X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=d0b3232b47d6658d3841be320b89b40e16b86086;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=8fe3bca0850a274c4b28bf37c82ea152bd69591d;hpb=26ba864a6c290121fe6cf616794d2d0bea65fb7d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8fe3bca..d0b3232 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -51,7 +51,6 @@ import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
 
 /**
  * Main class for Jalview Application <br>
@@ -68,6 +67,7 @@ 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 +75,7 @@ public class Jalview
         return (perms);
       }
 
+      @Override
       public void refresh()
       {
       }
@@ -89,6 +90,7 @@ 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") + " "
@@ -178,7 +180,7 @@ public class Jalview
     } catch (Exception ex)
     {
     }
-    if (new Platform().isAMac())
+    if (Platform.isAMac())
     {
       System.setProperty("com.apple.mrj.application.apple.menu.about.name",
               "Jalview");
@@ -187,10 +189,10 @@ public class Jalview
       {
         UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
                 .getLookAndFeel());
-      } catch (UnsupportedLookAndFeelException e)
+      } catch (Throwable e)
       {
-        // TODO Auto-generated catch block
-        e.printStackTrace();
+        System.err.println("Failed to set QuaQua look and feel: "
+                + e.toString());
       }
     }
 
@@ -514,20 +516,10 @@ public class Jalview
         {
           // Execute the groovy script after we've done all the rendering stuff
           // and before any images or figures are generated.
-          if (jalview.bin.Cache.groovyJarsPresent())
-          {
-            System.out.println("Executing script " + groovyscript);
-            executeGroovyScript(groovyscript, new Object[] { desktop, af });
-
-            System.out.println("CMD groovy[" + groovyscript
-                    + "] executed successfully!");
-          }
-          else
-          {
-            System.err
-                    .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
-                            + groovyscript);
-          }
+          System.out.println("Executing script " + groovyscript);
+          executeGroovyScript(groovyscript, new Object[] { desktop, af });
+          System.out.println("CMD groovy[" + groovyscript
+                  + "] executed successfully!");
           groovyscript = null;
         }
         String imageName = "unnamed.png";
@@ -729,6 +721,7 @@ 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 +731,7 @@ public class Jalview
               }
             }, new Runnable()
             {
+              @Override
               public void run()
               {
                 Cache.log.debug("Not enabling Google Tracking.");
@@ -1040,6 +1034,7 @@ public class Jalview
 
 class rnabuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
     System.out.println("Good idea ! ");
@@ -1049,6 +1044,7 @@ class rnabuttonlistener implements ActionListener
 
 class pbuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
 
@@ -1169,6 +1165,7 @@ class FeatureFetcher
     new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         synchronized (us)