X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples-jbake%2Fcontent%2FappletParameters.html;h=b936824b11421f914eb3ec1d11324796db020f19;hb=c1905ce5efcb38babec4f46a54ea47a1b83992e7;hp=7ed46b9f514c4455283d22c8839ec7bd6e1a5f7a;hpb=e0426a0637cfb6b9869bddd67bed435bd960dca7;p=jalview.git

diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html
index 7ed46b9..b936824 100644
--- a/examples-jbake/content/appletParameters.html
+++ b/examples-jbake/content/appletParameters.html
@@ -2,14 +2,15 @@ title=Applet Parameters
 type=page
 status=published
 ~~~~~~
+<h2>JalviewLite Applet Parameter Documentation</h2>
 <p>
-<ul>
-<li>Parameters are described <a href="#parameters">below</a></li>
-<li>The javascript API is described <a
-href="jalviewLiteJs.html">here</a></li>
-</ul></strong>
+The JalviewLite applet is configured through a series of applet parameters,
+which are described <a href="#parameters"> below</a>. Once initialised,
+the applet can be interacted with <em>via</em> its 
+<a href="jalviewLiteJs.html">Javascript API</a>.
+</p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the <a href="u_applets.html">unsigned applet examples</a>.
 </p>
-    <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+    <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
 	    <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
         <a name="parameters"></a>        <table width="97%" class="borderTable" align="center" >
           <tr> 
@@ -77,7 +78,7 @@ href="jalviewLiteJs.html">here</a></li>
             <td>defaultColour</td>
             <td> <em>One of: </em><br>
               Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix 
-              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
             <td>Default is no colour.</td>
           </tr>
           <tr>