JAL-2083 removed use of reflection for Groovy

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 462f5a7..6c8750f 100755 (executable)
--- 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()
       {
       }
@@ -178,7 +179,7 @@ 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 +188,10 @@ 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());
       }
     }
 
@@ -377,7 +378,7 @@ public class Jalview
 
       protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
 
-      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      format = new jalview.io.IdentifyFile().identify(file, protocol);
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
@@ -514,20 +515,10 @@ 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";
@@ -627,7 +618,7 @@ public class Jalview
       }
       else
       {
-        format = new jalview.io.IdentifyFile().Identify(file, protocol);
+        format = new jalview.io.IdentifyFile().identify(file, protocol);
       }
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -729,6 +720,7 @@ 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 +730,7 @@ public class Jalview
               }
             }, new Runnable()
             {
+              @Override
               public void run()
               {
                 Cache.log.debug("Not enabling Google Tracking.");
@@ -1040,6 +1033,7 @@ public class Jalview
 
 class rnabuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
     System.out.println("Good idea ! ");
@@ -1049,6 +1043,7 @@ class rnabuttonlistener implements ActionListener
 
 class pbuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
 
@@ -1169,6 +1164,7 @@ class FeatureFetcher
     new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         synchronized (us)