X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=8e014fae065b592e548efc727d0e0bd1eb766257;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=345c906b8c71344aa4e968264f39db971274afb3;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 345c906..8e014fa 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,33 +1,45 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.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;
 
+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
 {
@@ -51,7 +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);
@@ -70,8 +83,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     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);
 
@@ -125,12 +138,14 @@ 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);
 
     validate();
+    sliderValueChanged();
     // System.out.println("blob done "+ (System.currentTimeMillis()-start));
   }
 
@@ -143,19 +158,16 @@ 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);
 
   }
@@ -194,8 +206,9 @@ 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++)
       {
@@ -211,8 +224,8 @@ 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());
     }
 
   }
@@ -222,10 +235,12 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     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);