Merge branch 'develop' into features/JAL-2068groovyAnnotationWorker

[jalview.git] / examples / embeddedWJmol.html

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 9b7389d..f629312 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -103,7 +103,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
 
 
 <script src="javascript/deployJava.js"></script>
-<script src="jmol/Jmol.js"></script>
+<script src="jmol/Jmol2.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>
@@ -189,16 +189,11 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
   
 
 <script language="JavaScript">
-jmolInitialize("","JmolApplet-12.2.4.jar");
-function genHref()
-{
- var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
- for(i=0; i<11; i++)
- { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); 
- }
- window.location=href;
-}
-
+// instead of this, we use a custom JmolApplet spec
+// jmolInitialize('jmol');
+jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
+</script>
+<script>
  var loglevel=1;
  function dbg(lvl,string) {
   if (_console && lvl<=loglevel) {_console.value += string + "\n";}
@@ -218,19 +213,16 @@ function genHref()
  var jvstructassoc;
  var modeltofiles = new Array();
 
- //function lJvA() {
-  //jvfollower = document.getElementById("jvA");
-  //setConsole(document.getElementById("stdout"));
-  
-  //sep = jvfollower.getSeparator();
-  //jvapp.setSeparator(""+jvapp.getSeparator());
-//  linkJvJmol(jvfollower, "jmolView", modeltofiles);
-// };
+ function lJvA() {
+  jvfollower = document.getElementById("jvA");
+  setConsole(document.getElementById("stdout"));
+  linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
 
  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,java-json.jar,json_simple-1.1.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
@@ -270,7 +262,7 @@ 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>
@@ -282,12 +274,12 @@ function genHref()
 
 <div>
  <script>
-  jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+  jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
  </script>
 </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="mayscript" 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="java_arguments" value="-Xmx256m"/>
 <param name="externalstructureviewer" value="true"/>