Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d114a8a..86febed 100644 (file)
--- 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;
 
 /**
  * DOCUMENT ME!
@@ -92,6 +95,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 
+  protected JRadioButtonMenuItem annotationColour;
+
   protected JMenuItem modifyConservation = new JMenuItem();
 
   AlignmentPanel ap;
@@ -401,9 +406,20 @@ 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"));
@@ -419,7 +435,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             }
           }
         });
-
         add(menuItem);
       }
     }
@@ -1401,6 +1416,13 @@ 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()
@@ -1431,7 +1453,10 @@ 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);