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 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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142 setJMenuBar(alignFrameMenuBar);
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146 // dynamically fill save as menu with available formats
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147 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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149 item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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152 item.addActionListener(new java.awt.event.ActionListener()
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154 public void actionPerformed(ActionEvent e)
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156 outputText_actionPerformed(e);
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160 outputTextboxMenu.add(item);
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163 catch (Exception e)
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169 public void setColourSelected(String defaultColour)
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172 if (defaultColour != null)
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174 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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178 case ColourSchemeProperty.NONE:
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179 noColourmenuItem.setSelected(true);
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181 case ColourSchemeProperty.CLUSTAL:
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182 clustalColour.setSelected(true);
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186 case ColourSchemeProperty.BLOSUM:
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187 BLOSUM62Colour.setSelected(true);
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191 case ColourSchemeProperty.PID:
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192 PIDColour.setSelected(true);
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196 case ColourSchemeProperty.ZAPPO:
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197 zappoColour.setSelected(true);
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201 case ColourSchemeProperty.TAYLOR:
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202 taylorColour.setSelected(true);
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205 case ColourSchemeProperty.HYDROPHOBIC:
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206 hydrophobicityColour.setSelected(true);
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210 case ColourSchemeProperty.HELIX:
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211 helixColour.setSelected(true);
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215 case ColourSchemeProperty.STRAND:
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216 strandColour.setSelected(true);
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220 case ColourSchemeProperty.TURN:
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221 turnColour.setSelected(true);
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225 case ColourSchemeProperty.BURIED:
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226 buriedColour.setSelected(true);
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230 case ColourSchemeProperty.NUCLEOTIDE:
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231 nucleotideColour.setSelected(true);
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235 case ColourSchemeProperty.USER_DEFINED:
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236 userDefinedColour.setSelected(true);
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244 private void jbInit()
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247 fileMenu.setMnemonic('F');
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248 fileMenu.setText("File");
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249 saveAlignmentMenu.setMnemonic('L');
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250 saveAlignmentMenu.setText("Save As");
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251 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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252 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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253 saveAlignmentMenu.addActionListener(new ActionListener()
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255 public void actionPerformed(ActionEvent e)
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257 saveAlignmentMenu_actionPerformed(e);
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260 closeMenuItem.setMnemonic('C');
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261 closeMenuItem.setText("Close");
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262 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 closeMenuItem_actionPerformed(e);
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269 editMenu.setText("Edit");
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270 viewMenu.setText("View");
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271 colourMenu.setText("Colour");
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272 calculateMenu.setText("Calculate");
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273 webService.setText("Web Service");
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274 selectAllSequenceMenuItem.setText("Select all");
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275 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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276 java.awt.event.KeyEvent.VK_A,
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277 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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278 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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281 public void actionPerformed(ActionEvent e)
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283 selectAllSequenceMenuItem_actionPerformed(e);
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286 deselectAllSequenceMenuItem.setText("Deselect All");
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287 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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289 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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290 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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293 public void actionPerformed(ActionEvent e)
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295 deselectAllSequenceMenuItem_actionPerformed(e);
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298 invertSequenceMenuItem.setText("Invert Selection");
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299 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 invertSequenceMenuItem_actionPerformed(e);
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306 remove2LeftMenuItem.setText("Remove Left");
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307 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 remove2LeftMenuItem_actionPerformed(e);
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314 remove2RightMenuItem.setText("Remove Right");
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315 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 remove2RightMenuItem_actionPerformed(e);
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322 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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323 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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326 public void actionPerformed(ActionEvent e)
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328 removeGappedColumnMenuItem_actionPerformed(e);
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331 removeAllGapsMenuItem.setText("Remove All Gaps");
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332 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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334 public void actionPerformed(ActionEvent e)
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336 removeAllGapsMenuItem_actionPerformed(e);
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339 viewBoxesMenuItem.setText("Boxes");
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340 viewBoxesMenuItem.setState(true);
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341 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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343 public void actionPerformed(ActionEvent e)
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345 viewBoxesMenuItem_actionPerformed(e);
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348 viewTextMenuItem.setText("Text");
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349 viewTextMenuItem.setState(true);
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350 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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352 public void actionPerformed(ActionEvent e)
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354 viewTextMenuItem_actionPerformed(e);
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357 sortPairwiseMenuItem.setText("by Pairwise Identity");
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358 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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360 public void actionPerformed(ActionEvent e)
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362 sortPairwiseMenuItem_actionPerformed(e);
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365 sortIDMenuItem.setText("by ID");
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366 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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368 public void actionPerformed(ActionEvent e)
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370 sortIDMenuItem_actionPerformed(e);
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373 sortGroupMenuItem.setText("by Group");
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374 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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376 public void actionPerformed(ActionEvent e)
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378 sortGroupMenuItem_actionPerformed(e);
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381 removeRedundancyMenuItem.setText("Remove Redundancy...");
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382 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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385 public void actionPerformed(ActionEvent e)
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387 removeRedundancyMenuItem_actionPerformed(e);
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390 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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391 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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394 public void actionPerformed(ActionEvent e)
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396 pairwiseAlignmentMenuItem_actionPerformed(e);
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399 PCAMenuItem.setText("Principal Component Analysis");
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400 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 PCAMenuItem_actionPerformed(e);
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407 averageDistanceTreeMenuItem.setText(
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408 "Average Distance Using % Identity");
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409 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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412 public void actionPerformed(ActionEvent e)
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414 averageDistanceTreeMenuItem_actionPerformed(e);
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417 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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418 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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420 public void actionPerformed(ActionEvent e)
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422 neighbourTreeMenuItem_actionPerformed(e);
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425 clustalAlignMenuItem.setText("Clustal Alignment");
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426 clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
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428 public void actionPerformed(ActionEvent e)
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430 clustalAlignMenuItem_actionPerformed(e);
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433 this.getContentPane().setLayout(borderLayout1);
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434 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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435 alignFrameMenuBar.addAncestorListener(new AncestorListener()
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437 public void ancestorAdded(AncestorEvent event)
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439 alignFrameMenuBar_ancestorAdded(event);
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442 public void ancestorRemoved(AncestorEvent event)
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446 public void ancestorMoved(AncestorEvent event)
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450 statusBar.setBackground(Color.white);
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451 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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452 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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453 statusBar.setText("Status bar");
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454 outputTextboxMenu.setMnemonic('T');
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455 outputTextboxMenu.setText("Output to Textbox");
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456 clustalColour.setText("Clustalx");
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458 clustalColour.addActionListener(new java.awt.event.ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 clustalColour_actionPerformed(e);
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465 zappoColour.setText("Zappo");
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466 zappoColour.addActionListener(new java.awt.event.ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 zappoColour_actionPerformed(e);
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473 taylorColour.setText("Taylor");
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474 taylorColour.addActionListener(new java.awt.event.ActionListener()
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476 public void actionPerformed(ActionEvent e)
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478 taylorColour_actionPerformed(e);
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481 hydrophobicityColour.setText("Hydrophobicity");
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482 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 hydrophobicityColour_actionPerformed(e);
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489 helixColour.setText("Helix Propensity");
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490 helixColour.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 helixColour_actionPerformed(e);
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497 strandColour.setText("Strand Propensity");
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498 strandColour.addActionListener(new java.awt.event.ActionListener()
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500 public void actionPerformed(ActionEvent e)
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502 strandColour_actionPerformed(e);
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505 turnColour.setText("Turn Propensity");
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506 turnColour.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 turnColour_actionPerformed(e);
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513 buriedColour.setText("Buried Index");
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514 buriedColour.addActionListener(new java.awt.event.ActionListener()
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516 public void actionPerformed(ActionEvent e)
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518 buriedColour_actionPerformed(e);
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521 userDefinedColour.setText("User Defined...");
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522 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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524 public void actionPerformed(ActionEvent e)
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526 userDefinedColour_actionPerformed(e);
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529 PIDColour.setText("Percentage Identity");
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530 PIDColour.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 PIDColour_actionPerformed(e);
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537 BLOSUM62Colour.setText("BLOSUM62 Score");
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538 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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540 public void actionPerformed(ActionEvent e)
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542 BLOSUM62Colour_actionPerformed(e);
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545 avDistanceTreeBlosumMenuItem.setText(
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546 "Average Distance Using BLOSUM62");
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547 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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550 public void actionPerformed(ActionEvent e)
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552 avTreeBlosumMenuItem_actionPerformed(e);
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555 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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556 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 njTreeBlosumMenuItem_actionPerformed(e);
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563 annotationPanelMenuItem.setActionCommand("");
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564 annotationPanelMenuItem.setText("Show Annotations");
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565 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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566 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 annotationPanelMenuItem_actionPerformed(e);
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573 colourTextMenuItem.setText("Colour Text");
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574 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 colourTextMenuItem_actionPerformed(e);
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581 htmlMenuItem.setText("HTML");
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582 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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584 public void actionPerformed(ActionEvent e)
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586 htmlMenuItem_actionPerformed(e);
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589 overviewMenuItem.setText("Overview Window");
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590 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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592 public void actionPerformed(ActionEvent e)
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594 overviewMenuItem_actionPerformed(e);
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597 undoMenuItem.setEnabled(false);
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598 undoMenuItem.setMnemonic('Z');
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599 undoMenuItem.setText("Undo");
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600 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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601 java.awt.event.KeyEvent.VK_Z,
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602 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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603 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 undoMenuItem_actionPerformed(e);
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610 redoMenuItem.setEnabled(false);
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611 redoMenuItem.setMnemonic('0');
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612 redoMenuItem.setText("Redo");
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613 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 redoMenuItem_actionPerformed(e);
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620 conservationMenuItem.setText("By Conservation");
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621 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 conservationMenuItem_actionPerformed(e);
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628 noColourmenuItem.setText("None");
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629 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 noColourmenuItem_actionPerformed(e);
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636 wrapMenuItem.setText("Wrap");
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637 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 wrapMenuItem_actionPerformed(e);
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644 printMenuItem.setText("Print");
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645 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 printMenuItem_actionPerformed(e);
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652 renderGapsMenuItem.setText("Show Gaps");
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653 renderGapsMenuItem.setState(true);
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654 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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656 public void actionPerformed(ActionEvent e)
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658 renderGapsMenuItem_actionPerformed(e);
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661 findMenuItem.setText("Find...");
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662 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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663 java.awt.event.KeyEvent.VK_F,
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664 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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665 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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667 public void actionPerformed(ActionEvent e)
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669 findMenuItem_actionPerformed(e);
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672 searchMenu.setText("Search");
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674 abovePIDThreshold.setText("Above Identity Threshold");
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675 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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677 public void actionPerformed(ActionEvent e)
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679 abovePIDThreshold_actionPerformed(e);
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682 sequenceFeatures.setText("Sequence Features");
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683 sequenceFeatures.addActionListener(new ActionListener()
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685 public void actionPerformed(ActionEvent actionEvent)
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687 sequenceFeatures_actionPerformed(actionEvent);
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690 nucleotideColour.setText("Nucleotide");
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691 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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693 public void actionPerformed(ActionEvent e)
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695 nucleotideColour_actionPerformed(e);
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698 deleteGroups.setText("Undefine groups");
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699 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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701 public void actionPerformed(ActionEvent e)
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703 deleteGroups_actionPerformed(e);
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706 copy.setText("Copy");
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707 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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708 java.awt.event.KeyEvent.VK_C,
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709 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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710 copy.setMnemonic(KeyEvent.VK_C);
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712 copy.addActionListener(new java.awt.event.ActionListener()
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714 public void actionPerformed(ActionEvent e)
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716 copy_actionPerformed(e);
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719 cut.setText("Cut");
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720 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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721 java.awt.event.KeyEvent.VK_X,
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722 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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723 cut.setMnemonic(KeyEvent.VK_X);
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724 cut.addActionListener(new java.awt.event.ActionListener()
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726 public void actionPerformed(ActionEvent e)
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728 cut_actionPerformed(e);
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731 delete.setText("Delete");
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732 delete.addActionListener(new java.awt.event.ActionListener()
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734 public void actionPerformed(ActionEvent e)
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736 delete_actionPerformed(e);
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739 jMenu1.setMnemonic('V');
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740 jMenu1.setText("Paste");
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741 pasteNew.setText("To New Alignment");
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742 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
743 java.awt.event.KeyEvent.VK_V,
\r
744 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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745 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
747 public void actionPerformed(ActionEvent e)
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749 pasteNew_actionPerformed(e);
\r
752 pasteThis.setText("Add To This Alignment");
\r
753 pasteThis.addActionListener(new java.awt.event.ActionListener()
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755 public void actionPerformed(ActionEvent e)
\r
757 pasteThis_actionPerformed(e);
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760 applyToAllGroups.setText("Apply Colour To All Groups");
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761 applyToAllGroups.setState(true);
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762 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
764 public void actionPerformed(ActionEvent e)
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766 applyToAllGroups_actionPerformed(e);
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769 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
771 public void actionPerformed(ActionEvent e)
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776 createPNG.setActionCommand("Save As PNG Image");
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777 createPNG.setText("PNG");
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778 font.setText("Font...");
\r
779 font.addActionListener(new java.awt.event.ActionListener()
\r
781 public void actionPerformed(ActionEvent e)
\r
783 font_actionPerformed(e);
\r
786 fullSeqId.setText("Show Full Sequence ID");
\r
787 fullSeqId.setState(true);
\r
788 fullSeqId.addActionListener(new java.awt.event.ActionListener()
\r
790 public void actionPerformed(ActionEvent e)
\r
792 fullSeqId_actionPerformed(e);
\r
795 epsFile.setText("EPS");
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796 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
798 public void actionPerformed(ActionEvent e)
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803 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
804 LoadtreeMenuItem.setText("Load Assocated Tree");
\r
805 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
807 public void actionPerformed(ActionEvent e)
\r
809 LoadtreeMenuItem_actionPerformed(e);
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812 jnet.setText("JNet");
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813 jnet.addActionListener(new java.awt.event.ActionListener()
\r
815 public void actionPerformed(ActionEvent e)
\r
817 jpred_actionPerformed(e);
\r
820 scaleAbove.setVisible(false);
\r
821 scaleAbove.setText("Scale Above");
\r
822 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
824 public void actionPerformed(ActionEvent e)
\r
826 scaleAbove_actionPerformed(e);
\r
829 scaleLeft.setVisible(false);
\r
830 scaleLeft.setSelected(true);
\r
831 scaleLeft.setText("Scale Left");
\r
832 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
834 public void actionPerformed(ActionEvent e)
\r
836 scaleLeft_actionPerformed(e);
\r
839 scaleRight.setVisible(false);
\r
840 scaleRight.setSelected(true);
\r
841 scaleRight.setText("Scale Right");
\r
842 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
844 public void actionPerformed(ActionEvent e)
\r
846 scaleRight_actionPerformed(e);
\r
849 modifyPID.setText("Modify Identity Threshold...");
\r
850 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
852 public void actionPerformed(ActionEvent e)
\r
854 modifyPID_actionPerformed(e);
\r
857 modifyConservation.setText("Modify Conservation Threshold...");
\r
858 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
860 public void actionPerformed(ActionEvent e)
\r
862 modifyConservation_actionPerformed(e);
\r
865 sortByTreeMenu.setText("By Tree Order");
\r
866 sort.setText("Sort");
\r
867 calculate.setText("Calculate Tree");
\r
868 msaAlignMenuItem.setText("Muscle Alignment");
\r
869 msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
871 public void actionPerformed(ActionEvent e)
\r
873 msaAlignMenuItem_actionPerformed(e);
\r
876 jMenu2.setText("Export");
\r
877 padGapsMenuitem.setText("Pad Gaps");
\r
878 padGapsMenuitem.addActionListener(new ActionListener()
\r
880 public void actionPerformed(ActionEvent e)
\r
882 padGapsMenuitem_actionPerformed(e);
\r
885 ClustalRealign.setText("Clustal Realign");
\r
886 ClustalRealign.addActionListener(new ActionListener()
\r
888 public void actionPerformed(ActionEvent e)
\r
890 ClustalRealign_actionPerformed(e);
\r
893 alignFrameMenuBar.add(fileMenu);
\r
894 alignFrameMenuBar.add(editMenu);
\r
895 alignFrameMenuBar.add(searchMenu);
\r
896 alignFrameMenuBar.add(viewMenu);
\r
897 alignFrameMenuBar.add(colourMenu);
\r
898 alignFrameMenuBar.add(calculateMenu);
\r
899 fileMenu.add(saveAlignmentMenu);
\r
900 fileMenu.add(jMenu2);
\r
901 fileMenu.add(outputTextboxMenu);
\r
902 fileMenu.add(printMenuItem);
\r
903 fileMenu.addSeparator();
\r
904 fileMenu.add(LoadtreeMenuItem);
\r
905 fileMenu.addSeparator();
\r
906 fileMenu.add(closeMenuItem);
\r
907 editMenu.add(undoMenuItem);
\r
908 editMenu.add(redoMenuItem);
\r
910 editMenu.add(copy);
\r
911 editMenu.add(jMenu1);
\r
912 editMenu.add(delete);
\r
913 editMenu.addSeparator();
\r
914 editMenu.add(selectAllSequenceMenuItem);
\r
915 editMenu.add(deselectAllSequenceMenuItem);
\r
916 editMenu.add(invertSequenceMenuItem);
\r
917 editMenu.add(deleteGroups);
\r
918 editMenu.addSeparator();
\r
919 editMenu.add(remove2LeftMenuItem);
\r
920 editMenu.add(remove2RightMenuItem);
\r
921 editMenu.add(removeGappedColumnMenuItem);
\r
922 editMenu.add(removeAllGapsMenuItem);
\r
923 editMenu.add(removeRedundancyMenuItem);
\r
924 editMenu.addSeparator();
\r
925 editMenu.add(padGapsMenuitem);
\r
926 searchMenu.add(findMenuItem);
\r
927 viewMenu.add(font);
\r
928 viewMenu.addSeparator();
\r
929 viewMenu.add(wrapMenuItem);
\r
930 viewMenu.add(fullSeqId);
\r
931 viewMenu.add(scaleAbove);
\r
932 viewMenu.add(scaleLeft);
\r
933 viewMenu.add(scaleRight);
\r
934 viewMenu.add(viewBoxesMenuItem);
\r
935 viewMenu.add(viewTextMenuItem);
\r
936 viewMenu.add(colourTextMenuItem);
\r
937 viewMenu.add(renderGapsMenuItem);
\r
938 viewMenu.add(annotationPanelMenuItem);
\r
939 viewMenu.add(sequenceFeatures);
\r
940 viewMenu.addSeparator();
\r
941 viewMenu.add(overviewMenuItem);
\r
942 colourMenu.add(applyToAllGroups);
\r
943 colourMenu.addSeparator();
\r
944 colourMenu.add(noColourmenuItem);
\r
945 colourMenu.add(clustalColour);
\r
946 colourMenu.add(BLOSUM62Colour);
\r
947 colourMenu.add(PIDColour);
\r
948 colourMenu.add(zappoColour);
\r
949 colourMenu.add(taylorColour);
\r
950 colourMenu.add(hydrophobicityColour);
\r
951 colourMenu.add(helixColour);
\r
952 colourMenu.add(strandColour);
\r
953 colourMenu.add(turnColour);
\r
954 colourMenu.add(buriedColour);
\r
955 colourMenu.add(nucleotideColour);
\r
956 colourMenu.add(userDefinedColour);
\r
957 colourMenu.addSeparator();
\r
958 colourMenu.add(conservationMenuItem);
\r
959 colourMenu.add(modifyConservation);
\r
960 colourMenu.add(abovePIDThreshold);
\r
961 colourMenu.add(modifyPID);
\r
962 calculateMenu.add(sort);
\r
963 calculateMenu.add(calculate);
\r
964 calculateMenu.addSeparator();
\r
965 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
966 calculateMenu.add(PCAMenuItem);
\r
967 calculateMenu.addSeparator();
\r
968 calculateMenu.add(webService);
\r
969 webService.add(clustalAlignMenuItem);
\r
970 webService.add(msaAlignMenuItem);
\r
971 webService.add(jnet);
\r
972 webService.add(ClustalRealign);
\r
973 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
974 jMenu1.add(pasteNew);
\r
975 jMenu1.add(pasteThis);
\r
976 sort.add(sortIDMenuItem);
\r
977 sort.add(sortGroupMenuItem);
\r
978 sort.add(sortPairwiseMenuItem);
\r
979 calculate.add(averageDistanceTreeMenuItem);
\r
980 calculate.add(neighbourTreeMenuItem);
\r
981 calculate.add(avDistanceTreeBlosumMenuItem);
\r
982 calculate.add(njTreeBlosumMenuItem);
\r
983 jMenu2.add(htmlMenuItem);
\r
984 jMenu2.add(epsFile);
\r
985 jMenu2.add(createPNG);
\r
988 protected void outputText_actionPerformed(ActionEvent e)
\r
992 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
996 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1000 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1004 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1008 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1012 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1016 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1020 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1024 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1028 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1032 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1036 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1040 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1044 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1048 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1052 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1056 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1060 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1064 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1068 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1072 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1076 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1080 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1084 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1088 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1092 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1096 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1100 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1104 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1108 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1112 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1116 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1120 protected void helixColour_actionPerformed(ActionEvent e)
\r
1124 protected void strandColour_actionPerformed(ActionEvent e)
\r
1128 protected void turnColour_actionPerformed(ActionEvent e)
\r
1132 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1136 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1140 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1144 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1148 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1152 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1156 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1160 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1164 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1168 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1172 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1176 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1180 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1184 protected void copy_actionPerformed(ActionEvent e)
\r
1188 protected void cut_actionPerformed(ActionEvent e)
\r
1192 protected void delete_actionPerformed(ActionEvent e)
\r
1196 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1200 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1204 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1208 public void createPNG(java.io.File f)
\r
1212 protected void font_actionPerformed(ActionEvent e)
\r
1216 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1220 public void createEPS(java.io.File f)
\r
1224 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1228 protected void jpred_actionPerformed(ActionEvent e)
\r
1232 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1236 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1240 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1244 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1248 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1252 protected void preferences_actionPerformed(ActionEvent e)
\r
1256 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1260 protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
\r
1264 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1268 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1272 protected void ClustalRealign_actionPerformed(ActionEvent e)
\r