X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fbiojsmsa.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fbiojsmsa.html;h=f3b68162d4a74b5912e0691ba2b3c373b567d9c3;hb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;hp=0000000000000000000000000000000000000000;hpb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;p=jalview.git diff --git a/help/help/html/features/biojsmsa.html b/help/help/html/features/biojsmsa.html new file mode 100644 index 0000000..f3b6816 --- /dev/null +++ b/help/help/html/features/biojsmsa.html @@ -0,0 +1,58 @@ + + +BioJS MSA Viewer Export + +

+ 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/. +

+ +

+ 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).

+ +