1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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36 protected JMenuItem fontNameMenuItem = new JMenuItem();
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37 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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38 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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39 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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40 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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41 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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42 protected JMenuItem sortIDMenuItem = new JMenuItem();
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43 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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44 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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45 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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46 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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47 protected JMenuItem PCAMenuItem = new JMenuItem();
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48 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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49 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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50 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public JLabel statusBar = new JLabel();
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53 protected JMenu saveAlignmentMenu = new JMenu();
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54 protected JMenu outputTextboxMenu = new JMenu();
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55 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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66 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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67 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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68 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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69 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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70 JMenuItem htmlMenuItem = new JMenuItem();
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71 JMenuItem schemeKeyMenuItem = new JMenuItem();
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72 JMenuItem overviewMenuItem = new JMenuItem();
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73 protected JMenuItem undoMenuItem = new JMenuItem();
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74 protected JMenuItem redoMenuItem = new JMenuItem();
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75 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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76 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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77 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem pdbTest = new JMenuItem();
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79 JMenuItem printMenuItem = new JMenuItem();
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80 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem findMenuItem = new JMenuItem();
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82 JMenu searchMenu = new JMenu();
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83 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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84 protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
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85 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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86 JMenuItem deleteGroups = new JMenuItem();
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87 public GAlignFrame()
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92 setJMenuBar(alignFrameMenuBar);
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95 // dynamically fill save as menu with available formats
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96 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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97 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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98 saveAlignmentMenu.add( item );
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99 item.addActionListener(new java.awt.event.ActionListener()
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101 public void actionPerformed(ActionEvent e)
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103 saveAs_actionPerformed(e);
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107 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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108 item.addActionListener(new java.awt.event.ActionListener()
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110 public void actionPerformed(ActionEvent e)
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112 outputText_actionPerformed(e);
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116 outputTextboxMenu.add( item );
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122 e.printStackTrace();
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125 ButtonGroup colours = new ButtonGroup();
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126 colours.add(noColourmenuItem);
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127 colours.add(clustalColour);
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128 colours.add(zappoColour);
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129 colours.add(taylorColour);
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130 colours.add(hydrophobicityColour);
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131 colours.add(helixColour);
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132 colours.add(strandColour);
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133 colours.add(turnColour);
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134 colours.add(buriedColour);
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135 colours.add(userDefinedColour);
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136 colours.add(PIDColour);
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137 colours.add(BLOSUM62Colour);
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138 colours.add(nucleotideColour);
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140 private void jbInit() throws Exception
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142 fileMenu.setMnemonic('F');
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143 fileMenu.setText("File");
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144 saveAlignmentMenu.setMnemonic('L');
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145 saveAlignmentMenu.setText("Save alignment to local file");
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146 closeMenuItem.setMnemonic('C');
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147 closeMenuItem.setText("Close");
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148 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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150 public void actionPerformed(ActionEvent e)
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152 closeMenuItem_actionPerformed(e);
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155 editMenu.setText("Edit");
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156 fontMenu.setText("Font");
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157 viewMenu.setText("View");
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158 colourMenu.setText("Colour");
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159 calculateMenu.setText("Calculate");
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160 alignMenu.setText("Web Service");
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161 groupsMenuItem.setText("Groups");
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162 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 groupsMenuItem_actionPerformed(e);
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169 selectAllSequenceMenuItem.setText("Select all sequences");
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170 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 selectAllSequenceMenuItem_actionPerformed(e);
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177 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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178 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 deselectAllSequenceMenuItem_actionPerformed(e);
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185 invertSequenceMenuItem.setText("Invert sequence selection");
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186 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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188 public void actionPerformed(ActionEvent e)
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190 invertSequenceMenuItem_actionPerformed(e);
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193 deselectAllColumnsMenuItem.setText("Deselect all columns");
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194 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 deselectAllColumnsMenuItem_actionPerformed(e);
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201 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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202 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 remove2LeftMenuItem_actionPerformed(e);
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209 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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210 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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212 public void actionPerformed(ActionEvent e)
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214 remove2RightMenuItem_actionPerformed(e);
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217 removeGappedColumnMenuItem.setText("Remove gapped columns");
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218 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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220 public void actionPerformed(ActionEvent e)
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222 removeGappedColumnMenuItem_actionPerformed(e);
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225 removeAllGapsMenuItem.setText("Remove all gaps");
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226 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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228 public void actionPerformed(ActionEvent e)
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230 removeAllGapsMenuItem_actionPerformed(e);
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233 setGapCharMenuItem.setText("Set gap character to \".\"");
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234 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 setGapCharMenuItem_actionPerformed(e);
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241 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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243 public void actionPerformed(ActionEvent e)
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245 fontNameMenuItem_actionPerformed(e);
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248 fontSizeMenuItem.setText("10");
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249 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 fontSizeMenuItem_actionPerformed(e);
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256 fontStyleMenuItem.setText("Plain");
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257 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 fontStyleMenuItem_actionPerformed(e);
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264 viewBoxesMenuItem.setText("Boxes");
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265 viewBoxesMenuItem.setState(true);
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266 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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268 public void actionPerformed(ActionEvent e)
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270 viewBoxesMenuItem_actionPerformed(e);
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273 viewTextMenuItem.setText("Text");
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274 viewTextMenuItem.setState(true);
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275 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 viewTextMenuItem_actionPerformed(e);
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282 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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283 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 sortPairwiseMenuItem_actionPerformed(e);
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290 sortIDMenuItem.setText("Sort by ID");
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291 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 sortIDMenuItem_actionPerformed(e);
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298 sortGroupMenuItem.setText("Sort by group");
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299 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 sortGroupMenuItem_actionPerformed(e);
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306 sortTreeOrderMenuItem.setText("Sort by tree order");
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307 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 sortTreeOrderMenuItem_actionPerformed(e);
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314 removeRedundancyMenuItem.setText("Remove redundancy");
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315 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 removeRedundancyMenuItem_actionPerformed(e);
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322 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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323 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 pairwiseAlignmentMenuItem_actionPerformed(e);
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330 PCAMenuItem.setText("Principal component analysis");
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331 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 PCAMenuItem_actionPerformed(e);
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338 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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339 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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341 public void actionPerformed(ActionEvent e)
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343 averageDistanceTreeMenuItem_actionPerformed(e);
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346 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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347 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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349 public void actionPerformed(ActionEvent e)
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351 neighbourTreeMenuItem_actionPerformed(e);
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354 clustalAlignMenuItem.setText("Clustal alignment");
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355 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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357 public void actionPerformed(ActionEvent e)
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359 clustalAlignMenuItem_actionPerformed(e);
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362 this.getContentPane().setLayout(borderLayout1);
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363 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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364 statusBar.setBackground(Color.white);
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365 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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366 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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367 statusBar.setText("Status bar");
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368 outputTextboxMenu.setMnemonic('T');
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369 outputTextboxMenu.setText("Output alignment via textbox");
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370 clustalColour.setSelected(false);
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371 clustalColour.setText("Clustalx colours");
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372 clustalColour.addActionListener(new java.awt.event.ActionListener()
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374 public void actionPerformed(ActionEvent e)
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376 clustalColour_actionPerformed(e);
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379 zappoColour.setText("Zappo colour scheme");
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380 zappoColour.addActionListener(new java.awt.event.ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 zappoColour_actionPerformed(e);
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387 taylorColour.setText("Taylor colour scheme");
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388 taylorColour.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 taylorColour_actionPerformed(e);
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395 hydrophobicityColour.setText("By hydrophobicity");
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396 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 hydrophobicityColour_actionPerformed(e);
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403 helixColour.setText("Helix propensity");
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404 helixColour.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 helixColour_actionPerformed(e);
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411 strandColour.setText("Strand propensity");
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412 strandColour.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 strandColour_actionPerformed(e);
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419 turnColour.setText("Turn propensity");
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420 turnColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 turnColour_actionPerformed(e);
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427 buriedColour.setText("Buried index");
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428 buriedColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 buriedColour_actionPerformed(e);
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435 userDefinedColour.setText("User defined colours");
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436 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 userDefinedColour_actionPerformed(e);
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443 PIDColour.setText("Percentage Identity");
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444 PIDColour.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 PIDColour_actionPerformed(e);
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451 BLOSUM62Colour.setText("BLOSUM62 score");
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452 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 BLOSUM62Colour_actionPerformed(e);
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459 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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460 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 avTreeBlosumMenuItem_actionPerformed(e);
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467 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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468 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 njTreeBlosumMenuItem_actionPerformed(e);
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475 consensusGraphMenuItem.setActionCommand("");
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476 consensusGraphMenuItem.setText("Consensus graph");
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477 consensusGraphMenuItem.setState(true);
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478 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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480 public void actionPerformed(ActionEvent e)
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482 consensusGraphMenuItem_actionPerformed(e);
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485 colourTextMenuItem.setText("Colour text");
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486 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 colourTextMenuItem_actionPerformed(e);
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493 htmlMenuItem.setText("Output as HTML");
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494 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 htmlMenuItem_actionPerformed(e);
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501 schemeKeyMenuItem.setText("Colour Scheme Key");
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502 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 schemeKeyMenuItem_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.setEnabled(false);
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555 wrapMenuItem.setText("Wrap alignment");
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556 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 wrapMenuItem_actionPerformed(e);
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563 pdbTest.setText("PDB Test Viewer");
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564 pdbTest.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 pdbTest_actionPerformed(e);
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571 printMenuItem.setText("Print");
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572 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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574 public void actionPerformed(ActionEvent e)
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576 printMenuItem_actionPerformed(e);
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579 renderGapsMenuItem.setText("Render gaps");
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580 renderGapsMenuItem.setState(true);
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581 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 renderGapsMenuItem_actionPerformed(e);
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588 findMenuItem.setText("Find");
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589 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 findMenuItem_actionPerformed(e);
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596 searchMenu.setText("Search");
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598 abovePIDThreshold.setText("Above PID threshold");
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599 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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600 public void actionPerformed(ActionEvent e) {
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601 abovePIDThreshold_actionPerformed(e);
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604 secondaryStructure.setSelected(true);
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605 secondaryStructure.setText("Secondary Structure");
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606 secondaryStructure.addActionListener(new ActionListener()
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608 public void actionPerformed(ActionEvent actionEvent)
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610 secondaryStructure_actionPerformed(actionEvent);
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613 nucleotideColour.setText("Nucleotide colours");
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614 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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616 public void actionPerformed(ActionEvent e)
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618 nucleotideColour_actionPerformed(e);
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621 deleteGroups.setSelected(false);
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622 deleteGroups.setText("Delete all groups");
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623 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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625 public void actionPerformed(ActionEvent e)
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627 deleteGroups_actionPerformed(e);
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630 alignFrameMenuBar.add(fileMenu);
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631 alignFrameMenuBar.add(editMenu);
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632 alignFrameMenuBar.add(searchMenu);
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633 alignFrameMenuBar.add(fontMenu);
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634 alignFrameMenuBar.add(viewMenu);
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635 alignFrameMenuBar.add(colourMenu);
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636 alignFrameMenuBar.add(calculateMenu);
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637 alignFrameMenuBar.add(alignMenu);
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638 fileMenu.add(saveAlignmentMenu);
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639 fileMenu.add(outputTextboxMenu);
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640 fileMenu.add(htmlMenuItem);
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641 fileMenu.add(printMenuItem);
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642 fileMenu.addSeparator();
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643 fileMenu.add(closeMenuItem);
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644 editMenu.add(undoMenuItem);
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645 editMenu.add(redoMenuItem);
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646 editMenu.addSeparator();
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647 editMenu.add(deleteGroups);
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648 editMenu.add(groupsMenuItem);
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649 editMenu.addSeparator();
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650 editMenu.add(selectAllSequenceMenuItem);
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651 editMenu.add(deselectAllSequenceMenuItem);
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652 editMenu.add(invertSequenceMenuItem);
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653 editMenu.addSeparator();
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654 editMenu.add(deselectAllColumnsMenuItem);
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655 editMenu.add(remove2LeftMenuItem);
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656 editMenu.add(remove2RightMenuItem);
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657 editMenu.addSeparator();
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658 editMenu.add(removeGappedColumnMenuItem);
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659 editMenu.add(removeAllGapsMenuItem);
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660 editMenu.add(setGapCharMenuItem);
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661 searchMenu.add(findMenuItem);
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662 fontMenu.add(fontNameMenuItem);
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663 fontMenu.add(fontSizeMenuItem);
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664 fontMenu.add(fontStyleMenuItem);
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665 viewMenu.add(wrapMenuItem);
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666 viewMenu.add(viewBoxesMenuItem);
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667 viewMenu.add(viewTextMenuItem);
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668 viewMenu.add(colourTextMenuItem);
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669 viewMenu.add(renderGapsMenuItem);
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670 viewMenu.add(consensusGraphMenuItem);
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671 viewMenu.add(overviewMenuItem);
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672 viewMenu.add(secondaryStructure);
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673 colourMenu.add(noColourmenuItem);
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674 colourMenu.add(clustalColour);
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675 colourMenu.add(zappoColour);
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676 colourMenu.add(taylorColour);
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677 colourMenu.add(hydrophobicityColour);
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678 colourMenu.add(helixColour);
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679 colourMenu.add(strandColour);
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680 colourMenu.add(turnColour);
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681 colourMenu.add(buriedColour);
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682 colourMenu.add(nucleotideColour);
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683 colourMenu.add(userDefinedColour);
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684 colourMenu.add(PIDColour);
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685 colourMenu.add(BLOSUM62Colour);
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686 colourMenu.addSeparator();
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687 colourMenu.add(abovePIDThreshold);
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688 colourMenu.add(conservationMenuItem);
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689 colourMenu.addSeparator();
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690 colourMenu.add(schemeKeyMenuItem);
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691 calculateMenu.add(sortPairwiseMenuItem);
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692 calculateMenu.add(sortIDMenuItem);
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693 calculateMenu.add(sortGroupMenuItem);
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694 calculateMenu.add(sortTreeOrderMenuItem);
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695 calculateMenu.add(removeRedundancyMenuItem);
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696 calculateMenu.addSeparator();
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697 calculateMenu.add(pairwiseAlignmentMenuItem);
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698 calculateMenu.add(PCAMenuItem);
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699 calculateMenu.addSeparator();
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700 calculateMenu.add(averageDistanceTreeMenuItem);
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701 calculateMenu.add(neighbourTreeMenuItem);
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702 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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703 calculateMenu.add(njTreeBlosumMenuItem);
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704 alignMenu.add(clustalAlignMenuItem);
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705 alignMenu.add(pdbTest);
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706 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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709 protected void saveAs_actionPerformed(ActionEvent e)
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714 protected void outputText_actionPerformed(ActionEvent e)
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719 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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728 protected void closeMenuItem_actionPerformed(ActionEvent e)
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733 protected void redoMenuItem_actionPerformed(ActionEvent e)
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738 protected void undoMenuItem_actionPerformed(ActionEvent e)
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744 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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750 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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755 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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760 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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766 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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771 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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776 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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781 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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786 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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791 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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797 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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802 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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807 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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812 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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818 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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823 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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829 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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836 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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841 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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846 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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851 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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856 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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861 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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866 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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871 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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876 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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881 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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886 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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892 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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897 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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904 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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912 protected void clustalColour_actionPerformed(ActionEvent e)
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917 protected void zappoColour_actionPerformed(ActionEvent e)
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922 protected void taylorColour_actionPerformed(ActionEvent e)
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928 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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933 protected void helixColour_actionPerformed(ActionEvent e)
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938 protected void strandColour_actionPerformed(ActionEvent e)
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943 protected void turnColour_actionPerformed(ActionEvent e)
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948 protected void buriedColour_actionPerformed(ActionEvent e)
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955 protected void userDefinedColour_actionPerformed(ActionEvent e)
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960 protected void PIDColour_actionPerformed(ActionEvent e)
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965 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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970 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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975 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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980 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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985 protected void pdbTest_actionPerformed(ActionEvent e)
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990 protected void printMenuItem_actionPerformed(ActionEvent e)
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995 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1000 protected void findMenuItem_actionPerformed(ActionEvent e)
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1006 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1010 public void secondaryStructure_actionPerformed(ActionEvent actionEvent)
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1015 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1020 protected void deleteGroups_actionPerformed(ActionEvent e)
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