Dynamically build tree sort menu when sort menu is selected

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6b8eb09..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.
@@ -381,7 +380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       expandViews.setEnabled(true);
       gatherViews.setEnabled(true);
-      tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+      tabbedPane.addTab(ap.av.viewName, ap);
 
       ap.setVisible(false);
     }
@@ -401,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
-    tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
+    tabbedPane.addTab(first.av.viewName,first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
@@ -890,13 +889,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           int index = tabbedPane.getSelectedIndex();
 
-          tabbedPane.removeTabAt(index);
           alignPanels.removeElement(alignPanel);
           PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
           PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
           PaintRefresher.RemoveComponent(alignPanel);
           alignPanel = null;
           viewport = null;
+
+          tabbedPane.removeTabAt(index);
           tabbedPane.validate();
 
           if(index==tabbedPane.getTabCount())
@@ -977,7 +977,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,null);
+    originalSource.firePropertyChange("alignment", null,viewport.getAlignment().getSequences());
   }
 
   /**
@@ -995,7 +995,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null, null);
+    originalSource.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   AlignViewport getOriginatingSource(CommandI command)
@@ -1729,12 +1729,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new Jalview2XML().copyAlignPanel(alignPanel, true);
 
     if (viewport.viewName == null)
-      viewport.viewName = "View 1";
+      viewport.viewName = "Original";
 
     newap.av.historyList = viewport.historyList;
     newap.av.redoList = viewport.redoList;
-    newap.av.viewName = "View " +
-        (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
+
+    int index = Desktop.getViewCount(viewport.getSequenceSetId());
+    String newViewName = "View " +index;
+
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector existingNames = new Vector();
+    for(int i=0; i<comps.size(); i++)
+    {
+      if(comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+        if(!existingNames.contains(ap.av.viewName))
+          existingNames.addElement(ap.av.viewName);
+      }
+    }
+
+    while(existingNames.contains(newViewName))
+    {
+      newViewName = "View "+ (++index);
+    }
+
+    newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, false);
 
@@ -2615,9 +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);
   }
 
   /**
@@ -2655,51 +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)
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector treePanels = new Vector();
+    int i, iSize = comps.size();
+    for(i=0; i<iSize; i++)
     {
-      sort.add(sortByTreeMenu);
-    }
-
-    sortByTreeMenu.add(item);
-    item.addActionListener(new java.awt.event.ActionListener()
-    {
-      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);
+    }
   }
 
   /**
@@ -2855,7 +2879,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
         Desktop.addInternalFrame(tp, title, w, h);
-        addTreeMenuItem(tp, title);
       }
     }
     catch (Exception ex)