From d8d179f9c399205f61e7b936dd11a061bfb5de80 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Wed, 9 Sep 2015 10:12:50 +0100 Subject: [PATCH] updated Biojs msa help doc --- help/help.jhm | 1 + help/helpTOC.xml | 1 + help/html/features/biojsmsa.html | 50 ++++++++++++++++++-------------------- 3 files changed, 25 insertions(+), 27 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index fe465ec..622ed5a 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -141,6 +141,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 75ff4c4..60a0ae2 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -36,6 +36,7 @@ + diff --git a/help/html/features/biojsmsa.html b/help/html/features/biojsmsa.html index 7b383b0..fbbb135 100644 --- a/help/html/features/biojsmsa.html +++ b/help/html/features/biojsmsa.html @@ -1,48 +1,44 @@

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. +Since Jalview 2.9, BioJS MSA HTML files can be generated from an 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

    -
  • All JavaScripts necessary to visualise BioJS
    • +
  • All JavaScripts necessary to render and visualise BioJS data
  • JavaScripts to transform BioJSON data to BioJS MSA data
    • -
  • And a place holder for BioJSON data (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#'/>
      • -
    -
+
  • 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 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. +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 a new BioJS MSA template +The following steps can be taken to create or update a 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. -
        -
      • Publish the template and an equivalent VALID package.json file to a live URL
        • -
      • 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 jalview_properties file
        e.g. - biojs_template_git_repo="https://raw.githubusercontent.com/gituser/biojs-templates/package.json
        • -
      • Restart Jalview and ensure that the test templates are downloaded
        • +
      • 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. +
        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. +
        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
          6. -
      -
    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. +
    + +
  • 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 4iii to 4v above
    • 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. +When Jalview starts up, provided that there is an internet connection, Jalview 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