2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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23 import java.awt.event.*;
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24 import javax.swing.*;
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25 import javax.swing.event.*;
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27 import jalview.commands.*;
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28 import jalview.datamodel.*;
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29 import jalview.jbgui.*;
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30 import jalview.util.*;
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36 * @version $Revision$
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38 public class RedundancyPanel
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39 extends GSliderPanel implements Runnable
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43 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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45 SequenceI[] originalSequences;
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46 JInternalFrame frame;
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47 Vector redundantSeqs;
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50 * Creates a new RedundancyPanel object.
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52 * @param ap DOCUMENT ME!
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53 * @param af DOCUMENT ME!
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55 public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
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59 redundantSeqs = new Vector();
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61 slider.addChangeListener(new ChangeListener()
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63 public void stateChanged(ChangeEvent evt)
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65 valueField.setText(slider.getValue() + "");
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66 sliderValueChanged();
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70 applyButton.setText("Remove");
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71 allGroupsCheck.setVisible(false);
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72 slider.setMinimum(0);
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73 slider.setMaximum(100);
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74 slider.setValue(100);
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76 Thread worker = new Thread(this);
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79 frame = new JInternalFrame();
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80 frame.setContentPane(this);
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81 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
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83 frame.addInternalFrameListener(new InternalFrameAdapter()
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85 public void internalFrameClosing(InternalFrameEvent evt)
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87 ap.idPanel.idCanvas.setHighlighted(null);
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95 * This is a copy of remove redundancy in jalivew.datamodel.Alignment
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96 * except we dont want to remove redundancy, just calculate once
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97 * so we can use the slider to dynamically hide redundant sequences
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99 * @param threshold DOCUMENT ME!
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100 * @param sel DOCUMENT ME!
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102 * @return DOCUMENT ME!
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106 JProgressBar progress = new JProgressBar();
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107 progress.setIndeterminate(true);
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108 southPanel.add(progress, java.awt.BorderLayout.SOUTH);
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110 label.setText("Calculating....");
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112 slider.setVisible(false);
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113 applyButton.setEnabled(false);
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114 valueField.setVisible(false);
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118 String[] omitHidden = null;
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120 SequenceGroup sg = ap.av.getSelectionGroup();
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125 if ( (sg != null) && (sg.getSize() >= 1))
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127 originalSequences = sg.getSequencesInOrder(ap.av.alignment);
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128 start = sg.getStartRes();
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129 end = sg.getEndRes();
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133 originalSequences = ap.av.alignment.getSequencesArray();
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135 end = ap.av.alignment.getWidth();
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138 height = originalSequences.length;
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140 redundancy = new float[height];
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141 for (int i = 0; i < height; i++)
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143 redundancy[i] = 0f;
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146 if (ap.av.hasHiddenColumns)
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148 omitHidden = ap.av.getViewAsString(sg != null);
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151 // long start = System.currentTimeMillis();
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155 for (int i = 0; i < height; i++)
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158 for (int j = 0; j < i; j++)
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165 if (omitHidden == null)
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167 seqi = originalSequences[i].getSequenceAsString(start, end);
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168 seqj = originalSequences[j].getSequenceAsString(start, end);
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172 seqi = omitHidden[i];
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173 seqj = omitHidden[j];
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176 pid = Comparison.PID(seqi, seqj);
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178 if (seqj.length() < seqi.length())
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180 redundancy[j] = Math.max(pid, redundancy[j]);
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184 redundancy[i] = Math.max(pid, redundancy[i]);
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190 progress.setIndeterminate(false);
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191 progress.setVisible(false);
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194 label.setText("Enter the redundancy threshold");
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195 slider.setVisible(true);
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196 applyButton.setEnabled(true);
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197 valueField.setVisible(true);
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200 // System.out.println((System.currentTimeMillis()-start));
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203 void sliderValueChanged()
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205 if (redundancy == null)
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210 float value = slider.getValue();
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212 for (int i = 0; i < redundancy.length; i++)
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214 if (value > redundancy[i])
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216 redundantSeqs.remove(originalSequences[i]);
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218 else if (!redundantSeqs.contains(originalSequences[i]))
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220 redundantSeqs.add(originalSequences[i]);
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225 ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
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231 * @param e DOCUMENT ME!
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233 public void applyButton_actionPerformed(ActionEvent e)
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235 Vector del = new Vector();
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237 undoButton.setEnabled(true);
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239 float value = slider.getValue();
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240 SequenceGroup sg = ap.av.getSelectionGroup();
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242 for (int i = 0; i < redundancy.length; i++)
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244 if (value <= redundancy[i])
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246 del.addElement(originalSequences[i]);
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250 // This has to be done before the restoreHistoryItem method of alignFrame will
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251 // actually restore these sequences.
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252 if (del.size() > 0)
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254 SequenceI[] deleted = new SequenceI[del.size()];
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257 for (int i = 0; i < del.size(); i++)
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259 deleted[i] = (SequenceI) del.elementAt(i);
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260 if (deleted[i].getLength() > width)
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262 width = deleted[i].getLength();
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266 EditCommand cut = new EditCommand("Remove Redundancy",
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267 EditCommand.CUT, deleted, 0, width,
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270 for (int i = 0; i < del.size(); i++)
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272 ap.av.alignment.deleteSequence(deleted[i]);
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273 PaintRefresher.Refresh(this,
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274 ap.av.getSequenceSetId(),
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279 sg.deleteSequence(deleted[i], false);
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283 historyList.push(cut);
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285 ap.alignFrame.addHistoryItem(cut);
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287 ap.av.firePropertyChange("alignment", null,
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288 ap.av.getAlignment().getSequences());
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296 * @param e DOCUMENT ME!
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298 public void undoButton_actionPerformed(ActionEvent e)
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300 CommandI command = (CommandI) historyList.pop();
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301 command.undoCommand();
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303 if (ap.av.historyList.contains(command))
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305 ap.av.historyList.remove(command);
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306 af.updateEditMenuBar();
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309 ap.paintAlignment(true);
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311 if (historyList.size() == 0)
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313 undoButton.setEnabled(false);
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320 * @param e DOCUMENT ME!
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322 public void valueField_actionPerformed(ActionEvent e)
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326 int i = Integer.parseInt(valueField.getText());
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327 slider.setValue(i);
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329 catch (Exception ex)
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331 valueField.setText(slider.getValue() + "");
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