1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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36 protected JMenuItem fontNameMenuItem = new JMenuItem();
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37 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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38 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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39 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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40 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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41 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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42 protected JMenuItem sortIDMenuItem = new JMenuItem();
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43 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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44 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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45 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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46 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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47 protected JMenuItem PCAMenuItem = new JMenuItem();
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48 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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49 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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50 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public JLabel statusBar = new JLabel();
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53 protected JMenu saveAlignmentMenu = new JMenu();
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54 protected JMenu outputTextboxMenu = new JMenu();
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55 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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66 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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67 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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68 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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69 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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70 JMenuItem htmlMenuItem = new JMenuItem();
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71 JMenuItem overviewMenuItem = new JMenuItem();
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72 protected JMenuItem undoMenuItem = new JMenuItem();
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73 protected JMenuItem redoMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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75 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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76 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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77 JMenuItem pdbTest = new JMenuItem();
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78 JMenuItem printMenuItem = new JMenuItem();
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79 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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80 JMenuItem findMenuItem = new JMenuItem();
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81 JMenu searchMenu = new JMenu();
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82 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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83 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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84 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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85 JMenuItem deleteGroups = new JMenuItem();
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86 public GAlignFrame()
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93 setJMenuBar(alignFrameMenuBar);
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96 // dynamically fill save as menu with available formats
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97 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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98 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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99 saveAlignmentMenu.add( item );
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100 item.addActionListener(new java.awt.event.ActionListener()
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102 public void actionPerformed(ActionEvent e)
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104 saveAs_actionPerformed(e);
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108 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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109 item.addActionListener(new java.awt.event.ActionListener()
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111 public void actionPerformed(ActionEvent e)
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113 outputText_actionPerformed(e);
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117 outputTextboxMenu.add( item );
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123 e.printStackTrace();
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126 ButtonGroup colours = new ButtonGroup();
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127 colours.add(noColourmenuItem);
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128 colours.add(clustalColour);
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129 colours.add(zappoColour);
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130 colours.add(taylorColour);
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131 colours.add(hydrophobicityColour);
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132 colours.add(helixColour);
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133 colours.add(strandColour);
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134 colours.add(turnColour);
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135 colours.add(buriedColour);
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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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139 colours.add(nucleotideColour);
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141 private void jbInit() throws Exception
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143 fileMenu.setMnemonic('F');
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144 fileMenu.setText("File");
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145 saveAlignmentMenu.setMnemonic('L');
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146 saveAlignmentMenu.setText("Save alignment to local file");
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147 closeMenuItem.setMnemonic('C');
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148 closeMenuItem.setText("Close");
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149 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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151 public void actionPerformed(ActionEvent e)
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153 closeMenuItem_actionPerformed(e);
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156 editMenu.setText("Edit");
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157 fontMenu.setText("Font");
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158 viewMenu.setText("View");
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159 colourMenu.setText("Colour");
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160 calculateMenu.setText("Calculate");
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161 alignMenu.setText("Web Service");
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162 groupsMenuItem.setText("Groups");
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163 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 groupsMenuItem_actionPerformed(e);
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170 selectAllSequenceMenuItem.setText("Select all");
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171 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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173 public void actionPerformed(ActionEvent e)
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175 selectAllSequenceMenuItem_actionPerformed(e);
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178 deselectAllSequenceMenuItem.setText("Clear selection");
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179 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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181 public void actionPerformed(ActionEvent e)
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183 deselectAllSequenceMenuItem_actionPerformed(e);
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186 invertSequenceMenuItem.setText("Invert sequence selection");
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187 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 invertSequenceMenuItem_actionPerformed(e);
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194 deselectAllColumnsMenuItem.setText("Deselect all columns");
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195 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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197 public void actionPerformed(ActionEvent e)
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199 deselectAllColumnsMenuItem_actionPerformed(e);
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202 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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203 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 remove2LeftMenuItem_actionPerformed(e);
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210 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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211 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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213 public void actionPerformed(ActionEvent e)
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215 remove2RightMenuItem_actionPerformed(e);
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218 removeGappedColumnMenuItem.setText("Remove gapped columns");
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219 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 removeGappedColumnMenuItem_actionPerformed(e);
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226 removeAllGapsMenuItem.setText("Remove all gaps");
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227 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 removeAllGapsMenuItem_actionPerformed(e);
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234 setGapCharMenuItem.setText("Set gap character to \".\"");
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235 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 setGapCharMenuItem_actionPerformed(e);
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242 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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244 public void actionPerformed(ActionEvent e)
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246 fontNameMenuItem_actionPerformed(e);
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249 fontSizeMenuItem.setText("10");
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250 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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252 public void actionPerformed(ActionEvent e)
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254 fontSizeMenuItem_actionPerformed(e);
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257 fontStyleMenuItem.setText("Plain");
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258 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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260 public void actionPerformed(ActionEvent e)
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262 fontStyleMenuItem_actionPerformed(e);
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265 viewBoxesMenuItem.setText("Boxes");
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266 viewBoxesMenuItem.setState(true);
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267 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 viewBoxesMenuItem_actionPerformed(e);
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274 viewTextMenuItem.setText("Text");
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275 viewTextMenuItem.setState(true);
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276 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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278 public void actionPerformed(ActionEvent e)
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280 viewTextMenuItem_actionPerformed(e);
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283 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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284 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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286 public void actionPerformed(ActionEvent e)
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288 sortPairwiseMenuItem_actionPerformed(e);
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291 sortIDMenuItem.setText("Sort by ID");
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292 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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294 public void actionPerformed(ActionEvent e)
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296 sortIDMenuItem_actionPerformed(e);
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299 sortGroupMenuItem.setText("Sort by group");
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300 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(ActionEvent e)
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304 sortGroupMenuItem_actionPerformed(e);
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307 sortTreeOrderMenuItem.setText("Sort by tree order");
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308 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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310 public void actionPerformed(ActionEvent e)
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312 sortTreeOrderMenuItem_actionPerformed(e);
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315 removeRedundancyMenuItem.setText("Remove redundancy");
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316 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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318 public void actionPerformed(ActionEvent e)
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320 removeRedundancyMenuItem_actionPerformed(e);
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323 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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324 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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326 public void actionPerformed(ActionEvent e)
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328 pairwiseAlignmentMenuItem_actionPerformed(e);
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331 PCAMenuItem.setText("Principal component analysis");
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332 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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334 public void actionPerformed(ActionEvent e)
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336 PCAMenuItem_actionPerformed(e);
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339 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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340 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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342 public void actionPerformed(ActionEvent e)
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344 averageDistanceTreeMenuItem_actionPerformed(e);
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347 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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348 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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350 public void actionPerformed(ActionEvent e)
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352 neighbourTreeMenuItem_actionPerformed(e);
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355 clustalAlignMenuItem.setText("Clustal alignment");
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356 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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358 public void actionPerformed(ActionEvent e)
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360 clustalAlignMenuItem_actionPerformed(e);
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363 this.getContentPane().setLayout(borderLayout1);
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364 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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365 statusBar.setBackground(Color.white);
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366 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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367 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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368 statusBar.setText("Status bar");
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369 outputTextboxMenu.setMnemonic('T');
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370 outputTextboxMenu.setText("Output alignment via textbox");
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371 clustalColour.setSelected(false);
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372 clustalColour.setText("Clustalx colours");
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373 clustalColour.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 clustalColour_actionPerformed(e);
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380 zappoColour.setText("Zappo colour scheme");
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381 zappoColour.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 zappoColour_actionPerformed(e);
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388 taylorColour.setText("Taylor colour scheme");
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389 taylorColour.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 taylorColour_actionPerformed(e);
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396 hydrophobicityColour.setText("By hydrophobicity");
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397 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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399 public void actionPerformed(ActionEvent e)
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401 hydrophobicityColour_actionPerformed(e);
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404 helixColour.setText("Helix propensity");
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405 helixColour.addActionListener(new java.awt.event.ActionListener()
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407 public void actionPerformed(ActionEvent e)
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409 helixColour_actionPerformed(e);
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412 strandColour.setText("Strand propensity");
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413 strandColour.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 strandColour_actionPerformed(e);
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420 turnColour.setText("Turn propensity");
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421 turnColour.addActionListener(new java.awt.event.ActionListener()
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423 public void actionPerformed(ActionEvent e)
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425 turnColour_actionPerformed(e);
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428 buriedColour.setText("Buried index");
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429 buriedColour.addActionListener(new java.awt.event.ActionListener()
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431 public void actionPerformed(ActionEvent e)
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433 buriedColour_actionPerformed(e);
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436 userDefinedColour.setText("User defined colours");
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437 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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439 public void actionPerformed(ActionEvent e)
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441 userDefinedColour_actionPerformed(e);
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444 PIDColour.setText("Percentage Identity");
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445 PIDColour.addActionListener(new java.awt.event.ActionListener()
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447 public void actionPerformed(ActionEvent e)
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449 PIDColour_actionPerformed(e);
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452 BLOSUM62Colour.setText("BLOSUM62 score");
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453 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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455 public void actionPerformed(ActionEvent e)
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457 BLOSUM62Colour_actionPerformed(e);
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460 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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461 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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463 public void actionPerformed(ActionEvent e)
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465 avTreeBlosumMenuItem_actionPerformed(e);
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468 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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469 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 njTreeBlosumMenuItem_actionPerformed(e);
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476 consensusGraphMenuItem.setActionCommand("");
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477 consensusGraphMenuItem.setText("Consensus graph");
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478 consensusGraphMenuItem.setState(true);
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479 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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481 public void actionPerformed(ActionEvent e)
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483 consensusGraphMenuItem_actionPerformed(e);
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486 colourTextMenuItem.setText("Colour text");
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487 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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489 public void actionPerformed(ActionEvent e)
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491 colourTextMenuItem_actionPerformed(e);
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494 htmlMenuItem.setText("Output as HTML");
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495 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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497 public void actionPerformed(ActionEvent e)
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499 htmlMenuItem_actionPerformed(e);
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502 overviewMenuItem.setText("Overview window");
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503 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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505 public void actionPerformed(ActionEvent e)
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507 overviewMenuItem_actionPerformed(e);
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510 undoMenuItem.setEnabled(false);
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511 undoMenuItem.setMnemonic('Z');
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512 undoMenuItem.setText("Undo");
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513 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 undoMenuItem_actionPerformed(e);
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520 redoMenuItem.setEnabled(false);
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521 redoMenuItem.setMnemonic('0');
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522 redoMenuItem.setText("Redo");
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523 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 redoMenuItem_actionPerformed(e);
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530 conservationMenuItem.setText("By conservation");
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531 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 conservationMenuItem_actionPerformed(e);
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538 noColourmenuItem.setText("None");
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539 noColourmenuItem.setSelected(true);
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540 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 noColourmenuItem_actionPerformed(e);
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547 wrapMenuItem.setText("Wrap alignment");
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548 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 wrapMenuItem_actionPerformed(e);
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555 pdbTest.setText("PDB Test Viewer");
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556 pdbTest.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 pdbTest_actionPerformed(e);
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563 printMenuItem.setText("Print");
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564 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 printMenuItem_actionPerformed(e);
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571 renderGapsMenuItem.setText("Render gaps");
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572 renderGapsMenuItem.setState(true);
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573 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 renderGapsMenuItem_actionPerformed(e);
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580 findMenuItem.setText("Find");
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581 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 findMenuItem_actionPerformed(e);
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588 searchMenu.setText("Search");
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590 abovePIDThreshold.setText("Above PID threshold");
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591 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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592 public void actionPerformed(ActionEvent e) {
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593 abovePIDThreshold_actionPerformed(e);
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596 sequenceFeatures.setSelected(true);
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597 sequenceFeatures.setText("Sequence Features");
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598 sequenceFeatures.addActionListener(new ActionListener()
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600 public void actionPerformed(ActionEvent actionEvent)
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602 sequenceFeatures_actionPerformed(actionEvent);
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605 nucleotideColour.setText("Nucleotide colours");
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606 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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608 public void actionPerformed(ActionEvent e)
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610 nucleotideColour_actionPerformed(e);
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613 deleteGroups.setSelected(false);
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614 deleteGroups.setText("Delete all groups");
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615 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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617 public void actionPerformed(ActionEvent e)
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619 deleteGroups_actionPerformed(e);
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622 alignFrameMenuBar.add(fileMenu);
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623 alignFrameMenuBar.add(editMenu);
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624 alignFrameMenuBar.add(searchMenu);
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625 alignFrameMenuBar.add(fontMenu);
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626 alignFrameMenuBar.add(viewMenu);
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627 alignFrameMenuBar.add(colourMenu);
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628 alignFrameMenuBar.add(calculateMenu);
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629 alignFrameMenuBar.add(alignMenu);
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630 fileMenu.add(saveAlignmentMenu);
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631 fileMenu.add(outputTextboxMenu);
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632 fileMenu.add(htmlMenuItem);
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633 fileMenu.add(printMenuItem);
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634 fileMenu.addSeparator();
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635 fileMenu.add(closeMenuItem);
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636 editMenu.add(undoMenuItem);
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637 editMenu.add(redoMenuItem);
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638 editMenu.addSeparator();
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639 editMenu.add(deselectAllSequenceMenuItem);
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640 editMenu.add(selectAllSequenceMenuItem);
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641 editMenu.add(invertSequenceMenuItem);
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642 editMenu.add(deleteGroups);
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643 editMenu.add(groupsMenuItem);
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644 editMenu.addSeparator();
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645 editMenu.add(deselectAllColumnsMenuItem);
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646 editMenu.add(remove2LeftMenuItem);
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647 editMenu.add(remove2RightMenuItem);
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648 editMenu.addSeparator();
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649 editMenu.add(removeGappedColumnMenuItem);
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650 editMenu.add(removeAllGapsMenuItem);
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651 editMenu.add(setGapCharMenuItem);
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652 searchMenu.add(findMenuItem);
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653 fontMenu.add(fontNameMenuItem);
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654 fontMenu.add(fontSizeMenuItem);
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655 fontMenu.add(fontStyleMenuItem);
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656 viewMenu.add(wrapMenuItem);
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657 viewMenu.add(viewBoxesMenuItem);
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658 viewMenu.add(viewTextMenuItem);
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659 viewMenu.add(colourTextMenuItem);
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660 viewMenu.add(renderGapsMenuItem);
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661 viewMenu.add(consensusGraphMenuItem);
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662 viewMenu.add(overviewMenuItem);
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663 viewMenu.add(sequenceFeatures);
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664 colourMenu.add(noColourmenuItem);
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665 colourMenu.add(clustalColour);
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666 colourMenu.add(zappoColour);
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667 colourMenu.add(taylorColour);
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668 colourMenu.add(hydrophobicityColour);
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669 colourMenu.add(helixColour);
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670 colourMenu.add(strandColour);
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671 colourMenu.add(turnColour);
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672 colourMenu.add(buriedColour);
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673 colourMenu.add(nucleotideColour);
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674 colourMenu.add(userDefinedColour);
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675 colourMenu.add(PIDColour);
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676 colourMenu.add(BLOSUM62Colour);
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677 colourMenu.addSeparator();
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678 colourMenu.add(abovePIDThreshold);
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679 colourMenu.add(conservationMenuItem);
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680 calculateMenu.add(sortPairwiseMenuItem);
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681 calculateMenu.add(sortIDMenuItem);
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682 calculateMenu.add(sortGroupMenuItem);
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683 calculateMenu.add(sortTreeOrderMenuItem);
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684 calculateMenu.add(removeRedundancyMenuItem);
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685 calculateMenu.addSeparator();
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686 calculateMenu.add(pairwiseAlignmentMenuItem);
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687 calculateMenu.add(PCAMenuItem);
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688 calculateMenu.addSeparator();
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689 calculateMenu.add(averageDistanceTreeMenuItem);
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690 calculateMenu.add(neighbourTreeMenuItem);
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691 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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692 calculateMenu.add(njTreeBlosumMenuItem);
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693 alignMenu.add(clustalAlignMenuItem);
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694 alignMenu.add(pdbTest);
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695 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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698 protected void saveAs_actionPerformed(ActionEvent e)
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703 protected void outputText_actionPerformed(ActionEvent e)
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708 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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717 protected void closeMenuItem_actionPerformed(ActionEvent e)
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722 protected void redoMenuItem_actionPerformed(ActionEvent e)
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727 protected void undoMenuItem_actionPerformed(ActionEvent e)
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733 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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739 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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744 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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749 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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755 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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760 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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765 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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770 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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775 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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780 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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786 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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791 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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796 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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801 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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807 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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812 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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818 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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825 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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830 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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835 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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840 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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845 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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850 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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855 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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860 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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865 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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870 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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875 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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881 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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886 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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893 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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901 protected void clustalColour_actionPerformed(ActionEvent e)
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906 protected void zappoColour_actionPerformed(ActionEvent e)
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911 protected void taylorColour_actionPerformed(ActionEvent e)
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917 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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922 protected void helixColour_actionPerformed(ActionEvent e)
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927 protected void strandColour_actionPerformed(ActionEvent e)
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932 protected void turnColour_actionPerformed(ActionEvent e)
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937 protected void buriedColour_actionPerformed(ActionEvent e)
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944 protected void userDefinedColour_actionPerformed(ActionEvent e)
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949 protected void PIDColour_actionPerformed(ActionEvent e)
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954 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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960 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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965 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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970 protected void pdbTest_actionPerformed(ActionEvent e)
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975 protected void printMenuItem_actionPerformed(ActionEvent e)
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980 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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985 protected void findMenuItem_actionPerformed(ActionEvent e)
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991 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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995 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1000 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1005 protected void deleteGroups_actionPerformed(ActionEvent e)
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