1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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36 protected JMenuItem fontNameMenuItem = new JMenuItem();
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37 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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38 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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39 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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40 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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41 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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42 protected JMenuItem sortIDMenuItem = new JMenuItem();
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43 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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44 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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45 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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46 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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47 protected JMenuItem PCAMenuItem = new JMenuItem();
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48 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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49 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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50 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public JLabel statusBar = new JLabel();
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53 protected JMenu saveAlignmentMenu = new JMenu();
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54 protected JMenu outputTextboxMenu = new JMenu();
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55 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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66 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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67 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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68 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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69 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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70 JMenuItem htmlMenuItem = new JMenuItem();
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71 JMenuItem schemeKeyMenuItem = new JMenuItem();
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72 JMenuItem overviewMenuItem = new JMenuItem();
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73 protected JMenuItem undoMenuItem = new JMenuItem();
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74 protected JMenuItem redoMenuItem = new JMenuItem();
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75 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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76 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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77 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem pdbTest = new JMenuItem();
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79 JMenuItem printMenuItem = new JMenuItem();
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80 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem findMenuItem = new JMenuItem();
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82 JMenu searchMenu = new JMenu();
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83 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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84 protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
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85 public GAlignFrame()
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90 setJMenuBar(alignFrameMenuBar);
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93 // dynamically fill save as menu with available formats
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94 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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95 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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96 saveAlignmentMenu.add( item );
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97 item.addActionListener(new java.awt.event.ActionListener()
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99 public void actionPerformed(ActionEvent e)
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101 saveAs_actionPerformed(e);
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105 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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106 item.addActionListener(new java.awt.event.ActionListener()
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108 public void actionPerformed(ActionEvent e)
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110 outputText_actionPerformed(e);
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114 outputTextboxMenu.add( item );
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120 e.printStackTrace();
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123 ButtonGroup colours = new ButtonGroup();
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124 colours.add(noColourmenuItem);
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125 colours.add(clustalColour);
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126 colours.add(zappoColour);
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127 colours.add(taylorColour);
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128 colours.add(hydrophobicityColour);
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129 colours.add(helixColour);
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130 colours.add(strandColour);
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131 colours.add(turnColour);
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132 colours.add(buriedColour);
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133 colours.add(userDefinedColour);
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134 colours.add(PIDColour);
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135 colours.add(BLOSUM62Colour);
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137 private void jbInit() throws Exception
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139 fileMenu.setMnemonic('F');
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140 fileMenu.setText("File");
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141 saveAlignmentMenu.setMnemonic('L');
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142 saveAlignmentMenu.setText("Save alignment to local file");
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143 closeMenuItem.setMnemonic('C');
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144 closeMenuItem.setText("Close");
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145 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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147 public void actionPerformed(ActionEvent e)
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149 closeMenuItem_actionPerformed(e);
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152 editMenu.setText("Edit");
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153 fontMenu.setText("Font");
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154 viewMenu.setText("View");
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155 colourMenu.setText("Colour");
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156 calculateMenu.setText("Calculate");
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157 alignMenu.setText("Web Service");
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158 groupsMenuItem.setText("Groups");
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159 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 groupsMenuItem_actionPerformed(e);
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166 selectAllSequenceMenuItem.setText("Select all sequences");
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167 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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169 public void actionPerformed(ActionEvent e)
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171 selectAllSequenceMenuItem_actionPerformed(e);
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174 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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175 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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177 public void actionPerformed(ActionEvent e)
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179 deselectAllSequenceMenuItem_actionPerformed(e);
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182 invertSequenceMenuItem.setText("Invert sequence selection");
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183 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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185 public void actionPerformed(ActionEvent e)
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187 invertSequenceMenuItem_actionPerformed(e);
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190 deselectAllColumnsMenuItem.setText("Deselect all columns");
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191 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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193 public void actionPerformed(ActionEvent e)
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195 deselectAllColumnsMenuItem_actionPerformed(e);
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198 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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199 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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201 public void actionPerformed(ActionEvent e)
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203 remove2LeftMenuItem_actionPerformed(e);
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206 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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207 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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209 public void actionPerformed(ActionEvent e)
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211 remove2RightMenuItem_actionPerformed(e);
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214 removeGappedColumnMenuItem.setText("Remove gapped columns");
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215 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 removeGappedColumnMenuItem_actionPerformed(e);
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222 removeAllGapsMenuItem.setText("Remove all gaps");
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223 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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225 public void actionPerformed(ActionEvent e)
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227 removeAllGapsMenuItem_actionPerformed(e);
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230 setGapCharMenuItem.setText("Set gap character to \".\"");
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231 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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233 public void actionPerformed(ActionEvent e)
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235 setGapCharMenuItem_actionPerformed(e);
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238 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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240 public void actionPerformed(ActionEvent e)
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242 fontNameMenuItem_actionPerformed(e);
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245 fontSizeMenuItem.setText("10");
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246 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 fontSizeMenuItem_actionPerformed(e);
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253 fontStyleMenuItem.setText("Plain");
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254 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 fontStyleMenuItem_actionPerformed(e);
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261 viewBoxesMenuItem.setText("Boxes");
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262 viewBoxesMenuItem.setState(true);
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263 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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265 public void actionPerformed(ActionEvent e)
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267 viewBoxesMenuItem_actionPerformed(e);
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270 viewTextMenuItem.setText("Text");
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271 viewTextMenuItem.setState(true);
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272 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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274 public void actionPerformed(ActionEvent e)
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276 viewTextMenuItem_actionPerformed(e);
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279 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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280 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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282 public void actionPerformed(ActionEvent e)
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284 sortPairwiseMenuItem_actionPerformed(e);
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287 sortIDMenuItem.setText("Sort by ID");
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288 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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290 public void actionPerformed(ActionEvent e)
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292 sortIDMenuItem_actionPerformed(e);
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295 sortGroupMenuItem.setText("Sort by group");
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296 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 sortGroupMenuItem_actionPerformed(e);
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303 sortTreeOrderMenuItem.setText("Sort by tree order");
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304 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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306 public void actionPerformed(ActionEvent e)
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308 sortTreeOrderMenuItem_actionPerformed(e);
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311 removeRedundancyMenuItem.setText("Remove redundancy");
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312 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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314 public void actionPerformed(ActionEvent e)
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316 removeRedundancyMenuItem_actionPerformed(e);
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319 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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320 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 pairwiseAlignmentMenuItem_actionPerformed(e);
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327 PCAMenuItem.setText("Principal component analysis");
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328 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 PCAMenuItem_actionPerformed(e);
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335 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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336 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 averageDistanceTreeMenuItem_actionPerformed(e);
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343 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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344 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 neighbourTreeMenuItem_actionPerformed(e);
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351 clustalAlignMenuItem.setText("Clustal alignment");
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352 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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354 public void actionPerformed(ActionEvent e)
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356 clustalAlignMenuItem_actionPerformed(e);
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359 this.getContentPane().setLayout(borderLayout1);
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360 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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361 statusBar.setBackground(Color.white);
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362 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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363 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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364 statusBar.setText("Status bar");
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365 outputTextboxMenu.setMnemonic('T');
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366 outputTextboxMenu.setText("Output alignment via textbox");
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367 clustalColour.setSelected(false);
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368 clustalColour.setText("Clustalx colours");
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369 clustalColour.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 clustalColour_actionPerformed(e);
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376 zappoColour.setText("Zappo colour scheme");
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377 zappoColour.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 zappoColour_actionPerformed(e);
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384 taylorColour.setText("Taylor colour scheme");
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385 taylorColour.addActionListener(new java.awt.event.ActionListener()
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387 public void actionPerformed(ActionEvent e)
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389 taylorColour_actionPerformed(e);
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392 hydrophobicityColour.setText("By hydrophobicity");
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393 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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395 public void actionPerformed(ActionEvent e)
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397 hydrophobicityColour_actionPerformed(e);
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400 helixColour.setText("Helix propensity");
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401 helixColour.addActionListener(new java.awt.event.ActionListener()
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403 public void actionPerformed(ActionEvent e)
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405 helixColour_actionPerformed(e);
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408 strandColour.setText("Strand propensity");
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409 strandColour.addActionListener(new java.awt.event.ActionListener()
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411 public void actionPerformed(ActionEvent e)
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413 strandColour_actionPerformed(e);
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416 turnColour.setText("Turn propensity");
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417 turnColour.addActionListener(new java.awt.event.ActionListener()
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419 public void actionPerformed(ActionEvent e)
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421 turnColour_actionPerformed(e);
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424 buriedColour.setText("Buried index");
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425 buriedColour.addActionListener(new java.awt.event.ActionListener()
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427 public void actionPerformed(ActionEvent e)
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429 buriedColour_actionPerformed(e);
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432 userDefinedColour.setText("User defined colours");
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433 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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435 public void actionPerformed(ActionEvent e)
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437 userDefinedColour_actionPerformed(e);
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440 PIDColour.setText("Percentage Identity");
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441 PIDColour.addActionListener(new java.awt.event.ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 PIDColour_actionPerformed(e);
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448 BLOSUM62Colour.setText("BLOSUM62 score");
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449 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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451 public void actionPerformed(ActionEvent e)
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453 BLOSUM62Colour_actionPerformed(e);
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456 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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457 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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459 public void actionPerformed(ActionEvent e)
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461 avTreeBlosumMenuItem_actionPerformed(e);
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464 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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465 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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467 public void actionPerformed(ActionEvent e)
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469 njTreeBlosumMenuItem_actionPerformed(e);
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472 consensusGraphMenuItem.setActionCommand("");
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473 consensusGraphMenuItem.setText("Consensus graph");
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474 consensusGraphMenuItem.setState(true);
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475 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 consensusGraphMenuItem_actionPerformed(e);
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482 colourTextMenuItem.setText("Colour text");
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483 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 colourTextMenuItem_actionPerformed(e);
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490 htmlMenuItem.setText("Output as HTML");
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491 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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493 public void actionPerformed(ActionEvent e)
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495 htmlMenuItem_actionPerformed(e);
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498 schemeKeyMenuItem.setText("Colour Scheme Key");
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499 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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501 public void actionPerformed(ActionEvent e)
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503 schemeKeyMenuItem_actionPerformed(e);
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506 overviewMenuItem.setText("Overview window");
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507 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 overviewMenuItem_actionPerformed(e);
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514 undoMenuItem.setEnabled(false);
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515 undoMenuItem.setMnemonic('Z');
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516 undoMenuItem.setText("Undo");
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517 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 undoMenuItem_actionPerformed(e);
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524 redoMenuItem.setEnabled(false);
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525 redoMenuItem.setMnemonic('0');
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526 redoMenuItem.setText("Redo");
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527 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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529 public void actionPerformed(ActionEvent e)
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531 redoMenuItem_actionPerformed(e);
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534 conservationMenuItem.setText("By conservation");
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535 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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537 public void actionPerformed(ActionEvent e)
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539 conservationMenuItem_actionPerformed(e);
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542 noColourmenuItem.setText("None");
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543 noColourmenuItem.setSelected(true);
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544 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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546 public void actionPerformed(ActionEvent e)
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548 noColourmenuItem_actionPerformed(e);
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551 wrapMenuItem.setEnabled(false);
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552 wrapMenuItem.setText("Wrap alignment");
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553 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 wrapMenuItem_actionPerformed(e);
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560 pdbTest.setText("PDB Test Viewer");
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561 pdbTest.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 pdbTest_actionPerformed(e);
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568 printMenuItem.setText("Print");
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569 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 printMenuItem_actionPerformed(e);
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576 renderGapsMenuItem.setText("Render gaps");
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577 renderGapsMenuItem.setState(true);
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578 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 renderGapsMenuItem_actionPerformed(e);
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585 findMenuItem.setText("Find");
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586 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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588 public void actionPerformed(ActionEvent e)
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590 findMenuItem_actionPerformed(e);
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593 searchMenu.setText("Search");
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595 abovePIDThreshold.setText("Above PID threshold");
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596 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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597 public void actionPerformed(ActionEvent e) {
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598 abovePIDThreshold_actionPerformed(e);
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601 secondaryStructure.setSelected(true);
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602 secondaryStructure.setText("Secondary Structure");
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603 secondaryStructure.addActionListener(new ActionListener()
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605 public void actionPerformed(ActionEvent actionEvent)
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607 secondaryStructure_actionPerformed(actionEvent);
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610 alignFrameMenuBar.add(fileMenu);
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611 alignFrameMenuBar.add(editMenu);
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612 alignFrameMenuBar.add(searchMenu);
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613 alignFrameMenuBar.add(fontMenu);
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614 alignFrameMenuBar.add(viewMenu);
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615 alignFrameMenuBar.add(colourMenu);
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616 alignFrameMenuBar.add(calculateMenu);
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617 alignFrameMenuBar.add(alignMenu);
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618 fileMenu.add(saveAlignmentMenu);
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619 fileMenu.add(outputTextboxMenu);
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620 fileMenu.add(htmlMenuItem);
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621 fileMenu.add(printMenuItem);
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622 fileMenu.addSeparator();
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623 fileMenu.add(closeMenuItem);
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624 editMenu.add(undoMenuItem);
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625 editMenu.add(redoMenuItem);
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626 editMenu.addSeparator();
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627 editMenu.add(groupsMenuItem);
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628 editMenu.addSeparator();
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629 editMenu.add(selectAllSequenceMenuItem);
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630 editMenu.add(deselectAllSequenceMenuItem);
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631 editMenu.add(invertSequenceMenuItem);
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632 editMenu.addSeparator();
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633 editMenu.add(deselectAllColumnsMenuItem);
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634 editMenu.add(remove2LeftMenuItem);
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635 editMenu.add(remove2RightMenuItem);
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636 editMenu.addSeparator();
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637 editMenu.add(removeGappedColumnMenuItem);
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638 editMenu.add(removeAllGapsMenuItem);
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639 editMenu.add(setGapCharMenuItem);
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640 searchMenu.add(findMenuItem);
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641 fontMenu.add(fontNameMenuItem);
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642 fontMenu.add(fontSizeMenuItem);
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643 fontMenu.add(fontStyleMenuItem);
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644 viewMenu.add(wrapMenuItem);
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645 viewMenu.add(viewBoxesMenuItem);
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646 viewMenu.add(viewTextMenuItem);
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647 viewMenu.add(colourTextMenuItem);
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648 viewMenu.add(renderGapsMenuItem);
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649 viewMenu.add(consensusGraphMenuItem);
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650 viewMenu.add(overviewMenuItem);
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651 viewMenu.add(secondaryStructure);
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652 colourMenu.add(noColourmenuItem);
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653 colourMenu.add(clustalColour);
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654 colourMenu.add(zappoColour);
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655 colourMenu.add(taylorColour);
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656 colourMenu.add(hydrophobicityColour);
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657 colourMenu.add(helixColour);
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658 colourMenu.add(strandColour);
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659 colourMenu.add(turnColour);
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660 colourMenu.add(buriedColour);
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661 colourMenu.add(userDefinedColour);
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662 colourMenu.add(PIDColour);
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663 colourMenu.add(BLOSUM62Colour);
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664 colourMenu.addSeparator();
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665 colourMenu.add(abovePIDThreshold);
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666 colourMenu.add(conservationMenuItem);
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667 colourMenu.addSeparator();
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668 colourMenu.add(schemeKeyMenuItem);
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669 calculateMenu.add(sortPairwiseMenuItem);
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670 calculateMenu.add(sortIDMenuItem);
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671 calculateMenu.add(sortGroupMenuItem);
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672 calculateMenu.add(sortTreeOrderMenuItem);
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673 calculateMenu.add(removeRedundancyMenuItem);
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674 calculateMenu.addSeparator();
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675 calculateMenu.add(pairwiseAlignmentMenuItem);
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676 calculateMenu.add(PCAMenuItem);
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677 calculateMenu.addSeparator();
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678 calculateMenu.add(averageDistanceTreeMenuItem);
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679 calculateMenu.add(neighbourTreeMenuItem);
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680 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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681 calculateMenu.add(njTreeBlosumMenuItem);
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682 alignMenu.add(clustalAlignMenuItem);
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683 alignMenu.add(pdbTest);
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684 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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687 protected void saveAs_actionPerformed(ActionEvent e)
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692 protected void outputText_actionPerformed(ActionEvent e)
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697 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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706 protected void closeMenuItem_actionPerformed(ActionEvent e)
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711 protected void redoMenuItem_actionPerformed(ActionEvent e)
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716 protected void undoMenuItem_actionPerformed(ActionEvent e)
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722 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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728 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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733 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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738 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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744 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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749 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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754 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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759 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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764 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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769 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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775 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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780 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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785 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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790 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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796 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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801 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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807 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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814 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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819 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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824 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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829 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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834 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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839 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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844 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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849 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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854 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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859 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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864 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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870 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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875 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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882 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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890 protected void clustalColour_actionPerformed(ActionEvent e)
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895 protected void zappoColour_actionPerformed(ActionEvent e)
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900 protected void taylorColour_actionPerformed(ActionEvent e)
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906 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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911 protected void helixColour_actionPerformed(ActionEvent e)
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916 protected void strandColour_actionPerformed(ActionEvent e)
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921 protected void turnColour_actionPerformed(ActionEvent e)
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926 protected void buriedColour_actionPerformed(ActionEvent e)
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933 protected void userDefinedColour_actionPerformed(ActionEvent e)
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938 protected void PIDColour_actionPerformed(ActionEvent e)
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943 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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948 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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953 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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958 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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963 protected void pdbTest_actionPerformed(ActionEvent e)
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968 protected void printMenuItem_actionPerformed(ActionEvent e)
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973 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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978 protected void findMenuItem_actionPerformed(ActionEvent e)
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984 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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988 public void secondaryStructure_actionPerformed(ActionEvent actionEvent)
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