2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.jbappletgui;
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22 import java.awt.event.*;
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25 public class GAlignFrame extends Frame
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27 protected MenuBar alignFrameMenuBar = new MenuBar();
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28 protected Menu fileMenu = new Menu();
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29 protected MenuItem closeMenuItem = new MenuItem();
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30 protected Menu editMenu = new Menu();
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31 protected Menu viewMenu = new Menu();
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32 protected Menu colourMenu = new Menu();
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33 protected Menu calculateMenu = new Menu();
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34 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
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35 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
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36 protected MenuItem invertSequenceMenuItem = new MenuItem();
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37 protected MenuItem remove2LeftMenuItem = new MenuItem();
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38 protected MenuItem remove2RightMenuItem = new MenuItem();
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39 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
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40 protected MenuItem removeAllGapsMenuItem = new MenuItem();
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41 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
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42 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
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43 protected MenuItem sortPairwiseMenuItem = new MenuItem();
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44 protected MenuItem sortIDMenuItem = new MenuItem();
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45 protected MenuItem sortGroupMenuItem = new MenuItem();
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46 protected MenuItem removeRedundancyMenuItem = new MenuItem();
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47 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
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48 protected MenuItem PCAMenuItem = new MenuItem();
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49 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
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50 protected MenuItem neighbourTreeMenuItem = new MenuItem();
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51 BorderLayout borderLayout1 = new BorderLayout();
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52 public Label statusBar = new Label();
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53 protected Menu outputTextboxMenu = new Menu();
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54 protected MenuItem clustalColour = new MenuItem();
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55 protected MenuItem zappoColour = new MenuItem();
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56 protected MenuItem taylorColour = new MenuItem();
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57 protected MenuItem hydrophobicityColour = new MenuItem();
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58 protected MenuItem helixColour = new MenuItem();
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59 protected MenuItem strandColour = new MenuItem();
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60 protected MenuItem turnColour = new MenuItem();
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61 protected MenuItem buriedColour = new MenuItem();
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62 protected MenuItem userDefinedColour = new MenuItem();
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63 protected MenuItem PIDColour = new MenuItem();
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64 protected MenuItem BLOSUM62Colour = new MenuItem();
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65 MenuItem njTreeBlosumMenuItem = new MenuItem();
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66 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
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67 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
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68 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
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69 MenuItem overviewMenuItem = new MenuItem();
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70 protected MenuItem undoMenuItem = new MenuItem();
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71 protected MenuItem redoMenuItem = new MenuItem();
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72 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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73 MenuItem noColourmenuItem = new MenuItem();
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74 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
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75 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
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76 MenuItem findMenuItem = new MenuItem();
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77 Menu searchMenu = new Menu();
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78 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
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79 protected MenuItem nucleotideColour = new MenuItem();
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80 MenuItem deleteGroups = new MenuItem();
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81 MenuItem delete = new MenuItem();
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82 MenuItem copy = new MenuItem();
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83 MenuItem cut = new MenuItem();
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84 Menu Menu1 = new Menu();
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85 MenuItem pasteNew = new MenuItem();
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86 MenuItem pasteThis = new MenuItem();
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87 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
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88 protected MenuItem font = new MenuItem();
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89 protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
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90 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
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91 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
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92 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
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93 MenuItem modifyPID = new MenuItem();
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94 MenuItem modifyConservation = new MenuItem();
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95 protected Menu sortByTreeMenu = new Menu();
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96 Menu sort = new Menu();
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97 Menu calculate = new Menu();
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98 MenuItem inputText = new MenuItem();
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99 Menu helpMenu = new Menu();
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100 MenuItem documentation = new MenuItem();
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101 MenuItem about = new MenuItem();
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102 public GAlignFrame()
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107 setMenuBar(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.FormatAdapter.formats.size(); i++) {
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112 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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113 item.addActionListener(new java.awt.event.ActionListener()
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115 public void actionPerformed(ActionEvent e)
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117 saveAs_actionPerformed(e);
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121 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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122 item.addActionListener(new java.awt.event.ActionListener()
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124 public void actionPerformed(ActionEvent e)
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126 outputText_actionPerformed(e);
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130 outputTextboxMenu.add( item );
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136 e.printStackTrace();
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140 private void jbInit() throws Exception
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142 fileMenu.setLabel("File");
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143 closeMenuItem.setLabel("Close");
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144 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 closeMenuItem_actionPerformed(e);
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151 editMenu.setLabel("Edit");
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152 viewMenu.setLabel("View");
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153 colourMenu.setLabel("Colour");
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154 calculateMenu.setLabel("Calculate");
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155 selectAllSequenceMenuItem.setLabel("Select all");
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156 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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158 public void actionPerformed(ActionEvent e)
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160 selectAllSequenceMenuItem_actionPerformed(e);
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163 deselectAllSequenceMenuItem.setLabel("Deselect All");
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164 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 deselectAllSequenceMenuItem_actionPerformed(e);
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171 invertSequenceMenuItem.setLabel("Invert Selection");
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172 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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174 public void actionPerformed(ActionEvent e)
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176 invertSequenceMenuItem_actionPerformed(e);
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179 remove2LeftMenuItem.setLabel("Remove Left");
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180 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 remove2LeftMenuItem_actionPerformed(e);
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187 remove2RightMenuItem.setLabel("Remove Right");
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188 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 remove2RightMenuItem_actionPerformed(e);
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195 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
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196 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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198 public void actionPerformed(ActionEvent e)
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200 removeGappedColumnMenuItem_actionPerformed(e);
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203 removeAllGapsMenuItem.setLabel("Remove All Gaps");
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204 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 removeAllGapsMenuItem_actionPerformed(e);
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211 viewBoxesMenuItem.setLabel("Boxes");
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212 viewBoxesMenuItem.setState(true);
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213 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()
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215 public void itemStateChanged(ItemEvent e)
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217 viewBoxesMenuItem_actionPerformed(null);
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220 viewTextMenuItem.setLabel("Text");
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221 viewTextMenuItem.setState(true);
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222 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()
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224 public void itemStateChanged(ItemEvent e)
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226 viewTextMenuItem_actionPerformed(null);
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229 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
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230 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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232 public void actionPerformed(ActionEvent e)
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234 sortPairwiseMenuItem_actionPerformed(e);
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237 sortIDMenuItem.setLabel("by ID");
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238 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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240 public void actionPerformed(ActionEvent e)
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242 sortIDMenuItem_actionPerformed(e);
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245 sortGroupMenuItem.setLabel("by Group");
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246 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 sortGroupMenuItem_actionPerformed(e);
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253 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
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254 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 removeRedundancyMenuItem_actionPerformed(e);
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261 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
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262 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 pairwiseAlignmentMenuItem_actionPerformed(e);
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269 PCAMenuItem.setLabel("Principal Component Analysis...");
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270 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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272 public void actionPerformed(ActionEvent e)
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274 PCAMenuItem_actionPerformed(e);
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277 averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity...");
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278 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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280 public void actionPerformed(ActionEvent e)
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282 averageDistanceTreeMenuItem_actionPerformed(e);
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285 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
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286 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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288 public void actionPerformed(ActionEvent e)
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290 neighbourTreeMenuItem_actionPerformed(e);
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293 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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294 statusBar.setBackground(Color.white);
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295 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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296 statusBar.setText("Status bar");
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297 outputTextboxMenu.setLabel("Output to Textbox");
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298 clustalColour.setLabel("Clustalx");
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300 clustalColour.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(ActionEvent e)
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304 clustalColour_actionPerformed(e);
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307 zappoColour.setLabel("Zappo");
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308 zappoColour.addActionListener(new java.awt.event.ActionListener()
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310 public void actionPerformed(ActionEvent e)
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312 zappoColour_actionPerformed(e);
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315 taylorColour.setLabel("Taylor");
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316 taylorColour.addActionListener(new java.awt.event.ActionListener()
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318 public void actionPerformed(ActionEvent e)
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320 taylorColour_actionPerformed(e);
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323 hydrophobicityColour.setLabel("Hydrophobicity");
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324 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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326 public void actionPerformed(ActionEvent e)
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328 hydrophobicityColour_actionPerformed(e);
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331 helixColour.setLabel("Helix Propensity");
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332 helixColour.addActionListener(new java.awt.event.ActionListener()
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334 public void actionPerformed(ActionEvent e)
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336 helixColour_actionPerformed(e);
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339 strandColour.setLabel("Strand Propensity");
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340 strandColour.addActionListener(new java.awt.event.ActionListener()
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342 public void actionPerformed(ActionEvent e)
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344 strandColour_actionPerformed(e);
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347 turnColour.setLabel("Turn Propensity");
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348 turnColour.addActionListener(new java.awt.event.ActionListener()
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350 public void actionPerformed(ActionEvent e)
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352 turnColour_actionPerformed(e);
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355 buriedColour.setLabel("Buried Index");
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356 buriedColour.addActionListener(new java.awt.event.ActionListener()
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358 public void actionPerformed(ActionEvent e)
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360 buriedColour_actionPerformed(e);
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363 userDefinedColour.setLabel("User Defined...");
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364 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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366 public void actionPerformed(ActionEvent e)
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368 userDefinedColour_actionPerformed(e);
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371 PIDColour.setLabel("Percentage Identity");
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372 PIDColour.addActionListener(new java.awt.event.ActionListener()
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374 public void actionPerformed(ActionEvent e)
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376 PIDColour_actionPerformed(e);
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379 BLOSUM62Colour.setLabel("BLOSUM62 Score");
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380 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 BLOSUM62Colour_actionPerformed(e);
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387 avDistanceTreeBlosumMenuItem.setLabel("Average Distance Using BLOSUM62...");
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388 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 avTreeBlosumMenuItem_actionPerformed(e);
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395 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");
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396 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 njTreeBlosumMenuItem_actionPerformed(e);
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403 annotationPanelMenuItem.setActionCommand("");
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404 annotationPanelMenuItem.setState(true);
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405 annotationPanelMenuItem.setLabel("Show Annotations");
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406 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()
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408 public void itemStateChanged(ItemEvent e)
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410 annotationPanelMenuItem_actionPerformed(null);
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413 colourTextMenuItem.setLabel("Colour Text");
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414 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()
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416 public void itemStateChanged(ItemEvent e)
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418 colourTextMenuItem_actionPerformed(null);
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421 overviewMenuItem.setLabel("Overview Window...");
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422 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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424 public void actionPerformed(ActionEvent e)
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426 overviewMenuItem_actionPerformed(e);
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429 undoMenuItem.setEnabled(false);
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430 undoMenuItem.setLabel("Undo");
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431 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 undoMenuItem_actionPerformed(e);
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438 redoMenuItem.setEnabled(false);
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439 redoMenuItem.setLabel("Redo");
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440 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 redoMenuItem_actionPerformed(e);
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447 conservationMenuItem.setLabel("by Conservation");
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448 conservationMenuItem.addItemListener(new java.awt.event.ItemListener()
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450 public void itemStateChanged(ItemEvent e)
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452 conservationMenuItem_actionPerformed(null);
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455 noColourmenuItem.setLabel("None");
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456 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 noColourmenuItem_actionPerformed(e);
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463 wrapMenuItem.setLabel("Wrap");
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464 wrapMenuItem.addItemListener(new java.awt.event.ItemListener()
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466 public void itemStateChanged(ItemEvent e)
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468 wrapMenuItem_actionPerformed(null);
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471 renderGapsMenuItem.setLabel("Show Gaps");
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472 renderGapsMenuItem.setState(true);
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473 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()
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476 public void itemStateChanged(ItemEvent e)
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479 renderGapsMenuItem_actionPerformed(null);
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482 findMenuItem.setLabel("Find...");
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483 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 findMenuItem_actionPerformed(e);
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490 searchMenu.setLabel("Search");
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492 abovePIDThreshold.setLabel("Above Identity Threshold");
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493 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()
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495 public void itemStateChanged(ItemEvent e)
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497 abovePIDThreshold_actionPerformed(null);
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500 nucleotideColour.setLabel("Nucleotide");
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501 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 nucleotideColour_actionPerformed(e);
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508 deleteGroups.setLabel("Undefine Groups");
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509 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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511 public void actionPerformed(ActionEvent e)
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513 deleteGroups_actionPerformed(e);
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516 copy.setLabel("Copy");
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517 copy.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 copy_actionPerformed(e);
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524 cut.setLabel("Cut");
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525 cut.addActionListener(new java.awt.event.ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 cut_actionPerformed(e);
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532 delete.setLabel("Delete");
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533 delete.addActionListener(new java.awt.event.ActionListener()
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535 public void actionPerformed(ActionEvent e)
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537 delete_actionPerformed(e);
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540 Menu1.setLabel("Paste");
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541 pasteNew.setLabel("To New Alignment");
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542 pasteNew.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 pasteNew_actionPerformed(e);
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549 pasteThis.setLabel("Add To This Alignment");
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550 pasteThis.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 pasteThis_actionPerformed(e);
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557 applyToAllGroups.setLabel("Apply Colour To All Groups");
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558 applyToAllGroups.setState(true);
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559 applyToAllGroups.addItemListener(new java.awt.event.ItemListener()
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561 public void itemStateChanged(ItemEvent e)
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563 applyToAllGroups_actionPerformed(null);
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566 font.setLabel("Font...");
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567 font.addActionListener(new java.awt.event.ActionListener()
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569 public void actionPerformed(ActionEvent e)
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571 font_actionPerformed(e);
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574 fullSeqId.setLabel("Show Full Sequence ID");
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575 fullSeqId.setState(true);
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576 fullSeqId.addItemListener(new java.awt.event.ItemListener()
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579 public void itemStateChanged(ItemEvent e)
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581 fullSeqId_actionPerformed(null);
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584 scaleAbove.setLabel("Scale Above");
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585 scaleAbove.setState(true);
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586 scaleAbove.addItemListener(new java.awt.event.ItemListener()
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589 public void itemStateChanged(ItemEvent e)
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592 scaleAbove_actionPerformed(null);
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595 scaleLeft.setEnabled(false);
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596 scaleLeft.setState(true);
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597 scaleLeft.setLabel("Scale Left");
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598 scaleLeft.addItemListener(new java.awt.event.ItemListener()
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601 public void itemStateChanged(ItemEvent e)
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604 scaleLeft_actionPerformed(null);
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607 scaleRight.setEnabled(false);
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608 scaleRight.setState(true);
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609 scaleRight.setLabel("Scale Right");
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610 scaleRight.addItemListener(new java.awt.event.ItemListener()
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613 public void itemStateChanged(ItemEvent e)
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616 scaleRight_actionPerformed(null);
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619 modifyPID.setLabel("Modify Identity Threshold...");
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620 modifyPID.addActionListener(new java.awt.event.ActionListener()
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622 public void actionPerformed(ActionEvent e)
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624 modifyPID_actionPerformed(e);
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627 modifyConservation.setLabel("Modify Conservation Threshold...");
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628 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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630 public void actionPerformed(ActionEvent e)
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632 modifyConservation_actionPerformed(e);
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635 sortByTreeMenu.setLabel("By Tree Order");
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636 sort.setLabel("Sort");
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637 calculate.setLabel("Calculate Tree");
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638 inputText.setLabel("Input from textbox");
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639 inputText.addActionListener(new java.awt.event.ActionListener()
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641 public void actionPerformed(ActionEvent e)
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643 inputText_actionPerformed(e);
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647 helpMenu.setLabel("Help");
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648 documentation.setLabel("Documentation");
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649 documentation.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 documentation_actionPerformed(e);
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657 about.setLabel("About...");
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658 about.addActionListener(new java.awt.event.ActionListener()
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660 public void actionPerformed(ActionEvent e)
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662 about_actionPerformed(e);
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666 alignFrameMenuBar.add(fileMenu);
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667 alignFrameMenuBar.add(editMenu);
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668 alignFrameMenuBar.add(searchMenu);
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669 alignFrameMenuBar.add(viewMenu);
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670 alignFrameMenuBar.add(colourMenu);
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671 alignFrameMenuBar.add(calculateMenu);
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672 alignFrameMenuBar.add(helpMenu);
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673 fileMenu.add(inputText);
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674 fileMenu.add(outputTextboxMenu);
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675 fileMenu.addSeparator();
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676 fileMenu.add(closeMenuItem);
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677 editMenu.add(undoMenuItem);
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678 editMenu.add(redoMenuItem);
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680 editMenu.add(copy);
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681 editMenu.add(Menu1);
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682 editMenu.add(delete);
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683 editMenu.addSeparator();
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684 editMenu.add(selectAllSequenceMenuItem);
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685 editMenu.add(deselectAllSequenceMenuItem);
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686 editMenu.add(invertSequenceMenuItem);
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687 editMenu.add(deleteGroups);
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688 editMenu.addSeparator();
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689 editMenu.add(remove2LeftMenuItem);
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690 editMenu.add(remove2RightMenuItem);
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691 editMenu.add(removeGappedColumnMenuItem);
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692 editMenu.add(removeAllGapsMenuItem);
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693 editMenu.add(removeRedundancyMenuItem);
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694 searchMenu.add(findMenuItem);
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695 viewMenu.add(font);
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696 viewMenu.addSeparator();
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697 viewMenu.add(wrapMenuItem);
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698 viewMenu.add(scaleAbove);
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699 viewMenu.add(scaleLeft);
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700 viewMenu.add(scaleRight);
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701 viewMenu.addSeparator();
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702 viewMenu.add(fullSeqId);
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703 viewMenu.add(viewBoxesMenuItem);
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704 viewMenu.add(viewTextMenuItem);
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705 viewMenu.add(colourTextMenuItem);
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706 viewMenu.add(renderGapsMenuItem);
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707 viewMenu.add(annotationPanelMenuItem);
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708 viewMenu.addSeparator();
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709 viewMenu.add(overviewMenuItem);
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710 colourMenu.add(applyToAllGroups);
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711 colourMenu.addSeparator();
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712 colourMenu.add(noColourmenuItem);
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713 colourMenu.add(clustalColour);
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714 colourMenu.add(BLOSUM62Colour);
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715 colourMenu.add(PIDColour);
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716 colourMenu.add(zappoColour);
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717 colourMenu.add(taylorColour);
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718 colourMenu.add(hydrophobicityColour);
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719 colourMenu.add(helixColour);
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720 colourMenu.add(strandColour);
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721 colourMenu.add(turnColour);
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722 colourMenu.add(buriedColour);
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723 colourMenu.add(nucleotideColour);
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724 colourMenu.add(userDefinedColour);
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725 colourMenu.addSeparator();
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726 colourMenu.add(conservationMenuItem);
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727 colourMenu.add(modifyConservation);
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728 colourMenu.add(abovePIDThreshold);
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729 colourMenu.add(modifyPID);
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730 calculateMenu.add(sort);
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731 calculateMenu.add(calculate);
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732 calculateMenu.addSeparator();
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733 calculateMenu.add(pairwiseAlignmentMenuItem);
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734 calculateMenu.add(PCAMenuItem);
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735 this.add(statusBar, BorderLayout.SOUTH);
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736 Menu1.add(pasteNew);
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737 Menu1.add(pasteThis);
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738 sort.add(sortIDMenuItem);
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739 sort.add(sortByTreeMenu);
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740 sort.add(sortGroupMenuItem);
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741 sort.add(sortPairwiseMenuItem);
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742 calculate.add(averageDistanceTreeMenuItem);
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743 calculate.add(neighbourTreeMenuItem);
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744 calculate.add(avDistanceTreeBlosumMenuItem);
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745 calculate.add(njTreeBlosumMenuItem);
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746 helpMenu.add(documentation);
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747 helpMenu.add(about);
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750 protected void saveAs_actionPerformed(ActionEvent e)
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755 protected void outputText_actionPerformed(ActionEvent e)
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760 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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766 protected void closeMenuItem_actionPerformed(ActionEvent e)
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771 protected void redoMenuItem_actionPerformed(ActionEvent e)
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776 protected void undoMenuItem_actionPerformed(ActionEvent e)
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782 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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787 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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792 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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797 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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802 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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807 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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812 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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818 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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824 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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829 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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835 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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840 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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845 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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850 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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855 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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860 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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866 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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871 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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876 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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881 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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886 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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892 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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897 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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904 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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912 protected void clustalColour_actionPerformed(ActionEvent e)
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917 protected void zappoColour_actionPerformed(ActionEvent e)
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922 protected void taylorColour_actionPerformed(ActionEvent e)
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928 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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933 protected void helixColour_actionPerformed(ActionEvent e)
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938 protected void strandColour_actionPerformed(ActionEvent e)
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943 protected void turnColour_actionPerformed(ActionEvent e)
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948 protected void buriedColour_actionPerformed(ActionEvent e)
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955 protected void userDefinedColour_actionPerformed(ActionEvent e)
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960 protected void PIDColour_actionPerformed(ActionEvent e)
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965 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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971 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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976 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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982 protected void printMenuItem_actionPerformed(ActionEvent e)
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987 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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992 protected void findMenuItem_actionPerformed(ActionEvent e)
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998 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1002 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1007 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1012 protected void deleteGroups_actionPerformed(ActionEvent e)
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1017 protected void copy_actionPerformed(ActionEvent e)
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1023 protected void cut_actionPerformed(ActionEvent e)
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1028 protected void delete_actionPerformed(ActionEvent e)
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1033 protected void pasteNew_actionPerformed(ActionEvent e)
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1038 protected void pasteThis_actionPerformed(ActionEvent e)
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1043 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1048 protected void createPNG_actionPerformed(ActionEvent e)
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1053 protected void font_actionPerformed(ActionEvent e)
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1058 protected void fullSeqId_actionPerformed(ActionEvent e)
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1063 protected void epsFile_actionPerformed(ActionEvent e)
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1068 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
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1072 protected void jpred_actionPerformed(ActionEvent e)
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1077 protected void scaleAbove_actionPerformed(ActionEvent e)
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1082 protected void scaleLeft_actionPerformed(ActionEvent e)
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1087 protected void scaleRight_actionPerformed(ActionEvent e)
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1092 protected void modifyPID_actionPerformed(ActionEvent e)
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1097 protected void modifyConservation_actionPerformed(ActionEvent e)
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1102 protected void preferences_actionPerformed(ActionEvent e)
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1107 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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1111 protected void inputText_actionPerformed(ActionEvent e) {
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1115 protected void documentation_actionPerformed(ActionEvent e) {
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1119 protected void about_actionPerformed(ActionEvent e) {
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