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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20 package jalview.appletgui;
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24 import java.awt.event.*;
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26 import jalview.datamodel.*;
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28 public class RedundancyPanel extends SliderPanel
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32 SequenceI[] oldAlignment;
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34 public RedundancyPanel(AlignmentPanel ap)
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36 super(ap, 0, false, null);
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40 label.setText("Enter the redundancy threshold");
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42 slider.addAdjustmentListener(new AdjustmentListener()
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44 public void adjustmentValueChanged(AdjustmentEvent evt)
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46 valueField.setText(slider.getValue() + "");
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50 slider.setMinimum(0);
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51 slider.setMaximum(100);
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52 slider.setValue(100);
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56 public void applyButton_actionPerformed(ActionEvent e)
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58 float threshold = slider.getValue();
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61 oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
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62 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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64 oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
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65 ap.av.alignment.getSequenceAt(i).
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69 undoButton.setEnabled(true);
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71 SequenceGroup sg = ap.av.getSelectionGroup();
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72 if (sg != null && sg.getSize() > 1)
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75 del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
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76 for (int i = 0; i < del.size(); i++)
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78 if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
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80 sg.deleteSequence( (SequenceI) del.elementAt(i), true);
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87 Vector s = new Vector();
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89 while (i < ap.av.alignment.getHeight())
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91 s.addElement(ap.av.alignment.getSequenceAt(i));
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94 del = ap.av.alignment.removeRedundancy(threshold, s);
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95 for (int j = 0; j < del.size(); j++)
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97 if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
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99 sg.deleteSequence( (SequenceI) del.elementAt(j), true);
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109 public void undoButton_actionPerformed(ActionEvent e)
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111 undoButton.setEnabled(false);
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112 ap.av.setAlignment(new Alignment(oldAlignment));
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113 oldAlignment = null;
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117 public void valueField_actionPerformed(ActionEvent e)
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121 int i = Integer.parseInt(valueField.getText());
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122 slider.setValue(i);
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124 catch (Exception ex)
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126 valueField.setText(slider.getValue() + "");
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