fixes for Jalview command-line URI code

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 330919b..694fe00 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -87,34 +87,13 @@ import groovy.util.GroovyScriptEngine;
  */
 public class Jalview
 {
-  // @formatter:off
-       /**
-   * find first query parameter (if any) that doesn't start with j2s
-   * and set as space-delimited arguments to Jalview main
-   * 
-   * @j2sNative
-   *  var hr = decodeURI(document.location.href);
-   *  var pos = hr.indexOf("?");
-   *  if (pos > 0)
-   *  {
-   *     q = hr.substring(pos+1);
-   *     args = q.split("&");
-   *     for (i = 0 ; i < args.length; i++)
-   *     {
-   *      arg1 = args[i];
-   *      if (!arg1.startsWith("j2s"))
-   *      {
-   *       thisApplet.__Info.args = arg1.split(" ");
-   *       break;
-   *      }
-   *     }
-   *  }
-   */
-  // @formatter:on
+  static
+  {
+    Platform.getURLCommandArguments();
+  }
+
+  // singleton instance of this class
 
-  /*
-   * singleton instance of this class
-   */
   private static Jalview instance;
 
   private Desktop desktop;
@@ -127,7 +106,7 @@ public class Jalview
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       // grab all the rights we can for the JVM
@@ -239,12 +218,21 @@ public class Jalview
   @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
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
        {
                Logger.getLogger("").setLevel(Level.ALL);
@@ -292,7 +280,7 @@ public class Jalview
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       if (aparser.contains("help") || aparser.contains("h"))
@@ -435,7 +423,7 @@ public class Jalview
       /**
        * Java only
        * 
-       * @j2sNative
+       * @j2sIgnore
        */
       {
         desktop.startServiceDiscovery();
@@ -609,7 +597,7 @@ public class Jalview
         /**
          * ignore in JavaScript -- can't just file existence - could load it?
          * 
-         * @j2sNative
+         * @j2sIgnore
          */
       {
         if (!file.startsWith("http://") && !file.startsWith("https://"))
@@ -844,7 +832,7 @@ public class Jalview
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",