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 createPNG = new JMenuItem();
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89 protected JMenuItem font = new JMenuItem();
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90 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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91 JMenuItem epsFile = new JMenuItem();
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92 public GAlignFrame()
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99 setJMenuBar(alignFrameMenuBar);
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102 // dynamically fill save as menu with available formats
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103 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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104 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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105 saveAlignmentMenu.add( item );
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106 item.addActionListener(new java.awt.event.ActionListener()
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108 public void actionPerformed(ActionEvent e)
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110 saveAs_actionPerformed(e);
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114 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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115 item.addActionListener(new java.awt.event.ActionListener()
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117 public void actionPerformed(ActionEvent e)
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119 outputText_actionPerformed(e);
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123 outputTextboxMenu.add( item );
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129 e.printStackTrace();
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132 ButtonGroup colours = new ButtonGroup();
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133 colours.add(noColourmenuItem);
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134 colours.add(clustalColour);
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135 colours.add(zappoColour);
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136 colours.add(taylorColour);
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137 colours.add(hydrophobicityColour);
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138 colours.add(helixColour);
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139 colours.add(strandColour);
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140 colours.add(turnColour);
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141 colours.add(buriedColour);
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142 colours.add(userDefinedColour);
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143 colours.add(PIDColour);
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144 colours.add(BLOSUM62Colour);
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145 colours.add(nucleotideColour);
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147 private void jbInit() throws Exception
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149 fileMenu.setMnemonic('F');
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150 fileMenu.setText("File");
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151 saveAlignmentMenu.setMnemonic('L');
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152 saveAlignmentMenu.setText("Save alignment to local file");
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153 closeMenuItem.setMnemonic('C');
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154 closeMenuItem.setText("Close");
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155 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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157 public void actionPerformed(ActionEvent e)
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159 closeMenuItem_actionPerformed(e);
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162 editMenu.setText("Edit");
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163 viewMenu.setText("View");
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164 colourMenu.setText("Colour");
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165 calculateMenu.setText("Calculate");
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166 alignMenu.setText("Web Service");
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167 groupsMenuItem.setVisible(false);
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168 groupsMenuItem.setText("Groups");
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169 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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171 public void actionPerformed(ActionEvent e)
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173 groupsMenuItem_actionPerformed(e);
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176 selectAllSequenceMenuItem.setText("Select all");
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177 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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179 public void actionPerformed(ActionEvent e)
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181 selectAllSequenceMenuItem_actionPerformed(e);
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184 deselectAllSequenceMenuItem.setText("Clear selection");
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185 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 deselectAllSequenceMenuItem_actionPerformed(e);
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192 invertSequenceMenuItem.setText("Invert sequence selection");
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193 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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195 public void actionPerformed(ActionEvent e)
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197 invertSequenceMenuItem_actionPerformed(e);
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200 deselectAllColumnsMenuItem.setText("Deselect all columns");
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201 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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203 public void actionPerformed(ActionEvent e)
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205 deselectAllColumnsMenuItem_actionPerformed(e);
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208 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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209 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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211 public void actionPerformed(ActionEvent e)
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213 remove2LeftMenuItem_actionPerformed(e);
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216 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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217 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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219 public void actionPerformed(ActionEvent e)
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221 remove2RightMenuItem_actionPerformed(e);
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224 removeGappedColumnMenuItem.setText("Remove gapped columns");
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225 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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227 public void actionPerformed(ActionEvent e)
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229 removeGappedColumnMenuItem_actionPerformed(e);
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232 removeAllGapsMenuItem.setText("Remove all gaps");
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233 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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235 public void actionPerformed(ActionEvent e)
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237 removeAllGapsMenuItem_actionPerformed(e);
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240 setGapCharMenuItem.setText("Set gap character to \".\"");
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241 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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243 public void actionPerformed(ActionEvent e)
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245 setGapCharMenuItem_actionPerformed(e);
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248 viewBoxesMenuItem.setText("Boxes");
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249 viewBoxesMenuItem.setState(true);
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250 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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252 public void actionPerformed(ActionEvent e)
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254 viewBoxesMenuItem_actionPerformed(e);
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257 viewTextMenuItem.setText("Text");
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258 viewTextMenuItem.setState(true);
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259 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 viewTextMenuItem_actionPerformed(e);
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266 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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267 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 sortPairwiseMenuItem_actionPerformed(e);
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274 sortIDMenuItem.setText("Sort by ID");
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275 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 sortIDMenuItem_actionPerformed(e);
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282 sortGroupMenuItem.setText("Sort by group");
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283 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 sortGroupMenuItem_actionPerformed(e);
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290 sortTreeOrderMenuItem.setText("Sort by tree order");
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291 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 sortTreeOrderMenuItem_actionPerformed(e);
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298 removeRedundancyMenuItem.setText("Remove redundancy");
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299 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 removeRedundancyMenuItem_actionPerformed(e);
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306 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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307 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 pairwiseAlignmentMenuItem_actionPerformed(e);
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314 PCAMenuItem.setText("Principal component analysis");
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315 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 PCAMenuItem_actionPerformed(e);
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322 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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323 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 averageDistanceTreeMenuItem_actionPerformed(e);
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330 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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331 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 neighbourTreeMenuItem_actionPerformed(e);
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338 clustalAlignMenuItem.setText("Clustal alignment");
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339 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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341 public void actionPerformed(ActionEvent e)
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343 clustalAlignMenuItem_actionPerformed(e);
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346 this.getContentPane().setLayout(borderLayout1);
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347 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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348 statusBar.setBackground(Color.white);
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349 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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350 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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351 statusBar.setText("Status bar");
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352 outputTextboxMenu.setMnemonic('T');
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353 outputTextboxMenu.setText("Output alignment via textbox");
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354 clustalColour.setSelected(false);
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355 clustalColour.setText("Clustalx colours");
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356 clustalColour.addActionListener(new java.awt.event.ActionListener()
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358 public void actionPerformed(ActionEvent e)
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360 clustalColour_actionPerformed(e);
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363 zappoColour.setText("Zappo colour scheme");
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364 zappoColour.addActionListener(new java.awt.event.ActionListener()
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366 public void actionPerformed(ActionEvent e)
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368 zappoColour_actionPerformed(e);
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371 taylorColour.setText("Taylor colour scheme");
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372 taylorColour.addActionListener(new java.awt.event.ActionListener()
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374 public void actionPerformed(ActionEvent e)
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376 taylorColour_actionPerformed(e);
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379 hydrophobicityColour.setText("By hydrophobicity");
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380 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 hydrophobicityColour_actionPerformed(e);
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387 helixColour.setText("Helix propensity");
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388 helixColour.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 helixColour_actionPerformed(e);
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395 strandColour.setText("Strand propensity");
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396 strandColour.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 strandColour_actionPerformed(e);
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403 turnColour.setText("Turn propensity");
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404 turnColour.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 turnColour_actionPerformed(e);
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411 buriedColour.setText("Buried index");
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412 buriedColour.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 buriedColour_actionPerformed(e);
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419 userDefinedColour.setText("User defined colours");
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420 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 userDefinedColour_actionPerformed(e);
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427 PIDColour.setText("Percentage Identity");
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428 PIDColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 PIDColour_actionPerformed(e);
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435 BLOSUM62Colour.setText("BLOSUM62 score");
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436 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 BLOSUM62Colour_actionPerformed(e);
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443 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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444 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 avTreeBlosumMenuItem_actionPerformed(e);
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451 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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452 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 njTreeBlosumMenuItem_actionPerformed(e);
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459 consensusGraphMenuItem.setActionCommand("");
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460 consensusGraphMenuItem.setText("Consensus graph");
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461 consensusGraphMenuItem.setState(true);
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462 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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464 public void actionPerformed(ActionEvent e)
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466 consensusGraphMenuItem_actionPerformed(e);
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469 colourTextMenuItem.setText("Colour text");
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470 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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472 public void actionPerformed(ActionEvent e)
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474 colourTextMenuItem_actionPerformed(e);
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477 htmlMenuItem.setText("Output as HTML");
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478 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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480 public void actionPerformed(ActionEvent e)
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482 htmlMenuItem_actionPerformed(e);
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485 overviewMenuItem.setText("Overview window");
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486 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 overviewMenuItem_actionPerformed(e);
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493 undoMenuItem.setEnabled(false);
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494 undoMenuItem.setMnemonic('Z');
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495 undoMenuItem.setText("Undo");
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496 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 undoMenuItem_actionPerformed(e);
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503 redoMenuItem.setEnabled(false);
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504 redoMenuItem.setMnemonic('0');
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505 redoMenuItem.setText("Redo");
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506 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 redoMenuItem_actionPerformed(e);
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513 conservationMenuItem.setText("By conservation");
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514 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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516 public void actionPerformed(ActionEvent e)
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518 conservationMenuItem_actionPerformed(e);
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521 noColourmenuItem.setText("None");
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522 noColourmenuItem.setSelected(true);
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523 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 noColourmenuItem_actionPerformed(e);
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530 wrapMenuItem.setText("Wrap alignment");
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531 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 wrapMenuItem_actionPerformed(e);
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538 printMenuItem.setText("Print");
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539 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 printMenuItem_actionPerformed(e);
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546 renderGapsMenuItem.setText("Render gaps");
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547 renderGapsMenuItem.setState(true);
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548 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 renderGapsMenuItem_actionPerformed(e);
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555 findMenuItem.setText("Find");
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556 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 findMenuItem_actionPerformed(e);
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563 searchMenu.setText("Search");
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565 abovePIDThreshold.setText("Above PID threshold");
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566 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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567 public void actionPerformed(ActionEvent e) {
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568 abovePIDThreshold_actionPerformed(e);
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571 sequenceFeatures.setText("Sequence Features");
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572 sequenceFeatures.addActionListener(new ActionListener()
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574 public void actionPerformed(ActionEvent actionEvent)
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576 sequenceFeatures_actionPerformed(actionEvent);
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579 nucleotideColour.setText("Nucleotide colours");
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580 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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582 public void actionPerformed(ActionEvent e)
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584 nucleotideColour_actionPerformed(e);
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587 deleteGroups.setSelected(false);
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588 deleteGroups.setText("Delete all groups");
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589 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 deleteGroups_actionPerformed(e);
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596 copy.setText("Copy");
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597 copy.setMnemonic(KeyEvent.VK_C);
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599 copy.addActionListener(new java.awt.event.ActionListener()
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601 public void actionPerformed(ActionEvent e)
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603 copy_actionPerformed(e);
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606 cut.setText("Cut");
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607 cut.setMnemonic(KeyEvent.VK_X);
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608 cut.addActionListener(new java.awt.event.ActionListener()
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610 public void actionPerformed(ActionEvent e)
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612 cut_actionPerformed(e);
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615 delete.setText("Delete");
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616 delete.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 delete_actionPerformed(e);
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623 jMenu1.setMnemonic('V');
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624 jMenu1.setText("Paste");
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625 pasteNew.setText("to new alignment");
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626 pasteNew.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 pasteNew_actionPerformed(e);
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633 pasteThis.setText("add to this alignment");
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634 pasteThis.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 pasteThis_actionPerformed(e);
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641 applyToAllGroups.setText("Apply colour to all groups");
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642 applyToAllGroups.setState(true);
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643 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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645 public void actionPerformed(ActionEvent e)
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647 applyToAllGroups_actionPerformed(e);
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650 createPNG.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 createPNG_actionPerformed(e);
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657 createPNG.setActionCommand("Save as PNG Image");
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658 createPNG.setText("Save as PNG Image");
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659 font.setText("Change Font");
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660 font.addActionListener(new java.awt.event.ActionListener()
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662 public void actionPerformed(ActionEvent e)
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664 font_actionPerformed(e);
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667 fullSeqId.setText("Show full sequence id");
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668 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 fullSeqId_actionPerformed(e);
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675 epsFile.setText("Save as EPS file");
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676 epsFile.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 epsFile_actionPerformed(e);
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683 alignFrameMenuBar.add(fileMenu);
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684 alignFrameMenuBar.add(editMenu);
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685 alignFrameMenuBar.add(searchMenu);
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686 alignFrameMenuBar.add(viewMenu);
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687 alignFrameMenuBar.add(colourMenu);
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688 alignFrameMenuBar.add(calculateMenu);
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689 alignFrameMenuBar.add(alignMenu);
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690 fileMenu.add(saveAlignmentMenu);
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691 fileMenu.add(outputTextboxMenu);
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692 fileMenu.add(htmlMenuItem);
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693 fileMenu.add(epsFile);
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694 fileMenu.add(createPNG);
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695 fileMenu.add(printMenuItem);
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696 fileMenu.addSeparator();
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697 fileMenu.add(closeMenuItem);
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698 editMenu.add(copy);
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699 editMenu.add(jMenu1);
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701 editMenu.add(delete);
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702 editMenu.addSeparator();
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703 editMenu.add(undoMenuItem);
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704 editMenu.add(redoMenuItem);
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705 editMenu.addSeparator();
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706 editMenu.add(deselectAllSequenceMenuItem);
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707 editMenu.add(selectAllSequenceMenuItem);
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708 editMenu.add(invertSequenceMenuItem);
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709 editMenu.add(deleteGroups);
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710 editMenu.add(groupsMenuItem);
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711 editMenu.addSeparator();
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712 editMenu.add(deselectAllColumnsMenuItem);
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713 editMenu.add(remove2LeftMenuItem);
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714 editMenu.add(remove2RightMenuItem);
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715 editMenu.addSeparator();
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716 editMenu.add(removeGappedColumnMenuItem);
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717 editMenu.add(removeAllGapsMenuItem);
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718 editMenu.add(setGapCharMenuItem);
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719 searchMenu.add(findMenuItem);
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720 viewMenu.add(font);
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721 viewMenu.add(fullSeqId);
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722 viewMenu.add(wrapMenuItem);
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723 viewMenu.add(viewBoxesMenuItem);
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724 viewMenu.add(viewTextMenuItem);
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725 viewMenu.add(colourTextMenuItem);
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726 viewMenu.add(renderGapsMenuItem);
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727 viewMenu.add(consensusGraphMenuItem);
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728 viewMenu.add(overviewMenuItem);
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729 viewMenu.add(sequenceFeatures);
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730 colourMenu.add(applyToAllGroups);
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731 colourMenu.add(noColourmenuItem);
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732 colourMenu.add(clustalColour);
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733 colourMenu.add(zappoColour);
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734 colourMenu.add(taylorColour);
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735 colourMenu.add(hydrophobicityColour);
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736 colourMenu.add(helixColour);
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737 colourMenu.add(strandColour);
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738 colourMenu.add(turnColour);
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739 colourMenu.add(buriedColour);
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740 colourMenu.add(nucleotideColour);
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741 colourMenu.add(userDefinedColour);
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742 colourMenu.add(PIDColour);
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743 colourMenu.add(BLOSUM62Colour);
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744 colourMenu.addSeparator();
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745 colourMenu.add(abovePIDThreshold);
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746 colourMenu.add(conservationMenuItem);
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747 calculateMenu.add(sortPairwiseMenuItem);
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748 calculateMenu.add(sortIDMenuItem);
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749 calculateMenu.add(sortGroupMenuItem);
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750 calculateMenu.add(sortTreeOrderMenuItem);
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751 calculateMenu.add(removeRedundancyMenuItem);
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752 calculateMenu.addSeparator();
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753 calculateMenu.add(pairwiseAlignmentMenuItem);
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754 calculateMenu.add(PCAMenuItem);
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755 calculateMenu.addSeparator();
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756 calculateMenu.add(averageDistanceTreeMenuItem);
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757 calculateMenu.add(neighbourTreeMenuItem);
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758 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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759 calculateMenu.add(njTreeBlosumMenuItem);
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760 alignMenu.add(clustalAlignMenuItem);
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761 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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762 jMenu1.add(pasteNew);
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763 jMenu1.add(pasteThis);
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766 protected void saveAs_actionPerformed(ActionEvent e)
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771 protected void outputText_actionPerformed(ActionEvent e)
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776 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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785 protected void closeMenuItem_actionPerformed(ActionEvent e)
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790 protected void redoMenuItem_actionPerformed(ActionEvent e)
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795 protected void undoMenuItem_actionPerformed(ActionEvent e)
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801 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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807 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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812 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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817 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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823 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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828 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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833 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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838 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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843 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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848 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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857 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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863 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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868 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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874 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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881 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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886 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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891 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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896 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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901 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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906 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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911 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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916 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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921 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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926 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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931 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
937 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
942 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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949 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
957 protected void clustalColour_actionPerformed(ActionEvent e)
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962 protected void zappoColour_actionPerformed(ActionEvent e)
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967 protected void taylorColour_actionPerformed(ActionEvent e)
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973 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
978 protected void helixColour_actionPerformed(ActionEvent e)
\r
983 protected void strandColour_actionPerformed(ActionEvent e)
\r
988 protected void turnColour_actionPerformed(ActionEvent e)
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993 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1000 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1005 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1010 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1016 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1021 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1027 protected void printMenuItem_actionPerformed(ActionEvent e)
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1032 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1037 protected void findMenuItem_actionPerformed(ActionEvent e)
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1043 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1047 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1052 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1057 protected void deleteGroups_actionPerformed(ActionEvent e)
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1062 protected void copy_actionPerformed(ActionEvent e)
\r
1068 protected void cut_actionPerformed(ActionEvent e)
\r
1073 protected void delete_actionPerformed(ActionEvent e)
\r
1078 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1083 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1088 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1093 protected void createPNG_actionPerformed(ActionEvent e)
\r
1098 protected void font_actionPerformed(ActionEvent e)
\r
1103 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1108 protected void epsFile_actionPerformed(ActionEvent e)
\r