X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=16db1fa2c5125409ff2ab68d59ac0865ec129bb9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=e4ef46ec1dfa274f5a1cebbcb16f59898eeefcdc;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index e4ef46e..16db1fa 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,148 +1,341 @@
-/*
-* 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 java.awt.event.*;
-import java.util.*;
-import javax.swing.event.*;
-
-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");
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      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();
-    }
-    undoButton.setEnabled(true);
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() >= 1)
-    {
-
-      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
-      for (int i = 0; i < del.size(); i++)
-      {
-        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
-        {
-          sg.deleteSequence( (SequenceI) del.elementAt(i));
-        }
-      }
-
-    }
-    else
-    {
-      Vector s = new Vector();
-      int i = 0;
-      while (i < ap.av.alignment.getHeight())
-      {
-        s.addElement(ap.av.alignment.getSequenceAt(i));
-        i++;
-      }
-      del = ap.av.alignment.removeRedundancy(threshold, s);
-    }
-
-    // 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());
-    ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
-    if (ap.av.getAlignment().getHeight() < 1)
-    {
-      try
-      {
-        af.setClosed(true);
-      }
-      catch (Exception ex)
-      {}
-    }
-    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)
-    {
-      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)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+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!
+ * 
+ * @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;
+
+  /**
+   * 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()
+    {
+      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();
+
+    String[] omitHidden = null;
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
+
+    int start, end;
+
+    if ((sg != null) && (sg.getSize() >= 1))
+    {
+      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].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(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);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void applyButton_actionPerformed(ActionEvent e)
+  {
+    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());
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void undoButton_actionPerformed(ActionEvent e)
+  {
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand(af.getViewAlignments());
+
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.remove(command);
+      af.updateEditMenuBar();
+    }
+
+    ap.paintAlignment(true);
+
+    if (historyList.size() == 0)
+    {
+      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() + "");
+    }
+  }
+
+}