void changeCase(ActionEvent e

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4687b3c..db9e75e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -106,6 +106,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     viewport = ap.av;
     alignPanel = ap;
+    alignPanel.alignFrame = this;
     addAlignmentPanel(ap);
     init();
   }
@@ -824,10 +825,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   void updateEditMenuBar()
   {
+
     if (historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-
       CommandI command = (CommandI) historyList.peek();
       undoMenuItem.setText("Undo " + command.getDescription());
     }
@@ -874,12 +875,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     redoList.push(command);
     command.undoCommand();
 
-   // HistoryItem nh,hi = (HistoryItem) historyList.pop();
-   // redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
-   //                               HistoryItem.HIDE));
-   // if (hi.alColumnChanges!=null)
-   //   nh.alColumnChanges = hi.alColumnChanges.getInverse();
-   // restoreHistoryItem(hi);
+
    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
    updateEditMenuBar();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -894,15 +890,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     CommandI command = (CommandI) redoList.pop();
     historyList.push(command);
+    historyList.push(command);
     command.doCommand();
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
-   // HistoryItem nh,hi = (HistoryItem) redoList.pop();
-  //  historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
-  //      HistoryItem.HIDE));
-  //  if (hi.alColumnChanges!=null)
-  //    nh.alColumnChanges=hi.alColumnChanges.getInverse();
-  //  restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
@@ -1512,7 +1503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth();
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -1551,7 +1542,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth();
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)