X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=04cc235164ee30368f32b1253282173f3a7016d5;hb=refs%2Fheads%2Fdevelop;hp=cc95ecb808876d00c2839cd9a48df2dd179872f6;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index cc95ecb..04cc235 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -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>