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 JMenu searchMenu = new JMenu();
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92 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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93 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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94 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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95 JMenuItem deleteGroups = new JMenuItem();
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96 JMenuItem delete = new JMenuItem();
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97 JMenuItem copy = new JMenuItem();
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98 JMenuItem cut = new JMenuItem();
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99 JMenu jMenu1 = new JMenu();
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100 JMenuItem pasteNew = new JMenuItem();
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101 JMenuItem pasteThis = new JMenuItem();
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102 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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103 JMenuItem createPNG = new JMenuItem();
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104 protected JMenuItem font = new JMenuItem();
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105 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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106 JMenuItem epsFile = new JMenuItem();
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107 JMenuItem LoadtreeMenuItem = new JMenuItem();
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108 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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109 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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110 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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111 protected JMenuItem modifyPID = new JMenuItem();
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112 protected JMenuItem modifyConservation = new JMenuItem();
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113 protected JMenu sortByTreeMenu = new JMenu();
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114 protected JMenu sort = new JMenu();
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115 JMenu calculate = new JMenu();
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116 JMenu jMenu2 = new JMenu();
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117 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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118 protected ButtonGroup colours = new ButtonGroup();
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119 JMenuItem vamsasStore = new JMenuItem();
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120 protected JMenuItem showTranslation = new JMenuItem();
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121 public JMenuItem featureSettings = new JMenuItem();
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122 JMenuItem fetchSequence = new JMenuItem();
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123 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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124 JMenuItem annotationColour = new JMenuItem();
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125 JMenuItem associatedData = new JMenuItem();
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126 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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127 JMenu addSequenceMenu = new JMenu();
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128 JMenuItem addFromFile = new JMenuItem();
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129 JMenuItem addFromText = new JMenuItem();
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130 JMenuItem addFromURL = new JMenuItem();
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131 JMenuItem exportAnnotations = new JMenuItem();
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132 JMenuItem exportFeatures = new JMenuItem();
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133 protected JPanel statusPanel = new JPanel();
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134 GridLayout gridLayout1 = new GridLayout();
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135 JMenu jMenu3 = new JMenu();
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136 JMenuItem showAllSeqs = new JMenuItem();
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137 JMenuItem showAllColumns = new JMenuItem();
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138 JMenu hideMenu = new JMenu();
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139 JMenuItem hideSelSequences = new JMenuItem();
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140 JMenuItem hideSelColumns = new JMenuItem();
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141 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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142 JMenuItem invertColSel = new JMenuItem();
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143 protected JTabbedPane tabbedPane = new JTabbedPane();
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144 JMenuItem save = new JMenuItem();
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145 JMenuItem jMenuItem1 = new JMenuItem();
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146 JMenuItem reload = new JMenuItem();
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147 public GAlignFrame()
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152 setJMenuBar(alignFrameMenuBar);
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154 // dynamically fill save as menu with available formats
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155 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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157 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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159 item.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 outputText_actionPerformed(e);
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167 outputTextboxMenu.add(item);
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170 catch (Exception e)
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175 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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177 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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178 getUserColourSchemes().keys();
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180 while (userColours.hasMoreElements())
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182 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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183 nextElement().toString());
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184 radioItem.setName("USER_DEFINED");
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185 radioItem.addMouseListener(new MouseAdapter()
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187 public void mousePressed(MouseEvent evt)
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189 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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191 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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193 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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194 "Remove from default list?",
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195 "Remove user defined colour",
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196 JOptionPane.YES_NO_OPTION);
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197 if(option == JOptionPane.YES_OPTION)
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199 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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200 colourMenu.remove(radioItem);
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203 radioItem.addActionListener(new ActionListener()
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205 public void actionPerformed(ActionEvent evt)
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207 userDefinedColour_actionPerformed(evt);
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213 radioItem.addActionListener(new ActionListener()
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215 public void actionPerformed(ActionEvent evt)
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217 userDefinedColour_actionPerformed(evt);
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220 colourMenu.insert(radioItem, 15);
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221 colours.add(radioItem);
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224 colours.add(noColourmenuItem);
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225 colours.add(clustalColour);
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226 colours.add(zappoColour);
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227 colours.add(taylorColour);
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228 colours.add(hydrophobicityColour);
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229 colours.add(helixColour);
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230 colours.add(strandColour);
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231 colours.add(turnColour);
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232 colours.add(buriedColour);
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233 colours.add(userDefinedColour);
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234 colours.add(PIDColour);
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235 colours.add(BLOSUM62Colour);
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236 colours.add(nucleotideColour);
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238 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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243 public void setColourSelected(String defaultColour)
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246 if (defaultColour != null)
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248 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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252 case ColourSchemeProperty.NONE:
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253 noColourmenuItem.setSelected(true);
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255 case ColourSchemeProperty.CLUSTAL:
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256 clustalColour.setSelected(true);
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260 case ColourSchemeProperty.BLOSUM:
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261 BLOSUM62Colour.setSelected(true);
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265 case ColourSchemeProperty.PID:
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266 PIDColour.setSelected(true);
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270 case ColourSchemeProperty.ZAPPO:
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271 zappoColour.setSelected(true);
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275 case ColourSchemeProperty.TAYLOR:
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276 taylorColour.setSelected(true);
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279 case ColourSchemeProperty.HYDROPHOBIC:
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280 hydrophobicityColour.setSelected(true);
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284 case ColourSchemeProperty.HELIX:
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285 helixColour.setSelected(true);
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289 case ColourSchemeProperty.STRAND:
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290 strandColour.setSelected(true);
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294 case ColourSchemeProperty.TURN:
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295 turnColour.setSelected(true);
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299 case ColourSchemeProperty.BURIED:
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300 buriedColour.setSelected(true);
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304 case ColourSchemeProperty.NUCLEOTIDE:
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305 nucleotideColour.setSelected(true);
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309 case ColourSchemeProperty.USER_DEFINED:
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310 userDefinedColour.setSelected(true);
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318 private void jbInit()
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321 fileMenu.setText("File");
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322 saveAs.setText("Save As ...");
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323 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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324 KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));
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325 saveAs.addActionListener(new ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 saveAs_actionPerformed(e);
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332 closeMenuItem.setMnemonic('C');
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333 closeMenuItem.setText("Close");
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334 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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335 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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336 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 closeMenuItem_actionPerformed(e);
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343 editMenu.setText("Edit");
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344 viewMenu.setText("View");
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345 colourMenu.setText("Colour");
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346 calculateMenu.setText("Calculate");
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347 webService.setText("Web Service");
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348 selectAllSequenceMenuItem.setText("Select all");
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349 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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350 java.awt.event.KeyEvent.VK_A,
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351 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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352 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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355 public void actionPerformed(ActionEvent e)
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357 selectAllSequenceMenuItem_actionPerformed(e);
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360 deselectAllSequenceMenuItem.setText("Deselect All");
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361 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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363 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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364 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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367 public void actionPerformed(ActionEvent e)
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369 deselectAllSequenceMenuItem_actionPerformed(e);
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372 invertSequenceMenuItem.setText("Invert Sequence Selection");
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373 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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374 java.awt.event.KeyEvent.VK_I,
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375 java.awt.event.KeyEvent.SHIFT_MASK, false));
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376 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 invertSequenceMenuItem_actionPerformed(e);
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383 remove2LeftMenuItem.setText("Remove Left");
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384 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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385 awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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386 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 remove2LeftMenuItem_actionPerformed(e);
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393 remove2RightMenuItem.setText("Remove Right");
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394 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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395 awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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396 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 remove2RightMenuItem_actionPerformed(e);
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403 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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404 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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405 getKeyStroke(java.awt.event.
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406 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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407 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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410 public void actionPerformed(ActionEvent e)
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412 removeGappedColumnMenuItem_actionPerformed(e);
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415 removeAllGapsMenuItem.setText("Remove All Gaps");
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416 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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417 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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418 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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420 public void actionPerformed(ActionEvent e)
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422 removeAllGapsMenuItem_actionPerformed(e);
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425 viewBoxesMenuItem.setText("Boxes");
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426 viewBoxesMenuItem.setState(true);
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427 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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429 public void actionPerformed(ActionEvent e)
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431 viewBoxesMenuItem_actionPerformed(e);
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434 viewTextMenuItem.setText("Text");
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435 viewTextMenuItem.setState(true);
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436 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 viewTextMenuItem_actionPerformed(e);
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443 sortPairwiseMenuItem.setText("by Pairwise Identity");
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444 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 sortPairwiseMenuItem_actionPerformed(e);
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451 sortIDMenuItem.setText("by ID");
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452 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 sortIDMenuItem_actionPerformed(e);
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459 sortGroupMenuItem.setText("by Group");
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460 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 sortGroupMenuItem_actionPerformed(e);
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467 removeRedundancyMenuItem.setText("Remove Redundancy...");
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468 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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469 java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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470 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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473 public void actionPerformed(ActionEvent e)
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475 removeRedundancyMenuItem_actionPerformed(e);
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478 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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479 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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482 public void actionPerformed(ActionEvent e)
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484 pairwiseAlignmentMenuItem_actionPerformed(e);
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487 PCAMenuItem.setText("Principal Component Analysis");
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488 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 PCAMenuItem_actionPerformed(e);
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495 averageDistanceTreeMenuItem.setText(
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496 "Average Distance Using % Identity");
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497 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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500 public void actionPerformed(ActionEvent e)
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502 averageDistanceTreeMenuItem_actionPerformed(e);
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505 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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506 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 neighbourTreeMenuItem_actionPerformed(e);
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513 this.getContentPane().setLayout(borderLayout1);
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514 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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515 statusBar.setBackground(Color.white);
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516 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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517 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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518 statusBar.setText("Status bar");
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519 outputTextboxMenu.setMnemonic('T');
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520 outputTextboxMenu.setText("Output to Textbox");
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521 clustalColour.setText("Clustalx");
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523 clustalColour.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 clustalColour_actionPerformed(e);
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530 zappoColour.setText("Zappo");
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531 zappoColour.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 zappoColour_actionPerformed(e);
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538 taylorColour.setText("Taylor");
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539 taylorColour.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 taylorColour_actionPerformed(e);
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546 hydrophobicityColour.setText("Hydrophobicity");
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547 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 hydrophobicityColour_actionPerformed(e);
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554 helixColour.setText("Helix Propensity");
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555 helixColour.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 helixColour_actionPerformed(e);
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562 strandColour.setText("Strand Propensity");
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563 strandColour.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 strandColour_actionPerformed(e);
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570 turnColour.setText("Turn Propensity");
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571 turnColour.addActionListener(new java.awt.event.ActionListener()
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573 public void actionPerformed(ActionEvent e)
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575 turnColour_actionPerformed(e);
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578 buriedColour.setText("Buried Index");
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579 buriedColour.addActionListener(new java.awt.event.ActionListener()
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581 public void actionPerformed(ActionEvent e)
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583 buriedColour_actionPerformed(e);
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586 userDefinedColour.setText("User Defined...");
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587 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 userDefinedColour_actionPerformed(e);
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594 PIDColour.setText("Percentage Identity");
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595 PIDColour.addActionListener(new java.awt.event.ActionListener()
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597 public void actionPerformed(ActionEvent e)
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599 PIDColour_actionPerformed(e);
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602 BLOSUM62Colour.setText("BLOSUM62 Score");
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603 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 BLOSUM62Colour_actionPerformed(e);
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610 avDistanceTreeBlosumMenuItem.setText(
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611 "Average Distance Using BLOSUM62");
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612 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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615 public void actionPerformed(ActionEvent e)
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617 avTreeBlosumMenuItem_actionPerformed(e);
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620 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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621 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 njTreeBlosumMenuItem_actionPerformed(e);
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628 annotationPanelMenuItem.setActionCommand("");
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629 annotationPanelMenuItem.setText("Show Annotations");
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630 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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631 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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633 public void actionPerformed(ActionEvent e)
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635 annotationPanelMenuItem_actionPerformed(e);
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638 colourTextMenuItem.setText("Colour Text");
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639 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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641 public void actionPerformed(ActionEvent e)
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643 colourTextMenuItem_actionPerformed(e);
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646 htmlMenuItem.setText("HTML");
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647 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 htmlMenuItem_actionPerformed(e);
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654 overviewMenuItem.setText("Overview Window");
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655 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 overviewMenuItem_actionPerformed(e);
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662 undoMenuItem.setEnabled(false);
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663 undoMenuItem.setMnemonic('Z');
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664 undoMenuItem.setText("Undo");
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665 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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666 java.awt.event.KeyEvent.VK_Z,
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667 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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668 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 undoMenuItem_actionPerformed(e);
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675 redoMenuItem.setEnabled(false);
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676 redoMenuItem.setMnemonic('0');
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677 redoMenuItem.setText("Redo");
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678 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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679 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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680 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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682 public void actionPerformed(ActionEvent e)
\r
684 redoMenuItem_actionPerformed(e);
\r
687 conservationMenuItem.setText("By Conservation");
\r
688 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
690 public void actionPerformed(ActionEvent e)
\r
692 conservationMenuItem_actionPerformed(e);
\r
695 noColourmenuItem.setText("None");
\r
696 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
698 public void actionPerformed(ActionEvent e)
\r
700 noColourmenuItem_actionPerformed(e);
\r
703 wrapMenuItem.setText("Wrap");
\r
704 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
706 public void actionPerformed(ActionEvent e)
\r
708 wrapMenuItem_actionPerformed(e);
\r
711 printMenuItem.setText("Print");
\r
712 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
713 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
714 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
716 public void actionPerformed(ActionEvent e)
\r
718 printMenuItem_actionPerformed(e);
\r
721 renderGapsMenuItem.setText("Show Gaps");
\r
722 renderGapsMenuItem.setState(true);
\r
723 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
725 public void actionPerformed(ActionEvent e)
\r
727 renderGapsMenuItem_actionPerformed(e);
\r
730 findMenuItem.setText("Find...");
\r
731 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
732 java.awt.event.KeyEvent.VK_F,
\r
733 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
734 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
736 public void actionPerformed(ActionEvent e)
\r
738 findMenuItem_actionPerformed(e);
\r
741 searchMenu.setText("Search");
\r
743 abovePIDThreshold.setText("Above Identity Threshold");
\r
744 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
746 public void actionPerformed(ActionEvent e)
\r
748 abovePIDThreshold_actionPerformed(e);
\r
751 showSeqFeatures.setText("Show Sequence Features");
\r
752 showSeqFeatures.addActionListener(new ActionListener()
\r
754 public void actionPerformed(ActionEvent actionEvent)
\r
756 showSeqFeatures_actionPerformed(actionEvent);
\r
759 nucleotideColour.setText("Nucleotide");
\r
760 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
762 public void actionPerformed(ActionEvent e)
\r
764 nucleotideColour_actionPerformed(e);
\r
767 deleteGroups.setText("Undefine groups");
\r
768 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
769 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
770 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
772 public void actionPerformed(ActionEvent e)
\r
774 deleteGroups_actionPerformed(e);
\r
777 copy.setText("Copy");
\r
778 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
779 java.awt.event.KeyEvent.VK_C,
\r
780 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
781 copy.setMnemonic(KeyEvent.VK_C);
\r
783 copy.addActionListener(new java.awt.event.ActionListener()
\r
785 public void actionPerformed(ActionEvent e)
\r
787 copy_actionPerformed(e);
\r
790 cut.setText("Cut");
\r
791 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
792 java.awt.event.KeyEvent.VK_X,
\r
793 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
794 cut.setMnemonic(KeyEvent.VK_X);
\r
795 cut.addActionListener(new java.awt.event.ActionListener()
\r
797 public void actionPerformed(ActionEvent e)
\r
799 cut_actionPerformed(e);
\r
802 delete.setText("Delete");
\r
803 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
804 KeyEvent.VK_BACK_SPACE, 0, false));
\r
805 delete.addActionListener(new java.awt.event.ActionListener()
\r
807 public void actionPerformed(ActionEvent e)
\r
809 delete_actionPerformed(e);
\r
812 jMenu1.setMnemonic('V');
\r
813 jMenu1.setText("Paste");
\r
814 pasteNew.setText("To New Alignment");
\r
815 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
816 java.awt.event.KeyEvent.VK_V,
\r
817 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
818 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
820 public void actionPerformed(ActionEvent e)
\r
822 pasteNew_actionPerformed(e);
\r
825 pasteThis.setText("Add To This Alignment");
\r
826 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
828 public void actionPerformed(ActionEvent e)
\r
830 pasteThis_actionPerformed(e);
\r
833 applyToAllGroups.setText("Apply Colour To All Groups");
\r
834 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
836 public void actionPerformed(ActionEvent e)
\r
838 applyToAllGroups_actionPerformed(e);
\r
841 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
843 public void actionPerformed(ActionEvent e)
\r
848 createPNG.setActionCommand("Save As PNG Image");
\r
849 createPNG.setText("PNG");
\r
850 font.setText("Font...");
\r
851 font.addActionListener(new java.awt.event.ActionListener()
\r
853 public void actionPerformed(ActionEvent e)
\r
855 font_actionPerformed(e);
\r
859 seqLimits.setText("Show Sequence Limits");
\r
860 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
861 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
863 public void actionPerformed(ActionEvent e)
\r
865 seqLimit_actionPerformed(e);
\r
868 epsFile.setText("EPS");
\r
869 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
871 public void actionPerformed(ActionEvent e)
\r
876 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
877 LoadtreeMenuItem.setText("Load Associated Tree");
\r
878 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
880 public void actionPerformed(ActionEvent e)
\r
882 LoadtreeMenuItem_actionPerformed(e);
\r
885 scaleAbove.setVisible(false);
\r
886 scaleAbove.setText("Scale Above");
\r
887 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
889 public void actionPerformed(ActionEvent e)
\r
891 scaleAbove_actionPerformed(e);
\r
894 scaleLeft.setVisible(false);
\r
895 scaleLeft.setSelected(true);
\r
896 scaleLeft.setText("Scale Left");
\r
897 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
899 public void actionPerformed(ActionEvent e)
\r
901 scaleLeft_actionPerformed(e);
\r
904 scaleRight.setVisible(false);
\r
905 scaleRight.setSelected(true);
\r
906 scaleRight.setText("Scale Right");
\r
907 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
909 public void actionPerformed(ActionEvent e)
\r
911 scaleRight_actionPerformed(e);
\r
914 modifyPID.setText("Modify Identity Threshold...");
\r
915 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
917 public void actionPerformed(ActionEvent e)
\r
919 modifyPID_actionPerformed(e);
\r
922 modifyConservation.setText("Modify Conservation Threshold...");
\r
923 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
925 public void actionPerformed(ActionEvent e)
\r
927 modifyConservation_actionPerformed(e);
\r
930 sortByTreeMenu.setText("By Tree Order");
\r
931 sort.setText("Sort");
\r
932 calculate.setText("Calculate Tree");
\r
934 jMenu2.setText("Export Image");
\r
935 padGapsMenuitem.setText("Pad Gaps");
\r
936 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
937 padGapsMenuitem.addActionListener(new ActionListener()
\r
939 public void actionPerformed(ActionEvent e)
\r
941 padGapsMenuitem_actionPerformed(e);
\r
944 vamsasStore.setVisible(false);
\r
945 vamsasStore.setText("VAMSAS store");
\r
946 vamsasStore.addActionListener(new ActionListener()
\r
948 public void actionPerformed(ActionEvent e)
\r
950 vamsasStore_actionPerformed(e);
\r
953 showTranslation.setText("Translate cDNA");
\r
954 showTranslation.addActionListener(new ActionListener()
\r
956 public void actionPerformed(ActionEvent e)
\r
958 showTranslation_actionPerformed(e);
\r
963 featureSettings.setText("Feature Settings...");
\r
964 featureSettings.addActionListener(new ActionListener()
\r
966 public void actionPerformed(ActionEvent e)
\r
968 featureSettings_actionPerformed(e);
\r
971 fetchSequence.setText("Fetch Sequence(s)...");
\r
972 fetchSequence.addActionListener(new ActionListener()
\r
974 public void actionPerformed(ActionEvent e)
\r
976 fetchSequence_actionPerformed(e);
\r
979 smoothFont.setText("Smooth Fonts");
\r
980 smoothFont.addActionListener(new ActionListener()
\r
982 public void actionPerformed(ActionEvent e)
\r
984 smoothFont_actionPerformed(e);
\r
988 annotationColour.setText("By Annotation...");
\r
989 annotationColour.addActionListener(new ActionListener()
\r
991 public void actionPerformed(ActionEvent e)
\r
993 annotationColour_actionPerformed(e);
\r
996 associatedData.setText("Load Features / Annotations");
\r
997 associatedData.addActionListener(new ActionListener()
\r
999 public void actionPerformed(ActionEvent e)
\r
1001 associatedData_actionPerformed(e);
\r
1004 autoCalculate.setText("Autocalculate Consensus");
\r
1005 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1006 autoCalculate.addActionListener(new ActionListener()
\r
1008 public void actionPerformed(ActionEvent e)
\r
1010 autoCalculate_actionPerformed(e);
\r
1013 addSequenceMenu.setText("Add Sequences");
\r
1014 addFromFile.setText("From File");
\r
1015 addFromFile.addActionListener(new ActionListener()
\r
1017 public void actionPerformed(ActionEvent e)
\r
1019 addFromFile_actionPerformed(e);
\r
1022 addFromText.setText("From Textbox");
\r
1023 addFromText.addActionListener(new ActionListener()
\r
1025 public void actionPerformed(ActionEvent e)
\r
1027 addFromText_actionPerformed(e);
\r
1030 addFromURL.setText("From URL");
\r
1031 addFromURL.addActionListener(new ActionListener()
\r
1033 public void actionPerformed(ActionEvent e)
\r
1035 addFromURL_actionPerformed(e);
\r
1038 exportFeatures.setText("Export Features...");
\r
1039 exportFeatures.addActionListener(new ActionListener()
\r
1041 public void actionPerformed(ActionEvent e)
\r
1043 exportFeatures_actionPerformed(e);
\r
1046 exportAnnotations.setText("Export Annotations...");
\r
1047 exportAnnotations.addActionListener(new ActionListener()
\r
1049 public void actionPerformed(ActionEvent e)
\r
1051 exportAnnotations_actionPerformed(e);
\r
1054 statusPanel.setLayout(gridLayout1);
\r
1055 jMenu3.setText("Show");
\r
1056 showAllSeqs.setText("All Sequences");
\r
1057 showAllSeqs.addActionListener(new ActionListener()
\r
1059 public void actionPerformed(ActionEvent e)
\r
1061 showAllSeqs_actionPerformed(e);
\r
1064 showAllColumns.setText("All Columns");
\r
1065 showAllColumns.addActionListener(new ActionListener()
\r
1067 public void actionPerformed(ActionEvent e)
\r
1069 showAllColumns_actionPerformed(e);
\r
1072 hideMenu.setText("Hide");
\r
1073 hideSelSequences.setText("Selected Sequences");
\r
1074 hideSelSequences.addActionListener(new ActionListener()
\r
1076 public void actionPerformed(ActionEvent e)
\r
1078 hideSelSequences_actionPerformed(e);
\r
1081 hideSelColumns.setText("Selected Columns");
\r
1082 hideSelColumns.addActionListener(new ActionListener()
\r
1084 public void actionPerformed(ActionEvent e)
\r
1086 hideSelColumns_actionPerformed(e);
\r
1089 hiddenMarkers.setText("Hidden Markers");
\r
1090 hiddenMarkers.addActionListener(new ActionListener()
\r
1092 public void actionPerformed(ActionEvent e)
\r
1094 hiddenMarkers_actionPerformed(e);
\r
1097 invertColSel.setText("Invert Column Selection");
\r
1098 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1099 event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1100 invertColSel.addActionListener(new ActionListener()
\r
1102 public void actionPerformed(ActionEvent e)
\r
1104 invertColSel_actionPerformed(e);
\r
1107 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1109 public void stateChanged(ChangeEvent evt)
\r
1111 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1112 int sel = pane.getSelectedIndex();
\r
1113 tabSelectionChanged(sel);
\r
1116 tabbedPane.addMouseListener(new MouseAdapter()
\r
1118 public void mousePressed(MouseEvent e)
\r
1120 tabbedPane_mousePressed(e);
\r
1123 tabbedPane.addFocusListener(new FocusAdapter()
\r
1125 public void focusGained(FocusEvent e)
\r
1127 tabbedPane_focusGained(e);
\r
1130 save.setText("Save");
\r
1131 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1132 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1133 save.addActionListener(new ActionListener()
\r
1135 public void actionPerformed(ActionEvent e)
\r
1137 save_actionPerformed(e);
\r
1140 reload.setMnemonic('R');
\r
1141 reload.setText("Reload");
\r
1142 // reload.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1143 // KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1144 reload.addActionListener(new ActionListener()
\r
1146 public void actionPerformed(ActionEvent e)
\r
1148 reload_actionPerformed(e);
\r
1152 alignFrameMenuBar.add(fileMenu);
\r
1153 alignFrameMenuBar.add(editMenu);
\r
1154 alignFrameMenuBar.add(searchMenu);
\r
1155 alignFrameMenuBar.add(viewMenu);
\r
1156 alignFrameMenuBar.add(colourMenu);
\r
1157 alignFrameMenuBar.add(calculateMenu);
\r
1158 alignFrameMenuBar.add(webService);
\r
1159 fileMenu.add(fetchSequence);
\r
1160 fileMenu.add(addSequenceMenu);
\r
1161 fileMenu.add(reload);
\r
1162 fileMenu.addSeparator();
\r
1163 fileMenu.add(vamsasStore);
\r
1164 fileMenu.add(save);
\r
1165 fileMenu.add(saveAs);
\r
1166 fileMenu.add(outputTextboxMenu);
\r
1167 fileMenu.add(printMenuItem);
\r
1168 fileMenu.addSeparator();
\r
1169 fileMenu.add(jMenu2);
\r
1170 fileMenu.add(exportFeatures);
\r
1171 fileMenu.add(exportAnnotations);
\r
1172 fileMenu.add(LoadtreeMenuItem);
\r
1173 fileMenu.add(associatedData);
\r
1174 fileMenu.addSeparator();
\r
1175 fileMenu.add(closeMenuItem);
\r
1176 editMenu.add(undoMenuItem);
\r
1177 editMenu.add(redoMenuItem);
\r
1178 editMenu.add(cut);
\r
1179 editMenu.add(copy);
\r
1180 editMenu.add(jMenu1);
\r
1181 editMenu.add(delete);
\r
1182 editMenu.addSeparator();
\r
1183 editMenu.add(selectAllSequenceMenuItem);
\r
1184 editMenu.add(deselectAllSequenceMenuItem);
\r
1185 editMenu.add(invertSequenceMenuItem);
\r
1186 editMenu.add(invertColSel);
\r
1187 editMenu.add(deleteGroups);
\r
1188 editMenu.addSeparator();
\r
1189 editMenu.add(remove2LeftMenuItem);
\r
1190 editMenu.add(remove2RightMenuItem);
\r
1191 editMenu.add(removeGappedColumnMenuItem);
\r
1192 editMenu.add(removeAllGapsMenuItem);
\r
1193 editMenu.add(removeRedundancyMenuItem);
\r
1194 editMenu.addSeparator();
\r
1195 editMenu.add(padGapsMenuitem);
\r
1196 searchMenu.add(findMenuItem);
\r
1197 viewMenu.add(font);
\r
1198 viewMenu.add(smoothFont);
\r
1199 viewMenu.addSeparator();
\r
1200 viewMenu.add(jMenu3);
\r
1201 viewMenu.add(hideMenu);
\r
1202 viewMenu.add(hiddenMarkers);
\r
1203 viewMenu.addSeparator();
\r
1204 viewMenu.add(wrapMenuItem);
\r
1205 viewMenu.add(seqLimits);
\r
1206 viewMenu.add(scaleAbove);
\r
1207 viewMenu.add(scaleLeft);
\r
1208 viewMenu.add(scaleRight);
\r
1209 viewMenu.add(viewBoxesMenuItem);
\r
1210 viewMenu.add(viewTextMenuItem);
\r
1211 viewMenu.add(colourTextMenuItem);
\r
1212 viewMenu.add(renderGapsMenuItem);
\r
1213 viewMenu.add(annotationPanelMenuItem);
\r
1214 viewMenu.addSeparator();
\r
1215 viewMenu.add(showSeqFeatures);
\r
1216 viewMenu.add(featureSettings);
\r
1217 viewMenu.addSeparator();
\r
1218 viewMenu.add(overviewMenuItem);
\r
1219 colourMenu.add(applyToAllGroups);
\r
1220 colourMenu.addSeparator();
\r
1221 colourMenu.add(noColourmenuItem);
\r
1222 colourMenu.add(clustalColour);
\r
1223 colourMenu.add(BLOSUM62Colour);
\r
1224 colourMenu.add(PIDColour);
\r
1225 colourMenu.add(zappoColour);
\r
1226 colourMenu.add(taylorColour);
\r
1227 colourMenu.add(hydrophobicityColour);
\r
1228 colourMenu.add(helixColour);
\r
1229 colourMenu.add(strandColour);
\r
1230 colourMenu.add(turnColour);
\r
1231 colourMenu.add(buriedColour);
\r
1232 colourMenu.add(nucleotideColour);
\r
1233 colourMenu.add(userDefinedColour);
\r
1234 colourMenu.addSeparator();
\r
1235 colourMenu.add(conservationMenuItem);
\r
1236 colourMenu.add(modifyConservation);
\r
1237 colourMenu.add(abovePIDThreshold);
\r
1238 colourMenu.add(modifyPID);
\r
1239 colourMenu.add(annotationColour);
\r
1240 calculateMenu.add(sort);
\r
1241 calculateMenu.add(calculate);
\r
1242 calculateMenu.addSeparator();
\r
1243 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1244 calculateMenu.add(PCAMenuItem);
\r
1245 calculateMenu.addSeparator();
\r
1246 calculateMenu.add(showTranslation);
\r
1247 calculateMenu.add(autoCalculate);
\r
1248 webServiceNoServices=new JMenuItem("<No Services>");
\r
1249 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1250 jMenu1.add(pasteThis);
\r
1251 sort.add(sortIDMenuItem);
\r
1252 sort.add(sortGroupMenuItem);
\r
1253 sort.add(sortPairwiseMenuItem);
\r
1254 calculate.add(averageDistanceTreeMenuItem);
\r
1255 calculate.add(neighbourTreeMenuItem);
\r
1256 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1257 calculate.add(njTreeBlosumMenuItem);
\r
1258 jMenu2.add(htmlMenuItem);
\r
1259 jMenu2.add(epsFile);
\r
1260 jMenu2.add(createPNG);
\r
1261 addSequenceMenu.add(addFromFile);
\r
1262 addSequenceMenu.add(addFromText);
\r
1263 addSequenceMenu.add(addFromURL);
\r
1264 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1265 statusPanel.add(statusBar, null);
\r
1266 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1267 jMenu3.add(showAllColumns);
\r
1268 jMenu3.add(showAllSeqs);
\r
1269 hideMenu.add(hideSelColumns);
\r
1270 hideMenu.add(hideSelSequences);
\r
1273 protected void outputText_actionPerformed(ActionEvent e)
\r
1277 public void addFromFile_actionPerformed(ActionEvent e)
\r
1282 public void addFromText_actionPerformed(ActionEvent e)
\r
1287 public void addFromURL_actionPerformed(ActionEvent e)
\r
1292 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1297 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1302 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1306 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1310 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1314 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1318 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1322 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1326 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1330 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1334 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1338 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1342 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1346 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1350 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1354 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1358 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1362 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1366 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1370 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1374 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1378 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1382 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1386 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1390 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1394 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1398 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1402 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1406 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1410 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1414 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1418 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1422 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1426 protected void helixColour_actionPerformed(ActionEvent e)
\r
1430 protected void strandColour_actionPerformed(ActionEvent e)
\r
1434 protected void turnColour_actionPerformed(ActionEvent e)
\r
1438 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1442 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1446 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1450 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1454 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1458 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1462 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1466 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1470 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1474 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1478 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1482 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1486 protected void deleteGroups_actionPerformed(ActionEvent e)
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1490 protected void copy_actionPerformed(ActionEvent e)
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1494 protected void cut_actionPerformed(ActionEvent e)
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1498 protected void delete_actionPerformed(ActionEvent e)
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1502 protected void pasteNew_actionPerformed(ActionEvent e)
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1506 protected void pasteThis_actionPerformed(ActionEvent e)
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1510 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1514 public void createPNG(java.io.File f)
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1518 protected void font_actionPerformed(ActionEvent e)
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1522 protected void seqLimit_actionPerformed(ActionEvent e)
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1526 public void seqDBRef_actionPerformed(ActionEvent e)
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1532 public void createEPS(java.io.File f)
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1536 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1540 protected void jpred_actionPerformed(ActionEvent e)
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1544 protected void scaleAbove_actionPerformed(ActionEvent e)
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1548 protected void scaleLeft_actionPerformed(ActionEvent e)
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1552 protected void scaleRight_actionPerformed(ActionEvent e)
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1556 protected void modifyPID_actionPerformed(ActionEvent e)
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1560 protected void modifyConservation_actionPerformed(ActionEvent e)
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1566 protected void saveAs_actionPerformed(ActionEvent e)
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1570 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1575 public void vamsasStore_actionPerformed(ActionEvent e)
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1580 public void vamsasLoad_actionPerformed(ActionEvent e)
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1585 public void showTranslation_actionPerformed(ActionEvent e)
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1590 public void featureSettings_actionPerformed(ActionEvent e)
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1595 public void fetchSequence_actionPerformed(ActionEvent e)
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1600 public void smoothFont_actionPerformed(ActionEvent e)
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1605 public void annotationColour_actionPerformed(ActionEvent e)
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1611 public void associatedData_actionPerformed(ActionEvent e)
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1616 public void autoCalculate_actionPerformed(ActionEvent e)
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1621 public void showAllSeqs_actionPerformed(ActionEvent e)
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1626 public void showAllColumns_actionPerformed(ActionEvent e)
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1631 public void hideSelSequences_actionPerformed(ActionEvent e)
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1636 public void hideSelColumns_actionPerformed(ActionEvent e)
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1641 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1646 public void findPdbId_actionPerformed(ActionEvent e)
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1651 public void enterPdbId_actionPerformed(ActionEvent e)
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1656 public void pdbFile_actionPerformed(ActionEvent e)
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1661 public void invertColSel_actionPerformed(ActionEvent e)
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1666 public void tabSelectionChanged(int sel)
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1671 public void tabbedPane_mousePressed(MouseEvent e)
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1676 public void tabbedPane_focusGained(FocusEvent e)
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1681 public void save_actionPerformed(ActionEvent e)
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1686 public void reload_actionPerformed(ActionEvent e)
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