2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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28 public class GAlignFrame
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29 extends JInternalFrame
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31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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32 protected JMenu fileMenu = new JMenu();
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33 protected JMenuItem closeMenuItem = new JMenuItem();
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34 protected JMenu editMenu = new JMenu();
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35 protected JMenu viewMenu = new JMenu();
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36 protected JMenu colourMenu = new JMenu();
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37 protected JMenu calculateMenu = new JMenu();
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38 protected JMenu webService = new JMenu();
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39 protected JMenuItem webServiceNoServices;
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40 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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41 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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42 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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43 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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44 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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45 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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46 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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47 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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48 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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49 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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50 protected JMenuItem sortIDMenuItem = new JMenuItem();
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51 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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52 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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53 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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54 protected JMenuItem PCAMenuItem = new JMenuItem();
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55 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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56 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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57 BorderLayout borderLayout1 = new BorderLayout();
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58 public JLabel statusBar = new JLabel();
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59 protected JMenuItem saveAs = new JMenuItem();
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60 protected JMenu outputTextboxMenu = new JMenu();
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61 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem hydrophobicityColour = new
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65 JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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73 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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74 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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75 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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76 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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77 JMenuItem htmlMenuItem = new JMenuItem();
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78 JMenuItem overviewMenuItem = new JMenuItem();
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79 protected JMenuItem undoMenuItem = new JMenuItem();
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80 protected JMenuItem redoMenuItem = new JMenuItem();
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81 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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82 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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83 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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84 JMenuItem printMenuItem = new JMenuItem();
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85 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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86 JMenuItem findMenuItem = new JMenuItem();
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87 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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88 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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89 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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90 JMenuItem deleteGroups = new JMenuItem();
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91 JMenuItem delete = new JMenuItem();
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92 JMenuItem copy = new JMenuItem();
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93 JMenuItem cut = new JMenuItem();
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94 JMenu pasteMenu = new JMenu();
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95 JMenuItem pasteNew = new JMenuItem();
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96 JMenuItem pasteThis = new JMenuItem();
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97 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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98 JMenuItem createPNG = new JMenuItem();
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99 protected JMenuItem font = new JMenuItem();
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100 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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101 JMenuItem epsFile = new JMenuItem();
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102 JMenuItem LoadtreeMenuItem = new JMenuItem();
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103 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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104 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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105 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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106 protected JMenuItem modifyPID = new JMenuItem();
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107 protected JMenuItem modifyConservation = new JMenuItem();
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108 protected JMenu sortByTreeMenu = new JMenu();
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109 protected JMenu sort = new JMenu();
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110 JMenu calculate = new JMenu();
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111 JMenu jMenu2 = new JMenu();
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112 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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113 protected ButtonGroup colours = new ButtonGroup();
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114 JMenuItem vamsasStore = new JMenuItem();
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115 protected JMenuItem showTranslation = new JMenuItem();
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116 public JMenuItem featureSettings = new JMenuItem();
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117 JMenuItem fetchSequence = new JMenuItem();
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118 JMenuItem annotationColour = new JMenuItem();
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119 JMenuItem associatedData = new JMenuItem();
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120 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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121 JMenu addSequenceMenu = new JMenu();
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122 JMenuItem addFromFile = new JMenuItem();
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123 JMenuItem addFromText = new JMenuItem();
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124 JMenuItem addFromURL = new JMenuItem();
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125 JMenuItem exportAnnotations = new JMenuItem();
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126 JMenuItem exportFeatures = new JMenuItem();
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127 protected JPanel statusPanel = new JPanel();
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128 GridLayout gridLayout1 = new GridLayout();
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129 JMenu jMenu3 = new JMenu();
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130 JMenuItem showAllSeqs = new JMenuItem();
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131 JMenuItem showAllColumns = new JMenuItem();
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132 JMenu hideMenu = new JMenu();
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133 JMenuItem hideSelSequences = new JMenuItem();
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134 JMenuItem hideSelColumns = new JMenuItem();
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135 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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136 JMenuItem invertColSel = new JMenuItem();
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137 protected JTabbedPane tabbedPane = new JTabbedPane();
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138 JMenuItem save = new JMenuItem();
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139 protected JMenuItem reload = new JMenuItem();
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140 JMenuItem newView = new JMenuItem();
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141 JMenuItem textColour = new JMenuItem();
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142 JMenu formatMenu = new JMenu();
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143 JMenu selectMenu = new JMenu();
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144 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
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145 protected JMenuItem gatherViews = new JMenuItem();
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146 protected JMenuItem expandViews = new JMenuItem();
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147 JMenuItem pageSetup = new JMenuItem();
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148 JMenuItem alignmentProperties = new JMenuItem();
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149 public GAlignFrame()
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154 setJMenuBar(alignFrameMenuBar);
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156 // dynamically fill save as menu with available formats
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157 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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159 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
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160 WRITEABLE_FORMATS[i]);
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162 item.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 outputText_actionPerformed(e);
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170 outputTextboxMenu.add(item);
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173 catch (Exception e)
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177 if (!System.getProperty("os.name").startsWith("Mac"))
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179 closeMenuItem.setMnemonic('C');
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180 outputTextboxMenu.setMnemonic('T');
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181 undoMenuItem.setMnemonic('Z');
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182 redoMenuItem.setMnemonic('0');
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183 copy.setMnemonic('C');
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184 cut.setMnemonic('U');
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185 pasteMenu.setMnemonic('P');
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186 reload.setMnemonic('R');
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189 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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191 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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192 getUserColourSchemes().keys();
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194 while (userColours.hasMoreElements())
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196 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
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198 nextElement().toString());
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199 radioItem.setName("USER_DEFINED");
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200 radioItem.addMouseListener(new MouseAdapter()
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202 public void mousePressed(MouseEvent evt)
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204 if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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206 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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208 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
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210 "Remove from default list?",
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211 "Remove user defined colour",
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212 JOptionPane.YES_NO_OPTION);
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213 if (option == JOptionPane.YES_OPTION)
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215 jalview.gui.UserDefinedColours.removeColourFromDefaults(
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216 radioItem.getText());
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217 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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232 radioItem.addActionListener(new ActionListener()
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234 public void actionPerformed(ActionEvent evt)
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236 userDefinedColour_actionPerformed(evt);
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239 colourMenu.insert(radioItem, 15);
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240 colours.add(radioItem);
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243 colours.add(noColourmenuItem);
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244 colours.add(clustalColour);
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245 colours.add(zappoColour);
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246 colours.add(taylorColour);
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247 colours.add(hydrophobicityColour);
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248 colours.add(helixColour);
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249 colours.add(strandColour);
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250 colours.add(turnColour);
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251 colours.add(buriedColour);
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252 colours.add(userDefinedColour);
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253 colours.add(PIDColour);
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254 colours.add(BLOSUM62Colour);
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255 colours.add(nucleotideColour);
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257 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() |
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344 java.awt.event.KeyEvent.SHIFT_MASK, false));
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345 saveAs.addActionListener(new ActionListener()
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347 public void actionPerformed(ActionEvent e)
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349 saveAs_actionPerformed(e);
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352 closeMenuItem.setText("Close");
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353 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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354 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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355 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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357 public void actionPerformed(ActionEvent e)
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359 closeMenuItem_actionPerformed(false);
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362 editMenu.setText("Edit");
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363 viewMenu.setText("View");
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364 colourMenu.setText("Colour");
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365 calculateMenu.setText("Calculate");
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366 webService.setText("Web Service");
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367 selectAllSequenceMenuItem.setText("Select All");
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368 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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369 java.awt.event.KeyEvent.VK_A,
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370 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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371 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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374 public void actionPerformed(ActionEvent e)
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376 selectAllSequenceMenuItem_actionPerformed(e);
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379 deselectAllSequenceMenuItem.setText("Deselect All");
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380 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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382 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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383 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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386 public void actionPerformed(ActionEvent e)
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388 deselectAllSequenceMenuItem_actionPerformed(e);
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391 invertSequenceMenuItem.setText("Invert Sequence Selection");
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392 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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393 java.awt.event.KeyEvent.VK_I,
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394 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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395 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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397 public void actionPerformed(ActionEvent e)
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399 invertSequenceMenuItem_actionPerformed(e);
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402 remove2LeftMenuItem.setText("Remove Left");
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403 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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404 awt.event.KeyEvent.VK_L,
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405 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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406 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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408 public void actionPerformed(ActionEvent e)
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410 remove2LeftMenuItem_actionPerformed(e);
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413 remove2RightMenuItem.setText("Remove Right");
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414 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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415 awt.event.KeyEvent.VK_R,
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416 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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417 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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419 public void actionPerformed(ActionEvent e)
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421 remove2RightMenuItem_actionPerformed(e);
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424 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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425 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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426 getKeyStroke(java.awt.event.
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427 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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428 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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431 public void actionPerformed(ActionEvent e)
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433 removeGappedColumnMenuItem_actionPerformed(e);
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436 removeAllGapsMenuItem.setText("Remove All Gaps");
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437 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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438 java.awt.event.KeyEvent.VK_E,
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439 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
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440 java.awt.event.KeyEvent.SHIFT_MASK, false));
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441 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 removeAllGapsMenuItem_actionPerformed(e);
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448 viewBoxesMenuItem.setText("Boxes");
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449 viewBoxesMenuItem.setState(true);
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450 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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452 public void actionPerformed(ActionEvent e)
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454 viewBoxesMenuItem_actionPerformed(e);
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457 viewTextMenuItem.setText("Text");
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458 viewTextMenuItem.setState(true);
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459 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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461 public void actionPerformed(ActionEvent e)
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463 viewTextMenuItem_actionPerformed(e);
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466 sortPairwiseMenuItem.setText("by Pairwise Identity");
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467 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 sortPairwiseMenuItem_actionPerformed(e);
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474 sortIDMenuItem.setText("by ID");
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475 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 sortIDMenuItem_actionPerformed(e);
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482 sortGroupMenuItem.setText("by Group");
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483 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 sortGroupMenuItem_actionPerformed(e);
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490 removeRedundancyMenuItem.setText("Remove Redundancy...");
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491 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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492 java.awt.event.KeyEvent.VK_D,
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493 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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494 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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497 public void actionPerformed(ActionEvent e)
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499 removeRedundancyMenuItem_actionPerformed(e);
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502 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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503 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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506 public void actionPerformed(ActionEvent e)
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508 pairwiseAlignmentMenuItem_actionPerformed(e);
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511 PCAMenuItem.setText("Principal Component Analysis");
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512 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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514 public void actionPerformed(ActionEvent e)
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516 PCAMenuItem_actionPerformed(e);
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519 averageDistanceTreeMenuItem.setText(
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520 "Average Distance Using % Identity");
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521 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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524 public void actionPerformed(ActionEvent e)
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526 averageDistanceTreeMenuItem_actionPerformed(e);
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529 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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530 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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532 public void actionPerformed(ActionEvent e)
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534 neighbourTreeMenuItem_actionPerformed(e);
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537 this.getContentPane().setLayout(borderLayout1);
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538 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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539 statusBar.setBackground(Color.white);
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540 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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541 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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542 statusBar.setText("Status bar");
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543 outputTextboxMenu.setText("Output to Textbox");
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544 clustalColour.setText("Clustalx");
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546 clustalColour.addActionListener(new java.awt.event.ActionListener()
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548 public void actionPerformed(ActionEvent e)
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550 clustalColour_actionPerformed(e);
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553 zappoColour.setText("Zappo");
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554 zappoColour.addActionListener(new java.awt.event.ActionListener()
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556 public void actionPerformed(ActionEvent e)
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558 zappoColour_actionPerformed(e);
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561 taylorColour.setText("Taylor");
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562 taylorColour.addActionListener(new java.awt.event.ActionListener()
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564 public void actionPerformed(ActionEvent e)
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566 taylorColour_actionPerformed(e);
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569 hydrophobicityColour.setText("Hydrophobicity");
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570 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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572 public void actionPerformed(ActionEvent e)
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574 hydrophobicityColour_actionPerformed(e);
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577 helixColour.setText("Helix Propensity");
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578 helixColour.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 helixColour_actionPerformed(e);
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585 strandColour.setText("Strand Propensity");
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586 strandColour.addActionListener(new java.awt.event.ActionListener()
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588 public void actionPerformed(ActionEvent e)
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590 strandColour_actionPerformed(e);
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593 turnColour.setText("Turn Propensity");
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594 turnColour.addActionListener(new java.awt.event.ActionListener()
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596 public void actionPerformed(ActionEvent e)
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598 turnColour_actionPerformed(e);
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601 buriedColour.setText("Buried Index");
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602 buriedColour.addActionListener(new java.awt.event.ActionListener()
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604 public void actionPerformed(ActionEvent e)
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606 buriedColour_actionPerformed(e);
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609 userDefinedColour.setText("User Defined...");
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610 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 userDefinedColour_actionPerformed(e);
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617 PIDColour.setText("Percentage Identity");
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618 PIDColour.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 PIDColour_actionPerformed(e);
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625 BLOSUM62Colour.setText("BLOSUM62 Score");
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626 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 BLOSUM62Colour_actionPerformed(e);
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633 avDistanceTreeBlosumMenuItem.setText(
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634 "Average Distance Using BLOSUM62");
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635 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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638 public void actionPerformed(ActionEvent e)
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640 avTreeBlosumMenuItem_actionPerformed(e);
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643 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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644 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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646 public void actionPerformed(ActionEvent e)
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648 njTreeBlosumMenuItem_actionPerformed(e);
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651 annotationPanelMenuItem.setActionCommand("");
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652 annotationPanelMenuItem.setText("Show Annotations");
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653 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
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654 "SHOW_ANNOTATIONS", true));
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655 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 annotationPanelMenuItem_actionPerformed(e);
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662 colourTextMenuItem.setText("Colour Text");
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663 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 colourTextMenuItem_actionPerformed(e);
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670 htmlMenuItem.setText("HTML");
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671 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 htmlMenuItem_actionPerformed(e);
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678 overviewMenuItem.setText("Overview Window");
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679 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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681 public void actionPerformed(ActionEvent e)
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683 overviewMenuItem_actionPerformed(e);
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686 undoMenuItem.setEnabled(false);
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687 undoMenuItem.setText("Undo");
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688 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
689 java.awt.event.KeyEvent.VK_Z,
\r
690 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
691 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
693 public void actionPerformed(ActionEvent e)
\r
695 undoMenuItem_actionPerformed(e);
\r
698 redoMenuItem.setEnabled(false);
\r
699 redoMenuItem.setText("Redo");
\r
700 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
701 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
702 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
704 public void actionPerformed(ActionEvent e)
\r
706 redoMenuItem_actionPerformed(e);
\r
709 conservationMenuItem.setText("By Conservation");
\r
710 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
712 public void actionPerformed(ActionEvent e)
\r
714 conservationMenuItem_actionPerformed(e);
\r
717 noColourmenuItem.setText("None");
\r
718 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
720 public void actionPerformed(ActionEvent e)
\r
722 noColourmenuItem_actionPerformed(e);
\r
725 wrapMenuItem.setText("Wrap");
\r
726 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
728 public void actionPerformed(ActionEvent e)
\r
730 wrapMenuItem_actionPerformed(e);
\r
733 printMenuItem.setText("Print ...");
\r
734 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
735 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
736 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
738 public void actionPerformed(ActionEvent e)
\r
740 printMenuItem_actionPerformed(e);
\r
743 renderGapsMenuItem.setText("Show Gaps");
\r
744 renderGapsMenuItem.setState(true);
\r
745 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
747 public void actionPerformed(ActionEvent e)
\r
749 renderGapsMenuItem_actionPerformed(e);
\r
752 findMenuItem.setText("Find...");
\r
753 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
754 java.awt.event.KeyEvent.VK_F,
\r
755 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
756 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
758 public void actionPerformed(ActionEvent e)
\r
760 findMenuItem_actionPerformed(e);
\r
763 abovePIDThreshold.setText("Above Identity Threshold");
\r
764 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
766 public void actionPerformed(ActionEvent e)
\r
768 abovePIDThreshold_actionPerformed(e);
\r
771 showSeqFeatures.setText("Show Sequence Features");
\r
772 showSeqFeatures.addActionListener(new ActionListener()
\r
774 public void actionPerformed(ActionEvent actionEvent)
\r
776 showSeqFeatures_actionPerformed(actionEvent);
\r
779 nucleotideColour.setText("Nucleotide");
\r
780 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
782 public void actionPerformed(ActionEvent e)
\r
784 nucleotideColour_actionPerformed(e);
\r
787 deleteGroups.setText("Undefine groups");
\r
788 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
789 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
790 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
792 public void actionPerformed(ActionEvent e)
\r
794 deleteGroups_actionPerformed(e);
\r
797 copy.setText("Copy");
\r
798 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
799 java.awt.event.KeyEvent.VK_C,
\r
800 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
802 copy.addActionListener(new java.awt.event.ActionListener()
\r
804 public void actionPerformed(ActionEvent e)
\r
806 copy_actionPerformed(e);
\r
809 cut.setText("Cut");
\r
810 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
811 java.awt.event.KeyEvent.VK_X,
\r
812 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
813 cut.addActionListener(new java.awt.event.ActionListener()
\r
815 public void actionPerformed(ActionEvent e)
\r
817 cut_actionPerformed(e);
\r
820 delete.setText("Delete");
\r
821 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
822 KeyEvent.VK_BACK_SPACE, 0, false));
\r
823 delete.addActionListener(new java.awt.event.ActionListener()
\r
825 public void actionPerformed(ActionEvent e)
\r
827 delete_actionPerformed(e);
\r
830 pasteMenu.setText("Paste");
\r
831 pasteNew.setText("To New Alignment");
\r
832 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
833 java.awt.event.KeyEvent.VK_V,
\r
834 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
\r
835 java.awt.event.KeyEvent.SHIFT_MASK, false));
\r
836 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
838 public void actionPerformed(ActionEvent e)
\r
840 pasteNew_actionPerformed(e);
\r
843 pasteThis.setText("Add To This Alignment");
\r
844 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
845 java.awt.event.KeyEvent.VK_V,
\r
846 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
847 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
849 public void actionPerformed(ActionEvent e)
\r
851 pasteThis_actionPerformed(e);
\r
854 applyToAllGroups.setText("Apply Colour To All Groups");
\r
855 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
857 public void actionPerformed(ActionEvent e)
\r
859 applyToAllGroups_actionPerformed(e);
\r
862 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
864 public void actionPerformed(ActionEvent e)
\r
869 createPNG.setActionCommand("Save As PNG Image");
\r
870 createPNG.setText("PNG");
\r
871 font.setText("Font...");
\r
872 font.addActionListener(new java.awt.event.ActionListener()
\r
874 public void actionPerformed(ActionEvent e)
\r
876 font_actionPerformed(e);
\r
880 seqLimits.setText("Show Sequence Limits");
\r
881 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
\r
882 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
884 public void actionPerformed(ActionEvent e)
\r
886 seqLimit_actionPerformed(e);
\r
889 epsFile.setText("EPS");
\r
890 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
892 public void actionPerformed(ActionEvent e)
\r
897 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
898 LoadtreeMenuItem.setText("Load Associated Tree");
\r
899 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
901 public void actionPerformed(ActionEvent e)
\r
903 LoadtreeMenuItem_actionPerformed(e);
\r
906 scaleAbove.setVisible(false);
\r
907 scaleAbove.setText("Scale Above");
\r
908 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
910 public void actionPerformed(ActionEvent e)
\r
912 scaleAbove_actionPerformed(e);
\r
915 scaleLeft.setVisible(false);
\r
916 scaleLeft.setSelected(true);
\r
917 scaleLeft.setText("Scale Left");
\r
918 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
920 public void actionPerformed(ActionEvent e)
\r
922 scaleLeft_actionPerformed(e);
\r
925 scaleRight.setVisible(false);
\r
926 scaleRight.setSelected(true);
\r
927 scaleRight.setText("Scale Right");
\r
928 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
930 public void actionPerformed(ActionEvent e)
\r
932 scaleRight_actionPerformed(e);
\r
935 modifyPID.setText("Modify Identity Threshold...");
\r
936 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
938 public void actionPerformed(ActionEvent e)
\r
940 modifyPID_actionPerformed(e);
\r
943 modifyConservation.setText("Modify Conservation Threshold...");
\r
944 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
946 public void actionPerformed(ActionEvent e)
\r
948 modifyConservation_actionPerformed(e);
\r
951 sortByTreeMenu.setText("By Tree Order");
\r
952 sort.setText("Sort");
\r
953 sort.addMenuListener(new MenuListener()
\r
955 public void menuSelected(MenuEvent e)
\r
960 public void menuDeselected(MenuEvent e)
\r
964 public void menuCanceled(MenuEvent e)
\r
968 calculate.setText("Calculate Tree");
\r
970 jMenu2.setText("Export Image");
\r
971 padGapsMenuitem.setText("Pad Gaps");
\r
972 padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
973 padGapsMenuitem.addActionListener(new ActionListener()
\r
975 public void actionPerformed(ActionEvent e)
\r
977 padGapsMenuitem_actionPerformed(e);
\r
980 vamsasStore.setVisible(false);
\r
981 vamsasStore.setText("VAMSAS store");
\r
982 vamsasStore.addActionListener(new ActionListener()
\r
984 public void actionPerformed(ActionEvent e)
\r
986 vamsasStore_actionPerformed(e);
\r
989 showTranslation.setText("Translate cDNA");
\r
990 showTranslation.addActionListener(new ActionListener()
\r
992 public void actionPerformed(ActionEvent e)
\r
994 showTranslation_actionPerformed(e);
\r
998 featureSettings.setText("Feature Settings...");
\r
999 featureSettings.addActionListener(new ActionListener()
\r
1001 public void actionPerformed(ActionEvent e)
\r
1003 featureSettings_actionPerformed(e);
\r
1006 fetchSequence.setText("Fetch Sequence(s)...");
\r
1007 fetchSequence.addActionListener(new ActionListener()
\r
1009 public void actionPerformed(ActionEvent e)
\r
1011 fetchSequence_actionPerformed(e);
\r
1015 annotationColour.setText("By Annotation...");
\r
1016 annotationColour.addActionListener(new ActionListener()
\r
1018 public void actionPerformed(ActionEvent e)
\r
1020 annotationColour_actionPerformed(e);
\r
1023 associatedData.setText("Load Features / Annotations");
\r
1024 associatedData.addActionListener(new ActionListener()
\r
1026 public void actionPerformed(ActionEvent e)
\r
1028 associatedData_actionPerformed(e);
\r
1031 autoCalculate.setText("Autocalculate Consensus");
\r
1032 autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1033 autoCalculate.addActionListener(new ActionListener()
\r
1035 public void actionPerformed(ActionEvent e)
\r
1037 autoCalculate_actionPerformed(e);
\r
1040 addSequenceMenu.setText("Add Sequences");
\r
1041 addFromFile.setText("From File");
\r
1042 addFromFile.addActionListener(new ActionListener()
\r
1044 public void actionPerformed(ActionEvent e)
\r
1046 addFromFile_actionPerformed(e);
\r
1049 addFromText.setText("From Textbox");
\r
1050 addFromText.addActionListener(new ActionListener()
\r
1052 public void actionPerformed(ActionEvent e)
\r
1054 addFromText_actionPerformed(e);
\r
1057 addFromURL.setText("From URL");
\r
1058 addFromURL.addActionListener(new ActionListener()
\r
1060 public void actionPerformed(ActionEvent e)
\r
1062 addFromURL_actionPerformed(e);
\r
1065 exportFeatures.setText("Export Features...");
\r
1066 exportFeatures.addActionListener(new ActionListener()
\r
1068 public void actionPerformed(ActionEvent e)
\r
1070 exportFeatures_actionPerformed(e);
\r
1073 exportAnnotations.setText("Export Annotations...");
\r
1074 exportAnnotations.addActionListener(new ActionListener()
\r
1076 public void actionPerformed(ActionEvent e)
\r
1078 exportAnnotations_actionPerformed(e);
\r
1081 statusPanel.setLayout(gridLayout1);
\r
1082 jMenu3.setText("Show");
\r
1083 showAllSeqs.setText("All Sequences");
\r
1084 showAllSeqs.addActionListener(new ActionListener()
\r
1086 public void actionPerformed(ActionEvent e)
\r
1088 showAllSeqs_actionPerformed(e);
\r
1091 showAllColumns.setText("All Columns");
\r
1092 showAllColumns.addActionListener(new ActionListener()
\r
1094 public void actionPerformed(ActionEvent e)
\r
1096 showAllColumns_actionPerformed(e);
\r
1099 hideMenu.setText("Hide");
\r
1100 hideSelSequences.setText("Selected Sequences");
\r
1101 hideSelSequences.addActionListener(new ActionListener()
\r
1103 public void actionPerformed(ActionEvent e)
\r
1105 hideSelSequences_actionPerformed(e);
\r
1108 hideSelColumns.setText("Selected Columns");
\r
1109 hideSelColumns.addActionListener(new ActionListener()
\r
1111 public void actionPerformed(ActionEvent e)
\r
1113 hideSelColumns_actionPerformed(e);
\r
1116 hiddenMarkers.setText("Show Hidden Markers");
\r
1117 hiddenMarkers.addActionListener(new ActionListener()
\r
1119 public void actionPerformed(ActionEvent e)
\r
1121 hiddenMarkers_actionPerformed(e);
\r
1124 invertColSel.setText("Invert Column Selection");
\r
1125 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1126 event.KeyEvent.VK_I,
\r
1127 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
\r
1128 | java.awt.event.KeyEvent.ALT_MASK,
\r
1130 invertColSel.addActionListener(new ActionListener()
\r
1132 public void actionPerformed(ActionEvent e)
\r
1134 invertColSel_actionPerformed(e);
\r
1137 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1139 public void stateChanged(ChangeEvent evt)
\r
1141 JTabbedPane pane = (JTabbedPane) evt.getSource();
\r
1142 int sel = pane.getSelectedIndex();
\r
1143 tabSelectionChanged(sel);
\r
1146 tabbedPane.addMouseListener(new MouseAdapter()
\r
1148 public void mousePressed(MouseEvent e)
\r
1150 tabbedPane_mousePressed(e);
\r
1153 tabbedPane.addFocusListener(new FocusAdapter()
\r
1155 public void focusGained(FocusEvent e)
\r
1157 tabbedPane_focusGained(e);
\r
1160 save.setText("Save");
\r
1161 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1162 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1163 save.addActionListener(new ActionListener()
\r
1165 public void actionPerformed(ActionEvent e)
\r
1167 save_actionPerformed(e);
\r
1170 reload.setEnabled(false);
\r
1171 reload.setText("Reload");
\r
1172 reload.addActionListener(new ActionListener()
\r
1174 public void actionPerformed(ActionEvent e)
\r
1176 reload_actionPerformed(e);
\r
1179 newView.setText("New View");
\r
1180 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1181 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1182 newView.addActionListener(new ActionListener()
\r
1184 public void actionPerformed(ActionEvent e)
\r
1186 newView_actionPerformed(e);
\r
1189 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
\r
1191 "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
\r
1192 textColour.setText("Text Colour");
\r
1193 textColour.addActionListener(new ActionListener()
\r
1195 public void actionPerformed(ActionEvent e)
\r
1197 textColour_actionPerformed(e);
\r
1200 formatMenu.setText("Format");
\r
1201 selectMenu.setText("Select");
\r
1202 idRightAlign.setText("Right Align Sequence Id");
\r
1203 idRightAlign.addActionListener(new ActionListener()
\r
1205 public void actionPerformed(ActionEvent e)
\r
1207 idRightAlign_actionPerformed(e);
\r
1210 gatherViews.setEnabled(false);
\r
1211 gatherViews.setText("Gather Views");
\r
1212 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1213 event.KeyEvent.VK_G, 0, false));
\r
1214 gatherViews.addActionListener(new ActionListener()
\r
1216 public void actionPerformed(ActionEvent e)
\r
1218 gatherViews_actionPerformed(e);
\r
1221 expandViews.setEnabled(false);
\r
1222 expandViews.setText("Expand Views");
\r
1223 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1224 event.KeyEvent.VK_X, 0, false));
\r
1225 expandViews.addActionListener(new ActionListener()
\r
1227 public void actionPerformed(ActionEvent e)
\r
1229 expandViews_actionPerformed(e);
\r
1232 pageSetup.setText("Page Setup ...");
\r
1233 pageSetup.addActionListener(new ActionListener()
\r
1235 public void actionPerformed(ActionEvent e)
\r
1237 pageSetup_actionPerformed(e);
\r
1240 alignmentProperties.setText("Alignment Properties...");
\r
1241 alignmentProperties.addActionListener(new ActionListener()
\r
1243 public void actionPerformed(ActionEvent actionEvent)
\r
1245 alignmentProperties();
\r
1249 alignFrameMenuBar.add(fileMenu);
\r
1250 alignFrameMenuBar.add(editMenu);
\r
1251 alignFrameMenuBar.add(selectMenu);
\r
1252 alignFrameMenuBar.add(viewMenu);
\r
1253 alignFrameMenuBar.add(formatMenu);
\r
1254 alignFrameMenuBar.add(colourMenu);
\r
1255 alignFrameMenuBar.add(calculateMenu);
\r
1256 alignFrameMenuBar.add(webService);
\r
1257 fileMenu.add(fetchSequence);
\r
1258 fileMenu.add(addSequenceMenu);
\r
1259 fileMenu.add(reload);
\r
1260 fileMenu.addSeparator();
\r
1261 fileMenu.add(vamsasStore);
\r
1262 fileMenu.add(save);
\r
1263 fileMenu.add(saveAs);
\r
1264 fileMenu.add(outputTextboxMenu);
\r
1265 fileMenu.add(pageSetup);
\r
1266 fileMenu.add(printMenuItem);
\r
1267 fileMenu.addSeparator();
\r
1268 fileMenu.add(jMenu2);
\r
1269 fileMenu.add(exportFeatures);
\r
1270 fileMenu.add(exportAnnotations);
\r
1271 fileMenu.add(LoadtreeMenuItem);
\r
1272 fileMenu.add(associatedData);
\r
1273 fileMenu.addSeparator();
\r
1274 fileMenu.add(closeMenuItem);
\r
1275 editMenu.add(undoMenuItem);
\r
1276 editMenu.add(redoMenuItem);
\r
1277 editMenu.add(cut);
\r
1278 editMenu.add(copy);
\r
1279 editMenu.add(pasteMenu);
\r
1280 editMenu.add(delete);
\r
1281 editMenu.addSeparator();
\r
1282 editMenu.add(remove2LeftMenuItem);
\r
1283 editMenu.add(remove2RightMenuItem);
\r
1284 editMenu.add(removeGappedColumnMenuItem);
\r
1285 editMenu.add(removeAllGapsMenuItem);
\r
1286 editMenu.add(removeRedundancyMenuItem);
\r
1287 editMenu.addSeparator();
\r
1288 editMenu.add(padGapsMenuitem);
\r
1289 viewMenu.add(newView);
\r
1290 viewMenu.add(expandViews);
\r
1291 viewMenu.add(gatherViews);
\r
1292 viewMenu.addSeparator();
\r
1293 viewMenu.add(jMenu3);
\r
1294 viewMenu.add(hideMenu);
\r
1295 viewMenu.addSeparator();
\r
1296 viewMenu.add(annotationPanelMenuItem);
\r
1297 viewMenu.addSeparator();
\r
1298 viewMenu.add(showSeqFeatures);
\r
1299 viewMenu.add(featureSettings);
\r
1300 viewMenu.addSeparator();
\r
1301 viewMenu.add(alignmentProperties);
\r
1302 viewMenu.addSeparator();
\r
1303 viewMenu.add(overviewMenuItem);
\r
1304 colourMenu.add(applyToAllGroups);
\r
1305 colourMenu.add(textColour);
\r
1306 colourMenu.addSeparator();
\r
1307 colourMenu.add(noColourmenuItem);
\r
1308 colourMenu.add(clustalColour);
\r
1309 colourMenu.add(BLOSUM62Colour);
\r
1310 colourMenu.add(PIDColour);
\r
1311 colourMenu.add(zappoColour);
\r
1312 colourMenu.add(taylorColour);
\r
1313 colourMenu.add(hydrophobicityColour);
\r
1314 colourMenu.add(helixColour);
\r
1315 colourMenu.add(strandColour);
\r
1316 colourMenu.add(turnColour);
\r
1317 colourMenu.add(buriedColour);
\r
1318 colourMenu.add(nucleotideColour);
\r
1319 colourMenu.add(userDefinedColour);
\r
1320 colourMenu.addSeparator();
\r
1321 colourMenu.add(conservationMenuItem);
\r
1322 colourMenu.add(modifyConservation);
\r
1323 colourMenu.add(abovePIDThreshold);
\r
1324 colourMenu.add(modifyPID);
\r
1325 colourMenu.add(annotationColour);
\r
1326 calculateMenu.add(sort);
\r
1327 calculateMenu.add(calculate);
\r
1328 calculateMenu.addSeparator();
\r
1329 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1330 calculateMenu.add(PCAMenuItem);
\r
1331 calculateMenu.addSeparator();
\r
1332 calculateMenu.add(showTranslation);
\r
1333 calculateMenu.add(autoCalculate);
\r
1334 webServiceNoServices = new JMenuItem("<No Services>");
\r
1335 webService.add(webServiceNoServices);
\r
1336 pasteMenu.add(pasteNew);
\r
1337 pasteMenu.add(pasteThis);
\r
1338 sort.add(sortIDMenuItem);
\r
1339 sort.add(sortGroupMenuItem);
\r
1340 sort.add(sortPairwiseMenuItem);
\r
1341 sort.add(sortByTreeMenu);
\r
1342 calculate.add(averageDistanceTreeMenuItem);
\r
1343 calculate.add(neighbourTreeMenuItem);
\r
1344 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1345 calculate.add(njTreeBlosumMenuItem);
\r
1346 jMenu2.add(htmlMenuItem);
\r
1347 jMenu2.add(epsFile);
\r
1348 jMenu2.add(createPNG);
\r
1349 addSequenceMenu.add(addFromFile);
\r
1350 addSequenceMenu.add(addFromText);
\r
1351 addSequenceMenu.add(addFromURL);
\r
1352 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1353 statusPanel.add(statusBar, null);
\r
1354 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1355 jMenu3.add(showAllColumns);
\r
1356 jMenu3.add(showAllSeqs);
\r
1357 hideMenu.add(hideSelColumns);
\r
1358 hideMenu.add(hideSelSequences);
\r
1359 formatMenu.add(font);
\r
1360 formatMenu.addSeparator();
\r
1361 formatMenu.add(wrapMenuItem);
\r
1362 formatMenu.add(scaleAbove);
\r
1363 formatMenu.add(scaleLeft);
\r
1364 formatMenu.add(scaleRight);
\r
1365 formatMenu.add(seqLimits);
\r
1366 formatMenu.add(idRightAlign);
\r
1367 formatMenu.add(hiddenMarkers);
\r
1368 formatMenu.add(viewBoxesMenuItem);
\r
1369 formatMenu.add(viewTextMenuItem);
\r
1370 formatMenu.add(colourTextMenuItem);
\r
1371 formatMenu.add(renderGapsMenuItem);
\r
1372 selectMenu.add(findMenuItem);
\r
1373 selectMenu.addSeparator();
\r
1374 selectMenu.add(selectAllSequenceMenuItem);
\r
1375 selectMenu.add(deselectAllSequenceMenuItem);
\r
1376 selectMenu.add(invertSequenceMenuItem);
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1377 selectMenu.add(invertColSel);
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1378 selectMenu.add(deleteGroups);
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1381 protected void outputText_actionPerformed(ActionEvent e)
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1385 public void addFromFile_actionPerformed(ActionEvent e)
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1390 public void addFromText_actionPerformed(ActionEvent e)
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1395 public void addFromURL_actionPerformed(ActionEvent e)
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1400 public void exportFeatures_actionPerformed(ActionEvent e)
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1405 public void exportAnnotations_actionPerformed(ActionEvent e)
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1410 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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1414 protected void closeMenuItem_actionPerformed(boolean b)
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1418 protected void redoMenuItem_actionPerformed(ActionEvent e)
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1422 protected void undoMenuItem_actionPerformed(ActionEvent e)
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1426 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1430 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1434 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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1438 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1442 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1446 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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1450 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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1454 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1458 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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1462 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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1466 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1470 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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1474 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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1478 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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1482 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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1486 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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1490 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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1494 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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1498 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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1502 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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1506 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1510 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1514 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1518 protected void clustalColour_actionPerformed(ActionEvent e)
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1522 protected void zappoColour_actionPerformed(ActionEvent e)
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1526 protected void taylorColour_actionPerformed(ActionEvent e)
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1530 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1534 protected void helixColour_actionPerformed(ActionEvent e)
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1538 protected void strandColour_actionPerformed(ActionEvent e)
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1542 protected void turnColour_actionPerformed(ActionEvent e)
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1546 protected void buriedColour_actionPerformed(ActionEvent e)
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1550 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1554 protected void PIDColour_actionPerformed(ActionEvent e)
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1558 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1562 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1566 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1570 protected void printMenuItem_actionPerformed(ActionEvent e)
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1574 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1578 protected void findMenuItem_actionPerformed(ActionEvent e)
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1582 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
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1586 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
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1590 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1594 protected void deleteGroups_actionPerformed(ActionEvent e)
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1598 protected void copy_actionPerformed(ActionEvent e)
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1602 protected void cut_actionPerformed(ActionEvent e)
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1606 protected void delete_actionPerformed(ActionEvent e)
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1610 protected void pasteNew_actionPerformed(ActionEvent e)
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1614 protected void pasteThis_actionPerformed(ActionEvent e)
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1618 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1622 public void createPNG(java.io.File f)
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1626 protected void font_actionPerformed(ActionEvent e)
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1630 protected void seqLimit_actionPerformed(ActionEvent e)
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1634 public void seqDBRef_actionPerformed(ActionEvent e)
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1639 public void createEPS(java.io.File f)
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1643 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1647 protected void jpred_actionPerformed(ActionEvent e)
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1651 protected void scaleAbove_actionPerformed(ActionEvent e)
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1655 protected void scaleLeft_actionPerformed(ActionEvent e)
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1659 protected void scaleRight_actionPerformed(ActionEvent e)
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1663 protected void modifyPID_actionPerformed(ActionEvent e)
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1667 protected void modifyConservation_actionPerformed(ActionEvent e)
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1671 protected void saveAs_actionPerformed(ActionEvent e)
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1675 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1679 public void vamsasStore_actionPerformed(ActionEvent e)
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1684 public void vamsasLoad_actionPerformed(ActionEvent e)
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1689 public void showTranslation_actionPerformed(ActionEvent e)
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1694 public void featureSettings_actionPerformed(ActionEvent e)
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1699 public void fetchSequence_actionPerformed(ActionEvent e)
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1704 public void smoothFont_actionPerformed(ActionEvent e)
\r
1709 public void annotationColour_actionPerformed(ActionEvent e)
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1714 public void associatedData_actionPerformed(ActionEvent e)
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1719 public void autoCalculate_actionPerformed(ActionEvent e)
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1724 public void showAllSeqs_actionPerformed(ActionEvent e)
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1729 public void showAllColumns_actionPerformed(ActionEvent e)
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1734 public void hideSelSequences_actionPerformed(ActionEvent e)
\r
1739 public void hideSelColumns_actionPerformed(ActionEvent e)
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1744 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1749 public void findPdbId_actionPerformed(ActionEvent e)
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1754 public void enterPdbId_actionPerformed(ActionEvent e)
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1759 public void pdbFile_actionPerformed(ActionEvent e)
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1764 public void invertColSel_actionPerformed(ActionEvent e)
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1769 public void tabSelectionChanged(int sel)
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1774 public void tabbedPane_mousePressed(MouseEvent e)
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1779 public void tabbedPane_focusGained(FocusEvent e)
\r
1784 public void save_actionPerformed(ActionEvent e)
\r
1789 public void reload_actionPerformed(ActionEvent e)
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1794 public void newView_actionPerformed(ActionEvent e)
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1799 public void textColour_actionPerformed(ActionEvent e)
\r
1804 public void idRightAlign_actionPerformed(ActionEvent e)
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1809 public void expandViews_actionPerformed(ActionEvent e)
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1814 public void gatherViews_actionPerformed(ActionEvent e)
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1819 public void buildTreeMenu()
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1824 public void pageSetup_actionPerformed(ActionEvent e)
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1829 public void alignmentProperties()
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