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 177d56f..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());
       }
     }
 
@@ -240,8 +241,7 @@ public class Jalview
       }
       else
       {
-        System.err
-.println("CMD [-noquestionnaire] executed successfully!");
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
       desktop.checkForNews();
     }
@@ -358,7 +358,8 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+        desktop.setProgressBar(MessageManager
+                .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
@@ -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);
@@ -387,7 +388,7 @@ public class Jalview
       }
       else
       {
-
+        Desktop.setCurrentAlignFrame(af);
         data = aparser.getValue("colour", true);
         if (data != null)
         {
@@ -445,8 +446,7 @@ public class Jalview
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
           {
-            System.out
-.println("CMD [-sortbytree] executed successfully!");
+            System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
         if (aparser.contains("no-annotation"))
@@ -454,8 +454,7 @@ public class Jalview
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
           {
-            System.out
-.println("CMD no-annotation executed successfully!");
+            System.out.println("CMD no-annotation executed successfully!");
           }
         }
         if (aparser.contains("nosortbytree"))
@@ -516,21 +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";
@@ -630,7 +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,
@@ -655,8 +643,8 @@ public class Jalview
       if (jalview.bin.Cache.groovyJarsPresent())
       {
         System.out.println("Executing script " + groovyscript);
-        executeGroovyScript(groovyscript, new Object[]
-        { desktop, startUpAlframe });
+        executeGroovyScript(groovyscript, new Object[] { desktop,
+            startUpAlframe });
       }
       else
       {
@@ -732,6 +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
@@ -741,6 +730,7 @@ public class Jalview
               }
             }, new Runnable()
             {
+              @Override
               public void run()
               {
                 Cache.log.debug("Not enabling Google Tracking.");
@@ -865,8 +855,7 @@ public class Jalview
       Object[] binding;
       int blen = ((jalviewContext[0] == null) ? 0 : 1)
               + ((jalviewContext[1] == null) ? 0 : 1);
-      String cnames[] = new String[]
-      { "Jalview", "currentAlFrame" };
+      String cnames[] = new String[] { "Jalview", "currentAlFrame" };
       bspec = new Class[blen * 2];
       binding = new Object[blen * 2];
       blen = 0;
@@ -907,15 +896,15 @@ public class Jalview
       }
 
       Class<?> gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-      Constructor<?> gseccons = gsec.getConstructor(new Class[]
-      { URL[].class }); // String[].class });
-      Object gse = gseccons.newInstance(new Object[]
-      { new URL[]
-      { sfile } }); // .toString() } });
-      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
-      { String.class, gbindingc });
-      run.invoke(gse, new Object[]
-      { sfile.toString(), gbinding });
+      Constructor<?> gseccons = gsec
+              .getConstructor(new Class[] { URL[].class }); // String[].class
+                                                            // });
+      Object gse = gseccons
+              .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
+                                                                  // } });
+      java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+          String.class, gbindingc });
+      run.invoke(gse, new Object[] { sfile.toString(), gbinding });
       success = true;
     } catch (Exception e)
     {
@@ -1044,6 +1033,7 @@ public class Jalview
 
 class rnabuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
     System.out.println("Good idea ! ");
@@ -1053,6 +1043,7 @@ class rnabuttonlistener implements ActionListener
 
 class pbuttonlistener implements ActionListener
 {
+  @Override
   public void actionPerformed(ActionEvent arg0)
   {
 
@@ -1173,6 +1164,7 @@ class FeatureFetcher
     new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         synchronized (us)
@@ -1181,7 +1173,8 @@ class FeatureFetcher
           running++;
         }
 
-        af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+        af.setProgressBar(MessageManager
+                .getString("status.das_features_being_retrived"), id);
         af.featureSettings_actionPerformed(null);
         af.featureSettings.fetchDasFeatures(dasSources, true);
         af.setProgressBar(null, id);