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 viewMenu = new JMenu();
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22 protected JMenu colourMenu = new JMenu();
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23 protected JMenu calculateMenu = new JMenu();
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24 protected JMenu alignMenu = new JMenu();
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25 protected JMenuItem groupsMenuItem = new JMenuItem();
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26 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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27 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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30 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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31 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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32 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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33 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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34 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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35 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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36 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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37 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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38 protected JMenuItem sortIDMenuItem = new JMenuItem();
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39 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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40 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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41 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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42 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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43 protected JMenuItem PCAMenuItem = new JMenuItem();
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44 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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45 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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46 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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47 BorderLayout borderLayout1 = new BorderLayout();
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48 public JLabel statusBar = new JLabel();
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49 protected JMenu saveAlignmentMenu = new JMenu();
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50 protected JMenu outputTextboxMenu = new JMenu();
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51 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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62 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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63 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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64 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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65 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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66 JMenuItem htmlMenuItem = new JMenuItem();
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67 JMenuItem overviewMenuItem = new JMenuItem();
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68 protected JMenuItem undoMenuItem = new JMenuItem();
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69 protected JMenuItem redoMenuItem = new JMenuItem();
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70 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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71 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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72 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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73 JMenuItem printMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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75 JMenuItem findMenuItem = new JMenuItem();
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76 JMenu searchMenu = new JMenu();
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77 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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78 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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79 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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80 JMenuItem deleteGroups = new JMenuItem();
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81 JMenuItem delete = new JMenuItem();
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82 JMenuItem copy = new JMenuItem();
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83 JMenuItem cut = new JMenuItem();
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84 JMenu jMenu1 = new JMenu();
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85 JMenuItem pasteNew = new JMenuItem();
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86 JMenuItem pasteThis = new JMenuItem();
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87 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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88 JMenuItem createJPG = new JMenuItem();
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89 protected JMenuItem font = new JMenuItem();
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90 public GAlignFrame()
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97 setJMenuBar(alignFrameMenuBar);
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100 // dynamically fill save as menu with available formats
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101 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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102 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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103 saveAlignmentMenu.add( item );
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104 item.addActionListener(new java.awt.event.ActionListener()
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106 public void actionPerformed(ActionEvent e)
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108 saveAs_actionPerformed(e);
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112 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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113 item.addActionListener(new java.awt.event.ActionListener()
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115 public void actionPerformed(ActionEvent e)
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117 outputText_actionPerformed(e);
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121 outputTextboxMenu.add( item );
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127 e.printStackTrace();
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130 ButtonGroup colours = new ButtonGroup();
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131 colours.add(noColourmenuItem);
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132 colours.add(clustalColour);
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133 colours.add(zappoColour);
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134 colours.add(taylorColour);
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135 colours.add(hydrophobicityColour);
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136 colours.add(helixColour);
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137 colours.add(strandColour);
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138 colours.add(turnColour);
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139 colours.add(buriedColour);
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140 colours.add(userDefinedColour);
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141 colours.add(PIDColour);
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142 colours.add(BLOSUM62Colour);
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143 colours.add(nucleotideColour);
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145 private void jbInit() throws Exception
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147 fileMenu.setMnemonic('F');
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148 fileMenu.setText("File");
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149 saveAlignmentMenu.setMnemonic('L');
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150 saveAlignmentMenu.setText("Save alignment to local file");
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151 closeMenuItem.setMnemonic('C');
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152 closeMenuItem.setText("Close");
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153 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 closeMenuItem_actionPerformed(e);
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160 editMenu.setText("Edit");
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161 viewMenu.setText("View");
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162 colourMenu.setText("Colour");
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163 calculateMenu.setText("Calculate");
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164 alignMenu.setText("Web Service");
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165 groupsMenuItem.setVisible(false);
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166 groupsMenuItem.setText("Groups");
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167 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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169 public void actionPerformed(ActionEvent e)
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171 groupsMenuItem_actionPerformed(e);
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174 selectAllSequenceMenuItem.setText("Select all");
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175 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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177 public void actionPerformed(ActionEvent e)
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179 selectAllSequenceMenuItem_actionPerformed(e);
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182 deselectAllSequenceMenuItem.setText("Clear selection");
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183 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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185 public void actionPerformed(ActionEvent e)
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187 deselectAllSequenceMenuItem_actionPerformed(e);
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190 invertSequenceMenuItem.setText("Invert sequence selection");
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191 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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193 public void actionPerformed(ActionEvent e)
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195 invertSequenceMenuItem_actionPerformed(e);
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198 deselectAllColumnsMenuItem.setText("Deselect all columns");
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199 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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201 public void actionPerformed(ActionEvent e)
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203 deselectAllColumnsMenuItem_actionPerformed(e);
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206 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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207 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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209 public void actionPerformed(ActionEvent e)
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211 remove2LeftMenuItem_actionPerformed(e);
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214 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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215 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 remove2RightMenuItem_actionPerformed(e);
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222 removeGappedColumnMenuItem.setText("Remove gapped columns");
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223 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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225 public void actionPerformed(ActionEvent e)
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227 removeGappedColumnMenuItem_actionPerformed(e);
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230 removeAllGapsMenuItem.setText("Remove all gaps");
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231 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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233 public void actionPerformed(ActionEvent e)
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235 removeAllGapsMenuItem_actionPerformed(e);
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238 setGapCharMenuItem.setText("Set gap character to \".\"");
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239 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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241 public void actionPerformed(ActionEvent e)
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243 setGapCharMenuItem_actionPerformed(e);
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246 viewBoxesMenuItem.setText("Boxes");
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247 viewBoxesMenuItem.setState(true);
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248 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 viewBoxesMenuItem_actionPerformed(e);
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255 viewTextMenuItem.setText("Text");
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256 viewTextMenuItem.setState(true);
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257 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 viewTextMenuItem_actionPerformed(e);
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264 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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265 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 sortPairwiseMenuItem_actionPerformed(e);
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272 sortIDMenuItem.setText("Sort by ID");
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273 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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275 public void actionPerformed(ActionEvent e)
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277 sortIDMenuItem_actionPerformed(e);
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280 sortGroupMenuItem.setText("Sort by group");
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281 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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283 public void actionPerformed(ActionEvent e)
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285 sortGroupMenuItem_actionPerformed(e);
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288 sortTreeOrderMenuItem.setText("Sort by tree order");
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289 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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291 public void actionPerformed(ActionEvent e)
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293 sortTreeOrderMenuItem_actionPerformed(e);
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296 removeRedundancyMenuItem.setText("Remove redundancy");
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297 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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299 public void actionPerformed(ActionEvent e)
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301 removeRedundancyMenuItem_actionPerformed(e);
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304 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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305 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 pairwiseAlignmentMenuItem_actionPerformed(e);
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312 PCAMenuItem.setText("Principal component analysis");
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313 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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315 public void actionPerformed(ActionEvent e)
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317 PCAMenuItem_actionPerformed(e);
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320 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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321 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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323 public void actionPerformed(ActionEvent e)
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325 averageDistanceTreeMenuItem_actionPerformed(e);
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328 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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329 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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331 public void actionPerformed(ActionEvent e)
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333 neighbourTreeMenuItem_actionPerformed(e);
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336 clustalAlignMenuItem.setText("Clustal alignment");
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337 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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339 public void actionPerformed(ActionEvent e)
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341 clustalAlignMenuItem_actionPerformed(e);
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344 this.getContentPane().setLayout(borderLayout1);
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345 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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346 statusBar.setBackground(Color.white);
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347 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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348 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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349 statusBar.setText("Status bar");
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350 outputTextboxMenu.setMnemonic('T');
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351 outputTextboxMenu.setText("Output alignment via textbox");
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352 clustalColour.setSelected(false);
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353 clustalColour.setText("Clustalx colours");
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354 clustalColour.addActionListener(new java.awt.event.ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 clustalColour_actionPerformed(e);
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361 zappoColour.setText("Zappo colour scheme");
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362 zappoColour.addActionListener(new java.awt.event.ActionListener()
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364 public void actionPerformed(ActionEvent e)
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366 zappoColour_actionPerformed(e);
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369 taylorColour.setText("Taylor colour scheme");
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370 taylorColour.addActionListener(new java.awt.event.ActionListener()
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372 public void actionPerformed(ActionEvent e)
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374 taylorColour_actionPerformed(e);
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377 hydrophobicityColour.setText("By hydrophobicity");
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378 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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380 public void actionPerformed(ActionEvent e)
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382 hydrophobicityColour_actionPerformed(e);
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385 helixColour.setText("Helix propensity");
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386 helixColour.addActionListener(new java.awt.event.ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 helixColour_actionPerformed(e);
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393 strandColour.setText("Strand propensity");
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394 strandColour.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 strandColour_actionPerformed(e);
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401 turnColour.setText("Turn propensity");
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402 turnColour.addActionListener(new java.awt.event.ActionListener()
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404 public void actionPerformed(ActionEvent e)
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406 turnColour_actionPerformed(e);
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409 buriedColour.setText("Buried index");
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410 buriedColour.addActionListener(new java.awt.event.ActionListener()
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412 public void actionPerformed(ActionEvent e)
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414 buriedColour_actionPerformed(e);
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417 userDefinedColour.setText("User defined colours");
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418 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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420 public void actionPerformed(ActionEvent e)
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422 userDefinedColour_actionPerformed(e);
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425 PIDColour.setText("Percentage Identity");
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426 PIDColour.addActionListener(new java.awt.event.ActionListener()
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428 public void actionPerformed(ActionEvent e)
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430 PIDColour_actionPerformed(e);
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433 BLOSUM62Colour.setText("BLOSUM62 score");
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434 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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436 public void actionPerformed(ActionEvent e)
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438 BLOSUM62Colour_actionPerformed(e);
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441 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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442 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 avTreeBlosumMenuItem_actionPerformed(e);
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449 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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450 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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452 public void actionPerformed(ActionEvent e)
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454 njTreeBlosumMenuItem_actionPerformed(e);
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457 consensusGraphMenuItem.setActionCommand("");
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458 consensusGraphMenuItem.setText("Consensus graph");
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459 consensusGraphMenuItem.setState(true);
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460 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 consensusGraphMenuItem_actionPerformed(e);
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467 colourTextMenuItem.setText("Colour text");
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468 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 colourTextMenuItem_actionPerformed(e);
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475 htmlMenuItem.setText("Output as HTML");
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476 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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478 public void actionPerformed(ActionEvent e)
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480 htmlMenuItem_actionPerformed(e);
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483 overviewMenuItem.setText("Overview window");
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484 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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486 public void actionPerformed(ActionEvent e)
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488 overviewMenuItem_actionPerformed(e);
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491 undoMenuItem.setEnabled(false);
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492 undoMenuItem.setMnemonic('Z');
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493 undoMenuItem.setText("Undo");
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494 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 undoMenuItem_actionPerformed(e);
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501 redoMenuItem.setEnabled(false);
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502 redoMenuItem.setMnemonic('0');
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503 redoMenuItem.setText("Redo");
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504 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 redoMenuItem_actionPerformed(e);
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511 conservationMenuItem.setText("By conservation");
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512 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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514 public void actionPerformed(ActionEvent e)
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516 conservationMenuItem_actionPerformed(e);
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519 noColourmenuItem.setText("None");
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520 noColourmenuItem.setSelected(true);
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521 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 noColourmenuItem_actionPerformed(e);
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528 wrapMenuItem.setText("Wrap alignment");
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529 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 wrapMenuItem_actionPerformed(e);
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536 printMenuItem.setText("Print");
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537 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 printMenuItem_actionPerformed(e);
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544 renderGapsMenuItem.setText("Render gaps");
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545 renderGapsMenuItem.setState(true);
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546 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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548 public void actionPerformed(ActionEvent e)
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550 renderGapsMenuItem_actionPerformed(e);
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553 findMenuItem.setText("Find");
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554 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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556 public void actionPerformed(ActionEvent e)
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558 findMenuItem_actionPerformed(e);
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561 searchMenu.setText("Search");
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563 abovePIDThreshold.setText("Above PID threshold");
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564 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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565 public void actionPerformed(ActionEvent e) {
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566 abovePIDThreshold_actionPerformed(e);
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569 sequenceFeatures.setText("Sequence Features");
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570 sequenceFeatures.addActionListener(new ActionListener()
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572 public void actionPerformed(ActionEvent actionEvent)
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574 sequenceFeatures_actionPerformed(actionEvent);
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577 nucleotideColour.setText("Nucleotide colours");
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578 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 nucleotideColour_actionPerformed(e);
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585 deleteGroups.setSelected(false);
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586 deleteGroups.setText("Delete all groups");
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587 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 deleteGroups_actionPerformed(e);
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594 copy.setText("Copy");
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595 copy.setMnemonic(KeyEvent.VK_C);
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597 copy.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 copy_actionPerformed(e);
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604 cut.setText("Cut");
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605 cut.setMnemonic(KeyEvent.VK_X);
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606 cut.addActionListener(new java.awt.event.ActionListener()
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608 public void actionPerformed(ActionEvent e)
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610 cut_actionPerformed(e);
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613 delete.setText("Delete");
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614 delete.addActionListener(new java.awt.event.ActionListener()
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616 public void actionPerformed(ActionEvent e)
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618 delete_actionPerformed(e);
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621 jMenu1.setMnemonic('V');
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622 jMenu1.setText("Paste");
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623 pasteNew.setText("to new alignment");
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624 pasteNew.addActionListener(new java.awt.event.ActionListener()
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626 public void actionPerformed(ActionEvent e)
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628 pasteNew_actionPerformed(e);
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631 pasteThis.setText("add to this alignment");
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632 pasteThis.addActionListener(new java.awt.event.ActionListener()
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634 public void actionPerformed(ActionEvent e)
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636 pasteThis_actionPerformed(e);
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639 applyToAllGroups.setText("Apply colour to all groups");
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640 applyToAllGroups.setState(true);
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641 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 applyToAllGroups_actionPerformed(e);
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648 createJPG.addActionListener(new java.awt.event.ActionListener()
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650 public void actionPerformed(ActionEvent e)
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652 createJPG_actionPerformed(e);
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655 createJPG.setText("Save as JPG Image");
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656 font.setText("Change Font");
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657 font.addActionListener(new java.awt.event.ActionListener()
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659 public void actionPerformed(ActionEvent e)
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661 font_actionPerformed(e);
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664 alignFrameMenuBar.add(fileMenu);
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665 alignFrameMenuBar.add(editMenu);
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666 alignFrameMenuBar.add(searchMenu);
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667 alignFrameMenuBar.add(viewMenu);
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668 alignFrameMenuBar.add(colourMenu);
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669 alignFrameMenuBar.add(calculateMenu);
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670 alignFrameMenuBar.add(alignMenu);
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671 fileMenu.add(saveAlignmentMenu);
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672 fileMenu.add(outputTextboxMenu);
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673 fileMenu.add(htmlMenuItem);
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674 fileMenu.add(createJPG);
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675 fileMenu.add(printMenuItem);
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676 fileMenu.addSeparator();
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677 fileMenu.add(closeMenuItem);
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678 editMenu.add(copy);
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679 editMenu.add(jMenu1);
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681 editMenu.add(delete);
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682 editMenu.addSeparator();
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683 editMenu.add(undoMenuItem);
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684 editMenu.add(redoMenuItem);
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685 editMenu.addSeparator();
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686 editMenu.add(deselectAllSequenceMenuItem);
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687 editMenu.add(selectAllSequenceMenuItem);
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688 editMenu.add(invertSequenceMenuItem);
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689 editMenu.add(deleteGroups);
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690 editMenu.add(groupsMenuItem);
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691 editMenu.addSeparator();
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692 editMenu.add(deselectAllColumnsMenuItem);
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693 editMenu.add(remove2LeftMenuItem);
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694 editMenu.add(remove2RightMenuItem);
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695 editMenu.addSeparator();
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696 editMenu.add(removeGappedColumnMenuItem);
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697 editMenu.add(removeAllGapsMenuItem);
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698 editMenu.add(setGapCharMenuItem);
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699 searchMenu.add(findMenuItem);
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700 viewMenu.add(font);
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701 viewMenu.add(wrapMenuItem);
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702 viewMenu.add(viewBoxesMenuItem);
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703 viewMenu.add(viewTextMenuItem);
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704 viewMenu.add(colourTextMenuItem);
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705 viewMenu.add(renderGapsMenuItem);
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706 viewMenu.add(consensusGraphMenuItem);
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707 viewMenu.add(overviewMenuItem);
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708 viewMenu.add(sequenceFeatures);
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709 colourMenu.add(applyToAllGroups);
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710 colourMenu.add(noColourmenuItem);
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711 colourMenu.add(clustalColour);
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712 colourMenu.add(zappoColour);
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713 colourMenu.add(taylorColour);
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714 colourMenu.add(hydrophobicityColour);
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715 colourMenu.add(helixColour);
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716 colourMenu.add(strandColour);
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717 colourMenu.add(turnColour);
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718 colourMenu.add(buriedColour);
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719 colourMenu.add(nucleotideColour);
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720 colourMenu.add(userDefinedColour);
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721 colourMenu.add(PIDColour);
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722 colourMenu.add(BLOSUM62Colour);
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723 colourMenu.addSeparator();
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724 colourMenu.add(abovePIDThreshold);
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725 colourMenu.add(conservationMenuItem);
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726 calculateMenu.add(sortPairwiseMenuItem);
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727 calculateMenu.add(sortIDMenuItem);
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728 calculateMenu.add(sortGroupMenuItem);
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729 calculateMenu.add(sortTreeOrderMenuItem);
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730 calculateMenu.add(removeRedundancyMenuItem);
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731 calculateMenu.addSeparator();
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732 calculateMenu.add(pairwiseAlignmentMenuItem);
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733 calculateMenu.add(PCAMenuItem);
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734 calculateMenu.addSeparator();
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735 calculateMenu.add(averageDistanceTreeMenuItem);
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736 calculateMenu.add(neighbourTreeMenuItem);
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737 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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738 calculateMenu.add(njTreeBlosumMenuItem);
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739 alignMenu.add(clustalAlignMenuItem);
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740 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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741 jMenu1.add(pasteNew);
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742 jMenu1.add(pasteThis);
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745 protected void saveAs_actionPerformed(ActionEvent e)
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750 protected void outputText_actionPerformed(ActionEvent e)
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755 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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764 protected void closeMenuItem_actionPerformed(ActionEvent e)
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769 protected void redoMenuItem_actionPerformed(ActionEvent e)
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774 protected void undoMenuItem_actionPerformed(ActionEvent e)
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780 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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786 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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791 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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796 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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802 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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807 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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812 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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817 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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822 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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827 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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836 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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842 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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847 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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853 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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860 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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865 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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870 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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875 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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880 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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885 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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890 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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895 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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900 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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905 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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910 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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916 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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921 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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928 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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936 protected void clustalColour_actionPerformed(ActionEvent e)
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941 protected void zappoColour_actionPerformed(ActionEvent e)
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946 protected void taylorColour_actionPerformed(ActionEvent e)
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952 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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957 protected void helixColour_actionPerformed(ActionEvent e)
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962 protected void strandColour_actionPerformed(ActionEvent e)
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967 protected void turnColour_actionPerformed(ActionEvent e)
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972 protected void buriedColour_actionPerformed(ActionEvent e)
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979 protected void userDefinedColour_actionPerformed(ActionEvent e)
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984 protected void PIDColour_actionPerformed(ActionEvent e)
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989 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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995 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1000 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1006 protected void printMenuItem_actionPerformed(ActionEvent e)
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1011 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1016 protected void findMenuItem_actionPerformed(ActionEvent e)
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1022 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1026 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1031 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1036 protected void deleteGroups_actionPerformed(ActionEvent e)
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1041 protected void copy_actionPerformed(ActionEvent e)
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1047 protected void cut_actionPerformed(ActionEvent e)
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1052 protected void delete_actionPerformed(ActionEvent e)
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1057 protected void pasteNew_actionPerformed(ActionEvent e)
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1062 protected void pasteThis_actionPerformed(ActionEvent e)
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1067 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1072 protected void createJPG_actionPerformed(ActionEvent e)
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1077 protected void font_actionPerformed(ActionEvent e)
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