X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fapplets.html;h=b557efc72e4b3a9bca0b135b072e123eb3a0ffe7;hb=c45601b486d1a9fd51273134699ca980c872ea6f;hp=a57efb7d6ae72da88555a4f1732476c617945a39;hpb=b57c603c7d837e70f30a8ce7f4a1f0bb67167fb9;p=jalview.git

diff --git a/examples/applets.html b/examples/applets.html
index a57efb7..b557efc 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,21 +1,22 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <!--
-    * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-    * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-    * 
-    * This file is part of Jalview.
-    * 
-    * Jalview is free software: you can redistribute it and/or
-    * modify it under the terms of the GNU General Public License 
-    * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-    *  
-    * Jalview is distributed in the hope that it will be useful, but 
-    * WITHOUT ANY WARRANTY; without even the implied warranty 
-    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-    * PURPOSE.  See the GNU General Public License for more details.
-    * 
-    * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
-  -->
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
 <head>
   <TITLE>JalviewLite Examples</TITLE>
   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> 
@@ -188,7 +189,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td width="10%" valign="center">
 	<applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="treeFile" value="ferredoxin.nw"/>
@@ -214,7 +215,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="features" value="exampleFeatures.txt"/>
@@ -265,9 +266,10 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="jpred_msa.fasta"/>
+<param name="jnetfile" value="jpred_msa.seq.concise"/>
 <param name="showFullId" value="false"/>
 <param name="windowHeight" value="515"/>
 <param name="windowWidth" value="650"/>
@@ -295,7 +297,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar">
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="RF00031_folded.stk"/>
 <param name="showFullId" value="false"/>
@@ -311,6 +313,29 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
 	secondary structure annotation</td>
     </tr>
   </table>
+  <p>
+    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center"><applet
+   code="jalview.bin.JalviewLite" width="140" height="35"
+   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="estrogenReceptorCdna.fa"/>
+<param name="file2" value="estrogenReceptorProtein.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="300"/>
+<param name="windowWidth" value="800"/>
+<param name="showAnnotation" value="false"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+   <param name="APPLICATION_URL"
+     value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+    </tr>
+  </table>
 </div>
 <!-- content template end -->
 
