X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=0166e752e942835959ac7bc3f16aca208ced0a3e;hb=36c0eac11fb0d0ac6df2d971fabf524325db5e97;hp=e1b25602c07d181c7770916e52709332f52e81c8;hpb=90add82a33c05e218a92eb1cdb2c345da05465f8;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e1b2560..0166e75 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -71,6 +71,7 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -79,7 +80,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
 
@@ -1353,19 +1353,16 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(nucleotideMenuItem);
     if (ap.getAlignment().isNucleotide())
     {
-      // JBPNote - commented since the colourscheme isn't functional
       colourMenu.add(purinePyrimidineColour);
     }
-    colourMenu.add(userDefinedColour);
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
+            .getUserColourSchemes();
+    if (userColourSchemes != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
-      {
-        JMenuItem item = new JMenuItem(userColours.nextElement().toString());
+      for (String userColour : userColourSchemes.keySet())
+    {
+        JMenuItem item = new JMenuItem(userColour);
         item.addActionListener(new ActionListener()
         {
           @Override
@@ -1377,6 +1374,7 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(item);
       }
     }
+    colourMenu.add(userDefinedColour);
 
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
@@ -1408,8 +1406,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    clustalColour.setText(MessageManager
-            .getString("label.clustalx_colours"));
+    clustalColour.setText(MessageManager.getString("label.clustalx"));
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1514,7 +1511,8 @@ public class PopupMenu extends JPopupMenu
         PIDColour_actionPerformed();
       }
     });
-    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
+    BLOSUM62Colour
+            .setText(MessageManager.getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1576,7 +1574,7 @@ public class PopupMenu extends JPopupMenu
      * Temporary store to hold distinct calcId / type pairs for the tooltip.
      * Using TreeMap means calcIds are shown in alphabetical order.
      */
-    Map<String, String> tipEntries = new TreeMap<String, String>();
+    SortedMap<String, String> tipEntries = new TreeMap<String, String>();
     final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
     AlignmentI al = this.ap.av.getAlignment();
     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
@@ -1896,7 +1894,7 @@ public class PopupMenu extends JPopupMenu
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+      UserColourScheme udc = UserDefinedColours
               .getUserColourSchemes().get(e.getActionCommand());
 
       sg.cs = udc;