X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=6182532502a81606969b0ca232408b4446e5aecc;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=42ac7f4e56166458da5823bdbb4d27e3228577cb;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
old mode 100755
new mode 100644
index 42ac7f4..6182532
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,129 +1,291 @@
-/*
- * 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 jalview.datamodel.*;
-import jalview.jbappletgui.*;
-
-public class RedundancyPanel
- extends GSliderPanel
-{
- AlignmentPanel ap;
-
- SequenceI[] oldAlignment;
-
- public RedundancyPanel(AlignmentPanel ap)
- {
- this.ap = ap;
-
- label.setText("Enter the redundancy threshold");
-
- slider.addAdjustmentListener(new AdjustmentListener()
- {
- public void adjustmentValueChanged(AdjustmentEvent 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);
-
- 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);
- for (int j = 0; j < del.size(); j++)
- {
- if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
- {
- sg.deleteSequence( (SequenceI) del.elementAt(j));
- }
-
- }
- }
-
- ap.repaint();
-
- }
-
- public void undoButton_actionPerformed(ActionEvent e)
- {
- undoButton.setEnabled(false);
- ap.av.setAlignment(new Alignment(oldAlignment));
- oldAlignment = null;
- ap.repaint();
- }
-
- 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 2.8.2b1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+public class RedundancyPanel extends SliderPanel implements Runnable,
+ WindowListener
+{
+ 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(MessageManager
+ .getString("label.enter_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, MessageManager
+ .getString("label.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(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;
+
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
+ label.setText(MessageManager
+ .getString("label.enter_redundancy_threshold"));
+ slider.setVisible(true);
+ applyButton.setEnabled(true);
+ valueField.setVisible(true);
+
+ validate();
+ sliderValueChanged();
+ // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+ }
+
+ void sliderValueChanged()
+ {
+ if (redundancy == null)
+ {
+ return;
+ }
+
+ float value = slider.getValue();
+
+ List redundantSequences = new ArrayList();
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ redundantSequences.add(originalSequences[i]);
+ }
+ }
+
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
+ 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(MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
+ AlignmentI alignment = ap.av.getAlignment();
+ for (int i = 0; i < del.size(); i++)
+ {
+ alignment.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());
+ }
+
+ }
+
+ 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.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+ }
+
+ 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)
+ {
+ }
+}