JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add...

[jalview.git] / src / jalview / util / Platform.java

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index a65ee95..573e2d5 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -88,7 +88,8 @@ public class Platform
   public static boolean isLinux()
   {
     return (isLinux == null
-            ? (isLinux = (System.getProperty("os.name").indexOf("Linux") >= 0))
+            ? (isLinux = (System.getProperty("os.name")
+                    .indexOf("Linux") >= 0))
             : isLinux);
   }
 
@@ -522,8 +523,7 @@ public class Platform
 
   public static Object parseJSON(String json) throws ParseException
   {
-    return (isJS() ? JSON.parse(json)
-            : new JSONParser().parse(json));
+    return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
   }
 
   public static Object parseJSON(Reader r)
@@ -555,8 +555,8 @@ public class Platform
    * @param is
    * @param outFile
    * @throws IOException
-   *                       if the file cannot be created or there is a problem
-   *                       reading the input stream.
+   *           if the file cannot be created or there is a problem reading the
+   *           input stream.
    */
   public static void streamToFile(InputStream is, File outFile)
           throws IOException
@@ -600,8 +600,8 @@ public class Platform
     if (isJS())
     {
       System.out.println(
-            "Platform adding known access-control-allow-origin * for domain "
-                    + domain);
+              "Platform adding known access-control-allow-origin * for domain "
+                      + domain);
       /**
        * @j2sNative
        * 
@@ -613,23 +613,31 @@ public class Platform
 
   public static void getURLCommandArguments()
   {
-
-    /**
-     * Retrieve the first query field as command arguments to Jalview. Include
-     * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
-     * element to this value.
-     * 
-     * @j2sNative var a =
-     *            decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
-     *            + "?").split("?")[1].split("#")[0]); a &&
-     *            (J2S.thisApplet.__Info.args = a.split(" "));
-     */
-
+    try
+    {
+      /**
+       * Retrieve the first query field as command arguments to Jalview. Include
+       * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
+       * __Info.args element to this value.
+       * 
+       * @j2sNative var a =
+       *            decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+       *            + "?").split("?")[1].split("#")[0]); a &&
+       *            (System.out.println("URL arguments detected were "+a)) &&
+       *            (J2S.thisApplet.__Info.urlargs = a.split(" "));
+       *            (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args
+       *            == "" || J2S.thisApplet.__Info.args == "??") &&
+       *            (J2S.thisApplet.__Info.args = a) && (System.out.println("URL
+       *            arguments were passed to J2S main."));
+       */
+    } catch (Throwable t)
+    {
+    }
   }
 
   /**
-   * A (case sensitive) file path comparator that ignores the difference between /
-   * and \
+   * A (case sensitive) file path comparator that ignores the difference between
+   * / and \
    * 
    * @param path1
    * @param path2