From: jprocter <Jim Procter>
Date: Thu, 26 May 2005 17:19:40 +0000 (+0000)
Subject: fixed redundancy Undo and allowed it to work on UNALIGNED SEQUENCES
X-Git-Tag: Release_2_0~171
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d9e49c675fff2fabba281a6bfecaa0d65ce23c35;p=jalview.git

fixed redundancy Undo and allowed it to work on UNALIGNED SEQUENCES
(ho ho)
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1183cd8..6447005 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -419,11 +419,12 @@ public class AlignFrame extends GAlignFrame
   protected void delete_actionPerformed(ActionEvent e)
   {
     boolean seqsdeleted=false;
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
 
     if (viewport.getSelectionGroup() == null)
       return;
 
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
      SequenceGroup sg = viewport.getSelectionGroup();
      for (int i=0;i < sg.sequences.size(); i++)
      {
@@ -996,7 +997,7 @@ public class AlignFrame extends GAlignFrame
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 93ffd9c..f91f75d 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -6,98 +6,113 @@ import java.awt.event.*;
 import java.util.*;
 import javax.swing.event.*;
 
-public class RedundancyPanel extends GSliderPanel
+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;
+    historyList.push(new HistoryItem("Remove redundancy (" + threshold + "%)",
+                                      ap.av.alignment, HistoryItem.HIDE));
+
+    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));
         }
+      }
 
-        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);
+    }
+
+    // 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();
   }
 
-
   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() + "");
     }
   }
 }