X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=04cc235164ee30368f32b1253282173f3a7016d5;hb=9276cd700c1157d058538fc4e4676c3dce16deaa;hp=433f5a917f926b4ba361001be86b2a7fb721b813;hpb=62908e93f175753769436fd62193773b9f3ad26f;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 433f5a9..04cc235 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -28,7 +28,7 @@ which are described <a href="#parameters"> below</a>. Once initialised,
 the applet can be interacted with <em>via</em> its 
 <a href="javascript:doSubmit('jalviewLiteJs')">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 may not be compatible with these settings. </p>
-    <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
+    <p>For additional deployment notes, <a href="javascript:doSubmit('appletDeployment')">see Applet Deployment</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> 
@@ -91,8 +91,9 @@ the applet can be interacted with <em>via</em> its
             <td>jnetfile</td>
             <td>fileName</td>
             <td>Secondary structure predictions from a <a
-            href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise 
-              file will be added to the first sequence in the alignment.</td>
+            href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred</a> Concise 
+              file will be added to the first sequence in the alignment.<br/>
+              <em>jpredfile</em> can be used interchangeably with this parameter.</td>
           </tr>
           <tr> 
             <td>PDBfile(x)</td>
@@ -114,7 +115,7 @@ the applet can be interacted with <em>via</em> its
             <td>defaultColour</td>
             <td> <em>One of: </em><br>
               Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix 
-              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
+              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices</td>
             <td>Default is no colour.</td>
           </tr>
           <tr> 
@@ -158,6 +159,11 @@ the applet can be interacted with <em>via</em> its
             <td>Default is true.</td>
           </tr>
           <tr> 
+            <td>showOccupancy</td>
+            <td>true <em>or</em> false</td>
+            <td>Default is true.</td>
+          </tr>
+          <tr> 
             <td>sortBy</td>
             <td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
             <td> Sorts the alignment on startup</td>