X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=examples%2Fapplets.html;h=b789672812241dc3f9bdef1ed1ca327dab02dab2;hp=25440fb2c0f70ce9ab29ee29ab164d265447aac6;hb=5104921c5c24afc2066ad6dc127f2dcb9e07daa5;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914

diff --git a/examples/applets.html b/examples/applets.html
index 25440fb..b789672 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,6 +1,6 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
  * 
@@ -22,19 +22,14 @@
 
 <!-- boiler plate link to alternate demopage -->
 <div style="width: 100%">
-<div style="width:35%; align:left; float:right;">
-<div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
-<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
-</p></div>
 </div>
-</div>
-
 <!-- content template start -->
 
 <p align="left">
 <h2>JalviewLite Button Examples</h2>
-Try out JalviewLite by pressing one of the buttons below.<br/>
- For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+Try out JalviewLite by pressing one of the buttons below. 
+  <a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/applets.html">this page</a> and viewing the page source manually).<br/>
+ For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
 <p>&nbsp;</p><div align="center">
   <p align="center">
     <h2>Ferredoxins, chloroplast precursor related UniRef50
@@ -46,7 +41,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">  
+   	archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">  
 	<param name="permissions" value="sandbox"/>
 	<param name="file" value="uniref50.fa"/>
 	<param name="treeFile" value="ferredoxin.nw"/>
@@ -69,7 +64,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="features" value="exampleFeatures.txt"/>
@@ -94,7 +89,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="uniref50.fa"/>
 <param name="showFullId" value="false"/>
@@ -121,7 +116,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="jpred_msa.fasta"/>
 <param name="jnetfile" value="jpred_msa.seq.concise"/>
@@ -141,7 +136,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
 </applet>
 						       </td>
       <td valign="middle">Displays a Multiple Sequence Alignment
-	Based JNet Prediction for a Sequence</td>
+	Based JPred Prediction for a Sequence</td>
     </tr>
   </table>
   <p>
@@ -152,7 +147,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="RF00031_folded.stk"/>
 <param name="showFullId" value="false"/>
@@ -176,7 +171,7 @@ 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,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
@@ -187,7 +182,8 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
 <param name="windowWidth" value="800"/>
 <param name="showAnnotation" value="true"/>
 <param name="showSequenceLogo" value="true"/>
-<param name="defaultColour" value="Purine/Pyrimidine"/>
+<param name="defaultColourNuc" value="Purine/Pyrimidine"/>
+<param name="defaultColourProt" value="Clustal"/>
    <param name="APPLICATION_URL"
      value="http://www.jalview.org/services/launchApp"/>
 </applet>
@@ -195,7 +191,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td valign="center">Displays a split window view showing aligned protein
         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
-        via the Jalvew Desktop).<br />Data retrieved from Uniprot and
+        via the Jalview Desktop).<br />Data retrieved from Uniprot and
         ENA, after Thornton, Need and Crews, <a
         href="http://dx.doi.org/10.1126/science.1086185">Science 19
           September 2003: 301 (5640), 1714-1717</a>