2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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20 package jalview.appletgui;
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24 import java.awt.event.*;
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28 import jalview.datamodel.*;
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29 import jalview.appletgui.PaintRefresher;
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30 import jalview.commands.*;
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32 public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener
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36 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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37 float [] redundancy;
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38 SequenceI [] originalSequences;
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40 Vector redundantSeqs;
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42 public RedundancyPanel(AlignmentPanel ap)
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44 super(ap, 0, false, null);
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46 redundantSeqs = new Vector();
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48 undoButton.setVisible(true);
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49 applyButton.setVisible(true);
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50 allGroupsCheck.setVisible(false);
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52 label.setText("Enter the redundancy threshold");
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53 valueField.setText("100");
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55 slider.setVisibleAmount(1);
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56 slider.setMinimum(0);
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57 slider.setMaximum(100+slider.getVisibleAmount());
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58 slider.setValue(100);
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60 slider.addAdjustmentListener(new AdjustmentListener()
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62 public void adjustmentValueChanged(AdjustmentEvent evt)
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64 valueField.setText(slider.getValue() + "");
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65 sliderValueChanged();
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69 frame = new Frame();
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71 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
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74 frame.addWindowListener(this);
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76 Thread worker = new Thread(this);
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80 * This is a copy of remove redundancy in jalivew.datamodel.Alignment
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81 * except we dont want to remove redundancy, just calculate once
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82 * so we can use the slider to dynamically hide redundant sequences
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84 * @param threshold DOCUMENT ME!
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85 * @param sel DOCUMENT ME!
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87 * @return DOCUMENT ME!
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91 label.setText("Calculating....");
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93 slider.setVisible(false);
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94 applyButton.setEnabled(false);
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95 valueField.setVisible(false);
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99 String[] omitHidden = null;
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101 SequenceGroup sg = ap.av.getSelectionGroup();
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106 if ( (sg != null) && (sg.getSize(false) >= 1))
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108 originalSequences = sg.getSequencesInOrder(ap.av.alignment);
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109 start = sg.getStartRes();
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110 end = sg.getEndRes();
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114 originalSequences = ap.av.alignment.getSequencesArray();
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116 end = ap.av.alignment.getWidth();
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119 height = originalSequences.length;
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121 redundancy = new float[height];
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122 for (int i = 0; i < height; i++)
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124 redundancy[i] = 0f;
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127 // if (ap.av.hasHiddenColumns)
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129 // omitHidden = ap.av.getSelectionAsString();
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133 // long start = System.currentTimeMillis();
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137 for (int i = 0; i < height; i++)
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139 for (int j = 0; j < i; j++)
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144 if(omitHidden==null)
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146 seqi = originalSequences[i].getSequence(start, end);
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147 seqj = originalSequences[j].getSequence(start, end);
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151 seqi = omitHidden[i];
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152 seqj = omitHidden[j];
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155 pid = jalview.util.Comparison.PID( seqi, seqj );
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157 if(seqj.length() < seqi.length())
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158 redundancy[j] = Math.max(pid, redundancy[j]);
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160 redundancy[i] = Math.max(pid, redundancy[i]);
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166 label.setText("Enter the redundancy threshold");
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167 slider.setVisible(true);
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168 applyButton.setEnabled(true);
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169 valueField.setVisible(true);
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172 // System.out.println("blob done "+ (System.currentTimeMillis()-start));
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175 void sliderValueChanged()
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177 if(redundancy==null)
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180 float value = slider.getValue();
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182 for(int i=0; i<redundancy.length; i++)
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184 if (value > redundancy[i])
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185 redundantSeqs.removeElement(originalSequences[i]);
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186 else if(!redundantSeqs.contains(originalSequences[i]))
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187 redundantSeqs.addElement(originalSequences[i]);
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190 ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
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191 PaintRefresher.Refresh(this,
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192 ap.av.getSequenceSetId(),
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197 public void applyButton_actionPerformed()
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198 { Vector del = new Vector();
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200 undoButton.setEnabled(true);
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202 float value = slider.getValue();
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203 SequenceGroup sg = ap.av.getSelectionGroup();
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205 for (int i = 0; i < redundancy.length; i++)
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207 if (value <= redundancy[i])
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209 del.addElement(originalSequences[i]);
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213 // This has to be done before the restoreHistoryItem method of alignFrame will
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214 // actually restore these sequences.
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215 if (del.size() > 0)
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217 SequenceI [] deleted = new SequenceI[del.size()];
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220 for (int i = 0; i < del.size(); i++)
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222 deleted[i] = (SequenceI)del.elementAt(i);
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223 if(deleted[i].getLength()>width)
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224 width = deleted[i].getLength();
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227 EditCommand cut = new EditCommand("Remove Redundancy",
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228 EditCommand.CUT, deleted,0,width,ap.av.alignment);
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230 for (int i = 0; i < del.size(); i++)
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232 ap.av.alignment.deleteSequence( deleted[i] );
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233 PaintRefresher.Refresh(this,
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234 ap.av.getSequenceSetId(),
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239 sg.deleteSequence(deleted[i], false);
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243 historyList.push(cut);
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245 ap.alignFrame.addHistoryItem(cut);
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247 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
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252 public void undoButton_actionPerformed()
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254 CommandI command = (CommandI) historyList.pop();
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255 command.undoCommand();
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257 if (ap.av.historyList.contains(command))
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259 ap.av.historyList.removeElement(command);
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260 ap.alignFrame.updateEditMenuBar();
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265 if (historyList.size() == 0)
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267 undoButton.setEnabled(false);
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271 public void valueField_actionPerformed(ActionEvent e)
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275 int i = Integer.parseInt(valueField.getText());
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276 slider.setValue(i);
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278 catch (Exception ex)
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280 valueField.setText(slider.getValue() + "");
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285 public void windowOpened(WindowEvent evt)
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288 public void windowClosing(WindowEvent evt)
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290 ap.idPanel.idCanvas.setHighlighted(null);
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293 public void windowClosed(WindowEvent evt)
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296 public void windowActivated(WindowEvent evt)
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298 public void windowDeactivated(WindowEvent evt)
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300 public void windowIconified(WindowEvent evt)
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302 public void windowDeiconified(WindowEvent evt)
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