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 7cbbd7d..694fe00 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -87,22 +87,13 @@ import groovy.util.GroovyScriptEngine;
  */
 public class Jalview
 {
-       /**
-   * // 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; } } }
-   */
+  static
+  {
+    Platform.getURLCommandArguments();
+  }
+
+  // singleton instance of this class
 
-  /*
-   * singleton instance of this class
-   */
   private static Jalview instance;
 
   private Desktop desktop;
@@ -115,7 +106,7 @@ public class Jalview
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       // grab all the rights we can for the JVM
@@ -227,12 +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())// !(/** @j2sNative true ||*/false))
+    if (!Platform.isJS())
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
        {
                Logger.getLogger("").setLevel(Level.ALL);
@@ -278,9 +278,9 @@ public class Jalview
 
     if (!Platform.isJS())
     /**
-     * ignore in JavaScript
+     * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       if (aparser.contains("help") || aparser.contains("h"))
@@ -423,7 +423,7 @@ public class Jalview
       /**
        * Java only
        * 
-       * @j2sNative
+       * @j2sIgnore
        */
       {
         desktop.startServiceDiscovery();
@@ -597,7 +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://"))
@@ -826,13 +826,13 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!Platform.isJS() && // /** @j2sNative false && */ // BH 2018
-    !headless && file == null && vamsasImport == null
+    if (!Platform.isJS() && !headless && file == null
+            && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
      * 
-     * @j2sNative
+     * @j2sIgnore
      */
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",