X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fapplets.html;h=6882b55aa2c8e4a2b4919ae9f1eb520f92419395;hb=64fb69927bb37d8773a75b684a3e7ab3f0c5c212;hp=df3de4d3ed2dd204bc6cf6fb44512f707bf59e44;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/examples/applets.html b/examples/applets.html
index df3de4d..6882b55 100755
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,7 +1,7 @@
 <!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 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -189,7 +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"/>
@@ -215,7 +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"/>
@@ -266,9 +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"/>
@@ -296,7 +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"/>
@@ -312,6 +313,32 @@ 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="enableSplitFrame" value="true"/>
+<param name="scaleProteinAsCdna" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="300"/>
+<param name="windowWidth" value="800"/>
+<param name="showAnnotation" value="true"/>
+<param name="showSequenceLogo" value="true"/>
+<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 -->
 
