JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / examples / applets.html

diff --git a/examples/applets.html b/examples/applets.html
index 501dc40..25440fb 100644 (file)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -1,6 +1,6 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -17,11 +17,14 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 
+
+<div id="view_decorated" name="view_decorated"  style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#applets"> here</a> to view decorated page</b></div>
+
 <!-- 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-12.2.4.jar">JmolApplet.jar</a>
+<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>
@@ -43,7 +46,7 @@ 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-12.2.4.jar,java-json.jar,json_simple-1.1.jar">  
+       archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.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"/>
@@ -66,7 +69,7 @@ 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-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.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"/>
@@ -91,13 +94,14 @@ 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-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.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"/>
 <param name="windowHeight" value="500"/>
 <param name="windowWidth" value="650"/>
 <param name="wrap" value="true"/>
+<param name="debug" value="true"/>
 <param name="showAnnotation" value="false"/>
 <param name="defaultColour" value="Strand Propensity"/>
 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
@@ -117,7 +121,7 @@ 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-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.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"/>
@@ -148,7 +152,7 @@ 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-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.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"/>
@@ -165,17 +169,17 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     </tr>
   </table>
   <p>
-    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+    <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</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,java-json.jar,json_simple-1.1.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
-<param name="file" value="estrogenReceptorCdna.fa"/>
-<param name="file2" value="estrogenReceptorProtein.fa"/>
+<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
+<param name="file" value="estrogenReceptorProtein_frag.fa"/>
 <param name="enableSplitFrame" value="true"/>
 <param name="scaleProteinAsCdna" value="true"/>
 <param name="showFullId" value="false"/>
@@ -188,6 +192,13 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
      value="http://www.jalview.org/services/launchApp"/>
 </applet>
 </td>
-      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+      <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
+        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>
+      </td>
     </tr>
   </table>