2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import jalview.gui.*;
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27 import jalview.schemes.*;
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29 public class GAlignFrame
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30 extends JInternalFrame
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32 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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33 protected JMenu fileMenu = new JMenu();
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34 protected JMenuItem closeMenuItem = new JMenuItem();
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35 protected JMenu editMenu = new JMenu();
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36 protected JMenu viewMenu = new JMenu();
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37 protected JMenu colourMenu = new JMenu();
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38 protected JMenu calculateMenu = new JMenu();
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39 protected JMenu webService = new JMenu();
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40 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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41 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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42 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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43 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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44 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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45 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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46 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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47 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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48 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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49 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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50 protected JMenuItem sortIDMenuItem = new JMenuItem();
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51 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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52 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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53 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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54 protected JMenuItem PCAMenuItem = new JMenuItem();
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55 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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56 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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57 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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58 BorderLayout borderLayout1 = new BorderLayout();
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59 public JLabel statusBar = new JLabel();
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60 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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61 protected JMenu outputTextboxMenu = new JMenu();
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62 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem hydrophobicityColour = new
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66 JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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74 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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75 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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76 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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77 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem htmlMenuItem = new JMenuItem();
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79 JMenuItem overviewMenuItem = new JMenuItem();
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80 protected JMenuItem undoMenuItem = new JMenuItem();
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81 protected JMenuItem redoMenuItem = new JMenuItem();
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82 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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83 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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84 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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85 JMenuItem printMenuItem = new JMenuItem();
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86 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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87 JMenuItem findMenuItem = new JMenuItem();
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88 JMenu searchMenu = new JMenu();
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89 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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90 public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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91 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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92 JMenuItem deleteGroups = new JMenuItem();
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93 JMenuItem delete = new JMenuItem();
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94 JMenuItem copy = new JMenuItem();
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95 JMenuItem cut = new JMenuItem();
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96 JMenu jMenu1 = new JMenu();
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97 JMenuItem pasteNew = new JMenuItem();
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98 JMenuItem pasteThis = new JMenuItem();
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99 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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100 JMenuItem createPNG = new JMenuItem();
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101 protected JMenuItem font = new JMenuItem();
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102 public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
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103 JMenuItem epsFile = new JMenuItem();
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104 JMenuItem LoadtreeMenuItem = new JMenuItem();
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105 JMenuItem jnet = new JMenuItem();
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106 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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107 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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108 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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109 JMenuItem modifyPID = new JMenuItem();
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110 JMenuItem modifyConservation = new JMenuItem();
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111 protected JMenu sortByTreeMenu = new JMenu();
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112 protected JMenu sort = new JMenu();
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113 JMenu calculate = new JMenu();
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114 JMenuItem msaAlignMenuItem = new JMenuItem();
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115 JMenu jMenu2 = new JMenu();
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116 JMenuItem padGapsMenuitem = new JMenuItem();
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117 JMenuItem ClustalRealign = new JMenuItem();
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119 public GAlignFrame()
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121 ButtonGroup colours = new ButtonGroup();
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122 colours.add(noColourmenuItem);
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123 colours.add(clustalColour);
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124 colours.add(zappoColour);
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125 colours.add(taylorColour);
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126 colours.add(hydrophobicityColour);
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127 colours.add(helixColour);
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128 colours.add(strandColour);
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129 colours.add(turnColour);
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130 colours.add(buriedColour);
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131 colours.add(userDefinedColour);
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132 colours.add(PIDColour);
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133 colours.add(BLOSUM62Colour);
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134 colours.add(nucleotideColour);
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136 noColourmenuItem.setSelected(true);
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138 String defaultColour = Preferences.defaultColour;
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140 if (defaultColour != null)
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142 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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146 case ColourSchemeProperty.CLUSTAL:
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147 clustalColour.setSelected(true);
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151 case ColourSchemeProperty.BLOSUM:
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152 BLOSUM62Colour.setSelected(true);
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156 case ColourSchemeProperty.PID:
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157 PIDColour.setSelected(true);
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161 case ColourSchemeProperty.ZAPPO:
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162 zappoColour.setSelected(true);
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166 case ColourSchemeProperty.HYDROPHOBIC:
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167 hydrophobicityColour.setSelected(true);
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171 case ColourSchemeProperty.HELIX:
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172 helixColour.setSelected(true);
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176 case ColourSchemeProperty.STRAND:
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177 strandColour.setSelected(true);
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181 case ColourSchemeProperty.TURN:
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182 turnColour.setSelected(true);
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186 case ColourSchemeProperty.BURIED:
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187 buriedColour.setSelected(true);
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191 case ColourSchemeProperty.NUCLEOTIDE:
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192 nucleotideColour.setSelected(true);
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196 case ColourSchemeProperty.USER_DEFINED:
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197 userDefinedColour.setSelected(true);
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206 setJMenuBar(alignFrameMenuBar);
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210 // dynamically fill save as menu with available formats
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211 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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213 item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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216 item.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 outputText_actionPerformed(e);
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224 outputTextboxMenu.add(item);
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227 catch (Exception e)
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233 private void jbInit()
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236 fileMenu.setMnemonic('F');
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237 fileMenu.setText("File");
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238 saveAlignmentMenu.setMnemonic('L');
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239 saveAlignmentMenu.setText("Save As");
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240 saveAlignmentMenu.addActionListener(new ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 saveAlignmentMenu_actionPerformed(e);
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247 closeMenuItem.setMnemonic('C');
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248 closeMenuItem.setText("Close");
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249 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 closeMenuItem_actionPerformed(e);
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256 editMenu.setText("Edit");
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257 viewMenu.setText("View");
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258 colourMenu.setText("Colour");
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259 calculateMenu.setText("Calculate");
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260 webService.setText("Web Service");
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261 selectAllSequenceMenuItem.setText("Select all");
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262 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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263 java.awt.event.KeyEvent.VK_A,
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264 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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265 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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268 public void actionPerformed(ActionEvent e)
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270 selectAllSequenceMenuItem_actionPerformed(e);
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273 deselectAllSequenceMenuItem.setText("Deselect All");
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274 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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276 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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277 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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280 public void actionPerformed(ActionEvent e)
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282 deselectAllSequenceMenuItem_actionPerformed(e);
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285 invertSequenceMenuItem.setText("Invert Selection");
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286 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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288 public void actionPerformed(ActionEvent e)
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290 invertSequenceMenuItem_actionPerformed(e);
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293 remove2LeftMenuItem.setText("Remove Left");
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294 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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296 public void actionPerformed(ActionEvent e)
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298 remove2LeftMenuItem_actionPerformed(e);
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301 remove2RightMenuItem.setText("Remove Right");
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302 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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304 public void actionPerformed(ActionEvent e)
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306 remove2RightMenuItem_actionPerformed(e);
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309 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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310 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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313 public void actionPerformed(ActionEvent e)
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315 removeGappedColumnMenuItem_actionPerformed(e);
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318 removeAllGapsMenuItem.setText("Remove All Gaps");
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319 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 removeAllGapsMenuItem_actionPerformed(e);
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326 viewBoxesMenuItem.setText("Boxes");
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327 viewBoxesMenuItem.setState(true);
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328 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 viewBoxesMenuItem_actionPerformed(e);
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335 viewTextMenuItem.setText("Text");
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336 viewTextMenuItem.setState(true);
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337 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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339 public void actionPerformed(ActionEvent e)
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341 viewTextMenuItem_actionPerformed(e);
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344 sortPairwiseMenuItem.setText("by Pairwise Identity");
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345 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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347 public void actionPerformed(ActionEvent e)
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349 sortPairwiseMenuItem_actionPerformed(e);
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352 sortIDMenuItem.setText("by ID");
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353 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 sortIDMenuItem_actionPerformed(e);
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360 sortGroupMenuItem.setText("by Group");
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361 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 sortGroupMenuItem_actionPerformed(e);
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368 removeRedundancyMenuItem.setText("Remove Redundancy...");
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369 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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372 public void actionPerformed(ActionEvent e)
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374 removeRedundancyMenuItem_actionPerformed(e);
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377 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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378 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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381 public void actionPerformed(ActionEvent e)
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383 pairwiseAlignmentMenuItem_actionPerformed(e);
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386 PCAMenuItem.setText("Principal Component Analysis");
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387 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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389 public void actionPerformed(ActionEvent e)
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391 PCAMenuItem_actionPerformed(e);
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394 averageDistanceTreeMenuItem.setText(
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395 "Average Distance Using % Identity");
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396 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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399 public void actionPerformed(ActionEvent e)
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401 averageDistanceTreeMenuItem_actionPerformed(e);
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404 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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405 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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407 public void actionPerformed(ActionEvent e)
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409 neighbourTreeMenuItem_actionPerformed(e);
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412 clustalAlignMenuItem.setText("Clustal Alignment");
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413 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 clustalAlignMenuItem_actionPerformed(e);
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420 this.getContentPane().setLayout(borderLayout1);
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421 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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422 alignFrameMenuBar.addAncestorListener(new AncestorListener()
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424 public void ancestorAdded(AncestorEvent event)
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426 alignFrameMenuBar_ancestorAdded(event);
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429 public void ancestorRemoved(AncestorEvent event)
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433 public void ancestorMoved(AncestorEvent event)
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437 statusBar.setBackground(Color.white);
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438 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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439 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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440 statusBar.setText("Status bar");
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441 outputTextboxMenu.setMnemonic('T');
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442 outputTextboxMenu.setText("Output to Textbox");
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443 clustalColour.setText("Clustalx");
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445 clustalColour.addActionListener(new java.awt.event.ActionListener()
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447 public void actionPerformed(ActionEvent e)
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449 clustalColour_actionPerformed(e);
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452 zappoColour.setText("Zappo");
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453 zappoColour.addActionListener(new java.awt.event.ActionListener()
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455 public void actionPerformed(ActionEvent e)
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457 zappoColour_actionPerformed(e);
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460 taylorColour.setText("Taylor");
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461 taylorColour.addActionListener(new java.awt.event.ActionListener()
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463 public void actionPerformed(ActionEvent e)
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465 taylorColour_actionPerformed(e);
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468 hydrophobicityColour.setText("Hydrophobicity");
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469 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 hydrophobicityColour_actionPerformed(e);
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476 helixColour.setText("Helix Propensity");
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477 helixColour.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 helixColour_actionPerformed(e);
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484 strandColour.setText("Strand Propensity");
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485 strandColour.addActionListener(new java.awt.event.ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 strandColour_actionPerformed(e);
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492 turnColour.setText("Turn Propensity");
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493 turnColour.addActionListener(new java.awt.event.ActionListener()
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495 public void actionPerformed(ActionEvent e)
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497 turnColour_actionPerformed(e);
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500 buriedColour.setText("Buried Index");
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501 buriedColour.addActionListener(new java.awt.event.ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 buriedColour_actionPerformed(e);
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508 userDefinedColour.setText("User Defined...");
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509 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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511 public void actionPerformed(ActionEvent e)
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513 userDefinedColour_actionPerformed(e);
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516 PIDColour.setText("Percentage Identity");
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517 PIDColour.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 PIDColour_actionPerformed(e);
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524 BLOSUM62Colour.setText("BLOSUM62 Score");
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525 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 BLOSUM62Colour_actionPerformed(e);
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532 avDistanceTreeBlosumMenuItem.setText(
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533 "Average Distance Using BLOSUM62");
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534 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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537 public void actionPerformed(ActionEvent e)
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539 avTreeBlosumMenuItem_actionPerformed(e);
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542 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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543 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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545 public void actionPerformed(ActionEvent e)
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547 njTreeBlosumMenuItem_actionPerformed(e);
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550 annotationPanelMenuItem.setActionCommand("");
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551 annotationPanelMenuItem.setText("Show Annotations");
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552 annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);
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553 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 annotationPanelMenuItem_actionPerformed(e);
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560 colourTextMenuItem.setText("Colour Text");
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561 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 colourTextMenuItem_actionPerformed(e);
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568 htmlMenuItem.setText("HTML");
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569 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 htmlMenuItem_actionPerformed(e);
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576 overviewMenuItem.setText("Overview Window");
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577 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 overviewMenuItem_actionPerformed(e);
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584 undoMenuItem.setEnabled(false);
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585 undoMenuItem.setMnemonic('Z');
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586 undoMenuItem.setText("Undo");
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587 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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588 java.awt.event.KeyEvent.VK_Z,
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589 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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590 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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592 public void actionPerformed(ActionEvent e)
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594 undoMenuItem_actionPerformed(e);
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597 redoMenuItem.setEnabled(false);
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598 redoMenuItem.setMnemonic('0');
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599 redoMenuItem.setText("Redo");
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600 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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602 public void actionPerformed(ActionEvent e)
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604 redoMenuItem_actionPerformed(e);
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607 conservationMenuItem.setText("By Conservation");
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608 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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610 public void actionPerformed(ActionEvent e)
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612 conservationMenuItem_actionPerformed(e);
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615 noColourmenuItem.setText("None");
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616 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 noColourmenuItem_actionPerformed(e);
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623 wrapMenuItem.setText("Wrap");
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624 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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626 public void actionPerformed(ActionEvent e)
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628 wrapMenuItem_actionPerformed(e);
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631 printMenuItem.setText("Print");
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632 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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634 public void actionPerformed(ActionEvent e)
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636 printMenuItem_actionPerformed(e);
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639 renderGapsMenuItem.setText("Show Gaps");
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640 renderGapsMenuItem.setState(true);
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641 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 renderGapsMenuItem_actionPerformed(e);
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648 findMenuItem.setText("Find...");
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649 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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650 java.awt.event.KeyEvent.VK_F,
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651 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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652 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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654 public void actionPerformed(ActionEvent e)
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656 findMenuItem_actionPerformed(e);
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659 searchMenu.setText("Search");
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661 abovePIDThreshold.setText("Above Identity Threshold");
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662 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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664 public void actionPerformed(ActionEvent e)
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666 abovePIDThreshold_actionPerformed(e);
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669 sequenceFeatures.setText("Sequence Features");
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670 sequenceFeatures.addActionListener(new ActionListener()
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672 public void actionPerformed(ActionEvent actionEvent)
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674 sequenceFeatures_actionPerformed(actionEvent);
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677 nucleotideColour.setText("Nucleotide");
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678 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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680 public void actionPerformed(ActionEvent e)
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682 nucleotideColour_actionPerformed(e);
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685 deleteGroups.setText("Undefine groups");
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686 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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688 public void actionPerformed(ActionEvent e)
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690 deleteGroups_actionPerformed(e);
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693 copy.setText("Copy");
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694 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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695 java.awt.event.KeyEvent.VK_C,
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696 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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697 copy.setMnemonic(KeyEvent.VK_C);
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699 copy.addActionListener(new java.awt.event.ActionListener()
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701 public void actionPerformed(ActionEvent e)
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703 copy_actionPerformed(e);
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706 cut.setText("Cut");
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707 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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708 java.awt.event.KeyEvent.VK_X,
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709 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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710 cut.setMnemonic(KeyEvent.VK_X);
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711 cut.addActionListener(new java.awt.event.ActionListener()
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713 public void actionPerformed(ActionEvent e)
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715 cut_actionPerformed(e);
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718 delete.setText("Delete");
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719 delete.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 delete_actionPerformed(e);
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726 jMenu1.setMnemonic('V');
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727 jMenu1.setText("Paste");
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728 pasteNew.setText("To New Alignment");
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729 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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730 java.awt.event.KeyEvent.VK_V,
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731 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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732 pasteNew.addActionListener(new java.awt.event.ActionListener()
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734 public void actionPerformed(ActionEvent e)
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736 pasteNew_actionPerformed(e);
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739 pasteThis.setText("Add To This Alignment");
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740 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
742 public void actionPerformed(ActionEvent e)
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744 pasteThis_actionPerformed(e);
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747 applyToAllGroups.setText("Apply Colour To All Groups");
\r
748 applyToAllGroups.setState(true);
\r
749 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
751 public void actionPerformed(ActionEvent e)
\r
753 applyToAllGroups_actionPerformed(e);
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756 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
758 public void actionPerformed(ActionEvent e)
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763 createPNG.setActionCommand("Save As PNG Image");
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764 createPNG.setText("PNG");
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765 font.setText("Font...");
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766 font.addActionListener(new java.awt.event.ActionListener()
\r
768 public void actionPerformed(ActionEvent e)
\r
770 font_actionPerformed(e);
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773 fullSeqId.setText("Show Full Sequence ID");
\r
774 fullSeqId.setState(true);
\r
775 fullSeqId.addActionListener(new java.awt.event.ActionListener()
\r
777 public void actionPerformed(ActionEvent e)
\r
779 fullSeqId_actionPerformed(e);
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782 epsFile.setText("EPS");
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783 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
785 public void actionPerformed(ActionEvent e)
\r
790 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
791 LoadtreeMenuItem.setText("Load Assocated Tree");
\r
792 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
794 public void actionPerformed(ActionEvent e)
\r
796 LoadtreeMenuItem_actionPerformed(e);
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799 jnet.setText("JNet");
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800 jnet.addActionListener(new java.awt.event.ActionListener()
\r
802 public void actionPerformed(ActionEvent e)
\r
804 jpred_actionPerformed(e);
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807 scaleAbove.setVisible(false);
\r
808 scaleAbove.setText("Scale Above");
\r
809 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
811 public void actionPerformed(ActionEvent e)
\r
813 scaleAbove_actionPerformed(e);
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816 scaleLeft.setVisible(false);
\r
817 scaleLeft.setSelected(true);
\r
818 scaleLeft.setText("Scale Left");
\r
819 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
821 public void actionPerformed(ActionEvent e)
\r
823 scaleLeft_actionPerformed(e);
\r
826 scaleRight.setVisible(false);
\r
827 scaleRight.setSelected(true);
\r
828 scaleRight.setText("Scale Right");
\r
829 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
831 public void actionPerformed(ActionEvent e)
\r
833 scaleRight_actionPerformed(e);
\r
836 modifyPID.setText("Modify Identity Threshold...");
\r
837 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
839 public void actionPerformed(ActionEvent e)
\r
841 modifyPID_actionPerformed(e);
\r
844 modifyConservation.setText("Modify Conservation Threshold...");
\r
845 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
847 public void actionPerformed(ActionEvent e)
\r
849 modifyConservation_actionPerformed(e);
\r
852 sortByTreeMenu.setText("By Tree Order");
\r
853 sort.setText("Sort");
\r
854 calculate.setText("Calculate Tree");
\r
855 msaAlignMenuItem.setText("Muscle Alignment");
\r
856 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
858 public void actionPerformed(ActionEvent e)
\r
860 msaAlignMenuItem_actionPerformed(e);
\r
863 jMenu2.setText("Export");
\r
864 padGapsMenuitem.setText("Pad Gaps");
\r
865 padGapsMenuitem.addActionListener(new ActionListener()
\r
867 public void actionPerformed(ActionEvent e)
\r
869 padGapsMenuitem_actionPerformed(e);
\r
872 ClustalRealign.setText("Clustal Realign");
\r
873 ClustalRealign.addActionListener(new ActionListener()
\r
875 public void actionPerformed(ActionEvent e)
\r
877 ClustalRealign_actionPerformed(e);
\r
880 alignFrameMenuBar.add(fileMenu);
\r
881 alignFrameMenuBar.add(editMenu);
\r
882 alignFrameMenuBar.add(searchMenu);
\r
883 alignFrameMenuBar.add(viewMenu);
\r
884 alignFrameMenuBar.add(colourMenu);
\r
885 alignFrameMenuBar.add(calculateMenu);
\r
886 fileMenu.add(saveAlignmentMenu);
\r
887 fileMenu.add(jMenu2);
\r
888 fileMenu.add(outputTextboxMenu);
\r
889 fileMenu.add(printMenuItem);
\r
890 fileMenu.addSeparator();
\r
891 fileMenu.add(LoadtreeMenuItem);
\r
892 fileMenu.addSeparator();
\r
893 fileMenu.add(closeMenuItem);
\r
894 editMenu.add(undoMenuItem);
\r
895 editMenu.add(redoMenuItem);
\r
897 editMenu.add(copy);
\r
898 editMenu.add(jMenu1);
\r
899 editMenu.add(delete);
\r
900 editMenu.addSeparator();
\r
901 editMenu.add(selectAllSequenceMenuItem);
\r
902 editMenu.add(deselectAllSequenceMenuItem);
\r
903 editMenu.add(invertSequenceMenuItem);
\r
904 editMenu.add(deleteGroups);
\r
905 editMenu.addSeparator();
\r
906 editMenu.add(remove2LeftMenuItem);
\r
907 editMenu.add(remove2RightMenuItem);
\r
908 editMenu.add(removeGappedColumnMenuItem);
\r
909 editMenu.add(removeAllGapsMenuItem);
\r
910 editMenu.add(removeRedundancyMenuItem);
\r
911 editMenu.addSeparator();
\r
912 editMenu.add(padGapsMenuitem);
\r
913 searchMenu.add(findMenuItem);
\r
914 viewMenu.add(font);
\r
915 viewMenu.addSeparator();
\r
916 viewMenu.add(wrapMenuItem);
\r
917 viewMenu.add(fullSeqId);
\r
918 viewMenu.add(scaleAbove);
\r
919 viewMenu.add(scaleLeft);
\r
920 viewMenu.add(scaleRight);
\r
921 viewMenu.add(viewBoxesMenuItem);
\r
922 viewMenu.add(viewTextMenuItem);
\r
923 viewMenu.add(colourTextMenuItem);
\r
924 viewMenu.add(renderGapsMenuItem);
\r
925 viewMenu.add(annotationPanelMenuItem);
\r
926 viewMenu.add(sequenceFeatures);
\r
927 viewMenu.addSeparator();
\r
928 viewMenu.add(overviewMenuItem);
\r
929 colourMenu.add(applyToAllGroups);
\r
930 colourMenu.addSeparator();
\r
931 colourMenu.add(noColourmenuItem);
\r
932 colourMenu.add(clustalColour);
\r
933 colourMenu.add(BLOSUM62Colour);
\r
934 colourMenu.add(PIDColour);
\r
935 colourMenu.add(zappoColour);
\r
936 colourMenu.add(taylorColour);
\r
937 colourMenu.add(hydrophobicityColour);
\r
938 colourMenu.add(helixColour);
\r
939 colourMenu.add(strandColour);
\r
940 colourMenu.add(turnColour);
\r
941 colourMenu.add(buriedColour);
\r
942 colourMenu.add(nucleotideColour);
\r
943 colourMenu.add(userDefinedColour);
\r
944 colourMenu.addSeparator();
\r
945 colourMenu.add(conservationMenuItem);
\r
946 colourMenu.add(modifyConservation);
\r
947 colourMenu.add(abovePIDThreshold);
\r
948 colourMenu.add(modifyPID);
\r
949 calculateMenu.add(sort);
\r
950 calculateMenu.add(calculate);
\r
951 calculateMenu.addSeparator();
\r
952 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
953 calculateMenu.add(PCAMenuItem);
\r
954 calculateMenu.addSeparator();
\r
955 calculateMenu.add(webService);
\r
956 webService.add(clustalAlignMenuItem);
\r
957 webService.add(msaAlignMenuItem);
\r
958 webService.add(jnet);
\r
959 webService.add(ClustalRealign);
\r
960 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
961 jMenu1.add(pasteNew);
\r
962 jMenu1.add(pasteThis);
\r
963 sort.add(sortIDMenuItem);
\r
964 sort.add(sortGroupMenuItem);
\r
965 sort.add(sortPairwiseMenuItem);
\r
966 calculate.add(averageDistanceTreeMenuItem);
\r
967 calculate.add(neighbourTreeMenuItem);
\r
968 calculate.add(avDistanceTreeBlosumMenuItem);
\r
969 calculate.add(njTreeBlosumMenuItem);
\r
970 jMenu2.add(htmlMenuItem);
\r
971 jMenu2.add(epsFile);
\r
972 jMenu2.add(createPNG);
\r
975 protected void outputText_actionPerformed(ActionEvent e)
\r
979 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
983 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
987 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
991 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
995 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
999 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1003 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1007 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1011 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1015 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1019 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1023 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1027 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1031 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1035 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1039 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1043 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1047 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1051 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1055 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1059 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1063 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1067 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1071 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1075 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1079 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1083 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1087 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1091 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1095 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1099 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1103 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1107 protected void helixColour_actionPerformed(ActionEvent e)
\r
1111 protected void strandColour_actionPerformed(ActionEvent e)
\r
1115 protected void turnColour_actionPerformed(ActionEvent e)
\r
1119 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1123 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1127 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1131 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1135 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1139 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1143 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1147 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1151 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1155 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1159 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1163 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1167 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1171 protected void copy_actionPerformed(ActionEvent e)
\r
1175 protected void cut_actionPerformed(ActionEvent e)
\r
1179 protected void delete_actionPerformed(ActionEvent e)
\r
1183 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1187 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1191 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1195 public void createPNG(java.io.File f)
\r
1199 protected void font_actionPerformed(ActionEvent e)
\r
1203 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1207 public void createEPS(java.io.File f)
\r
1211 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1215 protected void jpred_actionPerformed(ActionEvent e)
\r
1219 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1223 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1227 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1231 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1235 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1239 protected void preferences_actionPerformed(ActionEvent e)
\r
1243 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1247 protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
\r
1251 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1255 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1259 protected void ClustalRealign_actionPerformed(ActionEvent e)
\r