Reorder popupmenu

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 018c1c2..5a98d55 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -77,11 +77,11 @@ public class PopupMenu extends JPopupMenu
   JMenuItem upperCase = new JMenuItem();\r
   JMenuItem lowerCase = new JMenuItem();\r
   JMenuItem toggle = new JMenuItem();\r
-  JMenu outputMenu = new JMenu();\r
   JMenu pdbMenu = new JMenu();\r
   JMenuItem pdbFromFile = new JMenuItem();\r
   JMenuItem enterPDB = new JMenuItem();\r
   JMenuItem discoverPDB = new JMenuItem();\r
+  JMenuItem jMenuItem1 = new JMenuItem();\r
 \r
   /**\r
      * Creates a new PopupMenu object.\r
@@ -128,8 +128,7 @@ public class PopupMenu extends JPopupMenu
             }\r
           });\r
 \r
-          outputMenu.add(item);\r
-        }\r
+    }\r
 \r
 \r
         try\r
@@ -144,6 +143,9 @@ public class PopupMenu extends JPopupMenu
 \r
         if (seq != null)\r
         {\r
+          int start = Math.max(sequence.getName().length()-15, 0);\r
+          sequenceMenu.setText(sequence.getName().substring(start));\r
+\r
           JMenuItem menuItem;\r
           if( seq.getDatasetSequence().getPDBId() != null)\r
           {\r
@@ -175,7 +177,7 @@ public class PopupMenu extends JPopupMenu
                   hideSequences(false);\r
                 }\r
               });\r
-          sequenceMenu.add(menuItem);\r
+          add(menuItem);\r
 \r
           if(ap.av.getSelectionGroup() !=null\r
              && ap.av.getSelectionGroup().getSize(false)>1)\r
@@ -198,7 +200,7 @@ public class PopupMenu extends JPopupMenu
             if (ap.av.adjustForHiddenSeqs(index) -\r
                 ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
             {\r
-              menuItem = new JMenuItem("Reveal");\r
+              menuItem = new JMenuItem("Reveal Sequences");\r
               menuItem.addActionListener(new ActionListener()\r
               {\r
                 public void actionPerformed(ActionEvent e)\r
@@ -209,7 +211,7 @@ public class PopupMenu extends JPopupMenu
                     ap.overviewPanel.updateOverviewImage();\r
                 }\r
               });\r
-              sequenceMenu.add(menuItem);\r
+              add(menuItem);\r
             }\r
 \r
             menuItem = new JMenuItem("Reveal All");\r
@@ -224,10 +226,7 @@ public class PopupMenu extends JPopupMenu
                       }\r
                 });\r
 \r
-            sequenceMenu.add(menuItem);\r
-\r
-\r
-\r
+            add(menuItem);\r
           }\r
 \r
 \r
@@ -309,10 +308,7 @@ public class PopupMenu extends JPopupMenu
         {\r
             unGroupMenuItem.setVisible(false);\r
         }\r
-        else\r
-        {\r
-            groupMenu.insertSeparator(3);\r
-        }\r
+\r
 \r
         if (seq == null)\r
         {\r
@@ -356,7 +352,7 @@ public class PopupMenu extends JPopupMenu
 \r
             linkMenu.add(item);\r
           }\r
-          add(linkMenu);\r
+          sequenceMenu.add(linkMenu);\r
         }\r
     }\r
 \r
@@ -369,7 +365,7 @@ public class PopupMenu extends JPopupMenu
     private void jbInit() throws Exception\r
     {\r
         groupMenu.setText("Group");\r
-        groupMenu.setText("Group");\r
+        groupMenu.setText("Selection");\r
         groupName.setText("Name");\r
         groupName.addActionListener(new java.awt.event.ActionListener()\r
             {\r
@@ -481,7 +477,6 @@ public class PopupMenu extends JPopupMenu
         toggle_actionPerformed(e);\r
       }\r
     });\r
-    outputMenu.setText("Output to Textbox...");\r
     pdbMenu.setText("Associate Structure with Sequence");\r
     pdbFromFile.setText("From File");\r
     pdbFromFile.addActionListener(new ActionListener()\r
@@ -507,24 +502,23 @@ public class PopupMenu extends JPopupMenu
         discoverPDB_actionPerformed(e);\r
       }\r
     });\r
+    jMenuItem1.setText("Output to Textbox...");\r
     add(groupMenu);\r
 \r
-    this.add(editMenu);\r
-    this.add(outputMenu);\r
     add(sequenceMenu);\r
-    this.add(pdbMenu);\r
+    groupMenu.add(editMenu);\r
+    groupMenu.add(jMenuItem1);\r
+    groupMenu.addSeparator();\r
     groupMenu.add(groupName);\r
-        groupMenu.addSeparator();\r
-        groupMenu.add(unGroupMenuItem);\r
+    groupMenu.add(unGroupMenuItem);\r
         groupMenu.add(colourMenu);\r
-        groupMenu.addSeparator();\r
-        groupMenu.add(showBoxes);\r
+    groupMenu.add(showBoxes);\r
         groupMenu.add(showText);\r
         groupMenu.add(showColourText);\r
-        groupMenu.addSeparator();\r
-        groupMenu.add(outline);\r
+    groupMenu.add(outline);\r
         sequenceMenu.add(sequenceName);\r
-        colourMenu.add(noColourmenuItem);\r
+    sequenceMenu.add(pdbMenu);\r
+    colourMenu.add(noColourmenuItem);\r
         colourMenu.add(clustalColour);\r
         colourMenu.add(BLOSUM62Colour);\r
         colourMenu.add(PIDColour);\r
@@ -1151,6 +1145,7 @@ public class PopupMenu extends JPopupMenu
         }\r
 \r
         ap.av.setSelectionGroup(null);\r
+        ap.repaint();\r
         refresh();\r
     }\r
 \r