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 65b32af..b0e9333 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,19 +1,22 @@
 /*
- * 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;
 
@@ -28,7 +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;
@@ -71,7 +73,11 @@ public class Jalview
       }
     });
   }
-  protected static boolean proteine;
+  /**
+   * Put protein=true for get a protein example
+   */
+  private static boolean protein=false;
+
 
   /**
    * main class for Jalview application
@@ -134,6 +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");
@@ -153,16 +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();
@@ -221,6 +228,7 @@ public class Jalview
           }
         }
       }
+      desktop.checkForNews();
     }
 
     String file = null, protocol = null, format = null, data = null;
@@ -521,27 +529,14 @@ public class Jalview
     // And the user
     // ////////////////////
   
-    JFrame Typechooser =new JFrame("choose molecule type"); 
-    FlowLayout fl = new FlowLayout();
-    Typechooser.setLayout(fl);
-    Typechooser.setSize(400,400);
-    Typechooser.setDefaultCloseOperation(Typechooser.DISPOSE_ON_CLOSE);
-    JLabel label = new JLabel("What would you open ? ");
-    JButton rnabutton = new JButton("RNA molecule");
-    JButton pbutton = new JButton("Proteine molecule");
-    
-    pbutton.addActionListener(new pbuttonlistener());
-    rnabutton.addActionListener(new rnabuttonlistener());
-    Typechooser.getContentPane().add(label);
-    Typechooser.getContentPane().add(rnabutton);
-    Typechooser.getContentPane().add(pbutton);
-    Typechooser.setVisible(true);
+
+ 
     
     
 
     
     if (!headless && file == null && vamsasImport == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true)
+            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && protein == true)
     {
       file = jalview.bin.Cache.getDefault(
               "STARTUP_FILE",
@@ -644,7 +639,7 @@ public class Jalview
                 Cache.log.info("Not enabling Google Tracking.");
               }
             }, null, true);
-    SwingUtilities.invokeLater(prompter);
+    desktop.addDialogThread(prompter);
   }
 
   /**