JAL-1517 source formatting

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5dc6c81..b6d6d3f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,23 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
@@ -69,6 +75,11 @@ public class Jalview
   }
 
   /**
+   * Put protein=true for get a protein example
+   */
+  private static boolean protein = false;
+
+  /**
    * main class for Jalview application
    * 
    * @param args
@@ -129,10 +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"))
+    if (aparser.contains("nodisplay") || aparser.contains("nogui")
+            || aparser.contains("headless"))
     {
       System.setProperty("java.awt.headless", "true");
-      headless=true;
+      headless = true;
     }
     Cache.loadProperties(aparser.getValue("props")); // must do this before
     // anything else!
@@ -158,7 +170,8 @@ public class Jalview
     {
       headless = true;
     }
-    System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
+    System.setProperty("http.agent",
+            "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
     try
     {
       Cache.initLogger();
@@ -517,8 +530,10 @@ 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",
@@ -903,6 +918,24 @@ 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;
@@ -1041,4 +1074,5 @@ class FeatureFetcher
   {
     return queued == 0 && running == 0;
   }
+
 };