1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu viewMenu = new JMenu();
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22 protected JMenu colourMenu = new JMenu();
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23 protected JMenu calculateMenu = new JMenu();
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24 protected JMenu alignMenu = new JMenu();
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25 protected JMenuItem groupsMenuItem = new JMenuItem();
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26 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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27 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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30 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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31 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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32 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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33 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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34 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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35 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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36 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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37 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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38 protected JMenuItem sortIDMenuItem = new JMenuItem();
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39 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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40 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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41 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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42 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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43 protected JMenuItem PCAMenuItem = new JMenuItem();
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44 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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45 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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46 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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47 BorderLayout borderLayout1 = new BorderLayout();
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48 public JLabel statusBar = new JLabel();
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49 protected JMenu saveAlignmentMenu = new JMenu();
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50 protected JMenu outputTextboxMenu = new JMenu();
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51 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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62 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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63 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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64 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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65 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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66 JMenuItem htmlMenuItem = new JMenuItem();
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67 JMenuItem overviewMenuItem = new JMenuItem();
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68 protected JMenuItem undoMenuItem = new JMenuItem();
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69 protected JMenuItem redoMenuItem = new JMenuItem();
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70 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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71 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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72 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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73 JMenuItem printMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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75 JMenuItem findMenuItem = new JMenuItem();
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76 JMenu searchMenu = new JMenu();
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77 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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78 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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79 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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80 JMenuItem deleteGroups = new JMenuItem();
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81 JMenuItem delete = new JMenuItem();
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82 JMenuItem copy = new JMenuItem();
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83 JMenuItem cut = new JMenuItem();
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84 JMenu jMenu1 = new JMenu();
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85 JMenuItem pasteNew = new JMenuItem();
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86 JMenuItem pasteThis = new JMenuItem();
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87 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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88 JMenuItem createJPG = new JMenuItem();
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89 protected JMenuItem font = new JMenuItem();
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90 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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91 public GAlignFrame()
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98 setJMenuBar(alignFrameMenuBar);
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101 // dynamically fill save as menu with available formats
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102 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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103 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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104 saveAlignmentMenu.add( item );
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105 item.addActionListener(new java.awt.event.ActionListener()
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107 public void actionPerformed(ActionEvent e)
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109 saveAs_actionPerformed(e);
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113 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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114 item.addActionListener(new java.awt.event.ActionListener()
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116 public void actionPerformed(ActionEvent e)
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118 outputText_actionPerformed(e);
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122 outputTextboxMenu.add( item );
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128 e.printStackTrace();
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131 ButtonGroup colours = new ButtonGroup();
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132 colours.add(noColourmenuItem);
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133 colours.add(clustalColour);
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134 colours.add(zappoColour);
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135 colours.add(taylorColour);
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136 colours.add(hydrophobicityColour);
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137 colours.add(helixColour);
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138 colours.add(strandColour);
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139 colours.add(turnColour);
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140 colours.add(buriedColour);
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141 colours.add(userDefinedColour);
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142 colours.add(PIDColour);
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143 colours.add(BLOSUM62Colour);
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144 colours.add(nucleotideColour);
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146 private void jbInit() throws Exception
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148 fileMenu.setMnemonic('F');
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149 fileMenu.setText("File");
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150 saveAlignmentMenu.setMnemonic('L');
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151 saveAlignmentMenu.setText("Save alignment to local file");
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152 closeMenuItem.setMnemonic('C');
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153 closeMenuItem.setText("Close");
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154 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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156 public void actionPerformed(ActionEvent e)
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158 closeMenuItem_actionPerformed(e);
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161 editMenu.setText("Edit");
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162 viewMenu.setText("View");
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163 colourMenu.setText("Colour");
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164 calculateMenu.setText("Calculate");
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165 alignMenu.setText("Web Service");
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166 groupsMenuItem.setVisible(false);
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167 groupsMenuItem.setText("Groups");
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168 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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170 public void actionPerformed(ActionEvent e)
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172 groupsMenuItem_actionPerformed(e);
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175 selectAllSequenceMenuItem.setText("Select all");
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176 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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178 public void actionPerformed(ActionEvent e)
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180 selectAllSequenceMenuItem_actionPerformed(e);
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183 deselectAllSequenceMenuItem.setText("Clear selection");
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184 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 deselectAllSequenceMenuItem_actionPerformed(e);
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191 invertSequenceMenuItem.setText("Invert sequence selection");
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192 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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194 public void actionPerformed(ActionEvent e)
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196 invertSequenceMenuItem_actionPerformed(e);
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199 deselectAllColumnsMenuItem.setText("Deselect all columns");
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200 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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202 public void actionPerformed(ActionEvent e)
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204 deselectAllColumnsMenuItem_actionPerformed(e);
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207 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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208 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 remove2LeftMenuItem_actionPerformed(e);
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215 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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216 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 remove2RightMenuItem_actionPerformed(e);
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223 removeGappedColumnMenuItem.setText("Remove gapped columns");
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224 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 removeGappedColumnMenuItem_actionPerformed(e);
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231 removeAllGapsMenuItem.setText("Remove all gaps");
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232 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 removeAllGapsMenuItem_actionPerformed(e);
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239 setGapCharMenuItem.setText("Set gap character to \".\"");
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240 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 setGapCharMenuItem_actionPerformed(e);
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247 viewBoxesMenuItem.setText("Boxes");
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248 viewBoxesMenuItem.setState(true);
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249 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 viewBoxesMenuItem_actionPerformed(e);
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256 viewTextMenuItem.setText("Text");
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257 viewTextMenuItem.setState(true);
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258 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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260 public void actionPerformed(ActionEvent e)
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262 viewTextMenuItem_actionPerformed(e);
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265 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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266 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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268 public void actionPerformed(ActionEvent e)
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270 sortPairwiseMenuItem_actionPerformed(e);
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273 sortIDMenuItem.setText("Sort by ID");
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274 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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276 public void actionPerformed(ActionEvent e)
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278 sortIDMenuItem_actionPerformed(e);
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281 sortGroupMenuItem.setText("Sort by group");
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282 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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284 public void actionPerformed(ActionEvent e)
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286 sortGroupMenuItem_actionPerformed(e);
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289 sortTreeOrderMenuItem.setText("Sort by tree order");
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290 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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292 public void actionPerformed(ActionEvent e)
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294 sortTreeOrderMenuItem_actionPerformed(e);
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297 removeRedundancyMenuItem.setText("Remove redundancy");
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298 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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300 public void actionPerformed(ActionEvent e)
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302 removeRedundancyMenuItem_actionPerformed(e);
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305 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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306 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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308 public void actionPerformed(ActionEvent e)
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310 pairwiseAlignmentMenuItem_actionPerformed(e);
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313 PCAMenuItem.setText("Principal component analysis");
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314 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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316 public void actionPerformed(ActionEvent e)
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318 PCAMenuItem_actionPerformed(e);
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321 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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322 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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324 public void actionPerformed(ActionEvent e)
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326 averageDistanceTreeMenuItem_actionPerformed(e);
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329 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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330 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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332 public void actionPerformed(ActionEvent e)
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334 neighbourTreeMenuItem_actionPerformed(e);
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337 clustalAlignMenuItem.setText("Clustal alignment");
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338 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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340 public void actionPerformed(ActionEvent e)
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342 clustalAlignMenuItem_actionPerformed(e);
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345 this.getContentPane().setLayout(borderLayout1);
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346 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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347 statusBar.setBackground(Color.white);
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348 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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349 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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350 statusBar.setText("Status bar");
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351 outputTextboxMenu.setMnemonic('T');
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352 outputTextboxMenu.setText("Output alignment via textbox");
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353 clustalColour.setSelected(false);
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354 clustalColour.setText("Clustalx colours");
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355 clustalColour.addActionListener(new java.awt.event.ActionListener()
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357 public void actionPerformed(ActionEvent e)
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359 clustalColour_actionPerformed(e);
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362 zappoColour.setText("Zappo colour scheme");
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363 zappoColour.addActionListener(new java.awt.event.ActionListener()
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365 public void actionPerformed(ActionEvent e)
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367 zappoColour_actionPerformed(e);
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370 taylorColour.setText("Taylor colour scheme");
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371 taylorColour.addActionListener(new java.awt.event.ActionListener()
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373 public void actionPerformed(ActionEvent e)
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375 taylorColour_actionPerformed(e);
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378 hydrophobicityColour.setText("By hydrophobicity");
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379 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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381 public void actionPerformed(ActionEvent e)
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383 hydrophobicityColour_actionPerformed(e);
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386 helixColour.setText("Helix propensity");
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387 helixColour.addActionListener(new java.awt.event.ActionListener()
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389 public void actionPerformed(ActionEvent e)
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391 helixColour_actionPerformed(e);
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394 strandColour.setText("Strand propensity");
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395 strandColour.addActionListener(new java.awt.event.ActionListener()
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397 public void actionPerformed(ActionEvent e)
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399 strandColour_actionPerformed(e);
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402 turnColour.setText("Turn propensity");
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403 turnColour.addActionListener(new java.awt.event.ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 turnColour_actionPerformed(e);
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410 buriedColour.setText("Buried index");
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411 buriedColour.addActionListener(new java.awt.event.ActionListener()
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413 public void actionPerformed(ActionEvent e)
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415 buriedColour_actionPerformed(e);
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418 userDefinedColour.setText("User defined colours");
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419 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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421 public void actionPerformed(ActionEvent e)
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423 userDefinedColour_actionPerformed(e);
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426 PIDColour.setText("Percentage Identity");
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427 PIDColour.addActionListener(new java.awt.event.ActionListener()
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429 public void actionPerformed(ActionEvent e)
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431 PIDColour_actionPerformed(e);
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434 BLOSUM62Colour.setText("BLOSUM62 score");
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435 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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437 public void actionPerformed(ActionEvent e)
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439 BLOSUM62Colour_actionPerformed(e);
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442 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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443 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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445 public void actionPerformed(ActionEvent e)
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447 avTreeBlosumMenuItem_actionPerformed(e);
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450 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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451 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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453 public void actionPerformed(ActionEvent e)
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455 njTreeBlosumMenuItem_actionPerformed(e);
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458 consensusGraphMenuItem.setActionCommand("");
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459 consensusGraphMenuItem.setText("Consensus graph");
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460 consensusGraphMenuItem.setState(true);
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461 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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463 public void actionPerformed(ActionEvent e)
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465 consensusGraphMenuItem_actionPerformed(e);
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468 colourTextMenuItem.setText("Colour text");
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469 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 colourTextMenuItem_actionPerformed(e);
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476 htmlMenuItem.setText("Output as HTML");
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477 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 htmlMenuItem_actionPerformed(e);
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484 overviewMenuItem.setText("Overview window");
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485 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 overviewMenuItem_actionPerformed(e);
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492 undoMenuItem.setEnabled(false);
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493 undoMenuItem.setMnemonic('Z');
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494 undoMenuItem.setText("Undo");
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495 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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497 public void actionPerformed(ActionEvent e)
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499 undoMenuItem_actionPerformed(e);
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502 redoMenuItem.setEnabled(false);
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503 redoMenuItem.setMnemonic('0');
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504 redoMenuItem.setText("Redo");
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505 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 redoMenuItem_actionPerformed(e);
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512 conservationMenuItem.setText("By conservation");
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513 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 conservationMenuItem_actionPerformed(e);
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520 noColourmenuItem.setText("None");
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521 noColourmenuItem.setSelected(true);
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522 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 noColourmenuItem_actionPerformed(e);
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529 wrapMenuItem.setText("Wrap alignment");
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530 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 wrapMenuItem_actionPerformed(e);
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537 printMenuItem.setText("Print");
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538 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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540 public void actionPerformed(ActionEvent e)
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542 printMenuItem_actionPerformed(e);
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545 renderGapsMenuItem.setText("Render gaps");
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546 renderGapsMenuItem.setState(true);
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547 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 renderGapsMenuItem_actionPerformed(e);
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554 findMenuItem.setText("Find");
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555 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 findMenuItem_actionPerformed(e);
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562 searchMenu.setText("Search");
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564 abovePIDThreshold.setText("Above PID threshold");
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565 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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566 public void actionPerformed(ActionEvent e) {
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567 abovePIDThreshold_actionPerformed(e);
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570 sequenceFeatures.setText("Sequence Features");
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571 sequenceFeatures.addActionListener(new ActionListener()
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573 public void actionPerformed(ActionEvent actionEvent)
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575 sequenceFeatures_actionPerformed(actionEvent);
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578 nucleotideColour.setText("Nucleotide colours");
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579 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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581 public void actionPerformed(ActionEvent e)
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583 nucleotideColour_actionPerformed(e);
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586 deleteGroups.setSelected(false);
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587 deleteGroups.setText("Delete all groups");
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588 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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590 public void actionPerformed(ActionEvent e)
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592 deleteGroups_actionPerformed(e);
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595 copy.setText("Copy");
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596 copy.setMnemonic(KeyEvent.VK_C);
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598 copy.addActionListener(new java.awt.event.ActionListener()
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600 public void actionPerformed(ActionEvent e)
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602 copy_actionPerformed(e);
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605 cut.setText("Cut");
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606 cut.setMnemonic(KeyEvent.VK_X);
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607 cut.addActionListener(new java.awt.event.ActionListener()
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609 public void actionPerformed(ActionEvent e)
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611 cut_actionPerformed(e);
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614 delete.setText("Delete");
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615 delete.addActionListener(new java.awt.event.ActionListener()
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617 public void actionPerformed(ActionEvent e)
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619 delete_actionPerformed(e);
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622 jMenu1.setMnemonic('V');
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623 jMenu1.setText("Paste");
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624 pasteNew.setText("to new alignment");
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625 pasteNew.addActionListener(new java.awt.event.ActionListener()
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627 public void actionPerformed(ActionEvent e)
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629 pasteNew_actionPerformed(e);
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632 pasteThis.setText("add to this alignment");
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633 pasteThis.addActionListener(new java.awt.event.ActionListener()
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635 public void actionPerformed(ActionEvent e)
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637 pasteThis_actionPerformed(e);
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640 applyToAllGroups.setText("Apply colour to all groups");
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641 applyToAllGroups.setState(true);
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642 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 applyToAllGroups_actionPerformed(e);
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649 createJPG.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 createJPG_actionPerformed(e);
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656 createJPG.setText("Save as JPG Image");
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657 font.setText("Change Font");
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658 font.addActionListener(new java.awt.event.ActionListener()
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660 public void actionPerformed(ActionEvent e)
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662 font_actionPerformed(e);
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665 fullSeqId.setText("Show full sequence id");
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666 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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668 public void actionPerformed(ActionEvent e)
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670 fullSeqId_actionPerformed(e);
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673 alignFrameMenuBar.add(fileMenu);
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674 alignFrameMenuBar.add(editMenu);
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675 alignFrameMenuBar.add(searchMenu);
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676 alignFrameMenuBar.add(viewMenu);
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677 alignFrameMenuBar.add(colourMenu);
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678 alignFrameMenuBar.add(calculateMenu);
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679 alignFrameMenuBar.add(alignMenu);
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680 fileMenu.add(saveAlignmentMenu);
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681 fileMenu.add(outputTextboxMenu);
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682 fileMenu.add(htmlMenuItem);
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683 fileMenu.add(createJPG);
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684 fileMenu.add(printMenuItem);
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685 fileMenu.addSeparator();
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686 fileMenu.add(closeMenuItem);
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687 editMenu.add(copy);
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688 editMenu.add(jMenu1);
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690 editMenu.add(delete);
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691 editMenu.addSeparator();
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692 editMenu.add(undoMenuItem);
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693 editMenu.add(redoMenuItem);
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694 editMenu.addSeparator();
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695 editMenu.add(deselectAllSequenceMenuItem);
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696 editMenu.add(selectAllSequenceMenuItem);
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697 editMenu.add(invertSequenceMenuItem);
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698 editMenu.add(deleteGroups);
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699 editMenu.add(groupsMenuItem);
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700 editMenu.addSeparator();
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701 editMenu.add(deselectAllColumnsMenuItem);
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702 editMenu.add(remove2LeftMenuItem);
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703 editMenu.add(remove2RightMenuItem);
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704 editMenu.addSeparator();
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705 editMenu.add(removeGappedColumnMenuItem);
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706 editMenu.add(removeAllGapsMenuItem);
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707 editMenu.add(setGapCharMenuItem);
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708 searchMenu.add(findMenuItem);
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709 viewMenu.add(font);
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710 viewMenu.add(fullSeqId);
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711 viewMenu.add(wrapMenuItem);
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712 viewMenu.add(viewBoxesMenuItem);
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713 viewMenu.add(viewTextMenuItem);
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714 viewMenu.add(colourTextMenuItem);
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715 viewMenu.add(renderGapsMenuItem);
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716 viewMenu.add(consensusGraphMenuItem);
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717 viewMenu.add(overviewMenuItem);
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718 viewMenu.add(sequenceFeatures);
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719 colourMenu.add(applyToAllGroups);
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720 colourMenu.add(noColourmenuItem);
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721 colourMenu.add(clustalColour);
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722 colourMenu.add(zappoColour);
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723 colourMenu.add(taylorColour);
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724 colourMenu.add(hydrophobicityColour);
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725 colourMenu.add(helixColour);
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726 colourMenu.add(strandColour);
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727 colourMenu.add(turnColour);
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728 colourMenu.add(buriedColour);
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729 colourMenu.add(nucleotideColour);
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730 colourMenu.add(userDefinedColour);
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731 colourMenu.add(PIDColour);
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732 colourMenu.add(BLOSUM62Colour);
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733 colourMenu.addSeparator();
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734 colourMenu.add(abovePIDThreshold);
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735 colourMenu.add(conservationMenuItem);
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736 calculateMenu.add(sortPairwiseMenuItem);
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737 calculateMenu.add(sortIDMenuItem);
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738 calculateMenu.add(sortGroupMenuItem);
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739 calculateMenu.add(sortTreeOrderMenuItem);
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740 calculateMenu.add(removeRedundancyMenuItem);
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741 calculateMenu.addSeparator();
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742 calculateMenu.add(pairwiseAlignmentMenuItem);
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743 calculateMenu.add(PCAMenuItem);
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744 calculateMenu.addSeparator();
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745 calculateMenu.add(averageDistanceTreeMenuItem);
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746 calculateMenu.add(neighbourTreeMenuItem);
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747 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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748 calculateMenu.add(njTreeBlosumMenuItem);
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749 alignMenu.add(clustalAlignMenuItem);
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750 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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751 jMenu1.add(pasteNew);
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752 jMenu1.add(pasteThis);
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755 protected void saveAs_actionPerformed(ActionEvent e)
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760 protected void outputText_actionPerformed(ActionEvent e)
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765 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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774 protected void closeMenuItem_actionPerformed(ActionEvent e)
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779 protected void redoMenuItem_actionPerformed(ActionEvent e)
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784 protected void undoMenuItem_actionPerformed(ActionEvent e)
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790 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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796 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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801 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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806 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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812 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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817 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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822 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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827 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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832 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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837 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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846 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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852 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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857 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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863 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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870 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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875 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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880 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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885 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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890 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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895 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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900 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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905 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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910 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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915 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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920 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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926 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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931 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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938 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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946 protected void clustalColour_actionPerformed(ActionEvent e)
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951 protected void zappoColour_actionPerformed(ActionEvent e)
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956 protected void taylorColour_actionPerformed(ActionEvent e)
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962 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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967 protected void helixColour_actionPerformed(ActionEvent e)
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972 protected void strandColour_actionPerformed(ActionEvent e)
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977 protected void turnColour_actionPerformed(ActionEvent e)
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982 protected void buriedColour_actionPerformed(ActionEvent e)
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989 protected void userDefinedColour_actionPerformed(ActionEvent e)
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994 protected void PIDColour_actionPerformed(ActionEvent e)
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999 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1005 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1010 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1016 protected void printMenuItem_actionPerformed(ActionEvent e)
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1021 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1026 protected void findMenuItem_actionPerformed(ActionEvent e)
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1032 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1036 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1041 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1046 protected void deleteGroups_actionPerformed(ActionEvent e)
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1051 protected void copy_actionPerformed(ActionEvent e)
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1057 protected void cut_actionPerformed(ActionEvent e)
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1062 protected void delete_actionPerformed(ActionEvent e)
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1067 protected void pasteNew_actionPerformed(ActionEvent e)
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1072 protected void pasteThis_actionPerformed(ActionEvent e)
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1077 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1082 protected void createJPG_actionPerformed(ActionEvent e)
\r
1087 protected void font_actionPerformed(ActionEvent e)
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1092 protected void fullSeqId_actionPerformed(ActionEvent e)
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