From fd6c33d8f91caaef0ee25a039956ac203ac9b7a6 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 08:20:45 +0000
Subject: [PATCH] hide annotation colouring options

---
 src/jalview/gui/PopupMenu.java |   44 +++++++++++++++++++++++++++++++++++-----
 1 file changed, 39 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1df8041..64339b3 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -84,8 +84,9 @@ public class PopupMenu
   JMenu jMenu1 = new JMenu();
   JMenu structureMenu = new JMenu();
   JMenu viewStructureMenu = new JMenu();
-  JMenu colStructureMenu = new JMenu();
+ // JMenu colStructureMenu = new JMenu();
   JMenuItem editSequence = new JMenuItem();
+ // JMenuItem annotationMenuItem = new JMenuItem();
 
   /**
    * Creates a new PopupMenu object.
@@ -192,7 +193,7 @@ public class PopupMenu
           });
           viewStructureMenu.add(menuItem);
 
-          menuItem = new JMenuItem();
+       /*   menuItem = new JMenuItem();
           menuItem.setText(pdb.getId());
           menuItem.addActionListener(new java.awt.event.ActionListener()
           {
@@ -201,9 +202,14 @@ public class PopupMenu
               colourByStructure(pdb.getId());
             }
           });
-          colStructureMenu.add(menuItem);
+          colStructureMenu.add(menuItem);*/
         }
       }
+      else
+      {
+        structureMenu.remove(viewStructureMenu);
+       // structureMenu.remove(colStructureMenu);
+      }
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -566,7 +572,7 @@ public class PopupMenu
     jMenu1.setText("Group");
     structureMenu.setText("Structure");
     viewStructureMenu.setText("View Structure");
-    colStructureMenu.setText("Colour By Structure");
+  //  colStructureMenu.setText("Colour By Structure");
     editSequence.setText("Edit Sequence...");
     editSequence.addActionListener(new ActionListener()
     {
@@ -575,6 +581,14 @@ public class PopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
+   /* annotationMenuItem.setText("By Annotation");
+    annotationMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        annotationMenuItem_actionPerformed(actionEvent);
+      }
+    });*/
 
     add(groupMenu);
 
@@ -623,6 +637,7 @@ public class PopupMenu
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
+    //colourMenu.add(annotationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
     editMenu.add(editSequence);
@@ -641,7 +656,7 @@ public class PopupMenu
     jMenu1.add(outline);
     structureMenu.add(pdbMenu);
     structureMenu.add(viewStructureMenu);
-    structureMenu.add(colStructureMenu);
+   // structureMenu.add(colStructureMenu);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -1009,6 +1024,23 @@ public class PopupMenu
     refresh();
   }
 
+  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+
+    acg.predefinedColours = true;
+    sg.cs = acg;
+
+    refresh();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -1448,4 +1480,6 @@ public class PopupMenu
         }
       }
   }
+
+
 }
-- 
1.7.10.2