X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2FbioJsonFormat.html;h=59b49365cfa4fb2d17a9843e53d7c58a70adcc7f;hb=b862b42c28778a3fddf89d10620854cea05a0250;hp=341e3e273d0d5b52cb099dd09a6ea100852ce884;hpb=3d8b21693c3c2cc27348b0fed1f5306932bc59a4;p=jalview.git
diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html
index 341e3e2..59b4936 100644
--- a/help/html/features/bioJsonFormat.html
+++ b/help/html/features/bioJsonFormat.html
@@ -20,33 +20,63 @@
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-BioJson-1.0 A JSON File Format
+BioJSON in Jalview
- BioJson (version-1.0)
- BioJson is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data.
- BioJSon-1.0 schema/documentation is available here.
- You can keep up to date with BioJson development and latest news here.
-
- Features supported
- Export/Import of the following alignment elements are supported in BioJson-1.0:
-
- - Alignment Sequences
- - Alignment Features
- - Alignment Annotations
- - Sequence Groups
- - Color Scheme
- - Hidden Sequences
- - Hidden Columns
-
+
+ BioJSON support in Jalview
+
+ BioJSON is a JavaScript Object Notation (JSON) specification
+ for the representation and exchange of multiple sequence alignment
+ data.
+
+ Jalview 2.9 includes support for reading and writing BioJSON v1.0
+ data directly, or embedded in HTML documents. It can also generate
+ HTML pages which employ the BioJS MSA
+ viewer for interactive display of BioJSON data.
+
+
+ Finding out more about BioJSON
+
+
+ The BioJSON specification is published at http://jalview.github.io/biojson/.
+
+
+ Import of BioJSON data from HTML pages
+
+ When importing embedded data in an HTML document, Jalview
+ searches for a hidden (usually) input or div element named
+ "seqData":
+
+ <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>
+
+ OR
+
+ <input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>
+
+ Jalview can also import BioJSON data directly.
- Features not yet supported
- Export/Import of the following alignment elements are not supported in BioJson-1.0:
-
- - Reference sequence
- - Representative sequence
- - Trees
- - 3D Structures
-
+
+ Jalview's Support for BioJSON v1.0
+
+ BioJSON exports of an alignment view include the following
+ additional data:
+
+ - Alignment Annotations
+ - Alignment Features
+ - Alignment Sequences
+ - Color Scheme
+ - Hidden Columns
+ - Hidden Sequences
+ - Sequence Groups
+
+ The following data are NOT currently preserved on export:
+
+ - Alignment Reference sequences
+ - Representative sequence groups
+ - Trees
+ - 3D Structures
+