Merge branch 'features/JAL-857_dynamic-example-files' into develop

diff --git a/examples-jbake/content/appletParameters.html b/examples-jbake/content/appletParameters.html
index b936824..00817a8 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 fdcdb33..a0f25d4 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -456,4 +456,4 @@ the applet can be interacted with <em>via</em> its
             </pre>(All the usual Jalview File formats are valid, however each 
             new line in an alignment file must be entered as a parameter)</li>
         </ul>
-<!-- content end -->
\ No newline at end of file
+<!-- content end -->

diff --git a/examples/applets.html b/examples/applets.html
index 501dc40..6ea7567 100644 (file)
--- 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 (file)
--- 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 1c1d663..31a627d 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -265,7 +265,7 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 <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>
@@ -282,7 +282,7 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 </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 (file)
--- 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/index.html b/examples/index.html
index 50f7cb5..492cbb6 100644 (file)
--- a/examples/index.html
+++ b/examples/index.html
@@ -100,12 +100,16 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
 //--><!]]>
 </script>
 <!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
-<script src="javascript/jquery-1.4.4.min.js"></script>
-
-<script src="javascript/jvcontroller.js"> </script>
-
 
 
+<script src="javascript/deployJava.js"></script>
+<script src="jmol/Jmol.js"></script>
+<script src="javascript/jquery-1.4.4.min.js"></script>
+<script src="javascript/jquery.timer.js"></script>
+<script src="javascript/jquery.blockUI.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script src="javascript/jvcontroller.js"> </script>
 
        
 
@@ -173,7 +177,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
                                                                                        class="field field-name-body field-type-text-with-summary field-label-hidden">
                                                                                        <div class="field-items">
                                                                                                <div class="field-item even" property="content:encoded">
-                                                                                               <div id="content"></div>
+                                                                                               <div id="content"></div>        
                                                                                                </div>
                                                                                        </div>
                                                                                </div>

diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 43d03bd..fa08a4d 100644 (file)
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -356,7 +356,7 @@ function _jmolMessagecallback(jmid, statmess) {
        var jvfollower = document.getElementById("jvfollower");
        //console.log(">>>>>>>> lJvApp" + jvapp);
        linkJvJmol(jvapp);
-    }, 100);
+    }, 200);
     setConsole(document.getElementById("stdout"));
   };
 
@@ -367,7 +367,7 @@ function _jmolMessagecallback(jmid, statmess) {
        var jvfollower = document.getElementById("jvfollower");
        console.log(">>>>>>> lJvFollow" + jvfollower);
        linkJvJmol(jvfollower);
-    }, 100);
+    }, 200);
   };
 
   function lJvA() {

diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index a7947bf..c6668ce 100644 (file)
--- 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 (file)
--- 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"/>