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 JMenuItem ClustalRealign = new JMenuItem();
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107 public GAlignFrame()
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109 ButtonGroup colours = new ButtonGroup();
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110 colours.add(noColourmenuItem);
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111 colours.add(clustalColour);
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112 colours.add(zappoColour);
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113 colours.add(taylorColour);
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114 colours.add(hydrophobicityColour);
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115 colours.add(helixColour);
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116 colours.add(strandColour);
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117 colours.add(turnColour);
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118 colours.add(buriedColour);
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119 colours.add(userDefinedColour);
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120 colours.add(PIDColour);
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121 colours.add(BLOSUM62Colour);
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122 colours.add(nucleotideColour);
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124 noColourmenuItem.setSelected(true);
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125 String defaultColour = Preferences.defaultColour;
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126 if(defaultColour!=null)
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128 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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131 case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
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132 case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
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133 case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
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134 case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
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135 case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
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136 case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
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137 case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
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138 case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
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139 case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
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140 case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
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141 case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
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149 setJMenuBar(alignFrameMenuBar);
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152 // dynamically fill save as menu with available formats
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153 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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154 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
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155 item.addActionListener(new java.awt.event.ActionListener()
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157 public void actionPerformed(ActionEvent e)
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159 outputText_actionPerformed(e);
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163 outputTextboxMenu.add( item );
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169 e.printStackTrace();
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173 private void jbInit() throws Exception
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175 fileMenu.setMnemonic('F');
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176 fileMenu.setText("File");
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177 saveAlignmentMenu.setMnemonic('L');
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178 saveAlignmentMenu.setText("Save As");
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179 saveAlignmentMenu.addActionListener(new ActionListener()
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181 public void actionPerformed(ActionEvent e)
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183 saveAlignmentMenu_actionPerformed(e);
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186 closeMenuItem.setMnemonic('C');
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187 closeMenuItem.setText("Close");
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188 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 closeMenuItem_actionPerformed(e);
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195 editMenu.setText("Edit");
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196 viewMenu.setText("View");
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197 colourMenu.setText("Colour");
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198 calculateMenu.setText("Calculate");
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199 webService.setText("Web Service");
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200 selectAllSequenceMenuItem.setText("Select all");
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201 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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202 java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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203 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 selectAllSequenceMenuItem_actionPerformed(e);
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210 deselectAllSequenceMenuItem.setText("Deselect All");
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211 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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212 getKeyStroke(java.awt.event.
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213 KeyEvent.VK_ESCAPE, 0, false));
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214 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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216 public void actionPerformed(ActionEvent e)
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218 deselectAllSequenceMenuItem_actionPerformed(e);
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221 invertSequenceMenuItem.setText("Invert Selection");
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222 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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224 public void actionPerformed(ActionEvent e)
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226 invertSequenceMenuItem_actionPerformed(e);
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229 remove2LeftMenuItem.setText("Remove Left");
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230 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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232 public void actionPerformed(ActionEvent e)
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234 remove2LeftMenuItem_actionPerformed(e);
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237 remove2RightMenuItem.setText("Remove Right");
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238 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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240 public void actionPerformed(ActionEvent e)
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242 remove2RightMenuItem_actionPerformed(e);
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245 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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246 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 removeGappedColumnMenuItem_actionPerformed(e);
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253 removeAllGapsMenuItem.setText("Remove All Gaps");
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254 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 removeAllGapsMenuItem_actionPerformed(e);
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261 viewBoxesMenuItem.setText("Boxes");
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262 viewBoxesMenuItem.setState(true);
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263 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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265 public void actionPerformed(ActionEvent e)
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267 viewBoxesMenuItem_actionPerformed(e);
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270 viewTextMenuItem.setText("Text");
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271 viewTextMenuItem.setState(true);
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272 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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274 public void actionPerformed(ActionEvent e)
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276 viewTextMenuItem_actionPerformed(e);
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279 sortPairwiseMenuItem.setText("by Pairwise Identity");
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280 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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282 public void actionPerformed(ActionEvent e)
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284 sortPairwiseMenuItem_actionPerformed(e);
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287 sortIDMenuItem.setText("by ID");
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288 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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290 public void actionPerformed(ActionEvent e)
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292 sortIDMenuItem_actionPerformed(e);
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295 sortGroupMenuItem.setText("by Group");
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296 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 sortGroupMenuItem_actionPerformed(e);
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303 removeRedundancyMenuItem.setText("Remove Redundancy...");
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304 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
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306 public void actionPerformed(ActionEvent e)
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308 removeRedundancyMenuItem_actionPerformed(e);
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311 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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312 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
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314 public void actionPerformed(ActionEvent e)
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316 pairwiseAlignmentMenuItem_actionPerformed(e);
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319 PCAMenuItem.setText("Principal Component Analysis...");
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320 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 PCAMenuItem_actionPerformed(e);
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327 averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
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328 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 averageDistanceTreeMenuItem_actionPerformed(e);
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335 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
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336 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 neighbourTreeMenuItem_actionPerformed(e);
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343 clustalAlignMenuItem.setText("Clustal Alignment...");
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344 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 clustalAlignMenuItem_actionPerformed(e);
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351 this.getContentPane().setLayout(borderLayout1);
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352 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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353 alignFrameMenuBar.addAncestorListener(new AncestorListener()
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355 public void ancestorAdded(AncestorEvent event)
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357 alignFrameMenuBar_ancestorAdded(event);
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360 public void ancestorRemoved(AncestorEvent event)
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364 public void ancestorMoved(AncestorEvent event)
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368 statusBar.setBackground(Color.white);
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369 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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370 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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371 statusBar.setText("Status bar");
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372 outputTextboxMenu.setMnemonic('T');
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373 outputTextboxMenu.setText("Output to Textbox");
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374 clustalColour.setText("Clustalx");
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376 clustalColour.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 clustalColour_actionPerformed(e);
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383 zappoColour.setText("Zappo");
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384 zappoColour.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 zappoColour_actionPerformed(e);
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391 taylorColour.setText("Taylor");
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392 taylorColour.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 taylorColour_actionPerformed(e);
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399 hydrophobicityColour.setText("Hydrophobicity");
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400 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 hydrophobicityColour_actionPerformed(e);
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407 helixColour.setText("Helix Propensity");
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408 helixColour.addActionListener(new java.awt.event.ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 helixColour_actionPerformed(e);
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415 strandColour.setText("Strand Propensity");
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416 strandColour.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 strandColour_actionPerformed(e);
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423 turnColour.setText("Turn Propensity");
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424 turnColour.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 turnColour_actionPerformed(e);
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431 buriedColour.setText("Buried Index");
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432 buriedColour.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 buriedColour_actionPerformed(e);
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439 userDefinedColour.setText("User Defined...");
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440 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 userDefinedColour_actionPerformed(e);
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447 PIDColour.setText("Percentage Identity");
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448 PIDColour.addActionListener(new java.awt.event.ActionListener()
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450 public void actionPerformed(ActionEvent e)
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452 PIDColour_actionPerformed(e);
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455 BLOSUM62Colour.setText("BLOSUM62 Score");
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456 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 BLOSUM62Colour_actionPerformed(e);
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463 avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62...");
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464 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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466 public void actionPerformed(ActionEvent e)
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468 avTreeBlosumMenuItem_actionPerformed(e);
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471 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
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472 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 njTreeBlosumMenuItem_actionPerformed(e);
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479 annotationPanelMenuItem.setActionCommand("");
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480 annotationPanelMenuItem.setText("Show Annotations");
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481 annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
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482 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 annotationPanelMenuItem_actionPerformed(e);
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489 colourTextMenuItem.setText("Colour Text");
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490 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 colourTextMenuItem_actionPerformed(e);
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497 htmlMenuItem.setText("HTML");
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498 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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500 public void actionPerformed(ActionEvent e)
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502 htmlMenuItem_actionPerformed(e);
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505 overviewMenuItem.setText("Overview Window...");
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506 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 overviewMenuItem_actionPerformed(e);
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513 undoMenuItem.setEnabled(false);
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514 undoMenuItem.setMnemonic('Z');
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515 undoMenuItem.setText("Undo");
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516 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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517 event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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518 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 undoMenuItem_actionPerformed(e);
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525 redoMenuItem.setEnabled(false);
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526 redoMenuItem.setMnemonic('0');
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527 redoMenuItem.setText("Redo");
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528 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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530 public void actionPerformed(ActionEvent e)
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532 redoMenuItem_actionPerformed(e);
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535 conservationMenuItem.setText("By Conservation");
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536 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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538 public void actionPerformed(ActionEvent e)
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540 conservationMenuItem_actionPerformed(e);
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543 noColourmenuItem.setText("None");
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544 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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546 public void actionPerformed(ActionEvent e)
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548 noColourmenuItem_actionPerformed(e);
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551 wrapMenuItem.setText("Wrap");
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552 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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554 public void actionPerformed(ActionEvent e)
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556 wrapMenuItem_actionPerformed(e);
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559 printMenuItem.setText("Print");
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560 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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562 public void actionPerformed(ActionEvent e)
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564 printMenuItem_actionPerformed(e);
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567 renderGapsMenuItem.setText("Show Gaps");
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568 renderGapsMenuItem.setState(true);
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569 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 renderGapsMenuItem_actionPerformed(e);
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576 findMenuItem.setText("Find...");
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577 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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578 event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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579 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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581 public void actionPerformed(ActionEvent e)
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583 findMenuItem_actionPerformed(e);
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586 searchMenu.setText("Search");
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588 abovePIDThreshold.setText("Above Identity Threshold");
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589 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
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590 public void actionPerformed(ActionEvent e) {
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591 abovePIDThreshold_actionPerformed(e);
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594 sequenceFeatures.setText("Sequence Features");
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595 sequenceFeatures.addActionListener(new ActionListener()
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597 public void actionPerformed(ActionEvent actionEvent)
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599 sequenceFeatures_actionPerformed(actionEvent);
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602 nucleotideColour.setText("Nucleotide");
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603 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 nucleotideColour_actionPerformed(e);
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610 deleteGroups.setText("Undefine groups");
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611 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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613 public void actionPerformed(ActionEvent e)
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615 deleteGroups_actionPerformed(e);
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618 copy.setText("Copy");
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619 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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620 KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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621 copy.setMnemonic(KeyEvent.VK_C);
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623 copy.addActionListener(new java.awt.event.ActionListener()
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625 public void actionPerformed(ActionEvent e)
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627 copy_actionPerformed(e);
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630 cut.setText("Cut");
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631 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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632 KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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633 cut.setMnemonic(KeyEvent.VK_X);
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634 cut.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 cut_actionPerformed(e);
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641 delete.setText("Delete");
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642 delete.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 delete_actionPerformed(e);
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649 jMenu1.setMnemonic('V');
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650 jMenu1.setText("Paste");
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651 pasteNew.setText("To New Alignment");
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652 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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653 KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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654 pasteNew.addActionListener(new java.awt.event.ActionListener()
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656 public void actionPerformed(ActionEvent e)
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658 pasteNew_actionPerformed(e);
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661 pasteThis.setText("Add To This Alignment");
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662 pasteThis.addActionListener(new java.awt.event.ActionListener()
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664 public void actionPerformed(ActionEvent e)
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666 pasteThis_actionPerformed(e);
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669 applyToAllGroups.setText("Apply Colour To All Groups");
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670 applyToAllGroups.setState(true);
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671 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 applyToAllGroups_actionPerformed(e);
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678 createPNG.addActionListener(new java.awt.event.ActionListener()
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680 public void actionPerformed(ActionEvent e)
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682 createPNG_actionPerformed(e);
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685 createPNG.setActionCommand("Save As PNG Image");
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686 createPNG.setText("PNG");
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687 font.setText("Font...");
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688 font.addActionListener(new java.awt.event.ActionListener()
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690 public void actionPerformed(ActionEvent e)
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692 font_actionPerformed(e);
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695 fullSeqId.setText("Show Full Sequence ID");
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696 fullSeqId.setState(true);
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697 fullSeqId.addActionListener(new java.awt.event.ActionListener()
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699 public void actionPerformed(ActionEvent e)
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701 fullSeqId_actionPerformed(e);
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704 epsFile.setText("EPS");
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705 epsFile.addActionListener(new java.awt.event.ActionListener()
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707 public void actionPerformed(ActionEvent e)
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709 epsFile_actionPerformed(e);
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712 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
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713 LoadtreeMenuItem.setText("Load Assocated Tree");
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714 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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715 public void actionPerformed(ActionEvent e)
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717 LoadtreeMenuItem_actionPerformed(e);
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720 jpred.setText("JPred...");
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721 jpred.addActionListener(new java.awt.event.ActionListener()
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723 public void actionPerformed(ActionEvent e)
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725 jpred_actionPerformed(e);
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728 scaleAbove.setVisible(false);
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729 scaleAbove.setText("Scale Above");
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730 scaleAbove.addActionListener(new java.awt.event.ActionListener()
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732 public void actionPerformed(ActionEvent e)
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734 scaleAbove_actionPerformed(e);
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737 scaleLeft.setVisible(false);
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738 scaleLeft.setSelected(true);
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739 scaleLeft.setText("Scale Left");
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740 scaleLeft.addActionListener(new java.awt.event.ActionListener()
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742 public void actionPerformed(ActionEvent e)
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744 scaleLeft_actionPerformed(e);
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747 scaleRight.setVisible(false);
\r
748 scaleRight.setSelected(true);
\r
749 scaleRight.setText("Scale Right");
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750 scaleRight.addActionListener(new java.awt.event.ActionListener()
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752 public void actionPerformed(ActionEvent e)
\r
754 scaleRight_actionPerformed(e);
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757 modifyPID.setText("Modify Identity Threshold...");
\r
758 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
760 public void actionPerformed(ActionEvent e)
\r
762 modifyPID_actionPerformed(e);
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765 modifyConservation.setText("Modify Conservation Threshold...");
\r
766 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
768 public void actionPerformed(ActionEvent e)
\r
770 modifyConservation_actionPerformed(e);
\r
773 sortByTreeMenu.setText("By Tree Order");
\r
774 sort.setText("Sort");
\r
775 calculate.setText("Calculate Tree");
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776 msaAlignMenuItem.setText("Muscle Alignment...");
\r
777 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
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778 public void actionPerformed(ActionEvent e) {
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779 msaAlignMenuItem_actionPerformed(e);
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782 jMenu2.setText("Export");
\r
783 padGapsMenuitem.setText("Pad Gaps");
\r
784 padGapsMenuitem.addActionListener(new ActionListener()
\r
786 public void actionPerformed(ActionEvent e)
\r
788 padGapsMenuitem_actionPerformed(e);
\r
791 ClustalRealign.setText("Clustal Realign...");
\r
792 ClustalRealign.addActionListener(new ActionListener()
\r
794 public void actionPerformed(ActionEvent e)
\r
796 ClustalRealign_actionPerformed(e);
\r
799 alignFrameMenuBar.add(fileMenu);
\r
800 alignFrameMenuBar.add(editMenu);
\r
801 alignFrameMenuBar.add(searchMenu);
\r
802 alignFrameMenuBar.add(viewMenu);
\r
803 alignFrameMenuBar.add(colourMenu);
\r
804 alignFrameMenuBar.add(calculateMenu);
\r
805 fileMenu.add(saveAlignmentMenu);
\r
806 fileMenu.add(jMenu2);
\r
807 fileMenu.add(outputTextboxMenu);
\r
808 fileMenu.add(printMenuItem);
\r
809 fileMenu.addSeparator();
\r
810 fileMenu.add(LoadtreeMenuItem);
\r
811 fileMenu.addSeparator();
\r
812 fileMenu.add(closeMenuItem);
\r
813 editMenu.add(undoMenuItem);
\r
814 editMenu.add(redoMenuItem);
\r
816 editMenu.add(copy);
\r
817 editMenu.add(jMenu1);
\r
818 editMenu.add(delete);
\r
819 editMenu.addSeparator();
\r
820 editMenu.add(selectAllSequenceMenuItem);
\r
821 editMenu.add(deselectAllSequenceMenuItem);
\r
822 editMenu.add(invertSequenceMenuItem);
\r
823 editMenu.add(deleteGroups);
\r
824 editMenu.addSeparator();
\r
825 editMenu.add(remove2LeftMenuItem);
\r
826 editMenu.add(remove2RightMenuItem);
\r
827 editMenu.add(removeGappedColumnMenuItem);
\r
828 editMenu.add(removeAllGapsMenuItem);
\r
829 editMenu.add(removeRedundancyMenuItem);
\r
830 editMenu.addSeparator();
\r
831 editMenu.add(padGapsMenuitem);
\r
832 searchMenu.add(findMenuItem);
\r
833 viewMenu.add(font);
\r
834 viewMenu.addSeparator();
\r
835 viewMenu.add(wrapMenuItem);
\r
836 viewMenu.add(fullSeqId);
\r
837 viewMenu.add(scaleAbove);
\r
838 viewMenu.add(scaleLeft);
\r
839 viewMenu.add(scaleRight);
\r
840 viewMenu.add(viewBoxesMenuItem);
\r
841 viewMenu.add(viewTextMenuItem);
\r
842 viewMenu.add(colourTextMenuItem);
\r
843 viewMenu.add(renderGapsMenuItem);
\r
844 viewMenu.add(annotationPanelMenuItem);
\r
845 viewMenu.add(sequenceFeatures);
\r
846 viewMenu.addSeparator();
\r
847 viewMenu.add(overviewMenuItem);
\r
848 colourMenu.add(applyToAllGroups);
\r
849 colourMenu.addSeparator();
\r
850 colourMenu.add(noColourmenuItem);
\r
851 colourMenu.add(clustalColour);
\r
852 colourMenu.add(BLOSUM62Colour);
\r
853 colourMenu.add(PIDColour);
\r
854 colourMenu.add(zappoColour);
\r
855 colourMenu.add(taylorColour);
\r
856 colourMenu.add(hydrophobicityColour);
\r
857 colourMenu.add(helixColour);
\r
858 colourMenu.add(strandColour);
\r
859 colourMenu.add(turnColour);
\r
860 colourMenu.add(buriedColour);
\r
861 colourMenu.add(nucleotideColour);
\r
862 colourMenu.add(userDefinedColour);
\r
863 colourMenu.addSeparator();
\r
864 colourMenu.add(conservationMenuItem);
\r
865 colourMenu.add(modifyConservation);
\r
866 colourMenu.add(abovePIDThreshold);
\r
867 colourMenu.add(modifyPID);
\r
868 calculateMenu.add(sort);
\r
869 calculateMenu.add(calculate);
\r
870 calculateMenu.addSeparator();
\r
871 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
872 calculateMenu.add(PCAMenuItem);
\r
873 calculateMenu.addSeparator();
\r
874 calculateMenu.add(webService);
\r
875 webService.add(clustalAlignMenuItem);
\r
876 webService.add(msaAlignMenuItem);
\r
877 webService.add(jpred);
\r
878 webService.add(ClustalRealign);
\r
879 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
880 jMenu1.add(pasteNew);
\r
881 jMenu1.add(pasteThis);
\r
882 sort.add(sortIDMenuItem);
\r
883 sort.add(sortGroupMenuItem);
\r
884 sort.add(sortPairwiseMenuItem);
\r
885 calculate.add(averageDistanceTreeMenuItem);
\r
886 calculate.add(neighbourTreeMenuItem);
\r
887 calculate.add(avDistanceTreeBlosumMenuItem);
\r
888 calculate.add(njTreeBlosumMenuItem);
\r
889 jMenu2.add(htmlMenuItem);
\r
890 jMenu2.add(epsFile);
\r
891 jMenu2.add(createPNG);
\r
894 protected void outputText_actionPerformed(ActionEvent e)
\r
899 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
905 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
910 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
915 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
921 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
926 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
931 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
936 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
941 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
946 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
951 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
957 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
963 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
968 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
974 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
979 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
984 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
989 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
994 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
999 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1005 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1010 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1015 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1020 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1025 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1031 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1036 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1043 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1051 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1056 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1061 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1067 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1072 protected void helixColour_actionPerformed(ActionEvent e)
\r
1077 protected void strandColour_actionPerformed(ActionEvent e)
\r
1082 protected void turnColour_actionPerformed(ActionEvent e)
\r
1087 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1094 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1099 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1104 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1110 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1115 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1121 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1126 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1131 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1137 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
\r
1141 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1146 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1151 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1156 protected void copy_actionPerformed(ActionEvent e)
\r
1162 protected void cut_actionPerformed(ActionEvent e)
\r
1167 protected void delete_actionPerformed(ActionEvent e)
\r
1172 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1177 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1182 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1187 protected void createPNG_actionPerformed(ActionEvent e)
\r
1192 protected void font_actionPerformed(ActionEvent e)
\r
1197 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1202 protected void epsFile_actionPerformed(ActionEvent e)
\r
1207 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1211 protected void jpred_actionPerformed(ActionEvent e)
\r
1216 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1221 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1226 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1231 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1236 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1241 protected void preferences_actionPerformed(ActionEvent e)
\r
1246 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
\r
1250 protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
\r
1255 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1260 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1265 protected void ClustalRealign_actionPerformed(ActionEvent e)
\r