JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1fcd875..4998bcc 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,18 +20,28 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
 import jalview.util.MessageManager;
 
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
 /**
  * DOCUMENT ME!
  * 
@@ -44,7 +54,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   AlignmentPanel ap;
 
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
+  Stack<CommandI> historyList = new Stack<CommandI>();
+
+  // simpler than synching with alignFrame.
 
   float[] redundancy;
 
@@ -95,7 +107,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       public void internalFrameClosing(InternalFrameEvent evt)
       {
-        ap.idPanel.idCanvas.setHighlighted(null);
+        ap.getIdPanel().getIdCanvas().setHighlighted(null);
       }
     });
 
@@ -159,7 +171,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_thereshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -185,7 +198,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         redundantSequences.add(originalSequences[i]);
       }
     }
-    ap.idPanel.idCanvas.setHighlighted(redundantSequences);
+    ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
   }
 
   /**
@@ -228,8 +241,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         }
       }
 
-      EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
-              EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+      EditCommand cut = new EditCommand(
+              MessageManager.getString("action.remove_redundancy"),
+              Action.CUT, deleted, 0, width, ap.av.getAlignment());
 
       for (int i = 0; i < del.size(); i++)
       {
@@ -245,8 +259,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-      // ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-      // .getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
@@ -259,12 +273,19 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI) historyList.pop();
-    command.undoCommand(af.getViewAlignments());
+    if (historyList == null || historyList.isEmpty())
+    {
+      undoButton.setEnabled(false);
+      return;
+    }
 
-    if (ap.av.historyList.contains(command))
+    CommandI command = historyList.pop();
+    if (ap.av.getHistoryList().contains(command))
     {
-      ap.av.historyList.remove(command);
+      command.undoCommand(af.getViewAlignments());
+      ap.av.getHistoryList().remove(command);
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
       af.updateEditMenuBar();
     }