X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=6f5b09d31f86110b06cd2851a752defe5bab2a97;hb=0896dd47a711b260d6f79e1e18d1bb8aa822e111;hp=b2482948bd9edc602be41b5fa7ff73e09371b7b1;hpb=7c05496d1da22f21ce5ae1a199afb9b16c8777ea;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index b248294..6f5b09d 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) 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
@@ -18,18 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
-
-import java.awt.event.*;
-
 import java.util.*;
 
-import javax.swing.event.*;
-import jalview.util.Comparison;
+import java.awt.event.*;
 import javax.swing.*;
+import javax.swing.event.*;
 
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.util.*;
 
 /**
  * DOCUMENT ME!
@@ -37,291 +35,301 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class RedundancyPanel extends GSliderPanel implements Runnable
+public class RedundancyPanel
+    extends GSliderPanel implements Runnable
 {
-    AlignFrame af;
-    AlignmentPanel ap;
-    Stack historyList = new Stack(); // simpler than synching with alignFrame.
-    float [] redundancy;
-    SequenceI [] originalSequences;
-    Hashtable originalColours;
-    JInternalFrame frame;
-
-    /**
-     * Creates a new RedundancyPanel object.
-     *
-     * @param ap DOCUMENT ME!
-     * @param af DOCUMENT ME!
-     */
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
+  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.
+   *
+   * @param ap DOCUMENT ME!
+   * @param af DOCUMENT ME!
+   */
+  public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
+  {
+    this.ap = ap;
+    this.af = af;
+    redundantSeqs = new Vector();
+
+    slider.addChangeListener(new ChangeListener()
     {
-        this.ap = ap;
-        this.af = af;
-
-        slider.addChangeListener(new ChangeListener()
-            {
-                public void stateChanged(ChangeEvent evt)
-                {
-                    valueField.setText(slider.getValue() + "");
-                    sliderValueChanged();
-                }
-            });
-
-        applyButton.setText("Remove");
-        allGroupsCheck.setVisible(false);
-        slider.setMinimum(60);
-        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)
-              {
-                resetColours();
-              }
-            }
-            );
-
+      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);
+      }
     }
+    );
+
+  }
+
+  /**
+   * 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);
+
+    label.setText("Calculating....");
+
+    slider.setVisible(false);
+    applyButton.setEnabled(false);
+    valueField.setVisible(false);
 
+    validate();
 
-    /**
-     * 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()
+    String[] omitHidden = null;
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
+
+    int start, end;
+
+    if ( (sg != null) && (sg.getSize() >= 1))
     {
-        JProgressBar progress = new JProgressBar();
-        progress.setIndeterminate(true);
-        southPanel.add(progress, java.awt.BorderLayout.SOUTH);
+      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();
+    }
 
-        label.setText("Calculating....");
+    height = originalSequences.length;
 
-        slider.setVisible(false);
-        applyButton.setEnabled(false);
-        valueField.setVisible(false);
+    redundancy = new float[height];
+    for (int i = 0; i < height; i++)
+    {
+      redundancy[i] = 0f;
+    }
 
-        validate();
+    if (ap.av.hasHiddenColumns)
+    {
+      omitHidden = ap.av.getViewAsString(sg != null);
+    }
 
-        String[] omitHidden = null;
+    // long start = System.currentTimeMillis();
 
-        SequenceGroup sg = ap.av.getSelectionGroup();
-        int height;
+    float pid;
+    String seqi, seqj;
+    for (int i = 0; i < height; i++)
+    {
 
-        originalColours = new Hashtable();
-        int start, end;
+      for (int j = 0; j < i; j++)
+      {
+        if (i == j)
+        {
+          continue;
+        }
 
-        if ( (sg != null) && (sg.getSize(false) >= 1))
+        if (omitHidden == null)
         {
-           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
-           start = sg.getStartRes();
-           end = sg.getEndRes();
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(start, end);
         }
         else
         {
-          originalSequences = ap.av.alignment.getSequencesArray();
-          start = 0;
-          end = ap.av.alignment.getWidth();
+          seqi = omitHidden[i];
+          seqj = omitHidden[j];
         }
 
-        height = originalSequences.length;
+        pid = Comparison.PID(seqi, seqj);
 
-        redundancy = new float[height];
-        for (int i = 0; i < height; i++)
+        if (seqj.length() < seqi.length())
         {
-          redundancy[i] = 0f;
+          redundancy[j] = Math.max(pid, redundancy[j]);
         }
-
-        if (ap.av.hasHiddenColumns)
+        else
         {
-          omitHidden = ap.av.getSelectionAsString();
+          redundancy[i] = Math.max(pid, redundancy[i]);
         }
 
+      }
+    }
 
-       // long start = System.currentTimeMillis();
-
-        float pid;
-        String seqi, seqj;
-        for (int i = 0; i < height; i++)
-        {
-            originalColours.put(originalSequences[i],
-                               originalSequences[i].getColor());
-
-            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;
+    progress.setIndeterminate(false);
+    progress.setVisible(false);
+    progress = null;
 
-        label.setText("Enter the redundancy threshold");
-        slider.setVisible(true);
-        applyButton.setEnabled(true);
-        valueField.setVisible(true);
+    label.setText("Enter the redundancy threshold");
+    slider.setVisible(true);
+    applyButton.setEnabled(true);
+    valueField.setVisible(true);
 
-        validate();
-       // System.out.println((System.currentTimeMillis()-start));
-    }
+    validate();
+    // System.out.println((System.currentTimeMillis()-start));
+  }
 
-    void sliderValueChanged()
+  void sliderValueChanged()
+  {
+    if (redundancy == null)
     {
-      if(redundancy==null)
-        return;
+      return;
+    }
 
-      float value = slider.getValue();
+    float value = slider.getValue();
 
-      for(int i=0; i<redundancy.length; i++)
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value > redundancy[i])
       {
-        if (value > redundancy[i])
-           originalSequences[i].setColor(java.awt.Color.white);
-        else
-          originalSequences[i].setColor(java.awt.Color.red);
+        redundantSeqs.remove(originalSequences[i]);
+      }
+      else if (!redundantSeqs.contains(originalSequences[i]))
+      {
+        redundantSeqs.add(originalSequences[i]);
       }
-
-      PaintRefresher.Refresh(null,ap.av.alignment);
 
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void applyButton_actionPerformed(ActionEvent e)
-    {
-        historyList.push(new HistoryItem("Remove redundancy",
-                    ap.av.alignment, HistoryItem.HIDE));
+    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+  }
 
-        if ((historyList.size() == 1) ||
-                !af.historyList.contains(historyList.firstElement()))
-        {
-            af.addHistoryItem((HistoryItem) historyList.firstElement());
-            af.updateEditMenuBar();
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void applyButton_actionPerformed(ActionEvent e)
+  {
+    Vector del = new Vector();
 
-        Vector del = new Vector();
+    undoButton.setEnabled(true);
 
-        undoButton.setEnabled(true);
+    float value = slider.getValue();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
-        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()];
 
-        for (int i = 0; i < redundancy.length; i++)
+      int width = 0;
+      for (int i = 0; i < del.size(); i++)
+      {
+        deleted[i] = (SequenceI) del.elementAt(i);
+        if (deleted[i].getLength() > width)
         {
-          if (value <= redundancy[i])
-          {
-            SequenceI seq = originalSequences[i];
-            ap.av.alignment.deleteSequence(seq);
-            del.add(seq);
-            if (sg != null)
-            {
-              sg.deleteSequence(seq, false);
-            }
-          }
+          width = deleted[i].getLength();
         }
+      }
 
+      EditCommand cut = new EditCommand("Remove Redundancy",
+                                        EditCommand.CUT, deleted, 0, width,
+                                        ap.av.alignment);
 
-        // This has to be done before the restoreHistoryItem method of alignFrame will
-        // actually restore these sequences.
-        if (del.size() > 0)
+      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)
         {
-            for (int i = 0, j = del.size(); i < j; i++)
-            {
-                SequenceI sq = (SequenceI) del.elementAt(i);
-                sq.deleteChars(0, sq.getLength());
-            }
+          sg.deleteSequence(deleted[i], false);
         }
+      }
 
-        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
-        af.updateEditMenuBar();
-    }
+      historyList.push(cut);
 
-    void resetColours()
-    {
-      for(int i=0; i<originalSequences.length; i++)
-      {
-        SequenceI seq = originalSequences[i];
-        seq.setColor( (java.awt.Color)originalColours.get(seq));
-      }
+      ap.alignFrame.addHistoryItem(cut);
 
-      PaintRefresher.Refresh(ap.av.alignment);
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void undoButton_actionPerformed(ActionEvent e)
-    {
-      HistoryItem hi = (HistoryItem) historyList.pop();
-      af.restoreHistoryItem(hi);
+  }
 
-      if (historyList.size() == 0)
-      {
-        undoButton.setEnabled(false);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void undoButton_actionPerformed(ActionEvent e)
+  {
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand();
 
-        if (af.historyList.contains(hi))
-        {
-          af.historyList.remove(hi);
-          af.updateEditMenuBar();
-        }
-      }
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.remove(command);
+      af.updateEditMenuBar();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void valueField_actionPerformed(ActionEvent e)
+    ap.paintAlignment(true);
+
+    if (historyList.size() == 0)
     {
-        try
-        {
-            int i = Integer.parseInt(valueField.getText());
-            slider.setValue(i);
-        }
-        catch (Exception ex)
-        {
-            valueField.setText(slider.getValue() + "");
-        }
+      undoButton.setEnabled(false);
     }
-
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void valueField_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    }
+    catch (Exception ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
 
 }