3 import jalview.jbgui.*;
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4 import jalview.datamodel.*;
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5 import java.awt.event.*;
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7 import javax.swing.event.*;
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9 public class RedundancyPanel
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10 extends GSliderPanel
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14 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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16 public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
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20 label.setText("Enter the redundancy threshold");
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22 slider.addChangeListener(new ChangeListener()
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24 public void stateChanged(ChangeEvent evt)
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26 valueField.setText(slider.getValue() + "");
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30 slider.setMinimum(0);
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31 slider.setMaximum(100);
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32 slider.setValue(100);
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36 public void applyButton_actionPerformed(ActionEvent e)
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38 float threshold = slider.getValue();
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40 historyList.push(new HistoryItem("Remove redundancy (" + threshold + "%)",
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41 ap.av.alignment, HistoryItem.HIDE));
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43 undoButton.setEnabled(true);
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44 SequenceGroup sg = ap.av.getSelectionGroup();
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45 if (sg != null && sg.getSize() >= 1)
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48 del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
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49 for (int i = 0; i < del.size(); i++)
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51 if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
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53 sg.deleteSequence( (SequenceI) del.elementAt(i));
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60 Vector s = new Vector();
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62 while (i < ap.av.alignment.getHeight())
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64 s.addElement(ap.av.alignment.getSequenceAt(i));
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67 del = ap.av.alignment.removeRedundancy(threshold, s);
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70 // This has to be done before the restoreHistoryItem method of alignFrame will
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71 // actually restore these sequences.
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74 for (int i=0,j=del.size(); i<j; i++) {
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75 SequenceI sq = (SequenceI) del.elementAt(i);
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76 sq.deleteChars(0,sq.getLength());
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79 ap.av.firePropertyChange("alignment", null,
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80 ap.av.getAlignment().getSequences());
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81 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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82 if (ap.av.getAlignment().getHeight() < 1)
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88 catch (Exception ex)
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91 ap.av.updateConservation();
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92 ap.av.updateConsensus();
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93 af.updateEditMenuBar();
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98 public void undoButton_actionPerformed(ActionEvent e)
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100 HistoryItem hi = (HistoryItem)historyList.pop();
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101 af.restoreHistoryItem(hi);
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102 if (historyList.size()==0)
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103 undoButton.setEnabled(false);
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106 public void valueField_actionPerformed(ActionEvent e)
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110 int i = Integer.parseInt(valueField.getText());
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111 slider.setValue(i);
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113 catch (Exception ex)
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115 valueField.setText(slider.getValue() + "");
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