Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 226888f..857bd84 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -67,6 +67,8 @@ import java.util.logging.Logger;
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
+import com.threerings.getdown.util.LaunchUtil;
+
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 
@@ -87,34 +89,13 @@ 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;
@@ -286,6 +267,23 @@ public class Jalview
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
 
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null && appdirString.length() > 0)
+    {
+      final File appdir = new File(appdirString);
+      new Thread()
+      {
+        @Override
+        public void run()
+        {
+          LaunchUtil.upgradeGetdown(
+                  new File(appdir, "getdown-launcher-old.jar"),
+                  new File(appdir, "getdown-launcher.jar"),
+                  new File(appdir, "getdown-launcher-new.jar"));
+        }
+      }.start();
+
+    }
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
@@ -438,6 +436,20 @@ public class Jalview
 //       }
       ;
       desktop.setInBatchMode(true); // indicate we are starting up
+
+      try
+      {
+        JalviewTaskbar.setTaskbar(this);
+      } catch (Exception e)
+      {
+        System.out.println("Cannot set Taskbar");
+        // e.printStackTrace();
+      } catch (Throwable t)
+      {
+        System.out.println("Cannot set Taskbar");
+        // t.printStackTrace();
+      }
+
       desktop.setVisible(true);
 
       if (!Platform.isJS())
@@ -1092,7 +1104,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<>();
+      Map<String, java.lang.Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {