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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