2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.analysis.AlignSeq;
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24 import jalview.bin.JalviewLite;
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25 import jalview.commands.CommandI;
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26 import jalview.commands.EditCommand;
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27 import jalview.commands.EditCommand.Action;
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28 import jalview.datamodel.AlignmentI;
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29 import jalview.datamodel.SequenceGroup;
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30 import jalview.datamodel.SequenceI;
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31 import jalview.util.MessageManager;
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33 import javax.swing.JFrame;
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34 import java.awt.event.ActionEvent;
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35 import java.awt.event.AdjustmentEvent;
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36 import java.awt.event.AdjustmentListener;
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37 import java.awt.event.WindowEvent;
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38 import java.awt.event.WindowListener;
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39 import java.util.ArrayList;
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40 import java.util.List;
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41 import java.util.Stack;
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42 import java.util.Vector;
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44 public class RedundancyPanel extends SliderPanel implements Runnable,
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47 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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51 SequenceI[] originalSequences;
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55 Vector redundantSeqs;
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57 public RedundancyPanel(AlignmentPanel ap)
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59 super(ap, 0, false, null);
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61 redundantSeqs = new Vector();
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63 undoButton.setVisible(true);
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64 applyButton.setVisible(true);
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65 allGroupsCheck.setVisible(false);
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67 label.setText(MessageManager
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68 .getString("label.enter_redundancy_threshold"));
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69 valueField.setText("100");
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71 slider.setVisibleAmount(1);
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72 slider.setMinimum(0);
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73 slider.setMaximum(100 + slider.getVisibleAmount());
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74 slider.setValue(100);
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76 slider.addAdjustmentListener(new AdjustmentListener()
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78 public void adjustmentValueChanged(AdjustmentEvent evt)
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80 valueField.setText(slider.getValue() + "");
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81 sliderValueChanged();
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85 frame = new JFrame();
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87 JalviewLite.addFrame(frame, MessageManager
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88 .getString("label.redundancy_threshold_selection"), 400, 100);
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90 frame.addWindowListener(this);
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92 Thread worker = new Thread(this);
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97 * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
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98 * we dont want to remove redundancy, just calculate once so we can use the
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99 * slider to dynamically hide redundant sequences
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106 * @return DOCUMENT ME!
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110 label.setText(MessageManager.getString("label.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.getAlignment());
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128 start = sg.getStartRes();
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129 end = sg.getEndRes();
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133 originalSequences = ap.av.getAlignment().getSequencesArray();
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135 end = ap.av.getAlignment().getWidth();
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138 height = originalSequences.length;
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140 redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
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141 omitHidden, start, end, false);
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142 label.setText(MessageManager
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143 .getString("label.enter_redundancy_threshold"));
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144 slider.setVisible(true);
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145 applyButton.setEnabled(true);
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146 valueField.setVisible(true);
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149 sliderValueChanged();
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150 // System.out.println("blob done "+ (System.currentTimeMillis()-start));
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153 void sliderValueChanged()
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155 if (redundancy == null)
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160 float value = slider.getValue();
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162 List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
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163 for (int i = 0; i < redundancy.length; i++)
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165 if (value <= redundancy[i])
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167 redundantSequences.add(originalSequences[i]);
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171 ap.idPanel.idCanvas.setHighlighted(redundantSequences);
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172 PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
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176 public void applyButton_actionPerformed()
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178 Vector del = new Vector();
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180 undoButton.setEnabled(true);
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182 float value = slider.getValue();
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183 SequenceGroup sg = ap.av.getSelectionGroup();
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185 for (int i = 0; i < redundancy.length; i++)
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187 if (value <= redundancy[i])
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189 del.addElement(originalSequences[i]);
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193 // This has to be done before the restoreHistoryItem method of alignFrame
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195 // actually restore these sequences.
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196 if (del.size() > 0)
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198 SequenceI[] deleted = new SequenceI[del.size()];
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201 for (int i = 0; i < del.size(); i++)
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203 deleted[i] = (SequenceI) del.elementAt(i);
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204 if (deleted[i].getLength() > width)
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206 width = deleted[i].getLength();
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210 EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
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211 Action.CUT, deleted, 0, width, ap.av.getAlignment());
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212 AlignmentI alignment = ap.av.getAlignment();
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213 for (int i = 0; i < del.size(); i++)
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215 alignment.deleteSequence(deleted[i]);
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218 sg.deleteSequence(deleted[i], false);
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222 historyList.push(cut);
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224 ap.alignFrame.addHistoryItem(cut);
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226 PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
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227 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
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232 public void undoButton_actionPerformed()
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234 CommandI command = (CommandI) historyList.pop();
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235 command.undoCommand(null);
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237 if (ap.av.getHistoryList().contains(command))
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239 ap.av.getHistoryList().remove(command);
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240 ap.alignFrame.updateEditMenuBar();
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241 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
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244 ap.paintAlignment(true);
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246 if (historyList.size() == 0)
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248 undoButton.setEnabled(false);
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252 public void valueField_actionPerformed(ActionEvent e)
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256 int i = Integer.parseInt(valueField.getText());
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257 slider.setValue(i);
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258 } catch (Exception ex)
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260 valueField.setText(slider.getValue() + "");
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264 public void windowOpened(WindowEvent evt)
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268 public void windowClosing(WindowEvent evt)
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270 ap.idPanel.idCanvas.setHighlighted(null);
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273 public void windowClosed(WindowEvent evt)
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277 public void windowActivated(WindowEvent evt)
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281 public void windowDeactivated(WindowEvent evt)
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285 public void windowIconified(WindowEvent evt)
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289 public void windowDeiconified(WindowEvent evt)
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