JAL-952 JAL-1268 document RNA Helices and T-Coffee Scores as valid colour scheme...

[jalview.git] / examples-jbake / content / appletParameters.html

diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html
index edf937b..b936824 100644 (file)
--- a/examples-jbake/content/appletParameters.html
+++ b/examples-jbake/content/appletParameters.html
@@ -1,19 +1,16 @@
 title=Applet Parameters
 type=page
-jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
 status=published
 ~~~~~~
-        <p>
-                                               <strong>Quick Links:<ul><li>Download the applet jar file from <a
-                                                       href="jalviewApplet.jar">here</a>
-                                               </li>
-                                               <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>
-                                       </p>
-     <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</a>.</p>
+<h2>JalviewLite Applet Parameter Documentation</h2>
+<p>
+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>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> 
@@ -81,7 +78,7 @@ status=published
             <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>