X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=28d029c1ac68d23c33fc0d31bd7d62f279c7e2a5;hb=7d52ef194d39e75fed7730041da25c48e456cf8c;hp=d9de4692f1a0ca23eab66edb1d3fa50c584c77c0;hpb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index d9de469..28d029c 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -83,9 +83,6 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
@@ -148,6 +145,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   private boolean noCalculation, noMenuBar, noStatus;
 
+  private boolean noAnnotation;
+
   public boolean getStartCalculations()
   {
     return !noCalculation;
@@ -163,6 +162,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return !noStatus;
   }
 
+  public boolean getShowAnnotation()
+  {
+    return !noAnnotation;
+  }
 
   public static AlignFrame getCurrentAlignFrame()
   {
@@ -269,51 +272,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    */
   public static void main(String[] args)
   {
-    // setLogging(); // BH - for event debugging in JavaScript
+    // Platform.startJavaLogging();
     getInstance().doMain(args);
   }
 
 
-  private static void logClass(String name)
-  {
-    // BH - for event debugging in JavaScript
-    ConsoleHandler consoleHandler = new ConsoleHandler();
-    consoleHandler.setLevel(Level.ALL);
-    Logger logger = Logger.getLogger(name);
-    logger.setLevel(Level.ALL);
-    logger.addHandler(consoleHandler);
-  }
-
   @SuppressWarnings("unused")
-  private static void setLogging()
-  {
-
-    /**
-     * @j2sIgnore
-     * 
-     */
-    {
-      System.out.println("not in js");
-    }
-
-    // BH - for event debugging in JavaScript (Java mode only)
-    if (!Platform.isJS())
-    /**
-     * Java only
-     * 
-     * @j2sIgnore
-     */
-    {
-      Logger.getLogger("").setLevel(Level.ALL);
-      logClass("java.awt.EventDispatchThread");
-      logClass("java.awt.EventQueue");
-      logClass("java.awt.Component");
-      logClass("java.awt.focus.Component");
-      logClass("java.awt.focus.DefaultKeyboardFocusManager");
-    }
-
-  }
-
   /**
    * @param args
    */
@@ -321,7 +285,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   {
 
     boolean isJS = Platform.isJS();
-    if (!isJS)
+    if (isJS)
+    {
+      Platform.setAppClass(this);
+    }
+    else
     {
       System.setSecurityManager(null);
     }
@@ -692,6 +660,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         System.out.println("CMD [nostatus] executed successfully!");
       }
 
+      if (aparser.contains(ArgsParser.NOANNOTATION)
+              || aparser.contains(ArgsParser.NOANNOTATION2))
+      {
+        noAnnotation = true;
+        System.out.println("CMD no-annotation executed successfully!");
+      }
       if (aparser.contains(ArgsParser.NOCALCULATION))
       {
         noCalculation = true;
@@ -792,18 +766,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        
+
         boolean doUpdateAnnotation = false;
-        
 
-        if (aparser.contains(ArgsParser.NOANNOTATION)
-                || aparser.contains(ArgsParser.NOANNOTATION2))
+        /**
+         * we do this earlier in JalviewJS because of a complication with
+         * SHOWOVERVIEW
+         * 
+         * For now, just fixing this in JalviewJS.
+         *
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          af.getViewport().setShowAnnotation(false);
-          if (!af.getViewport().isShowAnnotation())
+          if (aparser.contains(ArgsParser.NOANNOTATION)
+                  || aparser.contains(ArgsParser.NOANNOTATION2))
           {
-            doUpdateAnnotation = true;
-            System.out.println("CMD no-annotation executed successfully!");
+            af.getViewport().setShowAnnotation(false);
+            if (!af.getViewport().isShowAnnotation())
+            {
+              doUpdateAnnotation = true;
+              System.out
+                      .println("CMD no-annotation executed successfully!");
+            }
           }
         }
         if (aparser.contains(ArgsParser.NOSORTBYTREE))
@@ -2058,5 +2044,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   }
 
+  @Override
+  public void showOverview()
+  {
+    currentAlignFrame.overviewMenuItem_actionPerformed(null);
+  }
 
 }
+