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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14 import javax.swing.event.*;
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17 public class GAlignFrame extends JInternalFrame
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19 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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20 protected JMenu fileMenu = new JMenu();
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21 protected JMenuItem saveAsPostscriptMenuItem = new JMenuItem();
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22 protected JMenuItem closeMenuItem = new JMenuItem();
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23 protected JMenu editMenu = new JMenu();
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24 protected JMenu fontMenu = new JMenu();
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25 protected JMenu viewMenu = new JMenu();
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26 protected JMenu colourMenu = new JMenu();
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27 protected JMenu calculateMenu = new JMenu();
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28 protected JMenu alignMenu = new JMenu();
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29 protected JMenuItem groupsMenuItem = new JMenuItem();
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30 protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
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31 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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32 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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33 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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34 protected JMenuItem deleteSelectedMenuItem = new JMenuItem();
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35 protected JMenuItem moveSelectedMenuItem = new JMenuItem();
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36 protected JMenuItem copySelectedMenuItem = new JMenuItem();
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37 protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
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38 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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39 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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40 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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41 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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42 protected JMenuItem setGapCharMenuItem = new JMenuItem();
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43 protected JMenuItem fontNameMenuItem = new JMenuItem();
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44 protected JMenuItem fontSizeMenuItem = new JMenuItem();
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45 protected JMenuItem fontStyleMenuItem = new JMenuItem();
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46 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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47 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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48 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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49 protected JMenuItem sortIDMenuItem = new JMenuItem();
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50 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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51 protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
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52 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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53 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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54 protected JMenuItem PCAMenuItem = new JMenuItem();
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55 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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56 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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57 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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58 BorderLayout borderLayout1 = new BorderLayout();
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59 public JLabel statusBar = new JLabel();
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60 protected JMenu saveAlignmentMenu = new JMenu();
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61 protected JMenu outputTextboxMenu = new JMenu();
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62 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem conservationColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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75 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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76 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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77 JMenuItem conservationColourIncMenuItem = new JMenuItem();
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78 protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
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79 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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80 JMenuItem htmlMenuItem = new JMenuItem();
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81 JMenuItem schemeKeyMenuItem = new JMenuItem();
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82 JMenuItem overviewMenuItem = new JMenuItem();
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83 public GAlignFrame()
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88 setJMenuBar(alignFrameMenuBar);
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91 // dynamically fill save as menu with available formats
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92 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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93 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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94 saveAlignmentMenu.add( item );
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95 item.addActionListener(new java.awt.event.ActionListener()
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97 public void actionPerformed(ActionEvent e)
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99 saveAs_actionPerformed(e);
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103 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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104 item.addActionListener(new java.awt.event.ActionListener()
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106 public void actionPerformed(ActionEvent e)
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108 outputText_actionPerformed(e);
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112 outputTextboxMenu.add( item );
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118 e.printStackTrace();
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121 ButtonGroup colours = new ButtonGroup();
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122 colours.add(clustalColour);
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123 colours.add(zappoColour);
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124 colours.add(taylorColour);
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125 colours.add(hydrophobicityColour);
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126 colours.add(helixColour);
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127 colours.add(strandColour);
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128 colours.add(turnColour);
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129 colours.add(buriedColour);
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130 colours.add(conservationColour);
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131 colours.add(abovePIDColour);
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132 colours.add(userDefinedColour);
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133 colours.add(PIDColour);
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134 colours.add(BLOSUM62Colour);
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136 private void jbInit() throws Exception
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138 fileMenu.setMnemonic('F');
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139 fileMenu.setText("File");
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140 saveAlignmentMenu.setMnemonic('L');
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141 saveAlignmentMenu.setText("Save alignment to local file");
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142 saveAsPostscriptMenuItem.setMnemonic('P');
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143 saveAsPostscriptMenuItem.setText("Save alignment as postscript");
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144 saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 saveAsPostscriptMenuItem_actionPerformed(e);
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151 closeMenuItem.setMnemonic('C');
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152 closeMenuItem.setText("Close");
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153 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 closeMenuItem_actionPerformed(e);
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160 editMenu.setText("Edit");
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161 fontMenu.setText("Font");
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162 viewMenu.setText("View");
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163 colourMenu.setText("Colour");
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164 calculateMenu.setText("Calculate");
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165 alignMenu.setText("Web Service");
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166 groupsMenuItem.setEnabled(false);
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167 groupsMenuItem.setText("Groups");
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168 groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
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170 public void actionPerformed(ActionEvent e)
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172 groupsMenuItem_actionPerformed(e);
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175 groupEditingMenuItem.setEnabled(false);
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176 groupEditingMenuItem.setText("Group editing mode");
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177 groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
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179 public void actionPerformed(ActionEvent e)
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181 groupEditingMenuItem_actionPerformed(e);
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184 selectAllSequenceMenuItem.setText("Select all sequences");
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185 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 selectAllSequenceMenuItem_actionPerformed(e);
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192 deselectAllSequenceMenuItem.setText("Clear sequence selection");
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193 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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195 public void actionPerformed(ActionEvent e)
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197 deselectAllSequenceMenuItem_actionPerformed(e);
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200 invertSequenceMenuItem.setText("Invert sequence selection");
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201 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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203 public void actionPerformed(ActionEvent e)
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205 invertSequenceMenuItem_actionPerformed(e);
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208 deleteSelectedMenuItem.setText("Delete selected sequences");
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209 deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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211 public void actionPerformed(ActionEvent e)
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213 deleteSelectedMenuItem_actionPerformed(e);
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216 moveSelectedMenuItem.setText("Move selected sequences to new alignment");
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217 moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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219 public void actionPerformed(ActionEvent e)
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221 moveSelectedMenuItem_actionPerformed(e);
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224 copySelectedMenuItem.setText("Copy selected sequences to new alignment");
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225 copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
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227 public void actionPerformed(ActionEvent e)
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229 copySelectedMenuItem_actionPerformed(e);
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232 deselectAllColumnsMenuItem.setText("Deselect all columns");
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233 deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
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235 public void actionPerformed(ActionEvent e)
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237 deselectAllColumnsMenuItem_actionPerformed(e);
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240 remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
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241 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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243 public void actionPerformed(ActionEvent e)
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245 remove2LeftMenuItem_actionPerformed(e);
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248 remove2RightMenuItem.setText("Remove sequence -> right of selected column");
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249 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 remove2RightMenuItem_actionPerformed(e);
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256 removeGappedColumnMenuItem.setText("Remove gapped columns");
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257 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 removeGappedColumnMenuItem_actionPerformed(e);
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264 removeAllGapsMenuItem.setText("Remove all gaps");
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265 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 removeAllGapsMenuItem_actionPerformed(e);
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272 setGapCharMenuItem.setText("Set gap character to \"-\"");
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273 setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
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275 public void actionPerformed(ActionEvent e)
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277 setGapCharMenuItem_actionPerformed(e);
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280 fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
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282 public void actionPerformed(ActionEvent e)
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284 fontNameMenuItem_actionPerformed(e);
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287 fontSizeMenuItem.setText("10");
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288 fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
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290 public void actionPerformed(ActionEvent e)
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292 fontSizeMenuItem_actionPerformed(e);
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295 fontStyleMenuItem.setText("Plain");
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296 fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 fontStyleMenuItem_actionPerformed(e);
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303 viewBoxesMenuItem.setText("Boxes");
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304 viewBoxesMenuItem.setState(true);
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305 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 viewBoxesMenuItem_actionPerformed(e);
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312 viewTextMenuItem.setText("Text");
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313 viewTextMenuItem.setState(true);
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314 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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316 public void actionPerformed(ActionEvent e)
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318 viewTextMenuItem_actionPerformed(e);
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321 sortPairwiseMenuItem.setText("Sort by pairwise identity");
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322 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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324 public void actionPerformed(ActionEvent e)
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326 sortPairwiseMenuItem_actionPerformed(e);
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329 sortIDMenuItem.setText("Sort by ID");
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330 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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332 public void actionPerformed(ActionEvent e)
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334 sortIDMenuItem_actionPerformed(e);
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337 sortGroupMenuItem.setText("Sort by group");
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338 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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340 public void actionPerformed(ActionEvent e)
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342 sortGroupMenuItem_actionPerformed(e);
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345 sortTreeOrderMenuItem.setText("Sort by tree order");
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346 sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
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348 public void actionPerformed(ActionEvent e)
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350 sortTreeOrderMenuItem_actionPerformed(e);
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353 removeRedundancyMenuItem.setText("Remove redundancy");
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354 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 removeRedundancyMenuItem_actionPerformed(e);
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361 pairwiseAlignmentMenuItem.setText("Pairwise alignments");
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362 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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364 public void actionPerformed(ActionEvent e)
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366 pairwiseAlignmentMenuItem_actionPerformed(e);
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369 PCAMenuItem.setText("Principal component analysis");
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370 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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372 public void actionPerformed(ActionEvent e)
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374 PCAMenuItem_actionPerformed(e);
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377 averageDistanceTreeMenuItem.setText("Average distance tree using PID");
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378 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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380 public void actionPerformed(ActionEvent e)
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382 averageDistanceTreeMenuItem_actionPerformed(e);
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385 neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
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386 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 neighbourTreeMenuItem_actionPerformed(e);
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393 clustalAlignMenuItem.setText("Clustal alignment");
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394 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 clustalAlignMenuItem_actionPerformed(e);
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401 this.getContentPane().setLayout(borderLayout1);
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402 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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403 statusBar.setBackground(Color.white);
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404 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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405 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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406 statusBar.setText("Status bar");
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407 outputTextboxMenu.setMnemonic('T');
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408 outputTextboxMenu.setText("Output alignment via textbox");
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409 clustalColour.setSelected(false);
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410 clustalColour.setText("Clustalx colours");
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411 clustalColour.addActionListener(new java.awt.event.ActionListener()
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413 public void actionPerformed(ActionEvent e)
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415 clustalColour_actionPerformed(e);
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418 zappoColour.setSelected(true);
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419 zappoColour.setText("Zappo colour scheme");
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420 zappoColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 zappoColour_actionPerformed(e);
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427 taylorColour.setText("Taylor colour scheme");
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428 taylorColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 taylorColour_actionPerformed(e);
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435 hydrophobicityColour.setText("By hydrophobicity");
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436 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 hydrophobicityColour_actionPerformed(e);
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443 helixColour.setText("Helix propensity");
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444 helixColour.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 helixColour_actionPerformed(e);
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451 strandColour.setText("Strand propensity");
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452 strandColour.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 strandColour_actionPerformed(e);
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459 turnColour.setText("Turn propensity");
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460 turnColour.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 turnColour_actionPerformed(e);
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467 buriedColour.setText("Buried index");
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468 buriedColour.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 buriedColour_actionPerformed(e);
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475 conservationColour.setEnabled(false);
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476 conservationColour.setText("By conservation");
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477 conservationColour.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 conservationColour_actionPerformed(e);
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484 abovePIDColour.setEnabled(false);
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485 abovePIDColour.setText("Above PID threshold only");
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486 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 abovePIDColour_actionPerformed(e);
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493 userDefinedColour.setText("User defined colours");
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494 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 userDefinedColour_actionPerformed(e);
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501 PIDColour.setEnabled(false);
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502 PIDColour.setText("By PID");
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503 PIDColour.addActionListener(new java.awt.event.ActionListener()
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505 public void actionPerformed(ActionEvent e)
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507 PIDColour_actionPerformed(e);
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510 BLOSUM62Colour.setText("By BLOSUM62 score");
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511 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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513 public void actionPerformed(ActionEvent e)
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515 BLOSUM62Colour_actionPerformed(e);
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518 avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
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519 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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521 public void actionPerformed(ActionEvent e)
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523 avTreeBlosumMenuItem_actionPerformed(e);
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526 njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
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527 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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529 public void actionPerformed(ActionEvent e)
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531 njTreeBlosumMenuItem_actionPerformed(e);
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534 conservationColourIncMenuItem.setEnabled(false);
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535 conservationColourIncMenuItem.setText("Conservation Colour Increment");
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536 conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
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538 public void actionPerformed(ActionEvent e)
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540 conservationColourIncMenuItem_actionPerformed(e);
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543 consensusGraphMenuItem.setActionCommand("");
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544 consensusGraphMenuItem.setText("Consensus graph");
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545 consensusGraphMenuItem.setState(true);
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546 consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
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548 public void actionPerformed(ActionEvent e)
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550 consensusGraphMenuItem_actionPerformed(e);
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553 colourTextMenuItem.setText("Colour text");
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554 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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556 public void actionPerformed(ActionEvent e)
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558 colourTextMenuItem_actionPerformed(e);
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561 htmlMenuItem.setText("Output as HTML");
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562 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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564 public void actionPerformed(ActionEvent e)
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566 htmlMenuItem_actionPerformed(e);
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569 schemeKeyMenuItem.setText("Colour Scheme Key");
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570 schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
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572 public void actionPerformed(ActionEvent e)
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574 schemeKeyMenuItem_actionPerformed(e);
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577 overviewMenuItem.setText("Overview window");
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578 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 overviewMenuItem_actionPerformed(e);
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585 alignFrameMenuBar.add(fileMenu);
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586 alignFrameMenuBar.add(editMenu);
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587 alignFrameMenuBar.add(fontMenu);
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588 alignFrameMenuBar.add(viewMenu);
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589 alignFrameMenuBar.add(colourMenu);
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590 alignFrameMenuBar.add(calculateMenu);
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591 alignFrameMenuBar.add(alignMenu);
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592 fileMenu.add(saveAlignmentMenu);
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593 fileMenu.add(saveAsPostscriptMenuItem);
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594 fileMenu.add(outputTextboxMenu);
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595 fileMenu.add(htmlMenuItem);
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596 fileMenu.addSeparator();
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597 fileMenu.add(closeMenuItem);
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598 editMenu.add(groupsMenuItem);
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599 editMenu.add(groupEditingMenuItem);
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600 editMenu.addSeparator();
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601 editMenu.add(selectAllSequenceMenuItem);
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602 editMenu.add(deselectAllSequenceMenuItem);
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603 editMenu.add(invertSequenceMenuItem);
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604 editMenu.addSeparator();
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605 editMenu.add(copySelectedMenuItem);
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606 editMenu.add(moveSelectedMenuItem);
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607 editMenu.add(deleteSelectedMenuItem);
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608 editMenu.addSeparator();
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609 editMenu.add(deselectAllColumnsMenuItem);
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610 editMenu.add(remove2LeftMenuItem);
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611 editMenu.add(remove2RightMenuItem);
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612 editMenu.addSeparator();
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613 editMenu.add(removeGappedColumnMenuItem);
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614 editMenu.add(removeAllGapsMenuItem);
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615 editMenu.add(setGapCharMenuItem);
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616 fontMenu.add(fontNameMenuItem);
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617 fontMenu.add(fontSizeMenuItem);
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618 fontMenu.add(fontStyleMenuItem);
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619 fontMenu.addSeparator();
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620 fontMenu.add(colourTextMenuItem);
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621 viewMenu.add(viewBoxesMenuItem);
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622 viewMenu.add(viewTextMenuItem);
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623 viewMenu.add(consensusGraphMenuItem);
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624 viewMenu.add(overviewMenuItem);
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625 colourMenu.add(clustalColour);
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626 colourMenu.add(zappoColour);
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627 colourMenu.add(taylorColour);
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628 colourMenu.add(hydrophobicityColour);
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629 colourMenu.add(helixColour);
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630 colourMenu.add(strandColour);
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631 colourMenu.add(turnColour);
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632 colourMenu.add(buriedColour);
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633 colourMenu.add(userDefinedColour);
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634 colourMenu.addSeparator();
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635 colourMenu.add(conservationColour);
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636 colourMenu.add(conservationColourIncMenuItem);
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637 colourMenu.addSeparator();
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638 colourMenu.add(abovePIDColour);
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639 colourMenu.add(PIDColour);
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640 colourMenu.add(BLOSUM62Colour);
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641 colourMenu.addSeparator();
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642 colourMenu.add(schemeKeyMenuItem);
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643 calculateMenu.add(sortPairwiseMenuItem);
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644 calculateMenu.add(sortIDMenuItem);
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645 calculateMenu.add(sortGroupMenuItem);
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646 calculateMenu.add(sortTreeOrderMenuItem);
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647 calculateMenu.add(removeRedundancyMenuItem);
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648 calculateMenu.addSeparator();
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649 calculateMenu.add(pairwiseAlignmentMenuItem);
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650 calculateMenu.add(PCAMenuItem);
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651 calculateMenu.addSeparator();
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652 calculateMenu.add(averageDistanceTreeMenuItem);
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653 calculateMenu.add(neighbourTreeMenuItem);
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654 calculateMenu.add(avDistanceTreeBlosumMenuItem);
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655 calculateMenu.add(njTreeBlosumMenuItem);
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656 alignMenu.add(clustalAlignMenuItem);
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657 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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660 protected void saveAs_actionPerformed(ActionEvent e)
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665 protected void outputText_actionPerformed(ActionEvent e)
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670 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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677 protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
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683 protected void closeMenuItem_actionPerformed(ActionEvent e)
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688 protected void groupsMenuItem_actionPerformed(ActionEvent e)
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693 protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
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698 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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703 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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708 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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713 protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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718 protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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723 protected void copySelectedMenuItem_actionPerformed(ActionEvent e)
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728 protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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733 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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738 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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743 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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748 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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753 protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
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759 protected void fontNameMenuItem_actionPerformed(ActionEvent e)
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764 protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
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769 protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
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774 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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779 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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785 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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792 protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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797 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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802 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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807 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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812 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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817 protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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822 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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827 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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832 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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837 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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842 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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848 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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853 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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860 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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868 protected void clustalColour_actionPerformed(ActionEvent e)
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873 protected void zappoColour_actionPerformed(ActionEvent e)
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878 protected void taylorColour_actionPerformed(ActionEvent e)
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884 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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889 protected void helixColour_actionPerformed(ActionEvent e)
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894 protected void strandColour_actionPerformed(ActionEvent e)
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899 protected void turnColour_actionPerformed(ActionEvent e)
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904 protected void buriedColour_actionPerformed(ActionEvent e)
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909 protected void conservationColour_actionPerformed(ActionEvent e)
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914 protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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920 protected void abovePIDColour_actionPerformed(ActionEvent e)
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926 protected void userDefinedColour_actionPerformed(ActionEvent e)
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931 protected void PIDColour_actionPerformed(ActionEvent e)
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936 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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941 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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