JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bfa7b11..b0e9333 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,22 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.bin;
 
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -24,7 +31,6 @@ import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.lang.reflect.Constructor;
-import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URL;
 import java.net.URLDecoder;
@@ -67,6 +73,11 @@ public class Jalview
       }
     });
   }
+  /**
+   * Put protein=true for get a protein example
+   */
+  private static boolean protein=false;
+
 
   /**
    * main class for Jalview application
@@ -129,6 +140,11 @@ public class Jalview
                       + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }
+    if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
+    {
+      System.setProperty("java.awt.headless", "true");
+      headless=true;
+    }
     Cache.loadProperties(aparser.getValue("props")); // must do this before
     // anything else!
     String defs = aparser.getValue("setprop");
@@ -148,16 +164,12 @@ public class Jalview
       }
       defs = aparser.getValue("setprop");
     }
-    if (aparser.contains("nodisplay"))
-    {
-      System.setProperty("java.awt.headless", "true");
-    }
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
     {
       headless = true;
     }
-
+    System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
     try
     {
       Cache.initLogger();
@@ -516,8 +528,15 @@ public class Jalview
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
+  
+
+ 
+    
+    
+
+    
     if (!headless && file == null && vamsasImport == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && protein == true)
     {
       file = jalview.bin.Cache.getDefault(
               "STARTUP_FILE",
@@ -590,7 +609,8 @@ public class Jalview
       desktop.setInBatchMode(false);
     }
   }
-
+  
+  
   private static void startUsageStats(final Desktop desktop)
   {
     /**
@@ -902,6 +922,21 @@ public class Jalview
  * @author Andrew Waterhouse and JBP documented.
  * 
  */
+
+class rnabuttonlistener  implements ActionListener{
+         public void actionPerformed(ActionEvent arg0) {
+                 System.out.println("Good idea ! ");
+
+         }
+}
+
+class pbuttonlistener  implements ActionListener{
+         public void actionPerformed(ActionEvent arg0) {
+               
+         
+         }
+}
+
 class ArgsParser
 {
   Vector vargs = null;
@@ -1040,4 +1075,7 @@ class FeatureFetcher
   {
     return queued == 0 && running == 0;
   }
+  
+  
+  
 };