2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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.schemes.*;
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27 import java.awt.BorderLayout;
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32 public class GAlignFrame
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33 extends JInternalFrame
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35 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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36 protected JMenu fileMenu = new JMenu();
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37 protected JMenuItem closeMenuItem = new JMenuItem();
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38 protected JMenu editMenu = new JMenu();
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39 protected JMenu viewMenu = new JMenu();
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40 protected JMenu colourMenu = new JMenu();
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41 protected JMenu calculateMenu = new JMenu();
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42 protected JMenu webService = new JMenu();
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43 protected JMenuItem webServiceNoServices;
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44 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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45 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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46 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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47 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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48 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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49 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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50 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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51 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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52 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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53 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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54 protected JMenuItem sortIDMenuItem = new JMenuItem();
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55 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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56 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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57 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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58 protected JMenuItem PCAMenuItem = new JMenuItem();
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59 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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60 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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61 BorderLayout borderLayout1 = new BorderLayout();
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62 public JLabel statusBar = new JLabel();
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63 protected JMenuItem saveAs = new JMenuItem();
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64 protected JMenu outputTextboxMenu = new JMenu();
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65 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem hydrophobicityColour = new
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69 JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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75 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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76 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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77 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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78 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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79 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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80 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem htmlMenuItem = new JMenuItem();
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82 JMenuItem overviewMenuItem = new JMenuItem();
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83 protected JMenuItem undoMenuItem = new JMenuItem();
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84 protected JMenuItem redoMenuItem = new JMenuItem();
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85 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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86 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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87 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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88 JMenuItem printMenuItem = new JMenuItem();
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89 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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90 JMenuItem findMenuItem = new JMenuItem();
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91 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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92 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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93 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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94 JMenuItem deleteGroups = new JMenuItem();
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95 JMenuItem delete = new JMenuItem();
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96 JMenuItem copy = new JMenuItem();
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97 JMenuItem cut = new JMenuItem();
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98 JMenu pasteMenu = new JMenu();
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99 JMenuItem pasteNew = new JMenuItem();
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100 JMenuItem pasteThis = new JMenuItem();
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101 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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102 JMenuItem createPNG = new JMenuItem();
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103 protected JMenuItem font = new JMenuItem();
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104 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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105 JMenuItem epsFile = new JMenuItem();
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106 JMenuItem LoadtreeMenuItem = new JMenuItem();
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107 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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108 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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109 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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110 protected JMenuItem modifyPID = new JMenuItem();
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111 protected JMenuItem modifyConservation = new JMenuItem();
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112 protected JMenu sortByTreeMenu = new JMenu();
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113 protected JMenu sort = new JMenu();
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114 JMenu calculate = new JMenu();
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115 JMenu jMenu2 = new JMenu();
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116 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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117 protected ButtonGroup colours = new ButtonGroup();
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118 JMenuItem vamsasStore = new JMenuItem();
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119 protected JMenuItem showTranslation = new JMenuItem();
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120 public JMenuItem featureSettings = new JMenuItem();
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121 JMenuItem fetchSequence = new JMenuItem();
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122 JMenuItem annotationColour = new JMenuItem();
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123 JMenuItem associatedData = new JMenuItem();
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124 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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125 JMenu addSequenceMenu = new JMenu();
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126 JMenuItem addFromFile = new JMenuItem();
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127 JMenuItem addFromText = new JMenuItem();
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128 JMenuItem addFromURL = new JMenuItem();
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129 JMenuItem exportAnnotations = new JMenuItem();
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130 JMenuItem exportFeatures = new JMenuItem();
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131 protected JPanel statusPanel = new JPanel();
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132 GridLayout gridLayout1 = new GridLayout();
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133 JMenu jMenu3 = new JMenu();
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134 JMenuItem showAllSeqs = new JMenuItem();
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135 JMenuItem showAllColumns = new JMenuItem();
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136 JMenu hideMenu = new JMenu();
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137 JMenuItem hideSelSequences = new JMenuItem();
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138 JMenuItem hideSelColumns = new JMenuItem();
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139 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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140 JMenuItem invertColSel = new JMenuItem();
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141 protected JTabbedPane tabbedPane = new JTabbedPane();
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142 JMenuItem save = new JMenuItem();
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143 JMenuItem jMenuItem1 = new JMenuItem();
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144 protected JMenuItem reload = new JMenuItem();
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145 JMenuItem newView = new JMenuItem();
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146 JMenuItem textColour = new JMenuItem();
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147 JMenu formatMenu = new JMenu();
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148 JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();
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149 JMenu selectMenu = new JMenu();
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150 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
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151 protected JMenuItem gatherViews = new JMenuItem();
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152 protected JMenuItem expandViews = new JMenuItem();
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153 public GAlignFrame()
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158 setJMenuBar(alignFrameMenuBar);
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160 // dynamically fill save as menu with available formats
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161 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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163 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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165 item.addActionListener(new java.awt.event.ActionListener()
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167 public void actionPerformed(ActionEvent e)
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169 outputText_actionPerformed(e);
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173 outputTextboxMenu.add(item);
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176 catch (Exception e)
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180 if (!System.getProperty("os.name").startsWith("Mac"))
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182 closeMenuItem.setMnemonic('C');
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183 outputTextboxMenu.setMnemonic('T');
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184 undoMenuItem.setMnemonic('Z');
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185 redoMenuItem.setMnemonic('0');
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186 copy.setMnemonic('C');
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187 cut.setMnemonic('U');
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188 pasteMenu.setMnemonic('P');
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189 reload.setMnemonic('R');
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193 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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195 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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196 getUserColourSchemes().keys();
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198 while (userColours.hasMoreElements())
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200 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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201 nextElement().toString());
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202 radioItem.setName("USER_DEFINED");
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203 radioItem.addMouseListener(new MouseAdapter()
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205 public void mousePressed(MouseEvent evt)
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207 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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209 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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211 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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212 "Remove from default list?",
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213 "Remove user defined colour",
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214 JOptionPane.YES_NO_OPTION);
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215 if(option == JOptionPane.YES_OPTION)
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217 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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218 colourMenu.remove(radioItem);
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221 radioItem.addActionListener(new ActionListener()
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223 public void actionPerformed(ActionEvent evt)
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225 userDefinedColour_actionPerformed(evt);
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231 radioItem.addActionListener(new ActionListener()
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233 public void actionPerformed(ActionEvent evt)
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235 userDefinedColour_actionPerformed(evt);
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238 colourMenu.insert(radioItem, 15);
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239 colours.add(radioItem);
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242 colours.add(noColourmenuItem);
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243 colours.add(clustalColour);
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244 colours.add(zappoColour);
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245 colours.add(taylorColour);
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246 colours.add(hydrophobicityColour);
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247 colours.add(helixColour);
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248 colours.add(strandColour);
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249 colours.add(turnColour);
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250 colours.add(buriedColour);
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251 colours.add(userDefinedColour);
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252 colours.add(PIDColour);
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253 colours.add(BLOSUM62Colour);
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254 colours.add(nucleotideColour);
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256 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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261 public void setColourSelected(String defaultColour)
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264 if (defaultColour != null)
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266 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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270 case ColourSchemeProperty.NONE:
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271 noColourmenuItem.setSelected(true);
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273 case ColourSchemeProperty.CLUSTAL:
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274 clustalColour.setSelected(true);
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278 case ColourSchemeProperty.BLOSUM:
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279 BLOSUM62Colour.setSelected(true);
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283 case ColourSchemeProperty.PID:
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284 PIDColour.setSelected(true);
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288 case ColourSchemeProperty.ZAPPO:
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289 zappoColour.setSelected(true);
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293 case ColourSchemeProperty.TAYLOR:
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294 taylorColour.setSelected(true);
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297 case ColourSchemeProperty.HYDROPHOBIC:
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298 hydrophobicityColour.setSelected(true);
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302 case ColourSchemeProperty.HELIX:
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303 helixColour.setSelected(true);
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307 case ColourSchemeProperty.STRAND:
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308 strandColour.setSelected(true);
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312 case ColourSchemeProperty.TURN:
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313 turnColour.setSelected(true);
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317 case ColourSchemeProperty.BURIED:
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318 buriedColour.setSelected(true);
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322 case ColourSchemeProperty.NUCLEOTIDE:
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323 nucleotideColour.setSelected(true);
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327 case ColourSchemeProperty.USER_DEFINED:
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328 userDefinedColour.setSelected(true);
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336 private void jbInit()
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339 fileMenu.setText("File");
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340 saveAs.setText("Save As...");
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341 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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343 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
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344 saveAs.addActionListener(new ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 saveAs_actionPerformed(e);
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351 closeMenuItem.setText("Close");
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352 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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353 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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354 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 closeMenuItem_actionPerformed(false);
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361 editMenu.setText("Edit");
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362 viewMenu.setText("View");
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363 colourMenu.setText("Colour");
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364 calculateMenu.setText("Calculate");
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365 webService.setText("Web Service");
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366 selectAllSequenceMenuItem.setText("Select All");
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367 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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368 java.awt.event.KeyEvent.VK_A,
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369 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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370 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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373 public void actionPerformed(ActionEvent e)
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375 selectAllSequenceMenuItem_actionPerformed(e);
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378 deselectAllSequenceMenuItem.setText("Deselect All");
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379 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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381 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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382 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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385 public void actionPerformed(ActionEvent e)
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387 deselectAllSequenceMenuItem_actionPerformed(e);
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390 invertSequenceMenuItem.setText("Invert Sequence Selection");
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391 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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392 java.awt.event.KeyEvent.VK_I,
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393 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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394 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 invertSequenceMenuItem_actionPerformed(e);
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401 remove2LeftMenuItem.setText("Remove Left");
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402 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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403 awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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404 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 remove2LeftMenuItem_actionPerformed(e);
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411 remove2RightMenuItem.setText("Remove Right");
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412 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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413 awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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414 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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416 public void actionPerformed(ActionEvent e)
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418 remove2RightMenuItem_actionPerformed(e);
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421 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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422 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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423 getKeyStroke(java.awt.event.
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424 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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425 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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428 public void actionPerformed(ActionEvent e)
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430 removeGappedColumnMenuItem_actionPerformed(e);
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433 removeAllGapsMenuItem.setText("Remove All Gaps");
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434 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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435 java.awt.event.KeyEvent.VK_E,
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436 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
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437 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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439 public void actionPerformed(ActionEvent e)
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441 removeAllGapsMenuItem_actionPerformed(e);
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444 viewBoxesMenuItem.setText("Boxes");
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445 viewBoxesMenuItem.setState(true);
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446 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 viewBoxesMenuItem_actionPerformed(e);
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453 viewTextMenuItem.setText("Text");
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454 viewTextMenuItem.setState(true);
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455 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 viewTextMenuItem_actionPerformed(e);
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462 sortPairwiseMenuItem.setText("by Pairwise Identity");
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463 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 sortPairwiseMenuItem_actionPerformed(e);
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470 sortIDMenuItem.setText("by ID");
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471 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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473 public void actionPerformed(ActionEvent e)
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475 sortIDMenuItem_actionPerformed(e);
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478 sortGroupMenuItem.setText("by Group");
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479 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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481 public void actionPerformed(ActionEvent e)
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483 sortGroupMenuItem_actionPerformed(e);
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486 removeRedundancyMenuItem.setText("Remove Redundancy...");
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487 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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488 java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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489 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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492 public void actionPerformed(ActionEvent e)
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494 removeRedundancyMenuItem_actionPerformed(e);
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497 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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498 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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501 public void actionPerformed(ActionEvent e)
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503 pairwiseAlignmentMenuItem_actionPerformed(e);
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506 PCAMenuItem.setText("Principal Component Analysis");
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507 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 PCAMenuItem_actionPerformed(e);
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514 averageDistanceTreeMenuItem.setText(
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515 "Average Distance Using % Identity");
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516 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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519 public void actionPerformed(ActionEvent e)
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521 averageDistanceTreeMenuItem_actionPerformed(e);
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524 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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525 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 neighbourTreeMenuItem_actionPerformed(e);
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532 this.getContentPane().setLayout(borderLayout1);
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533 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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534 statusBar.setBackground(Color.white);
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535 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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536 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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537 statusBar.setText("Status bar");
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538 outputTextboxMenu.setText("Output to Textbox");
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539 clustalColour.setText("Clustalx");
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541 clustalColour.addActionListener(new java.awt.event.ActionListener()
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543 public void actionPerformed(ActionEvent e)
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545 clustalColour_actionPerformed(e);
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548 zappoColour.setText("Zappo");
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549 zappoColour.addActionListener(new java.awt.event.ActionListener()
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551 public void actionPerformed(ActionEvent e)
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553 zappoColour_actionPerformed(e);
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556 taylorColour.setText("Taylor");
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557 taylorColour.addActionListener(new java.awt.event.ActionListener()
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559 public void actionPerformed(ActionEvent e)
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561 taylorColour_actionPerformed(e);
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564 hydrophobicityColour.setText("Hydrophobicity");
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565 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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567 public void actionPerformed(ActionEvent e)
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569 hydrophobicityColour_actionPerformed(e);
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572 helixColour.setText("Helix Propensity");
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573 helixColour.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 helixColour_actionPerformed(e);
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580 strandColour.setText("Strand Propensity");
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581 strandColour.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 strandColour_actionPerformed(e);
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588 turnColour.setText("Turn Propensity");
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589 turnColour.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 turnColour_actionPerformed(e);
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596 buriedColour.setText("Buried Index");
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597 buriedColour.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 buriedColour_actionPerformed(e);
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604 userDefinedColour.setText("User Defined...");
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605 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 userDefinedColour_actionPerformed(e);
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612 PIDColour.setText("Percentage Identity");
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613 PIDColour.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 PIDColour_actionPerformed(e);
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620 BLOSUM62Colour.setText("BLOSUM62 Score");
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621 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 BLOSUM62Colour_actionPerformed(e);
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628 avDistanceTreeBlosumMenuItem.setText(
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629 "Average Distance Using BLOSUM62");
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630 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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633 public void actionPerformed(ActionEvent e)
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635 avTreeBlosumMenuItem_actionPerformed(e);
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638 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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639 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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641 public void actionPerformed(ActionEvent e)
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643 njTreeBlosumMenuItem_actionPerformed(e);
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646 annotationPanelMenuItem.setActionCommand("");
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647 annotationPanelMenuItem.setText("Show Annotations");
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648 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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649 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 annotationPanelMenuItem_actionPerformed(e);
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656 colourTextMenuItem.setText("Colour Text");
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657 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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659 public void actionPerformed(ActionEvent e)
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661 colourTextMenuItem_actionPerformed(e);
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664 htmlMenuItem.setText("HTML");
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665 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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667 public void actionPerformed(ActionEvent e)
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669 htmlMenuItem_actionPerformed(e);
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672 overviewMenuItem.setText("Overview Window");
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673 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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675 public void actionPerformed(ActionEvent e)
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677 overviewMenuItem_actionPerformed(e);
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680 undoMenuItem.setEnabled(false);
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681 undoMenuItem.setText("Undo");
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682 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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683 java.awt.event.KeyEvent.VK_Z,
\r
684 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
685 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
687 public void actionPerformed(ActionEvent e)
\r
689 undoMenuItem_actionPerformed(e);
\r
692 redoMenuItem.setEnabled(false);
\r
693 redoMenuItem.setText("Redo");
\r
694 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
695 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
696 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
698 public void actionPerformed(ActionEvent e)
\r
700 redoMenuItem_actionPerformed(e);
\r
703 conservationMenuItem.setText("By Conservation");
\r
704 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
706 public void actionPerformed(ActionEvent e)
\r
708 conservationMenuItem_actionPerformed(e);
\r
711 noColourmenuItem.setText("None");
\r
712 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
714 public void actionPerformed(ActionEvent e)
\r
716 noColourmenuItem_actionPerformed(e);
\r
719 wrapMenuItem.setText("Wrap");
\r
720 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
722 public void actionPerformed(ActionEvent e)
\r
724 wrapMenuItem_actionPerformed(e);
\r
727 printMenuItem.setText("Print");
\r
728 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
729 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
730 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
732 public void actionPerformed(ActionEvent e)
\r
734 printMenuItem_actionPerformed(e);
\r
737 renderGapsMenuItem.setText("Show Gaps");
\r
738 renderGapsMenuItem.setState(true);
\r
739 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
741 public void actionPerformed(ActionEvent e)
\r
743 renderGapsMenuItem_actionPerformed(e);
\r
746 findMenuItem.setText("Find...");
\r
747 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
748 java.awt.event.KeyEvent.VK_F,
\r
749 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
750 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
752 public void actionPerformed(ActionEvent e)
\r
754 findMenuItem_actionPerformed(e);
\r
757 abovePIDThreshold.setText("Above Identity Threshold");
\r
758 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
760 public void actionPerformed(ActionEvent e)
\r
762 abovePIDThreshold_actionPerformed(e);
\r
765 showSeqFeatures.setText("Show Sequence Features");
\r
766 showSeqFeatures.addActionListener(new ActionListener()
\r
768 public void actionPerformed(ActionEvent actionEvent)
\r
770 showSeqFeatures_actionPerformed(actionEvent);
\r
773 nucleotideColour.setText("Nucleotide");
\r
774 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
776 public void actionPerformed(ActionEvent e)
\r
778 nucleotideColour_actionPerformed(e);
\r
781 deleteGroups.setText("Undefine groups");
\r
782 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
783 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
784 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
786 public void actionPerformed(ActionEvent e)
\r
788 deleteGroups_actionPerformed(e);
\r
791 copy.setText("Copy");
\r
792 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
793 java.awt.event.KeyEvent.VK_C,
\r
794 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
796 copy.addActionListener(new java.awt.event.ActionListener()
\r
798 public void actionPerformed(ActionEvent e)
\r
800 copy_actionPerformed(e);
\r
803 cut.setText("Cut");
\r
804 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
805 java.awt.event.KeyEvent.VK_X,
\r
806 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
807 cut.addActionListener(new java.awt.event.ActionListener()
\r
809 public void actionPerformed(ActionEvent e)
\r
811 cut_actionPerformed(e);
\r
814 delete.setText("Delete");
\r
815 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
816 KeyEvent.VK_BACK_SPACE, 0, false));
\r
817 delete.addActionListener(new java.awt.event.ActionListener()
\r
819 public void actionPerformed(ActionEvent e)
\r
821 delete_actionPerformed(e);
\r
824 pasteMenu.setText("Paste");
\r
825 pasteNew.setText("To New Alignment");
\r
826 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
827 java.awt.event.KeyEvent.VK_V,
\r
828 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
\r
829 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
831 public void actionPerformed(ActionEvent e)
\r
833 pasteNew_actionPerformed(e);
\r
836 pasteThis.setText("Add To This Alignment");
\r
837 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
838 java.awt.event.KeyEvent.VK_V,
\r
839 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
840 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
842 public void actionPerformed(ActionEvent e)
\r
844 pasteThis_actionPerformed(e);
\r
847 applyToAllGroups.setText("Apply Colour To All Groups");
\r
848 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
850 public void actionPerformed(ActionEvent e)
\r
852 applyToAllGroups_actionPerformed(e);
\r
855 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
857 public void actionPerformed(ActionEvent e)
\r
862 createPNG.setActionCommand("Save As PNG Image");
\r
863 createPNG.setText("PNG");
\r
864 font.setText("Font...");
\r
865 font.addActionListener(new java.awt.event.ActionListener()
\r
867 public void actionPerformed(ActionEvent e)
\r
869 font_actionPerformed(e);
\r
873 seqLimits.setText("Show Sequence Limits");
\r
874 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
875 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
877 public void actionPerformed(ActionEvent e)
\r
879 seqLimit_actionPerformed(e);
\r
882 epsFile.setText("EPS");
\r
883 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
885 public void actionPerformed(ActionEvent e)
\r
890 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
891 LoadtreeMenuItem.setText("Load Associated Tree");
\r
892 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
894 public void actionPerformed(ActionEvent e)
\r
896 LoadtreeMenuItem_actionPerformed(e);
\r
899 scaleAbove.setVisible(false);
\r
900 scaleAbove.setText("Scale Above");
\r
901 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
903 public void actionPerformed(ActionEvent e)
\r
905 scaleAbove_actionPerformed(e);
\r
908 scaleLeft.setVisible(false);
\r
909 scaleLeft.setSelected(true);
\r
910 scaleLeft.setText("Scale Left");
\r
911 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
913 public void actionPerformed(ActionEvent e)
\r
915 scaleLeft_actionPerformed(e);
\r
918 scaleRight.setVisible(false);
\r
919 scaleRight.setSelected(true);
\r
920 scaleRight.setText("Scale Right");
\r
921 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
923 public void actionPerformed(ActionEvent e)
\r
925 scaleRight_actionPerformed(e);
\r
928 modifyPID.setText("Modify Identity Threshold...");
\r
929 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
931 public void actionPerformed(ActionEvent e)
\r
933 modifyPID_actionPerformed(e);
\r
936 modifyConservation.setText("Modify Conservation Threshold...");
\r
937 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
939 public void actionPerformed(ActionEvent e)
\r
941 modifyConservation_actionPerformed(e);
\r
944 sortByTreeMenu.setText("By Tree Order");
\r
945 sort.setText("Sort");
\r
946 calculate.setText("Calculate Tree");
\r
948 jMenu2.setText("Export Image");
\r
949 padGapsMenuitem.setText("Pad Gaps");
\r
950 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
951 padGapsMenuitem.addActionListener(new ActionListener()
\r
953 public void actionPerformed(ActionEvent e)
\r
955 padGapsMenuitem_actionPerformed(e);
\r
958 vamsasStore.setVisible(false);
\r
959 vamsasStore.setText("VAMSAS store");
\r
960 vamsasStore.addActionListener(new ActionListener()
\r
962 public void actionPerformed(ActionEvent e)
\r
964 vamsasStore_actionPerformed(e);
\r
967 showTranslation.setText("Translate cDNA");
\r
968 showTranslation.addActionListener(new ActionListener()
\r
970 public void actionPerformed(ActionEvent e)
\r
972 showTranslation_actionPerformed(e);
\r
977 featureSettings.setText("Feature Settings...");
\r
978 featureSettings.addActionListener(new ActionListener()
\r
980 public void actionPerformed(ActionEvent e)
\r
982 featureSettings_actionPerformed(e);
\r
985 fetchSequence.setText("Fetch Sequence(s)...");
\r
986 fetchSequence.addActionListener(new ActionListener()
\r
988 public void actionPerformed(ActionEvent e)
\r
990 fetchSequence_actionPerformed(e);
\r
994 annotationColour.setText("By Annotation...");
\r
995 annotationColour.addActionListener(new ActionListener()
\r
997 public void actionPerformed(ActionEvent e)
\r
999 annotationColour_actionPerformed(e);
\r
1002 associatedData.setText("Load Features / Annotations");
\r
1003 associatedData.addActionListener(new ActionListener()
\r
1005 public void actionPerformed(ActionEvent e)
\r
1007 associatedData_actionPerformed(e);
\r
1010 autoCalculate.setText("Autocalculate Consensus");
\r
1011 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1012 autoCalculate.addActionListener(new ActionListener()
\r
1014 public void actionPerformed(ActionEvent e)
\r
1016 autoCalculate_actionPerformed(e);
\r
1019 addSequenceMenu.setText("Add Sequences");
\r
1020 addFromFile.setText("From File");
\r
1021 addFromFile.addActionListener(new ActionListener()
\r
1023 public void actionPerformed(ActionEvent e)
\r
1025 addFromFile_actionPerformed(e);
\r
1028 addFromText.setText("From Textbox");
\r
1029 addFromText.addActionListener(new ActionListener()
\r
1031 public void actionPerformed(ActionEvent e)
\r
1033 addFromText_actionPerformed(e);
\r
1036 addFromURL.setText("From URL");
\r
1037 addFromURL.addActionListener(new ActionListener()
\r
1039 public void actionPerformed(ActionEvent e)
\r
1041 addFromURL_actionPerformed(e);
\r
1044 exportFeatures.setText("Export Features...");
\r
1045 exportFeatures.addActionListener(new ActionListener()
\r
1047 public void actionPerformed(ActionEvent e)
\r
1049 exportFeatures_actionPerformed(e);
\r
1052 exportAnnotations.setText("Export Annotations...");
\r
1053 exportAnnotations.addActionListener(new ActionListener()
\r
1055 public void actionPerformed(ActionEvent e)
\r
1057 exportAnnotations_actionPerformed(e);
\r
1060 statusPanel.setLayout(gridLayout1);
\r
1061 jMenu3.setText("Show");
\r
1062 showAllSeqs.setText("All Sequences");
\r
1063 showAllSeqs.addActionListener(new ActionListener()
\r
1065 public void actionPerformed(ActionEvent e)
\r
1067 showAllSeqs_actionPerformed(e);
\r
1070 showAllColumns.setText("All Columns");
\r
1071 showAllColumns.addActionListener(new ActionListener()
\r
1073 public void actionPerformed(ActionEvent e)
\r
1075 showAllColumns_actionPerformed(e);
\r
1078 hideMenu.setText("Hide");
\r
1079 hideSelSequences.setText("Selected Sequences");
\r
1080 hideSelSequences.addActionListener(new ActionListener()
\r
1082 public void actionPerformed(ActionEvent e)
\r
1084 hideSelSequences_actionPerformed(e);
\r
1087 hideSelColumns.setText("Selected Columns");
\r
1088 hideSelColumns.addActionListener(new ActionListener()
\r
1090 public void actionPerformed(ActionEvent e)
\r
1092 hideSelColumns_actionPerformed(e);
\r
1095 hiddenMarkers.setText("Show Hidden Markers");
\r
1096 hiddenMarkers.addActionListener(new ActionListener()
\r
1098 public void actionPerformed(ActionEvent e)
\r
1100 hiddenMarkers_actionPerformed(e);
\r
1103 invertColSel.setText("Invert Column Selection");
\r
1104 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1105 event.KeyEvent.VK_I,
\r
1106 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
\r
1107 |java.awt.event.KeyEvent.ALT_MASK,
\r
1109 invertColSel.addActionListener(new ActionListener()
\r
1111 public void actionPerformed(ActionEvent e)
\r
1113 invertColSel_actionPerformed(e);
\r
1116 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1118 public void stateChanged(ChangeEvent evt)
\r
1120 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1121 int sel = pane.getSelectedIndex();
\r
1122 tabSelectionChanged(sel);
\r
1125 tabbedPane.addMouseListener(new MouseAdapter()
\r
1127 public void mousePressed(MouseEvent e)
\r
1129 tabbedPane_mousePressed(e);
\r
1132 tabbedPane.addFocusListener(new FocusAdapter()
\r
1134 public void focusGained(FocusEvent e)
\r
1136 tabbedPane_focusGained(e);
\r
1139 save.setText("Save");
\r
1140 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1141 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1142 save.addActionListener(new ActionListener()
\r
1144 public void actionPerformed(ActionEvent e)
\r
1146 save_actionPerformed(e);
\r
1149 reload.setEnabled(false);
\r
1150 reload.setText("Reload");
\r
1151 reload.addActionListener(new ActionListener()
\r
1153 public void actionPerformed(ActionEvent e)
\r
1155 reload_actionPerformed(e);
\r
1158 newView.setText("New View");
\r
1159 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1160 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1161 newView.addActionListener(new ActionListener()
\r
1163 public void actionPerformed(ActionEvent e)
\r
1165 newView_actionPerformed(e);
\r
1168 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
\r
1169 +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
\r
1170 textColour.setText("Text Colour");
\r
1171 textColour.addActionListener(new ActionListener()
\r
1173 public void actionPerformed(ActionEvent e)
\r
1175 textColour_actionPerformed(e);
\r
1178 formatMenu.setText("Format");
\r
1179 jCheckBoxMenuItem1.setText("Right Align Ids");
\r
1180 selectMenu.setText("Select");
\r
1181 idRightAlign.setText("Right Align Sequence Id");
\r
1182 idRightAlign.addActionListener(new ActionListener()
\r
1184 public void actionPerformed(ActionEvent e)
\r
1186 idRightAlign_actionPerformed(e);
\r
1189 gatherViews.setEnabled(false);
\r
1190 gatherViews.setText("Gather Views");
\r
1191 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1192 event.KeyEvent.VK_G, 0, false));
\r
1193 gatherViews.addActionListener(new ActionListener()
\r
1195 public void actionPerformed(ActionEvent e)
\r
1197 gatherViews_actionPerformed(e);
\r
1200 expandViews.setEnabled(false);
\r
1201 expandViews.setText("Expand Views");
\r
1202 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1203 event.KeyEvent.VK_X, 0, false));
\r
1204 expandViews.addActionListener(new ActionListener()
\r
1206 public void actionPerformed(ActionEvent e)
\r
1208 expandViews_actionPerformed(e);
\r
1212 alignFrameMenuBar.add(fileMenu);
\r
1213 alignFrameMenuBar.add(editMenu);
\r
1214 alignFrameMenuBar.add(selectMenu);
\r
1215 alignFrameMenuBar.add(viewMenu);
\r
1216 alignFrameMenuBar.add(formatMenu);
\r
1217 alignFrameMenuBar.add(colourMenu);
\r
1218 alignFrameMenuBar.add(calculateMenu);
\r
1219 alignFrameMenuBar.add(webService);
\r
1220 fileMenu.add(fetchSequence);
\r
1221 fileMenu.add(addSequenceMenu);
\r
1222 fileMenu.add(reload);
\r
1223 fileMenu.addSeparator();
\r
1224 fileMenu.add(vamsasStore);
\r
1225 fileMenu.add(save);
\r
1226 fileMenu.add(saveAs);
\r
1227 fileMenu.add(outputTextboxMenu);
\r
1228 fileMenu.add(printMenuItem);
\r
1229 fileMenu.addSeparator();
\r
1230 fileMenu.add(jMenu2);
\r
1231 fileMenu.add(exportFeatures);
\r
1232 fileMenu.add(exportAnnotations);
\r
1233 fileMenu.add(LoadtreeMenuItem);
\r
1234 fileMenu.add(associatedData);
\r
1235 fileMenu.addSeparator();
\r
1236 fileMenu.add(closeMenuItem);
\r
1237 editMenu.add(undoMenuItem);
\r
1238 editMenu.add(redoMenuItem);
\r
1239 editMenu.add(cut);
\r
1240 editMenu.add(copy);
\r
1241 editMenu.add(pasteMenu);
\r
1242 editMenu.add(delete);
\r
1243 editMenu.addSeparator();
\r
1244 editMenu.add(remove2LeftMenuItem);
\r
1245 editMenu.add(remove2RightMenuItem);
\r
1246 editMenu.add(removeGappedColumnMenuItem);
\r
1247 editMenu.add(removeAllGapsMenuItem);
\r
1248 editMenu.add(removeRedundancyMenuItem);
\r
1249 editMenu.addSeparator();
\r
1250 editMenu.add(padGapsMenuitem);
\r
1251 viewMenu.add(newView);
\r
1252 viewMenu.add(expandViews);
\r
1253 viewMenu.add(gatherViews);
\r
1254 viewMenu.addSeparator();
\r
1255 viewMenu.add(jMenu3);
\r
1256 viewMenu.add(hideMenu);
\r
1257 viewMenu.addSeparator();
\r
1258 viewMenu.add(annotationPanelMenuItem);
\r
1259 viewMenu.addSeparator();
\r
1260 viewMenu.add(showSeqFeatures);
\r
1261 viewMenu.add(featureSettings);
\r
1262 viewMenu.addSeparator();
\r
1263 viewMenu.add(overviewMenuItem);
\r
1264 colourMenu.add(applyToAllGroups);
\r
1265 colourMenu.add(textColour);
\r
1266 colourMenu.addSeparator();
\r
1267 colourMenu.add(noColourmenuItem);
\r
1268 colourMenu.add(clustalColour);
\r
1269 colourMenu.add(BLOSUM62Colour);
\r
1270 colourMenu.add(PIDColour);
\r
1271 colourMenu.add(zappoColour);
\r
1272 colourMenu.add(taylorColour);
\r
1273 colourMenu.add(hydrophobicityColour);
\r
1274 colourMenu.add(helixColour);
\r
1275 colourMenu.add(strandColour);
\r
1276 colourMenu.add(turnColour);
\r
1277 colourMenu.add(buriedColour);
\r
1278 colourMenu.add(nucleotideColour);
\r
1279 colourMenu.add(userDefinedColour);
\r
1280 colourMenu.addSeparator();
\r
1281 colourMenu.add(conservationMenuItem);
\r
1282 colourMenu.add(modifyConservation);
\r
1283 colourMenu.add(abovePIDThreshold);
\r
1284 colourMenu.add(modifyPID);
\r
1285 colourMenu.add(annotationColour);
\r
1286 calculateMenu.add(sort);
\r
1287 calculateMenu.add(calculate);
\r
1288 calculateMenu.addSeparator();
\r
1289 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1290 calculateMenu.add(PCAMenuItem);
\r
1291 calculateMenu.addSeparator();
\r
1292 calculateMenu.add(showTranslation);
\r
1293 calculateMenu.add(autoCalculate);
\r
1294 webServiceNoServices=new JMenuItem("<No Services>");
\r
1295 webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
\r
1296 pasteMenu.add(pasteThis);
\r
1297 sort.add(sortIDMenuItem);
\r
1298 sort.add(sortGroupMenuItem);
\r
1299 sort.add(sortPairwiseMenuItem);
\r
1300 calculate.add(averageDistanceTreeMenuItem);
\r
1301 calculate.add(neighbourTreeMenuItem);
\r
1302 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1303 calculate.add(njTreeBlosumMenuItem);
\r
1304 jMenu2.add(htmlMenuItem);
\r
1305 jMenu2.add(epsFile);
\r
1306 jMenu2.add(createPNG);
\r
1307 addSequenceMenu.add(addFromFile);
\r
1308 addSequenceMenu.add(addFromText);
\r
1309 addSequenceMenu.add(addFromURL);
\r
1310 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1311 statusPanel.add(statusBar, null);
\r
1312 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1313 jMenu3.add(showAllColumns);
\r
1314 jMenu3.add(showAllSeqs);
\r
1315 hideMenu.add(hideSelColumns);
\r
1316 hideMenu.add(hideSelSequences);
\r
1317 formatMenu.add(font);
\r
1318 formatMenu.addSeparator();
\r
1319 formatMenu.add(wrapMenuItem);
\r
1320 formatMenu.add(scaleAbove);
\r
1321 formatMenu.add(scaleLeft);
\r
1322 formatMenu.add(scaleRight);
\r
1323 formatMenu.add(seqLimits);
\r
1324 formatMenu.add(idRightAlign);
\r
1325 formatMenu.add(hiddenMarkers);
\r
1326 formatMenu.add(viewBoxesMenuItem);
\r
1327 formatMenu.add(viewTextMenuItem);
\r
1328 formatMenu.add(colourTextMenuItem);
\r
1329 formatMenu.add(renderGapsMenuItem);
\r
1330 selectMenu.add(findMenuItem);
\r
1331 selectMenu.addSeparator();
\r
1332 selectMenu.add(selectAllSequenceMenuItem);
\r
1333 selectMenu.add(deselectAllSequenceMenuItem);
\r
1334 selectMenu.add(invertSequenceMenuItem);
\r
1335 selectMenu.add(invertColSel);
\r
1336 selectMenu.add(deleteGroups);
\r
1339 protected void outputText_actionPerformed(ActionEvent e)
\r
1343 public void addFromFile_actionPerformed(ActionEvent e)
\r
1348 public void addFromText_actionPerformed(ActionEvent e)
\r
1353 public void addFromURL_actionPerformed(ActionEvent e)
\r
1358 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1363 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1368 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1372 protected void closeMenuItem_actionPerformed(boolean b)
\r
1376 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1380 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1384 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1388 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1392 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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1396 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1400 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1404 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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1408 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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1412 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1416 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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1420 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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1424 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1428 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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1432 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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1436 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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1440 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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1444 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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1448 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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1452 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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1456 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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1460 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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1464 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1468 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1472 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1476 protected void clustalColour_actionPerformed(ActionEvent e)
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1480 protected void zappoColour_actionPerformed(ActionEvent e)
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1484 protected void taylorColour_actionPerformed(ActionEvent e)
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1488 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1492 protected void helixColour_actionPerformed(ActionEvent e)
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1496 protected void strandColour_actionPerformed(ActionEvent e)
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1500 protected void turnColour_actionPerformed(ActionEvent e)
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1504 protected void buriedColour_actionPerformed(ActionEvent e)
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1508 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1512 protected void PIDColour_actionPerformed(ActionEvent e)
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1516 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1520 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1524 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1528 protected void printMenuItem_actionPerformed(ActionEvent e)
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1532 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1536 protected void findMenuItem_actionPerformed(ActionEvent e)
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1540 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
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1544 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
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1548 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1552 protected void deleteGroups_actionPerformed(ActionEvent e)
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1556 protected void copy_actionPerformed(ActionEvent e)
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1560 protected void cut_actionPerformed(ActionEvent e)
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1564 protected void delete_actionPerformed(ActionEvent e)
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1568 protected void pasteNew_actionPerformed(ActionEvent e)
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1572 protected void pasteThis_actionPerformed(ActionEvent e)
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1576 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1580 public void createPNG(java.io.File f)
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1584 protected void font_actionPerformed(ActionEvent e)
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1588 protected void seqLimit_actionPerformed(ActionEvent e)
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1592 public void seqDBRef_actionPerformed(ActionEvent e)
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1598 public void createEPS(java.io.File f)
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1602 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1606 protected void jpred_actionPerformed(ActionEvent e)
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1610 protected void scaleAbove_actionPerformed(ActionEvent e)
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1614 protected void scaleLeft_actionPerformed(ActionEvent e)
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1618 protected void scaleRight_actionPerformed(ActionEvent e)
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1622 protected void modifyPID_actionPerformed(ActionEvent e)
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1626 protected void modifyConservation_actionPerformed(ActionEvent e)
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1632 protected void saveAs_actionPerformed(ActionEvent e)
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1636 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1641 public void vamsasStore_actionPerformed(ActionEvent e)
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1646 public void vamsasLoad_actionPerformed(ActionEvent e)
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1651 public void showTranslation_actionPerformed(ActionEvent e)
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1656 public void featureSettings_actionPerformed(ActionEvent e)
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1661 public void fetchSequence_actionPerformed(ActionEvent e)
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1666 public void smoothFont_actionPerformed(ActionEvent e)
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1671 public void annotationColour_actionPerformed(ActionEvent e)
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1677 public void associatedData_actionPerformed(ActionEvent e)
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1682 public void autoCalculate_actionPerformed(ActionEvent e)
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1687 public void showAllSeqs_actionPerformed(ActionEvent e)
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1692 public void showAllColumns_actionPerformed(ActionEvent e)
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1697 public void hideSelSequences_actionPerformed(ActionEvent e)
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1702 public void hideSelColumns_actionPerformed(ActionEvent e)
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1707 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1712 public void findPdbId_actionPerformed(ActionEvent e)
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1717 public void enterPdbId_actionPerformed(ActionEvent e)
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1722 public void pdbFile_actionPerformed(ActionEvent e)
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1727 public void invertColSel_actionPerformed(ActionEvent e)
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1732 public void tabSelectionChanged(int sel)
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1737 public void tabbedPane_mousePressed(MouseEvent e)
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1742 public void tabbedPane_focusGained(FocusEvent e)
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1747 public void save_actionPerformed(ActionEvent e)
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1752 public void reload_actionPerformed(ActionEvent e)
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1757 public void newView_actionPerformed(ActionEvent e)
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1762 public void textColour_actionPerformed(ActionEvent e)
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1767 public void idRightAlign_actionPerformed(ActionEvent e)
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1772 public void expandViews_actionPerformed(ActionEvent e)
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1777 public void gatherViews_actionPerformed(ActionEvent e)
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