X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=daee8623f3469e5939ec69d276fa06433e9d7643;hb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;hp=5d266f87a06d7c7503d7a8bc5f3efc91268cd897;hpb=b6c0570ea7dc3c805ead26348f849fe69daaf917;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 5d266f8..daee862 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,11 +1,31 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.*;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
+
+import java.awt.event.*;
 import javax.swing.event.*;
 
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
 public class RedundancyPanel
     extends GSliderPanel
 {
@@ -30,7 +50,6 @@ public class RedundancyPanel
     slider.setMinimum(0);
     slider.setMaximum(100);
     slider.setValue(100);
-
   }
 
   public void applyButton_actionPerformed(ActionEvent e)
@@ -38,52 +57,61 @@ public class RedundancyPanel
     float threshold = slider.getValue();
     Vector del;
     HistoryItem it;
-    historyList.push(it=new HistoryItem("Remove redundancy",
-                                      ap.av.alignment, HistoryItem.HIDE));
-    if (historyList.size()==1
-        || !af.historyList.contains(historyList.firstElement())) {
-      af.addHistoryItem((HistoryItem) historyList.firstElement());
+    historyList.push(it = new HistoryItem("Remove redundancy",
+                                          ap.av.alignment, HistoryItem.HIDE));
+
+    if ( (historyList.size() == 1) ||
+        !af.historyList.contains(historyList.firstElement()))
+    {
+      af.addHistoryItem( (HistoryItem) historyList.firstElement());
       af.updateEditMenuBar();
     }
+
     undoButton.setEnabled(true);
+
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() >= 1)
-    {
 
+    if ( (sg != null) && (sg.getSize() >= 1))
+    {
       del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+
       for (int i = 0; i < del.size(); i++)
       {
         if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
         {
-          sg.deleteSequence( (SequenceI) del.elementAt(i));
+          sg.deleteSequence( (SequenceI) del.elementAt(i), true);
         }
       }
-
     }
     else
     {
       Vector s = new Vector();
       int i = 0;
+
       while (i < ap.av.alignment.getHeight())
       {
         s.addElement(ap.av.alignment.getSequenceAt(i));
         i++;
       }
+
       del = ap.av.alignment.removeRedundancy(threshold, s);
     }
 
     // This has to be done before the restoreHistoryItem method of alignFrame will
     // actually restore these sequences.
-
-    if (del.size()>0)
-      for (int i=0,j=del.size(); i<j; i++) {
+    if (del.size() > 0)
+    {
+      for (int i = 0, j = del.size(); i < j; i++)
+      {
         SequenceI sq = (SequenceI) del.elementAt(i);
-        sq.deleteChars(0,sq.getLength());
+        sq.deleteChars(0, sq.getLength());
       }
+    }
 
     ap.av.firePropertyChange("alignment", null,
                              ap.av.getAlignment().getSequences());
     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
+
     if (ap.av.getAlignment().getHeight() < 1)
     {
       try
@@ -91,22 +119,25 @@ public class RedundancyPanel
         af.setClosed(true);
       }
       catch (Exception ex)
-      {}
+      {
+      }
     }
+
     ap.av.updateConservation();
     ap.av.updateConsensus();
     af.updateEditMenuBar();
     ap.repaint();
-
   }
 
   public void undoButton_actionPerformed(ActionEvent e)
   {
     HistoryItem hi = (HistoryItem) historyList.pop();
     af.restoreHistoryItem(hi);
+
     if (historyList.size() == 0)
     {
       undoButton.setEnabled(false);
+
       if (af.historyList.contains(hi))
       {
         af.historyList.remove(hi);
@@ -114,6 +145,7 @@ public class RedundancyPanel
       }
     }
   }
+
   public void valueField_actionPerformed(ActionEvent e)
   {
     try