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 deleteSelectedMenuItem = new JMenuItem();
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32 protected JMenuItem moveSelectedMenuItem = new JMenuItem();
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33 protected JMenuItem copySelectedMenuItem = new JMenuItem();
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34 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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35 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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36 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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37 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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38 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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39 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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40 protected JMenuItem fontNameMenuItem = new JMenuItem();
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41 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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42 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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43 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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44 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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45 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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46 protected JMenuItem sortIDMenuItem = new JMenuItem();
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47 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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48 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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49 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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50 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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51 protected JMenuItem PCAMenuItem = new JMenuItem();
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52 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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53 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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54 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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55 BorderLayout borderLayout1 = new BorderLayout();
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56 public JLabel statusBar = new JLabel();
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57 protected JMenu saveAlignmentMenu = new JMenu();
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58 protected JMenu outputTextboxMenu = new JMenu();
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59 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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71 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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72 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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73 protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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75 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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76 JMenuItem htmlMenuItem = new JMenuItem();
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77 JMenuItem schemeKeyMenuItem = new JMenuItem();
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78 JMenuItem overviewMenuItem = new JMenuItem();
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79 protected JMenuItem undoMenuItem = new JMenuItem();
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80 protected JMenuItem redoMenuItem = new JMenuItem();
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81 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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82 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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83 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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84 JMenuItem pdbTest = new JMenuItem();
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85 JMenuItem printMenuItem = new JMenuItem();
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86 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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87 JMenuItem findMenuItem = new JMenuItem();
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88 JMenu searchMenu = new JMenu();
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89 public GAlignFrame()
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94 setJMenuBar(alignFrameMenuBar);
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97 // dynamically fill save as menu with available formats
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98 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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99 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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100 saveAlignmentMenu.add( item );
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101 item.addActionListener(new java.awt.event.ActionListener()
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103 public void actionPerformed(ActionEvent e)
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105 saveAs_actionPerformed(e);
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109 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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110 item.addActionListener(new java.awt.event.ActionListener()
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112 public void actionPerformed(ActionEvent e)
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114 outputText_actionPerformed(e);
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118 outputTextboxMenu.add( item );
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124 e.printStackTrace();
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127 ButtonGroup colours = new ButtonGroup();
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128 colours.add(noColourmenuItem);
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129 colours.add(clustalColour);
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130 colours.add(zappoColour);
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131 colours.add(taylorColour);
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132 colours.add(hydrophobicityColour);
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133 colours.add(helixColour);
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134 colours.add(strandColour);
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135 colours.add(turnColour);
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136 colours.add(buriedColour);
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137 colours.add(abovePIDColour);
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138 colours.add(userDefinedColour);
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139 colours.add(PIDColour);
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140 colours.add(BLOSUM62Colour);
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142 private void jbInit() throws Exception
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144 fileMenu.setMnemonic('F');
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145 fileMenu.setText("File");
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146 saveAlignmentMenu.setMnemonic('L');
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147 saveAlignmentMenu.setText("Save alignment to local file");
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148 closeMenuItem.setMnemonic('C');
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149 closeMenuItem.setText("Close");
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150 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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152 public void actionPerformed(ActionEvent e)
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154 closeMenuItem_actionPerformed(e);
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157 editMenu.setText("Edit");
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158 fontMenu.setText("Font");
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159 viewMenu.setText("View");
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160 colourMenu.setText("Colour");
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161 calculateMenu.setText("Calculate");
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162 alignMenu.setText("Web Service");
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163 groupsMenuItem.setText("Groups");
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164 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 groupsMenuItem_actionPerformed(e);
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171 groupEditingMenuItem.setText("Group editing mode");
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172 groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
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174 public void actionPerformed(ActionEvent e)
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176 groupEditingMenuItem_actionPerformed(e);
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179 selectAllSequenceMenuItem.setText("Select all sequences");
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180 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 selectAllSequenceMenuItem_actionPerformed(e);
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187 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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188 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 deselectAllSequenceMenuItem_actionPerformed(e);
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195 invertSequenceMenuItem.setText("Invert sequence selection");
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196 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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198 public void actionPerformed(ActionEvent e)
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200 invertSequenceMenuItem_actionPerformed(e);
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203 deleteSelectedMenuItem.setText("Delete selected sequences");
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204 deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 deleteSelectedMenuItem_actionPerformed(e);
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211 moveSelectedMenuItem.setText("Move selected sequences to new alignment");
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212 moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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214 public void actionPerformed(ActionEvent e)
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216 moveSelectedMenuItem_actionPerformed(e);
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219 copySelectedMenuItem.setText("Copy selected sequences to new alignment");
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220 copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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222 public void actionPerformed(ActionEvent e)
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224 copySelectedMenuItem_actionPerformed(e);
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227 deselectAllColumnsMenuItem.setText("Deselect all columns");
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228 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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230 public void actionPerformed(ActionEvent e)
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232 deselectAllColumnsMenuItem_actionPerformed(e);
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235 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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236 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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238 public void actionPerformed(ActionEvent e)
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240 remove2LeftMenuItem_actionPerformed(e);
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243 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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244 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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246 public void actionPerformed(ActionEvent e)
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248 remove2RightMenuItem_actionPerformed(e);
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251 removeGappedColumnMenuItem.setText("Remove gapped columns");
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252 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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254 public void actionPerformed(ActionEvent e)
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256 removeGappedColumnMenuItem_actionPerformed(e);
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259 removeAllGapsMenuItem.setText("Remove all gaps");
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260 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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262 public void actionPerformed(ActionEvent e)
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264 removeAllGapsMenuItem_actionPerformed(e);
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267 setGapCharMenuItem.setText("Set gap character to \".\"");
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268 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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270 public void actionPerformed(ActionEvent e)
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272 setGapCharMenuItem_actionPerformed(e);
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275 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 fontNameMenuItem_actionPerformed(e);
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282 fontSizeMenuItem.setText("10");
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283 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 fontSizeMenuItem_actionPerformed(e);
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290 fontStyleMenuItem.setText("Plain");
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291 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 fontStyleMenuItem_actionPerformed(e);
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298 viewBoxesMenuItem.setText("Boxes");
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299 viewBoxesMenuItem.setState(true);
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300 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(ActionEvent e)
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304 viewBoxesMenuItem_actionPerformed(e);
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307 viewTextMenuItem.setText("Text");
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308 viewTextMenuItem.setState(true);
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309 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 viewTextMenuItem_actionPerformed(e);
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316 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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317 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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319 public void actionPerformed(ActionEvent e)
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321 sortPairwiseMenuItem_actionPerformed(e);
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324 sortIDMenuItem.setText("Sort by ID");
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325 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 sortIDMenuItem_actionPerformed(e);
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332 sortGroupMenuItem.setText("Sort by group");
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333 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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335 public void actionPerformed(ActionEvent e)
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337 sortGroupMenuItem_actionPerformed(e);
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340 sortTreeOrderMenuItem.setText("Sort by tree order");
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341 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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343 public void actionPerformed(ActionEvent e)
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345 sortTreeOrderMenuItem_actionPerformed(e);
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348 removeRedundancyMenuItem.setText("Remove redundancy");
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349 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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351 public void actionPerformed(ActionEvent e)
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353 removeRedundancyMenuItem_actionPerformed(e);
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356 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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357 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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359 public void actionPerformed(ActionEvent e)
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361 pairwiseAlignmentMenuItem_actionPerformed(e);
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364 PCAMenuItem.setText("Principal component analysis");
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365 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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367 public void actionPerformed(ActionEvent e)
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369 PCAMenuItem_actionPerformed(e);
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372 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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373 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 averageDistanceTreeMenuItem_actionPerformed(e);
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380 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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381 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 neighbourTreeMenuItem_actionPerformed(e);
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388 clustalAlignMenuItem.setText("Clustal alignment");
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389 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 clustalAlignMenuItem_actionPerformed(e);
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396 this.getContentPane().setLayout(borderLayout1);
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397 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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398 statusBar.setBackground(Color.white);
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399 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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400 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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401 statusBar.setText("Status bar");
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402 outputTextboxMenu.setMnemonic('T');
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403 outputTextboxMenu.setText("Output alignment via textbox");
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404 clustalColour.setEnabled(false);
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405 clustalColour.setSelected(false);
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406 clustalColour.setText("Clustalx colours");
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407 clustalColour.addActionListener(new java.awt.event.ActionListener()
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409 public void actionPerformed(ActionEvent e)
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411 clustalColour_actionPerformed(e);
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414 zappoColour.setText("Zappo colour scheme");
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415 zappoColour.addActionListener(new java.awt.event.ActionListener()
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417 public void actionPerformed(ActionEvent e)
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419 zappoColour_actionPerformed(e);
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422 taylorColour.setText("Taylor colour scheme");
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423 taylorColour.addActionListener(new java.awt.event.ActionListener()
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425 public void actionPerformed(ActionEvent e)
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427 taylorColour_actionPerformed(e);
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430 hydrophobicityColour.setText("By hydrophobicity");
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431 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 hydrophobicityColour_actionPerformed(e);
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438 helixColour.setText("Helix propensity");
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439 helixColour.addActionListener(new java.awt.event.ActionListener()
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441 public void actionPerformed(ActionEvent e)
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443 helixColour_actionPerformed(e);
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446 strandColour.setText("Strand propensity");
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447 strandColour.addActionListener(new java.awt.event.ActionListener()
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449 public void actionPerformed(ActionEvent e)
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451 strandColour_actionPerformed(e);
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454 turnColour.setText("Turn propensity");
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455 turnColour.addActionListener(new java.awt.event.ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 turnColour_actionPerformed(e);
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462 buriedColour.setText("Buried index");
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463 buriedColour.addActionListener(new java.awt.event.ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 buriedColour_actionPerformed(e);
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470 abovePIDColour.setEnabled(false);
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471 abovePIDColour.setText("Above PID threshold only");
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472 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 abovePIDColour_actionPerformed(e);
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479 userDefinedColour.setText("User defined colours");
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480 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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482 public void actionPerformed(ActionEvent e)
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484 userDefinedColour_actionPerformed(e);
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487 PIDColour.setEnabled(false);
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488 PIDColour.setText("By PID");
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489 PIDColour.addActionListener(new java.awt.event.ActionListener()
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491 public void actionPerformed(ActionEvent e)
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493 PIDColour_actionPerformed(e);
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496 BLOSUM62Colour.setText("By BLOSUM62 score");
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497 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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499 public void actionPerformed(ActionEvent e)
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501 BLOSUM62Colour_actionPerformed(e);
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504 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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505 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 avTreeBlosumMenuItem_actionPerformed(e);
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512 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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513 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 njTreeBlosumMenuItem_actionPerformed(e);
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520 conservationColourIncMenuItem.setEnabled(false);
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521 conservationColourIncMenuItem.setText("Conservation Colour Increment");
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522 conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 conservationColourIncMenuItem_actionPerformed(e);
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529 consensusGraphMenuItem.setActionCommand("");
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530 consensusGraphMenuItem.setText("Consensus graph");
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531 consensusGraphMenuItem.setState(true);
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532 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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534 public void actionPerformed(ActionEvent e)
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536 consensusGraphMenuItem_actionPerformed(e);
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539 colourTextMenuItem.setText("Colour text");
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540 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 colourTextMenuItem_actionPerformed(e);
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547 htmlMenuItem.setText("Output as HTML");
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548 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 htmlMenuItem_actionPerformed(e);
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555 schemeKeyMenuItem.setText("Colour Scheme Key");
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556 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 schemeKeyMenuItem_actionPerformed(e);
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563 overviewMenuItem.setText("Overview window");
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564 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 overviewMenuItem_actionPerformed(e);
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571 undoMenuItem.setEnabled(false);
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572 undoMenuItem.setMnemonic('Z');
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573 undoMenuItem.setText("Undo");
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574 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 undoMenuItem_actionPerformed(e);
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581 redoMenuItem.setEnabled(false);
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582 redoMenuItem.setMnemonic('0');
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583 redoMenuItem.setText("Redo");
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584 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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586 public void actionPerformed(ActionEvent e)
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588 redoMenuItem_actionPerformed(e);
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591 conservationMenuItem.setText("By conservation");
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592 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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594 public void actionPerformed(ActionEvent e)
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596 conservationMenuItem_actionPerformed(e);
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599 noColourmenuItem.setText("None");
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600 noColourmenuItem.setSelected(true);
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601 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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603 public void actionPerformed(ActionEvent e)
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605 noColourmenuItem_actionPerformed(e);
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608 wrapMenuItem.setEnabled(false);
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609 wrapMenuItem.setText("Wrap alignment");
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610 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 wrapMenuItem_actionPerformed(e);
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617 pdbTest.setText("PDB Test Viewer");
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618 pdbTest.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 pdbTest_actionPerformed(e);
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625 printMenuItem.setText("Print");
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626 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 printMenuItem_actionPerformed(e);
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633 renderGapsMenuItem.setText("Render gaps");
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634 renderGapsMenuItem.setState(true);
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635 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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637 public void actionPerformed(ActionEvent e)
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639 renderGapsMenuItem_actionPerformed(e);
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642 findMenuItem.setText("Find");
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643 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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645 public void actionPerformed(ActionEvent e)
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647 findMenuItem_actionPerformed(e);
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650 searchMenu.setText("Search");
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651 alignFrameMenuBar.add(fileMenu);
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652 alignFrameMenuBar.add(editMenu);
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653 alignFrameMenuBar.add(searchMenu);
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654 alignFrameMenuBar.add(fontMenu);
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655 alignFrameMenuBar.add(viewMenu);
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656 alignFrameMenuBar.add(colourMenu);
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657 alignFrameMenuBar.add(calculateMenu);
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658 alignFrameMenuBar.add(alignMenu);
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659 fileMenu.add(saveAlignmentMenu);
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660 fileMenu.add(outputTextboxMenu);
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661 fileMenu.add(htmlMenuItem);
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662 fileMenu.add(printMenuItem);
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663 fileMenu.addSeparator();
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664 fileMenu.add(closeMenuItem);
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665 editMenu.add(undoMenuItem);
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666 editMenu.add(redoMenuItem);
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667 editMenu.addSeparator();
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668 editMenu.add(groupsMenuItem);
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669 editMenu.add(groupEditingMenuItem);
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670 editMenu.addSeparator();
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671 editMenu.add(selectAllSequenceMenuItem);
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672 editMenu.add(deselectAllSequenceMenuItem);
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673 editMenu.add(invertSequenceMenuItem);
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674 editMenu.addSeparator();
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675 editMenu.add(copySelectedMenuItem);
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676 editMenu.add(moveSelectedMenuItem);
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677 editMenu.add(deleteSelectedMenuItem);
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678 editMenu.addSeparator();
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679 editMenu.add(deselectAllColumnsMenuItem);
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680 editMenu.add(remove2LeftMenuItem);
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681 editMenu.add(remove2RightMenuItem);
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682 editMenu.addSeparator();
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683 editMenu.add(removeGappedColumnMenuItem);
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684 editMenu.add(removeAllGapsMenuItem);
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685 editMenu.add(setGapCharMenuItem);
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686 searchMenu.add(findMenuItem);
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687 fontMenu.add(fontNameMenuItem);
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688 fontMenu.add(fontSizeMenuItem);
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689 fontMenu.add(fontStyleMenuItem);
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690 viewMenu.add(wrapMenuItem);
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691 viewMenu.add(viewBoxesMenuItem);
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692 viewMenu.add(viewTextMenuItem);
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693 viewMenu.add(colourTextMenuItem);
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694 viewMenu.add(renderGapsMenuItem);
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695 viewMenu.add(consensusGraphMenuItem);
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696 viewMenu.add(overviewMenuItem);
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697 colourMenu.add(noColourmenuItem);
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698 colourMenu.add(clustalColour);
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699 colourMenu.add(zappoColour);
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700 colourMenu.add(taylorColour);
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701 colourMenu.add(hydrophobicityColour);
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702 colourMenu.add(helixColour);
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703 colourMenu.add(strandColour);
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704 colourMenu.add(turnColour);
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705 colourMenu.add(buriedColour);
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706 colourMenu.add(userDefinedColour);
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707 colourMenu.addSeparator();
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708 colourMenu.add(conservationMenuItem);
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709 colourMenu.add(conservationColourIncMenuItem);
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710 colourMenu.addSeparator();
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711 colourMenu.add(abovePIDColour);
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712 colourMenu.add(PIDColour);
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713 colourMenu.add(BLOSUM62Colour);
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714 colourMenu.addSeparator();
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715 colourMenu.add(schemeKeyMenuItem);
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716 calculateMenu.add(sortPairwiseMenuItem);
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717 calculateMenu.add(sortIDMenuItem);
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718 calculateMenu.add(sortGroupMenuItem);
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719 calculateMenu.add(sortTreeOrderMenuItem);
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720 calculateMenu.add(removeRedundancyMenuItem);
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721 calculateMenu.addSeparator();
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722 calculateMenu.add(pairwiseAlignmentMenuItem);
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723 calculateMenu.add(PCAMenuItem);
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724 calculateMenu.addSeparator();
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725 calculateMenu.add(averageDistanceTreeMenuItem);
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726 calculateMenu.add(neighbourTreeMenuItem);
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727 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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728 calculateMenu.add(njTreeBlosumMenuItem);
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729 alignMenu.add(clustalAlignMenuItem);
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730 alignMenu.add(pdbTest);
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731 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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734 protected void saveAs_actionPerformed(ActionEvent e)
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739 protected void outputText_actionPerformed(ActionEvent e)
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744 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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753 protected void closeMenuItem_actionPerformed(ActionEvent e)
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758 protected void redoMenuItem_actionPerformed(ActionEvent e)
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763 protected void undoMenuItem_actionPerformed(ActionEvent e)
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769 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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774 protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
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779 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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784 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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789 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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794 protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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799 protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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804 protected void copySelectedMenuItem_actionPerformed(ActionEvent e)
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809 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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814 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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819 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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824 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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829 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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834 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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840 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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845 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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850 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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855 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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861 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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866 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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872 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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879 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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884 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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889 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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894 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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899 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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904 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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909 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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914 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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919 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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924 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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929 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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935 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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940 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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947 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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955 protected void clustalColour_actionPerformed(ActionEvent e)
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960 protected void zappoColour_actionPerformed(ActionEvent e)
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965 protected void taylorColour_actionPerformed(ActionEvent e)
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971 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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976 protected void helixColour_actionPerformed(ActionEvent e)
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981 protected void strandColour_actionPerformed(ActionEvent e)
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986 protected void turnColour_actionPerformed(ActionEvent e)
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991 protected void buriedColour_actionPerformed(ActionEvent e)
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997 protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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1003 protected void abovePIDColour_actionPerformed(ActionEvent e)
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1009 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1014 protected void PIDColour_actionPerformed(ActionEvent e)
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1019 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1024 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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1029 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1034 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1039 protected void pdbTest_actionPerformed(ActionEvent e)
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1044 protected void printMenuItem_actionPerformed(ActionEvent e)
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1049 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1054 protected void findMenuItem_actionPerformed(ActionEvent e)
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