JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26

diff --git a/.classpath b/.classpath
index 6583992..8aef745 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -64,7 +64,7 @@
        <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
        <classpathentry kind="lib" path="lib/java-json.jar"/>
-       <classpathentry kind="lib" path="lib/Jmol-14.2.14_2015.06.11.jar"/>
+       <classpathentry kind="lib" path="lib/Jmol-14.6.4_2016.10.26.jar"/>
        <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
        <classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
        <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 31ad2f5..38d5b93 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -10,7 +10,7 @@ ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Mor
 Licencing information for each library is given below:
 
 JGoogleAnalytics_0.3.jar       APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
-Jmol-14.2.14_2015.06.11.jar    GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+Jmol-14.6.4_2016.10.26.jar     GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
 VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
 activation.jar 
 apache-mime4j-0.6.jar

diff --git a/appletlib/JmolApplet-14.2.14_2015.06.11.jar b/appletlib/JmolApplet-14.2.14_2015.06.11.jar
deleted file mode 100644 (file)
index 5d6338c..0000000
Binary files a/appletlib/JmolApplet-14.2.14_2015.06.11.jar and /dev/null differ

diff --git a/appletlib/JmolApplet-14.6.4_2016.10.26.jar b/appletlib/JmolApplet-14.6.4_2016.10.26.jar
new file mode 100644 (file)
index 0000000..dd23a82
Binary files /dev/null and b/appletlib/JmolApplet-14.6.4_2016.10.26.jar differ

diff --git a/build.xml b/build.xml
index 1d4878b..3c18308 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -128,7 +128,7 @@
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
-    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
     <property name="varnaJar" value="VARNAv3-93.jar" />
     <property name="jsoup" value="jsoup-1.8.1.jar" />
     <property name="jsonSimple" value="json_simple-1.1.jar" />

diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html
index 7fcca00..7b4daee 100644 (file)
--- a/examples/appletDeployment.html
+++ b/examples/appletDeployment.html
@@ -33,7 +33,7 @@
     <td>Main Jalview Applet Jar</td>
   </tr>
   <tr>
-    <td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.2.14_2015.06.11.jar">JmolApplet-14.2.14_2015.06.11.jar</a> </td>
+    <td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.6.4_2016.10.26.jar">JmolApplet-14.6.4_2016.10.26.jar</a> </td>
     <td>Jmol Applet Jar</td>
   </tr>
   <tr>
@@ -48,7 +48,7 @@
 
 <p>To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.    
 <pre><code>
-&lt;applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"&gt;
+&lt;applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar"&gt;
        &lt;param name="permissions" value="sandbox" /&gt;
        &lt;param name="file" value="plantfdx.fa" /&gt;
        &lt;param name="features" value="plantfdx.features" /&gt;

diff --git a/examples/applets.html b/examples/applets.html
index 1f65565..d997f14 100644 (file)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -41,7 +41,7 @@ Try out JalviewLite by pressing one of the buttons below.
       <td width="10%" valign="center">
       <applet
        code="jalview.bin.JalviewLite" width="140" height="35"
-       archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">  
+       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="file" value="uniref50.fa"/>
        <param name="treeFile" value="ferredoxin.nw"/>
@@ -64,7 +64,7 @@ Try out JalviewLite by pressing one of the buttons below.
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file" value="uniref50.fa"/>
 <param name="features" value="exampleFeatures.txt"/>
@@ -89,7 +89,7 @@ Try out JalviewLite by pressing one of the buttons below.
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file" value="uniref50.fa"/>
 <param name="showFullId" value="false"/>
@@ -116,7 +116,7 @@ Try out JalviewLite by pressing one of the buttons below.
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file" value="jpred_msa.fasta"/>
 <param name="jnetfile" value="jpred_msa.seq.concise"/>
@@ -147,7 +147,7 @@ Try out JalviewLite by pressing one of the buttons below.
     <tr>
       <td width="10%" valign="center"><applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file" value="RF00031_folded.stk"/>
 <param name="showFullId" value="false"/>
@@ -171,7 +171,7 @@ Try out JalviewLite by pressing one of the buttons below.
       <td width="10%" valign="center">
 <applet
    code="jalview.bin.JalviewLite" width="140" height="35"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file2" value="estrogenReceptorCdna_frag.fa"/>
 <param name="file" value="estrogenReceptorProtein_frag.fa"/>

diff --git a/examples/embedded.html b/examples/embedded.html
index 0d5ddf3..0cea17d 100644 (file)
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -40,7 +40,7 @@
   <a href="view-source:http://www.jalview.org/builds/develop/examples/embedded.html" target="_blank">View the source code for this example here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/embedded.html">this page</a> and viewing the page source manually).<p>
   <applet
    code="jalview.bin.JalviewLite" width="756" height="560"
-   archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   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="file" value="plantfdx.fa"/>
 <param name="features" value="plantfdx.features"/>

diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 501c20e..6fdcc07 100644 (file)
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -211,7 +211,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
 <script language="JavaScript">
 // instead of this, we use a custom JmolApplet spec
 // jmolInitialize('jmol');
-jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
+jmolInitialize("","JmolApplet-14.6.4_2016.10.26.jar");
 </script>
 <script>
  var loglevel=1;
@@ -242,7 +242,7 @@ 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,java-json.jar,json_simple-1.1.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',
@@ -295,7 +295,7 @@ jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 </div>
 <div>
 <applet
-   code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.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"/>

diff --git a/examples/formComplete.html b/examples/formComplete.html
index 9e89990..65a3a45 100644 (file)
--- a/examples/formComplete.html
+++ b/examples/formComplete.html
@@ -36,7 +36,7 @@ instance on the page.</p>
   <a href="view-source:http://www.jalview.org/builds/develop/examples/formComplete.html" target="_blank">View the source here to see how it has been done</a>  (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/formComplete.html">this page</a> and viewing the page source manually).<br/>
 <a name="api">View the full <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite API documentation</a>.</a>
 <applet code="jalview.bin.JalviewLite" width="0" height="0"
-       archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar" name="Jalview">
+       archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar" name="Jalview">
   
   <param name="file" value="plantfdx.fa"/>
   <param name="features" value="plantfdx.features"/>

diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html
index 35b1d81..38f80b7 100644 (file)
--- a/examples/javascriptLaunch.html
+++ b/examples/javascriptLaunch.html
@@ -110,7 +110,7 @@ function startJalview(aligURL,title,alwvar) {
 </SCRIPT>
   <form name="Form1">
 <applet name="JalviewLite"  code="jalview.bin.JalviewLite"
-archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar" width="0" height="0">
+archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar" width="0" height="0">
 <param name="debug" value="true"/>
 <param name="showbutton" value="false"/>
 </applet>

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 5890515..8ddfd2f 100644 (file)
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -38,7 +38,7 @@
 
 
 <applet
-   code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="oninit" value="lJvApp"/>
 <param name="automaticScrolling" value="true"/>
 <param name="file" value="plantfdx.fa"/>
@@ -61,7 +61,7 @@
 
 
 <applet
-   code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+   code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 <param name="oninit" value="lJvFollow"/>
 <param name="file" value="plantfdx.fa"/>
 <param name="annotations" value="plantfdx.annotations"/>

diff --git a/lib/Jmol-14.2.14_2015.06.11.jar b/lib/Jmol-14.2.14_2015.06.11.jar
deleted file mode 100644 (file)
index 1470745..0000000
Binary files a/lib/Jmol-14.2.14_2015.06.11.jar and /dev/null differ

diff --git a/lib/Jmol-14.6.4_2016.10.26.jar b/lib/Jmol-14.6.4_2016.10.26.jar
new file mode 100644 (file)
index 0000000..0166a42
Binary files /dev/null and b/lib/Jmol-14.6.4_2016.10.26.jar differ

diff --git a/nbproject/project.properties b/nbproject/project.properties
index ac1a2e3..b569f55 100644 (file)
--- a/nbproject/project.properties
+++ b/nbproject/project.properties
@@ -59,8 +59,8 @@ file.reference.jalview-src=src
 file.reference.jaxrpc.jar=lib/jaxrpc.jar
 file.reference.JGoogleAnalytics_0.3.jar=lib/JGoogleAnalytics_0.3.jar
 file.reference.jhall.jar=lib/jhall.jar
-file.reference.Jmol-14.2.14_2015.06.11.jar=lib/Jmol-14.2.14_2015.06.11.jar
-file.reference.JmolApplet-14.2.14_2015.06.11.jar=appletlib/JmolApplet-14.2.14_2015.06.11.jar
+file.reference.Jmol-14.6.4_2016.10.26.jar=lib/Jmol-14.6.4_2016.10.26.jar
+file.reference.JmolApplet-14.6.4_2016.10.26.jar=appletlib/JmolApplet-14.6.4_2016.10.26.jar
 file.reference.log4j-1.2.8.jar=lib/log4j-1.2.8.jar
 file.reference.mail.jar=lib/mail.jar
 file.reference.min-jaba-client.jar=lib/min-jaba-client-2.0.jar
@@ -92,7 +92,7 @@ javac.classpath=\
     ${file.reference.jaxrpc.jar}:\
     ${file.reference.JGoogleAnalytics_0.3.jar}:\
     ${file.reference.jhall.jar}:\
-    ${file.reference.Jmol-14.2.14_2015.06.11.jar}:\
+    ${file.reference.Jmol-14.6.4_2016.10.26.jar}:\
     ${file.reference.miglayout-4.0-swing.jar}:\
     ${file.reference.log4j-1.2.8.jar}:\
     ${file.reference.mail.jar}:\
@@ -101,7 +101,7 @@ javac.classpath=\
     ${file.reference.xml-apis.jar}:\
     ${file.reference.xercesImpl.jar}:\
     ${file.reference.wsdl4j.jar}:\
-    ${file.reference.JmolApplet-14.2.14_2015.06.11.jar} \
+    ${file.reference.JmolApplet-14.6.4_2016.10.26.jar} \
     ${file.reference.varna-3.9-dev.jar}
 # Space-separated list of extra javac options
 javac.compilerargs=

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 6ec5b4d..ea3d3fa 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -29,8 +29,6 @@ import jalview.structure.StructureSelectionManager;
 import java.awt.Container;
 import java.util.Map;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.console.AppletConsole;
 import org.jmol.java.BS;
@@ -113,12 +111,14 @@ class AppletJmolBinding extends JalviewJmolBinding
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
     colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
@@ -143,6 +143,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     // do nothing.
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
@@ -183,7 +184,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // TODO Auto-generated method stub
     return null;

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fbac400..9ee0777 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -49,8 +49,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -1404,7 +1402,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // Jalview doesn't honour resize panel requests
     return null;

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index b2ba256..180da8f 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -38,8 +38,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
@@ -626,7 +624,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     return null;
   }

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index fc799bb..45b3425 100755 (executable)
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -1245,7 +1245,7 @@ and any path to a file to save to the file]]></string>
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
+                                                               <string><![CDATA[Jmol-14.6.4_2016.10.26.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@ -1263,7 +1263,7 @@ and any path to a file to save to the file]]></string>
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
+                                                               <string><![CDATA[Jmol-14.6.4_2016.10.26.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
                                                                <long>5417196</long>