X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=daee8623f3469e5939ec69d276fa06433e9d7643;hb=2fa86d263d7bd66fb270a5d26878df37b96a61f4;hp=93ffd9cad1df038c975ba53c65e62a71a75773f9;hpb=79f4b175e12f4c16d598b4cb56ffe62532b592a1;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 93ffd9c..daee862 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,103 +1,161 @@
+/*
+ * 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.*;
 
-public class RedundancyPanel extends GSliderPanel
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+public class RedundancyPanel
+    extends GSliderPanel
 {
+  AlignFrame af;
   AlignmentPanel ap;
+  Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
-  SequenceI[] oldAlignment;
-
-
-  public RedundancyPanel(AlignmentPanel ap)
+  public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
   {
     this.ap = ap;
-
+    this.af = af;
     label.setText("Enter the redundancy threshold");
 
     slider.addChangeListener(new ChangeListener()
     {
       public void stateChanged(ChangeEvent evt)
       {
-        valueField.setText( slider.getValue()+"" );
+        valueField.setText(slider.getValue() + "");
       }
     });
 
     slider.setMinimum(0);
     slider.setMaximum(100);
-    slider.setValue(100 );
-
+    slider.setValue(100);
   }
 
   public void applyButton_actionPerformed(ActionEvent e)
   {
-       float threshold = slider.getValue();
-       Vector del;
+    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());
+      af.updateEditMenuBar();
+    }
+
+    undoButton.setEnabled(true);
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    if ( (sg != null) && (sg.getSize() >= 1))
+    {
+      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
 
-       oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+      for (int i = 0; i < del.size(); i++)
+      {
+        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
         {
-           oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
-                                ap.av.alignment.getSequenceAt(i).
-                                getSequence());
+          sg.deleteSequence( (SequenceI) del.elementAt(i), true);
         }
+      }
+    }
+    else
+    {
+      Vector s = new Vector();
+      int i = 0;
 
-        undoButton.setEnabled(true);
-
-        SequenceGroup sg = ap.av.getSelectionGroup();
-       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));
-
-         }
-         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);
-           for (int j=0; j < del.size(); j++)
-           {
-               if (sg.sequences.contains((SequenceI)del.elementAt(j)))
-               sg.deleteSequence((SequenceI)del.elementAt(j));
-
-           }
-         }
-
-         ap.repaint();
+      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++)
+      {
+        SequenceI sq = (SequenceI) del.elementAt(i);
+        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
+      {
+        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);
-      ap.av.setAlignment( new Alignment(oldAlignment) );
-      oldAlignment = null;
-      ap.repaint();
-  }
 
+      if (af.historyList.contains(hi))
+      {
+        af.historyList.remove(hi);
+        af.updateEditMenuBar();
+      }
+    }
+  }
 
   public void valueField_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
-      valueField.setText( slider.getValue()+"" );
+      valueField.setText(slider.getValue() + "");
     }
   }
 }