Merge branch 'JAL-980_jmol_patch' into develop

Conflicts:
	.classpath
	examples/appletParameters.html

diff --cc .classpath
index 8af4838,d26fa6c..4e84fb8
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -39,11 -36,10 +37,13 @@@
        </classpathentry>
        <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
        <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
 -      <classpathentry kind="lib" path="lib/min-jaba-client.jar"/>
        <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
 -      <classpathentry kind="lib" path="appletlib/JmolApplet-12.2.0.jar" sourcepath="/Jmol"/>
 -      <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
 +      <classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
++      <classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
 +<!--  <classpathentry exported="true" kind="var" path="GROOVY_ECLIPSE_HOME/groovy-all-1.0.jar"/> -->
 +      <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.java"/>
 +      <classpathentry kind="lib" path="lib/VARNAv3-9.jar"/>
++      <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
        <classpathentry kind="output" path="classes"/>
  </classpath>

diff --cc build.xml
Simple merge

diff --cc examples/appletParameters.html
index 5b0af6c,3cc5403..261bfa3
--- 1/examples/appletParameters.html
--- 2/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@@ -19,7 -19,7 +19,7 @@@
              button by setting the embed parameter to true;<br>
              &lt;param name=&quot;embedded&quot;
            value=&quot;true&quot;&gt; </li>
-         </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7.1</font></strong></p>\r        <ul>\r        <li><font size="2">Normalised sequence logo display\r        </font></li>\r        <li><font size="2">RNA secondary structure annotation row\r        </font></li>\r        </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r        <ul>\r        <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</font></li>\r        <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (&lt;param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>\r        </li>\r        <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r        </font></li></ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r        <ul>\r        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r            the jar file in the applet archive argument thus:<br>\r            <pre><font size="2">archive=&quot;jalviewApplet.jar,Jmol-12.1.13.jar&quot;</font></pre>\r          </li>\r          <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have \r            Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the \r            original Jalview structure viewer will still be available. <br>\r          </li>\r          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r          the Jmol binary distribution available at the Jmol Sourceforge site, \r          or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r          <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>\r            </ul>
 -        </ul>\r        <p><strong><font size="2">** NEW FEATURES ** in Jalview 2.7.1</font></strong></p>\r        <ul><li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r            the jar file in the applet archive argument thus:<br>\r            <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre></font>\r          </li>\r          <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have \r            Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the \r            original Jalview structure viewer will still be available. <br>\r          </li>\r          \r        </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r        <ul>\r        <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>\r        <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (&lt;param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>\r        </li>\r        <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r        </font></li></ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r        <ul>\r        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>\r          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r          the Jmol binary distribution available at the Jmol Sourceforge site, \r          or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r          <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>\r         </ul>
++        </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.8</font></strong></p>\r        <ul>\r        <li><font size="2">Normalised sequence logo display\r        </font></li>\r        <li><font size="2">RNA secondary structure annotation row\r        </font></li>\r        </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7.1</font></strong></p>\r        <ul>\r<li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r            the jar file in the applet archive argument thus:<br>\r            <pre>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre></font>\r          </li>\r          <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have \r            Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the \r            original Jalview structure viewer will still be available. <br>\r          </li>\r          \r        </ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r        <ul>\r        <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>\r        <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (&lt;param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>\r        </li>\r        <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r        </font></li></ul>\r        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r        <ul>\r        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series</font></li>\r          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r          the Jmol binary distribution available at the Jmol Sourceforge site, \r          or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r          <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>\r         </ul>
          <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>\r        <ul>\r        <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>\r                </ul>        \r        <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
          <ul>
          <li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>

diff --cc examples/applets.html
Simple merge

diff --cc src/jalview/appletgui/AppletJmolBinding.java
Simple merge

diff --cc src/jalview/ext/jmol/JalviewJmolBinding.java
Simple merge

diff --cc src/jalview/gui/AppJmolBinding.java
Simple merge