X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=77c96913f13795809d21d2139198bee09b2c332d;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=273261243a5caf061ee9bf527e6fb64859b1945c;hpb=7928c1a7fab123e9e8baa935f37ab08a965341e7;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 2732612..77c9691 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,293 +1,325 @@
-/*
- * 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.appletgui;
-
-import java.util.*;
-
-import java.awt.event.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.appletgui.PaintRefresher;
-
-public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener
-{
-  AlignmentPanel ap;
-
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
-  Vector originalSequences;
-  Hashtable originalColours;
-  SequenceI[] oldAlignment;
-  float [] redundancy;
-  Frame frame;
-
-  public RedundancyPanel(AlignmentPanel ap)
-  {
-    super(ap, 0, false, null);
-
-    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(40);
-    slider.setMaximum(100+slider.getVisibleAmount());
-    slider.setValue(100);
-
-    slider.addAdjustmentListener(new AdjustmentListener()
-    {
-      public void adjustmentValueChanged(AdjustmentEvent evt)
-      {
-        valueField.setText(slider.getValue() + "");
-        sliderValueChanged();
-      }
-    });
-
-    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();
-  }
-  /**
-   * 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()
-  {
-      label.setText("Calculating....");
-
-      slider.setVisible(false);
-      applyButton.setEnabled(false);
-      valueField.setVisible(false);
-
-      validate();
-
-      Vector sel = new Vector();
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      int height;
-      originalSequences = new Vector();
-      originalColours = new Hashtable();
-
-      if ( (sg != null) && (sg.getSize() >= 1))
-      {
-         height = sg.getSize();
-        for (int i = 0; i < sg.getSize(); i++)
-        {
-          sel.addElement(sg.getSequenceAt(i));
-        }
-      }
-      else
-      {
-        height = ap.av.alignment.getHeight();
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-        {
-          sel.addElement(ap.av.alignment.getSequenceAt(i));
-        }
-      }
-
-      redundancy = new float[height];
-      for (int i = 0; i < height; i++)
-      {
-        redundancy[i] = 0f;
-      }
-
-
-     // long start = System.currentTimeMillis();
-
-      float pid;
-      SequenceI seqi, seqj;
-      for (int i = 0; i < sel.size(); i++)
-      {
-          originalSequences.addElement(sel.elementAt(i));
-          originalColours.put(sel.elementAt(i),
-                             ((SequenceI) sel.elementAt(i)).getColor());
-
-          for (int j = 0; j < i; j++)
-          {
-            if(i==j)
-              continue;
-
-            seqi = (SequenceI) sel.elementAt(i);
-            seqj = (SequenceI) sel.elementAt(j);
-
-            if (sg != null)
-            {
-              pid = jalview.util.Comparison.PID(seqi,
-                                                seqj,
-                                                sg.getStartRes(), sg.getEndRes());
-            }
-            else
-              pid = jalview.util.Comparison.PID( seqi,  seqj );
-
-
-            if(seqj.getLength() < seqi.getLength())
-              redundancy[j] = Math.max(pid, redundancy[j]);
-            else
-              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;
-
-    float value = slider.getValue();
-
-    for(int i=0; i<redundancy.length; i++)
-    {
-      if (value > redundancy[i])
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);
-      else
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);
-    }
-
-    PaintRefresher.Refresh(null,ap.av.alignment);
-
-    }
-  public void applyButton_actionPerformed()
-  {
-    historyList.push(new HistoryItem("Remove redundancy",
-                        ap.av.alignment, HistoryItem.HIDE));
-
-            if ((historyList.size() == 1) ||
-                    !ap.alignFrame.historyList.contains(historyList.firstElement()))
-            {
-                ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());
-                ap.alignFrame.updateEditMenuBar();
-            }
-
-            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 = (SequenceI) originalSequences.elementAt(i);
-                ap.av.alignment.deleteSequence(seq);
-                del.addElement(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());
-        ap.alignFrame.updateEditMenuBar();
-
-  }
-
-  public void undoButton_actionPerformed()
-  {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    ap.alignFrame.restoreHistoryItem(hi);
-
-    if (historyList.size() == 0)
-    {
-      undoButton.setEnabled(false);
-    }
-    ap.alignFrame.updateEditMenuBar();
-  }
-
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch (Exception ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-
-  public void windowOpened(WindowEvent evt)
-  {}
-
-  public void windowClosing(WindowEvent evt)
-  {
-    for(int i=0; i<originalSequences.size(); i++)
-    {
-      SequenceI seq = (SequenceI)originalSequences.elementAt(i);
-      seq.setColor( (java.awt.Color)originalColours.get(seq));
-    }
-
-    PaintRefresher.Refresh(ap.av.alignment);
-  }
-
-  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)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+
+public class RedundancyPanel extends SliderPanel implements Runnable,
+        WindowListener
+{
+  AlignmentPanel ap;
+
+  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();
+      }
+    });
+
+    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();
+  }
+
+  /**
+   * 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()
+  {
+    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.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 (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
+        {
+          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;
+    }
+
+    float value = slider.getValue();
+
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value > redundancy[i])
+      {
+        redundantSeqs.removeElement(originalSequences[i]);
+      }
+      else if (!redundantSeqs.contains(originalSequences[i]))
+      {
+        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)
+        {
+          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());
+    }
+
+  }
+
+  public void undoButton_actionPerformed()
+  {
+    CommandI command = (CommandI) historyList.pop();
+    command.undoCommand(null);
+
+    if (ap.av.historyList.contains(command))
+    {
+      ap.av.historyList.removeElement(command);
+      ap.alignFrame.updateEditMenuBar();
+    }
+
+    ap.paintAlignment(true);
+
+    if (historyList.size() == 0)
+    {
+      undoButton.setEnabled(false);
+    }
+  }
+
+  public void valueField_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    } catch (Exception ex)
+    {
+      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)
+  {
+  }
+}