Applet has main method, excutable

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 14a341d..289e761 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -48,40 +48,43 @@ public class AlignFrame
     add(alignPanel);\r
     alignPanel.validate();\r
 \r
-    String treeFile = applet.getParameter("treeFile");\r
-    if (treeFile != null)\r
+    if(applet!=null)\r
     {\r
-      try\r
+      String treeFile = applet.getParameter("treeFile");\r
+      if (treeFile != null)\r
       {\r
-        treeFile = treeFile;\r
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
-            getCodeBase() + treeFile, "URL");\r
-        fin.parse();\r
+        try\r
+        {\r
+          treeFile = treeFile;\r
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+              getCodeBase() + treeFile, "URL");\r
+          fin.parse();\r
 \r
-        if (fin.getTree() != null)\r
+          if (fin.getTree() != null)\r
+          {\r
+            TreePanel tp = null;\r
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+                               fin, "FromFile", applet.getCodeBase() + treeFile);\r
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+            addTreeMenuItem(tp, treeFile);\r
+          }\r
+        }\r
+        catch (Exception ex)\r
         {\r
-          TreePanel tp = null;\r
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
-                             fin, "FromFile", applet.getCodeBase() + treeFile);\r
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
-          addTreeMenuItem(tp, treeFile);\r
+          ex.printStackTrace();\r
         }\r
       }\r
-      catch (Exception ex)\r
+\r
+      String param = applet.getParameter("sortBy");\r
+      if (param != null)\r
       {\r
-        ex.printStackTrace();\r
+        if (param.equalsIgnoreCase("Id"))\r
+          sortIDMenuItem_actionPerformed(null);\r
+        else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+          sortPairwiseMenuItem_actionPerformed(null);\r
       }\r
     }\r
 \r
-    String param = applet.getParameter("sortBy");\r
-    if(param!=null)\r
-    {\r
-      if (param.equalsIgnoreCase("Id"))\r
-        sortIDMenuItem_actionPerformed(null);\r
-      else if (param.equalsIgnoreCase("Pairwise Identity"))\r
-        sortPairwiseMenuItem_actionPerformed(null);\r
-    }\r
-\r
     this.addWindowListener(new WindowAdapter()\r
     {\r
       public void windowClosing(WindowEvent e)\r
@@ -127,6 +130,8 @@ public class AlignFrame
   {\r
     PaintRefresher.components.remove(viewport.alignment);\r
     dispose();\r
+    if(PaintRefresher.components.size()==0 && applet==null)\r
+      System.exit(0);\r
   }\r
 \r
   Stack historyList = new Stack();\r