notes re JAL-629

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2c68662..6a59093 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -36,7 +36,7 @@ import java.util.*;
 import javax.swing.*;
 
 import jalview.gui.*;
-import jalview.io.AppletFormatAdapter;
+import jalview.util.Platform;
 
 /**
  * Main class for Jalview Application <br>
@@ -79,6 +79,11 @@ public class Jalview
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
+    if (new Platform().isAMac())
+    {
+       System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview");
+       System.setProperty("apple.laf.useScreenMenuBar", "true");
+    }
 
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
@@ -89,6 +94,7 @@ public class Jalview
               .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                       + "-nodisplay\tRun Jalview without User Interface.\n"
                       + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+                      + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                       + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                       + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
                       + "-features FILE\tUse the given file to mark features on the alignment.\n"
@@ -165,20 +171,15 @@ public class Jalview
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
-      // UIManager.getCrossPlatformLookAndFeelClassName()
-              // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
-              // "javax.swing.plaf.metal.MetalLookAndFeel"
-              // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
-              // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
-              );
+      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
     }
+
     if (!headless)
     {
       desktop = new Desktop();
+      desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -411,7 +412,7 @@ public class Jalview
           ex.printStackTrace(System.err);
         }
       }
-      // todo - load PDB structure to alignment
+      // TODO - load PDB structure(s) to alignment JAL-629
       // (associate with identical sequence in alignment, or a specified
       // sequence)
 
@@ -536,7 +537,7 @@ public class Jalview
         startFeatureFetching(getFeatures);
       }
     }
-    // execute a groovy script.
+    // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
@@ -551,8 +552,11 @@ public class Jalview
                         + groovyscript);
       }
     }
-
-    // Once all other stuff is done, execute any groovy scripts (in order)
+    // and finally, turn off batch mode indicator - if the desktop still exists
+    if (desktop!=null)
+    {
+      desktop.setInBatchMode(false);
+    }
   }
 
   private static void startUsageStats(final Desktop desktop)