JAL-2360 findColour() with no args removed from ColourSchemeI

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index b6fd5fc..f3927df 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -423,9 +423,16 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
 
-      if (sg.cs != null && sg.cs.conservationApplied())
+      if (sg.cs != null)
       {
-        conservationMenuItem.setSelected(true);
+        if (sg.cs.conservationApplied())
+        {
+          conservationMenuItem.setSelected(true);
+        }
+        if (sg.cs.getThreshold() > 0)
+        {
+          abovePIDColour.setSelected(true);
+        }
       }
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
@@ -987,15 +994,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     });
     createGroupMenuItem.setText(MessageManager
             .getString("action.create_group"));
-    createGroupMenuItem
-.addActionListener(new ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                createGroupMenuItem_actionPerformed();
-              }
-            });
+    createGroupMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        createGroupMenuItem_actionPerformed();
+      }
+    });
 
     outline.setText(MessageManager.getString("action.border_colour"));
     outline.addActionListener(new ActionListener()
@@ -1270,12 +1276,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    */
   protected void buildColourMenu()
   {
-    SequenceGroup sg = getGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+    {
+      /*
+       * popup menu with no sequence group scope
+       */
+      return;
+    }
     colourMenu.removeAll();
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, sg);
+    ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
 
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);