(JAL-980) update Jmol library to 12.2.16452 (built from SVN)

diff --git a/.classpath b/.classpath
index 1838768..f5f1631 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -17,8 +17,6 @@
        <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="lib/Jmol-12.1.13.jar" sourcepath="/Jmol"/>
-       <classpathentry kind="lib" path="appletlib/JmolApplet-12.1.13.jar"/>
        <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
        <classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
        <classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
@@ -40,7 +38,8 @@
        <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-12.2.16452.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="output" path="classes"/>
 </classpath>

diff --git a/appletlib/JmolApplet-12.1.13.jar b/appletlib/JmolApplet-12.1.13.jar
deleted file mode 100644 (file)
index 27c7bd6..0000000
Binary files a/appletlib/JmolApplet-12.1.13.jar and /dev/null differ

diff --git a/appletlib/JmolApplet-12.2.16452.jar b/appletlib/JmolApplet-12.2.16452.jar
new file mode 100644 (file)
index 0000000..697c8ce
Binary files /dev/null and b/appletlib/JmolApplet-12.2.16452.jar differ

diff --git a/build.xml b/build.xml
index 736b5e6..aa57423 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -101,7 +101,7 @@
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->
-               <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+               <property name="jmolJar" value="JmolApplet-12.2.16452.jar" />
                <property name="jalviewLiteJar" value="jalviewApplet.jar" />
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 24452b6..fe13955 100644 (file)
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -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</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 - <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-12.2.16452.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-12.2.16452.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 --git a/examples/applets.html b/examples/applets.html
index d67c8b1..a768be6 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -79,7 +79,7 @@
                   <tr>
                     <td width="100"> <applet code="jalview.bin.JalviewLite"
                                width="140" height="35"
-                               archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
+                               archive="jalviewApplet.jar,JmolApplet-12.2.16452.jar">
                         <param name="file" value="uniref50.fa">\r                        <!-- <param name="debug" value="true">
                         -->\r                        <param name="defaultColour" value="Strand Propensity">
                         <param name="wrap" value="true">

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 2a3e65a..3f3903d 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -19,7 +19,7 @@
 <script language="JavaScript">\r
 // instead of this, we use a custom JmolApplet spec\r
 // jmolInitialize('jmol');\r
-jmolInitialize("","JmolApplet-12.1.13.jar");\r
+jmolInitialize("","JmolApplet-12.2.16452.jar");\r
 function genHref()\r
 {\r
        var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";\r

diff --git a/lib/Jmol-12.1.13.jar b/lib/Jmol-12.2.16452.jar
similarity index 61%
rename from lib/Jmol-12.1.13.jar
rename to lib/Jmol-12.2.16452.jar
index a017034..7ed37f1 100644 (file)
Binary files a/lib/Jmol-12.1.13.jar and b/lib/Jmol-12.2.16452.jar differ