From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 8 Sep 2015 09:09:08 +0000 (+0100)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
X-Git-Tag: Release_2_10_0~465^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b2c06af3e4e5bff86a1d2fca0f2ada78bef8ab52;hp=01aa5959c9eff6e3e23db686f5b056f0f52fb91d;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
---

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index eef45b4..8ef18d9 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -222,7 +222,7 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
  var _jvA=new Object();
  _jvA.attributes = {
   code : 'jalview.bin.JalviewLite',
-  archive : 'jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar',
+  archive : 'u_jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar',
   width : '500',
   height : '350',
   mayscript : 'True',
@@ -274,12 +274,12 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 
 <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;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-14.2.14_2015.06.11.jar">
+   code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="u_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/javascript/jalview.js b/examples/javascript/jalview.js
index 26d87dc..7172948 100644
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -153,7 +153,7 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
 		var sep = applet.getSeparator();
 		var oldjm=jmolView;
 		// recover full id of Jmol applet
-		jmolView=jmolFindTarget(jmolView); // Jmol 14.2.14
+		jmolView=jmolFindTarget(jmolView)._id; // Jmol 14.2.14
 		var jmbinding=_jvjmols.get(jmolView);
 		if (!jmbinding)
 		{