Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5dc6c81..046d132 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;
@@ -38,6 +44,7 @@ import java.util.*;
 import javax.swing.*;
 
 import jalview.gui.*;
+import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 /**
@@ -69,6 +76,11 @@ 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 +141,11 @@ 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 +171,8 @@ 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();
@@ -327,7 +341,7 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar("Processing commandline arguments...",
+        desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
       System.out.println("Opening file: " + file);
@@ -517,8 +531,10 @@ 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 +919,24 @@ 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;
@@ -1025,7 +1059,7 @@ class FeatureFetcher
           running++;
         }
 
-        af.setProgressBar("DAS features being retrieved...", id);
+        af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
         af.featureSettings_actionPerformed(null);
         af.featureSettings.fetchDasFeatures(dasSources, true);
         af.setProgressBar(null, id);
@@ -1041,4 +1075,5 @@ class FeatureFetcher
   {
     return queued == 0 && running == 0;
   }
+
 };