X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=d2d4384e1f9ccbd40afd1d73d0db3aeb737900b7;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=42ac7f4e56166458da5823bdbb4d27e3228577cb;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 42ac7f4..d2d4384 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) 2007 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
@@ -21,97 +21,267 @@ package jalview.appletgui;
 
 import java.util.*;
 
+import java.awt.*;
 import java.awt.event.*;
 
+import jalview.commands.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
 
 public class RedundancyPanel
-    extends GSliderPanel
+    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);
+
+    Thread worker = new Thread(this);
+    worker.start();
   }
 
-  public void applyButton_actionPerformed(ActionEvent e)
+  /**
+   * 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....");
+
+    slider.setVisible(false);
+    applyButton.setEnabled(false);
+    valueField.setVisible(false);
+
+    validate();
+
+    String[] omitHidden = null;
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
 
-    oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
-    for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+    int start, end;
+
+    if ( (sg != null) && (sg.getSize() >= 1))
+    {
+      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      start = sg.getStartRes();
+      end = sg.getEndRes();
+    }
+    else
     {
-      oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
-                                     ap.av.alignment.getSequenceAt(i).
-                                     getSequence());
+      originalSequences = ap.av.alignment.getSequencesArray();
+      start = 0;
+      end = ap.av.alignment.getWidth();
     }
 
-    undoButton.setEnabled(true);
+    height = originalSequences.length;
 
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() > 1)
+    redundancy = new float[height];
+    for (int i = 0; i < height; i++)
     {
+      redundancy[i] = 0f;
+    }
 
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-      for (int i = 0; i < del.size(); i++)
+    //  if (ap.av.hasHiddenColumns)
+    {
+      //   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 (sg.sequences.contains( (SequenceI) del.elementAt(i)))
+        if (i == j)
+        {
+          continue;
+        }
+
+        if (omitHidden == null)
+        {
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(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
         {
-          sg.deleteSequence( (SequenceI) del.elementAt(i));
+          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;
     }
-    else
+
+    float value = slider.getValue();
+
+    for (int i = 0; i < redundancy.length; i++)
     {
-      Vector s = new Vector();
-      int i = 0;
-      while (i < ap.av.alignment.getHeight())
+      if (value > redundancy[i])
       {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
+        redundantSeqs.removeElement(originalSequences[i]);
       }
-      del = ap.av.alignment.removeRedundancy(threshold, s);
-      for (int j = 0; j < del.size(); j++)
+      else if (!redundantSeqs.contains(originalSequences[i]))
       {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
+        redundantSeqs.addElement(originalSequences[i]);
+      }
+    }
+
+    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)
         {
-          sg.deleteSequence( (SequenceI) del.elementAt(j));
+          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);
+        }
       }
-    }
 
-    ap.repaint();
+      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 +296,27 @@ 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)
+  {}
 }