2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import jalview.schemes.*;
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27 import java.awt.BorderLayout;
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32 public class GAlignFrame
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33 extends JInternalFrame
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35 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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36 protected JMenu fileMenu = new JMenu();
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37 protected JMenuItem closeMenuItem = new JMenuItem();
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38 protected JMenu editMenu = new JMenu();
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39 protected JMenu viewMenu = new JMenu();
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40 protected JMenu colourMenu = new JMenu();
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41 protected JMenu calculateMenu = new JMenu();
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42 protected JMenu webService = new JMenu();
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43 protected JMenuItem webServiceNoServices;
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44 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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45 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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46 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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47 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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48 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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49 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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50 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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51 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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52 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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53 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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54 protected JMenuItem sortIDMenuItem = new JMenuItem();
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55 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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56 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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57 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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58 protected JMenuItem PCAMenuItem = new JMenuItem();
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59 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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60 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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61 BorderLayout borderLayout1 = new BorderLayout();
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62 public JLabel statusBar = new JLabel();
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63 protected JMenuItem saveAs = new JMenuItem();
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64 protected JMenu outputTextboxMenu = new JMenu();
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65 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem hydrophobicityColour = new
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69 JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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75 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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76 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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77 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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78 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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79 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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80 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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81 JMenuItem htmlMenuItem = new JMenuItem();
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82 JMenuItem overviewMenuItem = new JMenuItem();
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83 protected JMenuItem undoMenuItem = new JMenuItem();
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84 protected JMenuItem redoMenuItem = new JMenuItem();
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85 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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86 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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87 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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88 JMenuItem printMenuItem = new JMenuItem();
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89 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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90 JMenuItem findMenuItem = new JMenuItem();
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91 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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92 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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93 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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94 JMenuItem deleteGroups = new JMenuItem();
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95 JMenuItem delete = new JMenuItem();
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96 JMenuItem copy = new JMenuItem();
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97 JMenuItem cut = new JMenuItem();
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98 JMenu pasteMenu = new JMenu();
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99 JMenuItem pasteNew = new JMenuItem();
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100 JMenuItem pasteThis = new JMenuItem();
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101 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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102 JMenuItem createPNG = new JMenuItem();
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103 protected JMenuItem font = new JMenuItem();
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104 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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105 JMenuItem epsFile = new JMenuItem();
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106 JMenuItem LoadtreeMenuItem = new JMenuItem();
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107 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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108 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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109 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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110 protected JMenuItem modifyPID = new JMenuItem();
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111 protected JMenuItem modifyConservation = new JMenuItem();
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112 protected JMenu sortByTreeMenu = new JMenu();
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113 protected JMenu sort = new JMenu();
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114 JMenu calculate = new JMenu();
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115 JMenu jMenu2 = new JMenu();
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116 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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117 protected ButtonGroup colours = new ButtonGroup();
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118 JMenuItem vamsasStore = new JMenuItem();
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119 protected JMenuItem showTranslation = new JMenuItem();
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120 public JMenuItem featureSettings = new JMenuItem();
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121 JMenuItem fetchSequence = new JMenuItem();
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122 JMenuItem annotationColour = new JMenuItem();
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123 JMenuItem associatedData = new JMenuItem();
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124 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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125 JMenu addSequenceMenu = new JMenu();
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126 JMenuItem addFromFile = new JMenuItem();
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127 JMenuItem addFromText = new JMenuItem();
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128 JMenuItem addFromURL = new JMenuItem();
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129 JMenuItem exportAnnotations = new JMenuItem();
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130 JMenuItem exportFeatures = new JMenuItem();
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131 protected JPanel statusPanel = new JPanel();
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132 GridLayout gridLayout1 = new GridLayout();
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133 JMenu jMenu3 = new JMenu();
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134 JMenuItem showAllSeqs = new JMenuItem();
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135 JMenuItem showAllColumns = new JMenuItem();
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136 JMenu hideMenu = new JMenu();
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137 JMenuItem hideSelSequences = new JMenuItem();
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138 JMenuItem hideSelColumns = new JMenuItem();
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139 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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140 JMenuItem invertColSel = new JMenuItem();
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141 protected JTabbedPane tabbedPane = new JTabbedPane();
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142 JMenuItem save = new JMenuItem();
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143 JMenuItem jMenuItem1 = new JMenuItem();
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144 protected JMenuItem reload = new JMenuItem();
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145 JMenuItem newView = new JMenuItem();
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146 JMenuItem textColour = new JMenuItem();
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147 JMenu jMenu1 = new JMenu();
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148 JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();
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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.WRITEABLE_FORMATS[i] );
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161 item.addActionListener(new java.awt.event.ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 outputText_actionPerformed(e);
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169 outputTextboxMenu.add(item);
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172 catch (Exception e)
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176 if (!System.getProperty("os.name").startsWith("Mac"))
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178 closeMenuItem.setMnemonic('C');
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179 outputTextboxMenu.setMnemonic('T');
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180 undoMenuItem.setMnemonic('Z');
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181 redoMenuItem.setMnemonic('0');
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182 copy.setMnemonic('C');
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183 cut.setMnemonic('U');
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184 pasteMenu.setMnemonic('P');
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185 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(userColours.
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197 nextElement().toString());
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198 radioItem.setName("USER_DEFINED");
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199 radioItem.addMouseListener(new MouseAdapter()
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201 public void mousePressed(MouseEvent evt)
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203 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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205 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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207 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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208 "Remove from default list?",
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209 "Remove user defined colour",
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210 JOptionPane.YES_NO_OPTION);
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211 if(option == JOptionPane.YES_OPTION)
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213 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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214 colourMenu.remove(radioItem);
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217 radioItem.addActionListener(new ActionListener()
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219 public void actionPerformed(ActionEvent evt)
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221 userDefinedColour_actionPerformed(evt);
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227 radioItem.addActionListener(new ActionListener()
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229 public void actionPerformed(ActionEvent evt)
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231 userDefinedColour_actionPerformed(evt);
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234 colourMenu.insert(radioItem, 15);
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235 colours.add(radioItem);
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238 colours.add(noColourmenuItem);
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239 colours.add(clustalColour);
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240 colours.add(zappoColour);
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241 colours.add(taylorColour);
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242 colours.add(hydrophobicityColour);
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243 colours.add(helixColour);
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244 colours.add(strandColour);
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245 colours.add(turnColour);
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246 colours.add(buriedColour);
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247 colours.add(userDefinedColour);
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248 colours.add(PIDColour);
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249 colours.add(BLOSUM62Colour);
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250 colours.add(nucleotideColour);
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252 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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257 public void setColourSelected(String defaultColour)
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260 if (defaultColour != null)
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262 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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266 case ColourSchemeProperty.NONE:
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267 noColourmenuItem.setSelected(true);
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269 case ColourSchemeProperty.CLUSTAL:
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270 clustalColour.setSelected(true);
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274 case ColourSchemeProperty.BLOSUM:
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275 BLOSUM62Colour.setSelected(true);
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279 case ColourSchemeProperty.PID:
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280 PIDColour.setSelected(true);
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284 case ColourSchemeProperty.ZAPPO:
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285 zappoColour.setSelected(true);
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289 case ColourSchemeProperty.TAYLOR:
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290 taylorColour.setSelected(true);
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293 case ColourSchemeProperty.HYDROPHOBIC:
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294 hydrophobicityColour.setSelected(true);
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298 case ColourSchemeProperty.HELIX:
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299 helixColour.setSelected(true);
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303 case ColourSchemeProperty.STRAND:
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304 strandColour.setSelected(true);
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308 case ColourSchemeProperty.TURN:
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309 turnColour.setSelected(true);
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313 case ColourSchemeProperty.BURIED:
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314 buriedColour.setSelected(true);
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318 case ColourSchemeProperty.NUCLEOTIDE:
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319 nucleotideColour.setSelected(true);
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323 case ColourSchemeProperty.USER_DEFINED:
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324 userDefinedColour.setSelected(true);
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332 private void jbInit()
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335 fileMenu.setText("File");
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336 saveAs.setText("Save As...");
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337 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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339 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
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340 saveAs.addActionListener(new ActionListener()
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342 public void actionPerformed(ActionEvent e)
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344 saveAs_actionPerformed(e);
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347 closeMenuItem.setText("Close");
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348 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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349 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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350 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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352 public void actionPerformed(ActionEvent e)
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354 closeMenuItem_actionPerformed(false);
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357 editMenu.setText("Edit");
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358 viewMenu.setText("View");
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359 colourMenu.setText("Colour");
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360 calculateMenu.setText("Calculate");
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361 webService.setText("Web Service");
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362 selectAllSequenceMenuItem.setText("Select All");
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363 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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364 java.awt.event.KeyEvent.VK_A,
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365 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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366 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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369 public void actionPerformed(ActionEvent e)
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371 selectAllSequenceMenuItem_actionPerformed(e);
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374 deselectAllSequenceMenuItem.setText("Deselect All");
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375 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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377 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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378 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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381 public void actionPerformed(ActionEvent e)
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383 deselectAllSequenceMenuItem_actionPerformed(e);
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386 invertSequenceMenuItem.setText("Invert Sequence Selection");
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387 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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388 java.awt.event.KeyEvent.VK_I,
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389 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
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390 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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392 public void actionPerformed(ActionEvent e)
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394 invertSequenceMenuItem_actionPerformed(e);
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397 remove2LeftMenuItem.setText("Remove Left");
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398 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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399 awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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400 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 remove2LeftMenuItem_actionPerformed(e);
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407 remove2RightMenuItem.setText("Remove Right");
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408 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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409 awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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410 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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412 public void actionPerformed(ActionEvent e)
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414 remove2RightMenuItem_actionPerformed(e);
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417 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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418 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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419 getKeyStroke(java.awt.event.
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420 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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421 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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424 public void actionPerformed(ActionEvent e)
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426 removeGappedColumnMenuItem_actionPerformed(e);
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429 removeAllGapsMenuItem.setText("Remove All Gaps");
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430 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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431 java.awt.event.KeyEvent.VK_E,
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432 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
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433 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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435 public void actionPerformed(ActionEvent e)
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437 removeAllGapsMenuItem_actionPerformed(e);
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440 viewBoxesMenuItem.setText("Boxes");
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441 viewBoxesMenuItem.setState(true);
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442 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 viewBoxesMenuItem_actionPerformed(e);
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449 viewTextMenuItem.setText("Text");
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450 viewTextMenuItem.setState(true);
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451 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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453 public void actionPerformed(ActionEvent e)
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455 viewTextMenuItem_actionPerformed(e);
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458 sortPairwiseMenuItem.setText("by Pairwise Identity");
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459 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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461 public void actionPerformed(ActionEvent e)
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463 sortPairwiseMenuItem_actionPerformed(e);
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466 sortIDMenuItem.setText("by ID");
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467 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 sortIDMenuItem_actionPerformed(e);
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474 sortGroupMenuItem.setText("by Group");
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475 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 sortGroupMenuItem_actionPerformed(e);
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482 removeRedundancyMenuItem.setText("Remove Redundancy...");
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483 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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484 java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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485 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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488 public void actionPerformed(ActionEvent e)
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490 removeRedundancyMenuItem_actionPerformed(e);
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493 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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494 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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497 public void actionPerformed(ActionEvent e)
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499 pairwiseAlignmentMenuItem_actionPerformed(e);
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502 PCAMenuItem.setText("Principal Component Analysis");
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503 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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505 public void actionPerformed(ActionEvent e)
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507 PCAMenuItem_actionPerformed(e);
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510 averageDistanceTreeMenuItem.setText(
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511 "Average Distance Using % Identity");
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512 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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515 public void actionPerformed(ActionEvent e)
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517 averageDistanceTreeMenuItem_actionPerformed(e);
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520 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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521 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 neighbourTreeMenuItem_actionPerformed(e);
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528 this.getContentPane().setLayout(borderLayout1);
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529 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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530 statusBar.setBackground(Color.white);
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531 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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532 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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533 statusBar.setText("Status bar");
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534 outputTextboxMenu.setText("Output to Textbox");
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535 clustalColour.setText("Clustalx");
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537 clustalColour.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 clustalColour_actionPerformed(e);
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544 zappoColour.setText("Zappo");
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545 zappoColour.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 zappoColour_actionPerformed(e);
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552 taylorColour.setText("Taylor");
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553 taylorColour.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 taylorColour_actionPerformed(e);
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560 hydrophobicityColour.setText("Hydrophobicity");
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561 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 hydrophobicityColour_actionPerformed(e);
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568 helixColour.setText("Helix Propensity");
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569 helixColour.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 helixColour_actionPerformed(e);
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576 strandColour.setText("Strand Propensity");
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577 strandColour.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 strandColour_actionPerformed(e);
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584 turnColour.setText("Turn Propensity");
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585 turnColour.addActionListener(new java.awt.event.ActionListener()
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587 public void actionPerformed(ActionEvent e)
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589 turnColour_actionPerformed(e);
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592 buriedColour.setText("Buried Index");
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593 buriedColour.addActionListener(new java.awt.event.ActionListener()
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595 public void actionPerformed(ActionEvent e)
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597 buriedColour_actionPerformed(e);
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600 userDefinedColour.setText("User Defined...");
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601 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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603 public void actionPerformed(ActionEvent e)
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605 userDefinedColour_actionPerformed(e);
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608 PIDColour.setText("Percentage Identity");
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609 PIDColour.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 PIDColour_actionPerformed(e);
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616 BLOSUM62Colour.setText("BLOSUM62 Score");
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617 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 BLOSUM62Colour_actionPerformed(e);
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624 avDistanceTreeBlosumMenuItem.setText(
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625 "Average Distance Using BLOSUM62");
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626 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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629 public void actionPerformed(ActionEvent e)
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631 avTreeBlosumMenuItem_actionPerformed(e);
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634 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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635 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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637 public void actionPerformed(ActionEvent e)
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639 njTreeBlosumMenuItem_actionPerformed(e);
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642 annotationPanelMenuItem.setActionCommand("");
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643 annotationPanelMenuItem.setText("Show Annotations");
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644 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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645 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 annotationPanelMenuItem_actionPerformed(e);
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652 colourTextMenuItem.setText("Colour Text");
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653 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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655 public void actionPerformed(ActionEvent e)
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657 colourTextMenuItem_actionPerformed(e);
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660 htmlMenuItem.setText("HTML");
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661 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 htmlMenuItem_actionPerformed(e);
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668 overviewMenuItem.setText("Overview Window");
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669 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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671 public void actionPerformed(ActionEvent e)
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673 overviewMenuItem_actionPerformed(e);
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676 undoMenuItem.setEnabled(false);
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677 undoMenuItem.setText("Undo");
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678 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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679 java.awt.event.KeyEvent.VK_Z,
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680 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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681 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
683 public void actionPerformed(ActionEvent e)
\r
685 undoMenuItem_actionPerformed(e);
\r
688 redoMenuItem.setEnabled(false);
\r
689 redoMenuItem.setText("Redo");
\r
690 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
691 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
692 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
694 public void actionPerformed(ActionEvent e)
\r
696 redoMenuItem_actionPerformed(e);
\r
699 conservationMenuItem.setText("By Conservation");
\r
700 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
702 public void actionPerformed(ActionEvent e)
\r
704 conservationMenuItem_actionPerformed(e);
\r
707 noColourmenuItem.setText("None");
\r
708 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
710 public void actionPerformed(ActionEvent e)
\r
712 noColourmenuItem_actionPerformed(e);
\r
715 wrapMenuItem.setText("Wrap");
\r
716 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
718 public void actionPerformed(ActionEvent e)
\r
720 wrapMenuItem_actionPerformed(e);
\r
723 printMenuItem.setText("Print");
\r
724 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
725 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
726 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
728 public void actionPerformed(ActionEvent e)
\r
730 printMenuItem_actionPerformed(e);
\r
733 renderGapsMenuItem.setText("Show Gaps");
\r
734 renderGapsMenuItem.setState(true);
\r
735 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
737 public void actionPerformed(ActionEvent e)
\r
739 renderGapsMenuItem_actionPerformed(e);
\r
742 findMenuItem.setText("Find...");
\r
743 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
744 java.awt.event.KeyEvent.VK_F,
\r
745 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
746 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
748 public void actionPerformed(ActionEvent e)
\r
750 findMenuItem_actionPerformed(e);
\r
753 abovePIDThreshold.setText("Above Identity Threshold");
\r
754 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
756 public void actionPerformed(ActionEvent e)
\r
758 abovePIDThreshold_actionPerformed(e);
\r
761 showSeqFeatures.setText("Show Sequence Features");
\r
762 showSeqFeatures.addActionListener(new ActionListener()
\r
764 public void actionPerformed(ActionEvent actionEvent)
\r
766 showSeqFeatures_actionPerformed(actionEvent);
\r
769 nucleotideColour.setText("Nucleotide");
\r
770 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
772 public void actionPerformed(ActionEvent e)
\r
774 nucleotideColour_actionPerformed(e);
\r
777 deleteGroups.setText("Undefine groups");
\r
778 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
779 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
780 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
782 public void actionPerformed(ActionEvent e)
\r
784 deleteGroups_actionPerformed(e);
\r
787 copy.setText("Copy");
\r
788 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
789 java.awt.event.KeyEvent.VK_C,
\r
790 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
792 copy.addActionListener(new java.awt.event.ActionListener()
\r
794 public void actionPerformed(ActionEvent e)
\r
796 copy_actionPerformed(e);
\r
799 cut.setText("Cut");
\r
800 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
801 java.awt.event.KeyEvent.VK_X,
\r
802 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
803 cut.addActionListener(new java.awt.event.ActionListener()
\r
805 public void actionPerformed(ActionEvent e)
\r
807 cut_actionPerformed(e);
\r
810 delete.setText("Delete");
\r
811 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
812 KeyEvent.VK_BACK_SPACE, 0, false));
\r
813 delete.addActionListener(new java.awt.event.ActionListener()
\r
815 public void actionPerformed(ActionEvent e)
\r
817 delete_actionPerformed(e);
\r
820 pasteMenu.setText("Paste");
\r
821 pasteNew.setText("To New Alignment");
\r
822 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
823 java.awt.event.KeyEvent.VK_V,
\r
824 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false));
\r
825 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
827 public void actionPerformed(ActionEvent e)
\r
829 pasteNew_actionPerformed(e);
\r
832 pasteThis.setText("Add To This Alignment");
\r
833 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
834 java.awt.event.KeyEvent.VK_V,
\r
835 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
836 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
838 public void actionPerformed(ActionEvent e)
\r
840 pasteThis_actionPerformed(e);
\r
843 applyToAllGroups.setText("Apply Colour To All Groups");
\r
844 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
846 public void actionPerformed(ActionEvent e)
\r
848 applyToAllGroups_actionPerformed(e);
\r
851 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
853 public void actionPerformed(ActionEvent e)
\r
858 createPNG.setActionCommand("Save As PNG Image");
\r
859 createPNG.setText("PNG");
\r
860 font.setText("Font...");
\r
861 font.addActionListener(new java.awt.event.ActionListener()
\r
863 public void actionPerformed(ActionEvent e)
\r
865 font_actionPerformed(e);
\r
869 seqLimits.setText("Show Sequence Limits");
\r
870 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
871 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
873 public void actionPerformed(ActionEvent e)
\r
875 seqLimit_actionPerformed(e);
\r
878 epsFile.setText("EPS");
\r
879 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
881 public void actionPerformed(ActionEvent e)
\r
886 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
887 LoadtreeMenuItem.setText("Load Associated Tree");
\r
888 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
890 public void actionPerformed(ActionEvent e)
\r
892 LoadtreeMenuItem_actionPerformed(e);
\r
895 scaleAbove.setVisible(false);
\r
896 scaleAbove.setText("Scale Above");
\r
897 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
899 public void actionPerformed(ActionEvent e)
\r
901 scaleAbove_actionPerformed(e);
\r
904 scaleLeft.setVisible(false);
\r
905 scaleLeft.setSelected(true);
\r
906 scaleLeft.setText("Scale Left");
\r
907 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
909 public void actionPerformed(ActionEvent e)
\r
911 scaleLeft_actionPerformed(e);
\r
914 scaleRight.setVisible(false);
\r
915 scaleRight.setSelected(true);
\r
916 scaleRight.setText("Scale Right");
\r
917 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
919 public void actionPerformed(ActionEvent e)
\r
921 scaleRight_actionPerformed(e);
\r
924 modifyPID.setText("Modify Identity Threshold...");
\r
925 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
927 public void actionPerformed(ActionEvent e)
\r
929 modifyPID_actionPerformed(e);
\r
932 modifyConservation.setText("Modify Conservation Threshold...");
\r
933 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
935 public void actionPerformed(ActionEvent e)
\r
937 modifyConservation_actionPerformed(e);
\r
940 sortByTreeMenu.setText("By Tree Order");
\r
941 sort.setText("Sort");
\r
942 calculate.setText("Calculate Tree");
\r
944 jMenu2.setText("Export Image");
\r
945 padGapsMenuitem.setText("Pad Gaps");
\r
946 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
947 padGapsMenuitem.addActionListener(new ActionListener()
\r
949 public void actionPerformed(ActionEvent e)
\r
951 padGapsMenuitem_actionPerformed(e);
\r
954 vamsasStore.setVisible(false);
\r
955 vamsasStore.setText("VAMSAS store");
\r
956 vamsasStore.addActionListener(new ActionListener()
\r
958 public void actionPerformed(ActionEvent e)
\r
960 vamsasStore_actionPerformed(e);
\r
963 showTranslation.setText("Translate cDNA");
\r
964 showTranslation.addActionListener(new ActionListener()
\r
966 public void actionPerformed(ActionEvent e)
\r
968 showTranslation_actionPerformed(e);
\r
973 featureSettings.setText("Feature Settings...");
\r
974 featureSettings.addActionListener(new ActionListener()
\r
976 public void actionPerformed(ActionEvent e)
\r
978 featureSettings_actionPerformed(e);
\r
981 fetchSequence.setText("Fetch Sequence(s)...");
\r
982 fetchSequence.addActionListener(new ActionListener()
\r
984 public void actionPerformed(ActionEvent e)
\r
986 fetchSequence_actionPerformed(e);
\r
990 annotationColour.setText("By Annotation...");
\r
991 annotationColour.addActionListener(new ActionListener()
\r
993 public void actionPerformed(ActionEvent e)
\r
995 annotationColour_actionPerformed(e);
\r
998 associatedData.setText("Load Features / Annotations");
\r
999 associatedData.addActionListener(new ActionListener()
\r
1001 public void actionPerformed(ActionEvent e)
\r
1003 associatedData_actionPerformed(e);
\r
1006 autoCalculate.setText("Autocalculate Consensus");
\r
1007 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1008 autoCalculate.addActionListener(new ActionListener()
\r
1010 public void actionPerformed(ActionEvent e)
\r
1012 autoCalculate_actionPerformed(e);
\r
1015 addSequenceMenu.setText("Add Sequences");
\r
1016 addFromFile.setText("From File");
\r
1017 addFromFile.addActionListener(new ActionListener()
\r
1019 public void actionPerformed(ActionEvent e)
\r
1021 addFromFile_actionPerformed(e);
\r
1024 addFromText.setText("From Textbox");
\r
1025 addFromText.addActionListener(new ActionListener()
\r
1027 public void actionPerformed(ActionEvent e)
\r
1029 addFromText_actionPerformed(e);
\r
1032 addFromURL.setText("From URL");
\r
1033 addFromURL.addActionListener(new ActionListener()
\r
1035 public void actionPerformed(ActionEvent e)
\r
1037 addFromURL_actionPerformed(e);
\r
1040 exportFeatures.setText("Export Features...");
\r
1041 exportFeatures.addActionListener(new ActionListener()
\r
1043 public void actionPerformed(ActionEvent e)
\r
1045 exportFeatures_actionPerformed(e);
\r
1048 exportAnnotations.setText("Export Annotations...");
\r
1049 exportAnnotations.addActionListener(new ActionListener()
\r
1051 public void actionPerformed(ActionEvent e)
\r
1053 exportAnnotations_actionPerformed(e);
\r
1056 statusPanel.setLayout(gridLayout1);
\r
1057 jMenu3.setText("Show");
\r
1058 showAllSeqs.setText("All Sequences");
\r
1059 showAllSeqs.addActionListener(new ActionListener()
\r
1061 public void actionPerformed(ActionEvent e)
\r
1063 showAllSeqs_actionPerformed(e);
\r
1066 showAllColumns.setText("All Columns");
\r
1067 showAllColumns.addActionListener(new ActionListener()
\r
1069 public void actionPerformed(ActionEvent e)
\r
1071 showAllColumns_actionPerformed(e);
\r
1074 hideMenu.setText("Hide");
\r
1075 hideSelSequences.setText("Selected Sequences");
\r
1076 hideSelSequences.addActionListener(new ActionListener()
\r
1078 public void actionPerformed(ActionEvent e)
\r
1080 hideSelSequences_actionPerformed(e);
\r
1083 hideSelColumns.setText("Selected Columns");
\r
1084 hideSelColumns.addActionListener(new ActionListener()
\r
1086 public void actionPerformed(ActionEvent e)
\r
1088 hideSelColumns_actionPerformed(e);
\r
1091 hiddenMarkers.setText("Show Hidden Markers");
\r
1092 hiddenMarkers.addActionListener(new ActionListener()
\r
1094 public void actionPerformed(ActionEvent e)
\r
1096 hiddenMarkers_actionPerformed(e);
\r
1099 invertColSel.setText("Invert Column Selection");
\r
1100 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1101 event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1102 invertColSel.addActionListener(new ActionListener()
\r
1104 public void actionPerformed(ActionEvent e)
\r
1106 invertColSel_actionPerformed(e);
\r
1109 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1111 public void stateChanged(ChangeEvent evt)
\r
1113 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1114 int sel = pane.getSelectedIndex();
\r
1115 tabSelectionChanged(sel);
\r
1118 tabbedPane.addMouseListener(new MouseAdapter()
\r
1120 public void mousePressed(MouseEvent e)
\r
1122 tabbedPane_mousePressed(e);
\r
1125 tabbedPane.addFocusListener(new FocusAdapter()
\r
1127 public void focusGained(FocusEvent e)
\r
1129 tabbedPane_focusGained(e);
\r
1132 save.setText("Save");
\r
1133 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1134 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1135 save.addActionListener(new ActionListener()
\r
1137 public void actionPerformed(ActionEvent e)
\r
1139 save_actionPerformed(e);
\r
1142 reload.setEnabled(false);
\r
1143 reload.setText("Reload");
\r
1144 reload.addActionListener(new ActionListener()
\r
1146 public void actionPerformed(ActionEvent e)
\r
1148 reload_actionPerformed(e);
\r
1151 newView.setText("New View");
\r
1152 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1153 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1154 newView.addActionListener(new ActionListener()
\r
1156 public void actionPerformed(ActionEvent e)
\r
1158 newView_actionPerformed(e);
\r
1161 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
\r
1162 +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
\r
1163 textColour.setText("Text Colour");
\r
1164 textColour.addActionListener(new ActionListener()
\r
1166 public void actionPerformed(ActionEvent e)
\r
1168 textColour_actionPerformed(e);
\r
1171 jMenu1.setText("Format");
\r
1172 jCheckBoxMenuItem1.setText("Right Align Ids");
\r
1174 alignFrameMenuBar.add(fileMenu);
\r
1175 alignFrameMenuBar.add(editMenu);
\r
1176 alignFrameMenuBar.add(viewMenu);
\r
1177 alignFrameMenuBar.add(jMenu1);
\r
1178 alignFrameMenuBar.add(colourMenu);
\r
1179 alignFrameMenuBar.add(calculateMenu);
\r
1180 alignFrameMenuBar.add(webService);
\r
1181 fileMenu.add(fetchSequence);
\r
1182 fileMenu.add(addSequenceMenu);
\r
1183 fileMenu.add(reload);
\r
1184 fileMenu.addSeparator();
\r
1185 fileMenu.add(vamsasStore);
\r
1186 fileMenu.add(save);
\r
1187 fileMenu.add(saveAs);
\r
1188 fileMenu.add(outputTextboxMenu);
\r
1189 fileMenu.add(printMenuItem);
\r
1190 fileMenu.addSeparator();
\r
1191 fileMenu.add(jMenu2);
\r
1192 fileMenu.add(exportFeatures);
\r
1193 fileMenu.add(exportAnnotations);
\r
1194 fileMenu.add(LoadtreeMenuItem);
\r
1195 fileMenu.add(associatedData);
\r
1196 fileMenu.addSeparator();
\r
1197 fileMenu.add(closeMenuItem);
\r
1198 editMenu.add(undoMenuItem);
\r
1199 editMenu.add(redoMenuItem);
\r
1200 editMenu.add(cut);
\r
1201 editMenu.add(copy);
\r
1202 editMenu.add(pasteMenu);
\r
1203 editMenu.add(delete);
\r
1204 editMenu.addSeparator();
\r
1205 editMenu.add(selectAllSequenceMenuItem);
\r
1206 editMenu.add(deselectAllSequenceMenuItem);
\r
1207 editMenu.add(invertSequenceMenuItem);
\r
1208 editMenu.add(invertColSel);
\r
1209 editMenu.add(deleteGroups);
\r
1210 editMenu.addSeparator();
\r
1211 editMenu.add(findMenuItem);
\r
1212 editMenu.addSeparator();
\r
1213 editMenu.add(remove2LeftMenuItem);
\r
1214 editMenu.add(remove2RightMenuItem);
\r
1215 editMenu.add(removeGappedColumnMenuItem);
\r
1216 editMenu.add(removeAllGapsMenuItem);
\r
1217 editMenu.add(removeRedundancyMenuItem);
\r
1218 editMenu.addSeparator();
\r
1219 editMenu.add(padGapsMenuitem);
\r
1220 viewMenu.add(newView);
\r
1221 viewMenu.addSeparator();
\r
1222 viewMenu.add(jMenu3);
\r
1223 viewMenu.add(hideMenu);
\r
1224 viewMenu.addSeparator();
\r
1225 viewMenu.add(annotationPanelMenuItem);
\r
1226 viewMenu.addSeparator();
\r
1227 viewMenu.add(showSeqFeatures);
\r
1228 viewMenu.add(featureSettings);
\r
1229 viewMenu.addSeparator();
\r
1230 viewMenu.add(overviewMenuItem);
\r
1231 colourMenu.add(applyToAllGroups);
\r
1232 colourMenu.add(textColour);
\r
1233 colourMenu.addSeparator();
\r
1234 colourMenu.add(noColourmenuItem);
\r
1235 colourMenu.add(clustalColour);
\r
1236 colourMenu.add(BLOSUM62Colour);
\r
1237 colourMenu.add(PIDColour);
\r
1238 colourMenu.add(zappoColour);
\r
1239 colourMenu.add(taylorColour);
\r
1240 colourMenu.add(hydrophobicityColour);
\r
1241 colourMenu.add(helixColour);
\r
1242 colourMenu.add(strandColour);
\r
1243 colourMenu.add(turnColour);
\r
1244 colourMenu.add(buriedColour);
\r
1245 colourMenu.add(nucleotideColour);
\r
1246 colourMenu.add(userDefinedColour);
\r
1247 colourMenu.addSeparator();
\r
1248 colourMenu.add(conservationMenuItem);
\r
1249 colourMenu.add(modifyConservation);
\r
1250 colourMenu.add(abovePIDThreshold);
\r
1251 colourMenu.add(modifyPID);
\r
1252 colourMenu.add(annotationColour);
\r
1253 calculateMenu.add(sort);
\r
1254 calculateMenu.add(calculate);
\r
1255 calculateMenu.addSeparator();
\r
1256 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1257 calculateMenu.add(PCAMenuItem);
\r
1258 calculateMenu.addSeparator();
\r
1259 calculateMenu.add(showTranslation);
\r
1260 calculateMenu.add(autoCalculate);
\r
1261 webServiceNoServices=new JMenuItem("<No Services>");
\r
1262 webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
\r
1263 pasteMenu.add(pasteThis);
\r
1264 sort.add(sortIDMenuItem);
\r
1265 sort.add(sortGroupMenuItem);
\r
1266 sort.add(sortPairwiseMenuItem);
\r
1267 calculate.add(averageDistanceTreeMenuItem);
\r
1268 calculate.add(neighbourTreeMenuItem);
\r
1269 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1270 calculate.add(njTreeBlosumMenuItem);
\r
1271 jMenu2.add(htmlMenuItem);
\r
1272 jMenu2.add(epsFile);
\r
1273 jMenu2.add(createPNG);
\r
1274 addSequenceMenu.add(addFromFile);
\r
1275 addSequenceMenu.add(addFromText);
\r
1276 addSequenceMenu.add(addFromURL);
\r
1277 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1278 statusPanel.add(statusBar, null);
\r
1279 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1280 jMenu3.add(showAllColumns);
\r
1281 jMenu3.add(showAllSeqs);
\r
1282 hideMenu.add(hideSelColumns);
\r
1283 hideMenu.add(hideSelSequences);
\r
1285 jMenu1.addSeparator();
\r
1286 jMenu1.add(seqLimits);
\r
1287 jMenu1.add(wrapMenuItem);
\r
1288 jMenu1.add(scaleAbove);
\r
1289 jMenu1.add(scaleLeft);
\r
1290 jMenu1.add(scaleRight);
\r
1291 jMenu1.add(hiddenMarkers);
\r
1292 jMenu1.add(viewBoxesMenuItem);
\r
1293 jMenu1.add(viewTextMenuItem);
\r
1294 jMenu1.add(colourTextMenuItem);
\r
1295 jMenu1.add(renderGapsMenuItem);
\r
1298 protected void outputText_actionPerformed(ActionEvent e)
\r
1302 public void addFromFile_actionPerformed(ActionEvent e)
\r
1307 public void addFromText_actionPerformed(ActionEvent e)
\r
1312 public void addFromURL_actionPerformed(ActionEvent e)
\r
1317 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1322 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1327 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1331 protected void closeMenuItem_actionPerformed(boolean b)
\r
1335 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1339 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1343 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1347 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1351 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1355 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1359 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1363 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1367 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1371 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1375 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1379 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1383 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1387 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1391 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1395 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1399 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1403 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1407 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1411 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1415 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1419 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1423 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1427 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1431 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1435 protected void clustalColour_actionPerformed(ActionEvent e)
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1439 protected void zappoColour_actionPerformed(ActionEvent e)
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1443 protected void taylorColour_actionPerformed(ActionEvent e)
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1447 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1451 protected void helixColour_actionPerformed(ActionEvent e)
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1455 protected void strandColour_actionPerformed(ActionEvent e)
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1459 protected void turnColour_actionPerformed(ActionEvent e)
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1463 protected void buriedColour_actionPerformed(ActionEvent e)
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1467 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1471 protected void PIDColour_actionPerformed(ActionEvent e)
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1475 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1479 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1483 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1487 protected void printMenuItem_actionPerformed(ActionEvent e)
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1491 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1495 protected void findMenuItem_actionPerformed(ActionEvent e)
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1499 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
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1503 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
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1507 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1511 protected void deleteGroups_actionPerformed(ActionEvent e)
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1515 protected void copy_actionPerformed(ActionEvent e)
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1519 protected void cut_actionPerformed(ActionEvent e)
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1523 protected void delete_actionPerformed(ActionEvent e)
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1527 protected void pasteNew_actionPerformed(ActionEvent e)
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1531 protected void pasteThis_actionPerformed(ActionEvent e)
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1535 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1539 public void createPNG(java.io.File f)
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1543 protected void font_actionPerformed(ActionEvent e)
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1547 protected void seqLimit_actionPerformed(ActionEvent e)
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1551 public void seqDBRef_actionPerformed(ActionEvent e)
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1557 public void createEPS(java.io.File f)
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1561 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1565 protected void jpred_actionPerformed(ActionEvent e)
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1569 protected void scaleAbove_actionPerformed(ActionEvent e)
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1573 protected void scaleLeft_actionPerformed(ActionEvent e)
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1577 protected void scaleRight_actionPerformed(ActionEvent e)
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1581 protected void modifyPID_actionPerformed(ActionEvent e)
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1585 protected void modifyConservation_actionPerformed(ActionEvent e)
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1591 protected void saveAs_actionPerformed(ActionEvent e)
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1595 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1600 public void vamsasStore_actionPerformed(ActionEvent e)
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1605 public void vamsasLoad_actionPerformed(ActionEvent e)
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1610 public void showTranslation_actionPerformed(ActionEvent e)
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1615 public void featureSettings_actionPerformed(ActionEvent e)
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1620 public void fetchSequence_actionPerformed(ActionEvent e)
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1625 public void smoothFont_actionPerformed(ActionEvent e)
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1630 public void annotationColour_actionPerformed(ActionEvent e)
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1636 public void associatedData_actionPerformed(ActionEvent e)
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1641 public void autoCalculate_actionPerformed(ActionEvent e)
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1646 public void showAllSeqs_actionPerformed(ActionEvent e)
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1651 public void showAllColumns_actionPerformed(ActionEvent e)
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1656 public void hideSelSequences_actionPerformed(ActionEvent e)
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1661 public void hideSelColumns_actionPerformed(ActionEvent e)
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1666 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1671 public void findPdbId_actionPerformed(ActionEvent e)
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1676 public void enterPdbId_actionPerformed(ActionEvent e)
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1681 public void pdbFile_actionPerformed(ActionEvent e)
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1686 public void invertColSel_actionPerformed(ActionEvent e)
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1691 public void tabSelectionChanged(int sel)
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1696 public void tabbedPane_mousePressed(MouseEvent e)
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1701 public void tabbedPane_focusGained(FocusEvent e)
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1706 public void save_actionPerformed(ActionEvent e)
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1711 public void reload_actionPerformed(ActionEvent e)
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1716 public void newView_actionPerformed(ActionEvent e)
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1721 public void textColour_actionPerformed(ActionEvent e)
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