From b21920d2355ae42bdada6dfc0c42614aa0539137 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 23 Nov 2006 15:18:17 +0000
Subject: [PATCH] If alignment is closed, then undo performed in visible
 window

---
 src/jalview/appletgui/AlignFrame.java |   11 ++++++++++-
 src/jalview/gui/AlignFrame.java       |   30 +++++++++++++++++++++++-------
 2 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index afc103e..3a1ab05 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -821,7 +821,7 @@ public void itemStateChanged(ItemEvent evt)
 
   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
@@ -842,7 +842,16 @@ public void itemStateChanged(ItemEvent evt)
           }
         }
       }
+      if (originalSource == null)
+      {
+        //The original view is closed, we must validate
+        //the current view against the closed view first
+        PaintRefresher.validateSequences(al, viewport.alignment);
+        originalSource = viewport;
+      }
+
     }
+
     return originalSource;
   }
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3291dca..4afaf92 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -974,10 +974,13 @@ 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);
+    }
   }
 
   /**
@@ -992,15 +995,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     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
@@ -1021,7 +1027,17 @@ 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
+        PaintRefresher.validateSequences(al, viewport.alignment);
+        originalSource = viewport;
+      }
+
     }
+
+
     return originalSource;
   }
 
-- 
1.7.10.2