Dynamically build tree sort menu when sort menu is selected

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3adc725..c1d1087 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,7 +64,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   String fileName = null;
 
-  private int treeCount = 0;
 
   /**
    * Creates a new AlignFrame object.
@@ -2636,9 +2635,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
-    addTreeMenuItem(tp, title);
+    title = title + " from " + this.title;
+    if(viewport.viewName!=null)
+      title+= " ("+viewport.viewName+")";
 
-    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
   /**
@@ -2676,51 +2677,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    * @param treePanel Displayed tree window.
    * @param title SortBy menu item title.
    */
-  void addTreeMenuItem(final TreePanel treePanel, String title)
+  public void buildTreeMenu()
   {
-    final JMenuItem item = new JMenuItem(title);
+    sortByTreeMenu.removeAll();
 
-    treeCount++;
-
-    if (treeCount == 1)
-    {
-      sort.add(sortByTreeMenu);
-    }
-
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector treePanels = new Vector();
+    int i, iSize = comps.size();
+    for(i=0; i<iSize; i++)
     {
-      public void actionPerformed(ActionEvent e)
+      if(comps.elementAt(i) instanceof TreePanel)
       {
-        SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByTree(viewport.getAlignment(),
-                                   treePanel.getTree());
+        treePanels.add(comps.elementAt(i));
+      }
+    }
 
-        addHistoryItem(new OrderCommand("Tree Sort",
-                                        oldOrder,
-                                        viewport.alignment));
+    iSize = treePanels.size();
 
+    if(iSize<1)
+    {
+      sortByTreeMenu.setVisible(false);
+      return;
+    }
 
-        alignPanel.repaint();
-      }
-    });
+    sortByTreeMenu.setVisible(true);
 
-    treePanel.addInternalFrameListener(new javax.swing.event.
-                                       InternalFrameAdapter()
+    for(i=0; i<treePanels.size(); i++)
     {
-      public void internalFrameClosed(
-          javax.swing.event.InternalFrameEvent evt)
+      TreePanel tp = (TreePanel)treePanels.elementAt(i);
+      final JMenuItem item = new JMenuItem(tp.getTitle());
+      final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+      item.addActionListener(new java.awt.event.ActionListener()
       {
-        treeCount--;
-        sortByTreeMenu.remove(item);
-
-        if (treeCount == 0)
+        public void actionPerformed(ActionEvent e)
         {
-          sort.remove(sortByTreeMenu);
+          SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+          AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+
+          addHistoryItem(new OrderCommand("Tree Sort",
+                                          oldOrder,
+                                          viewport.alignment));
+
+          alignPanel.repaint();
         }
-      }
-      ;
-    });
+      });
+
+      sortByTreeMenu.add(item);
+    }
   }
 
   /**
@@ -2876,7 +2879,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
         Desktop.addInternalFrame(tp, title, w, h);
-        addTreeMenuItem(tp, title);
       }
     }
     catch (Exception ex)