X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FembeddedWJmol.html;h=6fdcc0739345b254e260d5b8824521a44fe3e0ab;hb=7585bdc21653bdb66d604ed5efa95497f28c7eb5;hp=9b7389d4a4386d8beb8d0953c4622b225235061b;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 9b7389d..6fdcc07 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -1,5 +1,25 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
-<html lang="en" dir="ltr" version="HTML+RDFa 1.1"
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+ <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
 	xmlns:content="http://purl.org/rss/1.0/modules/content/"
 	xmlns:dc="http://purl.org/dc/terms/"
 	xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
@@ -103,7 +123,7 @@ 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 +209,11 @@ 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-14.6.4_2016.10.26.jar");
+</script>
+<script>
  var loglevel=1;
  function dbg(lvl,string) {
   if (_console && lvl<=loglevel) {_console.value += string + "\n";}
@@ -218,19 +233,16 @@ 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-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
@@ -268,11 +280,7 @@ function genHref()
   modeltofiles+="1gaq.txt";
 </script> 
 <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></div>
-</div>
+
 </div>
 
 <!-- content template start -->
@@ -282,12 +290,12 @@ 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-14.6.4_2016.10.26.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"/>
