X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=e574450b23297e947ebe9ee016b3ced2b20651f8;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=3adc7259afa11e219bd2fca04cd48281ca9bacbd;hpb=ecf2b981352e4d5d798e39e8c4597757cd629514;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3adc725..e574450 100755
--- 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.
@@ -619,7 +618,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null || currentFileFormat==null)
+    if(fileName==null
+       || currentFileFormat==null
+       || fileName.startsWith("http")
+        )
       saveAs_actionPerformed(null);
     else
       saveAlignment(fileName, currentFileFormat);
@@ -975,10 +977,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     command.undoCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
-
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,viewport.getAlignment().getSequences());
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment", null,null);
+    }
   }
 
   /**
@@ -988,29 +993,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.redoList.size()<1)
+      return;
+
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
 
     AlignViewport originalSource = getOriginatingSource(command);
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
-
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+    if(originalSource!=null)
+    {
+      originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      originalSource.firePropertyChange("alignment", null,null);
+    }
   }
 
   AlignViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = viewport;
+    AlignViewport originalSource = null;
     //For sequence removal and addition, we need to fire
    //the property change event FROM the viewport where the
    //original alignment was altered
+    AlignmentI al=null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
-      AlignmentI al = editCommand.getAlignment();
+      al = editCommand.getAlignment();
       Vector comps = (Vector) PaintRefresher.components
           .get(viewport.getSequenceSetId());
+
       for (int i = 0; i < comps.size(); i++)
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
@@ -1023,6 +1036,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       }
     }
+
+    if (originalSource == null)
+    {
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+        PaintRefresher.validateSequences(al, viewport.alignment);
+
+      originalSource = viewport;
+    }
+
     return originalSource;
   }
 
@@ -1456,7 +1480,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.sequenceColours.clear();
+    viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
     alignPanel.repaint();
@@ -2516,7 +2540,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       return;
     }
 
-     new PCAPanel(viewport);
+     new PCAPanel(alignPanel);
   }
 
 
@@ -2636,9 +2660,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
-    addTreeMenuItem(tp, title);
+    title += " from ";
+
+    if(viewport.viewName!=null)
+      title+= viewport.viewName+" of ";
 
-    Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+    title += this.title;
+
+    Desktop.addInternalFrame(tp, title, 600, 500);
   }
 
   /**
@@ -2676,51 +2705,53 @@ 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);
-
-    treeCount++;
-
-    if (treeCount == 1)
-    {
-      sort.add(sortByTreeMenu);
-    }
+    sortByTreeMenu.removeAll();
 
-    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 +2907,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
         Desktop.addInternalFrame(tp, title, w, h);
-        addTreeMenuItem(tp, title);
       }
     }
     catch (Exception ex)