1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 public class GAlignFrame extends JInternalFrame
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17 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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18 protected JMenu fileMenu = new JMenu();
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19 protected JMenuItem closeMenuItem = new JMenuItem();
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20 protected JMenu editMenu = new JMenu();
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21 protected JMenu fontMenu = new JMenu();
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22 protected JMenu viewMenu = new JMenu();
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23 protected JMenu colourMenu = new JMenu();
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24 protected JMenu calculateMenu = new JMenu();
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25 protected JMenu alignMenu = new JMenu();
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26 protected JMenuItem groupsMenuItem = new JMenuItem();
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27 protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
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28 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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31 protected JMenuItem deleteSelectedMenuItem = new JMenuItem();
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32 protected JMenuItem moveSelectedMenuItem = new JMenuItem();
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33 protected JMenuItem copySelectedMenuItem = new JMenuItem();
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34 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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35 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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36 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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37 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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38 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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39 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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40 protected JMenuItem fontNameMenuItem = new JMenuItem();
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41 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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42 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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43 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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44 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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45 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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46 protected JMenuItem sortIDMenuItem = new JMenuItem();
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47 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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48 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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49 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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50 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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51 protected JMenuItem PCAMenuItem = new JMenuItem();
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52 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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53 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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54 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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55 BorderLayout borderLayout1 = new BorderLayout();
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56 public JLabel statusBar = new JLabel();
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57 protected JMenu saveAlignmentMenu = new JMenu();
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58 protected JMenu outputTextboxMenu = new JMenu();
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59 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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71 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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72 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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73 protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
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74 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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75 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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76 JMenuItem htmlMenuItem = new JMenuItem();
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77 JMenuItem schemeKeyMenuItem = new JMenuItem();
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78 JMenuItem overviewMenuItem = new JMenuItem();
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79 protected JMenuItem undoMenuItem = new JMenuItem();
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80 protected JMenuItem redoMenuItem = new JMenuItem();
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81 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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82 JMenuItem noColourmenuItem = new JMenuItem();
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83 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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84 JMenuItem pdbTest = new JMenuItem();
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85 JMenuItem printMenuItem = new JMenuItem();
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86 public GAlignFrame()
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91 setJMenuBar(alignFrameMenuBar);
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94 // dynamically fill save as menu with available formats
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95 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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96 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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97 saveAlignmentMenu.add( item );
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98 item.addActionListener(new java.awt.event.ActionListener()
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100 public void actionPerformed(ActionEvent e)
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102 saveAs_actionPerformed(e);
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106 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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107 item.addActionListener(new java.awt.event.ActionListener()
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109 public void actionPerformed(ActionEvent e)
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111 outputText_actionPerformed(e);
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115 outputTextboxMenu.add( item );
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121 e.printStackTrace();
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124 ButtonGroup colours = new ButtonGroup();
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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(abovePIDColour);
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134 colours.add(userDefinedColour);
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135 colours.add(PIDColour);
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136 colours.add(BLOSUM62Colour);
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138 private void jbInit() throws Exception
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140 fileMenu.setMnemonic('F');
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141 fileMenu.setText("File");
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142 saveAlignmentMenu.setMnemonic('L');
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143 saveAlignmentMenu.setText("Save alignment to local file");
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144 closeMenuItem.setMnemonic('C');
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145 closeMenuItem.setText("Close");
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146 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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148 public void actionPerformed(ActionEvent e)
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150 closeMenuItem_actionPerformed(e);
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153 editMenu.setText("Edit");
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154 fontMenu.setText("Font");
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155 viewMenu.setText("View");
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156 colourMenu.setText("Colour");
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157 calculateMenu.setText("Calculate");
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158 alignMenu.setText("Web Service");
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159 groupsMenuItem.setText("Groups");
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160 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 groupsMenuItem_actionPerformed(e);
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167 groupEditingMenuItem.setText("Group editing mode");
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168 groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
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170 public void actionPerformed(ActionEvent e)
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172 groupEditingMenuItem_actionPerformed(e);
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175 selectAllSequenceMenuItem.setText("Select all sequences");
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176 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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178 public void actionPerformed(ActionEvent e)
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180 selectAllSequenceMenuItem_actionPerformed(e);
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183 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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184 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 deselectAllSequenceMenuItem_actionPerformed(e);
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191 invertSequenceMenuItem.setText("Invert sequence selection");
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192 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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194 public void actionPerformed(ActionEvent e)
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196 invertSequenceMenuItem_actionPerformed(e);
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199 deleteSelectedMenuItem.setText("Delete selected sequences");
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200 deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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202 public void actionPerformed(ActionEvent e)
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204 deleteSelectedMenuItem_actionPerformed(e);
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207 moveSelectedMenuItem.setText("Move selected sequences to new alignment");
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208 moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 moveSelectedMenuItem_actionPerformed(e);
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215 copySelectedMenuItem.setText("Copy selected sequences to new alignment");
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216 copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 copySelectedMenuItem_actionPerformed(e);
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223 deselectAllColumnsMenuItem.setText("Deselect all columns");
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224 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 deselectAllColumnsMenuItem_actionPerformed(e);
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231 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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232 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 remove2LeftMenuItem_actionPerformed(e);
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239 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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240 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 remove2RightMenuItem_actionPerformed(e);
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247 removeGappedColumnMenuItem.setText("Remove gapped columns");
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248 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 removeGappedColumnMenuItem_actionPerformed(e);
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255 removeAllGapsMenuItem.setText("Remove all gaps");
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256 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 removeAllGapsMenuItem_actionPerformed(e);
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263 setGapCharMenuItem.setText("Set gap character to \"-\"");
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264 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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266 public void actionPerformed(ActionEvent e)
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268 setGapCharMenuItem_actionPerformed(e);
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271 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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275 fontNameMenuItem_actionPerformed(e);
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278 fontSizeMenuItem.setText("10");
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279 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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281 public void actionPerformed(ActionEvent e)
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283 fontSizeMenuItem_actionPerformed(e);
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286 fontStyleMenuItem.setText("Plain");
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287 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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289 public void actionPerformed(ActionEvent e)
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291 fontStyleMenuItem_actionPerformed(e);
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294 viewBoxesMenuItem.setText("Boxes");
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295 viewBoxesMenuItem.setState(true);
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296 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 viewBoxesMenuItem_actionPerformed(e);
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303 viewTextMenuItem.setText("Text");
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304 viewTextMenuItem.setState(true);
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305 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 viewTextMenuItem_actionPerformed(e);
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312 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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313 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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315 public void actionPerformed(ActionEvent e)
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317 sortPairwiseMenuItem_actionPerformed(e);
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320 sortIDMenuItem.setText("Sort by ID");
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321 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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323 public void actionPerformed(ActionEvent e)
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325 sortIDMenuItem_actionPerformed(e);
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328 sortGroupMenuItem.setText("Sort by group");
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329 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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331 public void actionPerformed(ActionEvent e)
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333 sortGroupMenuItem_actionPerformed(e);
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336 sortTreeOrderMenuItem.setText("Sort by tree order");
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337 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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339 public void actionPerformed(ActionEvent e)
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341 sortTreeOrderMenuItem_actionPerformed(e);
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344 removeRedundancyMenuItem.setText("Remove redundancy");
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345 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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347 public void actionPerformed(ActionEvent e)
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349 removeRedundancyMenuItem_actionPerformed(e);
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352 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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353 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 pairwiseAlignmentMenuItem_actionPerformed(e);
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360 PCAMenuItem.setText("Principal component analysis");
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361 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 PCAMenuItem_actionPerformed(e);
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368 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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369 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 averageDistanceTreeMenuItem_actionPerformed(e);
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376 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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377 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 neighbourTreeMenuItem_actionPerformed(e);
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384 clustalAlignMenuItem.setText("Clustal alignment");
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385 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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387 public void actionPerformed(ActionEvent e)
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389 clustalAlignMenuItem_actionPerformed(e);
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392 this.getContentPane().setLayout(borderLayout1);
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393 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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394 statusBar.setBackground(Color.white);
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395 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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396 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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397 statusBar.setText("Status bar");
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398 outputTextboxMenu.setMnemonic('T');
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399 outputTextboxMenu.setText("Output alignment via textbox");
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400 clustalColour.setEnabled(false);
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401 clustalColour.setSelected(false);
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402 clustalColour.setText("Clustalx colours");
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403 clustalColour.addActionListener(new java.awt.event.ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 clustalColour_actionPerformed(e);
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410 zappoColour.setSelected(true);
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411 zappoColour.setText("Zappo colour scheme");
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412 zappoColour.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 zappoColour_actionPerformed(e);
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419 taylorColour.setText("Taylor colour scheme");
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420 taylorColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 taylorColour_actionPerformed(e);
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427 hydrophobicityColour.setText("By hydrophobicity");
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428 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 hydrophobicityColour_actionPerformed(e);
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435 helixColour.setText("Helix propensity");
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436 helixColour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 helixColour_actionPerformed(e);
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443 strandColour.setText("Strand propensity");
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444 strandColour.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 strandColour_actionPerformed(e);
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451 turnColour.setText("Turn propensity");
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452 turnColour.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 turnColour_actionPerformed(e);
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459 buriedColour.setText("Buried index");
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460 buriedColour.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 buriedColour_actionPerformed(e);
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467 abovePIDColour.setEnabled(false);
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468 abovePIDColour.setText("Above PID threshold only");
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469 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 abovePIDColour_actionPerformed(e);
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476 userDefinedColour.setText("User defined colours");
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477 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 userDefinedColour_actionPerformed(e);
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484 PIDColour.setEnabled(false);
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485 PIDColour.setText("By PID");
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486 PIDColour.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 PIDColour_actionPerformed(e);
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493 BLOSUM62Colour.setText("By BLOSUM62 score");
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494 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 BLOSUM62Colour_actionPerformed(e);
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501 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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502 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 avTreeBlosumMenuItem_actionPerformed(e);
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509 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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510 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 njTreeBlosumMenuItem_actionPerformed(e);
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517 conservationColourIncMenuItem.setEnabled(false);
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518 conservationColourIncMenuItem.setText("Conservation Colour Increment");
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519 conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
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521 public void actionPerformed(ActionEvent e)
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523 conservationColourIncMenuItem_actionPerformed(e);
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526 consensusGraphMenuItem.setActionCommand("");
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527 consensusGraphMenuItem.setText("Consensus graph");
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528 consensusGraphMenuItem.setState(true);
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529 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 consensusGraphMenuItem_actionPerformed(e);
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536 colourTextMenuItem.setText("Colour text");
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537 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 colourTextMenuItem_actionPerformed(e);
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544 htmlMenuItem.setText("Output as HTML");
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545 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 htmlMenuItem_actionPerformed(e);
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552 schemeKeyMenuItem.setText("Colour Scheme Key");
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553 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 schemeKeyMenuItem_actionPerformed(e);
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560 overviewMenuItem.setText("Overview window");
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561 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 overviewMenuItem_actionPerformed(e);
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568 undoMenuItem.setEnabled(false);
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569 undoMenuItem.setMnemonic('Z');
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570 undoMenuItem.setText("Undo");
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571 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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573 public void actionPerformed(ActionEvent e)
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575 undoMenuItem_actionPerformed(e);
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578 redoMenuItem.setEnabled(false);
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579 redoMenuItem.setMnemonic('0');
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580 redoMenuItem.setText("Redo");
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581 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 redoMenuItem_actionPerformed(e);
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588 conservationMenuItem.setText("By conservation");
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589 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 conservationMenuItem_actionPerformed(e);
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596 noColourmenuItem.setText("None");
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597 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 noColourmenuItem_actionPerformed(e);
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604 wrapMenuItem.setEnabled(false);
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605 wrapMenuItem.setText("Wrap alignment");
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606 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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608 public void actionPerformed(ActionEvent e)
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610 wrapMenuItem_actionPerformed(e);
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613 pdbTest.setText("PDB Test Viewer");
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614 pdbTest.addActionListener(new java.awt.event.ActionListener()
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616 public void actionPerformed(ActionEvent e)
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618 pdbTest_actionPerformed(e);
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621 printMenuItem.setText("Print");
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622 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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624 public void actionPerformed(ActionEvent e)
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626 printMenuItem_actionPerformed(e);
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629 alignFrameMenuBar.add(fileMenu);
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630 alignFrameMenuBar.add(editMenu);
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631 alignFrameMenuBar.add(fontMenu);
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632 alignFrameMenuBar.add(viewMenu);
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633 alignFrameMenuBar.add(colourMenu);
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634 alignFrameMenuBar.add(calculateMenu);
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635 alignFrameMenuBar.add(alignMenu);
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636 fileMenu.add(saveAlignmentMenu);
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637 fileMenu.add(outputTextboxMenu);
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638 fileMenu.add(htmlMenuItem);
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639 fileMenu.add(printMenuItem);
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640 fileMenu.addSeparator();
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641 fileMenu.add(closeMenuItem);
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642 editMenu.add(undoMenuItem);
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643 editMenu.add(redoMenuItem);
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644 editMenu.addSeparator();
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645 editMenu.add(groupsMenuItem);
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646 editMenu.add(groupEditingMenuItem);
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647 editMenu.addSeparator();
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648 editMenu.add(selectAllSequenceMenuItem);
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649 editMenu.add(deselectAllSequenceMenuItem);
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650 editMenu.add(invertSequenceMenuItem);
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651 editMenu.addSeparator();
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652 editMenu.add(copySelectedMenuItem);
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653 editMenu.add(moveSelectedMenuItem);
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654 editMenu.add(deleteSelectedMenuItem);
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655 editMenu.addSeparator();
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656 editMenu.add(deselectAllColumnsMenuItem);
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657 editMenu.add(remove2LeftMenuItem);
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658 editMenu.add(remove2RightMenuItem);
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659 editMenu.addSeparator();
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660 editMenu.add(removeGappedColumnMenuItem);
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661 editMenu.add(removeAllGapsMenuItem);
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662 editMenu.add(setGapCharMenuItem);
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663 fontMenu.add(fontNameMenuItem);
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664 fontMenu.add(fontSizeMenuItem);
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665 fontMenu.add(fontStyleMenuItem);
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666 viewMenu.add(wrapMenuItem);
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667 viewMenu.add(viewBoxesMenuItem);
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668 viewMenu.add(viewTextMenuItem);
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669 viewMenu.add(colourTextMenuItem);
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670 viewMenu.add(consensusGraphMenuItem);
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671 viewMenu.add(overviewMenuItem);
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672 colourMenu.add(noColourmenuItem);
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673 colourMenu.add(clustalColour);
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674 colourMenu.add(zappoColour);
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675 colourMenu.add(taylorColour);
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676 colourMenu.add(hydrophobicityColour);
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677 colourMenu.add(helixColour);
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678 colourMenu.add(strandColour);
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679 colourMenu.add(turnColour);
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680 colourMenu.add(buriedColour);
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681 colourMenu.add(userDefinedColour);
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682 colourMenu.addSeparator();
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683 colourMenu.add(conservationMenuItem);
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684 colourMenu.add(conservationColourIncMenuItem);
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685 colourMenu.addSeparator();
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686 colourMenu.add(abovePIDColour);
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687 colourMenu.add(PIDColour);
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688 colourMenu.add(BLOSUM62Colour);
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689 colourMenu.addSeparator();
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690 colourMenu.add(schemeKeyMenuItem);
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691 calculateMenu.add(sortPairwiseMenuItem);
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692 calculateMenu.add(sortIDMenuItem);
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693 calculateMenu.add(sortGroupMenuItem);
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694 calculateMenu.add(sortTreeOrderMenuItem);
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695 calculateMenu.add(removeRedundancyMenuItem);
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696 calculateMenu.addSeparator();
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697 calculateMenu.add(pairwiseAlignmentMenuItem);
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698 calculateMenu.add(PCAMenuItem);
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699 calculateMenu.addSeparator();
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700 calculateMenu.add(averageDistanceTreeMenuItem);
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701 calculateMenu.add(neighbourTreeMenuItem);
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702 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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703 calculateMenu.add(njTreeBlosumMenuItem);
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704 alignMenu.add(clustalAlignMenuItem);
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705 alignMenu.add(pdbTest);
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706 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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709 protected void saveAs_actionPerformed(ActionEvent e)
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714 protected void outputText_actionPerformed(ActionEvent e)
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719 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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728 protected void closeMenuItem_actionPerformed(ActionEvent e)
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733 protected void redoMenuItem_actionPerformed(ActionEvent e)
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738 protected void undoMenuItem_actionPerformed(ActionEvent e)
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744 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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749 protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
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754 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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759 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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764 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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769 protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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774 protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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779 protected void copySelectedMenuItem_actionPerformed(ActionEvent e)
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784 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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789 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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794 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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799 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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804 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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809 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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815 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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820 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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825 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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830 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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836 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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841 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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847 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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854 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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859 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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864 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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869 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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874 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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879 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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884 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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889 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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894 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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899 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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904 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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910 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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915 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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922 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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930 protected void clustalColour_actionPerformed(ActionEvent e)
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935 protected void zappoColour_actionPerformed(ActionEvent e)
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940 protected void taylorColour_actionPerformed(ActionEvent e)
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946 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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951 protected void helixColour_actionPerformed(ActionEvent e)
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956 protected void strandColour_actionPerformed(ActionEvent e)
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961 protected void turnColour_actionPerformed(ActionEvent e)
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966 protected void buriedColour_actionPerformed(ActionEvent e)
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972 protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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978 protected void abovePIDColour_actionPerformed(ActionEvent e)
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984 protected void userDefinedColour_actionPerformed(ActionEvent e)
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989 protected void PIDColour_actionPerformed(ActionEvent e)
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994 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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999 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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1004 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1009 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1014 protected void pdbTest_actionPerformed(ActionEvent e)
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1019 protected void printMenuItem_actionPerformed(ActionEvent e)
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