X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2Fbiojsmsa-templates.html;fp=doc%2Fbiojsmsa-templates.html;h=40e326dbee4eeb8a31a451fa98c59282889354f8;hb=dfb7b17a2c6b0019320d6fbdddbbd16b933dc62d;hp=0000000000000000000000000000000000000000;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git
diff --git a/doc/biojsmsa-templates.html b/doc/biojsmsa-templates.html
new file mode 100644
index 0000000..40e326d
--- /dev/null
+++ b/doc/biojsmsa-templates.html
@@ -0,0 +1,81 @@
+
+
The BioJS MSA Templating System
+
+ BioJS MSA Templates
+ 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.
+ 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 !
+ The components of a BioJS template file
+
+
+ The externalised BioJS MSA templates are available in the Github
+ repository
+ https://github.com/jalview/exporter-templates/tree/master/biojs.
+
Jalview processes the
+ package.json file at
+ https://github.com/jalview/exporter-templates/blob/master/biojs/package.json
+ to work out the available versions of BioJS MSA Viewer templates and
+ the latest release version to use for its exports.
+
+
+ Creating/Updating a new BioJS MSA Template
+ The following steps can be taken to create or update a BioJS MSA
+ template
+
+ - Add/update all BioJS MSA scripts to the template file
+ - Add/update codes for transforming BioJSON data to BioJS MSA
+ data (this requires knowledge of both data models)
+ - 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:
+
+ - Publish the template along with a valid package.json
+ file to an online repository
+ - Configure Jalview preferences to point to the raw URL
+ of package.json in your test repository. This is done by
+ creating/changing the property 'biojs_template_git_repo'
+ in the jalview_properties file
e.g. biojs_template_git_repo=https://raw.githubusercontent.com/gituser/biojs-templates/package.json
+
+ - Restart Jalview and ensure that the new templates are
+ downloaded
+ - Export an alignment to BioJS MSA
+ - Check that the exported file is valid and reflects all
+ the incorporated changes
+
+
+ - Commit the new template to the official Jalview-BioJS
+ Github template repository https://github.com/jalview/exporter-templates/tree/master/biojs
+
+ - Update the package.json of the official template repository
+ at https://github.com/jalview/exporter-templates/blob/master/biojs/package.json
+ accordingly
+
+ - Restore value for 'biojs_template_git_repo' in
+ jalview_properties to point to the official template repository
+
+ - Repeat steps 3iii to 3v above
+
+
+
+
\ No newline at end of file