2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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21 import jalview.datamodel.*;
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23 import jalview.jbgui.*;
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25 import java.awt.event.*;
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29 import javax.swing.event.*;
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30 import jalview.util.Comparison;
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31 import javax.swing.*;
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38 * @version $Revision$
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40 public class RedundancyPanel extends GSliderPanel implements Runnable
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44 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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45 float [] redundancy;
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46 SequenceI [] originalSequences;
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47 Hashtable originalColours;
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48 JInternalFrame frame;
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51 * Creates a new RedundancyPanel object.
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53 * @param ap DOCUMENT ME!
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54 * @param af DOCUMENT ME!
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56 public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
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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(60);
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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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96 * This is a copy of remove redundancy in jalivew.datamodel.Alignment
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97 * except we dont want to remove redundancy, just calculate once
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98 * so we can use the slider to dynamically hide redundant sequences
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100 * @param threshold DOCUMENT ME!
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101 * @param sel DOCUMENT ME!
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103 * @return DOCUMENT ME!
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107 JProgressBar progress = new JProgressBar();
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108 progress.setIndeterminate(true);
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109 southPanel.add(progress, java.awt.BorderLayout.SOUTH);
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111 label.setText("Calculating....");
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113 slider.setVisible(false);
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114 applyButton.setEnabled(false);
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115 valueField.setVisible(false);
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119 String[] omitHidden = null;
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121 SequenceGroup sg = ap.av.getSelectionGroup();
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124 originalColours = new Hashtable();
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127 if ( (sg != null) && (sg.getSize(false) >= 1))
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129 originalSequences = sg.getSequencesInOrder(ap.av.alignment);
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130 start = sg.getStartRes();
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131 end = sg.getEndRes();
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135 originalSequences = ap.av.alignment.getSequencesArray();
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137 end = ap.av.alignment.getWidth();
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140 height = originalSequences.length;
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142 redundancy = new float[height];
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143 for (int i = 0; i < height; i++)
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145 redundancy[i] = 0f;
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148 if (ap.av.hasHiddenColumns)
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150 omitHidden = ap.av.getSelectionAsString();
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154 // long start = System.currentTimeMillis();
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158 for (int i = 0; i < height; i++)
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160 originalColours.put(originalSequences[i],
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161 originalSequences[i].getColor());
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163 for (int j = 0; j < i; j++)
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168 if(omitHidden==null)
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170 seqi = originalSequences[i].getSequence(start, end);
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171 seqj = originalSequences[j].getSequence(start, end);
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175 seqi = omitHidden[i];
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176 seqj = omitHidden[j];
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179 pid = Comparison.PID( seqi, seqj );
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181 if(seqj.length() < seqi.length())
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182 redundancy[j] = Math.max(pid, redundancy[j]);
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184 redundancy[i] = Math.max(pid, redundancy[i]);
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189 progress.setIndeterminate(false);
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190 progress.setVisible(false);
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193 label.setText("Enter the redundancy threshold");
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194 slider.setVisible(true);
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195 applyButton.setEnabled(true);
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196 valueField.setVisible(true);
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199 // System.out.println((System.currentTimeMillis()-start));
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202 void sliderValueChanged()
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204 if(redundancy==null)
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207 float value = slider.getValue();
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209 for(int i=0; i<redundancy.length; i++)
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211 if (value > redundancy[i])
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212 originalSequences[i].setColor(java.awt.Color.white);
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214 originalSequences[i].setColor(java.awt.Color.red);
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217 PaintRefresher.Refresh(null,ap.av.alignment);
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224 * @param e DOCUMENT ME!
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226 public void applyButton_actionPerformed(ActionEvent e)
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228 historyList.push(new HistoryItem("Remove redundancy",
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229 ap.av.alignment, HistoryItem.HIDE));
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231 if ((historyList.size() == 1) ||
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232 !af.historyList.contains(historyList.firstElement()))
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234 af.addHistoryItem((HistoryItem) historyList.firstElement());
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235 af.updateEditMenuBar();
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238 Vector del = new Vector();
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240 undoButton.setEnabled(true);
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242 float value = slider.getValue();
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243 SequenceGroup sg = ap.av.getSelectionGroup();
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245 for (int i = 0; i < redundancy.length; i++)
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247 if (value <= redundancy[i])
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249 SequenceI seq = originalSequences[i];
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250 ap.av.alignment.deleteSequence(seq);
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254 sg.deleteSequence(seq, false);
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260 // This has to be done before the restoreHistoryItem method of alignFrame will
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261 // actually restore these sequences.
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262 if (del.size() > 0)
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264 for (int i = 0, j = del.size(); i < j; i++)
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266 SequenceI sq = (SequenceI) del.elementAt(i);
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267 sq.deleteChars(0, sq.getLength());
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271 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
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272 af.updateEditMenuBar();
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275 void resetColours()
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277 for(int i=0; i<originalSequences.length; i++)
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279 SequenceI seq = originalSequences[i];
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280 seq.setColor( (java.awt.Color)originalColours.get(seq));
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283 PaintRefresher.Refresh(ap.av.alignment);
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289 * @param e DOCUMENT ME!
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291 public void undoButton_actionPerformed(ActionEvent e)
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293 HistoryItem hi = (HistoryItem) historyList.pop();
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294 af.restoreHistoryItem(hi);
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296 if (historyList.size() == 0)
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298 undoButton.setEnabled(false);
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300 if (af.historyList.contains(hi))
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302 af.historyList.remove(hi);
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303 af.updateEditMenuBar();
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311 * @param e DOCUMENT ME!
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313 public void valueField_actionPerformed(ActionEvent e)
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317 int i = Integer.parseInt(valueField.getText());
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318 slider.setValue(i);
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320 catch (Exception ex)
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322 valueField.setText(slider.getValue() + "");
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