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 30620a1..2007814 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -77,6 +77,9 @@ import groovy.util.GroovyScriptEngine;
  */
 public class Jalview
 {
+
+  // BH 6/19/2018 starting to work on JS version - just discovering issues
+
   /*
    * singleton instance of this class
    */
@@ -86,8 +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()
     {
@@ -104,6 +113,8 @@ public class Jalview
       {
       }
     });
+
+    }
   }
 
   /**
@@ -188,7 +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") + " "