1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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36 protected JMenuItem fontNameMenuItem = new JMenuItem();
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37 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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38 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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39 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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40 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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41 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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42 protected JMenuItem sortIDMenuItem = new JMenuItem();
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43 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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44 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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45 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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46 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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47 protected JMenuItem PCAMenuItem = new JMenuItem();
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48 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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49 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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50 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public JLabel statusBar = new JLabel();
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53 protected JMenu saveAlignmentMenu = new JMenu();
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54 protected JMenu outputTextboxMenu = new JMenu();
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55 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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66 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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67 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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68 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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69 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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70 JMenuItem htmlMenuItem = new JMenuItem();
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71 JMenuItem schemeKeyMenuItem = new JMenuItem();
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72 JMenuItem overviewMenuItem = new JMenuItem();
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73 protected JMenuItem undoMenuItem = new JMenuItem();
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74 protected JMenuItem redoMenuItem = new JMenuItem();
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75 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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76 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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77 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem pdbTest = new JMenuItem();
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79 JMenuItem printMenuItem = new JMenuItem();
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80 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem findMenuItem = new JMenuItem();
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82 JMenu searchMenu = new JMenu();
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83 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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84 protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
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85 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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86 JMenuItem deleteGroups = new JMenuItem();
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87 public GAlignFrame()
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94 setJMenuBar(alignFrameMenuBar);
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97 // dynamically fill save as menu with available formats
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98 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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99 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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100 saveAlignmentMenu.add( item );
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101 item.addActionListener(new java.awt.event.ActionListener()
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103 public void actionPerformed(ActionEvent e)
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105 saveAs_actionPerformed(e);
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109 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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110 item.addActionListener(new java.awt.event.ActionListener()
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112 public void actionPerformed(ActionEvent e)
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114 outputText_actionPerformed(e);
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118 outputTextboxMenu.add( item );
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124 e.printStackTrace();
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127 ButtonGroup colours = new ButtonGroup();
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128 colours.add(noColourmenuItem);
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129 colours.add(clustalColour);
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130 colours.add(zappoColour);
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131 colours.add(taylorColour);
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132 colours.add(hydrophobicityColour);
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133 colours.add(helixColour);
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134 colours.add(strandColour);
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135 colours.add(turnColour);
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136 colours.add(buriedColour);
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137 colours.add(userDefinedColour);
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138 colours.add(PIDColour);
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139 colours.add(BLOSUM62Colour);
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140 colours.add(nucleotideColour);
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142 private void jbInit() throws Exception
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144 fileMenu.setMnemonic('F');
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145 fileMenu.setText("File");
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146 saveAlignmentMenu.setMnemonic('L');
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147 saveAlignmentMenu.setText("Save alignment to local file");
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148 closeMenuItem.setMnemonic('C');
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149 closeMenuItem.setText("Close");
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150 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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152 public void actionPerformed(ActionEvent e)
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154 closeMenuItem_actionPerformed(e);
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157 editMenu.setText("Edit");
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158 fontMenu.setText("Font");
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159 viewMenu.setText("View");
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160 colourMenu.setText("Colour");
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161 calculateMenu.setText("Calculate");
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162 alignMenu.setText("Web Service");
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163 groupsMenuItem.setText("Groups");
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164 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 groupsMenuItem_actionPerformed(e);
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171 selectAllSequenceMenuItem.setText("Select all");
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172 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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174 public void actionPerformed(ActionEvent e)
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176 selectAllSequenceMenuItem_actionPerformed(e);
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179 deselectAllSequenceMenuItem.setText("Clear selection");
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180 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 deselectAllSequenceMenuItem_actionPerformed(e);
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187 invertSequenceMenuItem.setText("Invert sequence selection");
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188 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 invertSequenceMenuItem_actionPerformed(e);
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195 deselectAllColumnsMenuItem.setText("Deselect all columns");
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196 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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198 public void actionPerformed(ActionEvent e)
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200 deselectAllColumnsMenuItem_actionPerformed(e);
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203 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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204 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 remove2LeftMenuItem_actionPerformed(e);
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211 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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212 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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214 public void actionPerformed(ActionEvent e)
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216 remove2RightMenuItem_actionPerformed(e);
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219 removeGappedColumnMenuItem.setText("Remove gapped columns");
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220 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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222 public void actionPerformed(ActionEvent e)
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224 removeGappedColumnMenuItem_actionPerformed(e);
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227 removeAllGapsMenuItem.setText("Remove all gaps");
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228 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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230 public void actionPerformed(ActionEvent e)
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232 removeAllGapsMenuItem_actionPerformed(e);
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235 setGapCharMenuItem.setText("Set gap character to \".\"");
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236 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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238 public void actionPerformed(ActionEvent e)
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240 setGapCharMenuItem_actionPerformed(e);
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243 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 fontNameMenuItem_actionPerformed(e);
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250 fontSizeMenuItem.setText("10");
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251 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 fontSizeMenuItem_actionPerformed(e);
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258 fontStyleMenuItem.setText("Plain");
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259 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 fontStyleMenuItem_actionPerformed(e);
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266 viewBoxesMenuItem.setText("Boxes");
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267 viewBoxesMenuItem.setState(true);
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268 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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270 public void actionPerformed(ActionEvent e)
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272 viewBoxesMenuItem_actionPerformed(e);
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275 viewTextMenuItem.setText("Text");
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276 viewTextMenuItem.setState(true);
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277 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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279 public void actionPerformed(ActionEvent e)
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281 viewTextMenuItem_actionPerformed(e);
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284 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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285 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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287 public void actionPerformed(ActionEvent e)
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289 sortPairwiseMenuItem_actionPerformed(e);
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292 sortIDMenuItem.setText("Sort by ID");
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293 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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295 public void actionPerformed(ActionEvent e)
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297 sortIDMenuItem_actionPerformed(e);
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300 sortGroupMenuItem.setText("Sort by group");
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301 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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303 public void actionPerformed(ActionEvent e)
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305 sortGroupMenuItem_actionPerformed(e);
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308 sortTreeOrderMenuItem.setText("Sort by tree order");
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309 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 sortTreeOrderMenuItem_actionPerformed(e);
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316 removeRedundancyMenuItem.setText("Remove redundancy");
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317 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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319 public void actionPerformed(ActionEvent e)
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321 removeRedundancyMenuItem_actionPerformed(e);
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324 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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325 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 pairwiseAlignmentMenuItem_actionPerformed(e);
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332 PCAMenuItem.setText("Principal component analysis");
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333 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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335 public void actionPerformed(ActionEvent e)
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337 PCAMenuItem_actionPerformed(e);
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340 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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341 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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343 public void actionPerformed(ActionEvent e)
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345 averageDistanceTreeMenuItem_actionPerformed(e);
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348 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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349 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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351 public void actionPerformed(ActionEvent e)
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353 neighbourTreeMenuItem_actionPerformed(e);
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356 clustalAlignMenuItem.setText("Clustal alignment");
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357 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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359 public void actionPerformed(ActionEvent e)
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361 clustalAlignMenuItem_actionPerformed(e);
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364 this.getContentPane().setLayout(borderLayout1);
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365 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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366 statusBar.setBackground(Color.white);
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367 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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368 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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369 statusBar.setText("Status bar");
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370 outputTextboxMenu.setMnemonic('T');
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371 outputTextboxMenu.setText("Output alignment via textbox");
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372 clustalColour.setSelected(false);
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373 clustalColour.setText("Clustalx colours");
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374 clustalColour.addActionListener(new java.awt.event.ActionListener()
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376 public void actionPerformed(ActionEvent e)
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378 clustalColour_actionPerformed(e);
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381 zappoColour.setText("Zappo colour scheme");
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382 zappoColour.addActionListener(new java.awt.event.ActionListener()
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384 public void actionPerformed(ActionEvent e)
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386 zappoColour_actionPerformed(e);
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389 taylorColour.setText("Taylor colour scheme");
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390 taylorColour.addActionListener(new java.awt.event.ActionListener()
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392 public void actionPerformed(ActionEvent e)
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394 taylorColour_actionPerformed(e);
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397 hydrophobicityColour.setText("By hydrophobicity");
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398 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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400 public void actionPerformed(ActionEvent e)
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402 hydrophobicityColour_actionPerformed(e);
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405 helixColour.setText("Helix propensity");
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406 helixColour.addActionListener(new java.awt.event.ActionListener()
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408 public void actionPerformed(ActionEvent e)
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410 helixColour_actionPerformed(e);
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413 strandColour.setText("Strand propensity");
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414 strandColour.addActionListener(new java.awt.event.ActionListener()
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416 public void actionPerformed(ActionEvent e)
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418 strandColour_actionPerformed(e);
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421 turnColour.setText("Turn propensity");
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422 turnColour.addActionListener(new java.awt.event.ActionListener()
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424 public void actionPerformed(ActionEvent e)
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426 turnColour_actionPerformed(e);
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429 buriedColour.setText("Buried index");
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430 buriedColour.addActionListener(new java.awt.event.ActionListener()
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432 public void actionPerformed(ActionEvent e)
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434 buriedColour_actionPerformed(e);
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437 userDefinedColour.setText("User defined colours");
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438 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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440 public void actionPerformed(ActionEvent e)
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442 userDefinedColour_actionPerformed(e);
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445 PIDColour.setText("Percentage Identity");
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446 PIDColour.addActionListener(new java.awt.event.ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 PIDColour_actionPerformed(e);
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453 BLOSUM62Colour.setText("BLOSUM62 score");
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454 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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456 public void actionPerformed(ActionEvent e)
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458 BLOSUM62Colour_actionPerformed(e);
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461 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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462 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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464 public void actionPerformed(ActionEvent e)
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466 avTreeBlosumMenuItem_actionPerformed(e);
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469 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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470 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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472 public void actionPerformed(ActionEvent e)
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474 njTreeBlosumMenuItem_actionPerformed(e);
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477 consensusGraphMenuItem.setActionCommand("");
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478 consensusGraphMenuItem.setText("Consensus graph");
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479 consensusGraphMenuItem.setState(true);
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480 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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482 public void actionPerformed(ActionEvent e)
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484 consensusGraphMenuItem_actionPerformed(e);
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487 colourTextMenuItem.setText("Colour text");
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488 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 colourTextMenuItem_actionPerformed(e);
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495 htmlMenuItem.setText("Output as HTML");
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496 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 htmlMenuItem_actionPerformed(e);
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503 schemeKeyMenuItem.setText("Colour Scheme Key");
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504 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 schemeKeyMenuItem_actionPerformed(e);
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511 overviewMenuItem.setText("Overview window");
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512 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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514 public void actionPerformed(ActionEvent e)
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516 overviewMenuItem_actionPerformed(e);
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519 undoMenuItem.setEnabled(false);
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520 undoMenuItem.setMnemonic('Z');
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521 undoMenuItem.setText("Undo");
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522 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 undoMenuItem_actionPerformed(e);
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529 redoMenuItem.setEnabled(false);
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530 redoMenuItem.setMnemonic('0');
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531 redoMenuItem.setText("Redo");
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532 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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534 public void actionPerformed(ActionEvent e)
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536 redoMenuItem_actionPerformed(e);
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539 conservationMenuItem.setText("By conservation");
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540 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 conservationMenuItem_actionPerformed(e);
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547 noColourmenuItem.setText("None");
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548 noColourmenuItem.setSelected(true);
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549 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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551 public void actionPerformed(ActionEvent e)
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553 noColourmenuItem_actionPerformed(e);
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556 wrapMenuItem.setEnabled(false);
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557 wrapMenuItem.setText("Wrap alignment");
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558 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 wrapMenuItem_actionPerformed(e);
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565 pdbTest.setText("PDB Test Viewer");
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566 pdbTest.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 pdbTest_actionPerformed(e);
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573 printMenuItem.setText("Print");
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574 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 printMenuItem_actionPerformed(e);
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581 renderGapsMenuItem.setText("Render gaps");
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582 renderGapsMenuItem.setState(true);
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583 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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585 public void actionPerformed(ActionEvent e)
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587 renderGapsMenuItem_actionPerformed(e);
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590 findMenuItem.setText("Find");
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591 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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593 public void actionPerformed(ActionEvent e)
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595 findMenuItem_actionPerformed(e);
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598 searchMenu.setText("Search");
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600 abovePIDThreshold.setText("Above PID threshold");
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601 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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602 public void actionPerformed(ActionEvent e) {
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603 abovePIDThreshold_actionPerformed(e);
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606 secondaryStructure.setSelected(true);
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607 secondaryStructure.setText("Secondary Structure");
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608 secondaryStructure.addActionListener(new ActionListener()
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610 public void actionPerformed(ActionEvent actionEvent)
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612 secondaryStructure_actionPerformed(actionEvent);
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615 nucleotideColour.setText("Nucleotide colours");
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616 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 nucleotideColour_actionPerformed(e);
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623 deleteGroups.setSelected(false);
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624 deleteGroups.setText("Delete all groups");
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625 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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627 public void actionPerformed(ActionEvent e)
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629 deleteGroups_actionPerformed(e);
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632 alignFrameMenuBar.add(fileMenu);
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633 alignFrameMenuBar.add(editMenu);
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634 alignFrameMenuBar.add(searchMenu);
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635 alignFrameMenuBar.add(fontMenu);
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636 alignFrameMenuBar.add(viewMenu);
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637 alignFrameMenuBar.add(colourMenu);
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638 alignFrameMenuBar.add(calculateMenu);
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639 alignFrameMenuBar.add(alignMenu);
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640 fileMenu.add(saveAlignmentMenu);
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641 fileMenu.add(outputTextboxMenu);
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642 fileMenu.add(htmlMenuItem);
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643 fileMenu.add(printMenuItem);
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644 fileMenu.addSeparator();
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645 fileMenu.add(closeMenuItem);
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646 editMenu.add(undoMenuItem);
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647 editMenu.add(redoMenuItem);
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648 editMenu.addSeparator();
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649 editMenu.add(deselectAllSequenceMenuItem);
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650 editMenu.add(selectAllSequenceMenuItem);
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651 editMenu.add(invertSequenceMenuItem);
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652 editMenu.add(deleteGroups);
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653 editMenu.add(groupsMenuItem);
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654 editMenu.addSeparator();
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655 editMenu.add(deselectAllColumnsMenuItem);
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656 editMenu.add(remove2LeftMenuItem);
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657 editMenu.add(remove2RightMenuItem);
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658 editMenu.addSeparator();
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659 editMenu.add(removeGappedColumnMenuItem);
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660 editMenu.add(removeAllGapsMenuItem);
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661 editMenu.add(setGapCharMenuItem);
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662 searchMenu.add(findMenuItem);
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663 fontMenu.add(fontNameMenuItem);
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664 fontMenu.add(fontSizeMenuItem);
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665 fontMenu.add(fontStyleMenuItem);
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666 viewMenu.add(wrapMenuItem);
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667 viewMenu.add(viewBoxesMenuItem);
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668 viewMenu.add(viewTextMenuItem);
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669 viewMenu.add(colourTextMenuItem);
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670 viewMenu.add(renderGapsMenuItem);
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671 viewMenu.add(consensusGraphMenuItem);
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672 viewMenu.add(overviewMenuItem);
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673 viewMenu.add(secondaryStructure);
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674 colourMenu.add(noColourmenuItem);
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675 colourMenu.add(clustalColour);
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676 colourMenu.add(zappoColour);
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677 colourMenu.add(taylorColour);
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678 colourMenu.add(hydrophobicityColour);
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679 colourMenu.add(helixColour);
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680 colourMenu.add(strandColour);
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681 colourMenu.add(turnColour);
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682 colourMenu.add(buriedColour);
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683 colourMenu.add(nucleotideColour);
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684 colourMenu.add(userDefinedColour);
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685 colourMenu.add(PIDColour);
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686 colourMenu.add(BLOSUM62Colour);
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687 colourMenu.addSeparator();
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688 colourMenu.add(abovePIDThreshold);
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689 colourMenu.add(conservationMenuItem);
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690 colourMenu.addSeparator();
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691 colourMenu.add(schemeKeyMenuItem);
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692 calculateMenu.add(sortPairwiseMenuItem);
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693 calculateMenu.add(sortIDMenuItem);
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694 calculateMenu.add(sortGroupMenuItem);
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695 calculateMenu.add(sortTreeOrderMenuItem);
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696 calculateMenu.add(removeRedundancyMenuItem);
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697 calculateMenu.addSeparator();
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698 calculateMenu.add(pairwiseAlignmentMenuItem);
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699 calculateMenu.add(PCAMenuItem);
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700 calculateMenu.addSeparator();
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701 calculateMenu.add(averageDistanceTreeMenuItem);
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702 calculateMenu.add(neighbourTreeMenuItem);
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703 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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704 calculateMenu.add(njTreeBlosumMenuItem);
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705 alignMenu.add(clustalAlignMenuItem);
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706 alignMenu.add(pdbTest);
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707 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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710 protected void saveAs_actionPerformed(ActionEvent e)
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715 protected void outputText_actionPerformed(ActionEvent e)
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720 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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729 protected void closeMenuItem_actionPerformed(ActionEvent e)
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734 protected void redoMenuItem_actionPerformed(ActionEvent e)
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739 protected void undoMenuItem_actionPerformed(ActionEvent e)
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745 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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751 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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756 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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761 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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767 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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772 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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777 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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782 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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787 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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792 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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798 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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803 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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808 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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813 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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819 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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824 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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830 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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837 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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842 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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847 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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852 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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857 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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862 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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867 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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872 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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877 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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882 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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887 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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893 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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898 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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905 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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913 protected void clustalColour_actionPerformed(ActionEvent e)
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918 protected void zappoColour_actionPerformed(ActionEvent e)
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923 protected void taylorColour_actionPerformed(ActionEvent e)
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929 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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934 protected void helixColour_actionPerformed(ActionEvent e)
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939 protected void strandColour_actionPerformed(ActionEvent e)
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944 protected void turnColour_actionPerformed(ActionEvent e)
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949 protected void buriedColour_actionPerformed(ActionEvent e)
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956 protected void userDefinedColour_actionPerformed(ActionEvent e)
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961 protected void PIDColour_actionPerformed(ActionEvent e)
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966 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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971 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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976 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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981 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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986 protected void pdbTest_actionPerformed(ActionEvent e)
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991 protected void printMenuItem_actionPerformed(ActionEvent e)
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996 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1001 protected void findMenuItem_actionPerformed(ActionEvent e)
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1007 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1011 public void secondaryStructure_actionPerformed(ActionEvent actionEvent)
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1016 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1021 protected void deleteGroups_actionPerformed(ActionEvent e)
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