please get in contact with the developers if you're interested in
+ creating your own templates so we can improve this documentation !</p>
+ <h3>The components of a BioJS template file</h3>
+ <ul>
+ <li>All JavaScripts necessary to render and visualise BioJS
+ data</li>
+ <li>JavaScripts to transform BioJSON data to BioJS MSA data</li>
+ <li>Place holder for BioJSON data (this can be a div or input
+ element as show 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#'/>
+</code>
+ </pre>
+ </li>
+ </ul>
+
+ The externalised BioJS MSA templates are available in the Github
+ repository
+ <a
+ href="https://github.com/jalview/exporter-templates/tree/master/biojs">https://github.com/jalview/exporter-templates/tree/master/biojs</a>.
+ <br />Jalview processes the
+ <b>package.json</b> file at
+ <a
+ href="https://github.com/jalview/exporter-templates/blob/master/biojs/package.json">https://github.com/jalview/exporter-templates/blob/master/biojs/package.json</a>
+ to work out the available versions of BioJS MSA Viewer templates and
+ the latest release version to use for its exports.
+
+
+ <h2>Creating/Updating a new BioJS MSA Template</h2>
+ The following steps can be taken to create or update a BioJS MSA
+ template
+ <ol>
+ <li>Add/update all BioJS MSA scripts to the template file</li>
+ <li>Add/update codes for transforming BioJSON data to BioJS MSA
+ data (this requires knowledge of both data models)</li>
+ <li>Ensure that the new template created can be employed by
+ Jalview to generate valid BioJS MSA files. This can be achieved by
+ following the steps below to deploy the new export template to a
+ test repository and subsequently configure Jalview to use the test
+ repository for testing the template:
+ <ol type="i">
+ <li>Publish the template along with a valid package.json
+ file to an online repository</li>
+ <li>Configure Jalview preferences to point to the raw URL
+ of package.json in your test repository. This is done by
+ creating/changing the property <b>'biojs_template_git_repo'</b>
+ in the <b>jalview_properties</b> file <br />e.g. <b>biojs_template_git_repo=https://raw.githubusercontent.com/gituser/biojs-templates/package.json</b>
+ </li>
+ <li>Restart Jalview and ensure that the new templates are
+ downloaded</li>
+ <li>Export an alignment to BioJS MSA</li>
+ <li>Check that the exported file is valid and reflects all
+ the incorporated changes</li>
+ </ol>
+ </li>
+ <li>Commit the new template to the official Jalview-BioJS
+ Github template repository <a
+ href="https://github.com/jalview/exporter-templates/tree/master/biojs">https://github.com/jalview/exporter-templates/tree/master/biojs</a>
+ </li>
+ <li>Update the package.json of the official template repository
+ at <a
+ href="https://github.com/jalview/exporter-templates/blob/master/biojs/package.json">https://github.com/jalview/exporter-templates/blob/master/biojs/package.json</a>
+ accordingly
+ </li>
+ <li>Restore value for <b>'biojs_template_git_repo'</b> in
+ jalview_properties to point to the official template repository
+ </li>
+ <li>Repeat steps 3iii to 3v above</li>
+ </ol>
+
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff