Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4

diff --git a/.classpath b/.classpath
index cad9e2b..d973eeb 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -12,7 +12,6 @@
        <classpathentry kind="lib" path="lib/regex.jar"/>
        <classpathentry kind="lib" path="lib/saaj.jar"/>
        <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-       <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
        <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"/>
@@ -39,7 +38,7 @@
        <classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
        <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
-       <classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
+       <classpathentry kind="lib" path="/Users/jprocter/git/jalview/lib/groovy-all-2.4.6-indy.jar"/>
        <classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.jar" sourcepath="/clustengine"/>
        <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
        <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>

diff --git a/lib/groovy-all-1.8.2.jar b/lib/groovy-all-1.8.2.jar
deleted file mode 100755 (executable)
index 85af249..0000000
Binary files a/lib/groovy-all-1.8.2.jar and /dev/null differ

diff --git a/lib/groovy-all-2.4.6-indy.jar b/lib/groovy-all-2.4.6-indy.jar
new file mode 100644 (file)
index 0000000..5f3d51c
Binary files /dev/null and b/lib/groovy-all-2.4.6-indy.jar differ

diff --git a/lib/xercesImpl.jar b/lib/xercesImpl.jar
deleted file mode 100755 (executable)
index 0aaa990..0000000
Binary files a/lib/xercesImpl.jar and /dev/null differ

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8fe3bca..229c6c2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -68,6 +68,7 @@ public class Jalview
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
     {
+      @Override
       public PermissionCollection getPermissions(CodeSource codesource)
       {
         Permissions perms = new Permissions();
@@ -75,6 +76,7 @@ public class Jalview
         return (perms);
       }
 
+      @Override
       public void refresh()
       {
       }
@@ -89,6 +91,7 @@ public class Jalview
    */
   public static void main(String[] args)
   {
+    System.setSecurityManager(null);
     System.out.println("Java version: "
             + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -729,6 +732,7 @@ public class Jalview
                     + "\n\n(you can enable or disable usage tracking in the preferences)",
             new Runnable()
             {
+              @Override
               public void run()
               {
                 Cache.log
@@ -738,6 +742,7 @@ public class Jalview
               }
             }, new Runnable()
             {
+              @Override
               public void run()
               {
                 Cache.log.debug("Not enabling Google Tracking.");
@@ -1040,6 +1045,7 @@ public class Jalview
 
 class rnabuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
     System.out.println("Good idea ! ");
@@ -1049,6 +1055,7 @@ class rnabuttonlistener implements ActionListener
 
 class pbuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
 
@@ -1169,6 +1176,7 @@ class FeatureFetcher
     new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         synchronized (us)

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index 83d1a98..428b998 100755 (executable)
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2025,7 +2025,7 @@ and any path to a file to save to the file]]></string>
                                                                <string><![CDATA[664]]></string>
                                                        </property>
                                                        <property name="sourceName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
                                                        </property>
                                                        <property name="overrideUnixPermissions">
                                                                <boolean>false</boolean>
@@ -2043,7 +2043,7 @@ and any path to a file to save to the file]]></string>
                                                                <boolean>true</boolean>
                                                        </property>
                                                        <property name="destinationName">
-                                                               <string><![CDATA[groovy-all-1.8.2.jar]]></string>
+                                                               <string><![CDATA[groovy-all-2.4.6-indy.jar]]></string>
                                                        </property>
                                                        <property name="fileSize">
                                                                <long>6149494</long>