JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 0038939..a9d2690 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,34 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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!
  * 
@@ -41,7 +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;
 
@@ -85,13 +100,14 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400,
-            100, false);
+    Desktop.addInternalFrame(frame, MessageManager
+            .getString("label.redundancy_threshold_selection"), 400, 100,
+            false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent evt)
       {
-        ap.idPanel.idCanvas.setHighlighted(null);
+        ap.getIdPanel().getIdCanvas().setHighlighted(null);
       }
     });
 
@@ -155,12 +171,14 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText("Enter the redundancy threshold");
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
 
     validate();
+    sliderValueChanged();
     // System.out.println((System.currentTimeMillis()-start));
   }
 
@@ -172,21 +190,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     }
 
     float value = slider.getValue();
-
+    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
     for (int i = 0; i < redundancy.length; i++)
     {
-      if (value > redundancy[i])
-      {
-        redundantSeqs.remove(originalSequences[i]);
-      }
-      else if (!redundantSeqs.contains(originalSequences[i]))
+      if (value <= redundancy[i])
       {
-        redundantSeqs.add(originalSequences[i]);
+        redundantSequences.add(originalSequences[i]);
       }
-
     }
-
-    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+    ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
   }
 
   /**
@@ -229,8 +241,9 @@ public class RedundancyPanel extends GSliderPanel 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());
 
       for (int i = 0; i < del.size(); i++)
       {
@@ -246,8 +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());
     }
 
   }
@@ -260,12 +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();
     }