X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=8aed73065ab8370e97ecf8b7090a17306c2282f4;hb=ef23c17739a6fba3a8d455b725782bce4607ac9f;hp=735a5790459e23fe66ca837be501531211ec7378;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 735a579..8aed730 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,36 +1,38 @@
 /*
-* 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
-*/
+ * 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.appletgui;
 
-import jalview.jbappletgui.*;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
 
-public class RedundancyPanel extends GSliderPanel
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
+
+public class RedundancyPanel
+    extends GSliderPanel
 {
   AlignmentPanel ap;
 
   SequenceI[] oldAlignment;
 
-
   public RedundancyPanel(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -41,81 +43,87 @@ public class RedundancyPanel extends GSliderPanel
     {
       public void adjustmentValueChanged(AdjustmentEvent 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;
+
+    oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
+    for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+    {
+      oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
+                                     ap.av.alignment.getSequenceAt(i).
+                                     getSequence());
+    }
+
+    undoButton.setEnabled(true);
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg != null && sg.getSize() > 1)
+    {
 
-       oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+      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);
         }
+      }
 
-        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();
+    }
+    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), true);
+        }
+
+      }
+    }
+
+    ap.repaint();
 
   }
 
   public void undoButton_actionPerformed(ActionEvent e)
   {
-      undoButton.setEnabled(false);
-      ap.av.setAlignment( new Alignment(oldAlignment) );
-      oldAlignment = null;
-      ap.repaint();
+    undoButton.setEnabled(false);
+    ap.av.setAlignment(new Alignment(oldAlignment));
+    oldAlignment = null;
+    ap.repaint();
   }
 
-
   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() + "");
     }
   }
 }