1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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36 protected JMenuItem fontNameMenuItem = new JMenuItem();
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37 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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38 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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39 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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40 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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41 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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42 protected JMenuItem sortIDMenuItem = new JMenuItem();
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43 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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44 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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45 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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46 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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47 protected JMenuItem PCAMenuItem = new JMenuItem();
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48 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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49 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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50 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public JLabel statusBar = new JLabel();
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53 protected JMenu saveAlignmentMenu = new JMenu();
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54 protected JMenu outputTextboxMenu = new JMenu();
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55 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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66 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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67 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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68 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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69 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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70 JMenuItem htmlMenuItem = new JMenuItem();
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71 JMenuItem schemeKeyMenuItem = new JMenuItem();
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72 JMenuItem overviewMenuItem = new JMenuItem();
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73 protected JMenuItem undoMenuItem = new JMenuItem();
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74 protected JMenuItem redoMenuItem = new JMenuItem();
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75 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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76 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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77 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem pdbTest = new JMenuItem();
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79 JMenuItem printMenuItem = new JMenuItem();
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80 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem findMenuItem = new JMenuItem();
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82 JMenu searchMenu = new JMenu();
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83 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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84 public GAlignFrame()
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89 setJMenuBar(alignFrameMenuBar);
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92 // dynamically fill save as menu with available formats
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93 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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94 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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95 saveAlignmentMenu.add( item );
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96 item.addActionListener(new java.awt.event.ActionListener()
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98 public void actionPerformed(ActionEvent e)
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100 saveAs_actionPerformed(e);
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104 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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105 item.addActionListener(new java.awt.event.ActionListener()
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107 public void actionPerformed(ActionEvent e)
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109 outputText_actionPerformed(e);
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113 outputTextboxMenu.add( item );
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119 e.printStackTrace();
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122 ButtonGroup colours = new ButtonGroup();
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123 colours.add(noColourmenuItem);
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124 colours.add(clustalColour);
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125 colours.add(zappoColour);
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126 colours.add(taylorColour);
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127 colours.add(hydrophobicityColour);
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128 colours.add(helixColour);
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129 colours.add(strandColour);
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130 colours.add(turnColour);
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131 colours.add(buriedColour);
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132 colours.add(userDefinedColour);
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133 colours.add(PIDColour);
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134 colours.add(BLOSUM62Colour);
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136 private void jbInit() throws Exception
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138 fileMenu.setMnemonic('F');
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139 fileMenu.setText("File");
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140 saveAlignmentMenu.setMnemonic('L');
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141 saveAlignmentMenu.setText("Save alignment to local file");
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142 closeMenuItem.setMnemonic('C');
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143 closeMenuItem.setText("Close");
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144 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 closeMenuItem_actionPerformed(e);
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151 editMenu.setText("Edit");
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152 fontMenu.setText("Font");
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153 viewMenu.setText("View");
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154 colourMenu.setText("Colour");
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155 calculateMenu.setText("Calculate");
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156 alignMenu.setText("Web Service");
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157 groupsMenuItem.setText("Groups");
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158 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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160 public void actionPerformed(ActionEvent e)
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162 groupsMenuItem_actionPerformed(e);
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165 selectAllSequenceMenuItem.setText("Select all sequences");
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166 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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168 public void actionPerformed(ActionEvent e)
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170 selectAllSequenceMenuItem_actionPerformed(e);
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173 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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174 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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176 public void actionPerformed(ActionEvent e)
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178 deselectAllSequenceMenuItem_actionPerformed(e);
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181 invertSequenceMenuItem.setText("Invert sequence selection");
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182 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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184 public void actionPerformed(ActionEvent e)
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186 invertSequenceMenuItem_actionPerformed(e);
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189 deselectAllColumnsMenuItem.setText("Deselect all columns");
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190 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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192 public void actionPerformed(ActionEvent e)
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194 deselectAllColumnsMenuItem_actionPerformed(e);
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197 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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198 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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200 public void actionPerformed(ActionEvent e)
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202 remove2LeftMenuItem_actionPerformed(e);
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205 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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206 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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208 public void actionPerformed(ActionEvent e)
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210 remove2RightMenuItem_actionPerformed(e);
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213 removeGappedColumnMenuItem.setText("Remove gapped columns");
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214 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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216 public void actionPerformed(ActionEvent e)
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218 removeGappedColumnMenuItem_actionPerformed(e);
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221 removeAllGapsMenuItem.setText("Remove all gaps");
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222 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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224 public void actionPerformed(ActionEvent e)
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226 removeAllGapsMenuItem_actionPerformed(e);
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229 setGapCharMenuItem.setText("Set gap character to \".\"");
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230 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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232 public void actionPerformed(ActionEvent e)
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234 setGapCharMenuItem_actionPerformed(e);
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237 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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239 public void actionPerformed(ActionEvent e)
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241 fontNameMenuItem_actionPerformed(e);
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244 fontSizeMenuItem.setText("10");
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245 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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247 public void actionPerformed(ActionEvent e)
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249 fontSizeMenuItem_actionPerformed(e);
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252 fontStyleMenuItem.setText("Plain");
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253 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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255 public void actionPerformed(ActionEvent e)
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257 fontStyleMenuItem_actionPerformed(e);
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260 viewBoxesMenuItem.setText("Boxes");
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261 viewBoxesMenuItem.setState(true);
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262 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 viewBoxesMenuItem_actionPerformed(e);
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269 viewTextMenuItem.setText("Text");
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270 viewTextMenuItem.setState(true);
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271 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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275 viewTextMenuItem_actionPerformed(e);
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278 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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279 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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281 public void actionPerformed(ActionEvent e)
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283 sortPairwiseMenuItem_actionPerformed(e);
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286 sortIDMenuItem.setText("Sort by ID");
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287 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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289 public void actionPerformed(ActionEvent e)
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291 sortIDMenuItem_actionPerformed(e);
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294 sortGroupMenuItem.setText("Sort by group");
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295 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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297 public void actionPerformed(ActionEvent e)
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299 sortGroupMenuItem_actionPerformed(e);
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302 sortTreeOrderMenuItem.setText("Sort by tree order");
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303 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 sortTreeOrderMenuItem_actionPerformed(e);
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310 removeRedundancyMenuItem.setText("Remove redundancy");
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311 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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313 public void actionPerformed(ActionEvent e)
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315 removeRedundancyMenuItem_actionPerformed(e);
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318 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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319 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 pairwiseAlignmentMenuItem_actionPerformed(e);
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326 PCAMenuItem.setText("Principal component analysis");
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327 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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329 public void actionPerformed(ActionEvent e)
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331 PCAMenuItem_actionPerformed(e);
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334 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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335 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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337 public void actionPerformed(ActionEvent e)
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339 averageDistanceTreeMenuItem_actionPerformed(e);
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342 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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343 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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345 public void actionPerformed(ActionEvent e)
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347 neighbourTreeMenuItem_actionPerformed(e);
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350 clustalAlignMenuItem.setText("Clustal alignment");
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351 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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353 public void actionPerformed(ActionEvent e)
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355 clustalAlignMenuItem_actionPerformed(e);
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358 this.getContentPane().setLayout(borderLayout1);
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359 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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360 statusBar.setBackground(Color.white);
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361 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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362 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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363 statusBar.setText("Status bar");
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364 outputTextboxMenu.setMnemonic('T');
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365 outputTextboxMenu.setText("Output alignment via textbox");
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366 clustalColour.setSelected(false);
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367 clustalColour.setText("Clustalx colours");
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368 clustalColour.addActionListener(new java.awt.event.ActionListener()
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370 public void actionPerformed(ActionEvent e)
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372 clustalColour_actionPerformed(e);
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375 zappoColour.setText("Zappo colour scheme");
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376 zappoColour.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 zappoColour_actionPerformed(e);
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383 taylorColour.setText("Taylor colour scheme");
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384 taylorColour.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 taylorColour_actionPerformed(e);
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391 hydrophobicityColour.setText("By hydrophobicity");
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392 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 hydrophobicityColour_actionPerformed(e);
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399 helixColour.setText("Helix propensity");
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400 helixColour.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 helixColour_actionPerformed(e);
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407 strandColour.setText("Strand propensity");
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408 strandColour.addActionListener(new java.awt.event.ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 strandColour_actionPerformed(e);
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415 turnColour.setText("Turn propensity");
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416 turnColour.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 turnColour_actionPerformed(e);
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423 buriedColour.setText("Buried index");
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424 buriedColour.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 buriedColour_actionPerformed(e);
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431 userDefinedColour.setText("User defined colours");
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432 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 userDefinedColour_actionPerformed(e);
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439 PIDColour.setText("Percentage Identity");
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440 PIDColour.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 PIDColour_actionPerformed(e);
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447 BLOSUM62Colour.setText("BLOSUM62 score");
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448 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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450 public void actionPerformed(ActionEvent e)
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452 BLOSUM62Colour_actionPerformed(e);
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455 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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456 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 avTreeBlosumMenuItem_actionPerformed(e);
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463 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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464 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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466 public void actionPerformed(ActionEvent e)
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468 njTreeBlosumMenuItem_actionPerformed(e);
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471 consensusGraphMenuItem.setActionCommand("");
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472 consensusGraphMenuItem.setText("Consensus graph");
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473 consensusGraphMenuItem.setState(true);
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474 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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476 public void actionPerformed(ActionEvent e)
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478 consensusGraphMenuItem_actionPerformed(e);
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481 colourTextMenuItem.setText("Colour text");
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482 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 colourTextMenuItem_actionPerformed(e);
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489 htmlMenuItem.setText("Output as HTML");
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490 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 htmlMenuItem_actionPerformed(e);
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497 schemeKeyMenuItem.setText("Colour Scheme Key");
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498 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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500 public void actionPerformed(ActionEvent e)
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502 schemeKeyMenuItem_actionPerformed(e);
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505 overviewMenuItem.setText("Overview window");
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506 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 overviewMenuItem_actionPerformed(e);
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513 undoMenuItem.setEnabled(false);
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514 undoMenuItem.setMnemonic('Z');
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515 undoMenuItem.setText("Undo");
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516 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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518 public void actionPerformed(ActionEvent e)
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520 undoMenuItem_actionPerformed(e);
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523 redoMenuItem.setEnabled(false);
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524 redoMenuItem.setMnemonic('0');
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525 redoMenuItem.setText("Redo");
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526 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 redoMenuItem_actionPerformed(e);
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533 conservationMenuItem.setText("By conservation");
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534 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 conservationMenuItem_actionPerformed(e);
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541 noColourmenuItem.setText("None");
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542 noColourmenuItem.setSelected(true);
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543 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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545 public void actionPerformed(ActionEvent e)
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547 noColourmenuItem_actionPerformed(e);
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550 wrapMenuItem.setEnabled(false);
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551 wrapMenuItem.setText("Wrap alignment");
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552 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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554 public void actionPerformed(ActionEvent e)
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556 wrapMenuItem_actionPerformed(e);
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559 pdbTest.setText("PDB Test Viewer");
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560 pdbTest.addActionListener(new java.awt.event.ActionListener()
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562 public void actionPerformed(ActionEvent e)
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564 pdbTest_actionPerformed(e);
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567 printMenuItem.setText("Print");
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568 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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570 public void actionPerformed(ActionEvent e)
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572 printMenuItem_actionPerformed(e);
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575 renderGapsMenuItem.setText("Render gaps");
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576 renderGapsMenuItem.setState(true);
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577 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 renderGapsMenuItem_actionPerformed(e);
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584 findMenuItem.setText("Find");
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585 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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587 public void actionPerformed(ActionEvent e)
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589 findMenuItem_actionPerformed(e);
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592 searchMenu.setText("Search");
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594 abovePIDThreshold.setText("Above PID threshold");
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595 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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596 public void actionPerformed(ActionEvent e) {
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597 abovePIDThreshold_actionPerformed(e);
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600 alignFrameMenuBar.add(fileMenu);
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601 alignFrameMenuBar.add(editMenu);
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602 alignFrameMenuBar.add(searchMenu);
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603 alignFrameMenuBar.add(fontMenu);
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604 alignFrameMenuBar.add(viewMenu);
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605 alignFrameMenuBar.add(colourMenu);
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606 alignFrameMenuBar.add(calculateMenu);
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607 alignFrameMenuBar.add(alignMenu);
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608 fileMenu.add(saveAlignmentMenu);
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609 fileMenu.add(outputTextboxMenu);
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610 fileMenu.add(htmlMenuItem);
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611 fileMenu.add(printMenuItem);
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612 fileMenu.addSeparator();
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613 fileMenu.add(closeMenuItem);
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614 editMenu.add(undoMenuItem);
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615 editMenu.add(redoMenuItem);
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616 editMenu.addSeparator();
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617 editMenu.add(groupsMenuItem);
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618 editMenu.addSeparator();
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619 editMenu.add(selectAllSequenceMenuItem);
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620 editMenu.add(deselectAllSequenceMenuItem);
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621 editMenu.add(invertSequenceMenuItem);
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622 editMenu.addSeparator();
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623 editMenu.add(deselectAllColumnsMenuItem);
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624 editMenu.add(remove2LeftMenuItem);
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625 editMenu.add(remove2RightMenuItem);
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626 editMenu.addSeparator();
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627 editMenu.add(removeGappedColumnMenuItem);
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628 editMenu.add(removeAllGapsMenuItem);
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629 editMenu.add(setGapCharMenuItem);
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630 searchMenu.add(findMenuItem);
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631 fontMenu.add(fontNameMenuItem);
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632 fontMenu.add(fontSizeMenuItem);
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633 fontMenu.add(fontStyleMenuItem);
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634 viewMenu.add(wrapMenuItem);
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635 viewMenu.add(viewBoxesMenuItem);
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636 viewMenu.add(viewTextMenuItem);
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637 viewMenu.add(colourTextMenuItem);
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638 viewMenu.add(renderGapsMenuItem);
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639 viewMenu.add(consensusGraphMenuItem);
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640 viewMenu.add(overviewMenuItem);
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641 colourMenu.add(noColourmenuItem);
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642 colourMenu.add(clustalColour);
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643 colourMenu.add(zappoColour);
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644 colourMenu.add(taylorColour);
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645 colourMenu.add(hydrophobicityColour);
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646 colourMenu.add(helixColour);
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647 colourMenu.add(strandColour);
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648 colourMenu.add(turnColour);
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649 colourMenu.add(buriedColour);
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650 colourMenu.add(userDefinedColour);
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651 colourMenu.add(PIDColour);
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652 colourMenu.add(BLOSUM62Colour);
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653 colourMenu.addSeparator();
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654 colourMenu.add(abovePIDThreshold);
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655 colourMenu.add(conservationMenuItem);
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656 colourMenu.addSeparator();
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657 colourMenu.add(schemeKeyMenuItem);
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658 calculateMenu.add(sortPairwiseMenuItem);
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659 calculateMenu.add(sortIDMenuItem);
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660 calculateMenu.add(sortGroupMenuItem);
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661 calculateMenu.add(sortTreeOrderMenuItem);
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662 calculateMenu.add(removeRedundancyMenuItem);
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663 calculateMenu.addSeparator();
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664 calculateMenu.add(pairwiseAlignmentMenuItem);
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665 calculateMenu.add(PCAMenuItem);
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666 calculateMenu.addSeparator();
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667 calculateMenu.add(averageDistanceTreeMenuItem);
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668 calculateMenu.add(neighbourTreeMenuItem);
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669 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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670 calculateMenu.add(njTreeBlosumMenuItem);
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671 alignMenu.add(clustalAlignMenuItem);
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672 alignMenu.add(pdbTest);
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673 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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676 protected void saveAs_actionPerformed(ActionEvent e)
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681 protected void outputText_actionPerformed(ActionEvent e)
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686 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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695 protected void closeMenuItem_actionPerformed(ActionEvent e)
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700 protected void redoMenuItem_actionPerformed(ActionEvent e)
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705 protected void undoMenuItem_actionPerformed(ActionEvent e)
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711 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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717 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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722 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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727 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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733 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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738 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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743 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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748 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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753 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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758 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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764 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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769 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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774 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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779 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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785 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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790 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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796 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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803 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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808 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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813 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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818 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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823 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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828 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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833 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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838 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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843 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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848 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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853 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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859 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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864 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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871 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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879 protected void clustalColour_actionPerformed(ActionEvent e)
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884 protected void zappoColour_actionPerformed(ActionEvent e)
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889 protected void taylorColour_actionPerformed(ActionEvent e)
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895 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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900 protected void helixColour_actionPerformed(ActionEvent e)
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905 protected void strandColour_actionPerformed(ActionEvent e)
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910 protected void turnColour_actionPerformed(ActionEvent e)
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915 protected void buriedColour_actionPerformed(ActionEvent e)
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922 protected void userDefinedColour_actionPerformed(ActionEvent e)
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927 protected void PIDColour_actionPerformed(ActionEvent e)
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932 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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937 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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942 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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947 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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952 protected void pdbTest_actionPerformed(ActionEvent e)
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957 protected void printMenuItem_actionPerformed(ActionEvent e)
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962 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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967 protected void findMenuItem_actionPerformed(ActionEvent e)
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973 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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