X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1377de2b1fef0fab631c3e63a3efced38ca90076;hb=e1124a62486322d2d28482529d2d6b850ce1719b;hp=26fc93c4a22b1fc8a1daa7d445e84807d12ecf91;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 26fc93c..1377de2 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -172,7 +172,7 @@ public class PopupMenu extends JPopupMenu
                 noColourmenuItem.setSelected(true);
             }
 
-            if (sg.cs instanceof ConservationColourScheme)
+            if (sg.cs!=null && sg.cs.conservationApplied())
             {
                 conservationMenuItem.setSelected(true);
             }
@@ -339,6 +339,28 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(buriedColour);
         colourMenu.add(nucleotideMenuItem);
         colourMenu.add(userDefinedColour);
+
+        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+        {
+          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+              getUserColourSchemes().keys();
+
+          while (userColours.hasMoreElements())
+          {
+            JMenuItem item = new JMenuItem(userColours.
+                nextElement().toString());
+            item.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent evt)
+              {
+                userDefinedColour_actionPerformed(evt);
+              }
+            });
+            colourMenu.add(item);
+          }
+        }
+
+
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
@@ -423,7 +445,7 @@ public class PopupMenu extends JPopupMenu
                     abovePIDColour_actionPerformed(e);
                 }
             });
-        userDefinedColour.setText("User Defined");
+        userDefinedColour.setText("User Defined...");
         userDefinedColour.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -472,6 +494,9 @@ public class PopupMenu extends JPopupMenu
             superG.setSuperGroupProperties(sg);
           }
         }
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
+
         ap.seqPanel.repaint();
     }
 
@@ -584,6 +609,8 @@ public class PopupMenu extends JPopupMenu
     protected void abovePIDColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (abovePIDColour.isSelected())
         {
@@ -593,22 +620,13 @@ public class PopupMenu extends JPopupMenu
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
 
-            if (sg.cs instanceof ResidueColourScheme)
-            {
-                ((ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-            }
-            else if (sg.cs instanceof ScoreColourScheme)
-            {
-                ((ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-            }
+           sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
             SliderPanel.showPIDSlider();
         }
         else // remove PIDColouring
         {
-            ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-            rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-            sg.cs = rcs;
+            sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
         }
 
         refresh();
@@ -621,9 +639,18 @@ public class PopupMenu extends JPopupMenu
      */
     protected void userDefinedColour_actionPerformed(ActionEvent e)
     {
-        new UserDefinedColours(ap, getGroup());
-    }
-
+       SequenceGroup sg = getGroup();
+
+       if (e.getActionCommand().equals("User Defined..."))
+         new UserDefinedColours(ap, sg);
+       else
+       {
+         UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+             getUserColourSchemes().get(e.getActionCommand());
+
+         sg.cs = udc;
+       }
+     }
     /**
      * DOCUMENT ME!
      *
@@ -674,6 +701,8 @@ public class PopupMenu extends JPopupMenu
     protected void conservationMenuItem_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
+        if(sg.cs==null)
+          return;
 
         if (conservationMenuItem.isSelected())
         {
@@ -684,17 +713,14 @@ public class PopupMenu extends JPopupMenu
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
 
-            ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-            sg.cs = ccs;
+            sg.cs.setConservation(c);
 
-            SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+            SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
             SliderPanel.showConservationSlider();
         }
         else // remove ConservationColouring
         {
-            ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
-            sg.cs = ccs.cs;
+            sg.cs.setConservation(null);
         }
 
         refresh();