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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36 * @version $Revision$
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38 public class RedundancyPanel extends GSliderPanel
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42 Stack historyList = new Stack(); // simpler than synching with alignFrame.
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45 * Creates a new RedundancyPanel object.
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47 * @param ap DOCUMENT ME!
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48 * @param af DOCUMENT ME!
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50 public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
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54 label.setText("Enter the redundancy threshold");
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56 slider.addChangeListener(new ChangeListener()
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58 public void stateChanged(ChangeEvent evt)
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60 valueField.setText(slider.getValue() + "");
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64 slider.setMinimum(0);
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65 slider.setMaximum(100);
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66 slider.setValue(100);
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72 * @param e DOCUMENT ME!
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74 public void applyButton_actionPerformed(ActionEvent e)
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76 float threshold = slider.getValue();
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78 historyList.push(new HistoryItem("Remove redundancy",
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79 ap.av.alignment, HistoryItem.HIDE));
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81 if ((historyList.size() == 1) ||
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82 !af.historyList.contains(historyList.firstElement()))
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84 af.addHistoryItem((HistoryItem) historyList.firstElement());
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85 af.updateEditMenuBar();
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88 undoButton.setEnabled(true);
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90 SequenceGroup sg = ap.av.getSelectionGroup();
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92 if ((sg != null) && (sg.getSize() >= 1))
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94 del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
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96 for (int i = 0; i < del.size(); i++)
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98 if (sg.sequences.contains((SequenceI) del.elementAt(i)))
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100 sg.deleteSequence((SequenceI) del.elementAt(i), true);
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106 Vector s = new Vector();
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109 while (i < ap.av.alignment.getHeight())
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111 s.addElement(ap.av.alignment.getSequenceAt(i));
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115 del = ap.av.alignment.removeRedundancy(threshold, s);
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118 // This has to be done before the restoreHistoryItem method of alignFrame will
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119 // actually restore these sequences.
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120 if (del.size() > 0)
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122 for (int i = 0, j = del.size(); i < j; i++)
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124 SequenceI sq = (SequenceI) del.elementAt(i);
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125 sq.deleteChars(0, sq.getLength());
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129 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
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130 af.updateEditMenuBar();
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133 if (ap.av.getAlignment().getHeight() < 1)
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137 af.setClosed(true);
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139 catch (Exception ex)
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148 * @param e DOCUMENT ME!
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150 public void undoButton_actionPerformed(ActionEvent e)
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152 HistoryItem hi = (HistoryItem) historyList.pop();
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153 af.restoreHistoryItem(hi);
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155 if (historyList.size() == 0)
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157 undoButton.setEnabled(false);
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159 if (af.historyList.contains(hi))
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161 af.historyList.remove(hi);
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162 af.updateEditMenuBar();
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170 * @param e DOCUMENT ME!
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172 public void valueField_actionPerformed(ActionEvent e)
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176 int i = Integer.parseInt(valueField.getText());
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177 slider.setValue(i);
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179 catch (Exception ex)
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181 valueField.setText(slider.getValue() + "");
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