1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
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28 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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31 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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32 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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33 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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34 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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35 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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36 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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37 protected JMenuItem fontNameMenuItem = new JMenuItem();
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38 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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39 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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40 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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41 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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42 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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43 protected JMenuItem sortIDMenuItem = new JMenuItem();
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44 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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45 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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46 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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47 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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48 protected JMenuItem PCAMenuItem = new JMenuItem();
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49 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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50 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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51 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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52 BorderLayout borderLayout1 = new BorderLayout();
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53 public JLabel statusBar = new JLabel();
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54 protected JMenu saveAlignmentMenu = new JMenu();
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55 protected JMenu outputTextboxMenu = new JMenu();
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56 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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68 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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69 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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70 protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
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71 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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72 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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73 JMenuItem htmlMenuItem = new JMenuItem();
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74 JMenuItem schemeKeyMenuItem = new JMenuItem();
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75 JMenuItem overviewMenuItem = new JMenuItem();
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76 protected JMenuItem undoMenuItem = new JMenuItem();
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77 protected JMenuItem redoMenuItem = new JMenuItem();
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78 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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79 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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80 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem pdbTest = new JMenuItem();
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82 JMenuItem printMenuItem = new JMenuItem();
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83 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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84 JMenuItem findMenuItem = new JMenuItem();
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85 JMenu searchMenu = new JMenu();
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86 protected JCheckBoxMenuItem modifyAlignmentMenuItem = new JCheckBoxMenuItem();
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87 public GAlignFrame()
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92 setJMenuBar(alignFrameMenuBar);
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95 // dynamically fill save as menu with available formats
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96 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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97 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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98 saveAlignmentMenu.add( item );
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99 item.addActionListener(new java.awt.event.ActionListener()
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101 public void actionPerformed(ActionEvent e)
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103 saveAs_actionPerformed(e);
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107 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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108 item.addActionListener(new java.awt.event.ActionListener()
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110 public void actionPerformed(ActionEvent e)
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112 outputText_actionPerformed(e);
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116 outputTextboxMenu.add( item );
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122 e.printStackTrace();
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125 ButtonGroup colours = new ButtonGroup();
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126 colours.add(noColourmenuItem);
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127 colours.add(clustalColour);
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128 colours.add(zappoColour);
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129 colours.add(taylorColour);
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130 colours.add(hydrophobicityColour);
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131 colours.add(helixColour);
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132 colours.add(strandColour);
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133 colours.add(turnColour);
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134 colours.add(buriedColour);
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135 colours.add(abovePIDColour);
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136 colours.add(userDefinedColour);
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137 colours.add(PIDColour);
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138 colours.add(BLOSUM62Colour);
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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 groupEditingMenuItem.setText("Group editing mode");
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170 groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 groupEditingMenuItem_actionPerformed(e);
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177 selectAllSequenceMenuItem.setText("Select all sequences");
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178 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 selectAllSequenceMenuItem_actionPerformed(e);
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185 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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186 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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188 public void actionPerformed(ActionEvent e)
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190 deselectAllSequenceMenuItem_actionPerformed(e);
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193 invertSequenceMenuItem.setText("Invert sequence selection");
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194 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 invertSequenceMenuItem_actionPerformed(e);
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201 deselectAllColumnsMenuItem.setText("Deselect all columns");
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202 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 deselectAllColumnsMenuItem_actionPerformed(e);
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209 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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210 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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212 public void actionPerformed(ActionEvent e)
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214 remove2LeftMenuItem_actionPerformed(e);
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217 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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218 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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220 public void actionPerformed(ActionEvent e)
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222 remove2RightMenuItem_actionPerformed(e);
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225 removeGappedColumnMenuItem.setText("Remove gapped columns");
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226 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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228 public void actionPerformed(ActionEvent e)
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230 removeGappedColumnMenuItem_actionPerformed(e);
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233 removeAllGapsMenuItem.setText("Remove all gaps");
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234 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 removeAllGapsMenuItem_actionPerformed(e);
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241 setGapCharMenuItem.setText("Set gap character to \".\"");
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242 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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244 public void actionPerformed(ActionEvent e)
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246 setGapCharMenuItem_actionPerformed(e);
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249 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 fontNameMenuItem_actionPerformed(e);
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256 fontSizeMenuItem.setText("10");
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257 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 fontSizeMenuItem_actionPerformed(e);
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264 fontStyleMenuItem.setText("Plain");
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265 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 fontStyleMenuItem_actionPerformed(e);
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272 viewBoxesMenuItem.setText("Boxes");
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273 viewBoxesMenuItem.setState(true);
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274 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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276 public void actionPerformed(ActionEvent e)
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278 viewBoxesMenuItem_actionPerformed(e);
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281 viewTextMenuItem.setText("Text");
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282 viewTextMenuItem.setState(true);
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283 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 viewTextMenuItem_actionPerformed(e);
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290 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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291 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 sortPairwiseMenuItem_actionPerformed(e);
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298 sortIDMenuItem.setText("Sort by ID");
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299 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 sortIDMenuItem_actionPerformed(e);
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306 sortGroupMenuItem.setText("Sort by group");
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307 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 sortGroupMenuItem_actionPerformed(e);
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314 sortTreeOrderMenuItem.setText("Sort by tree order");
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315 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 sortTreeOrderMenuItem_actionPerformed(e);
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322 removeRedundancyMenuItem.setText("Remove redundancy");
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323 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 removeRedundancyMenuItem_actionPerformed(e);
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330 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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331 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 pairwiseAlignmentMenuItem_actionPerformed(e);
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338 PCAMenuItem.setText("Principal component analysis");
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339 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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341 public void actionPerformed(ActionEvent e)
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343 PCAMenuItem_actionPerformed(e);
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346 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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347 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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349 public void actionPerformed(ActionEvent e)
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351 averageDistanceTreeMenuItem_actionPerformed(e);
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354 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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355 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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357 public void actionPerformed(ActionEvent e)
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359 neighbourTreeMenuItem_actionPerformed(e);
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362 clustalAlignMenuItem.setText("Clustal alignment");
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363 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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365 public void actionPerformed(ActionEvent e)
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367 clustalAlignMenuItem_actionPerformed(e);
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370 this.getContentPane().setLayout(borderLayout1);
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371 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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372 statusBar.setBackground(Color.white);
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373 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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374 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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375 statusBar.setText("Status bar");
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376 outputTextboxMenu.setMnemonic('T');
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377 outputTextboxMenu.setText("Output alignment via textbox");
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378 clustalColour.setEnabled(false);
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379 clustalColour.setSelected(false);
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380 clustalColour.setText("Clustalx colours");
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381 clustalColour.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 clustalColour_actionPerformed(e);
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388 zappoColour.setText("Zappo colour scheme");
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389 zappoColour.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 zappoColour_actionPerformed(e);
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396 taylorColour.setText("Taylor colour scheme");
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397 taylorColour.addActionListener(new java.awt.event.ActionListener()
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399 public void actionPerformed(ActionEvent e)
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401 taylorColour_actionPerformed(e);
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404 hydrophobicityColour.setText("By hydrophobicity");
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405 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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407 public void actionPerformed(ActionEvent e)
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409 hydrophobicityColour_actionPerformed(e);
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412 helixColour.setText("Helix propensity");
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413 helixColour.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 helixColour_actionPerformed(e);
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420 strandColour.setText("Strand propensity");
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421 strandColour.addActionListener(new java.awt.event.ActionListener()
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423 public void actionPerformed(ActionEvent e)
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425 strandColour_actionPerformed(e);
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428 turnColour.setText("Turn propensity");
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429 turnColour.addActionListener(new java.awt.event.ActionListener()
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431 public void actionPerformed(ActionEvent e)
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433 turnColour_actionPerformed(e);
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436 buriedColour.setText("Buried index");
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437 buriedColour.addActionListener(new java.awt.event.ActionListener()
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439 public void actionPerformed(ActionEvent e)
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441 buriedColour_actionPerformed(e);
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444 abovePIDColour.setEnabled(false);
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445 abovePIDColour.setText("Above PID threshold only");
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446 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 abovePIDColour_actionPerformed(e);
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453 userDefinedColour.setText("User defined colours");
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454 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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456 public void actionPerformed(ActionEvent e)
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458 userDefinedColour_actionPerformed(e);
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461 PIDColour.setEnabled(false);
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462 PIDColour.setText("By PID");
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463 PIDColour.addActionListener(new java.awt.event.ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 PIDColour_actionPerformed(e);
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470 BLOSUM62Colour.setText("By BLOSUM62 score");
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471 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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473 public void actionPerformed(ActionEvent e)
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475 BLOSUM62Colour_actionPerformed(e);
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478 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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479 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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481 public void actionPerformed(ActionEvent e)
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483 avTreeBlosumMenuItem_actionPerformed(e);
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486 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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487 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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489 public void actionPerformed(ActionEvent e)
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491 njTreeBlosumMenuItem_actionPerformed(e);
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494 conservationColourIncMenuItem.setEnabled(false);
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495 conservationColourIncMenuItem.setText("Conservation Colour Increment");
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496 conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 conservationColourIncMenuItem_actionPerformed(e);
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503 consensusGraphMenuItem.setActionCommand("");
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504 consensusGraphMenuItem.setText("Consensus graph");
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505 consensusGraphMenuItem.setState(true);
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506 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 consensusGraphMenuItem_actionPerformed(e);
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513 colourTextMenuItem.setText("Colour text");
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514 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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516 public void actionPerformed(ActionEvent e)
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518 colourTextMenuItem_actionPerformed(e);
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521 htmlMenuItem.setText("Output as HTML");
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522 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 htmlMenuItem_actionPerformed(e);
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529 schemeKeyMenuItem.setText("Colour Scheme Key");
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530 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 schemeKeyMenuItem_actionPerformed(e);
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537 overviewMenuItem.setText("Overview window");
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538 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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540 public void actionPerformed(ActionEvent e)
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542 overviewMenuItem_actionPerformed(e);
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545 undoMenuItem.setEnabled(false);
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546 undoMenuItem.setMnemonic('Z');
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547 undoMenuItem.setText("Undo");
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548 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 undoMenuItem_actionPerformed(e);
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555 redoMenuItem.setEnabled(false);
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556 redoMenuItem.setMnemonic('0');
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557 redoMenuItem.setText("Redo");
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558 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 redoMenuItem_actionPerformed(e);
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565 conservationMenuItem.setText("By conservation");
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566 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 conservationMenuItem_actionPerformed(e);
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573 noColourmenuItem.setText("None");
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574 noColourmenuItem.setSelected(true);
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575 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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577 public void actionPerformed(ActionEvent e)
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579 noColourmenuItem_actionPerformed(e);
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582 wrapMenuItem.setEnabled(false);
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583 wrapMenuItem.setText("Wrap alignment");
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584 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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586 public void actionPerformed(ActionEvent e)
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588 wrapMenuItem_actionPerformed(e);
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591 pdbTest.setText("PDB Test Viewer");
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592 pdbTest.addActionListener(new java.awt.event.ActionListener()
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594 public void actionPerformed(ActionEvent e)
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596 pdbTest_actionPerformed(e);
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599 printMenuItem.setText("Print");
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600 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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602 public void actionPerformed(ActionEvent e)
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604 printMenuItem_actionPerformed(e);
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607 renderGapsMenuItem.setText("Render gaps");
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608 renderGapsMenuItem.setState(true);
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609 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 renderGapsMenuItem_actionPerformed(e);
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616 findMenuItem.setText("Find");
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617 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 findMenuItem_actionPerformed(e);
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624 searchMenu.setText("Search");
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625 modifyAlignmentMenuItem.setText("Modify alignment");
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626 modifyAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 modifyAlignmentMenuItem_actionPerformed(e);
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633 alignFrameMenuBar.add(fileMenu);
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634 alignFrameMenuBar.add(editMenu);
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635 alignFrameMenuBar.add(searchMenu);
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636 alignFrameMenuBar.add(fontMenu);
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637 alignFrameMenuBar.add(viewMenu);
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638 alignFrameMenuBar.add(colourMenu);
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639 alignFrameMenuBar.add(calculateMenu);
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640 alignFrameMenuBar.add(alignMenu);
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641 fileMenu.add(saveAlignmentMenu);
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642 fileMenu.add(outputTextboxMenu);
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643 fileMenu.add(htmlMenuItem);
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644 fileMenu.add(printMenuItem);
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645 fileMenu.addSeparator();
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646 fileMenu.add(closeMenuItem);
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647 editMenu.add(undoMenuItem);
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648 editMenu.add(redoMenuItem);
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649 editMenu.addSeparator();
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650 editMenu.add(modifyAlignmentMenuItem);
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651 editMenu.add(groupsMenuItem);
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652 editMenu.add(groupEditingMenuItem);
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653 editMenu.addSeparator();
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654 editMenu.add(selectAllSequenceMenuItem);
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655 editMenu.add(deselectAllSequenceMenuItem);
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656 editMenu.add(invertSequenceMenuItem);
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657 editMenu.addSeparator();
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658 editMenu.add(deselectAllColumnsMenuItem);
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659 editMenu.add(remove2LeftMenuItem);
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660 editMenu.add(remove2RightMenuItem);
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661 editMenu.addSeparator();
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662 editMenu.add(removeGappedColumnMenuItem);
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663 editMenu.add(removeAllGapsMenuItem);
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664 editMenu.add(setGapCharMenuItem);
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665 searchMenu.add(findMenuItem);
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666 fontMenu.add(fontNameMenuItem);
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667 fontMenu.add(fontSizeMenuItem);
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668 fontMenu.add(fontStyleMenuItem);
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669 viewMenu.add(wrapMenuItem);
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670 viewMenu.add(viewBoxesMenuItem);
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671 viewMenu.add(viewTextMenuItem);
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672 viewMenu.add(colourTextMenuItem);
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673 viewMenu.add(renderGapsMenuItem);
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674 viewMenu.add(consensusGraphMenuItem);
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675 viewMenu.add(overviewMenuItem);
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676 colourMenu.add(noColourmenuItem);
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677 colourMenu.add(clustalColour);
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678 colourMenu.add(zappoColour);
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679 colourMenu.add(taylorColour);
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680 colourMenu.add(hydrophobicityColour);
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681 colourMenu.add(helixColour);
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682 colourMenu.add(strandColour);
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683 colourMenu.add(turnColour);
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684 colourMenu.add(buriedColour);
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685 colourMenu.add(userDefinedColour);
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686 colourMenu.addSeparator();
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687 colourMenu.add(conservationMenuItem);
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688 colourMenu.add(conservationColourIncMenuItem);
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689 colourMenu.addSeparator();
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690 colourMenu.add(abovePIDColour);
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691 colourMenu.add(PIDColour);
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692 colourMenu.add(BLOSUM62Colour);
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693 colourMenu.addSeparator();
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694 colourMenu.add(schemeKeyMenuItem);
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695 calculateMenu.add(sortPairwiseMenuItem);
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696 calculateMenu.add(sortIDMenuItem);
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697 calculateMenu.add(sortGroupMenuItem);
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698 calculateMenu.add(sortTreeOrderMenuItem);
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699 calculateMenu.add(removeRedundancyMenuItem);
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700 calculateMenu.addSeparator();
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701 calculateMenu.add(pairwiseAlignmentMenuItem);
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702 calculateMenu.add(PCAMenuItem);
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703 calculateMenu.addSeparator();
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704 calculateMenu.add(averageDistanceTreeMenuItem);
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705 calculateMenu.add(neighbourTreeMenuItem);
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706 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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707 calculateMenu.add(njTreeBlosumMenuItem);
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708 alignMenu.add(clustalAlignMenuItem);
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709 alignMenu.add(pdbTest);
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710 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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713 protected void saveAs_actionPerformed(ActionEvent e)
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718 protected void outputText_actionPerformed(ActionEvent e)
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723 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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732 protected void closeMenuItem_actionPerformed(ActionEvent e)
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737 protected void redoMenuItem_actionPerformed(ActionEvent e)
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742 protected void undoMenuItem_actionPerformed(ActionEvent e)
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748 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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753 protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
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758 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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763 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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768 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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774 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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779 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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784 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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789 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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794 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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799 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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805 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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810 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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815 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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820 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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826 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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831 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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837 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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844 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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849 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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854 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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859 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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864 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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869 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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874 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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879 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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884 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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889 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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894 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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900 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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905 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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912 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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920 protected void clustalColour_actionPerformed(ActionEvent e)
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925 protected void zappoColour_actionPerformed(ActionEvent e)
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930 protected void taylorColour_actionPerformed(ActionEvent e)
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936 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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941 protected void helixColour_actionPerformed(ActionEvent e)
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946 protected void strandColour_actionPerformed(ActionEvent e)
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951 protected void turnColour_actionPerformed(ActionEvent e)
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956 protected void buriedColour_actionPerformed(ActionEvent e)
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962 protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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968 protected void abovePIDColour_actionPerformed(ActionEvent e)
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974 protected void userDefinedColour_actionPerformed(ActionEvent e)
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979 protected void PIDColour_actionPerformed(ActionEvent e)
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984 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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989 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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994 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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999 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1004 protected void pdbTest_actionPerformed(ActionEvent e)
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1009 protected void printMenuItem_actionPerformed(ActionEvent e)
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1014 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1019 protected void findMenuItem_actionPerformed(ActionEvent e)
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1024 protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
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