X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=f59c37f16cae5d38c3848d231c4e168a08e9f57c;hb=4dd96dd41cb37178a6dc0298ce08c8bfcdfab715;hp=060d6ad91de0ed04babf071c0f44089b05b0586b;hpb=7a5cac232c59bba9964ec32ecdd787b8028cde48;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 060d6ad..f59c37f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
@@ -304,6 +305,15 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
+
+    if (aparser.contains(ArgsParser.NODISPLAY)
+            || aparser.contains(ArgsParser.NOGUI)
+            || aparser.contains(ArgsParser.HEADLESS)
+            || "true".equals(System.getProperty("java.awt.headless")))
+    {
+      headless = true;
+    }
+
     if (isJS)
     {
       isJavaAppletTag = aparser.isApplet();
@@ -335,13 +345,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains(ArgsParser.NODISPLAY)
-              || aparser.contains(ArgsParser.NOGUI)
-              || aparser.contains(ArgsParser.HEADLESS)
-              || "true".equals(System.getProperty("java.awt.headless")))
-      {
-        headless = true;
-      }
+
 
       // anything else!
 
@@ -397,7 +401,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      if (!isJS && Platform.isWin())
+       {
+        UIManager.setLookAndFeel(
+                headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+                        : UIManager.getSystemLookAndFeelClassName());
+//      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      }
     } catch (Exception ex)
     {
       System.err.println("Unexpected Look and Feel Exception");
@@ -640,14 +650,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         // TODO ?
       }
 
-      if (aparser.contains(ArgsParser.SHOWOVERVIEW))
-      {
-        jalview.bin.Cache.setPropertyNoSave(Preferences.SHOW_OVERVIEW,
-                "true");
-
-        System.out.println("CMD [showoverview] executed successfully!");
-      }
-
       if (aparser.contains(ArgsParser.NOMENUBAR))
       {
         noMenuBar = true;
@@ -757,6 +759,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
           System.out.println(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
+
+        if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+        {
+          af.overviewMenuItem_actionPerformed(null);
+          System.out.println("CMD [showoverview] executed successfully!");
+        }
+
         // set or clear the sortbytree flag.
         if (aparser.contains(ArgsParser.SORTBYTREE))
         {
@@ -849,11 +858,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          checkOutputFile(aparser, af, format);
-          while (aparser.getSize() > 0)
-          {
-            System.out.println("Unknown arg: " + aparser.nextValue());
-          }
+        }
+        checkOutputFile(aparser, af, format);
+        while (aparser.getSize() > 0)
+        {
+          System.out.println("Unknown arg: " + aparser.nextValue());
         }
       }
     }
@@ -1043,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       // biojsmsa filename
       String outputFormat = aparser.nextValue();
       String file = aparser.nextValue();
+      System.out.println("format " + outputFormat);
+
       if (outputFormat.equalsIgnoreCase("png"))
       {
         af.createPNG(new File(file));
@@ -2044,6 +2055,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   }
 
+  @Override
+  public void showOverview()
+  {
+    currentAlignFrame.overviewMenuItem_actionPerformed(null);
+  }
+
+  public void notifyWorker(AlignCalcWorkerI worker, String status)
+  {
+    // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+    // + " " + status);
+  }
 
 }