From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 20:31:18 +0000 (+0100)
Subject: JAL-1645 rejig biojson/biojsmsa docs
X-Git-Tag: Release_2_10_0~448
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=849a6a5ae80818bfb40f3843690c0ebee00c3d16;p=jalview.git

JAL-1645 rejig biojson/biojsmsa docs
---

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fe42110..1f1a8b7 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -35,7 +35,6 @@
 		</tocitem>
 		
 		<tocitem text="Making Figures" target="export" expand="false">
-			<tocitem text="BioJSON v1.0" target="biojson" />
 			<tocitem text="BioJS MSA Viewer" target="biojsmsa" />
 		</tocitem>
 		
diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html
index 7828f50..efbfb8c 100644
--- a/help/html/features/bioJsonFormat.html
+++ b/help/html/features/bioJsonFormat.html
@@ -29,10 +29,12 @@
   <p>BioJSON is a JavaScript Object Notation (JSON) specification
     for the representation and exchange of multiple sequence alignment
     data.</p>
-  <p>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 <a href="biojsmsa.html">BioJS MSA viewer</a> for
-    interactive display of BioJSON data.</p>
+  <p>
+    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 <a href="biojsmsa.html">BioJS MSA
+      viewer</a> for interactive display of BioJSON data.
+  </p>
   <p>
     <strong>Finding out more about BioJSON</strong>
   </p>
@@ -41,10 +43,24 @@
       href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
   </p>
   <p>
+    <em>Import of BioJSON data from HTML pages</em>
+  </p>
+  <p>When importing embedded data in an HTML document, Jalview
+    searches for a hidden (usually) input or div element named "seqData":</p>
+  <pre>
+    <code>&lt;div name="seqData" id="seqData" style="display: none;"&gt;#valid BioJSON data#&lt;/div&gt;</code>
+  </pre>
+  <strong>OR</strong>
+  <pre>
+    <code>&lt;input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/&gt;</code>
+  </pre>
+  <p>Jalview can also import BioJSON data directly.</p>
+
+  <p>
     <strong>Jalview's Support for BioJSON v1.0</strong>
   </p>
-  <p>BioJSON exports of an alignment view include
-    the following additional data:</p>
+  <p>BioJSON exports of an alignment view include the following
+    additional data:</p>
   <ul>
     <li>Alignment Annotations</li>
     <li>Alignment Features</li>
diff --git a/help/html/features/biojsmsa.html b/help/html/features/biojsmsa.html
index ff4d8da..f97c7b3 100644
--- a/help/html/features/biojsmsa.html
+++ b/help/html/features/biojsmsa.html
@@ -5,18 +5,24 @@
     <strong>Exporting Alignments for viewing with the BioJS MSA
       Viewer</strong>
   </p>
-  <p>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'. 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.</p>
+  <p>
+    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 <a href="bioJsonFormat.html">BioJSON</a>, 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.
+  </p>
   <p>
     To find out more about the BioJS MSA Viewer, please go to <a
       href="http://msa.biojs.net/">http://msa.biojs.net/</a>.
+  </p>
+
   <p>
-    <strong>Making sure your BioJS MSA exports uses the latest
+    <strong>Making sure your BioJS MSA export uses the latest
       BioJS MSA Viewer</strong>
   </p>
   <p>In order to allow Jalview to export data with the latest
diff --git a/help/html/io/export.html b/help/html/io/export.html
index c3270c7..71d5c55 100755
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -69,21 +69,7 @@
   </p>
   <p>
 
-  <p>
-    <em>Import of BioJSON data from HTML pages</em>
-  </p>
-  <p>When importing embedded data in an HTML document, Jalview
-    searches for a hidden input or div element named "seqData":
-  <pre>
-    <code>&lt;div name="seqData" id="seqData" style="display: none;"&gt;#valid BioJSON data#&lt;/div&gt;</code>
-  </pre>
-  <strong>OR</strong>
-  <pre>
-    <code>&lt;input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/&gt;</code>
-  </pre>
-  Jalview can also import JSON data directly if it conforms to the BioJSON specification.
-</p>
-<p><em>Tips for working with EPS Files</em></p>
+<p><strong>Tips for working with EPS Files</strong></p>
 <li>The EPS file generated by Jalview contains vector graphics which are directly 
   editable in graphics applications such as Adobe Illustrator.</li>
 <li>EPS files can be produced as &quot;Text&quot; or &quot;Lineart&quot;. Use