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 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 public GAlignFrame()
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107 ButtonGroup colours = new ButtonGroup();
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108 colours.add(noColourmenuItem);
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109 colours.add(clustalColour);
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110 colours.add(zappoColour);
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111 colours.add(taylorColour);
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112 colours.add(hydrophobicityColour);
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113 colours.add(helixColour);
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114 colours.add(strandColour);
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115 colours.add(turnColour);
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116 colours.add(buriedColour);
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117 colours.add(userDefinedColour);
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118 colours.add(PIDColour);
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119 colours.add(BLOSUM62Colour);
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120 colours.add(nucleotideColour);
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122 noColourmenuItem.setSelected(true);
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123 String defaultColour = Preferences.defaultColour;
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124 if(defaultColour!=null)
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126 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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129 case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
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130 case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
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131 case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
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132 case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
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133 case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
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134 case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
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135 case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
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136 case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
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137 case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
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138 case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
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139 case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
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147 setJMenuBar(alignFrameMenuBar);
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150 // dynamically fill save as menu with available formats
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151 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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152 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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153 item.addActionListener(new java.awt.event.ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 outputText_actionPerformed(e);
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161 outputTextboxMenu.add( item );
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167 e.printStackTrace();
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171 private void jbInit() throws Exception
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173 fileMenu.setMnemonic('F');
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174 fileMenu.setText("File");
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175 saveAlignmentMenu.setMnemonic('L');
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176 saveAlignmentMenu.setText("Save As");
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177 saveAlignmentMenu.addActionListener(new ActionListener()
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179 public void actionPerformed(ActionEvent e)
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181 saveAlignmentMenu_actionPerformed(e);
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184 closeMenuItem.setMnemonic('C');
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185 closeMenuItem.setText("Close");
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186 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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188 public void actionPerformed(ActionEvent e)
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190 closeMenuItem_actionPerformed(e);
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193 editMenu.setText("Edit");
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194 viewMenu.setText("View");
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195 colourMenu.setText("Colour");
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196 calculateMenu.setText("Calculate");
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197 webService.setText("Web Service");
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198 selectAllSequenceMenuItem.setText("Select all");
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199 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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200 java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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201 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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203 public void actionPerformed(ActionEvent e)
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205 selectAllSequenceMenuItem_actionPerformed(e);
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208 deselectAllSequenceMenuItem.setText("Deselect All");
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209 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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210 getKeyStroke(java.awt.event.
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211 KeyEvent.VK_ESCAPE, 0, false));
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212 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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214 public void actionPerformed(ActionEvent e)
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216 deselectAllSequenceMenuItem_actionPerformed(e);
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219 invertSequenceMenuItem.setText("Invert Selection");
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220 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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222 public void actionPerformed(ActionEvent e)
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224 invertSequenceMenuItem_actionPerformed(e);
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227 remove2LeftMenuItem.setText("Remove Left");
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228 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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230 public void actionPerformed(ActionEvent e)
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232 remove2LeftMenuItem_actionPerformed(e);
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235 remove2RightMenuItem.setText("Remove Right");
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236 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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238 public void actionPerformed(ActionEvent e)
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240 remove2RightMenuItem_actionPerformed(e);
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243 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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244 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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246 public void actionPerformed(ActionEvent e)
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248 removeGappedColumnMenuItem_actionPerformed(e);
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251 removeAllGapsMenuItem.setText("Remove All Gaps");
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252 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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254 public void actionPerformed(ActionEvent e)
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256 removeAllGapsMenuItem_actionPerformed(e);
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259 viewBoxesMenuItem.setText("Boxes");
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260 viewBoxesMenuItem.setState(true);
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261 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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263 public void actionPerformed(ActionEvent e)
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265 viewBoxesMenuItem_actionPerformed(e);
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268 viewTextMenuItem.setText("Text");
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269 viewTextMenuItem.setState(true);
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270 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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272 public void actionPerformed(ActionEvent e)
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274 viewTextMenuItem_actionPerformed(e);
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277 sortPairwiseMenuItem.setText("By Pairwise Identity");
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278 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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280 public void actionPerformed(ActionEvent e)
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282 sortPairwiseMenuItem_actionPerformed(e);
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285 sortIDMenuItem.setText("By ID");
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286 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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288 public void actionPerformed(ActionEvent e)
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290 sortIDMenuItem_actionPerformed(e);
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293 sortGroupMenuItem.setText("By Group");
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294 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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296 public void actionPerformed(ActionEvent e)
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298 sortGroupMenuItem_actionPerformed(e);
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301 removeRedundancyMenuItem.setText("Remove Redundancy...");
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302 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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304 public void actionPerformed(ActionEvent e)
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306 removeRedundancyMenuItem_actionPerformed(e);
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309 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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310 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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312 public void actionPerformed(ActionEvent e)
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314 pairwiseAlignmentMenuItem_actionPerformed(e);
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317 PCAMenuItem.setText("Principal Component Analysis...");
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318 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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320 public void actionPerformed(ActionEvent e)
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322 PCAMenuItem_actionPerformed(e);
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325 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
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326 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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328 public void actionPerformed(ActionEvent e)
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330 averageDistanceTreeMenuItem_actionPerformed(e);
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333 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
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334 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 neighbourTreeMenuItem_actionPerformed(e);
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341 clustalAlignMenuItem.setText("Clustal Alignment...");
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342 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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344 public void actionPerformed(ActionEvent e)
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346 clustalAlignMenuItem_actionPerformed(e);
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349 this.getContentPane().setLayout(borderLayout1);
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350 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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351 alignFrameMenuBar.addAncestorListener(new AncestorListener()
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353 public void ancestorAdded(AncestorEvent event)
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355 alignFrameMenuBar_ancestorAdded(event);
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358 public void ancestorRemoved(AncestorEvent event)
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362 public void ancestorMoved(AncestorEvent event)
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366 statusBar.setBackground(Color.white);
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367 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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368 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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369 statusBar.setText("Status bar");
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370 outputTextboxMenu.setMnemonic('T');
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371 outputTextboxMenu.setText("Output to Textbox");
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372 clustalColour.setText("Clustalx");
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374 clustalColour.addActionListener(new java.awt.event.ActionListener()
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376 public void actionPerformed(ActionEvent e)
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378 clustalColour_actionPerformed(e);
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381 zappoColour.setText("Zappo");
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382 zappoColour.addActionListener(new java.awt.event.ActionListener()
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384 public void actionPerformed(ActionEvent e)
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386 zappoColour_actionPerformed(e);
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389 taylorColour.setText("Taylor");
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390 taylorColour.addActionListener(new java.awt.event.ActionListener()
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392 public void actionPerformed(ActionEvent e)
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394 taylorColour_actionPerformed(e);
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397 hydrophobicityColour.setText("Hydrophobicity");
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398 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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400 public void actionPerformed(ActionEvent e)
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402 hydrophobicityColour_actionPerformed(e);
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405 helixColour.setText("Helix Propensity");
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406 helixColour.addActionListener(new java.awt.event.ActionListener()
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408 public void actionPerformed(ActionEvent e)
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410 helixColour_actionPerformed(e);
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413 strandColour.setText("Strand Propensity");
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414 strandColour.addActionListener(new java.awt.event.ActionListener()
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416 public void actionPerformed(ActionEvent e)
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418 strandColour_actionPerformed(e);
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421 turnColour.setText("Turn Propensity");
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422 turnColour.addActionListener(new java.awt.event.ActionListener()
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424 public void actionPerformed(ActionEvent e)
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426 turnColour_actionPerformed(e);
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429 buriedColour.setText("Buried Index");
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430 buriedColour.addActionListener(new java.awt.event.ActionListener()
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432 public void actionPerformed(ActionEvent e)
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434 buriedColour_actionPerformed(e);
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437 userDefinedColour.setText("User Defined...");
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438 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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440 public void actionPerformed(ActionEvent e)
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442 userDefinedColour_actionPerformed(e);
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445 PIDColour.setText("Percentage Identity");
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446 PIDColour.addActionListener(new java.awt.event.ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 PIDColour_actionPerformed(e);
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453 BLOSUM62Colour.setText("BLOSUM62 Score");
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454 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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456 public void actionPerformed(ActionEvent e)
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458 BLOSUM62Colour_actionPerformed(e);
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461 avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
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462 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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464 public void actionPerformed(ActionEvent e)
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466 avTreeBlosumMenuItem_actionPerformed(e);
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469 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
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470 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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472 public void actionPerformed(ActionEvent e)
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474 njTreeBlosumMenuItem_actionPerformed(e);
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477 annotationPanelMenuItem.setActionCommand("");
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478 annotationPanelMenuItem.setText("Show Annotations");
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479 annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
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480 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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482 public void actionPerformed(ActionEvent e)
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484 annotationPanelMenuItem_actionPerformed(e);
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487 colourTextMenuItem.setText("Colour Text");
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488 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 colourTextMenuItem_actionPerformed(e);
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495 htmlMenuItem.setText("HTML");
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496 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 htmlMenuItem_actionPerformed(e);
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503 overviewMenuItem.setText("Overview Window...");
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504 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 overviewMenuItem_actionPerformed(e);
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511 undoMenuItem.setEnabled(false);
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512 undoMenuItem.setMnemonic('Z');
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513 undoMenuItem.setText("Undo");
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514 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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515 event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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516 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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518 public void actionPerformed(ActionEvent e)
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520 undoMenuItem_actionPerformed(e);
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523 redoMenuItem.setEnabled(false);
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524 redoMenuItem.setMnemonic('0');
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525 redoMenuItem.setText("Redo");
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526 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 redoMenuItem_actionPerformed(e);
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533 conservationMenuItem.setText("By Conservation");
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534 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 conservationMenuItem_actionPerformed(e);
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541 noColourmenuItem.setText("None");
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542 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 noColourmenuItem_actionPerformed(e);
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549 wrapMenuItem.setText("Wrap");
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550 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 wrapMenuItem_actionPerformed(e);
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557 printMenuItem.setText("Print");
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558 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 printMenuItem_actionPerformed(e);
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565 renderGapsMenuItem.setText("Show Gaps");
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566 renderGapsMenuItem.setState(true);
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567 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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569 public void actionPerformed(ActionEvent e)
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571 renderGapsMenuItem_actionPerformed(e);
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574 findMenuItem.setText("Find...");
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575 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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576 event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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577 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 findMenuItem_actionPerformed(e);
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584 searchMenu.setText("Search");
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586 abovePIDThreshold.setText("Above Identity Threshold");
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587 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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588 public void actionPerformed(ActionEvent e) {
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589 abovePIDThreshold_actionPerformed(e);
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592 sequenceFeatures.setText("Sequence Features");
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593 sequenceFeatures.addActionListener(new ActionListener()
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595 public void actionPerformed(ActionEvent actionEvent)
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597 sequenceFeatures_actionPerformed(actionEvent);
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600 nucleotideColour.setText("Nucleotide");
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601 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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603 public void actionPerformed(ActionEvent e)
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605 nucleotideColour_actionPerformed(e);
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608 deleteGroups.setText("Undefine groups");
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609 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 deleteGroups_actionPerformed(e);
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616 copy.setText("Copy");
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617 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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618 KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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619 copy.setMnemonic(KeyEvent.VK_C);
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621 copy.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 copy_actionPerformed(e);
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628 cut.setText("Cut");
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629 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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630 KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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631 cut.setMnemonic(KeyEvent.VK_X);
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632 cut.addActionListener(new java.awt.event.ActionListener()
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634 public void actionPerformed(ActionEvent e)
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636 cut_actionPerformed(e);
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639 delete.setText("Delete");
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640 delete.addActionListener(new java.awt.event.ActionListener()
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642 public void actionPerformed(ActionEvent e)
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644 delete_actionPerformed(e);
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647 jMenu1.setMnemonic('V');
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648 jMenu1.setText("Paste");
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649 pasteNew.setText("to new alignment");
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650 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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651 KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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652 pasteNew.addActionListener(new java.awt.event.ActionListener()
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654 public void actionPerformed(ActionEvent e)
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656 pasteNew_actionPerformed(e);
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659 pasteThis.setText("add to this alignment");
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660 pasteThis.addActionListener(new java.awt.event.ActionListener()
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662 public void actionPerformed(ActionEvent e)
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664 pasteThis_actionPerformed(e);
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667 applyToAllGroups.setText("Apply Colour To All Groups");
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668 applyToAllGroups.setState(true);
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669 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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671 public void actionPerformed(ActionEvent e)
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673 applyToAllGroups_actionPerformed(e);
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676 createPNG.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 createPNG_actionPerformed(e);
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683 createPNG.setActionCommand("Save As PNG Image");
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684 createPNG.setText("PNG");
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685 font.setText("Font...");
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686 font.addActionListener(new java.awt.event.ActionListener()
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688 public void actionPerformed(ActionEvent e)
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690 font_actionPerformed(e);
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693 fullSeqId.setText("Show Full Sequence ID");
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694 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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696 public void actionPerformed(ActionEvent e)
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698 fullSeqId_actionPerformed(e);
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701 epsFile.setText("EPS");
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702 epsFile.addActionListener(new java.awt.event.ActionListener()
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704 public void actionPerformed(ActionEvent e)
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706 epsFile_actionPerformed(e);
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709 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
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710 LoadtreeMenuItem.setText("Load Assocated Tree");
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711 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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712 public void actionPerformed(ActionEvent e)
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714 LoadtreeMenuItem_actionPerformed(e);
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717 jpred.setText("JPred...");
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718 jpred.addActionListener(new java.awt.event.ActionListener()
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720 public void actionPerformed(ActionEvent e)
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722 jpred_actionPerformed(e);
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725 scaleAbove.setVisible(false);
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726 scaleAbove.setText("Scale Above");
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727 scaleAbove.addActionListener(new java.awt.event.ActionListener()
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729 public void actionPerformed(ActionEvent e)
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731 scaleAbove_actionPerformed(e);
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734 scaleLeft.setVisible(false);
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735 scaleLeft.setSelected(true);
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736 scaleLeft.setText("Scale Left");
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737 scaleLeft.addActionListener(new java.awt.event.ActionListener()
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739 public void actionPerformed(ActionEvent e)
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741 scaleLeft_actionPerformed(e);
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744 scaleRight.setVisible(false);
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745 scaleRight.setSelected(true);
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746 scaleRight.setText("Scale Right");
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747 scaleRight.addActionListener(new java.awt.event.ActionListener()
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749 public void actionPerformed(ActionEvent e)
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751 scaleRight_actionPerformed(e);
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754 modifyPID.setText("Modify Identity Threshold...");
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755 modifyPID.addActionListener(new java.awt.event.ActionListener()
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757 public void actionPerformed(ActionEvent e)
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759 modifyPID_actionPerformed(e);
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762 modifyConservation.setText("Modify Conservation Threshold...");
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763 modifyConservation.addActionListener(new java.awt.event.ActionListener()
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765 public void actionPerformed(ActionEvent e)
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767 modifyConservation_actionPerformed(e);
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770 sortByTreeMenu.setText("By Tree Order");
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771 sort.setText("Sort");
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772 calculate.setText("Calculate Tree");
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773 msaAlignMenuItem.setText("Muscle Alignment...");
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774 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
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775 public void actionPerformed(ActionEvent e) {
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776 msaAlignMenuItem_actionPerformed(e);
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779 jMenu2.setText("Export");
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780 alignFrameMenuBar.add(fileMenu);
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781 alignFrameMenuBar.add(editMenu);
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782 alignFrameMenuBar.add(searchMenu);
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783 alignFrameMenuBar.add(viewMenu);
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784 alignFrameMenuBar.add(colourMenu);
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785 alignFrameMenuBar.add(calculateMenu);
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786 fileMenu.add(saveAlignmentMenu);
\r
787 fileMenu.add(jMenu2);
\r
788 fileMenu.add(outputTextboxMenu);
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789 fileMenu.add(printMenuItem);
\r
790 fileMenu.addSeparator();
\r
791 fileMenu.add(LoadtreeMenuItem);
\r
792 fileMenu.addSeparator();
\r
793 fileMenu.add(closeMenuItem);
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794 editMenu.add(undoMenuItem);
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795 editMenu.add(redoMenuItem);
\r
797 editMenu.add(copy);
\r
798 editMenu.add(jMenu1);
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799 editMenu.add(delete);
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800 editMenu.addSeparator();
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801 editMenu.add(selectAllSequenceMenuItem);
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802 editMenu.add(deselectAllSequenceMenuItem);
\r
803 editMenu.add(invertSequenceMenuItem);
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804 editMenu.add(deleteGroups);
\r
805 editMenu.addSeparator();
\r
806 editMenu.add(remove2LeftMenuItem);
\r
807 editMenu.add(remove2RightMenuItem);
\r
808 editMenu.add(removeGappedColumnMenuItem);
\r
809 editMenu.add(removeAllGapsMenuItem);
\r
810 editMenu.add(removeRedundancyMenuItem);
\r
811 searchMenu.add(findMenuItem);
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812 viewMenu.add(font);
\r
813 viewMenu.add(fullSeqId);
\r
814 viewMenu.addSeparator();
\r
815 viewMenu.add(wrapMenuItem);
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816 viewMenu.add(scaleAbove);
\r
817 viewMenu.add(scaleLeft);
\r
818 viewMenu.add(scaleRight);
\r
819 viewMenu.addSeparator();
\r
820 viewMenu.add(viewBoxesMenuItem);
\r
821 viewMenu.add(viewTextMenuItem);
\r
822 viewMenu.add(colourTextMenuItem);
\r
823 viewMenu.add(renderGapsMenuItem);
\r
824 viewMenu.add(annotationPanelMenuItem);
\r
825 viewMenu.add(sequenceFeatures);
\r
826 viewMenu.addSeparator();
\r
827 viewMenu.add(overviewMenuItem);
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828 colourMenu.add(applyToAllGroups);
\r
829 colourMenu.add(noColourmenuItem);
\r
830 colourMenu.addSeparator();
\r
831 colourMenu.add(clustalColour);
\r
832 colourMenu.add(BLOSUM62Colour);
\r
833 colourMenu.add(PIDColour);
\r
834 colourMenu.add(zappoColour);
\r
835 colourMenu.add(taylorColour);
\r
836 colourMenu.add(hydrophobicityColour);
\r
837 colourMenu.add(helixColour);
\r
838 colourMenu.add(strandColour);
\r
839 colourMenu.add(turnColour);
\r
840 colourMenu.add(buriedColour);
\r
841 colourMenu.add(nucleotideColour);
\r
842 colourMenu.add(userDefinedColour);
\r
843 colourMenu.addSeparator();
\r
844 colourMenu.add(conservationMenuItem);
\r
845 colourMenu.add(modifyConservation);
\r
846 colourMenu.add(abovePIDThreshold);
\r
847 colourMenu.add(modifyPID);
\r
848 calculateMenu.add(sort);
\r
849 calculateMenu.add(calculate);
\r
850 calculateMenu.addSeparator();
\r
851 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
852 calculateMenu.add(PCAMenuItem);
\r
853 calculateMenu.addSeparator();
\r
854 calculateMenu.add(webService);
\r
855 webService.add(clustalAlignMenuItem);
\r
856 webService.add(jpred);
\r
857 webService.add(msaAlignMenuItem);
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858 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
859 jMenu1.add(pasteNew);
\r
860 jMenu1.add(pasteThis);
\r
861 sort.add(sortIDMenuItem);
\r
862 sort.add(sortByTreeMenu);
\r
863 sort.add(sortGroupMenuItem);
\r
864 sort.add(sortPairwiseMenuItem);
\r
865 calculate.add(averageDistanceTreeMenuItem);
\r
866 calculate.add(neighbourTreeMenuItem);
\r
867 calculate.add(avDistanceTreeBlosumMenuItem);
\r
868 calculate.add(njTreeBlosumMenuItem);
\r
869 jMenu2.add(htmlMenuItem);
\r
870 jMenu2.add(epsFile);
\r
871 jMenu2.add(createPNG);
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874 protected void outputText_actionPerformed(ActionEvent e)
\r
879 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
885 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
890 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
895 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
901 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
906 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
911 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
916 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
921 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
926 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
931 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
937 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
943 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
948 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
954 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
959 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
964 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
969 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
974 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
979 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
985 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
990 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
995 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1000 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1005 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1011 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1016 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1023 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1031 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1036 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1041 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1047 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1052 protected void helixColour_actionPerformed(ActionEvent e)
\r
1057 protected void strandColour_actionPerformed(ActionEvent e)
\r
1062 protected void turnColour_actionPerformed(ActionEvent e)
\r
1067 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1074 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1079 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1084 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1090 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1095 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1101 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1106 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1111 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1117 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
1121 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1126 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1131 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1136 protected void copy_actionPerformed(ActionEvent e)
\r
1142 protected void cut_actionPerformed(ActionEvent e)
\r
1147 protected void delete_actionPerformed(ActionEvent e)
\r
1152 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1157 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1162 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1167 protected void createPNG_actionPerformed(ActionEvent e)
\r
1172 protected void font_actionPerformed(ActionEvent e)
\r
1177 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1182 protected void epsFile_actionPerformed(ActionEvent e)
\r
1187 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1191 protected void jpred_actionPerformed(ActionEvent e)
\r
1196 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1201 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1206 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1211 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1216 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1221 protected void preferences_actionPerformed(ActionEvent e)
\r
1226 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
\r
1230 public void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
\r
1235 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r