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 overviewMenuItem = new JMenuItem();
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72 protected JMenuItem undoMenuItem = new JMenuItem();
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73 protected JMenuItem redoMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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75 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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76 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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77 JMenuItem pdbTest = new JMenuItem();
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78 JMenuItem printMenuItem = new JMenuItem();
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79 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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80 JMenuItem findMenuItem = new JMenuItem();
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81 JMenu searchMenu = new JMenu();
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82 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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83 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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84 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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85 JMenuItem deleteGroups = new JMenuItem();
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86 JMenuItem delete = new JMenuItem();
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87 JMenuItem copy = new JMenuItem();
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88 JMenuItem cut = new JMenuItem();
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89 JMenu jMenu1 = new JMenu();
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90 JMenuItem pasteNew = new JMenuItem();
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91 JMenuItem pasteThis = new JMenuItem();
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92 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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93 public GAlignFrame()
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100 setJMenuBar(alignFrameMenuBar);
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103 // dynamically fill save as menu with available formats
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104 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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105 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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106 saveAlignmentMenu.add( item );
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107 item.addActionListener(new java.awt.event.ActionListener()
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109 public void actionPerformed(ActionEvent e)
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111 saveAs_actionPerformed(e);
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115 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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116 item.addActionListener(new java.awt.event.ActionListener()
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118 public void actionPerformed(ActionEvent e)
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120 outputText_actionPerformed(e);
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124 outputTextboxMenu.add( item );
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130 e.printStackTrace();
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133 ButtonGroup colours = new ButtonGroup();
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134 colours.add(noColourmenuItem);
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135 colours.add(clustalColour);
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136 colours.add(zappoColour);
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137 colours.add(taylorColour);
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138 colours.add(hydrophobicityColour);
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139 colours.add(helixColour);
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140 colours.add(strandColour);
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141 colours.add(turnColour);
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142 colours.add(buriedColour);
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143 colours.add(userDefinedColour);
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144 colours.add(PIDColour);
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145 colours.add(BLOSUM62Colour);
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146 colours.add(nucleotideColour);
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148 private void jbInit() throws Exception
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150 fileMenu.setMnemonic('F');
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151 fileMenu.setText("File");
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152 saveAlignmentMenu.setMnemonic('L');
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153 saveAlignmentMenu.setText("Save alignment to local file");
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154 closeMenuItem.setMnemonic('C');
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155 closeMenuItem.setText("Close");
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156 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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158 public void actionPerformed(ActionEvent e)
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160 closeMenuItem_actionPerformed(e);
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163 editMenu.setText("Edit");
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164 fontMenu.setText("Font");
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165 viewMenu.setText("View");
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166 colourMenu.setText("Colour");
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167 calculateMenu.setText("Calculate");
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168 alignMenu.setText("Web Service");
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169 groupsMenuItem.setText("Groups");
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170 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 groupsMenuItem_actionPerformed(e);
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177 selectAllSequenceMenuItem.setText("Select all");
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178 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 selectAllSequenceMenuItem_actionPerformed(e);
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185 deselectAllSequenceMenuItem.setText("Clear selection");
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186 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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188 public void actionPerformed(ActionEvent e)
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190 deselectAllSequenceMenuItem_actionPerformed(e);
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193 invertSequenceMenuItem.setText("Invert sequence selection");
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194 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 invertSequenceMenuItem_actionPerformed(e);
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201 deselectAllColumnsMenuItem.setText("Deselect all columns");
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202 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 deselectAllColumnsMenuItem_actionPerformed(e);
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209 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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210 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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212 public void actionPerformed(ActionEvent e)
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214 remove2LeftMenuItem_actionPerformed(e);
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217 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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218 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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220 public void actionPerformed(ActionEvent e)
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222 remove2RightMenuItem_actionPerformed(e);
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225 removeGappedColumnMenuItem.setText("Remove gapped columns");
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226 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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228 public void actionPerformed(ActionEvent e)
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230 removeGappedColumnMenuItem_actionPerformed(e);
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233 removeAllGapsMenuItem.setText("Remove all gaps");
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234 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 removeAllGapsMenuItem_actionPerformed(e);
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241 setGapCharMenuItem.setText("Set gap character to \".\"");
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242 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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244 public void actionPerformed(ActionEvent e)
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246 setGapCharMenuItem_actionPerformed(e);
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249 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 fontNameMenuItem_actionPerformed(e);
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256 fontSizeMenuItem.setText("10");
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257 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 fontSizeMenuItem_actionPerformed(e);
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264 fontStyleMenuItem.setText("Plain");
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265 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 fontStyleMenuItem_actionPerformed(e);
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272 viewBoxesMenuItem.setText("Boxes");
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273 viewBoxesMenuItem.setState(true);
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274 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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276 public void actionPerformed(ActionEvent e)
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278 viewBoxesMenuItem_actionPerformed(e);
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281 viewTextMenuItem.setText("Text");
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282 viewTextMenuItem.setState(true);
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283 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 viewTextMenuItem_actionPerformed(e);
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290 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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291 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 sortPairwiseMenuItem_actionPerformed(e);
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298 sortIDMenuItem.setText("Sort by ID");
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299 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 sortIDMenuItem_actionPerformed(e);
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306 sortGroupMenuItem.setText("Sort by group");
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307 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 sortGroupMenuItem_actionPerformed(e);
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314 sortTreeOrderMenuItem.setText("Sort by tree order");
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315 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 sortTreeOrderMenuItem_actionPerformed(e);
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322 removeRedundancyMenuItem.setText("Remove redundancy");
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323 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 removeRedundancyMenuItem_actionPerformed(e);
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330 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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331 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 pairwiseAlignmentMenuItem_actionPerformed(e);
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338 PCAMenuItem.setText("Principal component analysis");
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339 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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341 public void actionPerformed(ActionEvent e)
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343 PCAMenuItem_actionPerformed(e);
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346 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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347 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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349 public void actionPerformed(ActionEvent e)
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351 averageDistanceTreeMenuItem_actionPerformed(e);
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354 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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355 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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357 public void actionPerformed(ActionEvent e)
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359 neighbourTreeMenuItem_actionPerformed(e);
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362 clustalAlignMenuItem.setText("Clustal alignment");
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363 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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365 public void actionPerformed(ActionEvent e)
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367 clustalAlignMenuItem_actionPerformed(e);
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370 this.getContentPane().setLayout(borderLayout1);
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371 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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372 statusBar.setBackground(Color.white);
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373 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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374 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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375 statusBar.setText("Status bar");
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376 outputTextboxMenu.setMnemonic('T');
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377 outputTextboxMenu.setText("Output alignment via textbox");
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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("Percentage Identity");
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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("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 consensusGraphMenuItem.setActionCommand("");
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484 consensusGraphMenuItem.setText("Consensus graph");
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485 consensusGraphMenuItem.setState(true);
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486 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 consensusGraphMenuItem_actionPerformed(e);
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493 colourTextMenuItem.setText("Colour text");
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494 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 colourTextMenuItem_actionPerformed(e);
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501 htmlMenuItem.setText("Output as HTML");
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502 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 htmlMenuItem_actionPerformed(e);
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509 overviewMenuItem.setText("Overview window");
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510 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 overviewMenuItem_actionPerformed(e);
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517 undoMenuItem.setEnabled(false);
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518 undoMenuItem.setMnemonic('Z');
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519 undoMenuItem.setText("Undo");
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520 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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522 public void actionPerformed(ActionEvent e)
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524 undoMenuItem_actionPerformed(e);
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527 redoMenuItem.setEnabled(false);
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528 redoMenuItem.setMnemonic('0');
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529 redoMenuItem.setText("Redo");
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530 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 redoMenuItem_actionPerformed(e);
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537 conservationMenuItem.setText("By conservation");
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538 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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540 public void actionPerformed(ActionEvent e)
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542 conservationMenuItem_actionPerformed(e);
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545 noColourmenuItem.setText("None");
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546 noColourmenuItem.setSelected(true);
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547 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 noColourmenuItem_actionPerformed(e);
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554 wrapMenuItem.setText("Wrap alignment");
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555 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 wrapMenuItem_actionPerformed(e);
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562 pdbTest.setText("PDB Test Viewer");
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563 pdbTest.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 pdbTest_actionPerformed(e);
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570 printMenuItem.setText("Print");
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571 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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573 public void actionPerformed(ActionEvent e)
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575 printMenuItem_actionPerformed(e);
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578 renderGapsMenuItem.setText("Render gaps");
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579 renderGapsMenuItem.setState(true);
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580 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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582 public void actionPerformed(ActionEvent e)
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584 renderGapsMenuItem_actionPerformed(e);
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587 findMenuItem.setText("Find");
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588 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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590 public void actionPerformed(ActionEvent e)
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592 findMenuItem_actionPerformed(e);
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595 searchMenu.setText("Search");
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597 abovePIDThreshold.setText("Above PID threshold");
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598 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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599 public void actionPerformed(ActionEvent e) {
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600 abovePIDThreshold_actionPerformed(e);
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603 sequenceFeatures.setSelected(true);
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604 sequenceFeatures.setText("Sequence Features");
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605 sequenceFeatures.addActionListener(new ActionListener()
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607 public void actionPerformed(ActionEvent actionEvent)
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609 sequenceFeatures_actionPerformed(actionEvent);
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612 nucleotideColour.setText("Nucleotide colours");
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613 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 nucleotideColour_actionPerformed(e);
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620 deleteGroups.setSelected(false);
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621 deleteGroups.setText("Delete all groups");
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622 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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624 public void actionPerformed(ActionEvent e)
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626 deleteGroups_actionPerformed(e);
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629 copy.setText("Copy");
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630 copy.setMnemonic(KeyEvent.VK_C);
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632 copy.addActionListener(new java.awt.event.ActionListener()
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634 public void actionPerformed(ActionEvent e)
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636 copy_actionPerformed(e);
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639 cut.setText("Cut");
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640 cut.setMnemonic(KeyEvent.VK_X);
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641 cut.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 cut_actionPerformed(e);
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648 delete.setText("Delete");
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649 delete.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 delete_actionPerformed(e);
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656 jMenu1.setMnemonic('V');
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657 jMenu1.setText("Paste");
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658 pasteNew.setText("to new alignment");
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659 pasteNew.addActionListener(new java.awt.event.ActionListener()
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661 public void actionPerformed(ActionEvent e)
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663 pasteNew_actionPerformed(e);
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666 pasteThis.setText("add to this alignment");
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667 pasteThis.addActionListener(new java.awt.event.ActionListener()
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669 public void actionPerformed(ActionEvent e)
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671 pasteThis_actionPerformed(e);
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674 applyToAllGroups.setText("Apply colour to all groups");
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675 applyToAllGroups.setState(true);
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676 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 applyToAllGroups_actionPerformed(e);
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683 alignFrameMenuBar.add(fileMenu);
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684 alignFrameMenuBar.add(editMenu);
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685 alignFrameMenuBar.add(searchMenu);
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686 alignFrameMenuBar.add(fontMenu);
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687 alignFrameMenuBar.add(viewMenu);
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688 alignFrameMenuBar.add(colourMenu);
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689 alignFrameMenuBar.add(calculateMenu);
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690 alignFrameMenuBar.add(alignMenu);
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691 fileMenu.add(saveAlignmentMenu);
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692 fileMenu.add(outputTextboxMenu);
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693 fileMenu.add(htmlMenuItem);
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694 fileMenu.add(printMenuItem);
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695 fileMenu.addSeparator();
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696 fileMenu.add(closeMenuItem);
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697 editMenu.add(copy);
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698 editMenu.add(jMenu1);
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700 editMenu.add(delete);
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701 editMenu.addSeparator();
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702 editMenu.add(undoMenuItem);
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703 editMenu.add(redoMenuItem);
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704 editMenu.addSeparator();
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705 editMenu.add(deselectAllSequenceMenuItem);
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706 editMenu.add(selectAllSequenceMenuItem);
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707 editMenu.add(invertSequenceMenuItem);
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708 editMenu.add(deleteGroups);
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709 editMenu.add(groupsMenuItem);
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710 editMenu.addSeparator();
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711 editMenu.add(deselectAllColumnsMenuItem);
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712 editMenu.add(remove2LeftMenuItem);
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713 editMenu.add(remove2RightMenuItem);
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714 editMenu.addSeparator();
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715 editMenu.add(removeGappedColumnMenuItem);
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716 editMenu.add(removeAllGapsMenuItem);
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717 editMenu.add(setGapCharMenuItem);
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718 searchMenu.add(findMenuItem);
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719 fontMenu.add(fontNameMenuItem);
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720 fontMenu.add(fontSizeMenuItem);
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721 fontMenu.add(fontStyleMenuItem);
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722 viewMenu.add(wrapMenuItem);
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723 viewMenu.add(viewBoxesMenuItem);
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724 viewMenu.add(viewTextMenuItem);
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725 viewMenu.add(colourTextMenuItem);
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726 viewMenu.add(renderGapsMenuItem);
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727 viewMenu.add(consensusGraphMenuItem);
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728 viewMenu.add(overviewMenuItem);
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729 viewMenu.add(sequenceFeatures);
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730 colourMenu.add(applyToAllGroups);
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731 colourMenu.add(noColourmenuItem);
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732 colourMenu.add(clustalColour);
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733 colourMenu.add(zappoColour);
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734 colourMenu.add(taylorColour);
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735 colourMenu.add(hydrophobicityColour);
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736 colourMenu.add(helixColour);
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737 colourMenu.add(strandColour);
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738 colourMenu.add(turnColour);
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739 colourMenu.add(buriedColour);
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740 colourMenu.add(nucleotideColour);
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741 colourMenu.add(userDefinedColour);
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742 colourMenu.add(PIDColour);
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743 colourMenu.add(BLOSUM62Colour);
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744 colourMenu.addSeparator();
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745 colourMenu.add(abovePIDThreshold);
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746 colourMenu.add(conservationMenuItem);
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747 calculateMenu.add(sortPairwiseMenuItem);
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748 calculateMenu.add(sortIDMenuItem);
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749 calculateMenu.add(sortGroupMenuItem);
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750 calculateMenu.add(sortTreeOrderMenuItem);
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751 calculateMenu.add(removeRedundancyMenuItem);
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752 calculateMenu.addSeparator();
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753 calculateMenu.add(pairwiseAlignmentMenuItem);
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754 calculateMenu.add(PCAMenuItem);
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755 calculateMenu.addSeparator();
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756 calculateMenu.add(averageDistanceTreeMenuItem);
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757 calculateMenu.add(neighbourTreeMenuItem);
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758 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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759 calculateMenu.add(njTreeBlosumMenuItem);
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760 alignMenu.add(clustalAlignMenuItem);
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761 alignMenu.add(pdbTest);
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762 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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763 jMenu1.add(pasteNew);
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764 jMenu1.add(pasteThis);
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767 protected void saveAs_actionPerformed(ActionEvent e)
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772 protected void outputText_actionPerformed(ActionEvent e)
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777 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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786 protected void closeMenuItem_actionPerformed(ActionEvent e)
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791 protected void redoMenuItem_actionPerformed(ActionEvent e)
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796 protected void undoMenuItem_actionPerformed(ActionEvent e)
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802 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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808 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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813 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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818 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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824 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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829 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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834 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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839 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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844 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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849 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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855 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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860 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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865 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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870 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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876 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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881 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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887 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
894 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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899 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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904 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
909 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
914 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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919 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
924 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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929 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
934 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
939 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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944 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
950 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
955 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
962 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
970 protected void clustalColour_actionPerformed(ActionEvent e)
\r
975 protected void zappoColour_actionPerformed(ActionEvent e)
\r
980 protected void taylorColour_actionPerformed(ActionEvent e)
\r
986 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
991 protected void helixColour_actionPerformed(ActionEvent e)
\r
996 protected void strandColour_actionPerformed(ActionEvent e)
\r
1001 protected void turnColour_actionPerformed(ActionEvent e)
\r
1006 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1013 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1018 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1023 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1029 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1034 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1039 protected void pdbTest_actionPerformed(ActionEvent e)
\r
1044 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1049 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1054 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1060 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
1064 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1069 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1074 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1079 protected void copy_actionPerformed(ActionEvent e)
\r
1085 protected void cut_actionPerformed(ActionEvent e)
\r
1090 protected void delete_actionPerformed(ActionEvent e)
\r
1095 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1100 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1105 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r