1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbappletgui;
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11 import java.awt.event.*;
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14 public class GAlignFrame extends Frame
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16 protected MenuBar alignFrameMenuBar = new MenuBar();
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17 protected Menu fileMenu = new Menu();
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18 protected MenuItem closeMenuItem = new MenuItem();
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19 protected Menu editMenu = new Menu();
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20 protected Menu viewMenu = new Menu();
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21 protected Menu colourMenu = new Menu();
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22 protected Menu calculateMenu = new Menu();
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23 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
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24 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
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25 protected MenuItem invertSequenceMenuItem = new MenuItem();
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26 protected MenuItem remove2LeftMenuItem = new MenuItem();
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27 protected MenuItem remove2RightMenuItem = new MenuItem();
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28 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
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29 protected MenuItem removeAllGapsMenuItem = new MenuItem();
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30 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
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31 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
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32 protected MenuItem sortPairwiseMenuItem = new MenuItem();
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33 protected MenuItem sortIDMenuItem = new MenuItem();
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34 protected MenuItem sortGroupMenuItem = new MenuItem();
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35 protected MenuItem removeRedundancyMenuItem = new MenuItem();
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36 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
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37 protected MenuItem PCAMenuItem = new MenuItem();
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38 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
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39 protected MenuItem neighbourTreeMenuItem = new MenuItem();
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40 BorderLayout borderLayout1 = new BorderLayout();
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41 public Label statusBar = new Label();
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42 protected Menu outputTextboxMenu = new Menu();
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43 protected MenuItem clustalColour = new MenuItem();
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44 protected MenuItem zappoColour = new MenuItem();
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45 protected MenuItem taylorColour = new MenuItem();
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46 protected MenuItem hydrophobicityColour = new MenuItem();
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47 protected MenuItem helixColour = new MenuItem();
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48 protected MenuItem strandColour = new MenuItem();
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49 protected MenuItem turnColour = new MenuItem();
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50 protected MenuItem buriedColour = new MenuItem();
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51 protected MenuItem userDefinedColour = new MenuItem();
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52 protected MenuItem PIDColour = new MenuItem();
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53 protected MenuItem BLOSUM62Colour = new MenuItem();
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54 MenuItem njTreeBlosumMenuItem = new MenuItem();
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55 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
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56 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
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57 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
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58 MenuItem overviewMenuItem = new MenuItem();
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59 protected MenuItem undoMenuItem = new MenuItem();
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60 protected MenuItem redoMenuItem = new MenuItem();
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61 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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62 MenuItem noColourmenuItem = new MenuItem();
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63 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
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64 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
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65 MenuItem findMenuItem = new MenuItem();
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66 Menu searchMenu = new Menu();
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67 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
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68 protected MenuItem nucleotideColour = new MenuItem();
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69 MenuItem deleteGroups = new MenuItem();
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70 MenuItem delete = new MenuItem();
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71 MenuItem copy = new MenuItem();
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72 MenuItem cut = new MenuItem();
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73 Menu Menu1 = new Menu();
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74 MenuItem pasteNew = new MenuItem();
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75 MenuItem pasteThis = new MenuItem();
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76 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
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77 protected MenuItem font = new MenuItem();
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78 protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
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79 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
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80 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
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81 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
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82 MenuItem modifyPID = new MenuItem();
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83 MenuItem modifyConservation = new MenuItem();
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84 protected Menu sortByTreeMenu = new Menu();
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85 Menu sort = new Menu();
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86 Menu calculate = new Menu();
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87 MenuItem inputText = new MenuItem();
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88 Menu helpMenu = new Menu();
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89 MenuItem documentation = new MenuItem();
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90 MenuItem about = new MenuItem();
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91 public GAlignFrame()
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96 setMenuBar(alignFrameMenuBar);
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99 // dynamically fill save as menu with available formats
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100 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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101 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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102 item.addActionListener(new java.awt.event.ActionListener()
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104 public void actionPerformed(ActionEvent e)
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106 saveAs_actionPerformed(e);
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110 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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111 item.addActionListener(new java.awt.event.ActionListener()
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113 public void actionPerformed(ActionEvent e)
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115 outputText_actionPerformed(e);
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119 outputTextboxMenu.add( item );
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125 e.printStackTrace();
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129 private void jbInit() throws Exception
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131 fileMenu.setLabel("File");
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132 closeMenuItem.setLabel("Close");
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133 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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135 public void actionPerformed(ActionEvent e)
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137 closeMenuItem_actionPerformed(e);
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140 editMenu.setLabel("Edit");
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141 viewMenu.setLabel("View");
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142 colourMenu.setLabel("Colour");
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143 calculateMenu.setLabel("Calculate");
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144 selectAllSequenceMenuItem.setLabel("Select all");
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145 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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147 public void actionPerformed(ActionEvent e)
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149 selectAllSequenceMenuItem_actionPerformed(e);
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152 deselectAllSequenceMenuItem.setLabel("Deselect All");
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153 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 deselectAllSequenceMenuItem_actionPerformed(e);
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160 invertSequenceMenuItem.setLabel("Invert Selection");
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161 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 invertSequenceMenuItem_actionPerformed(e);
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168 remove2LeftMenuItem.setLabel("Remove Left");
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169 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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171 public void actionPerformed(ActionEvent e)
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173 remove2LeftMenuItem_actionPerformed(e);
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176 remove2RightMenuItem.setLabel("Remove Right");
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177 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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179 public void actionPerformed(ActionEvent e)
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181 remove2RightMenuItem_actionPerformed(e);
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184 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
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185 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 removeGappedColumnMenuItem_actionPerformed(e);
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192 removeAllGapsMenuItem.setLabel("Remove All Gaps");
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193 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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195 public void actionPerformed(ActionEvent e)
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197 removeAllGapsMenuItem_actionPerformed(e);
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200 viewBoxesMenuItem.setLabel("Boxes");
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201 viewBoxesMenuItem.setState(true);
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202 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()
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204 public void itemStateChanged(ItemEvent e)
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206 viewBoxesMenuItem_actionPerformed(null);
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209 viewTextMenuItem.setLabel("Text");
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210 viewTextMenuItem.setState(true);
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211 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()
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213 public void itemStateChanged(ItemEvent e)
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215 viewTextMenuItem_actionPerformed(null);
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218 sortPairwiseMenuItem.setLabel("By Pairwise Identity");
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219 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 sortPairwiseMenuItem_actionPerformed(e);
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226 sortIDMenuItem.setLabel("By ID");
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227 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 sortIDMenuItem_actionPerformed(e);
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234 sortGroupMenuItem.setLabel("By Group");
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235 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 sortGroupMenuItem_actionPerformed(e);
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242 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
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243 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 removeRedundancyMenuItem_actionPerformed(e);
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250 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
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251 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 pairwiseAlignmentMenuItem_actionPerformed(e);
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258 PCAMenuItem.setLabel("Principal Component Analysis...");
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259 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 PCAMenuItem_actionPerformed(e);
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266 averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity...");
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267 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 averageDistanceTreeMenuItem_actionPerformed(e);
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274 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
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275 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 neighbourTreeMenuItem_actionPerformed(e);
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282 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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283 statusBar.setBackground(Color.white);
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284 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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285 statusBar.setText("Status bar");
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286 outputTextboxMenu.setLabel("Output to Textbox");
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287 clustalColour.setLabel("Clustalx");
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289 clustalColour.addActionListener(new java.awt.event.ActionListener()
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291 public void actionPerformed(ActionEvent e)
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293 clustalColour_actionPerformed(e);
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296 zappoColour.setLabel("Zappo");
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297 zappoColour.addActionListener(new java.awt.event.ActionListener()
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299 public void actionPerformed(ActionEvent e)
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301 zappoColour_actionPerformed(e);
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304 taylorColour.setLabel("Taylor");
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305 taylorColour.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 taylorColour_actionPerformed(e);
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312 hydrophobicityColour.setLabel("Hydrophobicity");
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313 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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315 public void actionPerformed(ActionEvent e)
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317 hydrophobicityColour_actionPerformed(e);
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320 helixColour.setLabel("Helix Propensity");
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321 helixColour.addActionListener(new java.awt.event.ActionListener()
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323 public void actionPerformed(ActionEvent e)
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325 helixColour_actionPerformed(e);
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328 strandColour.setLabel("Strand Propensity");
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329 strandColour.addActionListener(new java.awt.event.ActionListener()
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331 public void actionPerformed(ActionEvent e)
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333 strandColour_actionPerformed(e);
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336 turnColour.setLabel("Turn Propensity");
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337 turnColour.addActionListener(new java.awt.event.ActionListener()
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339 public void actionPerformed(ActionEvent e)
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341 turnColour_actionPerformed(e);
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344 buriedColour.setLabel("Buried Index");
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345 buriedColour.addActionListener(new java.awt.event.ActionListener()
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347 public void actionPerformed(ActionEvent e)
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349 buriedColour_actionPerformed(e);
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352 userDefinedColour.setLabel("User Defined...");
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353 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 userDefinedColour_actionPerformed(e);
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360 PIDColour.setLabel("Percentage Identity");
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361 PIDColour.addActionListener(new java.awt.event.ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 PIDColour_actionPerformed(e);
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368 BLOSUM62Colour.setLabel("BLOSUM62 Score");
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369 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 BLOSUM62Colour_actionPerformed(e);
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376 avDistanceTreeBlosumMenuItem.setLabel("Average Distance using BLOSUM62...");
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377 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 avTreeBlosumMenuItem_actionPerformed(e);
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384 njTreeBlosumMenuItem.setLabel("Neighbour Joining using BLOSUM62...");
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385 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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387 public void actionPerformed(ActionEvent e)
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389 njTreeBlosumMenuItem_actionPerformed(e);
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392 annotationPanelMenuItem.setActionCommand("");
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393 annotationPanelMenuItem.setState(true);
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394 annotationPanelMenuItem.setLabel("Show Annotations");
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395 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()
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397 public void itemStateChanged(ItemEvent e)
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399 annotationPanelMenuItem_actionPerformed(null);
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402 colourTextMenuItem.setLabel("Colour Text");
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403 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()
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405 public void itemStateChanged(ItemEvent e)
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407 colourTextMenuItem_actionPerformed(null);
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410 overviewMenuItem.setLabel("Overview Window...");
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411 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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413 public void actionPerformed(ActionEvent e)
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415 overviewMenuItem_actionPerformed(e);
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418 undoMenuItem.setEnabled(false);
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419 undoMenuItem.setLabel("Undo");
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420 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 undoMenuItem_actionPerformed(e);
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427 redoMenuItem.setEnabled(false);
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428 redoMenuItem.setLabel("Redo");
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429 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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431 public void actionPerformed(ActionEvent e)
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433 redoMenuItem_actionPerformed(e);
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436 conservationMenuItem.setLabel("By Conservation");
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437 conservationMenuItem.addItemListener(new java.awt.event.ItemListener()
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439 public void itemStateChanged(ItemEvent e)
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441 conservationMenuItem_actionPerformed(null);
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444 noColourmenuItem.setLabel("None");
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445 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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447 public void actionPerformed(ActionEvent e)
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449 noColourmenuItem_actionPerformed(e);
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452 wrapMenuItem.setLabel("Wrap");
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453 wrapMenuItem.addItemListener(new java.awt.event.ItemListener()
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455 public void itemStateChanged(ItemEvent e)
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457 wrapMenuItem_actionPerformed(null);
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460 renderGapsMenuItem.setLabel("Show Gaps");
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461 renderGapsMenuItem.setState(true);
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462 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()
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465 public void itemStateChanged(ItemEvent e)
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468 renderGapsMenuItem_actionPerformed(null);
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471 findMenuItem.setLabel("Find...");
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472 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 findMenuItem_actionPerformed(e);
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479 searchMenu.setLabel("Search");
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481 abovePIDThreshold.setLabel("Above Identity Threshold");
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482 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()
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484 public void itemStateChanged(ItemEvent e)
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486 abovePIDThreshold_actionPerformed(null);
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489 nucleotideColour.setLabel("Nucleotide");
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490 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 nucleotideColour_actionPerformed(e);
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497 deleteGroups.setLabel("Undefine groups");
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498 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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500 public void actionPerformed(ActionEvent e)
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502 deleteGroups_actionPerformed(e);
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505 copy.setLabel("Copy");
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506 copy.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 copy_actionPerformed(e);
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513 cut.setLabel("Cut");
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514 cut.addActionListener(new java.awt.event.ActionListener()
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516 public void actionPerformed(ActionEvent e)
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518 cut_actionPerformed(e);
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521 delete.setLabel("Delete");
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522 delete.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 delete_actionPerformed(e);
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529 Menu1.setLabel("Paste");
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530 pasteNew.setLabel("to new alignment");
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531 pasteNew.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 pasteNew_actionPerformed(e);
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538 pasteThis.setLabel("add to this alignment");
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539 pasteThis.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 pasteThis_actionPerformed(e);
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546 applyToAllGroups.setLabel("Apply Colour To All Groups");
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547 applyToAllGroups.setState(true);
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548 applyToAllGroups.addItemListener(new java.awt.event.ItemListener()
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550 public void itemStateChanged(ItemEvent e)
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552 applyToAllGroups_actionPerformed(null);
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555 font.setLabel("Font...");
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556 font.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 font_actionPerformed(e);
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563 fullSeqId.setLabel("Show Full Sequence ID");
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564 fullSeqId.setState(true);
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565 fullSeqId.addItemListener(new java.awt.event.ItemListener()
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568 public void itemStateChanged(ItemEvent e)
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570 fullSeqId_actionPerformed(null);
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573 scaleAbove.setLabel("Scale Above");
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574 scaleAbove.setState(true);
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575 scaleAbove.addItemListener(new java.awt.event.ItemListener()
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578 public void itemStateChanged(ItemEvent e)
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581 scaleAbove_actionPerformed(null);
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584 scaleLeft.setEnabled(false);
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585 scaleLeft.setState(true);
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586 scaleLeft.setLabel("Scale Left");
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587 scaleLeft.addItemListener(new java.awt.event.ItemListener()
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590 public void itemStateChanged(ItemEvent e)
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593 scaleLeft_actionPerformed(null);
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596 scaleRight.setEnabled(false);
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597 scaleRight.setState(true);
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598 scaleRight.setLabel("Scale Right");
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599 scaleRight.addItemListener(new java.awt.event.ItemListener()
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602 public void itemStateChanged(ItemEvent e)
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605 scaleRight_actionPerformed(null);
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608 modifyPID.setLabel("Modify Identity Threshold...");
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609 modifyPID.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 modifyPID_actionPerformed(e);
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616 modifyConservation.setLabel("Modify Conservation Threshold...");
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617 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 modifyConservation_actionPerformed(e);
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624 sortByTreeMenu.setLabel("By Tree Order");
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625 sort.setLabel("Sort");
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626 calculate.setLabel("Calculate Tree");
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627 inputText.setLabel("Input from textbox");
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628 inputText.addActionListener(new java.awt.event.ActionListener()
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630 public void actionPerformed(ActionEvent e)
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632 inputText_actionPerformed(e);
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636 helpMenu.setLabel("Help");
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637 documentation.setLabel("Documentation");
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638 documentation.addActionListener(new java.awt.event.ActionListener()
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640 public void actionPerformed(ActionEvent e)
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642 documentation_actionPerformed(e);
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646 about.setLabel("About...");
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647 about.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 about_actionPerformed(e);
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655 alignFrameMenuBar.add(fileMenu);
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656 alignFrameMenuBar.add(editMenu);
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657 alignFrameMenuBar.add(searchMenu);
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658 alignFrameMenuBar.add(viewMenu);
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659 alignFrameMenuBar.add(colourMenu);
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660 alignFrameMenuBar.add(calculateMenu);
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661 alignFrameMenuBar.add(helpMenu);
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662 fileMenu.add(inputText);
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663 fileMenu.add(outputTextboxMenu);
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664 fileMenu.addSeparator();
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665 fileMenu.add(closeMenuItem);
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666 editMenu.add(undoMenuItem);
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667 editMenu.add(redoMenuItem);
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669 editMenu.add(copy);
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670 editMenu.add(Menu1);
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671 editMenu.add(delete);
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672 editMenu.addSeparator();
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673 editMenu.add(selectAllSequenceMenuItem);
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674 editMenu.add(deselectAllSequenceMenuItem);
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675 editMenu.add(invertSequenceMenuItem);
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676 editMenu.add(deleteGroups);
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677 editMenu.addSeparator();
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678 editMenu.add(remove2LeftMenuItem);
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679 editMenu.add(remove2RightMenuItem);
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680 editMenu.add(removeGappedColumnMenuItem);
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681 editMenu.add(removeAllGapsMenuItem);
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682 editMenu.add(removeRedundancyMenuItem);
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683 searchMenu.add(findMenuItem);
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684 viewMenu.add(font);
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685 viewMenu.add(fullSeqId);
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686 viewMenu.addSeparator();
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687 viewMenu.add(wrapMenuItem);
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688 viewMenu.add(scaleAbove);
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689 viewMenu.add(scaleLeft);
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690 viewMenu.add(scaleRight);
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691 viewMenu.addSeparator();
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692 viewMenu.add(viewBoxesMenuItem);
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693 viewMenu.add(viewTextMenuItem);
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694 viewMenu.add(colourTextMenuItem);
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695 viewMenu.add(renderGapsMenuItem);
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696 viewMenu.add(annotationPanelMenuItem);
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697 viewMenu.addSeparator();
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698 viewMenu.add(overviewMenuItem);
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699 colourMenu.add(applyToAllGroups);
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700 colourMenu.add(noColourmenuItem);
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701 colourMenu.addSeparator();
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702 colourMenu.add(clustalColour);
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703 colourMenu.add(BLOSUM62Colour);
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704 colourMenu.add(PIDColour);
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705 colourMenu.add(zappoColour);
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706 colourMenu.add(taylorColour);
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707 colourMenu.add(hydrophobicityColour);
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708 colourMenu.add(helixColour);
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709 colourMenu.add(strandColour);
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710 colourMenu.add(turnColour);
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711 colourMenu.add(buriedColour);
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712 colourMenu.add(nucleotideColour);
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713 colourMenu.add(userDefinedColour);
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714 colourMenu.addSeparator();
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715 colourMenu.add(conservationMenuItem);
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716 colourMenu.add(modifyConservation);
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717 colourMenu.add(abovePIDThreshold);
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718 colourMenu.add(modifyPID);
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719 calculateMenu.add(sort);
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720 calculateMenu.add(calculate);
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721 calculateMenu.addSeparator();
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722 calculateMenu.add(pairwiseAlignmentMenuItem);
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723 calculateMenu.add(PCAMenuItem);
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724 this.add(statusBar, BorderLayout.SOUTH);
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725 Menu1.add(pasteNew);
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726 Menu1.add(pasteThis);
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727 sort.add(sortIDMenuItem);
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728 sort.add(sortByTreeMenu);
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729 sort.add(sortGroupMenuItem);
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730 sort.add(sortPairwiseMenuItem);
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731 calculate.add(averageDistanceTreeMenuItem);
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732 calculate.add(neighbourTreeMenuItem);
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733 calculate.add(avDistanceTreeBlosumMenuItem);
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734 calculate.add(njTreeBlosumMenuItem);
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735 helpMenu.add(documentation);
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736 helpMenu.add(about);
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739 protected void saveAs_actionPerformed(ActionEvent e)
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744 protected void outputText_actionPerformed(ActionEvent e)
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749 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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755 protected void closeMenuItem_actionPerformed(ActionEvent e)
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760 protected void redoMenuItem_actionPerformed(ActionEvent e)
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765 protected void undoMenuItem_actionPerformed(ActionEvent e)
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771 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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776 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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781 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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786 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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791 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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796 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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801 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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807 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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813 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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818 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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824 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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829 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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834 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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839 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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844 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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849 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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855 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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860 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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865 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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870 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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875 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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881 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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886 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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893 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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901 protected void clustalColour_actionPerformed(ActionEvent e)
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906 protected void zappoColour_actionPerformed(ActionEvent e)
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911 protected void taylorColour_actionPerformed(ActionEvent e)
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917 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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922 protected void helixColour_actionPerformed(ActionEvent e)
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927 protected void strandColour_actionPerformed(ActionEvent e)
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932 protected void turnColour_actionPerformed(ActionEvent e)
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937 protected void buriedColour_actionPerformed(ActionEvent e)
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944 protected void userDefinedColour_actionPerformed(ActionEvent e)
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949 protected void PIDColour_actionPerformed(ActionEvent e)
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954 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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960 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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965 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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971 protected void printMenuItem_actionPerformed(ActionEvent e)
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976 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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981 protected void findMenuItem_actionPerformed(ActionEvent e)
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987 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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991 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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996 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1001 protected void deleteGroups_actionPerformed(ActionEvent e)
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1006 protected void copy_actionPerformed(ActionEvent e)
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1012 protected void cut_actionPerformed(ActionEvent e)
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1017 protected void delete_actionPerformed(ActionEvent e)
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1022 protected void pasteNew_actionPerformed(ActionEvent e)
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1027 protected void pasteThis_actionPerformed(ActionEvent e)
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1032 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1037 protected void createPNG_actionPerformed(ActionEvent e)
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1042 protected void font_actionPerformed(ActionEvent e)
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1047 protected void fullSeqId_actionPerformed(ActionEvent e)
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1052 protected void epsFile_actionPerformed(ActionEvent e)
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1057 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
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1061 protected void jpred_actionPerformed(ActionEvent e)
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1066 protected void scaleAbove_actionPerformed(ActionEvent e)
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1071 protected void scaleLeft_actionPerformed(ActionEvent e)
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1076 protected void scaleRight_actionPerformed(ActionEvent e)
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1081 protected void modifyPID_actionPerformed(ActionEvent e)
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1086 protected void modifyConservation_actionPerformed(ActionEvent e)
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1091 protected void preferences_actionPerformed(ActionEvent e)
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1096 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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1100 protected void inputText_actionPerformed(ActionEvent e) {
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1104 protected void documentation_actionPerformed(ActionEvent e) {
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1108 protected void about_actionPerformed(ActionEvent e) {
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