X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=bd36b0d4b6dfb5b76c107ad228f8fa6cdfa20354;hb=483ecb5e4541537778844529cc93204f9124b68d;hp=d6882616e706b10a64050f18e31341a1eedeed8c;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index d688261..bd36b0d 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,18 +20,28 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
-public class RedundancyPanel extends SliderPanel implements Runnable,
-        WindowListener
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+public class RedundancyPanel extends SliderPanel
+        implements Runnable, WindowListener
 {
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
@@ -53,7 +63,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     applyButton.setVisible(true);
     allGroupsCheck.setVisible(false);
 
-    label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
@@ -63,17 +74,18 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     slider.addAdjustmentListener(new AdjustmentListener()
     {
+      @Override
       public void adjustmentValueChanged(AdjustmentEvent evt)
       {
-        valueField.setText(slider.getValue() + "");
+        valueField.setText(String.valueOf(slider.getValue()));
         sliderValueChanged();
       }
     });
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
-            MessageManager.getString("label.redundancy_threshold_selection"), 400, 100);
+    jalview.bin.JalviewLite.addFrame(frame, MessageManager
+            .getString("label.redundancy_threshold_selection"), 400, 100);
 
     frame.addWindowListener(this);
 
@@ -93,6 +105,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     label.setText(MessageManager.getString("label.calculating"));
@@ -127,7 +140,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
             omitHidden, start, end, false);
-    label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -146,7 +160,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     float value = slider.getValue();
 
-    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
+    List<SequenceI> redundantSequences = new ArrayList<>();
     for (int i = 0; i < redundancy.length; i++)
     {
       if (value <= redundancy[i])
@@ -160,6 +174,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
   }
 
+  @Override
   public void applyButton_actionPerformed()
   {
     Vector del = new Vector();
@@ -194,8 +209,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
         }
       }
 
-      EditCommand cut = new EditCommand("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());
       AlignmentI alignment = ap.av.getAlignment();
       for (int i = 0; i < del.size(); i++)
       {
@@ -211,24 +227,27 @@ public class RedundancyPanel extends SliderPanel 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());
     }
 
   }
 
+  @Override
   public void undoButton_actionPerformed()
   {
     CommandI command = (CommandI) historyList.pop();
     command.undoCommand(null);
 
-    if (ap.av.historyList.contains(command))
+    if (ap.av.getHistoryList().contains(command))
     {
-      ap.av.historyList.removeElement(command);
+      ap.av.getHistoryList().remove(command);
       ap.alignFrame.updateEditMenuBar();
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {
@@ -248,31 +267,38 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     }
   }
 
+  @Override
   public void windowOpened(WindowEvent evt)
   {
   }
 
+  @Override
   public void windowClosing(WindowEvent evt)
   {
     ap.idPanel.idCanvas.setHighlighted(null);
   }
 
+  @Override
   public void windowClosed(WindowEvent evt)
   {
   }
 
+  @Override
   public void windowActivated(WindowEvent evt)
   {
   }
 
+  @Override
   public void windowDeactivated(WindowEvent evt)
   {
   }
 
+  @Override
   public void windowIconified(WindowEvent evt)
   {
   }
 
+  @Override
   public void windowDeiconified(WindowEvent evt)
   {
   }