JAL-1250 Redundancy removal bug fix for Applet version

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index ef00017..1547862
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,30 +1,34 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 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.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.util.MessageManager;
 
 public class RedundancyPanel extends SliderPanel implements Runnable,
         WindowListener
@@ -49,7 +53,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     applyButton.setVisible(true);
     allGroupsCheck.setVisible(false);
 
-    label.setText("Enter the redundancy threshold");
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_threshold"));
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
@@ -68,8 +73,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
-            "Redundancy threshold selection", 400, 100);
+    jalview.bin.JalviewLite.addFrame(frame, MessageManager
+            .getString("label.redundancy_threshold_selection"), 400, 100);
 
     frame.addWindowListener(this);
 
@@ -91,7 +96,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
    */
   public void run()
   {
-    label.setText("Calculating....");
+    label.setText(MessageManager.getString("label.calculating"));
 
     slider.setVisible(false);
     applyButton.setEnabled(false);
@@ -123,12 +128,14 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
             omitHidden, start, end, false);
-    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("blob done "+ (System.currentTimeMillis()-start));
   }
 
@@ -141,19 +148,16 @@ public class RedundancyPanel extends SliderPanel 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.removeElement(originalSequences[i]);
-      }
-      else if (!redundantSeqs.contains(originalSequences[i]))
+      if (value <= redundancy[i])
       {
-        redundantSeqs.addElement(originalSequences[i]);
+        redundantSequences.add(originalSequences[i]);
       }
     }
 
-    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+    ap.idPanel.idCanvas.setHighlighted(redundantSequences);
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
 
   }
@@ -192,7 +196,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
         }
       }
 
-      EditCommand cut = new EditCommand("Remove Redundancy",
+      EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
               EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
       AlignmentI alignment = ap.av.getAlignment();
       for (int i = 0; i < del.size(); i++)
@@ -209,8 +213,7 @@ 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());
     }
 
   }
@@ -224,6 +227,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     {
       ap.av.historyList.removeElement(command);
       ap.alignFrame.updateEditMenuBar();
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
     }
 
     ap.paintAlignment(true);