X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fbiojsmsa.html;h=f3b68162d4a74b5912e0691ba2b3c373b567d9c3;hb=53e232c25d1956fdcc239b0db8d6b18cecc601a4;hp=fbbb1351e15671fed5212d61fbfcc35d3a40e1b5;hpb=d8d179f9c399205f61e7b936dd11a061bfb5de80;p=jalview.git diff --git a/help/html/features/biojsmsa.html b/help/html/features/biojsmsa.html index fbbb135..f3b6816 100644 --- a/help/html/features/biojsmsa.html +++ b/help/html/features/biojsmsa.html @@ -1,44 +1,58 @@ -
+ Exporting Alignments for viewing with the BioJS MSA + Viewer +
++ Since Jalview 2.9, HTML files can be generated from an alignment + within the Jalview desktop application that show the alignment in an + interactive viewer called 'BioJS-MSA'. These pages embed Jalview's + alignment data as BioJSON, which + can be imported back into Jalview, and also interpreted by the BioJS + MSA viewer. The BioJS MSA Viewer is a full-featured JavaScript based + multiple sequence alignment visualisation system created by a + community of biological data visualisation developers, and is + developed independently of Jalview. +
++ To find out more about the BioJS MSA Viewer, please go to http://msa.biojs.net/. +
-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.
- -<div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div> OR
-<input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>
-
+ Making sure your BioJS MSA export uses the latest + BioJS MSA Viewer +
+In order to allow Jalview to export data with the latest + version of the MSA viewer, the Jalview Desktop will download + templates for HTML export from our public GitHub Repository. + Normally, this should happen without you needing to do anything, but + if you do encounter problems, then please get in contact via the + jalview-discuss mailing list, or file a bug report.
+Templates are downloaded to a directory called + '.biojs_templates' in your user's home storage space (e.g. + ~/.biojs_templates).
+