X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=ec896d596f591b07148f892554478e05e3750da8;hb=f5a39f4861d0f1ffdb3c5b542e00907b2cc18a73;hp=3901b1f23803004291025e46cf7ebf4a35be08aa;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 3901b1f..ec896d5 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/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
@@ -19,8 +19,9 @@
 package jalview.gui;
 
 import jalview.datamodel.*;
-
 import jalview.jbgui.*;
+import jalview.util.Comparison;
+import jalview.commands.*;
 
 import java.awt.event.*;
 
@@ -28,6 +29,8 @@ import java.util.*;
 
 import javax.swing.event.*;
 
+import javax.swing.*;
+
 
 /**
  * DOCUMENT ME!
@@ -35,11 +38,15 @@ import javax.swing.event.*;
  * @author $author$
  * @version $Revision$
  */
-public class RedundancyPanel extends GSliderPanel
+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;
 
     /**
      * Creates a new RedundancyPanel object.
@@ -47,99 +54,167 @@ public class RedundancyPanel extends GSliderPanel
      * @param ap DOCUMENT ME!
      * @param af DOCUMENT ME!
      */
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
     {
         this.ap = ap;
         this.af = af;
-        label.setText("Enter the redundancy threshold");
+        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);
+              }
+            }
+            );
+
     }
 
+
     /**
-     * DOCUMENT ME!
+     * 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 e DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     * @param sel DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
      */
-    public void applyButton_actionPerformed(ActionEvent e)
+    public void run()
     {
-        float threshold = slider.getValue();
-        Vector del;
-        historyList.push(new HistoryItem("Remove redundancy",
-                    ap.av.alignment, HistoryItem.HIDE));
+        JProgressBar progress = new JProgressBar();
+        progress.setIndeterminate(true);
+        southPanel.add(progress, java.awt.BorderLayout.SOUTH);
 
-        if ((historyList.size() == 1) ||
-                !af.historyList.contains(historyList.firstElement()))
-        {
-            af.addHistoryItem((HistoryItem) historyList.firstElement());
-            af.updateEditMenuBar();
-        }
+        label.setText("Calculating....");
 
-        undoButton.setEnabled(true);
+        slider.setVisible(false);
+        applyButton.setEnabled(false);
+        valueField.setVisible(false);
+
+        validate();
+
+        String[] omitHidden = null;
 
         SequenceGroup sg = ap.av.getSelectionGroup();
+        int height;
 
-        if ((sg != null) && (sg.getSize() >= 1))
-        {
-            del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+        int start, end;
 
-            for (int i = 0; i < del.size(); i++)
-            {
-                if (sg.sequences.contains((SequenceI) del.elementAt(i)))
-                {
-                    sg.deleteSequence((SequenceI) del.elementAt(i), true);
-                }
-            }
+        if ( (sg != null) && (sg.getSize(false) >= 1))
+        {
+           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+           start = sg.getStartRes();
+           end = sg.getEndRes();
         }
         else
         {
-            Vector s = new Vector();
-            int i = 0;
+          originalSequences = ap.av.alignment.getSequencesArray();
+          start = 0;
+          end = ap.av.alignment.getWidth();
+        }
 
-            while (i < ap.av.alignment.getHeight())
-            {
-                s.addElement(ap.av.alignment.getSequenceAt(i));
-                i++;
-            }
+        height = originalSequences.length;
 
-            del = ap.av.alignment.removeRedundancy(threshold, s);
+        redundancy = new float[height];
+        for (int i = 0; i < height; i++)
+        {
+          redundancy[i] = 0f;
         }
 
-        // This has to be done before the restoreHistoryItem method of alignFrame will
-        // actually restore these sequences.
-        if (del.size() > 0)
+        if (ap.av.hasHiddenColumns)
         {
-            for (int i = 0, j = del.size(); i < j; i++)
-            {
-                SequenceI sq = (SequenceI) del.elementAt(i);
-                sq.deleteChars(0, sq.getLength());
-            }
+          omitHidden = ap.av.getViewAsString(sg!=null);
         }
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
-        af.updateEditMenuBar();
 
+       // long start = System.currentTimeMillis();
 
-        if (ap.av.getAlignment().getHeight() < 1)
+        float pid;
+        String seqi, seqj;
+        for (int i = 0; i < height; i++)
         {
-            try
-            {
-                af.setClosed(true);
-            }
-            catch (Exception ex)
+
+            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));
+    }
+
+    void sliderValueChanged()
+    {
+      if(redundancy==null)
+        return;
+
+      float value = slider.getValue();
+
+      for(int i=0; i<redundancy.length; i++)
+      {
+        if (value > redundancy[i])
+          redundantSeqs.remove(originalSequences[i]);
+        else if(!redundantSeqs.contains(originalSequences[i]))
+          redundantSeqs.add(originalSequences[i]);
+
+      }
+
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
     }
 
     /**
@@ -147,21 +222,86 @@ public class RedundancyPanel extends GSliderPanel
      *
      * @param e DOCUMENT ME!
      */
-    public void undoButton_actionPerformed(ActionEvent e)
+    public void applyButton_actionPerformed(ActionEvent e)
     {
-        HistoryItem hi = (HistoryItem) historyList.pop();
-        af.restoreHistoryItem(hi);
+        Vector del = new Vector();
+
+        undoButton.setEnabled(true);
+
+        float value = slider.getValue();
+        SequenceGroup sg = ap.av.getSelectionGroup();
 
-        if (historyList.size() == 0)
+        for (int i = 0; i < redundancy.length; i++)
         {
-            undoButton.setEnabled(false);
+          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);
 
-            if (af.historyList.contains(hi))
+          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)
             {
-                af.historyList.remove(hi);
-                af.updateEditMenuBar();
+              sg.deleteSequence(deleted[i], false);
             }
+          }
+
+          historyList.push(cut);
+
+          ap.alignFrame.addHistoryItem(cut);
+
+          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
         }
+
+
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void undoButton_actionPerformed(ActionEvent e)
+    {
+      CommandI command = (CommandI) historyList.pop();
+      command.undoCommand();
+
+      if (ap.av.historyList.contains(command))
+      {
+        ap.av.historyList.remove(command);
+        af.updateEditMenuBar();
+      }
+
+      ap.repaint();
+
+      if (historyList.size() == 0)
+      {
+        undoButton.setEnabled(false);
+      }
     }
 
     /**
@@ -181,4 +321,6 @@ public class RedundancyPanel extends GSliderPanel
             valueField.setText(slider.getValue() + "");
         }
     }
+
+
 }