From 4647e218f2e25f3a2bbd76ae3324678c94e59ed9 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 8 Sep 2015 19:51:52 +0100 Subject: [PATCH] JAL-1541 doc for biojs msa --- help/html/features/biojsmsa.html | 48 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 help/html/features/biojsmsa.html diff --git a/help/html/features/biojsmsa.html b/help/html/features/biojsmsa.html new file mode 100644 index 0000000..7b383b0 --- /dev/null +++ b/help/html/features/biojsmsa.html @@ -0,0 +1,48 @@ + +

BioJS MSA Viewer

+ +Since Jalview 2.9, BioJS MSA HTML files can be generated from alignment within the Jalview desktop application. BioJS MSA Viewer is a JavaScript based multiple sequence alignment visualisation system. Jalview generates BioJS HTML files by parsing a BioJS MSA export template file and embedding BioJSON data from a given alignment on the Jalview desktop application. + +

To ensure that the BioJS MSA export mechanism is easily extensible, the export templates are externalised from the Jalview codebase. Consequently, new versions of BioJS MSA Viewer can easily be integrated into Jalview without having to deploy a new version of Jalview.

+ +

What constitutes a BioJS MSA Template

+ + + + + +The externalised BioJS MSA templates are available in the github repository https://github.com/jalview/exporter-templates/tree/master/biojs. +
Jalview looks at 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 a new BioJS MSA template +
    +
  1. Add/update all BioJS MSA scripts to the template file
    2. +
  2. Update codes for transforming BioJSON data to BioJS MSA data (this requires knowledge of both data models)
    3. +
  3. Ensure that the new template created can be employed by Jalivew to generate valid BioJS MSA files. This can be achieved by following the steps below to deploy the new export template to a test repo and subsequently configure jalview to use the test repo for testing the template:
    4. + +
  4. Commit the new template to the official Jalview-BioJS github template repository https://github.com/jalview/exporter-templates/tree/master/biojs
    5. +
  5. Update the package.json of the official template repo at https://github.com/jalview/exporter-templates/blob/master/biojs/package.json accordingly
    6. +
  6. Restore value for 'biojs_template_git_repo' in jalview_properties to point to the official template repo
    7. +
  7. Restart Jalview
    8. +
+ +Note: +Whenever Jalview starts up, if internet connection is available, it checks if there are new updates of BioJS MSA template added to the repository and downloads them to a local user directory for subsequent offline use. + -- 1.7.10.2