From 472f47fc68c6f117334a76c0faffed5c86511fcd Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 3 Sep 2015 16:24:47 +0100
Subject: [PATCH] JAL-1859 JAL-857 updated all reference of
 JmolApplet-12.2.4.jar to JmolApplet-14.2.14_2015.06.11.jar

---
 examples-jbake/content/appletParameters.html   |    2 +-
 examples-jbake/content/applets.html            |    2 +-
 examples-jbake/content/embedded.html           |    2 +-
 examples-jbake/content/embeddedWJmol.html      |    2 +-
 examples-jbake/content/formComplete.html       |    2 +-
 examples-jbake/content/javascriptLaunch.html   |    2 +-
 examples-jbake/content/linkedapplets_ng.html   |    2 +-
 examples-jbake/content/u_applets.html          |    2 +-
 examples-jbake/content/u_embedded.html         |    2 +-
 examples-jbake/content/u_embeddedWJmol.html    |    2 +-
 examples-jbake/content/u_formComplete.html     |    2 +-
 examples-jbake/content/u_javascriptLaunch.html |    2 +-
 examples-jbake/content/u_linkedapplets_ng.html |    2 +-
 examples/appletParameters.html                 |    2 +-
 examples/applets.html                          |   14 +++++++-------
 examples/embedded.html                         |    4 ++--
 examples/embeddedWJmol.html                    |    8 ++++----
 examples/formComplete.html                     |    4 ++--
 examples/javascriptLaunch.html                 |    4 ++--
 examples/linkedapplets_ng.html                 |    6 +++---
 20 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html
index b936824..00817a8 100644
--- a/examples-jbake/content/appletParameters.html
+++ b/examples-jbake/content/appletParameters.html
@@ -334,7 +334,7 @@ the applet can be interacted with <em>via</em> its
         </li>
         <li>RNA secondary structure annotation row
         </li>
-<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
+<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-14.2.14_2015.06.11.jar">download the JmolApplet here</a></li>
 <li>To use Jmol as the structure viewer for Jalview, you must include 
             the jar file in the applet archive argument thus:<br>
             <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre>
diff --git a/examples-jbake/content/applets.html b/examples-jbake/content/applets.html
index 011c10e..5049e30 100644
--- a/examples-jbake/content/applets.html
+++ b/examples-jbake/content/applets.html
@@ -1,7 +1,7 @@
 title=JalviewLite Examples
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 status=published
 level=0
 class=jvl_examples.ftl
diff --git a/examples-jbake/content/embedded.html b/examples-jbake/content/embedded.html
index 3b6fc63..90a7fd0 100644
--- a/examples-jbake/content/embedded.html
+++ b/examples-jbake/content/embedded.html
@@ -1,7 +1,7 @@
 title=Embedded Alignment
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 class=jvl_embedded.ftl
 status=published
 level=2
diff --git a/examples-jbake/content/embeddedWJmol.html b/examples-jbake/content/embeddedWJmol.html
index ecc5769..6e42245 100644
--- a/examples-jbake/content/embeddedWJmol.html
+++ b/examples-jbake/content/embeddedWJmol.html
@@ -1,7 +1,7 @@
 title=Jalview and Jmol
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 class=jvl_embeddedWJmol.ftl
 hclass=jvl_embeddedWJmol_hdr.ftl
 status=published
diff --git a/examples-jbake/content/formComplete.html b/examples-jbake/content/formComplete.html
index c2ee860..6a3f71e 100644
--- a/examples-jbake/content/formComplete.html
+++ b/examples-jbake/content/formComplete.html
@@ -1,7 +1,7 @@
 title=Access from Javascript
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 class=jvl_formComplete.ftl
 status=published
 level=2
diff --git a/examples-jbake/content/javascriptLaunch.html b/examples-jbake/content/javascriptLaunch.html
index 6a0dc9b..1315ee9 100644
--- a/examples-jbake/content/javascriptLaunch.html
+++ b/examples-jbake/content/javascriptLaunch.html
@@ -1,7 +1,7 @@
 title=Javascript Launch
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 class=jvl_javascriptLaunch.ftl
 status=published
 level=2
diff --git a/examples-jbake/content/linkedapplets_ng.html b/examples-jbake/content/linkedapplets_ng.html
index 310ffd6..f220c75 100644
--- a/examples-jbake/content/linkedapplets_ng.html
+++ b/examples-jbake/content/linkedapplets_ng.html
@@ -1,7 +1,7 @@
 title=Linked JalviewLites
 type=page
 jvl=jalviewApplet.jar
-jmol=JmolApplet-12.2.4.jar
+jmol=JmolApplet-14.2.14_2015.06.11.jar
 class=jvl_linkedapplets_ng.ftl
 status=published
 level=1
diff --git a/examples-jbake/content/u_applets.html b/examples-jbake/content/u_applets.html
index 149cafa..1a48358 100644
--- a/examples-jbake/content/u_applets.html
+++ b/examples-jbake/content/u_applets.html
@@ -1,7 +1,7 @@
 title=JalviewLite Examples
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 status=published
 level=0
diff --git a/examples-jbake/content/u_embedded.html b/examples-jbake/content/u_embedded.html
index 0b68657..d295406 100644
--- a/examples-jbake/content/u_embedded.html
+++ b/examples-jbake/content/u_embedded.html
@@ -1,7 +1,7 @@
 title=Embedded Alignment
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 class=jvl_embedded.ftl
 status=published
diff --git a/examples-jbake/content/u_embeddedWJmol.html b/examples-jbake/content/u_embeddedWJmol.html
index af9fe88..0b54b60 100644
--- a/examples-jbake/content/u_embeddedWJmol.html
+++ b/examples-jbake/content/u_embeddedWJmol.html
@@ -1,7 +1,7 @@
 title=Jalview and Jmol
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 class=jvl_embeddedWJmol.ftl
 hclass=jvl_embeddedWJmol_hdr.ftl
diff --git a/examples-jbake/content/u_formComplete.html b/examples-jbake/content/u_formComplete.html
index c4f5ba6..86700e2 100644
--- a/examples-jbake/content/u_formComplete.html
+++ b/examples-jbake/content/u_formComplete.html
@@ -1,7 +1,7 @@
 title=Access from Javascript
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 class=jvl_formComplete.ftl
 status=published
diff --git a/examples-jbake/content/u_javascriptLaunch.html b/examples-jbake/content/u_javascriptLaunch.html
index 080cd3b..075b8ca 100644
--- a/examples-jbake/content/u_javascriptLaunch.html
+++ b/examples-jbake/content/u_javascriptLaunch.html
@@ -1,7 +1,7 @@
 title=Javascript Launch
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 class=jvl_javascriptLaunch.ftl
 status=published
diff --git a/examples-jbake/content/u_linkedapplets_ng.html b/examples-jbake/content/u_linkedapplets_ng.html
index 43e1ef5..69003f9 100644
--- a/examples-jbake/content/u_linkedapplets_ng.html
+++ b/examples-jbake/content/u_linkedapplets_ng.html
@@ -1,7 +1,7 @@
 title=Linked JalviewLites
 type=page
 jvl=u_jalviewApplet.jar
-jmol=u_JmolApplet-12.2.4.jar
+jmol=u_JmolApplet-14.2.14_2015.06.11.jar
 alteg=true
 class=jvl_linkedapplets_ng.ftl
 status=published
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index a0f25d4..976d8f9 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -358,7 +358,7 @@ the applet can be interacted with <em>via</em> its
         </li>
         <li>RNA secondary structure annotation row
         </li>
-<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></li>
+<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-14.2.14_2015.06.11.jar">download the JmolApplet here</a></li>
 <li>To use Jmol as the structure viewer for Jalview, you must include 
             the jar file in the applet archive argument thus:<br>
             <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre>
diff --git a/examples/applets.html b/examples/applets.html
index 501dc40..6ea7567 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -21,7 +21,7 @@
 <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 +43,7 @@ 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 +66,7 @@ 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"/>
@@ -91,7 +91,7 @@ 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="showFullId" value="false"/>
@@ -117,7 +117,7 @@ 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 +148,7 @@ 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"/>
@@ -172,7 +172,7 @@ 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="estrogenReceptorCdna.fa"/>
 <param name="file2" value="estrogenReceptorProtein.fa"/>
diff --git a/examples/embedded.html b/examples/embedded.html
index 4b0531c..5891225 100644
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -22,7 +22,7 @@
 <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>
@@ -40,7 +40,7 @@
   </ul>
   <applet
    code="jalview.bin.JalviewLite" width="756" height="560"
-   archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar">
 <param name="permissions" value="sandbox"/>
 <param name="file" value="plantfdx.fa"/>
 <param name="features" value="plantfdx.features"/>
diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 9b7389d..1c4c692 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -189,7 +189,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
   
 
 <script language="JavaScript">
-jmolInitialize("","JmolApplet-12.2.4.jar");
+jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 function genHref()
 {
  var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
@@ -230,7 +230,7 @@ function genHref()
  var _jvA=new Object();
  _jvA.attributes = {
   code : 'jalview.bin.JalviewLite',
-  archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
+  archive : 'jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
@@ -270,7 +270,7 @@ function genHref()
 <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>
@@ -287,7 +287,7 @@ function genHref()
 </div>
 <div>
 <applet
-   code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+   code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar">
 <param name="permissions" value="sandbox"/>
 <param name="java_arguments" value="-Xmx256m"/>
 <param name="externalstructureviewer" value="true"/>
diff --git a/examples/formComplete.html b/examples/formComplete.html
index 37b4450..8a0ae03 100644
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -22,7 +22,7 @@
 <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>
@@ -35,7 +35,7 @@ instance on the page.</p>
 View the source in your browser to see how it has been done. <br/>
 <a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
 <applet code="jalview.bin.JalviewLite" width="0" height="0"
-	archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" name="Jalview">
+	archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar" name="Jalview">
   
   <param name="file" value="plantfdx.fa"/>
   <param name="features" value="plantfdx.features"/>
diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index a7947bf..c6668ce 100644
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -22,7 +22,7 @@
 <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>
@@ -113,7 +113,7 @@ function startJalview(aligURL,title,alwvar) {
 </SCRIPT>
   <form name="Form1">
 <applet name="JalviewLite"  code="jalview.bin.JalviewLite"
-archive="jalviewApplet.jar,JmolApplet-12.2.4.jar" width="0" height="0">
+archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar" width="0" height="0">
 <param name="debug" value="true"/>
 <param name="showbutton" value="false"/>
 </applet>
diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 5da9e59..770c9b9 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -21,7 +21,7 @@
 <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>
@@ -38,7 +38,7 @@
 
 
 <applet
-   code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+   code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar">
 <param name="oninit" value="lJvApp"/>
 <param name="automaticScrolling" value="true"/>
 <param name="file" value="plantfdx.fa"/>
@@ -61,7 +61,7 @@
 
 
 <applet
-   code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+   code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar">
 <param name="oninit" value="lJvFollow"/>
 <param name="file" value="plantfdx.fa"/>
 <param name="annotations" value="plantfdx.annotations"/>
-- 
1.7.10.2