X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=702773b6af1cf47e727f2a63bb6877513f20580c;hp=4e02d21250aeab598121cd7e89a097515b9737e9;hb=383fd91269f510b189450fbe174e9c051103c7eb;hpb=bfb35471fbb8dd6cc4252b9a12b81057922e8f5e

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4e02d21..702773b 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -46,6 +46,7 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -68,11 +69,13 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
+import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
 
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
@@ -90,6 +93,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 
+  protected JRadioButtonMenuItem annotationColour;
+
   protected JMenuItem modifyConservation = new JMenuItem();
 
   AlignmentPanel ap;
@@ -580,9 +585,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
       }
     }
-    // for the case when no sequences are even visible
+
+    /*
+     * offer 'Reveal All'
+     * - in the IdPanel (seq not null) if any sequence is hidden
+     * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+     */
     if (alignPanel.av.hasHiddenRows())
     {
+      boolean addOption = seq != null;
+      if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
+      {
+        addOption = true;
+      }
+      if (addOption)
       {
         menuItem = new JMenuItem(
                 MessageManager.getString("action.reveal_all"));
@@ -598,7 +614,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             }
           }
         });
-
         add(menuItem);
       }
     }
@@ -1439,6 +1454,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     });
 
+    annotationColour = new JRadioButtonMenuItem(
+            MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+    annotationColour.setEnabled(false);
+    annotationColour.setToolTipText(
+            MessageManager.getString("label.by_annotation_tooltip"));
+
     modifyConservation.setText(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
@@ -1469,7 +1491,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+            false);
+    bg.add(annotationColour);
+    colourMenu.add(annotationColour);
 
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -2148,7 +2173,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * switch to the chosen colour scheme (or null for None)
      */
     ColourSchemeI colourScheme = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, sg,
+            .getColourScheme(colourSchemeName, ap.av, sg,
                     ap.av.getHiddenRepSequences());
     sg.setColourScheme(colourScheme);
     if (colourScheme instanceof Blosum62ColourScheme