update of javajs package; adds org.apache.harmony, org.xml.sax.helpers

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9ec0033..2007814 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -64,8 +61,12 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
+import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
@@ -76,6 +77,9 @@ import javax.swing.UIManager;
  */
 public class Jalview
 {
+
+  // BH 6/19/2018 starting to work on JS version - just discovering issues
+
   /*
    * singleton instance of this class
    */
@@ -85,8 +89,14 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
+  public static boolean isJS = /** @j2sNative true || */ // BH 2018
+          false;
+
   static
   {
+
+    if (!isJS)
+    { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
     {
@@ -103,6 +113,8 @@ public class Jalview
       {
       }
     });
+
+    }
   }
 
   /**
@@ -187,7 +199,12 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
+
+    if (!isJS)
+    {
+      System.setSecurityManager(null);
+    }
+
     System.out
             .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -275,20 +292,43 @@ public class Jalview
       UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
     }
     if (Platform.isAMac())
     {
+
+      LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+              .getLookAndFeel();
       System.setProperty("com.apple.mrj.application.apple.menu.about.name",
               "Jalview");
       System.setProperty("apple.laf.useScreenMenuBar", "true");
-      try
+      if (lookAndFeel != null)
       {
-        UIManager.setLookAndFeel(
-                ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
-      } catch (Throwable e)
+        try
+        {
+          UIManager.setLookAndFeel(lookAndFeel);
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to set QuaQua look and feel: " + e.toString());
+        }
+      }
+      if (lookAndFeel == null || !(lookAndFeel.getClass()
+              .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+              || !UIManager.getLookAndFeel().getClass().toString()
+                      .toLowerCase().contains("quaqua"))
       {
-        System.err.println(
-                "Failed to set QuaQua look and feel: " + e.toString());
+        try
+        {
+          System.err.println(
+                  "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+          UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to reset look and feel: " + e.toString());
+        }
       }
     }
 
@@ -970,7 +1010,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -1036,7 +1076,7 @@ public class Jalview
                         + nickname + "|" + url);
         if (source == null)
         {
-          source = new Vector<String>();
+          source = new Vector<>();
         }
         source.addElement(nickname);
       }
@@ -1054,7 +1094,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }