patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

diff --git a/build.xml b/build.xml
index 3894e21..08cd98e 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -100,7 +100,7 @@
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->
-               <property name="jmolJar" value="JmolApplet-12.1.5.jar" />
+               <property name="jmolJar" value="JmolApplet-12.1.11_dev_patched.jar" />
                <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->