X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=a9d26908a1cac6d286d066e2aaceea292bb1b16f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=6cb2c220c427a8fe3af49b82aab53dd8a8c89754;hpb=a013236e12d46fbb87df79447cc3031c542606e1;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 6cb2c22..a9d2690 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,102 +1,318 @@
-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
-{
-  AlignmentPanel ap;
-
-  SequenceI[] oldAlignment;
-
-
-  public RedundancyPanel(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    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;
-
-       oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-        {
-           oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
-                                ap.av.alignment.getSequenceAt(i).
-                                getSequence());
-        }
-
-        undoButton.setEnabled(true);
-
-       if (ap.av.sel != null && ap.av.sel.size() > 1)
-       {
-
-         del = ap.av.alignment.removeRedundancy(threshold, ap.av.sel.asVector());
-         for (int i = 0; i < del.size(); i++)
-           if (ap.av.sel.contains( (SequenceI) del.elementAt(i)))
-             ap.av.sel.removeElement( (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);
-           for (int j=0; j < del.size(); j++)
-           {
-               if (ap.av.sel.contains((SequenceI)del.elementAt(j)))
-               ap.av.sel.removeElement((SequenceI)del.elementAt(j));
-
-           }
-         }
-
-         ap.RefreshPanels();
-
-  }
-
-  public void undoButton_actionPerformed(ActionEvent e)
-  {
-      undoButton.setEnabled(false);
-      ap.av.setAlignment( new Alignment(oldAlignment) );
-      oldAlignment = null;
-      ap.RefreshPanels();
-  }
-
-
-  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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel implements Runnable
+{
+  AlignFrame af;
+
+  AlignmentPanel ap;
+
+  Stack<CommandI> historyList = new Stack<CommandI>();
+
+  // 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(MessageManager.getString("action.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, MessageManager
+            .getString("label.redundancy_threshold_selection"), 400, 100,
+            false);
+    frame.addInternalFrameListener(new InternalFrameAdapter()
+    {
+      public void internalFrameClosing(InternalFrameEvent evt)
+      {
+        ap.getIdPanel().getIdCanvas().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(MessageManager.getString("label.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.getAlignment());
+      start = sg.getStartRes();
+      end = sg.getEndRes();
+    }
+    else
+    {
+      originalSequences = ap.av.getAlignment().getSequencesArray();
+      start = 0;
+      end = ap.av.getAlignment().getWidth();
+    }
+
+    height = originalSequences.length;
+    if (ap.av.hasHiddenColumns())
+    {
+      omitHidden = ap.av.getViewAsString(sg != null);
+    }
+    redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+            omitHidden, start, end, false);
+
+    progress.setIndeterminate(false);
+    progress.setVisible(false);
+    progress = null;
+
+    label.setText(MessageManager
+            .getString("label.enter_redundancy_threshold"));
+    slider.setVisible(true);
+    applyButton.setEnabled(true);
+    valueField.setVisible(true);
+
+    validate();
+    sliderValueChanged();
+    // System.out.println((System.currentTimeMillis()-start));
+  }
+
+  void sliderValueChanged()
+  {
+    if (redundancy == null)
+    {
+      return;
+    }
+
+    float value = slider.getValue();
+    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value <= redundancy[i])
+      {
+        redundantSequences.add(originalSequences[i]);
+      }
+    }
+    ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
+  }
+
+  /**
+   * 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(
+              MessageManager.getString("action.remove_redundancy"),
+              Action.CUT, deleted, 0, width, ap.av.getAlignment());
+
+      for (int i = 0; i < del.size(); i++)
+      {
+        ap.av.getAlignment().deleteSequence(deleted[i]);
+        if (sg != null)
+        {
+          sg.deleteSequence(deleted[i], false);
+        }
+      }
+
+      historyList.push(cut);
+
+      ap.alignFrame.addHistoryItem(cut);
+
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void undoButton_actionPerformed(ActionEvent e)
+  {
+    if (historyList == null || historyList.isEmpty())
+    {
+      undoButton.setEnabled(false);
+      return;
+    }
+
+    CommandI command = historyList.pop();
+    if (ap.av.getHistoryList().contains(command))
+    {
+      command.undoCommand(af.getViewAlignments());
+      ap.av.getHistoryList().remove(command);
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
+      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() + "");
+    }
+  }
+
+}