look for startup file

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4ce1984..23c7547 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -120,6 +120,24 @@ public class Jalview extends JApplet
          frame.LoadFile(file, protocol, format);\r
      }\r
 \r
+     if(jalview.gui.Preferences.showStartupFile)\r
+     {\r
+       String file = jalview.gui.Preferences.startupFile;\r
+       String protocol = "File";\r
+       if (file.indexOf("http:") > -1)\r
+         protocol = "URL";\r
+\r
+       if(file.endsWith(".jar"))\r
+         Jalview2XML.LoadJalviewAlign(file);\r
+       else\r
+       {\r
+         String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+         frame.LoadFile(file, protocol, format);\r
+       }\r
+     }\r
+\r
+\r
+\r
    }\r
 \r
 }\r