From: tcofoegbu Date: Thu, 27 Oct 2016 16:30:02 +0000 (+0100) Subject: JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26 X-Git-Tag: Release_2_10_1~10^2~4^2~3 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2681593fa6810815547b688b89424c837cac1240 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 --- a/.classpath +++ b/.classpath @@ -64,7 +64,7 @@ - + diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index 31ad2f5..38d5b93 100644 --- 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 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 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 --- a/build.xml +++ b/build.xml @@ -128,7 +128,7 @@ - + diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html index 7fcca00..7b4daee 100644 --- a/examples/appletDeployment.html +++ b/examples/appletDeployment.html @@ -33,7 +33,7 @@ Main Jalview Applet Jar - JmolApplet-14.2.14_2015.06.11.jar + JmolApplet-14.6.4_2016.10.26.jar Jmol Applet Jar @@ -48,7 +48,7 @@

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. 


-<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">
+<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">
 	<param name="permissions" value="sandbox" />
 	<param name="file" value="plantfdx.fa" />
 	<param name="features" value="plantfdx.features" />
diff --git a/examples/applets.html b/examples/applets.html
index 1f65565..d997f14 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -41,7 +41,7 @@ Try out JalviewLite by pressing one of the buttons below.
       
         
+   	archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">  
 	
 	
 	
@@ -64,7 +64,7 @@ Try out JalviewLite by pressing one of the buttons below.
     
       
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
@@ -89,7 +89,7 @@ Try out JalviewLite by pressing one of the buttons below.
     
       
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
@@ -116,7 +116,7 @@ Try out JalviewLite by pressing one of the buttons below.
     
       
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
@@ -147,7 +147,7 @@ Try out JalviewLite by pressing one of the buttons below.
     
       
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
@@ -171,7 +171,7 @@ Try out JalviewLite by pressing one of the buttons below.
       
 
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
diff --git a/examples/embedded.html b/examples/embedded.html
index 0d5ddf3..0cea17d 100644
--- a/examples/embedded.html
+++ b/examples/embedded.html
@@ -40,7 +40,7 @@
   View the source code for this example here (If the link doesn't work on your browser try going to this page and viewing the page source manually).

   
+   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
 
 
 
diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html
index 501c20e..6fdcc07 100644
--- a/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@ -211,7 +211,7 @@ jQuery.extend(Drupal.settings, {"basePath":"\/","pathPrefix":"","ajaxPageState":
 
 
   

 
+archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar" width="0" height="0">
 
 
 
diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 5890515..8ddfd2f 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -38,7 +38,7 @@
 
 
 
+   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">
 
 
 
@@ -61,7 +61,7 @@
 
 
 
+   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">
 
 
 
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
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
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
--- 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
--- 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
--- 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
--- 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
--- 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]]>
 								
 							
 							
-								
+								
 							
 							
 								false
@@ -1263,7 +1263,7 @@ and any path to a file to save to the file]]>
 								true
 							
 							
-								
+								
 							
 							
 								5417196