The BioJS MSA Templating System

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2Fbiojsmsa-templates.html;fp=doc%2Fbiojsmsa-templates.html;h=161c30948c4f723086e4c9084ac0c18f4f1a0bdf;hb=9623cea766a766683243235557ad48e6f7659e6a;hp=0000000000000000000000000000000000000000;hpb=6066400ed6b0fe288ebbea82389f59838a534706;p=jalview.git diff --git a/doc/biojsmsa-templates.html b/doc/biojsmsa-templates.html new file mode 100644 index 0000000..161c309 --- /dev/null +++ b/doc/biojsmsa-templates.html @@ -0,0 +1,101 @@ + + +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

All JavaScripts necessary to render and visualise BioJS + data
JavaScripts to transform BioJSON data to BioJS MSA data

Place holder for BioJSON data (this can be a div or input + element as show below):

+        <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>  OR
+<input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>
+
+

+ + 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: +
1. Publish the template along with a valid package.json + file to an online repository
2. 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 +
3. Restart Jalview and ensure that the new templates are + downloaded
4. Export an alignment to BioJS MSA
5. 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

+ + +