X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=efabb9b0b7bd2e972363f12ecf4ae0bc2d19d2b6;hb=559b96a91b710f3f2e116790c9cf7e3aa6c76766;hp=3e3691b47b6112dabaccb9c2f26384e3987f6f68;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 3e3691b..efabb9b 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -23,95 +23,234 @@ import java.util.*;
 
 import java.awt.event.*;
 
+import java.awt.*;
+
 import jalview.datamodel.*;
+import jalview.appletgui.PaintRefresher;
 
-public class RedundancyPanel extends SliderPanel
+public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener
 {
   AlignmentPanel ap;
 
-  SequenceI[] oldAlignment;
+  Stack historyList = new Stack(); // simpler than synching with alignFrame.
+  float [] redundancy;
+  SequenceI [] originalSequences;
+  Frame frame;
+  Vector redundantSeqs;
 
   public RedundancyPanel(AlignmentPanel ap)
   {
     super(ap, 0, false, null);
 
+    redundantSeqs = new Vector();
     this.ap = ap;
+    undoButton.setVisible(true);
+    applyButton.setVisible(true);
+    allGroupsCheck.setVisible(false);
 
     label.setText("Enter the redundancy threshold");
+    valueField.setText("100");
+
+    slider.setVisibleAmount(1);
+    slider.setMinimum(0);
+    slider.setMaximum(100+slider.getVisibleAmount());
+    slider.setValue(100);
 
     slider.addAdjustmentListener(new AdjustmentListener()
     {
       public void adjustmentValueChanged(AdjustmentEvent evt)
       {
         valueField.setText(slider.getValue() + "");
+        sliderValueChanged();
       }
     });
 
-    slider.setMinimum(0);
-    slider.setMaximum(100);
-    slider.setValue(100);
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
+                                     400, 100);
 
-  }
+    frame.addWindowListener(this);
 
-  public void applyButton_actionPerformed(ActionEvent e)
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+  /**
+   * This is a copy of remove redundancy in jalivew.datamodel.Alignment
+   * except we dont want to remove redundancy, just calculate once
+   * so we can use the slider to dynamically hide redundant sequences
+   *
+   * @param threshold DOCUMENT ME!
+   * @param sel DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public void run()
   {
-    float threshold = slider.getValue();
-    Vector del;
+      label.setText("Calculating....");
 
-    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());
-    }
+      slider.setVisible(false);
+      applyButton.setEnabled(false);
+      valueField.setVisible(false);
 
-    undoButton.setEnabled(true);
+      validate();
 
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() > 1)
-    {
+      String[] omitHidden = null;
+
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      int height;
 
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-      for (int i = 0; i < del.size(); i++)
+      int start, end;
+
+      if ( (sg != null) && (sg.getSize(false) >= 1))
+      {
+         originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+         start = sg.getStartRes();
+         end = sg.getEndRes();
+      }
+      else
       {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
-        {
-          sg.deleteSequence( (SequenceI) del.elementAt(i), true);
-        }
+        originalSequences = ap.av.alignment.getSequencesArray();
+        start = 0;
+        end = ap.av.alignment.getWidth();
       }
 
-    }
-    else
-    {
-      Vector s = new Vector();
-      int i = 0;
-      while (i < ap.av.alignment.getHeight())
+      height = originalSequences.length;
+
+      redundancy = new float[height];
+      for (int i = 0; i < height; i++)
       {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
+        redundancy[i] = 0f;
       }
-      del = ap.av.alignment.removeRedundancy(threshold, s);
-      for (int j = 0; j < del.size(); j++)
+
+    //  if (ap.av.hasHiddenColumns)
+      {
+     //   omitHidden = ap.av.getSelectionAsString();
+      }
+
+
+     // long start = System.currentTimeMillis();
+
+      float pid;
+      String seqi, seqj;
+      for (int i = 0; i < height; i++)
       {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
-        {
-          sg.deleteSequence( (SequenceI) del.elementAt(j), true);
-        }
+          for (int j = 0; j < i; j++)
+          {
+            if(i==j)
+              continue;
+
+            if(omitHidden==null)
+            {
+              seqi = originalSequences[i].getSequence(start, end);
+              seqj = originalSequences[j].getSequence(start, end);
+            }
+            else
+            {
+              seqi = omitHidden[i];
+              seqj = omitHidden[j];
+            }
+
+            pid = jalview.util.Comparison.PID( seqi,  seqj );
 
+            if(seqj.length() < seqi.length())
+              redundancy[j] = Math.max(pid, redundancy[j]);
+            else
+              redundancy[i] = Math.max(pid, redundancy[i]);
+
+          }
       }
+
+
+      label.setText("Enter the redundancy threshold");
+      slider.setVisible(true);
+      applyButton.setEnabled(true);
+      valueField.setVisible(true);
+
+      validate();
+     // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+  }
+
+  void sliderValueChanged()
+  {
+    if(redundancy==null)
+      return;
+
+    float value = slider.getValue();
+
+    for(int i=0; i<redundancy.length; i++)
+    {
+      if (value > redundancy[i])
+         redundantSeqs.removeElement(originalSequences[i]);
+      else if(!redundantSeqs.contains(originalSequences[i]))
+         redundantSeqs.addElement(originalSequences[i]);
     }
 
-    ap.repaint();
+    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+
+    PaintRefresher.Refresh(null,ap.av.alignment);
+
+    }
+  public void applyButton_actionPerformed()
+  {
+    historyList.push(new HistoryItem("Remove redundancy",
+                        ap.av.alignment, HistoryItem.HIDE));
+
+            if ((historyList.size() == 1) ||
+                    !ap.alignFrame.historyList.contains(historyList.firstElement()))
+            {
+                ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());
+                ap.alignFrame.updateEditMenuBar();
+            }
+
+            Vector del = new Vector();
+
+            undoButton.setEnabled(true);
+
+            float value = slider.getValue();
+            SequenceGroup sg = ap.av.getSelectionGroup();
+
+            for (int i = 0; i < redundancy.length; i++)
+            {
+              if (value <= redundancy[i])
+              {
+                SequenceI seq = originalSequences[i];
+                ap.av.alignment.deleteSequence(seq);
+                del.addElement(seq);
+                if (sg != null)
+                {
+                  sg.deleteSequence(seq, false);
+                }
+              }
+            }
+
+
+            // 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.alignFrame.updateEditMenuBar();
 
   }
 
-  public void undoButton_actionPerformed(ActionEvent e)
+  public void undoButton_actionPerformed()
   {
-    undoButton.setEnabled(false);
-    ap.av.setAlignment(new Alignment(oldAlignment));
-    oldAlignment = null;
-    ap.repaint();
+    HistoryItem hi = (HistoryItem) historyList.pop();
+    ap.alignFrame.restoreHistoryItem(hi);
+
+    if (historyList.size() == 0)
+    {
+      undoButton.setEnabled(false);
+    }
+    ap.alignFrame.updateEditMenuBar();
   }
 
   public void valueField_actionPerformed(ActionEvent e)
@@ -126,4 +265,25 @@ public class RedundancyPanel extends SliderPanel
       valueField.setText(slider.getValue() + "");
     }
   }
+
+
+  public void windowOpened(WindowEvent evt)
+  {}
+
+  public void windowClosing(WindowEvent evt)
+  {
+    ap.idPanel.idCanvas.setHighlighted(null);
+  }
+
+  public void windowClosed(WindowEvent evt)
+  {}
+
+  public void windowActivated(WindowEvent evt)
+  {}
+  public void windowDeactivated(WindowEvent evt)
+  {}
+  public void windowIconified(WindowEvent evt)
+  {}
+  public void windowDeiconified(WindowEvent evt)
+  {}
 }