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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17 import javax.swing.event.AncestorListener;
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18 import javax.swing.event.AncestorEvent;
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20 public class GAlignFrame extends JInternalFrame
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22 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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23 protected JMenu fileMenu = new JMenu();
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24 protected JMenuItem closeMenuItem = new JMenuItem();
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25 protected JMenu editMenu = new JMenu();
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26 protected JMenu viewMenu = new JMenu();
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27 protected JMenu colourMenu = new JMenu();
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28 protected JMenu calculateMenu = new JMenu();
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29 protected JMenu webService = new JMenu();
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30 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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31 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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32 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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33 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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34 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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35 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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36 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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37 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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38 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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39 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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40 protected JMenuItem sortIDMenuItem = new JMenuItem();
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41 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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42 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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43 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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44 protected JMenuItem PCAMenuItem = new JMenuItem();
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45 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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46 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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47 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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48 BorderLayout borderLayout1 = new BorderLayout();
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49 public JLabel statusBar = new JLabel();
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50 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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51 protected JMenu outputTextboxMenu = new JMenu();
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52 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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61 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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63 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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64 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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65 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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66 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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67 JMenuItem htmlMenuItem = new JMenuItem();
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68 JMenuItem overviewMenuItem = new JMenuItem();
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69 protected JMenuItem undoMenuItem = new JMenuItem();
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70 protected JMenuItem redoMenuItem = new JMenuItem();
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71 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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72 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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73 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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74 JMenuItem printMenuItem = new JMenuItem();
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75 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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76 JMenuItem findMenuItem = new JMenuItem();
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77 JMenu searchMenu = new JMenu();
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78 protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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79 protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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80 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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81 JMenuItem deleteGroups = new JMenuItem();
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82 JMenuItem delete = new JMenuItem();
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83 JMenuItem copy = new JMenuItem();
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84 JMenuItem cut = new JMenuItem();
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85 JMenu jMenu1 = new JMenu();
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86 JMenuItem pasteNew = new JMenuItem();
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87 JMenuItem pasteThis = new JMenuItem();
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88 protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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89 JMenuItem createPNG = new JMenuItem();
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90 protected JMenuItem font = new JMenuItem();
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91 protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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92 JMenuItem epsFile = new JMenuItem();
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93 JMenuItem LoadtreeMenuItem = new JMenuItem();
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94 JMenuItem jpred = new JMenuItem();
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95 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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96 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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97 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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98 JMenuItem modifyPID = new JMenuItem();
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99 JMenuItem modifyConservation = new JMenuItem();
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100 protected JMenu sortByTreeMenu = new JMenu();
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101 protected JMenu sort = new JMenu();
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102 JMenu calculate = new JMenu();
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103 JMenuItem msaAlignMenuItem = new JMenuItem();
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104 JMenu jMenu2 = new JMenu();
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105 JMenuItem padGapsMenuitem = new JMenuItem();
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106 public GAlignFrame()
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108 ButtonGroup colours = new ButtonGroup();
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109 colours.add(noColourmenuItem);
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110 colours.add(clustalColour);
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111 colours.add(zappoColour);
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112 colours.add(taylorColour);
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113 colours.add(hydrophobicityColour);
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114 colours.add(helixColour);
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115 colours.add(strandColour);
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116 colours.add(turnColour);
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117 colours.add(buriedColour);
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118 colours.add(userDefinedColour);
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119 colours.add(PIDColour);
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120 colours.add(BLOSUM62Colour);
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121 colours.add(nucleotideColour);
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123 noColourmenuItem.setSelected(true);
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124 String defaultColour = Preferences.defaultColour;
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125 if(defaultColour!=null)
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127 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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130 case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
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131 case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
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132 case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
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133 case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
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134 case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
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135 case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
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136 case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
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137 case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
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138 case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
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139 case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
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140 case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
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148 setJMenuBar(alignFrameMenuBar);
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151 // dynamically fill save as menu with available formats
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152 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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153 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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154 item.addActionListener(new java.awt.event.ActionListener()
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156 public void actionPerformed(ActionEvent e)
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158 outputText_actionPerformed(e);
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162 outputTextboxMenu.add( item );
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168 e.printStackTrace();
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172 private void jbInit() throws Exception
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174 fileMenu.setMnemonic('F');
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175 fileMenu.setText("File");
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176 saveAlignmentMenu.setMnemonic('L');
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177 saveAlignmentMenu.setText("Save As");
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178 saveAlignmentMenu.addActionListener(new ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 saveAlignmentMenu_actionPerformed(e);
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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("by 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("by 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("by 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 alignFrameMenuBar.addAncestorListener(new AncestorListener()
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354 public void ancestorAdded(AncestorEvent event)
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356 alignFrameMenuBar_ancestorAdded(event);
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359 public void ancestorRemoved(AncestorEvent event)
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363 public void ancestorMoved(AncestorEvent event)
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367 statusBar.setBackground(Color.white);
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368 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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369 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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370 statusBar.setText("Status bar");
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371 outputTextboxMenu.setMnemonic('T');
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372 outputTextboxMenu.setText("Output to Textbox");
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373 clustalColour.setText("Clustalx");
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375 clustalColour.addActionListener(new java.awt.event.ActionListener()
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377 public void actionPerformed(ActionEvent e)
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379 clustalColour_actionPerformed(e);
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382 zappoColour.setText("Zappo");
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383 zappoColour.addActionListener(new java.awt.event.ActionListener()
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385 public void actionPerformed(ActionEvent e)
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387 zappoColour_actionPerformed(e);
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390 taylorColour.setText("Taylor");
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391 taylorColour.addActionListener(new java.awt.event.ActionListener()
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393 public void actionPerformed(ActionEvent e)
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395 taylorColour_actionPerformed(e);
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398 hydrophobicityColour.setText("Hydrophobicity");
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399 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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401 public void actionPerformed(ActionEvent e)
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403 hydrophobicityColour_actionPerformed(e);
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406 helixColour.setText("Helix Propensity");
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407 helixColour.addActionListener(new java.awt.event.ActionListener()
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409 public void actionPerformed(ActionEvent e)
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411 helixColour_actionPerformed(e);
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414 strandColour.setText("Strand Propensity");
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415 strandColour.addActionListener(new java.awt.event.ActionListener()
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417 public void actionPerformed(ActionEvent e)
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419 strandColour_actionPerformed(e);
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422 turnColour.setText("Turn Propensity");
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423 turnColour.addActionListener(new java.awt.event.ActionListener()
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425 public void actionPerformed(ActionEvent e)
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427 turnColour_actionPerformed(e);
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430 buriedColour.setText("Buried Index");
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431 buriedColour.addActionListener(new java.awt.event.ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 buriedColour_actionPerformed(e);
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438 userDefinedColour.setText("User Defined...");
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439 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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441 public void actionPerformed(ActionEvent e)
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443 userDefinedColour_actionPerformed(e);
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446 PIDColour.setText("Percentage Identity");
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447 PIDColour.addActionListener(new java.awt.event.ActionListener()
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449 public void actionPerformed(ActionEvent e)
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451 PIDColour_actionPerformed(e);
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454 BLOSUM62Colour.setText("BLOSUM62 Score");
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455 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 BLOSUM62Colour_actionPerformed(e);
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462 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
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463 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 avTreeBlosumMenuItem_actionPerformed(e);
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470 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
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471 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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473 public void actionPerformed(ActionEvent e)
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475 njTreeBlosumMenuItem_actionPerformed(e);
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478 annotationPanelMenuItem.setActionCommand("");
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479 annotationPanelMenuItem.setText("Show Annotations");
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480 annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
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481 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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483 public void actionPerformed(ActionEvent e)
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485 annotationPanelMenuItem_actionPerformed(e);
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488 colourTextMenuItem.setText("Colour Text");
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489 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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491 public void actionPerformed(ActionEvent e)
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493 colourTextMenuItem_actionPerformed(e);
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496 htmlMenuItem.setText("HTML");
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497 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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499 public void actionPerformed(ActionEvent e)
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501 htmlMenuItem_actionPerformed(e);
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504 overviewMenuItem.setText("Overview Window...");
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505 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 overviewMenuItem_actionPerformed(e);
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512 undoMenuItem.setEnabled(false);
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513 undoMenuItem.setMnemonic('Z');
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514 undoMenuItem.setText("Undo");
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515 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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516 event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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517 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 undoMenuItem_actionPerformed(e);
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524 redoMenuItem.setEnabled(false);
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525 redoMenuItem.setMnemonic('0');
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526 redoMenuItem.setText("Redo");
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527 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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529 public void actionPerformed(ActionEvent e)
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531 redoMenuItem_actionPerformed(e);
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534 conservationMenuItem.setText("By Conservation");
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535 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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537 public void actionPerformed(ActionEvent e)
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539 conservationMenuItem_actionPerformed(e);
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542 noColourmenuItem.setText("None");
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543 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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545 public void actionPerformed(ActionEvent e)
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547 noColourmenuItem_actionPerformed(e);
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550 wrapMenuItem.setText("Wrap");
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551 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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553 public void actionPerformed(ActionEvent e)
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555 wrapMenuItem_actionPerformed(e);
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558 printMenuItem.setText("Print");
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559 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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561 public void actionPerformed(ActionEvent e)
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563 printMenuItem_actionPerformed(e);
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566 renderGapsMenuItem.setText("Show Gaps");
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567 renderGapsMenuItem.setState(true);
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568 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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570 public void actionPerformed(ActionEvent e)
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572 renderGapsMenuItem_actionPerformed(e);
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575 findMenuItem.setText("Find...");
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576 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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577 event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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578 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 findMenuItem_actionPerformed(e);
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585 searchMenu.setText("Search");
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587 abovePIDThreshold.setText("Above Identity Threshold");
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588 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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589 public void actionPerformed(ActionEvent e) {
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590 abovePIDThreshold_actionPerformed(e);
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593 sequenceFeatures.setText("Sequence Features");
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594 sequenceFeatures.addActionListener(new ActionListener()
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596 public void actionPerformed(ActionEvent actionEvent)
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598 sequenceFeatures_actionPerformed(actionEvent);
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601 nucleotideColour.setText("Nucleotide");
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602 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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604 public void actionPerformed(ActionEvent e)
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606 nucleotideColour_actionPerformed(e);
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609 deleteGroups.setText("Undefine groups");
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610 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 deleteGroups_actionPerformed(e);
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617 copy.setText("Copy");
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618 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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619 KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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620 copy.setMnemonic(KeyEvent.VK_C);
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622 copy.addActionListener(new java.awt.event.ActionListener()
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624 public void actionPerformed(ActionEvent e)
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626 copy_actionPerformed(e);
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629 cut.setText("Cut");
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630 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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631 KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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632 cut.setMnemonic(KeyEvent.VK_X);
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633 cut.addActionListener(new java.awt.event.ActionListener()
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635 public void actionPerformed(ActionEvent e)
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637 cut_actionPerformed(e);
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640 delete.setText("Delete");
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641 delete.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 delete_actionPerformed(e);
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648 jMenu1.setMnemonic('V');
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649 jMenu1.setText("Paste");
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650 pasteNew.setText("to new alignment");
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651 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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652 KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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653 pasteNew.addActionListener(new java.awt.event.ActionListener()
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655 public void actionPerformed(ActionEvent e)
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657 pasteNew_actionPerformed(e);
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660 pasteThis.setText("add to this alignment");
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661 pasteThis.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 pasteThis_actionPerformed(e);
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668 applyToAllGroups.setText("Apply Colour To All Groups");
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669 applyToAllGroups.setState(true);
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670 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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672 public void actionPerformed(ActionEvent e)
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674 applyToAllGroups_actionPerformed(e);
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677 createPNG.addActionListener(new java.awt.event.ActionListener()
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679 public void actionPerformed(ActionEvent e)
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681 createPNG_actionPerformed(e);
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684 createPNG.setActionCommand("Save As PNG Image");
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685 createPNG.setText("PNG");
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686 font.setText("Font...");
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687 font.addActionListener(new java.awt.event.ActionListener()
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689 public void actionPerformed(ActionEvent e)
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691 font_actionPerformed(e);
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694 fullSeqId.setText("Show Full Sequence ID");
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695 fullSeqId.setState(true);
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696 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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698 public void actionPerformed(ActionEvent e)
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700 fullSeqId_actionPerformed(e);
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703 epsFile.setText("EPS");
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704 epsFile.addActionListener(new java.awt.event.ActionListener()
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706 public void actionPerformed(ActionEvent e)
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708 epsFile_actionPerformed(e);
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711 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
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712 LoadtreeMenuItem.setText("Load Assocated Tree");
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713 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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714 public void actionPerformed(ActionEvent e)
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716 LoadtreeMenuItem_actionPerformed(e);
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719 jpred.setText("JPred...");
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720 jpred.addActionListener(new java.awt.event.ActionListener()
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722 public void actionPerformed(ActionEvent e)
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724 jpred_actionPerformed(e);
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727 scaleAbove.setVisible(false);
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728 scaleAbove.setText("Scale Above");
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729 scaleAbove.addActionListener(new java.awt.event.ActionListener()
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731 public void actionPerformed(ActionEvent e)
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733 scaleAbove_actionPerformed(e);
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736 scaleLeft.setVisible(false);
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737 scaleLeft.setSelected(true);
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738 scaleLeft.setText("Scale Left");
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739 scaleLeft.addActionListener(new java.awt.event.ActionListener()
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741 public void actionPerformed(ActionEvent e)
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743 scaleLeft_actionPerformed(e);
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746 scaleRight.setVisible(false);
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747 scaleRight.setSelected(true);
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748 scaleRight.setText("Scale Right");
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749 scaleRight.addActionListener(new java.awt.event.ActionListener()
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751 public void actionPerformed(ActionEvent e)
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753 scaleRight_actionPerformed(e);
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756 modifyPID.setText("Modify Identity Threshold...");
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757 modifyPID.addActionListener(new java.awt.event.ActionListener()
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759 public void actionPerformed(ActionEvent e)
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761 modifyPID_actionPerformed(e);
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764 modifyConservation.setText("Modify Conservation Threshold...");
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765 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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767 public void actionPerformed(ActionEvent e)
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769 modifyConservation_actionPerformed(e);
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772 sortByTreeMenu.setText("By Tree Order");
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773 sort.setText("Sort");
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774 calculate.setText("Calculate Tree");
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775 msaAlignMenuItem.setText("Muscle Alignment...");
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776 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
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777 public void actionPerformed(ActionEvent e) {
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778 msaAlignMenuItem_actionPerformed(e);
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781 jMenu2.setText("Export");
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782 padGapsMenuitem.setText("Pad Gaps");
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783 padGapsMenuitem.addActionListener(new ActionListener()
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785 public void actionPerformed(ActionEvent e)
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787 padGapsMenuitem_actionPerformed(e);
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790 alignFrameMenuBar.add(fileMenu);
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791 alignFrameMenuBar.add(editMenu);
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792 alignFrameMenuBar.add(searchMenu);
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793 alignFrameMenuBar.add(viewMenu);
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794 alignFrameMenuBar.add(colourMenu);
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795 alignFrameMenuBar.add(calculateMenu);
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796 fileMenu.add(saveAlignmentMenu);
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797 fileMenu.add(jMenu2);
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798 fileMenu.add(outputTextboxMenu);
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799 fileMenu.add(printMenuItem);
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800 fileMenu.addSeparator();
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801 fileMenu.add(LoadtreeMenuItem);
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802 fileMenu.addSeparator();
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803 fileMenu.add(closeMenuItem);
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804 editMenu.add(undoMenuItem);
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805 editMenu.add(redoMenuItem);
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807 editMenu.add(copy);
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808 editMenu.add(jMenu1);
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809 editMenu.add(delete);
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810 editMenu.addSeparator();
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811 editMenu.add(selectAllSequenceMenuItem);
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812 editMenu.add(deselectAllSequenceMenuItem);
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813 editMenu.add(invertSequenceMenuItem);
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814 editMenu.add(deleteGroups);
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815 editMenu.addSeparator();
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816 editMenu.add(remove2LeftMenuItem);
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817 editMenu.add(remove2RightMenuItem);
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818 editMenu.add(removeGappedColumnMenuItem);
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819 editMenu.add(removeAllGapsMenuItem);
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820 editMenu.add(removeRedundancyMenuItem);
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821 editMenu.addSeparator();
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822 editMenu.add(padGapsMenuitem);
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823 searchMenu.add(findMenuItem);
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824 viewMenu.add(font);
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825 viewMenu.addSeparator();
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826 viewMenu.add(wrapMenuItem);
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827 viewMenu.add(fullSeqId);
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828 viewMenu.add(scaleAbove);
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829 viewMenu.add(scaleLeft);
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830 viewMenu.add(scaleRight);
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831 viewMenu.add(viewBoxesMenuItem);
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832 viewMenu.add(viewTextMenuItem);
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833 viewMenu.add(colourTextMenuItem);
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834 viewMenu.add(renderGapsMenuItem);
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835 viewMenu.add(annotationPanelMenuItem);
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836 viewMenu.add(sequenceFeatures);
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837 viewMenu.addSeparator();
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838 viewMenu.add(overviewMenuItem);
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839 colourMenu.add(applyToAllGroups);
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840 colourMenu.addSeparator();
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841 colourMenu.add(noColourmenuItem);
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842 colourMenu.add(clustalColour);
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843 colourMenu.add(BLOSUM62Colour);
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844 colourMenu.add(PIDColour);
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845 colourMenu.add(zappoColour);
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846 colourMenu.add(taylorColour);
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847 colourMenu.add(hydrophobicityColour);
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848 colourMenu.add(helixColour);
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849 colourMenu.add(strandColour);
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850 colourMenu.add(turnColour);
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851 colourMenu.add(buriedColour);
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852 colourMenu.add(nucleotideColour);
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853 colourMenu.add(userDefinedColour);
\r
854 colourMenu.addSeparator();
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855 colourMenu.add(conservationMenuItem);
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856 colourMenu.add(modifyConservation);
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857 colourMenu.add(abovePIDThreshold);
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858 colourMenu.add(modifyPID);
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859 calculateMenu.add(sort);
\r
860 calculateMenu.add(calculate);
\r
861 calculateMenu.addSeparator();
\r
862 calculateMenu.add(pairwiseAlignmentMenuItem);
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863 calculateMenu.add(PCAMenuItem);
\r
864 calculateMenu.addSeparator();
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865 calculateMenu.add(webService);
\r
866 webService.add(clustalAlignMenuItem);
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867 webService.add(jpred);
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868 webService.add(msaAlignMenuItem);
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869 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
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870 jMenu1.add(pasteNew);
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871 jMenu1.add(pasteThis);
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872 sort.add(sortIDMenuItem);
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873 sort.add(sortGroupMenuItem);
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874 sort.add(sortPairwiseMenuItem);
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875 calculate.add(averageDistanceTreeMenuItem);
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876 calculate.add(neighbourTreeMenuItem);
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877 calculate.add(avDistanceTreeBlosumMenuItem);
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878 calculate.add(njTreeBlosumMenuItem);
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879 jMenu2.add(htmlMenuItem);
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880 jMenu2.add(epsFile);
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881 jMenu2.add(createPNG);
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884 protected void outputText_actionPerformed(ActionEvent e)
\r
889 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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895 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
900 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
905 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
911 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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916 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
921 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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926 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
931 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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936 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
941 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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947 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
953 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
958 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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964 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
969 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
974 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
979 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
984 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
989 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
995 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1000 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1005 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1010 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1015 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1021 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1026 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1033 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1041 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1046 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1051 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1057 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1062 protected void helixColour_actionPerformed(ActionEvent e)
\r
1067 protected void strandColour_actionPerformed(ActionEvent e)
\r
1072 protected void turnColour_actionPerformed(ActionEvent e)
\r
1077 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1084 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1089 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1094 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1100 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1105 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1111 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1116 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1121 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1127 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
1131 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1136 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1141 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1146 protected void copy_actionPerformed(ActionEvent e)
\r
1152 protected void cut_actionPerformed(ActionEvent e)
\r
1157 protected void delete_actionPerformed(ActionEvent e)
\r
1162 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1167 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1172 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1177 protected void createPNG_actionPerformed(ActionEvent e)
\r
1182 protected void font_actionPerformed(ActionEvent e)
\r
1187 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1192 protected void epsFile_actionPerformed(ActionEvent e)
\r
1197 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1201 protected void jpred_actionPerformed(ActionEvent e)
\r
1206 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1211 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1216 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1221 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1226 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1231 protected void preferences_actionPerformed(ActionEvent e)
\r
1236 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
\r
1240 protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
\r
1245 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1250 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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