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 viewMenu = new JMenu();
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22 protected JMenu colourMenu = new JMenu();
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23 protected JMenu calculateMenu = new JMenu();
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24 protected JMenu webService = new JMenu();
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25 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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26 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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27 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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28 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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29 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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30 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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31 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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32 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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33 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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34 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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35 protected JMenuItem sortIDMenuItem = new JMenuItem();
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36 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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37 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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38 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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39 protected JMenuItem PCAMenuItem = new JMenuItem();
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40 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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41 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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42 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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43 BorderLayout borderLayout1 = new BorderLayout();
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44 public JLabel statusBar = new JLabel();
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45 protected JMenu saveAlignmentMenu = new JMenu();
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46 protected JMenu outputTextboxMenu = new JMenu();
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47 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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49 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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58 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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59 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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60 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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61 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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62 JMenuItem htmlMenuItem = new JMenuItem();
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63 JMenuItem overviewMenuItem = new JMenuItem();
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64 protected JMenuItem undoMenuItem = new JMenuItem();
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65 protected JMenuItem redoMenuItem = new JMenuItem();
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66 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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67 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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68 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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69 JMenuItem printMenuItem = new JMenuItem();
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70 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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71 JMenuItem findMenuItem = new JMenuItem();
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72 JMenu searchMenu = new JMenu();
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73 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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74 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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75 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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76 JMenuItem deleteGroups = new JMenuItem();
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77 JMenuItem delete = new JMenuItem();
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78 JMenuItem copy = new JMenuItem();
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79 JMenuItem cut = new JMenuItem();
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80 JMenu jMenu1 = new JMenu();
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81 JMenuItem pasteNew = new JMenuItem();
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82 JMenuItem pasteThis = new JMenuItem();
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83 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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84 JMenuItem createPNG = new JMenuItem();
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85 protected JMenuItem font = new JMenuItem();
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86 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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87 JMenuItem epsFile = new JMenuItem();
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88 JMenuItem LoadtreeMenuItem = new JMenuItem();
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89 JMenuItem jpred = new JMenuItem();
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90 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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91 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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92 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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93 JMenuItem modifyPID = new JMenuItem();
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94 JMenuItem modifyConservation = new JMenuItem();
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95 protected JMenu sortByTreeMenu = new JMenu();
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96 JMenu jMenu2 = new JMenu();
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97 JMenu sort = new JMenu();
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98 JMenu calculate = new JMenu();
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99 JMenuItem msaAlignMenuItem = new JMenuItem();
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100 public GAlignFrame()
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107 setJMenuBar(alignFrameMenuBar);
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110 // dynamically fill save as menu with available formats
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111 for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
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112 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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113 saveAlignmentMenu.add( item );
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114 item.addActionListener(new java.awt.event.ActionListener()
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116 public void actionPerformed(ActionEvent e)
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118 saveAs_actionPerformed(e);
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122 item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
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123 item.addActionListener(new java.awt.event.ActionListener()
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125 public void actionPerformed(ActionEvent e)
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127 outputText_actionPerformed(e);
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131 outputTextboxMenu.add( item );
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137 e.printStackTrace();
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140 ButtonGroup colours = new ButtonGroup();
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141 colours.add(noColourmenuItem);
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142 colours.add(clustalColour);
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143 colours.add(zappoColour);
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144 colours.add(taylorColour);
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145 colours.add(hydrophobicityColour);
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146 colours.add(helixColour);
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147 colours.add(strandColour);
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148 colours.add(turnColour);
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149 colours.add(buriedColour);
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150 colours.add(userDefinedColour);
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151 colours.add(PIDColour);
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152 colours.add(BLOSUM62Colour);
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153 colours.add(nucleotideColour);
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155 private void jbInit() throws Exception
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157 fileMenu.setMnemonic('F');
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158 fileMenu.setText("File");
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159 saveAlignmentMenu.setMnemonic('L');
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160 saveAlignmentMenu.setText("Save");
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161 closeMenuItem.setMnemonic('C');
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162 closeMenuItem.setText("Close");
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163 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 closeMenuItem_actionPerformed(e);
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170 editMenu.setText("Edit");
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171 viewMenu.setText("View");
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172 colourMenu.setText("Colour");
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173 calculateMenu.setText("Calculate");
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174 webService.setText("Web Service");
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175 selectAllSequenceMenuItem.setText("Select all");
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176 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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177 java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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178 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 selectAllSequenceMenuItem_actionPerformed(e);
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185 deselectAllSequenceMenuItem.setText("Deselect All");
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186 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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187 getKeyStroke(java.awt.event.
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188 KeyEvent.VK_ESCAPE, 0, false));
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189 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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191 public void actionPerformed(ActionEvent e)
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193 deselectAllSequenceMenuItem_actionPerformed(e);
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196 invertSequenceMenuItem.setText("Invert Selection");
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197 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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199 public void actionPerformed(ActionEvent e)
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201 invertSequenceMenuItem_actionPerformed(e);
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204 remove2LeftMenuItem.setText("Remove Left");
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205 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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207 public void actionPerformed(ActionEvent e)
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209 remove2LeftMenuItem_actionPerformed(e);
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212 remove2RightMenuItem.setText("Remove Right");
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213 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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215 public void actionPerformed(ActionEvent e)
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217 remove2RightMenuItem_actionPerformed(e);
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220 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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221 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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223 public void actionPerformed(ActionEvent e)
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225 removeGappedColumnMenuItem_actionPerformed(e);
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228 removeAllGapsMenuItem.setText("Remove All Gaps");
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229 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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231 public void actionPerformed(ActionEvent e)
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233 removeAllGapsMenuItem_actionPerformed(e);
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236 viewBoxesMenuItem.setText("Boxes");
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237 viewBoxesMenuItem.setState(true);
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238 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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240 public void actionPerformed(ActionEvent e)
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242 viewBoxesMenuItem_actionPerformed(e);
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245 viewTextMenuItem.setText("Text");
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246 viewTextMenuItem.setState(true);
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247 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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249 public void actionPerformed(ActionEvent e)
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251 viewTextMenuItem_actionPerformed(e);
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254 sortPairwiseMenuItem.setText("Pairwise Identity");
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255 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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257 public void actionPerformed(ActionEvent e)
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259 sortPairwiseMenuItem_actionPerformed(e);
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262 sortIDMenuItem.setText("ID");
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263 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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265 public void actionPerformed(ActionEvent e)
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267 sortIDMenuItem_actionPerformed(e);
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270 sortGroupMenuItem.setText("Group");
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271 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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275 sortGroupMenuItem_actionPerformed(e);
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278 removeRedundancyMenuItem.setText("Remove Redundancy...");
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279 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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281 public void actionPerformed(ActionEvent e)
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283 removeRedundancyMenuItem_actionPerformed(e);
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286 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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287 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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289 public void actionPerformed(ActionEvent e)
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291 pairwiseAlignmentMenuItem_actionPerformed(e);
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294 PCAMenuItem.setText("Principal Component Analysis...");
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295 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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297 public void actionPerformed(ActionEvent e)
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299 PCAMenuItem_actionPerformed(e);
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302 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
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303 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 averageDistanceTreeMenuItem_actionPerformed(e);
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310 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
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311 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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313 public void actionPerformed(ActionEvent e)
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315 neighbourTreeMenuItem_actionPerformed(e);
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318 clustalAlignMenuItem.setText("Clustal Alignment...");
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319 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 clustalAlignMenuItem_actionPerformed(e);
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326 this.getContentPane().setLayout(borderLayout1);
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327 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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328 statusBar.setBackground(Color.white);
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329 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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330 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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331 statusBar.setText("Status bar");
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332 outputTextboxMenu.setMnemonic('T');
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333 outputTextboxMenu.setText("Output to Textbox");
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334 clustalColour.setSelected(false);
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335 clustalColour.setText("Clustalx");
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336 clustalColour.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 clustalColour_actionPerformed(e);
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343 zappoColour.setText("Zappo");
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344 zappoColour.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 zappoColour_actionPerformed(e);
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351 taylorColour.setText("Taylor");
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352 taylorColour.addActionListener(new java.awt.event.ActionListener()
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354 public void actionPerformed(ActionEvent e)
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356 taylorColour_actionPerformed(e);
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359 hydrophobicityColour.setText("Hydrophobicity");
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360 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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362 public void actionPerformed(ActionEvent e)
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364 hydrophobicityColour_actionPerformed(e);
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367 helixColour.setText("Helix Propensity");
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368 helixColour.addActionListener(new java.awt.event.ActionListener()
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370 public void actionPerformed(ActionEvent e)
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372 helixColour_actionPerformed(e);
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375 strandColour.setText("Strand Propensity");
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376 strandColour.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 strandColour_actionPerformed(e);
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383 turnColour.setText("Turn Propensity");
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384 turnColour.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 turnColour_actionPerformed(e);
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391 buriedColour.setText("Buried Index");
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392 buriedColour.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 buriedColour_actionPerformed(e);
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399 userDefinedColour.setText("User Defined...");
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400 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 userDefinedColour_actionPerformed(e);
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407 PIDColour.setText("Percentage Identity");
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408 PIDColour.addActionListener(new java.awt.event.ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 PIDColour_actionPerformed(e);
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415 BLOSUM62Colour.setText("BLOSUM62 Score");
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416 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 BLOSUM62Colour_actionPerformed(e);
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423 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
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424 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 avTreeBlosumMenuItem_actionPerformed(e);
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431 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
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432 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 njTreeBlosumMenuItem_actionPerformed(e);
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439 annotationPanelMenuItem.setActionCommand("");
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440 annotationPanelMenuItem.setText("Show Annotations");
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441 annotationPanelMenuItem.setState(true);
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442 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 annotationPanelMenuItem_actionPerformed(e);
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449 colourTextMenuItem.setText("Colour Text");
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450 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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452 public void actionPerformed(ActionEvent e)
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454 colourTextMenuItem_actionPerformed(e);
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457 htmlMenuItem.setText("HTML");
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458 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 htmlMenuItem_actionPerformed(e);
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465 overviewMenuItem.setText("Overview Window...");
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466 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 overviewMenuItem_actionPerformed(e);
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473 undoMenuItem.setEnabled(false);
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474 undoMenuItem.setMnemonic('Z');
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475 undoMenuItem.setText("Undo");
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476 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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477 event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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478 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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480 public void actionPerformed(ActionEvent e)
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482 undoMenuItem_actionPerformed(e);
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485 redoMenuItem.setEnabled(false);
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486 redoMenuItem.setMnemonic('0');
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487 redoMenuItem.setText("Redo");
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488 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 redoMenuItem_actionPerformed(e);
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495 conservationMenuItem.setText("By Conservation");
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496 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 conservationMenuItem_actionPerformed(e);
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503 noColourmenuItem.setText("None");
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504 noColourmenuItem.setSelected(true);
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505 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 noColourmenuItem_actionPerformed(e);
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512 wrapMenuItem.setText("Wrap");
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513 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 wrapMenuItem_actionPerformed(e);
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520 printMenuItem.setText("Print");
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521 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 printMenuItem_actionPerformed(e);
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528 renderGapsMenuItem.setText("Show Gaps");
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529 renderGapsMenuItem.setState(true);
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530 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 renderGapsMenuItem_actionPerformed(e);
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537 findMenuItem.setText("Find...");
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538 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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539 event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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540 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 findMenuItem_actionPerformed(e);
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547 searchMenu.setText("Search");
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549 abovePIDThreshold.setText("Above Identity threshold");
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550 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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551 public void actionPerformed(ActionEvent e) {
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552 abovePIDThreshold_actionPerformed(e);
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555 sequenceFeatures.setText("Sequence Features");
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556 sequenceFeatures.addActionListener(new ActionListener()
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558 public void actionPerformed(ActionEvent actionEvent)
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560 sequenceFeatures_actionPerformed(actionEvent);
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563 nucleotideColour.setText("Nucleotide");
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564 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 nucleotideColour_actionPerformed(e);
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571 deleteGroups.setSelected(false);
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572 deleteGroups.setText("Undefine groups");
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573 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 deleteGroups_actionPerformed(e);
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580 copy.setText("Copy");
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581 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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582 KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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583 copy.setMnemonic(KeyEvent.VK_C);
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585 copy.addActionListener(new java.awt.event.ActionListener()
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587 public void actionPerformed(ActionEvent e)
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589 copy_actionPerformed(e);
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592 cut.setText("Cut");
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593 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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594 KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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595 cut.setMnemonic(KeyEvent.VK_X);
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596 cut.addActionListener(new java.awt.event.ActionListener()
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598 public void actionPerformed(ActionEvent e)
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600 cut_actionPerformed(e);
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603 delete.setText("Delete");
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604 delete.addActionListener(new java.awt.event.ActionListener()
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606 public void actionPerformed(ActionEvent e)
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608 delete_actionPerformed(e);
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611 jMenu1.setMnemonic('V');
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612 jMenu1.setText("Paste");
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613 pasteNew.setText("to new alignment");
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614 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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615 KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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616 pasteNew.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 pasteNew_actionPerformed(e);
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623 pasteThis.setText("add to this alignment");
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624 pasteThis.addActionListener(new java.awt.event.ActionListener()
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626 public void actionPerformed(ActionEvent e)
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628 pasteThis_actionPerformed(e);
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631 applyToAllGroups.setText("Apply Colour To All Groups");
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632 applyToAllGroups.setState(true);
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633 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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635 public void actionPerformed(ActionEvent e)
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637 applyToAllGroups_actionPerformed(e);
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640 createPNG.addActionListener(new java.awt.event.ActionListener()
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642 public void actionPerformed(ActionEvent e)
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644 createPNG_actionPerformed(e);
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647 createPNG.setActionCommand("Save as PNG Image");
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648 createPNG.setText("PNG");
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649 font.setText("Font...");
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650 font.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 font_actionPerformed(e);
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657 fullSeqId.setText("Show Full Sequence ID");
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658 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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660 public void actionPerformed(ActionEvent e)
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662 fullSeqId_actionPerformed(e);
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665 epsFile.setText("EPS");
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666 epsFile.addActionListener(new java.awt.event.ActionListener()
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668 public void actionPerformed(ActionEvent e)
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670 epsFile_actionPerformed(e);
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673 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
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674 LoadtreeMenuItem.setText("Load Assocated Tree");
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675 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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676 public void actionPerformed(ActionEvent e)
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678 LoadtreeMenuItem_actionPerformed(e);
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681 jpred.setText("JPred...");
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682 jpred.addActionListener(new java.awt.event.ActionListener()
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684 public void actionPerformed(ActionEvent e)
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686 jpred_actionPerformed(e);
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689 scaleAbove.setVisible(false);
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690 scaleAbove.setText("Scale Above");
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691 scaleAbove.addActionListener(new java.awt.event.ActionListener()
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693 public void actionPerformed(ActionEvent e)
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695 scaleAbove_actionPerformed(e);
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698 scaleLeft.setVisible(false);
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699 scaleLeft.setSelected(true);
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700 scaleLeft.setText("Scale Left");
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701 scaleLeft.addActionListener(new java.awt.event.ActionListener()
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703 public void actionPerformed(ActionEvent e)
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705 scaleLeft_actionPerformed(e);
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708 scaleRight.setVisible(false);
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709 scaleRight.setSelected(true);
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710 scaleRight.setText("Scale Right");
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711 scaleRight.addActionListener(new java.awt.event.ActionListener()
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713 public void actionPerformed(ActionEvent e)
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715 scaleRight_actionPerformed(e);
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718 modifyPID.setText("Modify Identity Threshold...");
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719 modifyPID.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 modifyPID_actionPerformed(e);
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726 modifyConservation.setText("Modify Conservation Threshold...");
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727 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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729 public void actionPerformed(ActionEvent e)
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731 modifyConservation_actionPerformed(e);
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734 sortByTreeMenu.setText("Tree Order");
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735 jMenu2.setText("Save as");
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736 sort.setText("Sort");
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737 calculate.setText("Calculate Tree");
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738 msaAlignMenuItem.setText("Muscle Alignment...");
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739 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
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740 public void actionPerformed(ActionEvent e) {
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741 msaAlignMenuItem_actionPerformed(e);
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744 alignFrameMenuBar.add(fileMenu);
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745 alignFrameMenuBar.add(editMenu);
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746 alignFrameMenuBar.add(searchMenu);
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747 alignFrameMenuBar.add(viewMenu);
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748 alignFrameMenuBar.add(colourMenu);
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749 alignFrameMenuBar.add(calculateMenu);
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750 fileMenu.add(saveAlignmentMenu);
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751 fileMenu.add(jMenu2);
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752 fileMenu.add(outputTextboxMenu);
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753 fileMenu.add(printMenuItem);
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754 fileMenu.addSeparator();
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755 fileMenu.add(LoadtreeMenuItem);
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756 fileMenu.addSeparator();
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757 fileMenu.add(closeMenuItem);
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758 editMenu.add(undoMenuItem);
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759 editMenu.add(redoMenuItem);
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761 editMenu.add(copy);
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762 editMenu.add(jMenu1);
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763 editMenu.add(delete);
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764 editMenu.add(selectAllSequenceMenuItem);
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765 editMenu.add(deselectAllSequenceMenuItem);
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766 editMenu.add(invertSequenceMenuItem);
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767 editMenu.add(deleteGroups);
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768 editMenu.addSeparator();
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769 editMenu.add(remove2LeftMenuItem);
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770 editMenu.add(remove2RightMenuItem);
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771 editMenu.add(removeGappedColumnMenuItem);
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772 editMenu.add(removeAllGapsMenuItem);
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773 editMenu.add(removeRedundancyMenuItem);
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774 searchMenu.add(findMenuItem);
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775 viewMenu.add(font);
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776 viewMenu.add(fullSeqId);
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777 viewMenu.addSeparator();
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778 viewMenu.add(wrapMenuItem);
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779 viewMenu.add(scaleAbove);
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780 viewMenu.add(scaleLeft);
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781 viewMenu.add(scaleRight);
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782 viewMenu.addSeparator();
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783 viewMenu.add(viewBoxesMenuItem);
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784 viewMenu.add(viewTextMenuItem);
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785 viewMenu.add(colourTextMenuItem);
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786 viewMenu.add(renderGapsMenuItem);
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787 viewMenu.add(annotationPanelMenuItem);
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788 viewMenu.add(sequenceFeatures);
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789 viewMenu.addSeparator();
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790 viewMenu.add(overviewMenuItem);
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791 colourMenu.add(applyToAllGroups);
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792 colourMenu.add(noColourmenuItem);
\r
793 colourMenu.addSeparator();
\r
794 colourMenu.add(clustalColour);
\r
795 colourMenu.add(BLOSUM62Colour);
\r
796 colourMenu.add(PIDColour);
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797 colourMenu.add(zappoColour);
\r
798 colourMenu.add(taylorColour);
\r
799 colourMenu.add(hydrophobicityColour);
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800 colourMenu.add(helixColour);
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801 colourMenu.add(strandColour);
\r
802 colourMenu.add(turnColour);
\r
803 colourMenu.add(buriedColour);
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804 colourMenu.add(nucleotideColour);
\r
805 colourMenu.add(userDefinedColour);
\r
806 colourMenu.addSeparator();
\r
807 colourMenu.add(conservationMenuItem);
\r
808 colourMenu.add(modifyConservation);
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809 colourMenu.add(abovePIDThreshold);
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810 colourMenu.add(modifyPID);
\r
811 calculateMenu.add(sort);
\r
812 calculateMenu.add(calculate);
\r
813 calculateMenu.addSeparator();
\r
814 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
815 calculateMenu.add(PCAMenuItem);
\r
816 calculateMenu.addSeparator();
\r
817 calculateMenu.add(webService);
\r
818 webService.add(clustalAlignMenuItem);
\r
819 webService.add(jpred);
\r
820 webService.add(msaAlignMenuItem);
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821 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
822 jMenu1.add(pasteNew);
\r
823 jMenu1.add(pasteThis);
\r
824 jMenu2.add(htmlMenuItem);
\r
825 jMenu2.add(epsFile);
\r
826 jMenu2.add(createPNG);
\r
827 sort.add(sortIDMenuItem);
\r
828 sort.add(sortGroupMenuItem);
\r
829 sort.add(sortByTreeMenu);
\r
830 sort.add(sortPairwiseMenuItem);
\r
831 calculate.add(averageDistanceTreeMenuItem);
\r
832 calculate.add(neighbourTreeMenuItem);
\r
833 calculate.add(avDistanceTreeBlosumMenuItem);
\r
834 calculate.add(njTreeBlosumMenuItem);
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837 protected void saveAs_actionPerformed(ActionEvent e)
\r
842 protected void outputText_actionPerformed(ActionEvent e)
\r
847 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
853 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
858 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
863 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
869 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
874 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
879 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
884 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
889 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
894 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
899 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
905 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
911 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
916 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
922 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
927 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
932 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
937 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
942 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
947 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
953 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
958 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
963 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
968 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
973 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
979 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
984 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
991 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
999 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1004 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1009 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1015 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1020 protected void helixColour_actionPerformed(ActionEvent e)
\r
1025 protected void strandColour_actionPerformed(ActionEvent e)
\r
1030 protected void turnColour_actionPerformed(ActionEvent e)
\r
1035 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1042 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1047 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1052 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1058 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1063 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1069 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1074 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1079 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1085 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
1089 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1094 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1099 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1104 protected void copy_actionPerformed(ActionEvent e)
\r
1110 protected void cut_actionPerformed(ActionEvent e)
\r
1115 protected void delete_actionPerformed(ActionEvent e)
\r
1120 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1125 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1130 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1135 protected void createPNG_actionPerformed(ActionEvent e)
\r
1140 protected void font_actionPerformed(ActionEvent e)
\r
1145 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1150 protected void epsFile_actionPerformed(ActionEvent e)
\r
1155 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1159 protected void jpred_actionPerformed(ActionEvent e)
\r
1164 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1169 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1174 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1179 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1184 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1189 protected void preferences_actionPerformed(ActionEvent e)
\r
1194 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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