1 /********************
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2 * 2004 Jalview Reengineered
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9 package jalview.jbgui;
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11 import javax.swing.*;
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12 import java.awt.event.*;
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15 import jalview.gui.Preferences;
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16 import jalview.schemes.ColourSchemeProperty;
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18 public class GAlignFrame extends JInternalFrame
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20 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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21 protected JMenu fileMenu = new JMenu();
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22 protected JMenuItem closeMenuItem = new JMenuItem();
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23 protected JMenu editMenu = new JMenu();
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24 protected JMenu viewMenu = new JMenu();
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25 protected JMenu colourMenu = new JMenu();
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26 protected JMenu calculateMenu = new JMenu();
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27 protected JMenu webService = new JMenu();
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28 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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29 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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30 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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31 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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32 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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33 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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34 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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35 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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36 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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37 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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38 protected JMenuItem sortIDMenuItem = new JMenuItem();
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39 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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40 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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41 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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42 protected JMenuItem PCAMenuItem = new JMenuItem();
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43 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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44 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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45 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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46 BorderLayout borderLayout1 = new BorderLayout();
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47 public JLabel statusBar = new JLabel();
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48 protected JMenu saveAlignmentMenu = new JMenu();
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49 protected JMenu outputTextboxMenu = new JMenu();
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50 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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61 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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62 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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63 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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64 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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65 JMenuItem htmlMenuItem = new JMenuItem();
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66 JMenuItem overviewMenuItem = new JMenuItem();
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67 protected JMenuItem undoMenuItem = new JMenuItem();
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68 protected JMenuItem redoMenuItem = new JMenuItem();
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69 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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70 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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71 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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72 JMenuItem printMenuItem = new JMenuItem();
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73 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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74 JMenuItem findMenuItem = new JMenuItem();
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75 JMenu searchMenu = new JMenu();
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76 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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77 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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78 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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79 JMenuItem deleteGroups = new JMenuItem();
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80 JMenuItem delete = new JMenuItem();
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81 JMenuItem copy = new JMenuItem();
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82 JMenuItem cut = new JMenuItem();
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83 JMenu jMenu1 = new JMenu();
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84 JMenuItem pasteNew = new JMenuItem();
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85 JMenuItem pasteThis = new JMenuItem();
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86 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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87 JMenuItem createPNG = new JMenuItem();
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88 protected JMenuItem font = new JMenuItem();
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89 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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90 JMenuItem epsFile = new JMenuItem();
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91 JMenuItem LoadtreeMenuItem = new JMenuItem();
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92 JMenuItem jpred = new JMenuItem();
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93 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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94 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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95 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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96 JMenuItem modifyPID = new JMenuItem();
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97 JMenuItem modifyConservation = new JMenuItem();
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98 protected JMenu sortByTreeMenu = new JMenu();
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99 JMenu jMenu2 = new JMenu();
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100 JMenu sort = new JMenu();
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101 JMenu calculate = new JMenu();
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102 JMenuItem msaAlignMenuItem = new JMenuItem();
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103 public GAlignFrame()
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105 ButtonGroup colours = new ButtonGroup();
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106 colours.add(noColourmenuItem);
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107 colours.add(clustalColour);
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108 colours.add(zappoColour);
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109 colours.add(taylorColour);
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110 colours.add(hydrophobicityColour);
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111 colours.add(helixColour);
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112 colours.add(strandColour);
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113 colours.add(turnColour);
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114 colours.add(buriedColour);
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115 colours.add(userDefinedColour);
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116 colours.add(PIDColour);
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117 colours.add(BLOSUM62Colour);
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118 colours.add(nucleotideColour);
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120 noColourmenuItem.setSelected(true);
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121 String defaultColour = Preferences.defaultColour;
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122 if(defaultColour!=null)
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124 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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127 case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
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128 case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
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129 case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
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130 case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
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131 case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
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132 case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
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133 case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
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134 case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
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135 case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
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136 case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
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137 case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
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145 setJMenuBar(alignFrameMenuBar);
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148 // dynamically fill save as menu with available formats
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149 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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150 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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151 saveAlignmentMenu.add( item );
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152 item.addActionListener(new java.awt.event.ActionListener()
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154 public void actionPerformed(ActionEvent e)
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156 saveAs_actionPerformed(e);
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160 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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161 item.addActionListener(new java.awt.event.ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 outputText_actionPerformed(e);
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169 outputTextboxMenu.add( item );
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175 e.printStackTrace();
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179 private void jbInit() throws Exception
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181 fileMenu.setMnemonic('F');
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182 fileMenu.setText("File");
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183 saveAlignmentMenu.setMnemonic('L');
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184 saveAlignmentMenu.setText("Save");
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185 closeMenuItem.setMnemonic('C');
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186 closeMenuItem.setText("Close");
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187 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 closeMenuItem_actionPerformed(e);
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194 editMenu.setText("Edit");
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195 viewMenu.setText("View");
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196 colourMenu.setText("Colour");
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197 calculateMenu.setText("Calculate");
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198 webService.setText("Web Service");
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199 selectAllSequenceMenuItem.setText("Select all");
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200 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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201 java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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202 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 selectAllSequenceMenuItem_actionPerformed(e);
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209 deselectAllSequenceMenuItem.setText("Deselect All");
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210 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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211 getKeyStroke(java.awt.event.
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212 KeyEvent.VK_ESCAPE, 0, false));
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213 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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215 public void actionPerformed(ActionEvent e)
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217 deselectAllSequenceMenuItem_actionPerformed(e);
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220 invertSequenceMenuItem.setText("Invert Selection");
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221 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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223 public void actionPerformed(ActionEvent e)
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225 invertSequenceMenuItem_actionPerformed(e);
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228 remove2LeftMenuItem.setText("Remove Left");
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229 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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231 public void actionPerformed(ActionEvent e)
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233 remove2LeftMenuItem_actionPerformed(e);
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236 remove2RightMenuItem.setText("Remove Right");
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237 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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239 public void actionPerformed(ActionEvent e)
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241 remove2RightMenuItem_actionPerformed(e);
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244 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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245 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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247 public void actionPerformed(ActionEvent e)
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249 removeGappedColumnMenuItem_actionPerformed(e);
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252 removeAllGapsMenuItem.setText("Remove All Gaps");
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253 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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255 public void actionPerformed(ActionEvent e)
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257 removeAllGapsMenuItem_actionPerformed(e);
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260 viewBoxesMenuItem.setText("Boxes");
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261 viewBoxesMenuItem.setState(true);
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262 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 viewBoxesMenuItem_actionPerformed(e);
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269 viewTextMenuItem.setText("Text");
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270 viewTextMenuItem.setState(true);
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271 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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275 viewTextMenuItem_actionPerformed(e);
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278 sortPairwiseMenuItem.setText("Pairwise Identity");
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279 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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281 public void actionPerformed(ActionEvent e)
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283 sortPairwiseMenuItem_actionPerformed(e);
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286 sortIDMenuItem.setText("ID");
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287 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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289 public void actionPerformed(ActionEvent e)
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291 sortIDMenuItem_actionPerformed(e);
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294 sortGroupMenuItem.setText("Group");
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295 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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297 public void actionPerformed(ActionEvent e)
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299 sortGroupMenuItem_actionPerformed(e);
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302 removeRedundancyMenuItem.setText("Remove Redundancy...");
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303 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 removeRedundancyMenuItem_actionPerformed(e);
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310 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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311 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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313 public void actionPerformed(ActionEvent e)
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315 pairwiseAlignmentMenuItem_actionPerformed(e);
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318 PCAMenuItem.setText("Principal Component Analysis...");
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319 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 PCAMenuItem_actionPerformed(e);
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326 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
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327 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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329 public void actionPerformed(ActionEvent e)
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331 averageDistanceTreeMenuItem_actionPerformed(e);
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334 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
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335 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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337 public void actionPerformed(ActionEvent e)
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339 neighbourTreeMenuItem_actionPerformed(e);
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342 clustalAlignMenuItem.setText("Clustal Alignment...");
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343 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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345 public void actionPerformed(ActionEvent e)
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347 clustalAlignMenuItem_actionPerformed(e);
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350 this.getContentPane().setLayout(borderLayout1);
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351 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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352 statusBar.setBackground(Color.white);
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353 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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354 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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355 statusBar.setText("Status bar");
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356 outputTextboxMenu.setMnemonic('T');
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357 outputTextboxMenu.setText("Output to Textbox");
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358 clustalColour.setText("Clustalx");
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360 clustalColour.addActionListener(new java.awt.event.ActionListener()
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362 public void actionPerformed(ActionEvent e)
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364 clustalColour_actionPerformed(e);
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367 zappoColour.setText("Zappo");
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368 zappoColour.addActionListener(new java.awt.event.ActionListener()
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370 public void actionPerformed(ActionEvent e)
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372 zappoColour_actionPerformed(e);
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375 taylorColour.setText("Taylor");
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376 taylorColour.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 taylorColour_actionPerformed(e);
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383 hydrophobicityColour.setText("Hydrophobicity");
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384 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 hydrophobicityColour_actionPerformed(e);
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391 helixColour.setText("Helix Propensity");
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392 helixColour.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 helixColour_actionPerformed(e);
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399 strandColour.setText("Strand Propensity");
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400 strandColour.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 strandColour_actionPerformed(e);
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407 turnColour.setText("Turn Propensity");
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408 turnColour.addActionListener(new java.awt.event.ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 turnColour_actionPerformed(e);
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415 buriedColour.setText("Buried Index");
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416 buriedColour.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 buriedColour_actionPerformed(e);
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423 userDefinedColour.setText("User Defined...");
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424 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 userDefinedColour_actionPerformed(e);
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431 PIDColour.setText("Percentage Identity");
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432 PIDColour.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 PIDColour_actionPerformed(e);
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439 BLOSUM62Colour.setText("BLOSUM62 Score");
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440 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 BLOSUM62Colour_actionPerformed(e);
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447 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
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448 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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450 public void actionPerformed(ActionEvent e)
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452 avTreeBlosumMenuItem_actionPerformed(e);
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455 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
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456 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 njTreeBlosumMenuItem_actionPerformed(e);
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463 annotationPanelMenuItem.setActionCommand("");
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464 annotationPanelMenuItem.setText("Show Annotations");
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465 annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
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466 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 annotationPanelMenuItem_actionPerformed(e);
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473 colourTextMenuItem.setText("Colour Text");
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474 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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476 public void actionPerformed(ActionEvent e)
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478 colourTextMenuItem_actionPerformed(e);
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481 htmlMenuItem.setText("HTML");
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482 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 htmlMenuItem_actionPerformed(e);
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489 overviewMenuItem.setText("Overview Window...");
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490 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 overviewMenuItem_actionPerformed(e);
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497 undoMenuItem.setEnabled(false);
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498 undoMenuItem.setMnemonic('Z');
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499 undoMenuItem.setText("Undo");
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500 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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501 event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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502 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 undoMenuItem_actionPerformed(e);
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509 redoMenuItem.setEnabled(false);
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510 redoMenuItem.setMnemonic('0');
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511 redoMenuItem.setText("Redo");
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512 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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514 public void actionPerformed(ActionEvent e)
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516 redoMenuItem_actionPerformed(e);
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519 conservationMenuItem.setText("By Conservation");
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520 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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522 public void actionPerformed(ActionEvent e)
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524 conservationMenuItem_actionPerformed(e);
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527 noColourmenuItem.setText("None");
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528 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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530 public void actionPerformed(ActionEvent e)
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532 noColourmenuItem_actionPerformed(e);
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535 wrapMenuItem.setText("Wrap");
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536 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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538 public void actionPerformed(ActionEvent e)
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540 wrapMenuItem_actionPerformed(e);
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543 printMenuItem.setText("Print");
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544 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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546 public void actionPerformed(ActionEvent e)
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548 printMenuItem_actionPerformed(e);
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551 renderGapsMenuItem.setText("Show Gaps");
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552 renderGapsMenuItem.setState(true);
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553 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 renderGapsMenuItem_actionPerformed(e);
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560 findMenuItem.setText("Find...");
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561 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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562 event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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563 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 findMenuItem_actionPerformed(e);
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570 searchMenu.setText("Search");
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572 abovePIDThreshold.setText("Above Identity threshold");
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573 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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574 public void actionPerformed(ActionEvent e) {
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575 abovePIDThreshold_actionPerformed(e);
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578 sequenceFeatures.setText("Sequence Features");
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579 sequenceFeatures.addActionListener(new ActionListener()
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581 public void actionPerformed(ActionEvent actionEvent)
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583 sequenceFeatures_actionPerformed(actionEvent);
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586 nucleotideColour.setText("Nucleotide");
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587 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 nucleotideColour_actionPerformed(e);
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594 deleteGroups.setText("Undefine groups");
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595 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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597 public void actionPerformed(ActionEvent e)
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599 deleteGroups_actionPerformed(e);
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602 copy.setText("Copy");
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603 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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604 KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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605 copy.setMnemonic(KeyEvent.VK_C);
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607 copy.addActionListener(new java.awt.event.ActionListener()
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609 public void actionPerformed(ActionEvent e)
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611 copy_actionPerformed(e);
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614 cut.setText("Cut");
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615 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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616 KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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617 cut.setMnemonic(KeyEvent.VK_X);
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618 cut.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 cut_actionPerformed(e);
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625 delete.setText("Delete");
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626 delete.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 delete_actionPerformed(e);
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633 jMenu1.setMnemonic('V');
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634 jMenu1.setText("Paste");
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635 pasteNew.setText("to new alignment");
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636 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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637 KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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638 pasteNew.addActionListener(new java.awt.event.ActionListener()
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640 public void actionPerformed(ActionEvent e)
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642 pasteNew_actionPerformed(e);
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645 pasteThis.setText("add to this alignment");
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646 pasteThis.addActionListener(new java.awt.event.ActionListener()
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648 public void actionPerformed(ActionEvent e)
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650 pasteThis_actionPerformed(e);
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653 applyToAllGroups.setText("Apply Colour To All Groups");
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654 applyToAllGroups.setState(true);
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655 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 applyToAllGroups_actionPerformed(e);
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662 createPNG.addActionListener(new java.awt.event.ActionListener()
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664 public void actionPerformed(ActionEvent e)
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666 createPNG_actionPerformed(e);
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669 createPNG.setActionCommand("Save as PNG Image");
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670 createPNG.setText("PNG");
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671 font.setText("Font...");
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672 font.addActionListener(new java.awt.event.ActionListener()
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674 public void actionPerformed(ActionEvent e)
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676 font_actionPerformed(e);
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679 fullSeqId.setText("Show Full Sequence ID");
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680 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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682 public void actionPerformed(ActionEvent e)
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684 fullSeqId_actionPerformed(e);
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687 epsFile.setText("EPS");
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688 epsFile.addActionListener(new java.awt.event.ActionListener()
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690 public void actionPerformed(ActionEvent e)
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692 epsFile_actionPerformed(e);
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695 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
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696 LoadtreeMenuItem.setText("Load Assocated Tree");
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697 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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698 public void actionPerformed(ActionEvent e)
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700 LoadtreeMenuItem_actionPerformed(e);
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703 jpred.setText("JPred...");
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704 jpred.addActionListener(new java.awt.event.ActionListener()
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706 public void actionPerformed(ActionEvent e)
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708 jpred_actionPerformed(e);
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711 scaleAbove.setVisible(false);
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712 scaleAbove.setText("Scale Above");
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713 scaleAbove.addActionListener(new java.awt.event.ActionListener()
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715 public void actionPerformed(ActionEvent e)
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717 scaleAbove_actionPerformed(e);
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720 scaleLeft.setVisible(false);
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721 scaleLeft.setSelected(true);
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722 scaleLeft.setText("Scale Left");
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723 scaleLeft.addActionListener(new java.awt.event.ActionListener()
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725 public void actionPerformed(ActionEvent e)
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727 scaleLeft_actionPerformed(e);
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730 scaleRight.setVisible(false);
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731 scaleRight.setSelected(true);
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732 scaleRight.setText("Scale Right");
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733 scaleRight.addActionListener(new java.awt.event.ActionListener()
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735 public void actionPerformed(ActionEvent e)
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737 scaleRight_actionPerformed(e);
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740 modifyPID.setText("Modify Identity Threshold...");
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741 modifyPID.addActionListener(new java.awt.event.ActionListener()
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743 public void actionPerformed(ActionEvent e)
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745 modifyPID_actionPerformed(e);
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748 modifyConservation.setText("Modify Conservation Threshold...");
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749 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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751 public void actionPerformed(ActionEvent e)
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753 modifyConservation_actionPerformed(e);
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756 sortByTreeMenu.setText("Tree Order");
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757 jMenu2.setText("Save as");
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758 sort.setText("Sort");
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759 calculate.setText("Calculate Tree");
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760 msaAlignMenuItem.setText("Muscle Alignment...");
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761 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
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762 public void actionPerformed(ActionEvent e) {
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763 msaAlignMenuItem_actionPerformed(e);
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766 alignFrameMenuBar.add(fileMenu);
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767 alignFrameMenuBar.add(editMenu);
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768 alignFrameMenuBar.add(searchMenu);
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769 alignFrameMenuBar.add(viewMenu);
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770 alignFrameMenuBar.add(colourMenu);
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771 alignFrameMenuBar.add(calculateMenu);
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772 fileMenu.add(saveAlignmentMenu);
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773 fileMenu.add(jMenu2);
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774 fileMenu.add(outputTextboxMenu);
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775 fileMenu.add(printMenuItem);
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776 fileMenu.addSeparator();
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777 fileMenu.add(LoadtreeMenuItem);
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778 fileMenu.addSeparator();
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779 fileMenu.add(closeMenuItem);
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780 editMenu.add(undoMenuItem);
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781 editMenu.add(redoMenuItem);
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783 editMenu.add(copy);
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784 editMenu.add(jMenu1);
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785 editMenu.add(delete);
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786 editMenu.addSeparator();
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787 editMenu.add(selectAllSequenceMenuItem);
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788 editMenu.add(deselectAllSequenceMenuItem);
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789 editMenu.add(invertSequenceMenuItem);
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790 editMenu.add(deleteGroups);
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791 editMenu.addSeparator();
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792 editMenu.add(remove2LeftMenuItem);
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793 editMenu.add(remove2RightMenuItem);
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794 editMenu.add(removeGappedColumnMenuItem);
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795 editMenu.add(removeAllGapsMenuItem);
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796 editMenu.add(removeRedundancyMenuItem);
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797 searchMenu.add(findMenuItem);
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798 viewMenu.add(font);
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799 viewMenu.add(fullSeqId);
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800 viewMenu.addSeparator();
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801 viewMenu.add(wrapMenuItem);
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802 viewMenu.add(scaleAbove);
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803 viewMenu.add(scaleLeft);
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804 viewMenu.add(scaleRight);
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805 viewMenu.addSeparator();
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806 viewMenu.add(viewBoxesMenuItem);
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807 viewMenu.add(viewTextMenuItem);
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808 viewMenu.add(colourTextMenuItem);
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809 viewMenu.add(renderGapsMenuItem);
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810 viewMenu.add(annotationPanelMenuItem);
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811 viewMenu.add(sequenceFeatures);
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812 viewMenu.addSeparator();
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813 viewMenu.add(overviewMenuItem);
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814 colourMenu.add(applyToAllGroups);
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815 colourMenu.add(noColourmenuItem);
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816 colourMenu.addSeparator();
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817 colourMenu.add(clustalColour);
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818 colourMenu.add(BLOSUM62Colour);
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819 colourMenu.add(PIDColour);
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820 colourMenu.add(zappoColour);
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821 colourMenu.add(taylorColour);
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822 colourMenu.add(hydrophobicityColour);
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823 colourMenu.add(helixColour);
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824 colourMenu.add(strandColour);
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825 colourMenu.add(turnColour);
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826 colourMenu.add(buriedColour);
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827 colourMenu.add(nucleotideColour);
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828 colourMenu.add(userDefinedColour);
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829 colourMenu.addSeparator();
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830 colourMenu.add(conservationMenuItem);
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831 colourMenu.add(modifyConservation);
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832 colourMenu.add(abovePIDThreshold);
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833 colourMenu.add(modifyPID);
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834 calculateMenu.add(sort);
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835 calculateMenu.add(calculate);
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836 calculateMenu.addSeparator();
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837 calculateMenu.add(pairwiseAlignmentMenuItem);
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838 calculateMenu.add(PCAMenuItem);
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839 calculateMenu.addSeparator();
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840 calculateMenu.add(webService);
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841 webService.add(clustalAlignMenuItem);
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842 webService.add(jpred);
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843 webService.add(msaAlignMenuItem);
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844 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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845 jMenu1.add(pasteNew);
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846 jMenu1.add(pasteThis);
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847 jMenu2.add(htmlMenuItem);
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848 jMenu2.add(epsFile);
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849 jMenu2.add(createPNG);
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850 sort.add(sortIDMenuItem);
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851 sort.add(sortGroupMenuItem);
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852 sort.add(sortByTreeMenu);
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853 sort.add(sortPairwiseMenuItem);
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854 calculate.add(averageDistanceTreeMenuItem);
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855 calculate.add(neighbourTreeMenuItem);
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856 calculate.add(avDistanceTreeBlosumMenuItem);
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857 calculate.add(njTreeBlosumMenuItem);
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860 protected void saveAs_actionPerformed(ActionEvent e)
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865 protected void outputText_actionPerformed(ActionEvent e)
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870 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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876 protected void closeMenuItem_actionPerformed(ActionEvent e)
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881 protected void redoMenuItem_actionPerformed(ActionEvent e)
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886 protected void undoMenuItem_actionPerformed(ActionEvent e)
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892 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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897 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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902 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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907 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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912 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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917 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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922 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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928 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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934 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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939 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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945 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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950 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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955 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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960 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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965 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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970 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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976 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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981 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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986 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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991 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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996 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1002 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1007 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1014 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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1022 protected void clustalColour_actionPerformed(ActionEvent e)
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1027 protected void zappoColour_actionPerformed(ActionEvent e)
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1032 protected void taylorColour_actionPerformed(ActionEvent e)
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1038 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1043 protected void helixColour_actionPerformed(ActionEvent e)
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1048 protected void strandColour_actionPerformed(ActionEvent e)
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1053 protected void turnColour_actionPerformed(ActionEvent e)
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1058 protected void buriedColour_actionPerformed(ActionEvent e)
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1065 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1070 protected void PIDColour_actionPerformed(ActionEvent e)
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1075 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1081 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1086 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1092 protected void printMenuItem_actionPerformed(ActionEvent e)
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1097 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1102 protected void findMenuItem_actionPerformed(ActionEvent e)
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1108 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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1112 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
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1117 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1122 protected void deleteGroups_actionPerformed(ActionEvent e)
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1127 protected void copy_actionPerformed(ActionEvent e)
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1133 protected void cut_actionPerformed(ActionEvent e)
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1138 protected void delete_actionPerformed(ActionEvent e)
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1143 protected void pasteNew_actionPerformed(ActionEvent e)
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1148 protected void pasteThis_actionPerformed(ActionEvent e)
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1153 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1158 protected void createPNG_actionPerformed(ActionEvent e)
\r
1163 protected void font_actionPerformed(ActionEvent e)
\r
1168 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1173 protected void epsFile_actionPerformed(ActionEvent e)
\r
1178 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
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1182 protected void jpred_actionPerformed(ActionEvent e)
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1187 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1192 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1197 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1202 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1207 protected void modifyConservation_actionPerformed(ActionEvent e)
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1212 protected void preferences_actionPerformed(ActionEvent e)
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1217 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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