X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=0e55cf89f733d8dc081b57a6ad261a9a3e97208a;hb=f511799b8f00b4a224f0f902ad6f25df862c60ed;hp=46cf18fcfda15398690645e8ed0e9f1b1f8559bf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 46cf18f..0e55cf8 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.gui;
 
@@ -27,7 +30,7 @@ import jalview.analysis.AlignSeq;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
-import jalview.util.*;
+import jalview.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -74,7 +77,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       }
     });
 
-    applyButton.setText("Remove");
+    applyButton.setText(MessageManager.getString("action.remove"));
     allGroupsCheck.setVisible(false);
     slider.setMinimum(0);
     slider.setMaximum(100);
@@ -85,8 +88,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "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)
@@ -115,7 +119,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setIndeterminate(true);
     southPanel.add(progress, java.awt.BorderLayout.SOUTH);
 
-    label.setText("Calculating....");
+    label.setText(MessageManager.getString("label.calculating"));
 
     slider.setVisible(false);
     applyButton.setEnabled(false);
@@ -155,12 +159,13 @@ 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_thereshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
 
     validate();
+    sliderValueChanged();
     // System.out.println((System.currentTimeMillis()-start));
   }
 
@@ -172,21 +177,15 @@ 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.idPanel.idCanvas.setHighlighted(redundantSequences);
   }
 
   /**
@@ -229,7 +228,7 @@ public class RedundancyPanel extends GSliderPanel 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());
 
       for (int i = 0; i < del.size(); i++)
@@ -246,8 +245,7 @@ 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 +258,17 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
+    if(historyList == null || historyList.isEmpty()){
+        undoButton.setEnabled(false);
+    	return;
+    }
+    
     CommandI command = (CommandI) historyList.pop();
-    command.undoCommand(af.getViewAlignments());
-
     if (ap.av.historyList.contains(command))
     {
+      command.undoCommand(af.getViewAlignments());
       ap.av.historyList.remove(command);
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
       af.updateEditMenuBar();
     }