X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=5423dc96e02598a42b843b47256bee816224958c;hb=2ef43e1e505af2742f1c3a59619c8a4357ea82c4;hp=e4ef46ec1dfa274f5a1cebbcb16f59898eeefcdc;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index e4ef46e..5423dc9 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,148 +1,315 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.*;
 import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
 import java.awt.event.*;
+
 import java.util.*;
+
 import javax.swing.event.*;
+import jalview.util.Comparison;
+import javax.swing.*;
 
-public class RedundancyPanel
-    extends GSliderPanel
-{
-  AlignFrame af;
-  AlignmentPanel ap;
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
-  public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
-  {
-    this.ap = ap;
-    this.af = af;
-    label.setText("Enter the redundancy threshold");
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel implements Runnable
+{
+    AlignFrame af;
+    AlignmentPanel ap;
+    Stack historyList = new Stack(); // simpler than synching with alignFrame.
+    float [] redundancy;
+    SequenceI [] originalSequences;
+    JInternalFrame frame;
+    Vector redundantSeqs;
 
-    slider.addChangeListener(new ChangeListener()
+    /**
+     * Creates a new RedundancyPanel object.
+     *
+     * @param ap DOCUMENT ME!
+     * @param af DOCUMENT ME!
+     */
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
     {
-      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())) {
-      af.addHistoryItem((HistoryItem) historyList.firstElement());
-      af.updateEditMenuBar();
+        this.ap = ap;
+        this.af = af;
+        redundantSeqs = new Vector();
+
+        slider.addChangeListener(new ChangeListener()
+            {
+                public void stateChanged(ChangeEvent evt)
+                {
+                    valueField.setText(slider.getValue() + "");
+                    sliderValueChanged();
+                }
+            });
+
+        applyButton.setText("Remove");
+        allGroupsCheck.setVisible(false);
+        slider.setMinimum(0);
+        slider.setMaximum(100);
+        slider.setValue(100);
+
+        Thread worker = new Thread(this);
+        worker.start();
+
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
+                         100, false);
+        frame.addInternalFrameListener(new InternalFrameAdapter()
+            {
+              public void internalFrameClosing(InternalFrameEvent evt)
+              {
+               ap.idPanel.idCanvas.setHighlighted(null);
+              }
+            }
+            );
+
     }
-    undoButton.setEnabled(true);
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() >= 1)
+
+
+    /**
+     * 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()
     {
+        JProgressBar progress = new JProgressBar();
+        progress.setIndeterminate(true);
+        southPanel.add(progress, java.awt.BorderLayout.SOUTH);
 
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-      for (int i = 0; i < del.size(); i++)
-      {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
+        label.setText("Calculating....");
+
+        slider.setVisible(false);
+        applyButton.setEnabled(false);
+        valueField.setVisible(false);
+
+        validate();
+
+        String[] omitHidden = null;
+
+        SequenceGroup sg = ap.av.getSelectionGroup();
+        int height;
+
+        int start, end;
+
+        if ( (sg != null) && (sg.getSize(false) >= 1))
         {
-          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();
+        }
+
+        height = originalSequences.length;
+
+        redundancy = new float[height];
+        for (int i = 0; i < height; i++)
+        {
+          redundancy[i] = 0f;
+        }
+
+        if (ap.av.hasHiddenColumns)
+        {
+          omitHidden = ap.av.getViewAsString(sg!=null);
+        }
+
+
+       // 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 = Comparison.PID( seqi,  seqj );
+
+              if(seqj.length() < seqi.length())
+                redundancy[j] = Math.max(pid, redundancy[j]);
+              else
+                redundancy[i] = Math.max(pid, redundancy[i]);
 
+            }
+        }
+
+        progress.setIndeterminate(false);
+        progress.setVisible(false);
+        progress = null;
+
+        label.setText("Enter the redundancy threshold");
+        slider.setVisible(true);
+        applyButton.setEnabled(true);
+        valueField.setVisible(true);
+
+        validate();
+       // System.out.println((System.currentTimeMillis()-start));
     }
-    else
+
+    void sliderValueChanged()
     {
-      Vector s = new Vector();
-      int i = 0;
-      while (i < ap.av.alignment.getHeight())
+      if(redundancy==null)
+        return;
+
+      float value = slider.getValue();
+
+      for(int i=0; i<redundancy.length; i++)
       {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
+        if (value > redundancy[i])
+          redundantSeqs.remove(originalSequences[i]);
+        else if(!redundantSeqs.contains(originalSequences[i]))
+          redundantSeqs.add(originalSequences[i]);
+
       }
-      del = ap.av.alignment.removeRedundancy(threshold, s);
+
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
     }
 
-    // This has to be done before the restoreHistoryItem method of alignFrame will
-    // actually restore these sequences.
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void applyButton_actionPerformed(ActionEvent e)
+    {
+        historyList.push(new HistoryItem("Remove redundancy",
+                    ap.av.alignment, HistoryItem.HIDE));
 
-    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 ((historyList.size() == 1) ||
+                !af.historyList.contains(historyList.firstElement()))
+        {
+            af.addHistoryItem((HistoryItem) historyList.firstElement());
+            af.updateEditMenuBar();
+        }
 
-    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)
-      {}
+        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.add(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());
+        af.updateEditMenuBar();
     }
-    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)
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void undoButton_actionPerformed(ActionEvent e)
     {
-      undoButton.setEnabled(false);
-      if (af.historyList.contains(hi))
+      HistoryItem hi = (HistoryItem) historyList.pop();
+      af.restoreHistoryItem(hi);
+
+      if (historyList.size() == 0)
       {
-        af.historyList.remove(hi);
-        af.updateEditMenuBar();
+        undoButton.setEnabled(false);
+
+        if (af.historyList.contains(hi))
+        {
+          af.historyList.remove(hi);
+          af.updateEditMenuBar();
+        }
       }
     }
-  }
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    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() + "");
+        }
     }
-  }
+
+
 }