JAL-1432 updated copyright notices

[jalview.git] / src / jalview / gui / UserDefinedColours.java

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 88bf6e2..a26517b 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,34 +1,49 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- * 
+ *  
  * 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.
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 /**
  * DOCUMENT ME!
@@ -297,9 +312,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
         JButton button = (JButton) buttonPanel.getComponent(b);
         if (!selectedButtons.contains(button))
         {
-          button
-                  .setForeground(button.getBackground().brighter()
-                          .brighter());
+          button.setForeground(button.getBackground().brighter().brighter());
           selectedButtons.add(button);
         }
       }
@@ -325,9 +338,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       }
       else
       {
-        pressed
-                .setForeground(pressed.getBackground().brighter()
-                        .brighter());
+        pressed.setForeground(pressed.getBackground().brighter().brighter());
         selectedButtons.addElement(pressed);
       }
     }
@@ -376,7 +387,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         try
         {
-          col = oldColourScheme.findColour(aa.charAt(0), -1);
+          col = oldColourScheme.findColour(aa.charAt(0), -1, null);
         } catch (Exception ex)
         {
         }
@@ -487,10 +498,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
     upperCaseButtons = new Vector();
     lowerCaseButtons = new Vector();
 
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"), new String[]
-    { "jc" }, new String[]
-    { "Jalview User Colours" }, "Jalview User Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "jc" }, new String[]
+            { "Jalview User Colours" }, "Jalview User Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load colour scheme");
     chooser.setToolTipText("Load");
@@ -708,7 +719,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     if (userColourSchemes != null
             && userColourSchemes.containsKey(schemeName.getText()))
     {
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+      int reply = JOptionPane.showInternalConfirmDialog(
+              Desktop.desktop,
               "Colour scheme " + schemeName.getText() + " exists."
                       + "\nContinue saving colour scheme as "
                       + schemeName.getText() + "?",
@@ -720,10 +732,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
       userColourSchemes.remove(schemeName.getText());
     }
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"), new String[]
-    { "jc" }, new String[]
-    { "Jalview User Colours" }, "Jalview User Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "jc" }, new String[]
+            { "Jalview User Colours" }, "Jalview User Colours");
 
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save colour scheme");
@@ -856,8 +868,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (coloursFound.toString().length() > 1)
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound
-                .toString());
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+                coloursFound.toString());
       }
       else
       {
@@ -876,8 +888,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     userColourSchemes = new Hashtable();
 
     StringBuffer coloursFound = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(jalview.bin.Cache
-            .getProperty("USER_DEFINED_COLOURS"), "|");
+    StringTokenizer st = new StringTokenizer(
+            jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
 
     while (st.hasMoreElements())
     {
@@ -902,8 +914,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (coloursFound.toString().length() > 1)
     {
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound
-              .toString());
+      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+              coloursFound.toString());
     }
     else
     {