1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
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28 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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31 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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32 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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33 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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34 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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35 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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36 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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37 protected JMenuItem fontNameMenuItem = new JMenuItem();
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38 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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39 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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40 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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41 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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42 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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43 protected JMenuItem sortIDMenuItem = new JMenuItem();
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44 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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45 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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46 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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47 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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48 protected JMenuItem PCAMenuItem = new JMenuItem();
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49 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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50 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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51 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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52 BorderLayout borderLayout1 = new BorderLayout();
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53 public JLabel statusBar = new JLabel();
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54 protected JMenu saveAlignmentMenu = new JMenu();
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55 protected JMenu outputTextboxMenu = new JMenu();
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56 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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67 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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68 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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69 protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
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70 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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71 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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72 JMenuItem htmlMenuItem = new JMenuItem();
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73 JMenuItem schemeKeyMenuItem = new JMenuItem();
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74 JMenuItem overviewMenuItem = new JMenuItem();
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75 protected JMenuItem undoMenuItem = new JMenuItem();
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76 protected JMenuItem redoMenuItem = new JMenuItem();
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77 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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78 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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79 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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80 JMenuItem pdbTest = new JMenuItem();
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81 JMenuItem printMenuItem = new JMenuItem();
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82 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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83 JMenuItem findMenuItem = new JMenuItem();
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84 JMenu searchMenu = new JMenu();
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85 protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();
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86 JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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87 public GAlignFrame()
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92 setJMenuBar(alignFrameMenuBar);
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95 // dynamically fill save as menu with available formats
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96 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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97 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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98 saveAlignmentMenu.add( item );
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99 item.addActionListener(new java.awt.event.ActionListener()
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101 public void actionPerformed(ActionEvent e)
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103 saveAs_actionPerformed(e);
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107 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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108 item.addActionListener(new java.awt.event.ActionListener()
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110 public void actionPerformed(ActionEvent e)
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112 outputText_actionPerformed(e);
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116 outputTextboxMenu.add( item );
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122 e.printStackTrace();
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125 ButtonGroup colours = new ButtonGroup();
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126 colours.add(noColourmenuItem);
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127 colours.add(clustalColour);
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128 colours.add(zappoColour);
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129 colours.add(taylorColour);
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130 colours.add(hydrophobicityColour);
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131 colours.add(helixColour);
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132 colours.add(strandColour);
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133 colours.add(turnColour);
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134 colours.add(buriedColour);
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135 colours.add(userDefinedColour);
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136 colours.add(PIDColour);
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137 colours.add(BLOSUM62Colour);
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139 private void jbInit() throws Exception
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141 fileMenu.setMnemonic('F');
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142 fileMenu.setText("File");
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143 saveAlignmentMenu.setMnemonic('L');
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144 saveAlignmentMenu.setText("Save alignment to local file");
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145 closeMenuItem.setMnemonic('C');
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146 closeMenuItem.setText("Close");
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147 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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149 public void actionPerformed(ActionEvent e)
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151 closeMenuItem_actionPerformed(e);
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154 editMenu.setText("Edit");
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155 fontMenu.setText("Font");
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156 viewMenu.setText("View");
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157 colourMenu.setText("Colour");
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158 calculateMenu.setText("Calculate");
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159 alignMenu.setText("Web Service");
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160 groupsMenuItem.setText("Groups");
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161 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 groupsMenuItem_actionPerformed(e);
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168 groupEditingMenuItem.setText("Group editing mode");
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169 groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
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171 public void actionPerformed(ActionEvent e)
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173 groupEditingMenuItem_actionPerformed(e);
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176 selectAllSequenceMenuItem.setText("Select all sequences");
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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 sequence 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 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 fontNameMenuItem_actionPerformed(e);
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255 fontSizeMenuItem.setText("10");
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256 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 fontSizeMenuItem_actionPerformed(e);
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263 fontStyleMenuItem.setText("Plain");
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264 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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266 public void actionPerformed(ActionEvent e)
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268 fontStyleMenuItem_actionPerformed(e);
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271 viewBoxesMenuItem.setText("Boxes");
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272 viewBoxesMenuItem.setState(true);
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273 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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275 public void actionPerformed(ActionEvent e)
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277 viewBoxesMenuItem_actionPerformed(e);
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280 viewTextMenuItem.setText("Text");
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281 viewTextMenuItem.setState(true);
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282 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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284 public void actionPerformed(ActionEvent e)
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286 viewTextMenuItem_actionPerformed(e);
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289 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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290 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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292 public void actionPerformed(ActionEvent e)
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294 sortPairwiseMenuItem_actionPerformed(e);
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297 sortIDMenuItem.setText("Sort by ID");
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298 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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300 public void actionPerformed(ActionEvent e)
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302 sortIDMenuItem_actionPerformed(e);
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305 sortGroupMenuItem.setText("Sort by group");
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306 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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308 public void actionPerformed(ActionEvent e)
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310 sortGroupMenuItem_actionPerformed(e);
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313 sortTreeOrderMenuItem.setText("Sort by tree order");
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314 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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316 public void actionPerformed(ActionEvent e)
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318 sortTreeOrderMenuItem_actionPerformed(e);
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321 removeRedundancyMenuItem.setText("Remove redundancy");
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322 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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324 public void actionPerformed(ActionEvent e)
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326 removeRedundancyMenuItem_actionPerformed(e);
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329 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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330 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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332 public void actionPerformed(ActionEvent e)
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334 pairwiseAlignmentMenuItem_actionPerformed(e);
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337 PCAMenuItem.setText("Principal component analysis");
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338 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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340 public void actionPerformed(ActionEvent e)
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342 PCAMenuItem_actionPerformed(e);
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345 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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346 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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348 public void actionPerformed(ActionEvent e)
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350 averageDistanceTreeMenuItem_actionPerformed(e);
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353 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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354 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 neighbourTreeMenuItem_actionPerformed(e);
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361 clustalAlignMenuItem.setText("Clustal alignment");
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362 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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364 public void actionPerformed(ActionEvent e)
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366 clustalAlignMenuItem_actionPerformed(e);
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369 this.getContentPane().setLayout(borderLayout1);
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370 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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371 statusBar.setBackground(Color.white);
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372 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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373 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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374 statusBar.setText("Status bar");
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375 outputTextboxMenu.setMnemonic('T');
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376 outputTextboxMenu.setText("Output alignment via textbox");
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377 clustalColour.setEnabled(false);
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378 clustalColour.setSelected(false);
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379 clustalColour.setText("Clustalx colours");
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380 clustalColour.addActionListener(new java.awt.event.ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 clustalColour_actionPerformed(e);
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387 zappoColour.setText("Zappo colour scheme");
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388 zappoColour.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 zappoColour_actionPerformed(e);
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395 taylorColour.setText("Taylor colour scheme");
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396 taylorColour.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 taylorColour_actionPerformed(e);
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403 hydrophobicityColour.setText("By hydrophobicity");
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404 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 hydrophobicityColour_actionPerformed(e);
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411 helixColour.setText("Helix propensity");
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412 helixColour.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 helixColour_actionPerformed(e);
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419 strandColour.setText("Strand propensity");
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420 strandColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 strandColour_actionPerformed(e);
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427 turnColour.setText("Turn propensity");
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428 turnColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 turnColour_actionPerformed(e);
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435 buriedColour.setText("Buried index");
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436 buriedColour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 buriedColour_actionPerformed(e);
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443 userDefinedColour.setText("User defined colours");
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444 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 userDefinedColour_actionPerformed(e);
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451 PIDColour.setText("By PID");
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452 PIDColour.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 PIDColour_actionPerformed(e);
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459 BLOSUM62Colour.setText("By BLOSUM62 score");
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460 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 BLOSUM62Colour_actionPerformed(e);
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467 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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468 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 avTreeBlosumMenuItem_actionPerformed(e);
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475 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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476 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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478 public void actionPerformed(ActionEvent e)
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480 njTreeBlosumMenuItem_actionPerformed(e);
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483 conservationColourIncMenuItem.setEnabled(false);
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484 conservationColourIncMenuItem.setText("Conservation Colour Increment");
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485 conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 conservationColourIncMenuItem_actionPerformed(e);
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492 consensusGraphMenuItem.setActionCommand("");
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493 consensusGraphMenuItem.setText("Consensus graph");
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494 consensusGraphMenuItem.setState(true);
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495 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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497 public void actionPerformed(ActionEvent e)
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499 consensusGraphMenuItem_actionPerformed(e);
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502 colourTextMenuItem.setText("Colour text");
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503 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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505 public void actionPerformed(ActionEvent e)
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507 colourTextMenuItem_actionPerformed(e);
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510 htmlMenuItem.setText("Output as HTML");
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511 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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513 public void actionPerformed(ActionEvent e)
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515 htmlMenuItem_actionPerformed(e);
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518 schemeKeyMenuItem.setText("Colour Scheme Key");
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519 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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521 public void actionPerformed(ActionEvent e)
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523 schemeKeyMenuItem_actionPerformed(e);
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526 overviewMenuItem.setText("Overview window");
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527 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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529 public void actionPerformed(ActionEvent e)
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531 overviewMenuItem_actionPerformed(e);
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534 undoMenuItem.setEnabled(false);
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535 undoMenuItem.setMnemonic('Z');
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536 undoMenuItem.setText("Undo");
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537 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 undoMenuItem_actionPerformed(e);
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544 redoMenuItem.setEnabled(false);
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545 redoMenuItem.setMnemonic('0');
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546 redoMenuItem.setText("Redo");
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547 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 redoMenuItem_actionPerformed(e);
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554 conservationMenuItem.setText("By conservation");
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555 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 conservationMenuItem_actionPerformed(e);
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562 noColourmenuItem.setText("None");
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563 noColourmenuItem.setSelected(true);
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564 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 noColourmenuItem_actionPerformed(e);
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571 wrapMenuItem.setEnabled(false);
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572 wrapMenuItem.setText("Wrap alignment");
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573 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 wrapMenuItem_actionPerformed(e);
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580 pdbTest.setText("PDB Test Viewer");
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581 pdbTest.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 pdbTest_actionPerformed(e);
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588 printMenuItem.setText("Print");
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589 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 printMenuItem_actionPerformed(e);
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596 renderGapsMenuItem.setText("Render gaps");
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597 renderGapsMenuItem.setState(true);
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598 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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600 public void actionPerformed(ActionEvent e)
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602 renderGapsMenuItem_actionPerformed(e);
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605 findMenuItem.setText("Find");
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606 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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608 public void actionPerformed(ActionEvent e)
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610 findMenuItem_actionPerformed(e);
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613 searchMenu.setText("Search");
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614 modifyAlignmentMenuItem.setText("Modify alignment");
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615 modifyAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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617 public void actionPerformed(ActionEvent e)
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619 modifyAlignmentMenuItem_actionPerformed(e);
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622 abovePIDThreshold.setEnabled(false);
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623 abovePIDThreshold.setText("Above PID threshold");
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624 alignFrameMenuBar.add(fileMenu);
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625 alignFrameMenuBar.add(editMenu);
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626 alignFrameMenuBar.add(searchMenu);
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627 alignFrameMenuBar.add(fontMenu);
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628 alignFrameMenuBar.add(viewMenu);
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629 alignFrameMenuBar.add(colourMenu);
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630 alignFrameMenuBar.add(calculateMenu);
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631 alignFrameMenuBar.add(alignMenu);
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632 fileMenu.add(saveAlignmentMenu);
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633 fileMenu.add(outputTextboxMenu);
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634 fileMenu.add(htmlMenuItem);
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635 fileMenu.add(printMenuItem);
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636 fileMenu.addSeparator();
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637 fileMenu.add(closeMenuItem);
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638 editMenu.add(undoMenuItem);
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639 editMenu.add(redoMenuItem);
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640 editMenu.addSeparator();
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641 editMenu.add(modifyAlignmentMenuItem);
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642 editMenu.add(groupsMenuItem);
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643 editMenu.add(groupEditingMenuItem);
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644 editMenu.addSeparator();
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645 editMenu.add(selectAllSequenceMenuItem);
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646 editMenu.add(deselectAllSequenceMenuItem);
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647 editMenu.add(invertSequenceMenuItem);
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648 editMenu.addSeparator();
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649 editMenu.add(deselectAllColumnsMenuItem);
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650 editMenu.add(remove2LeftMenuItem);
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651 editMenu.add(remove2RightMenuItem);
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652 editMenu.addSeparator();
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653 editMenu.add(removeGappedColumnMenuItem);
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654 editMenu.add(removeAllGapsMenuItem);
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655 editMenu.add(setGapCharMenuItem);
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656 searchMenu.add(findMenuItem);
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657 fontMenu.add(fontNameMenuItem);
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658 fontMenu.add(fontSizeMenuItem);
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659 fontMenu.add(fontStyleMenuItem);
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660 viewMenu.add(wrapMenuItem);
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661 viewMenu.add(viewBoxesMenuItem);
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662 viewMenu.add(viewTextMenuItem);
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663 viewMenu.add(colourTextMenuItem);
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664 viewMenu.add(renderGapsMenuItem);
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665 viewMenu.add(consensusGraphMenuItem);
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666 viewMenu.add(overviewMenuItem);
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667 colourMenu.add(noColourmenuItem);
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668 colourMenu.add(clustalColour);
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669 colourMenu.add(zappoColour);
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670 colourMenu.add(taylorColour);
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671 colourMenu.add(hydrophobicityColour);
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672 colourMenu.add(helixColour);
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673 colourMenu.add(strandColour);
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674 colourMenu.add(turnColour);
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675 colourMenu.add(buriedColour);
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676 colourMenu.add(userDefinedColour);
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677 colourMenu.add(abovePIDThreshold);
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678 colourMenu.addSeparator();
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679 colourMenu.add(conservationMenuItem);
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680 colourMenu.add(conservationColourIncMenuItem);
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681 colourMenu.addSeparator();
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683 colourMenu.add(PIDColour);
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684 colourMenu.add(BLOSUM62Colour);
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685 colourMenu.addSeparator();
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686 colourMenu.add(schemeKeyMenuItem);
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687 calculateMenu.add(sortPairwiseMenuItem);
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688 calculateMenu.add(sortIDMenuItem);
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689 calculateMenu.add(sortGroupMenuItem);
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690 calculateMenu.add(sortTreeOrderMenuItem);
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691 calculateMenu.add(removeRedundancyMenuItem);
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692 calculateMenu.addSeparator();
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693 calculateMenu.add(pairwiseAlignmentMenuItem);
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694 calculateMenu.add(PCAMenuItem);
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695 calculateMenu.addSeparator();
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696 calculateMenu.add(averageDistanceTreeMenuItem);
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697 calculateMenu.add(neighbourTreeMenuItem);
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698 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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699 calculateMenu.add(njTreeBlosumMenuItem);
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700 alignMenu.add(clustalAlignMenuItem);
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701 alignMenu.add(pdbTest);
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702 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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705 protected void saveAs_actionPerformed(ActionEvent e)
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710 protected void outputText_actionPerformed(ActionEvent e)
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715 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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724 protected void closeMenuItem_actionPerformed(ActionEvent e)
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729 protected void redoMenuItem_actionPerformed(ActionEvent e)
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734 protected void undoMenuItem_actionPerformed(ActionEvent e)
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740 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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745 protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
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750 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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755 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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760 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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766 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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771 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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776 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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781 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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786 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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791 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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797 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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802 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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807 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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812 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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818 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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823 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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829 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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836 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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841 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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846 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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851 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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856 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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861 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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866 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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871 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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876 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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881 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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886 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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892 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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897 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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904 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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912 protected void clustalColour_actionPerformed(ActionEvent e)
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917 protected void zappoColour_actionPerformed(ActionEvent e)
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922 protected void taylorColour_actionPerformed(ActionEvent e)
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928 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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933 protected void helixColour_actionPerformed(ActionEvent e)
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938 protected void strandColour_actionPerformed(ActionEvent e)
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943 protected void turnColour_actionPerformed(ActionEvent e)
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948 protected void buriedColour_actionPerformed(ActionEvent e)
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954 protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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962 protected void userDefinedColour_actionPerformed(ActionEvent e)
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967 protected void PIDColour_actionPerformed(ActionEvent e)
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972 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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977 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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982 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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987 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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992 protected void pdbTest_actionPerformed(ActionEvent e)
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997 protected void printMenuItem_actionPerformed(ActionEvent e)
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1002 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1007 protected void findMenuItem_actionPerformed(ActionEvent e)
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1012 protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
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