X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=3901b1f23803004291025e46cf7ebf4a35be08aa;hb=b2319fcc38be5c500ed7cafc014cf9da96a4ce98;hp=44aa4477b4382fbe738bb0453c209051fc75c704;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 44aa447..3901b1f 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -18,144 +18,167 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
 
 import java.awt.event.*;
-import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import java.util.*;
 
-public class RedundancyPanel
-    extends GSliderPanel
-{
-  AlignFrame af;
-  AlignmentPanel ap;
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
+import javax.swing.event.*;
 
-  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() + "");
-      }
-    });
-
-    slider.setMinimum(0);
-    slider.setMaximum(100);
-    slider.setValue(100);
-  }
-
-  public void applyButton_actionPerformed(ActionEvent e)
-  {
-    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()))
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel
+{
+    AlignFrame af;
+    AlignmentPanel ap;
+    Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
+    /**
+     * Creates a new RedundancyPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param af DOCUMENT ME!
+     */
+    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
     {
-      af.addHistoryItem( (HistoryItem) historyList.firstElement());
-      af.updateEditMenuBar();
+        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() + "");
+                }
+            });
+
+        slider.setMinimum(0);
+        slider.setMaximum(100);
+        slider.setValue(100);
     }
 
-    undoButton.setEnabled(true);
-
-    SequenceGroup sg = ap.av.getSelectionGroup();
-
-    if ( (sg != null) && (sg.getSize() >= 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void applyButton_actionPerformed(ActionEvent e)
     {
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+        float threshold = slider.getValue();
+        Vector del;
+        historyList.push(new HistoryItem("Remove redundancy",
+                    ap.av.alignment, HistoryItem.HIDE));
 
-      for (int i = 0; i < del.size(); i++)
-      {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
+        if ((historyList.size() == 1) ||
+                !af.historyList.contains(historyList.firstElement()))
         {
-          sg.deleteSequence( (SequenceI) del.elementAt(i));
+            af.addHistoryItem((HistoryItem) historyList.firstElement());
+            af.updateEditMenuBar();
         }
-      }
-    }
-    else
-    {
-      Vector s = new Vector();
-      int i = 0;
 
-      while (i < ap.av.alignment.getHeight())
-      {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
-      }
+        undoButton.setEnabled(true);
 
-      del = ap.av.alignment.removeRedundancy(threshold, s);
-    }
+        SequenceGroup sg = ap.av.getSelectionGroup();
 
-    // 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());
-      }
-    }
+        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), true);
+                }
+            }
+        }
+        else
+        {
+            Vector s = new Vector();
+            int i = 0;
 
-    ap.av.firePropertyChange("alignment", null,
-                             ap.av.getAlignment().getSequences());
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
+            while (i < ap.av.alignment.getHeight())
+            {
+                s.addElement(ap.av.alignment.getSequenceAt(i));
+                i++;
+            }
 
-    if (ap.av.getAlignment().getHeight() < 1)
-    {
-      try
-      {
-        af.setClosed(true);
-      }
-      catch (Exception ex)
-      {
-      }
-    }
+            del = ap.av.alignment.removeRedundancy(threshold, s);
+        }
 
-    ap.av.updateConservation();
-    ap.av.updateConsensus();
-    af.updateEditMenuBar();
-    ap.repaint();
-  }
+        // 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());
+            }
+        }
 
-  public void undoButton_actionPerformed(ActionEvent e)
-  {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    af.restoreHistoryItem(hi);
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+        af.updateEditMenuBar();
 
-    if (historyList.size() == 0)
-    {
-      undoButton.setEnabled(false);
 
-      if (af.historyList.contains(hi))
-      {
-        af.historyList.remove(hi);
-        af.updateEditMenuBar();
-      }
+        if (ap.av.getAlignment().getHeight() < 1)
+        {
+            try
+            {
+                af.setClosed(true);
+            }
+            catch (Exception ex)
+            {
+            }
+        }
     }
-  }
 
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void undoButton_actionPerformed(ActionEvent e)
     {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
+        HistoryItem hi = (HistoryItem) historyList.pop();
+        af.restoreHistoryItem(hi);
+
+        if (historyList.size() == 0)
+        {
+            undoButton.setEnabled(false);
+
+            if (af.historyList.contains(hi))
+            {
+                af.historyList.remove(hi);
+                af.updateEditMenuBar();
+            }
+        }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void valueField_actionPerformed(ActionEvent e)
     {
-      valueField.setText(slider.getValue() + "");
+        try
+        {
+            int i = Integer.parseInt(valueField.getText());
+            slider.setValue(i);
+        }
+        catch (Exception ex)
+        {
+            valueField.setText(slider.getValue() + "");
+        }
     }
-  }
 }