remove redundant menuitems

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b6d43ea..83e4407 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -9,10 +9,6 @@ import java.awt.event.*;
 public class APopupMenu extends java.awt.PopupMenu\r
 {\r
   Menu groupMenu = new Menu();\r
-  Menu analyze = new Menu();\r
-  Menu defineMenu = new Menu();\r
-  Menu groupName = new Menu();\r
-  Menu groupAnnotation = new Menu();\r
   protected MenuItem clustalColour = new MenuItem();\r
   protected MenuItem zappoColour = new MenuItem();\r
   protected MenuItem taylorColour = new MenuItem();\r
@@ -32,12 +28,8 @@ public class APopupMenu extends java.awt.PopupMenu
   AlignmentPanel ap;\r
   Menu sequenceMenu = new Menu();\r
   MenuItem sequenceName = new MenuItem();\r
-  Menu residueMenu = new Menu();\r
-  MenuItem annotateResidue = new MenuItem();\r
-\r
   Sequence sequence;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
-  MenuItem outline = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
 \r
   public APopupMenu(AlignmentPanel ap, Sequence seq)\r
@@ -58,54 +50,23 @@ public class APopupMenu extends java.awt.PopupMenu
     {    e.printStackTrace();    }\r
 \r
 \r
-    if(seq!=null)\r
-      residueMenu.setEnabled(false);\r
-    else\r
-      sequenceMenu.setEnabled(false);\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+    if( !ap.av.alignment.getGroups().contains(sg))\r
+        groupMenu.remove(unGroupMenuItem);\r
+\r
+    if(seq==null)\r
+       remove(sequenceMenu);\r
+\r
 \r
   }\r
   private void jbInit() throws Exception\r
   {\r
     groupMenu.setLabel("Group");\r
-    analyze.setLabel("Analyze");\r
-    analyze.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        analyze_actionPerformed(e);\r
-      }\r
-    });\r
-    defineMenu.setLabel("Define");\r
-    groupName.setLabel("Name");\r
-    groupName.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupName_actionPerformed(e);\r
-      }\r
-    });\r
-    groupAnnotation.setEnabled(false);\r
-    groupAnnotation.setLabel("Annotation");\r
-    groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        groupAnnotation_actionPerformed(e);\r
-      }\r
-    });\r
+    groupMenu.setLabel("Define");\r
+\r
     sequenceMenu.setLabel("Sequence");\r
     sequenceName.setLabel("Edit name");\r
-    sequenceName.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        sequenceName_actionPerformed(e);\r
-      }\r
-    });\r
-    residueMenu.setLabel("Residue");\r
-    annotateResidue.setEnabled(false);\r
-    annotateResidue.setActionCommand("annotate residue");\r
-    annotateResidue.setLabel("annotate residue???");\r
     unGroupMenuItem.setLabel("Remove Group");\r
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -115,14 +76,7 @@ public class APopupMenu extends java.awt.PopupMenu
       }\r
     });\r
 \r
-    outline.setLabel("Border colour");\r
-    outline.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        outline_actionPerformed(e);\r
-      }\r
-    });\r
+\r
     nucleotideMenuItem.setLabel("Nucleotide");\r
     nucleotideMenuItem.addActionListener(new ActionListener()\r
     {\r
@@ -134,38 +88,28 @@ public class APopupMenu extends java.awt.PopupMenu
 \r
     add(groupMenu);\r
     this.add(sequenceMenu);\r
-    this.add(residueMenu);\r
-    groupMenu.add(defineMenu);\r
     groupMenu.add(unGroupMenuItem);\r
+    groupMenu.add(noColourmenuItem);\r
+    groupMenu.add(clustalColour);\r
+    groupMenu.add(BLOSUM62Colour);\r
+    groupMenu.add(PIDColour);\r
+\r
+    groupMenu.add(zappoColour);\r
+    groupMenu.add(taylorColour);\r
+    groupMenu.add(hydrophobicityColour);\r
+    groupMenu.add(helixColour);\r
+    groupMenu.add(strandColour);\r
+    groupMenu.add(turnColour);\r
+    groupMenu.add(buriedColour);\r
+    groupMenu.add(nucleotideMenuItem);\r
+\r
+    groupMenu.add(userDefinedColour);\r
+\r
     groupMenu.addSeparator();\r
-    groupMenu.add(analyze);\r
-    defineMenu.add(groupName);\r
-    defineMenu.add(groupAnnotation);\r
-    defineMenu.addSeparator();\r
-    defineMenu.add(outline);\r
-    defineMenu.addSeparator();\r
-    defineMenu.add(noColourmenuItem);\r
-    defineMenu.add(clustalColour);\r
-    defineMenu.add(BLOSUM62Colour);\r
-    defineMenu.add(PIDColour);\r
-\r
-    defineMenu.add(zappoColour);\r
-    defineMenu.add(taylorColour);\r
-    defineMenu.add(hydrophobicityColour);\r
-    defineMenu.add(helixColour);\r
-    defineMenu.add(strandColour);\r
-    defineMenu.add(turnColour);\r
-    defineMenu.add(buriedColour);\r
-    defineMenu.add(nucleotideMenuItem);\r
-\r
-    defineMenu.add(userDefinedColour);\r
-\r
-    defineMenu.addSeparator();\r
-    defineMenu.add(abovePIDColour);\r
-    defineMenu.add(conservationMenuItem);\r
+    groupMenu.add(abovePIDColour);\r
+    groupMenu.add(conservationMenuItem);\r
 \r
     sequenceMenu.add(sequenceName);\r
-    residueMenu.add(annotateResidue);\r
 \r
     noColourmenuItem.setLabel("None");\r
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -292,7 +236,7 @@ public class APopupMenu extends java.awt.PopupMenu
     if( superG !=null)\r
       superG.setSuperGroupProperties( sg );\r
 \r
-    ap.seqPanel.repaint();\r
+    ap.seqPanel.seqCanvas.repaint();\r
   }\r
 \r
   protected void clustalColour_actionPerformed(ActionEvent e)\r
@@ -442,22 +386,6 @@ public class APopupMenu extends java.awt.PopupMenu
      refresh();\r
   }\r
 \r
-  protected void groupAnnotation_actionPerformed(ActionEvent e)\r
-  {\r
-\r
-  }\r
-\r
-  protected void groupName_actionPerformed(ActionEvent e)\r
-  {\r
-  /*  SequenceGroup sg = getGroup();\r
-    String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
-    if(reply==null)\r
-      return;\r
-\r
-    sg.setName(reply);\r
-    groupName.setLabel(reply);*/\r
-  }\r
-\r
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
@@ -490,26 +418,6 @@ public class APopupMenu extends java.awt.PopupMenu
     return sg;\r
   }\r
 \r
-  void sequenceName_actionPerformed(ActionEvent e)\r
-  {\r
-  /*  String id = sequence.getName();\r
-    String s = (String)JOptionPane.showInternalInputDialog(\r
-                ap,\r
-                "Edit sequence name",\r
-                "Edit sequence name ("+sequence.getName()+")",\r
-                JOptionPane.PLAIN_MESSAGE,\r
-                null,\r
-                null,\r
-                id);\r
-\r
-    if(s!=null)\r
-    {\r
-      sequence.setName(s);\r
-      ap.repaint();\r
-    }*/\r
-\r
-  }\r
-\r
   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
   {\r
      SequenceGroup sg = ap.av.getSelectionGroup();\r
@@ -519,12 +427,4 @@ public class APopupMenu extends java.awt.PopupMenu
   }\r
 \r
 \r
-  protected void outline_actionPerformed(ActionEvent e)\r
-  {\r
-  /*  SequenceGroup sg = getGroup();\r
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
-    if(col!=null)\r
-      sg.setOutlineColour(col);*/\r
-  }\r
-\r
 }\r