Merge branch 'JAL-429_phylip-file-support' into Release_2_8_2_Branch

[jalview.git] / src / jalview / io / JalviewFileChooser.java

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index c84e542..df8decf 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,19 +1,19 @@
 /*
  * 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 
+ * 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.
- *  
- * 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 
+ *
+ * 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/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
@@ -23,21 +23,31 @@ package jalview.io;
 
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.HeadlessException;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JFileChooser;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
 
 /**
  * Enhanced file chooser dialog box.
- * 
+ *
  * NOTE: bug on Windows systems when filechooser opened on directory to view
  * files with colons in title.
- * 
+ *
  * @author AMW
- * 
+ *
  */
 public class JalviewFileChooser extends JFileChooser
 {
@@ -104,6 +114,7 @@ public class JalviewFileChooser extends JFileChooser
     setAccessory(new RecentlyOpened());
   }
 
+  @Override
   public void setFileFilter(javax.swing.filechooser.FileFilter filter)
   {
     super.setFileFilter(filter);
@@ -122,6 +133,7 @@ public class JalviewFileChooser extends JFileChooser
 
         EventQueue.invokeLater(new Thread()
         {
+          @Override
           public void run()
           {
             String currentName = ui.getFileName();
@@ -176,10 +188,15 @@ public class JalviewFileChooser extends JFileChooser
     {
       format = "PFAM";
     }
+    else if (format.toUpperCase().startsWith(PhylipFile.FILE_DESC))
+    {
+      format = PhylipFile.FILE_DESC;
+    }
 
     return format;
   }
 
+  @Override
   public int showSaveDialog(Component parent) throws HeadlessException
   {
     this.setAccessory(null);
@@ -265,6 +282,7 @@ public class JalviewFileChooser extends JFileChooser
 
       list.addMouseListener(new MouseAdapter()
       {
+        @Override
         public void mousePressed(MouseEvent evt)
         {
           recentListSelectionChanged(list.getSelectedValue());
@@ -279,6 +297,7 @@ public class JalviewFileChooser extends JFileChooser
 
       javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
+        @Override
         public void run()
         {
           scroller.getHorizontalScrollBar().setValue(