From a9edbad08eca203164152905ecd4d734ce72ecf5 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 8 Sep 2015 14:40:38 +0100 Subject: [PATCH] updated help to include BioJS option in export.html --- help/html/io/export.html | 15 ++++++++++++++- help/html/io/fileformats.html | 3 ++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/help/html/io/export.html b/help/html/io/export.html index a7a5a1a..7a3efa7 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -37,7 +37,20 @@ diagrams and powerpoint presentations diagrams and publications.
  • SVG - a Scalable Vector Graphics document
    For high quality diagrams in publications and on the web. -
    • + +
  • BioJS - A JavaScript based multiple sequence alignment visualiser.
    For viewing in a web browser. Get more info about BioJS at http://msa.biojs.net/ +
    • + + + +

    From Jalview 2.9, the HTML exporting system was re-implemented to use SVG rendering. Also, optional embedding of BioJSON data to the generated HTML file was introduced. +This is achieved using a hidden input or div element which MUST be named "seqData" as seen in the examples 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#'/>
    +HTML file embedded with BioJSON can be imported back to Jalview at a later date. During the import operation, Jalview uses an API called JSoup to traverse through the HTML file and extract the embedded BioJSON data from the target div or input element named 'seqData'. The extracted data is then parsed as a BioJSON format. + +

    Tips for working with EPS Files

  • The EPS file generated by Jalview contains vector graphics which are directly diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html index 16e9cc6..f1cf5dc 100755 --- a/help/html/io/fileformats.html +++ b/help/html/io/fileformats.html @@ -79,9 +79,10 @@ THISISASEQUENCE
    JSON -Data starts with '{'
    Data ends with '}'

    See BioJson for more info about Jalview JSON format
    +Data starts with '{'
    Data ends with '}'

    See BioJSON for more infomation about the Jalview JSON format
    .json +

    The file extensions are used to associate Jalview alignment icons with alignment files: -- 1.7.10.2