2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import jalview.schemes.*;
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27 import java.awt.BorderLayout;
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32 public class GAlignFrame
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33 extends JInternalFrame
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35 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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36 protected JMenu fileMenu = new JMenu();
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37 protected JMenuItem closeMenuItem = new JMenuItem();
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38 protected JMenu editMenu = new JMenu();
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39 protected JMenu viewMenu = new JMenu();
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40 protected JMenu colourMenu = new JMenu();
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41 protected JMenu calculateMenu = new JMenu();
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42 protected JMenu webService = new JMenu();
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43 protected JMenuItem webServiceNoServices;
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44 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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45 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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46 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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47 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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48 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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49 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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50 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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51 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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52 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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53 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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54 protected JMenuItem sortIDMenuItem = new JMenuItem();
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55 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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56 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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57 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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58 protected JMenuItem PCAMenuItem = new JMenuItem();
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59 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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60 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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61 BorderLayout borderLayout1 = new BorderLayout();
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62 public JLabel statusBar = new JLabel();
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63 protected JMenuItem saveAs = new JMenuItem();
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64 protected JMenu outputTextboxMenu = new JMenu();
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65 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem hydrophobicityColour = new
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69 JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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75 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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76 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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77 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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78 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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79 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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80 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem htmlMenuItem = new JMenuItem();
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82 JMenuItem overviewMenuItem = new JMenuItem();
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83 protected JMenuItem undoMenuItem = new JMenuItem();
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84 protected JMenuItem redoMenuItem = new JMenuItem();
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85 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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86 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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87 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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88 JMenuItem printMenuItem = new JMenuItem();
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89 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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90 JMenuItem findMenuItem = new JMenuItem();
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91 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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92 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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93 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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94 JMenuItem deleteGroups = new JMenuItem();
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95 JMenuItem delete = new JMenuItem();
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96 JMenuItem copy = new JMenuItem();
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97 JMenuItem cut = new JMenuItem();
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98 JMenu pasteMenu = new JMenu();
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99 JMenuItem pasteNew = new JMenuItem();
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100 JMenuItem pasteThis = new JMenuItem();
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101 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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102 JMenuItem createPNG = new JMenuItem();
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103 protected JMenuItem font = new JMenuItem();
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104 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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105 JMenuItem epsFile = new JMenuItem();
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106 JMenuItem LoadtreeMenuItem = new JMenuItem();
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107 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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108 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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109 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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110 protected JMenuItem modifyPID = new JMenuItem();
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111 protected JMenuItem modifyConservation = new JMenuItem();
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112 protected JMenu sortByTreeMenu = new JMenu();
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113 protected JMenu sort = new JMenu();
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114 JMenu calculate = new JMenu();
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115 JMenu jMenu2 = new JMenu();
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116 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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117 protected ButtonGroup colours = new ButtonGroup();
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118 JMenuItem vamsasStore = new JMenuItem();
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119 protected JMenuItem showTranslation = new JMenuItem();
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120 public JMenuItem featureSettings = new JMenuItem();
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121 JMenuItem fetchSequence = new JMenuItem();
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122 JMenuItem annotationColour = new JMenuItem();
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123 JMenuItem associatedData = new JMenuItem();
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124 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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125 JMenu addSequenceMenu = new JMenu();
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126 JMenuItem addFromFile = new JMenuItem();
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127 JMenuItem addFromText = new JMenuItem();
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128 JMenuItem addFromURL = new JMenuItem();
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129 JMenuItem exportAnnotations = new JMenuItem();
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130 JMenuItem exportFeatures = new JMenuItem();
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131 protected JPanel statusPanel = new JPanel();
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132 GridLayout gridLayout1 = new GridLayout();
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133 JMenu jMenu3 = new JMenu();
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134 JMenuItem showAllSeqs = new JMenuItem();
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135 JMenuItem showAllColumns = new JMenuItem();
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136 JMenu hideMenu = new JMenu();
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137 JMenuItem hideSelSequences = new JMenuItem();
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138 JMenuItem hideSelColumns = new JMenuItem();
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139 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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140 JMenuItem invertColSel = new JMenuItem();
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141 protected JTabbedPane tabbedPane = new JTabbedPane();
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142 JMenuItem save = new JMenuItem();
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143 protected JMenuItem reload = new JMenuItem();
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144 JMenuItem newView = new JMenuItem();
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145 JMenuItem textColour = new JMenuItem();
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146 JMenu formatMenu = new JMenu();
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147 JMenu selectMenu = new JMenu();
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148 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
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149 protected JMenuItem gatherViews = new JMenuItem();
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150 protected JMenuItem expandViews = new JMenuItem();
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151 public GAlignFrame()
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156 setJMenuBar(alignFrameMenuBar);
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158 // dynamically fill save as menu with available formats
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159 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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161 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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163 item.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 outputText_actionPerformed(e);
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171 outputTextboxMenu.add(item);
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174 catch (Exception e)
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178 if (!System.getProperty("os.name").startsWith("Mac"))
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180 closeMenuItem.setMnemonic('C');
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181 outputTextboxMenu.setMnemonic('T');
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182 undoMenuItem.setMnemonic('Z');
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183 redoMenuItem.setMnemonic('0');
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184 copy.setMnemonic('C');
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185 cut.setMnemonic('U');
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186 pasteMenu.setMnemonic('P');
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187 reload.setMnemonic('R');
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191 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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193 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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194 getUserColourSchemes().keys();
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196 while (userColours.hasMoreElements())
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198 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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199 nextElement().toString());
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200 radioItem.setName("USER_DEFINED");
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201 radioItem.addMouseListener(new MouseAdapter()
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203 public void mousePressed(MouseEvent evt)
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205 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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207 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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209 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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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(radioItem.getText());
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216 colourMenu.remove(radioItem);
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219 radioItem.addActionListener(new ActionListener()
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221 public void actionPerformed(ActionEvent evt)
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223 userDefinedColour_actionPerformed(evt);
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229 radioItem.addActionListener(new ActionListener()
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231 public void actionPerformed(ActionEvent evt)
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233 userDefinedColour_actionPerformed(evt);
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236 colourMenu.insert(radioItem, 15);
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237 colours.add(radioItem);
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240 colours.add(noColourmenuItem);
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241 colours.add(clustalColour);
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242 colours.add(zappoColour);
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243 colours.add(taylorColour);
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244 colours.add(hydrophobicityColour);
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245 colours.add(helixColour);
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246 colours.add(strandColour);
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247 colours.add(turnColour);
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248 colours.add(buriedColour);
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249 colours.add(userDefinedColour);
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250 colours.add(PIDColour);
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251 colours.add(BLOSUM62Colour);
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252 colours.add(nucleotideColour);
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254 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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259 public void setColourSelected(String defaultColour)
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262 if (defaultColour != null)
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264 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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268 case ColourSchemeProperty.NONE:
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269 noColourmenuItem.setSelected(true);
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271 case ColourSchemeProperty.CLUSTAL:
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272 clustalColour.setSelected(true);
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276 case ColourSchemeProperty.BLOSUM:
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277 BLOSUM62Colour.setSelected(true);
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281 case ColourSchemeProperty.PID:
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282 PIDColour.setSelected(true);
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286 case ColourSchemeProperty.ZAPPO:
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287 zappoColour.setSelected(true);
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291 case ColourSchemeProperty.TAYLOR:
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292 taylorColour.setSelected(true);
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295 case ColourSchemeProperty.HYDROPHOBIC:
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296 hydrophobicityColour.setSelected(true);
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300 case ColourSchemeProperty.HELIX:
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301 helixColour.setSelected(true);
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305 case ColourSchemeProperty.STRAND:
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306 strandColour.setSelected(true);
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310 case ColourSchemeProperty.TURN:
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311 turnColour.setSelected(true);
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315 case ColourSchemeProperty.BURIED:
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316 buriedColour.setSelected(true);
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320 case ColourSchemeProperty.NUCLEOTIDE:
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321 nucleotideColour.setSelected(true);
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325 case ColourSchemeProperty.USER_DEFINED:
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326 userDefinedColour.setSelected(true);
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334 private void jbInit()
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337 fileMenu.setText("File");
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338 saveAs.setText("Save As...");
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339 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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341 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
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342 saveAs.addActionListener(new ActionListener()
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344 public void actionPerformed(ActionEvent e)
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346 saveAs_actionPerformed(e);
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349 closeMenuItem.setText("Close");
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350 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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351 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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352 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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354 public void actionPerformed(ActionEvent e)
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356 closeMenuItem_actionPerformed(false);
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359 editMenu.setText("Edit");
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360 viewMenu.setText("View");
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361 colourMenu.setText("Colour");
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362 calculateMenu.setText("Calculate");
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363 webService.setText("Web Service");
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364 selectAllSequenceMenuItem.setText("Select All");
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365 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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366 java.awt.event.KeyEvent.VK_A,
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367 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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368 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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371 public void actionPerformed(ActionEvent e)
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373 selectAllSequenceMenuItem_actionPerformed(e);
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376 deselectAllSequenceMenuItem.setText("Deselect All");
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377 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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379 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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380 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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383 public void actionPerformed(ActionEvent e)
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385 deselectAllSequenceMenuItem_actionPerformed(e);
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388 invertSequenceMenuItem.setText("Invert Sequence Selection");
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389 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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390 java.awt.event.KeyEvent.VK_I,
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391 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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392 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 invertSequenceMenuItem_actionPerformed(e);
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399 remove2LeftMenuItem.setText("Remove Left");
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400 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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401 awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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402 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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404 public void actionPerformed(ActionEvent e)
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406 remove2LeftMenuItem_actionPerformed(e);
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409 remove2RightMenuItem.setText("Remove Right");
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410 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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411 awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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412 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 remove2RightMenuItem_actionPerformed(e);
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419 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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420 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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421 getKeyStroke(java.awt.event.
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422 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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423 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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426 public void actionPerformed(ActionEvent e)
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428 removeGappedColumnMenuItem_actionPerformed(e);
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431 removeAllGapsMenuItem.setText("Remove All Gaps");
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432 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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433 java.awt.event.KeyEvent.VK_E,
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434 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
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435 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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437 public void actionPerformed(ActionEvent e)
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439 removeAllGapsMenuItem_actionPerformed(e);
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442 viewBoxesMenuItem.setText("Boxes");
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443 viewBoxesMenuItem.setState(true);
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444 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 viewBoxesMenuItem_actionPerformed(e);
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451 viewTextMenuItem.setText("Text");
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452 viewTextMenuItem.setState(true);
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453 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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455 public void actionPerformed(ActionEvent e)
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457 viewTextMenuItem_actionPerformed(e);
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460 sortPairwiseMenuItem.setText("by Pairwise Identity");
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461 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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463 public void actionPerformed(ActionEvent e)
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465 sortPairwiseMenuItem_actionPerformed(e);
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468 sortIDMenuItem.setText("by ID");
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469 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 sortIDMenuItem_actionPerformed(e);
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476 sortGroupMenuItem.setText("by Group");
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477 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 sortGroupMenuItem_actionPerformed(e);
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484 removeRedundancyMenuItem.setText("Remove Redundancy...");
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485 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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486 java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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487 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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490 public void actionPerformed(ActionEvent e)
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492 removeRedundancyMenuItem_actionPerformed(e);
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495 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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496 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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499 public void actionPerformed(ActionEvent e)
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501 pairwiseAlignmentMenuItem_actionPerformed(e);
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504 PCAMenuItem.setText("Principal Component Analysis");
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505 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 PCAMenuItem_actionPerformed(e);
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512 averageDistanceTreeMenuItem.setText(
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513 "Average Distance Using % Identity");
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514 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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517 public void actionPerformed(ActionEvent e)
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519 averageDistanceTreeMenuItem_actionPerformed(e);
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522 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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523 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 neighbourTreeMenuItem_actionPerformed(e);
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530 this.getContentPane().setLayout(borderLayout1);
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531 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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532 statusBar.setBackground(Color.white);
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533 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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534 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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535 statusBar.setText("Status bar");
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536 outputTextboxMenu.setText("Output to Textbox");
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537 clustalColour.setText("Clustalx");
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539 clustalColour.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 clustalColour_actionPerformed(e);
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546 zappoColour.setText("Zappo");
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547 zappoColour.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 zappoColour_actionPerformed(e);
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554 taylorColour.setText("Taylor");
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555 taylorColour.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 taylorColour_actionPerformed(e);
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562 hydrophobicityColour.setText("Hydrophobicity");
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563 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 hydrophobicityColour_actionPerformed(e);
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570 helixColour.setText("Helix Propensity");
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571 helixColour.addActionListener(new java.awt.event.ActionListener()
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573 public void actionPerformed(ActionEvent e)
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575 helixColour_actionPerformed(e);
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578 strandColour.setText("Strand Propensity");
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579 strandColour.addActionListener(new java.awt.event.ActionListener()
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581 public void actionPerformed(ActionEvent e)
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583 strandColour_actionPerformed(e);
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586 turnColour.setText("Turn Propensity");
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587 turnColour.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 turnColour_actionPerformed(e);
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594 buriedColour.setText("Buried Index");
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595 buriedColour.addActionListener(new java.awt.event.ActionListener()
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597 public void actionPerformed(ActionEvent e)
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599 buriedColour_actionPerformed(e);
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602 userDefinedColour.setText("User Defined...");
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603 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 userDefinedColour_actionPerformed(e);
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610 PIDColour.setText("Percentage Identity");
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611 PIDColour.addActionListener(new java.awt.event.ActionListener()
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613 public void actionPerformed(ActionEvent e)
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615 PIDColour_actionPerformed(e);
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618 BLOSUM62Colour.setText("BLOSUM62 Score");
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619 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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621 public void actionPerformed(ActionEvent e)
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623 BLOSUM62Colour_actionPerformed(e);
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626 avDistanceTreeBlosumMenuItem.setText(
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627 "Average Distance Using BLOSUM62");
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628 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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631 public void actionPerformed(ActionEvent e)
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633 avTreeBlosumMenuItem_actionPerformed(e);
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636 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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637 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 njTreeBlosumMenuItem_actionPerformed(e);
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644 annotationPanelMenuItem.setActionCommand("");
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645 annotationPanelMenuItem.setText("Show Annotations");
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646 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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647 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 annotationPanelMenuItem_actionPerformed(e);
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654 colourTextMenuItem.setText("Colour Text");
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655 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 colourTextMenuItem_actionPerformed(e);
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662 htmlMenuItem.setText("HTML");
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663 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 htmlMenuItem_actionPerformed(e);
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670 overviewMenuItem.setText("Overview Window");
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671 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 overviewMenuItem_actionPerformed(e);
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678 undoMenuItem.setEnabled(false);
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679 undoMenuItem.setText("Undo");
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680 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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681 java.awt.event.KeyEvent.VK_Z,
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682 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
683 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
685 public void actionPerformed(ActionEvent e)
\r
687 undoMenuItem_actionPerformed(e);
\r
690 redoMenuItem.setEnabled(false);
\r
691 redoMenuItem.setText("Redo");
\r
692 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
693 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
694 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
696 public void actionPerformed(ActionEvent e)
\r
698 redoMenuItem_actionPerformed(e);
\r
701 conservationMenuItem.setText("By Conservation");
\r
702 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
704 public void actionPerformed(ActionEvent e)
\r
706 conservationMenuItem_actionPerformed(e);
\r
709 noColourmenuItem.setText("None");
\r
710 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
712 public void actionPerformed(ActionEvent e)
\r
714 noColourmenuItem_actionPerformed(e);
\r
717 wrapMenuItem.setText("Wrap");
\r
718 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
720 public void actionPerformed(ActionEvent e)
\r
722 wrapMenuItem_actionPerformed(e);
\r
725 printMenuItem.setText("Print");
\r
726 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
727 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
728 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
730 public void actionPerformed(ActionEvent e)
\r
732 printMenuItem_actionPerformed(e);
\r
735 renderGapsMenuItem.setText("Show Gaps");
\r
736 renderGapsMenuItem.setState(true);
\r
737 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
739 public void actionPerformed(ActionEvent e)
\r
741 renderGapsMenuItem_actionPerformed(e);
\r
744 findMenuItem.setText("Find...");
\r
745 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
746 java.awt.event.KeyEvent.VK_F,
\r
747 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
748 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
750 public void actionPerformed(ActionEvent e)
\r
752 findMenuItem_actionPerformed(e);
\r
755 abovePIDThreshold.setText("Above Identity Threshold");
\r
756 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
758 public void actionPerformed(ActionEvent e)
\r
760 abovePIDThreshold_actionPerformed(e);
\r
763 showSeqFeatures.setText("Show Sequence Features");
\r
764 showSeqFeatures.addActionListener(new ActionListener()
\r
766 public void actionPerformed(ActionEvent actionEvent)
\r
768 showSeqFeatures_actionPerformed(actionEvent);
\r
771 nucleotideColour.setText("Nucleotide");
\r
772 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
774 public void actionPerformed(ActionEvent e)
\r
776 nucleotideColour_actionPerformed(e);
\r
779 deleteGroups.setText("Undefine groups");
\r
780 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
781 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
782 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
784 public void actionPerformed(ActionEvent e)
\r
786 deleteGroups_actionPerformed(e);
\r
789 copy.setText("Copy");
\r
790 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
791 java.awt.event.KeyEvent.VK_C,
\r
792 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
794 copy.addActionListener(new java.awt.event.ActionListener()
\r
796 public void actionPerformed(ActionEvent e)
\r
798 copy_actionPerformed(e);
\r
801 cut.setText("Cut");
\r
802 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
803 java.awt.event.KeyEvent.VK_X,
\r
804 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
805 cut.addActionListener(new java.awt.event.ActionListener()
\r
807 public void actionPerformed(ActionEvent e)
\r
809 cut_actionPerformed(e);
\r
812 delete.setText("Delete");
\r
813 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
814 KeyEvent.VK_BACK_SPACE, 0, false));
\r
815 delete.addActionListener(new java.awt.event.ActionListener()
\r
817 public void actionPerformed(ActionEvent e)
\r
819 delete_actionPerformed(e);
\r
822 pasteMenu.setText("Paste");
\r
823 pasteNew.setText("To New Alignment");
\r
824 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
825 java.awt.event.KeyEvent.VK_V,
\r
826 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
\r
827 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
829 public void actionPerformed(ActionEvent e)
\r
831 pasteNew_actionPerformed(e);
\r
834 pasteThis.setText("Add To This Alignment");
\r
835 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
836 java.awt.event.KeyEvent.VK_V,
\r
837 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
838 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
840 public void actionPerformed(ActionEvent e)
\r
842 pasteThis_actionPerformed(e);
\r
845 applyToAllGroups.setText("Apply Colour To All Groups");
\r
846 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
848 public void actionPerformed(ActionEvent e)
\r
850 applyToAllGroups_actionPerformed(e);
\r
853 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
855 public void actionPerformed(ActionEvent e)
\r
860 createPNG.setActionCommand("Save As PNG Image");
\r
861 createPNG.setText("PNG");
\r
862 font.setText("Font...");
\r
863 font.addActionListener(new java.awt.event.ActionListener()
\r
865 public void actionPerformed(ActionEvent e)
\r
867 font_actionPerformed(e);
\r
871 seqLimits.setText("Show Sequence Limits");
\r
872 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
873 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
875 public void actionPerformed(ActionEvent e)
\r
877 seqLimit_actionPerformed(e);
\r
880 epsFile.setText("EPS");
\r
881 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
883 public void actionPerformed(ActionEvent e)
\r
888 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
889 LoadtreeMenuItem.setText("Load Associated Tree");
\r
890 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
892 public void actionPerformed(ActionEvent e)
\r
894 LoadtreeMenuItem_actionPerformed(e);
\r
897 scaleAbove.setVisible(false);
\r
898 scaleAbove.setText("Scale Above");
\r
899 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
901 public void actionPerformed(ActionEvent e)
\r
903 scaleAbove_actionPerformed(e);
\r
906 scaleLeft.setVisible(false);
\r
907 scaleLeft.setSelected(true);
\r
908 scaleLeft.setText("Scale Left");
\r
909 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
911 public void actionPerformed(ActionEvent e)
\r
913 scaleLeft_actionPerformed(e);
\r
916 scaleRight.setVisible(false);
\r
917 scaleRight.setSelected(true);
\r
918 scaleRight.setText("Scale Right");
\r
919 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
921 public void actionPerformed(ActionEvent e)
\r
923 scaleRight_actionPerformed(e);
\r
926 modifyPID.setText("Modify Identity Threshold...");
\r
927 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
929 public void actionPerformed(ActionEvent e)
\r
931 modifyPID_actionPerformed(e);
\r
934 modifyConservation.setText("Modify Conservation Threshold...");
\r
935 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
937 public void actionPerformed(ActionEvent e)
\r
939 modifyConservation_actionPerformed(e);
\r
942 sortByTreeMenu.setText("By Tree Order");
\r
943 sort.setText("Sort");
\r
944 sort.addMenuListener(new MenuListener()
\r
946 public void menuSelected(MenuEvent e)
\r
951 public void menuDeselected(MenuEvent e)
\r
955 public void menuCanceled(MenuEvent e)
\r
959 calculate.setText("Calculate Tree");
\r
961 jMenu2.setText("Export Image");
\r
962 padGapsMenuitem.setText("Pad Gaps");
\r
963 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
964 padGapsMenuitem.addActionListener(new ActionListener()
\r
966 public void actionPerformed(ActionEvent e)
\r
968 padGapsMenuitem_actionPerformed(e);
\r
971 vamsasStore.setVisible(false);
\r
972 vamsasStore.setText("VAMSAS store");
\r
973 vamsasStore.addActionListener(new ActionListener()
\r
975 public void actionPerformed(ActionEvent e)
\r
977 vamsasStore_actionPerformed(e);
\r
980 showTranslation.setText("Translate cDNA");
\r
981 showTranslation.addActionListener(new ActionListener()
\r
983 public void actionPerformed(ActionEvent e)
\r
985 showTranslation_actionPerformed(e);
\r
990 featureSettings.setText("Feature Settings...");
\r
991 featureSettings.addActionListener(new ActionListener()
\r
993 public void actionPerformed(ActionEvent e)
\r
995 featureSettings_actionPerformed(e);
\r
998 fetchSequence.setText("Fetch Sequence(s)...");
\r
999 fetchSequence.addActionListener(new ActionListener()
\r
1001 public void actionPerformed(ActionEvent e)
\r
1003 fetchSequence_actionPerformed(e);
\r
1007 annotationColour.setText("By Annotation...");
\r
1008 annotationColour.addActionListener(new ActionListener()
\r
1010 public void actionPerformed(ActionEvent e)
\r
1012 annotationColour_actionPerformed(e);
\r
1015 associatedData.setText("Load Features / Annotations");
\r
1016 associatedData.addActionListener(new ActionListener()
\r
1018 public void actionPerformed(ActionEvent e)
\r
1020 associatedData_actionPerformed(e);
\r
1023 autoCalculate.setText("Autocalculate Consensus");
\r
1024 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1025 autoCalculate.addActionListener(new ActionListener()
\r
1027 public void actionPerformed(ActionEvent e)
\r
1029 autoCalculate_actionPerformed(e);
\r
1032 addSequenceMenu.setText("Add Sequences");
\r
1033 addFromFile.setText("From File");
\r
1034 addFromFile.addActionListener(new ActionListener()
\r
1036 public void actionPerformed(ActionEvent e)
\r
1038 addFromFile_actionPerformed(e);
\r
1041 addFromText.setText("From Textbox");
\r
1042 addFromText.addActionListener(new ActionListener()
\r
1044 public void actionPerformed(ActionEvent e)
\r
1046 addFromText_actionPerformed(e);
\r
1049 addFromURL.setText("From URL");
\r
1050 addFromURL.addActionListener(new ActionListener()
\r
1052 public void actionPerformed(ActionEvent e)
\r
1054 addFromURL_actionPerformed(e);
\r
1057 exportFeatures.setText("Export Features...");
\r
1058 exportFeatures.addActionListener(new ActionListener()
\r
1060 public void actionPerformed(ActionEvent e)
\r
1062 exportFeatures_actionPerformed(e);
\r
1065 exportAnnotations.setText("Export Annotations...");
\r
1066 exportAnnotations.addActionListener(new ActionListener()
\r
1068 public void actionPerformed(ActionEvent e)
\r
1070 exportAnnotations_actionPerformed(e);
\r
1073 statusPanel.setLayout(gridLayout1);
\r
1074 jMenu3.setText("Show");
\r
1075 showAllSeqs.setText("All Sequences");
\r
1076 showAllSeqs.addActionListener(new ActionListener()
\r
1078 public void actionPerformed(ActionEvent e)
\r
1080 showAllSeqs_actionPerformed(e);
\r
1083 showAllColumns.setText("All Columns");
\r
1084 showAllColumns.addActionListener(new ActionListener()
\r
1086 public void actionPerformed(ActionEvent e)
\r
1088 showAllColumns_actionPerformed(e);
\r
1091 hideMenu.setText("Hide");
\r
1092 hideSelSequences.setText("Selected Sequences");
\r
1093 hideSelSequences.addActionListener(new ActionListener()
\r
1095 public void actionPerformed(ActionEvent e)
\r
1097 hideSelSequences_actionPerformed(e);
\r
1100 hideSelColumns.setText("Selected Columns");
\r
1101 hideSelColumns.addActionListener(new ActionListener()
\r
1103 public void actionPerformed(ActionEvent e)
\r
1105 hideSelColumns_actionPerformed(e);
\r
1108 hiddenMarkers.setText("Show Hidden Markers");
\r
1109 hiddenMarkers.addActionListener(new ActionListener()
\r
1111 public void actionPerformed(ActionEvent e)
\r
1113 hiddenMarkers_actionPerformed(e);
\r
1116 invertColSel.setText("Invert Column Selection");
\r
1117 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1118 event.KeyEvent.VK_I,
\r
1119 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
\r
1120 |java.awt.event.KeyEvent.ALT_MASK,
\r
1122 invertColSel.addActionListener(new ActionListener()
\r
1124 public void actionPerformed(ActionEvent e)
\r
1126 invertColSel_actionPerformed(e);
\r
1129 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1131 public void stateChanged(ChangeEvent evt)
\r
1133 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1134 int sel = pane.getSelectedIndex();
\r
1135 tabSelectionChanged(sel);
\r
1138 tabbedPane.addMouseListener(new MouseAdapter()
\r
1140 public void mousePressed(MouseEvent e)
\r
1142 tabbedPane_mousePressed(e);
\r
1145 tabbedPane.addFocusListener(new FocusAdapter()
\r
1147 public void focusGained(FocusEvent e)
\r
1149 tabbedPane_focusGained(e);
\r
1152 save.setText("Save");
\r
1153 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1154 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1155 save.addActionListener(new ActionListener()
\r
1157 public void actionPerformed(ActionEvent e)
\r
1159 save_actionPerformed(e);
\r
1162 reload.setEnabled(false);
\r
1163 reload.setText("Reload");
\r
1164 reload.addActionListener(new ActionListener()
\r
1166 public void actionPerformed(ActionEvent e)
\r
1168 reload_actionPerformed(e);
\r
1171 newView.setText("New View");
\r
1172 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1173 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1174 newView.addActionListener(new ActionListener()
\r
1176 public void actionPerformed(ActionEvent e)
\r
1178 newView_actionPerformed(e);
\r
1181 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
\r
1182 +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
\r
1183 textColour.setText("Text Colour");
\r
1184 textColour.addActionListener(new ActionListener()
\r
1186 public void actionPerformed(ActionEvent e)
\r
1188 textColour_actionPerformed(e);
\r
1191 formatMenu.setText("Format");
\r
1192 selectMenu.setText("Select");
\r
1193 idRightAlign.setText("Right Align Sequence Id");
\r
1194 idRightAlign.addActionListener(new ActionListener()
\r
1196 public void actionPerformed(ActionEvent e)
\r
1198 idRightAlign_actionPerformed(e);
\r
1201 gatherViews.setEnabled(false);
\r
1202 gatherViews.setText("Gather Views");
\r
1203 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1204 event.KeyEvent.VK_G, 0, false));
\r
1205 gatherViews.addActionListener(new ActionListener()
\r
1207 public void actionPerformed(ActionEvent e)
\r
1209 gatherViews_actionPerformed(e);
\r
1212 expandViews.setEnabled(false);
\r
1213 expandViews.setText("Expand Views");
\r
1214 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1215 event.KeyEvent.VK_X, 0, false));
\r
1216 expandViews.addActionListener(new ActionListener()
\r
1218 public void actionPerformed(ActionEvent e)
\r
1220 expandViews_actionPerformed(e);
\r
1224 alignFrameMenuBar.add(fileMenu);
\r
1225 alignFrameMenuBar.add(editMenu);
\r
1226 alignFrameMenuBar.add(selectMenu);
\r
1227 alignFrameMenuBar.add(viewMenu);
\r
1228 alignFrameMenuBar.add(formatMenu);
\r
1229 alignFrameMenuBar.add(colourMenu);
\r
1230 alignFrameMenuBar.add(calculateMenu);
\r
1231 alignFrameMenuBar.add(webService);
\r
1232 fileMenu.add(fetchSequence);
\r
1233 fileMenu.add(addSequenceMenu);
\r
1234 fileMenu.add(reload);
\r
1235 fileMenu.addSeparator();
\r
1236 fileMenu.add(vamsasStore);
\r
1237 fileMenu.add(save);
\r
1238 fileMenu.add(saveAs);
\r
1239 fileMenu.add(outputTextboxMenu);
\r
1240 fileMenu.add(printMenuItem);
\r
1241 fileMenu.addSeparator();
\r
1242 fileMenu.add(jMenu2);
\r
1243 fileMenu.add(exportFeatures);
\r
1244 fileMenu.add(exportAnnotations);
\r
1245 fileMenu.add(LoadtreeMenuItem);
\r
1246 fileMenu.add(associatedData);
\r
1247 fileMenu.addSeparator();
\r
1248 fileMenu.add(closeMenuItem);
\r
1249 editMenu.add(undoMenuItem);
\r
1250 editMenu.add(redoMenuItem);
\r
1251 editMenu.add(cut);
\r
1252 editMenu.add(copy);
\r
1253 editMenu.add(pasteMenu);
\r
1254 editMenu.add(delete);
\r
1255 editMenu.addSeparator();
\r
1256 editMenu.add(remove2LeftMenuItem);
\r
1257 editMenu.add(remove2RightMenuItem);
\r
1258 editMenu.add(removeGappedColumnMenuItem);
\r
1259 editMenu.add(removeAllGapsMenuItem);
\r
1260 editMenu.add(removeRedundancyMenuItem);
\r
1261 editMenu.addSeparator();
\r
1262 editMenu.add(padGapsMenuitem);
\r
1263 viewMenu.add(newView);
\r
1264 viewMenu.add(expandViews);
\r
1265 viewMenu.add(gatherViews);
\r
1266 viewMenu.addSeparator();
\r
1267 viewMenu.add(jMenu3);
\r
1268 viewMenu.add(hideMenu);
\r
1269 viewMenu.addSeparator();
\r
1270 viewMenu.add(annotationPanelMenuItem);
\r
1271 viewMenu.addSeparator();
\r
1272 viewMenu.add(showSeqFeatures);
\r
1273 viewMenu.add(featureSettings);
\r
1274 viewMenu.addSeparator();
\r
1275 viewMenu.add(overviewMenuItem);
\r
1276 colourMenu.add(applyToAllGroups);
\r
1277 colourMenu.add(textColour);
\r
1278 colourMenu.addSeparator();
\r
1279 colourMenu.add(noColourmenuItem);
\r
1280 colourMenu.add(clustalColour);
\r
1281 colourMenu.add(BLOSUM62Colour);
\r
1282 colourMenu.add(PIDColour);
\r
1283 colourMenu.add(zappoColour);
\r
1284 colourMenu.add(taylorColour);
\r
1285 colourMenu.add(hydrophobicityColour);
\r
1286 colourMenu.add(helixColour);
\r
1287 colourMenu.add(strandColour);
\r
1288 colourMenu.add(turnColour);
\r
1289 colourMenu.add(buriedColour);
\r
1290 colourMenu.add(nucleotideColour);
\r
1291 colourMenu.add(userDefinedColour);
\r
1292 colourMenu.addSeparator();
\r
1293 colourMenu.add(conservationMenuItem);
\r
1294 colourMenu.add(modifyConservation);
\r
1295 colourMenu.add(abovePIDThreshold);
\r
1296 colourMenu.add(modifyPID);
\r
1297 colourMenu.add(annotationColour);
\r
1298 calculateMenu.add(sort);
\r
1299 calculateMenu.add(calculate);
\r
1300 calculateMenu.addSeparator();
\r
1301 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1302 calculateMenu.add(PCAMenuItem);
\r
1303 calculateMenu.addSeparator();
\r
1304 calculateMenu.add(showTranslation);
\r
1305 calculateMenu.add(autoCalculate);
\r
1306 webServiceNoServices=new JMenuItem("<No Services>");
\r
1307 webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
\r
1308 pasteMenu.add(pasteThis);
\r
1309 sort.add(sortIDMenuItem);
\r
1310 sort.add(sortGroupMenuItem);
\r
1311 sort.add(sortPairwiseMenuItem);
\r
1312 sort.add(sortByTreeMenu);
\r
1313 calculate.add(averageDistanceTreeMenuItem);
\r
1314 calculate.add(neighbourTreeMenuItem);
\r
1315 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1316 calculate.add(njTreeBlosumMenuItem);
\r
1317 jMenu2.add(htmlMenuItem);
\r
1318 jMenu2.add(epsFile);
\r
1319 jMenu2.add(createPNG);
\r
1320 addSequenceMenu.add(addFromFile);
\r
1321 addSequenceMenu.add(addFromText);
\r
1322 addSequenceMenu.add(addFromURL);
\r
1323 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1324 statusPanel.add(statusBar, null);
\r
1325 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1326 jMenu3.add(showAllColumns);
\r
1327 jMenu3.add(showAllSeqs);
\r
1328 hideMenu.add(hideSelColumns);
\r
1329 hideMenu.add(hideSelSequences);
\r
1330 formatMenu.add(font);
\r
1331 formatMenu.addSeparator();
\r
1332 formatMenu.add(wrapMenuItem);
\r
1333 formatMenu.add(scaleAbove);
\r
1334 formatMenu.add(scaleLeft);
\r
1335 formatMenu.add(scaleRight);
\r
1336 formatMenu.add(seqLimits);
\r
1337 formatMenu.add(idRightAlign);
\r
1338 formatMenu.add(hiddenMarkers);
\r
1339 formatMenu.add(viewBoxesMenuItem);
\r
1340 formatMenu.add(viewTextMenuItem);
\r
1341 formatMenu.add(colourTextMenuItem);
\r
1342 formatMenu.add(renderGapsMenuItem);
\r
1343 selectMenu.add(findMenuItem);
\r
1344 selectMenu.addSeparator();
\r
1345 selectMenu.add(selectAllSequenceMenuItem);
\r
1346 selectMenu.add(deselectAllSequenceMenuItem);
\r
1347 selectMenu.add(invertSequenceMenuItem);
\r
1348 selectMenu.add(invertColSel);
\r
1349 selectMenu.add(deleteGroups);
\r
1352 protected void outputText_actionPerformed(ActionEvent e)
\r
1356 public void addFromFile_actionPerformed(ActionEvent e)
\r
1361 public void addFromText_actionPerformed(ActionEvent e)
\r
1366 public void addFromURL_actionPerformed(ActionEvent e)
\r
1371 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1376 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1381 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1385 protected void closeMenuItem_actionPerformed(boolean b)
\r
1389 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1393 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1397 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1401 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1405 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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1409 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1413 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1417 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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1421 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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1425 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1429 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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1433 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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1437 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1441 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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1445 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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1449 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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1453 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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1457 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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1461 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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1465 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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1469 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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1473 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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1477 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1481 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1485 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1489 protected void clustalColour_actionPerformed(ActionEvent e)
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1493 protected void zappoColour_actionPerformed(ActionEvent e)
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1497 protected void taylorColour_actionPerformed(ActionEvent e)
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1501 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1505 protected void helixColour_actionPerformed(ActionEvent e)
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1509 protected void strandColour_actionPerformed(ActionEvent e)
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1513 protected void turnColour_actionPerformed(ActionEvent e)
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1517 protected void buriedColour_actionPerformed(ActionEvent e)
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1521 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1525 protected void PIDColour_actionPerformed(ActionEvent e)
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1529 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1533 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1537 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1541 protected void printMenuItem_actionPerformed(ActionEvent e)
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1545 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1549 protected void findMenuItem_actionPerformed(ActionEvent e)
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1553 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
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1557 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
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1561 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1565 protected void deleteGroups_actionPerformed(ActionEvent e)
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1569 protected void copy_actionPerformed(ActionEvent e)
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1573 protected void cut_actionPerformed(ActionEvent e)
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1577 protected void delete_actionPerformed(ActionEvent e)
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1581 protected void pasteNew_actionPerformed(ActionEvent e)
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1585 protected void pasteThis_actionPerformed(ActionEvent e)
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1589 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1593 public void createPNG(java.io.File f)
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1597 protected void font_actionPerformed(ActionEvent e)
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1601 protected void seqLimit_actionPerformed(ActionEvent e)
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1605 public void seqDBRef_actionPerformed(ActionEvent e)
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1611 public void createEPS(java.io.File f)
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1615 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1619 protected void jpred_actionPerformed(ActionEvent e)
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1623 protected void scaleAbove_actionPerformed(ActionEvent e)
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1627 protected void scaleLeft_actionPerformed(ActionEvent e)
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1631 protected void scaleRight_actionPerformed(ActionEvent e)
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1635 protected void modifyPID_actionPerformed(ActionEvent e)
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1639 protected void modifyConservation_actionPerformed(ActionEvent e)
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1645 protected void saveAs_actionPerformed(ActionEvent e)
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1649 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1654 public void vamsasStore_actionPerformed(ActionEvent e)
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1659 public void vamsasLoad_actionPerformed(ActionEvent e)
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1664 public void showTranslation_actionPerformed(ActionEvent e)
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1669 public void featureSettings_actionPerformed(ActionEvent e)
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1674 public void fetchSequence_actionPerformed(ActionEvent e)
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1679 public void smoothFont_actionPerformed(ActionEvent e)
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1684 public void annotationColour_actionPerformed(ActionEvent e)
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1690 public void associatedData_actionPerformed(ActionEvent e)
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1695 public void autoCalculate_actionPerformed(ActionEvent e)
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1700 public void showAllSeqs_actionPerformed(ActionEvent e)
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1705 public void showAllColumns_actionPerformed(ActionEvent e)
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1710 public void hideSelSequences_actionPerformed(ActionEvent e)
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1715 public void hideSelColumns_actionPerformed(ActionEvent e)
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1720 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1725 public void findPdbId_actionPerformed(ActionEvent e)
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1730 public void enterPdbId_actionPerformed(ActionEvent e)
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1735 public void pdbFile_actionPerformed(ActionEvent e)
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1740 public void invertColSel_actionPerformed(ActionEvent e)
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1745 public void tabSelectionChanged(int sel)
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1750 public void tabbedPane_mousePressed(MouseEvent e)
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1755 public void tabbedPane_focusGained(FocusEvent e)
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1760 public void save_actionPerformed(ActionEvent e)
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1765 public void reload_actionPerformed(ActionEvent e)
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1770 public void newView_actionPerformed(ActionEvent e)
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1775 public void textColour_actionPerformed(ActionEvent e)
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1780 public void idRightAlign_actionPerformed(ActionEvent e)
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1785 public void expandViews_actionPerformed(ActionEvent e)
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1790 public void gatherViews_actionPerformed(ActionEvent e)
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1795 public void buildTreeMenu()
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