X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=fccc30f4fedb226cb54a3da1e358b734953d7dba;hb=32a72d077d2371f4566688fbd103103d8505b27f;hp=42ac7f4e56166458da5823bdbb4d27e3228577cb;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 42ac7f4..fccc30f 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -23,95 +23,249 @@ import java.util.*;
 
 import java.awt.event.*;
 
+import java.awt.*;
+
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
+import jalview.appletgui.PaintRefresher;
+import jalview.commands.*;
 
-public class RedundancyPanel
-    extends GSliderPanel
+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;
+
+      int start, end;
 
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-      for (int i = 0; i < del.size(); i++)
+      if ( (sg != null) && (sg.getSize(false) >= 1))
       {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
-        {
-          sg.deleteSequence( (SequenceI) del.elementAt(i));
-        }
+         originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+         start = sg.getStartRes();
+         end = sg.getEndRes();
+      }
+      else
+      {
+        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)
       {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
-        {
-          sg.deleteSequence( (SequenceI) del.elementAt(j));
-        }
+     //   omitHidden = ap.av.getSelectionAsString();
+      }
+
+
+     // long start = System.currentTimeMillis();
 
+      float pid;
+      String seqi, seqj;
+      for (int i = 0; i < height; i++)
+      {
+          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(this,
+                           ap.av.getSequenceSetId(),
+                           true,
+                           true);
+
+    }
+  public void applyButton_actionPerformed()
+  {        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])
+          {
+            del.addElement(originalSequences[i]);
+          }
+        }
+
+        // This has to be done before the restoreHistoryItem method of alignFrame will
+        // actually restore these sequences.
+        if (del.size() > 0)
+        {
+          SequenceI [] deleted = new SequenceI[del.size()];
+
+          int width = 0;
+          for (int i = 0; i < del.size(); i++)
+          {
+            deleted[i] = (SequenceI)del.elementAt(i);
+            if(deleted[i].getLength()>width)
+              width = deleted[i].getLength();
+          }
+
+          EditCommand cut = new EditCommand("Remove Redundancy",
+              EditCommand.CUT, deleted,0,width,ap.av.alignment);
+
+          for (int i = 0; i < del.size(); i++)
+          {
+            ap.av.alignment.deleteSequence( deleted[i] );
+            PaintRefresher.Refresh(this,
+                                   ap.av.getSequenceSetId(),
+                                   true,
+                                   true);
+            if (sg != null)
+            {
+              sg.deleteSequence(deleted[i], false);
+            }
+          }
+
+          historyList.push(cut);
+
+          ap.alignFrame.addHistoryItem(cut);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+        }
 
   }
 
-  public void undoButton_actionPerformed(ActionEvent e)
+  public void undoButton_actionPerformed()
   {
-    undoButton.setEnabled(false);
-    ap.av.setAlignment(new Alignment(oldAlignment));
-    oldAlignment = null;
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand();
+
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.removeElement(command);
+      ap.alignFrame.updateEditMenuBar();
+    }
+
     ap.repaint();
+
+    if (historyList.size() == 0)
+    {
+      undoButton.setEnabled(false);
+      }
   }
 
   public void valueField_actionPerformed(ActionEvent e)
@@ -126,4 +280,25 @@ public class RedundancyPanel
       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)
+  {}
 }