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 JMenuItem pageSetup = new JMenuItem();
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152 public GAlignFrame()
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157 setJMenuBar(alignFrameMenuBar);
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159 // dynamically fill save as menu with available formats
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160 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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162 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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164 item.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 outputText_actionPerformed(e);
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172 outputTextboxMenu.add(item);
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175 catch (Exception e)
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179 if (!System.getProperty("os.name").startsWith("Mac"))
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181 closeMenuItem.setMnemonic('C');
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182 outputTextboxMenu.setMnemonic('T');
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183 undoMenuItem.setMnemonic('Z');
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184 redoMenuItem.setMnemonic('0');
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185 copy.setMnemonic('C');
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186 cut.setMnemonic('U');
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187 pasteMenu.setMnemonic('P');
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188 reload.setMnemonic('R');
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192 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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194 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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195 getUserColourSchemes().keys();
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197 while (userColours.hasMoreElements())
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199 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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200 nextElement().toString());
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201 radioItem.setName("USER_DEFINED");
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202 radioItem.addMouseListener(new MouseAdapter()
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204 public void mousePressed(MouseEvent evt)
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206 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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208 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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210 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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211 "Remove from default list?",
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212 "Remove user defined colour",
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213 JOptionPane.YES_NO_OPTION);
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214 if(option == JOptionPane.YES_OPTION)
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216 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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217 colourMenu.remove(radioItem);
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220 radioItem.addActionListener(new ActionListener()
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222 public void actionPerformed(ActionEvent evt)
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224 userDefinedColour_actionPerformed(evt);
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230 radioItem.addActionListener(new ActionListener()
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232 public void actionPerformed(ActionEvent evt)
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234 userDefinedColour_actionPerformed(evt);
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237 colourMenu.insert(radioItem, 15);
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238 colours.add(radioItem);
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241 colours.add(noColourmenuItem);
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242 colours.add(clustalColour);
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243 colours.add(zappoColour);
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244 colours.add(taylorColour);
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245 colours.add(hydrophobicityColour);
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246 colours.add(helixColour);
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247 colours.add(strandColour);
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248 colours.add(turnColour);
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249 colours.add(buriedColour);
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250 colours.add(userDefinedColour);
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251 colours.add(PIDColour);
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252 colours.add(BLOSUM62Colour);
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253 colours.add(nucleotideColour);
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255 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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260 public void setColourSelected(String defaultColour)
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263 if (defaultColour != null)
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265 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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269 case ColourSchemeProperty.NONE:
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270 noColourmenuItem.setSelected(true);
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272 case ColourSchemeProperty.CLUSTAL:
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273 clustalColour.setSelected(true);
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277 case ColourSchemeProperty.BLOSUM:
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278 BLOSUM62Colour.setSelected(true);
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282 case ColourSchemeProperty.PID:
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283 PIDColour.setSelected(true);
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287 case ColourSchemeProperty.ZAPPO:
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288 zappoColour.setSelected(true);
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292 case ColourSchemeProperty.TAYLOR:
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293 taylorColour.setSelected(true);
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296 case ColourSchemeProperty.HYDROPHOBIC:
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297 hydrophobicityColour.setSelected(true);
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301 case ColourSchemeProperty.HELIX:
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302 helixColour.setSelected(true);
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306 case ColourSchemeProperty.STRAND:
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307 strandColour.setSelected(true);
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311 case ColourSchemeProperty.TURN:
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312 turnColour.setSelected(true);
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316 case ColourSchemeProperty.BURIED:
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317 buriedColour.setSelected(true);
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321 case ColourSchemeProperty.NUCLEOTIDE:
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322 nucleotideColour.setSelected(true);
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326 case ColourSchemeProperty.USER_DEFINED:
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327 userDefinedColour.setSelected(true);
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335 private void jbInit()
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338 fileMenu.setText("File");
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339 saveAs.setText("Save As...");
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340 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
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342 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
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343 saveAs.addActionListener(new ActionListener()
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345 public void actionPerformed(ActionEvent e)
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347 saveAs_actionPerformed(e);
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350 closeMenuItem.setText("Close");
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351 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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352 event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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353 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 closeMenuItem_actionPerformed(false);
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360 editMenu.setText("Edit");
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361 viewMenu.setText("View");
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362 colourMenu.setText("Colour");
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363 calculateMenu.setText("Calculate");
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364 webService.setText("Web Service");
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365 selectAllSequenceMenuItem.setText("Select All");
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366 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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367 java.awt.event.KeyEvent.VK_A,
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368 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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369 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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372 public void actionPerformed(ActionEvent e)
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374 selectAllSequenceMenuItem_actionPerformed(e);
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377 deselectAllSequenceMenuItem.setText("Deselect All");
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378 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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380 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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381 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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384 public void actionPerformed(ActionEvent e)
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386 deselectAllSequenceMenuItem_actionPerformed(e);
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389 invertSequenceMenuItem.setText("Invert Sequence Selection");
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390 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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391 java.awt.event.KeyEvent.VK_I,
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392 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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393 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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395 public void actionPerformed(ActionEvent e)
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397 invertSequenceMenuItem_actionPerformed(e);
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400 remove2LeftMenuItem.setText("Remove Left");
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401 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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402 awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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403 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 remove2LeftMenuItem_actionPerformed(e);
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410 remove2RightMenuItem.setText("Remove Right");
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411 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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412 awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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413 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 remove2RightMenuItem_actionPerformed(e);
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420 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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421 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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422 getKeyStroke(java.awt.event.
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423 KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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424 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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427 public void actionPerformed(ActionEvent e)
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429 removeGappedColumnMenuItem_actionPerformed(e);
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432 removeAllGapsMenuItem.setText("Remove All Gaps");
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433 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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434 java.awt.event.KeyEvent.VK_E,
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435 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
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436 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 removeAllGapsMenuItem_actionPerformed(e);
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443 viewBoxesMenuItem.setText("Boxes");
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444 viewBoxesMenuItem.setState(true);
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445 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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447 public void actionPerformed(ActionEvent e)
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449 viewBoxesMenuItem_actionPerformed(e);
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452 viewTextMenuItem.setText("Text");
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453 viewTextMenuItem.setState(true);
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454 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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456 public void actionPerformed(ActionEvent e)
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458 viewTextMenuItem_actionPerformed(e);
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461 sortPairwiseMenuItem.setText("by Pairwise Identity");
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462 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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464 public void actionPerformed(ActionEvent e)
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466 sortPairwiseMenuItem_actionPerformed(e);
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469 sortIDMenuItem.setText("by ID");
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470 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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472 public void actionPerformed(ActionEvent e)
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474 sortIDMenuItem_actionPerformed(e);
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477 sortGroupMenuItem.setText("by Group");
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478 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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480 public void actionPerformed(ActionEvent e)
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482 sortGroupMenuItem_actionPerformed(e);
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485 removeRedundancyMenuItem.setText("Remove Redundancy...");
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486 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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487 java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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488 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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491 public void actionPerformed(ActionEvent e)
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493 removeRedundancyMenuItem_actionPerformed(e);
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496 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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497 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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500 public void actionPerformed(ActionEvent e)
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502 pairwiseAlignmentMenuItem_actionPerformed(e);
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505 PCAMenuItem.setText("Principal Component Analysis");
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506 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 PCAMenuItem_actionPerformed(e);
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513 averageDistanceTreeMenuItem.setText(
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514 "Average Distance Using % Identity");
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515 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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518 public void actionPerformed(ActionEvent e)
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520 averageDistanceTreeMenuItem_actionPerformed(e);
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523 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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524 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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526 public void actionPerformed(ActionEvent e)
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528 neighbourTreeMenuItem_actionPerformed(e);
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531 this.getContentPane().setLayout(borderLayout1);
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532 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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533 statusBar.setBackground(Color.white);
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534 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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535 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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536 statusBar.setText("Status bar");
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537 outputTextboxMenu.setText("Output to Textbox");
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538 clustalColour.setText("Clustalx");
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540 clustalColour.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 clustalColour_actionPerformed(e);
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547 zappoColour.setText("Zappo");
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548 zappoColour.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 zappoColour_actionPerformed(e);
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555 taylorColour.setText("Taylor");
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556 taylorColour.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 taylorColour_actionPerformed(e);
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563 hydrophobicityColour.setText("Hydrophobicity");
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564 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 hydrophobicityColour_actionPerformed(e);
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571 helixColour.setText("Helix Propensity");
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572 helixColour.addActionListener(new java.awt.event.ActionListener()
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574 public void actionPerformed(ActionEvent e)
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576 helixColour_actionPerformed(e);
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579 strandColour.setText("Strand Propensity");
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580 strandColour.addActionListener(new java.awt.event.ActionListener()
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582 public void actionPerformed(ActionEvent e)
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584 strandColour_actionPerformed(e);
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587 turnColour.setText("Turn Propensity");
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588 turnColour.addActionListener(new java.awt.event.ActionListener()
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590 public void actionPerformed(ActionEvent e)
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592 turnColour_actionPerformed(e);
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595 buriedColour.setText("Buried Index");
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596 buriedColour.addActionListener(new java.awt.event.ActionListener()
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598 public void actionPerformed(ActionEvent e)
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600 buriedColour_actionPerformed(e);
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603 userDefinedColour.setText("User Defined...");
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604 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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606 public void actionPerformed(ActionEvent e)
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608 userDefinedColour_actionPerformed(e);
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611 PIDColour.setText("Percentage Identity");
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612 PIDColour.addActionListener(new java.awt.event.ActionListener()
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614 public void actionPerformed(ActionEvent e)
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616 PIDColour_actionPerformed(e);
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619 BLOSUM62Colour.setText("BLOSUM62 Score");
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620 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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622 public void actionPerformed(ActionEvent e)
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624 BLOSUM62Colour_actionPerformed(e);
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627 avDistanceTreeBlosumMenuItem.setText(
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628 "Average Distance Using BLOSUM62");
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629 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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632 public void actionPerformed(ActionEvent e)
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634 avTreeBlosumMenuItem_actionPerformed(e);
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637 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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638 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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640 public void actionPerformed(ActionEvent e)
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642 njTreeBlosumMenuItem_actionPerformed(e);
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645 annotationPanelMenuItem.setActionCommand("");
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646 annotationPanelMenuItem.setText("Show Annotations");
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647 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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648 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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650 public void actionPerformed(ActionEvent e)
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652 annotationPanelMenuItem_actionPerformed(e);
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655 colourTextMenuItem.setText("Colour Text");
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656 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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658 public void actionPerformed(ActionEvent e)
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660 colourTextMenuItem_actionPerformed(e);
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663 htmlMenuItem.setText("HTML");
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664 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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666 public void actionPerformed(ActionEvent e)
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668 htmlMenuItem_actionPerformed(e);
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671 overviewMenuItem.setText("Overview Window");
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672 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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674 public void actionPerformed(ActionEvent e)
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676 overviewMenuItem_actionPerformed(e);
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679 undoMenuItem.setEnabled(false);
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680 undoMenuItem.setText("Undo");
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681 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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682 java.awt.event.KeyEvent.VK_Z,
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683 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
684 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
686 public void actionPerformed(ActionEvent e)
\r
688 undoMenuItem_actionPerformed(e);
\r
691 redoMenuItem.setEnabled(false);
\r
692 redoMenuItem.setText("Redo");
\r
693 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
694 event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
695 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
697 public void actionPerformed(ActionEvent e)
\r
699 redoMenuItem_actionPerformed(e);
\r
702 conservationMenuItem.setText("By Conservation");
\r
703 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
705 public void actionPerformed(ActionEvent e)
\r
707 conservationMenuItem_actionPerformed(e);
\r
710 noColourmenuItem.setText("None");
\r
711 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
713 public void actionPerformed(ActionEvent e)
\r
715 noColourmenuItem_actionPerformed(e);
\r
718 wrapMenuItem.setText("Wrap");
\r
719 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
721 public void actionPerformed(ActionEvent e)
\r
723 wrapMenuItem_actionPerformed(e);
\r
726 printMenuItem.setText("Print ...");
\r
727 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
728 event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
729 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
731 public void actionPerformed(ActionEvent e)
\r
733 printMenuItem_actionPerformed(e);
\r
736 renderGapsMenuItem.setText("Show Gaps");
\r
737 renderGapsMenuItem.setState(true);
\r
738 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
740 public void actionPerformed(ActionEvent e)
\r
742 renderGapsMenuItem_actionPerformed(e);
\r
745 findMenuItem.setText("Find...");
\r
746 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
747 java.awt.event.KeyEvent.VK_F,
\r
748 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
749 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
751 public void actionPerformed(ActionEvent e)
\r
753 findMenuItem_actionPerformed(e);
\r
756 abovePIDThreshold.setText("Above Identity Threshold");
\r
757 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
759 public void actionPerformed(ActionEvent e)
\r
761 abovePIDThreshold_actionPerformed(e);
\r
764 showSeqFeatures.setText("Show Sequence Features");
\r
765 showSeqFeatures.addActionListener(new ActionListener()
\r
767 public void actionPerformed(ActionEvent actionEvent)
\r
769 showSeqFeatures_actionPerformed(actionEvent);
\r
772 nucleotideColour.setText("Nucleotide");
\r
773 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
775 public void actionPerformed(ActionEvent e)
\r
777 nucleotideColour_actionPerformed(e);
\r
780 deleteGroups.setText("Undefine groups");
\r
781 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
782 event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
783 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
785 public void actionPerformed(ActionEvent e)
\r
787 deleteGroups_actionPerformed(e);
\r
790 copy.setText("Copy");
\r
791 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
792 java.awt.event.KeyEvent.VK_C,
\r
793 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
795 copy.addActionListener(new java.awt.event.ActionListener()
\r
797 public void actionPerformed(ActionEvent e)
\r
799 copy_actionPerformed(e);
\r
802 cut.setText("Cut");
\r
803 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
804 java.awt.event.KeyEvent.VK_X,
\r
805 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
806 cut.addActionListener(new java.awt.event.ActionListener()
\r
808 public void actionPerformed(ActionEvent e)
\r
810 cut_actionPerformed(e);
\r
813 delete.setText("Delete");
\r
814 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
815 KeyEvent.VK_BACK_SPACE, 0, false));
\r
816 delete.addActionListener(new java.awt.event.ActionListener()
\r
818 public void actionPerformed(ActionEvent e)
\r
820 delete_actionPerformed(e);
\r
823 pasteMenu.setText("Paste");
\r
824 pasteNew.setText("To New Alignment");
\r
825 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
826 java.awt.event.KeyEvent.VK_V,
\r
827 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
\r
828 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
830 public void actionPerformed(ActionEvent e)
\r
832 pasteNew_actionPerformed(e);
\r
835 pasteThis.setText("Add To This Alignment");
\r
836 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
837 java.awt.event.KeyEvent.VK_V,
\r
838 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
839 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
841 public void actionPerformed(ActionEvent e)
\r
843 pasteThis_actionPerformed(e);
\r
846 applyToAllGroups.setText("Apply Colour To All Groups");
\r
847 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
849 public void actionPerformed(ActionEvent e)
\r
851 applyToAllGroups_actionPerformed(e);
\r
854 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
856 public void actionPerformed(ActionEvent e)
\r
861 createPNG.setActionCommand("Save As PNG Image");
\r
862 createPNG.setText("PNG");
\r
863 font.setText("Font...");
\r
864 font.addActionListener(new java.awt.event.ActionListener()
\r
866 public void actionPerformed(ActionEvent e)
\r
868 font_actionPerformed(e);
\r
872 seqLimits.setText("Show Sequence Limits");
\r
873 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
874 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
876 public void actionPerformed(ActionEvent e)
\r
878 seqLimit_actionPerformed(e);
\r
881 epsFile.setText("EPS");
\r
882 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
884 public void actionPerformed(ActionEvent e)
\r
889 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
890 LoadtreeMenuItem.setText("Load Associated Tree");
\r
891 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
893 public void actionPerformed(ActionEvent e)
\r
895 LoadtreeMenuItem_actionPerformed(e);
\r
898 scaleAbove.setVisible(false);
\r
899 scaleAbove.setText("Scale Above");
\r
900 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
902 public void actionPerformed(ActionEvent e)
\r
904 scaleAbove_actionPerformed(e);
\r
907 scaleLeft.setVisible(false);
\r
908 scaleLeft.setSelected(true);
\r
909 scaleLeft.setText("Scale Left");
\r
910 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
912 public void actionPerformed(ActionEvent e)
\r
914 scaleLeft_actionPerformed(e);
\r
917 scaleRight.setVisible(false);
\r
918 scaleRight.setSelected(true);
\r
919 scaleRight.setText("Scale Right");
\r
920 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
922 public void actionPerformed(ActionEvent e)
\r
924 scaleRight_actionPerformed(e);
\r
927 modifyPID.setText("Modify Identity Threshold...");
\r
928 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
930 public void actionPerformed(ActionEvent e)
\r
932 modifyPID_actionPerformed(e);
\r
935 modifyConservation.setText("Modify Conservation Threshold...");
\r
936 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
938 public void actionPerformed(ActionEvent e)
\r
940 modifyConservation_actionPerformed(e);
\r
943 sortByTreeMenu.setText("By Tree Order");
\r
944 sort.setText("Sort");
\r
945 sort.addMenuListener(new MenuListener()
\r
947 public void menuSelected(MenuEvent e)
\r
952 public void menuDeselected(MenuEvent e)
\r
956 public void menuCanceled(MenuEvent e)
\r
960 calculate.setText("Calculate Tree");
\r
962 jMenu2.setText("Export Image");
\r
963 padGapsMenuitem.setText("Pad Gaps");
\r
964 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
965 padGapsMenuitem.addActionListener(new ActionListener()
\r
967 public void actionPerformed(ActionEvent e)
\r
969 padGapsMenuitem_actionPerformed(e);
\r
972 vamsasStore.setVisible(false);
\r
973 vamsasStore.setText("VAMSAS store");
\r
974 vamsasStore.addActionListener(new ActionListener()
\r
976 public void actionPerformed(ActionEvent e)
\r
978 vamsasStore_actionPerformed(e);
\r
981 showTranslation.setText("Translate cDNA");
\r
982 showTranslation.addActionListener(new ActionListener()
\r
984 public void actionPerformed(ActionEvent e)
\r
986 showTranslation_actionPerformed(e);
\r
991 featureSettings.setText("Feature Settings...");
\r
992 featureSettings.addActionListener(new ActionListener()
\r
994 public void actionPerformed(ActionEvent e)
\r
996 featureSettings_actionPerformed(e);
\r
999 fetchSequence.setText("Fetch Sequence(s)...");
\r
1000 fetchSequence.addActionListener(new ActionListener()
\r
1002 public void actionPerformed(ActionEvent e)
\r
1004 fetchSequence_actionPerformed(e);
\r
1008 annotationColour.setText("By Annotation...");
\r
1009 annotationColour.addActionListener(new ActionListener()
\r
1011 public void actionPerformed(ActionEvent e)
\r
1013 annotationColour_actionPerformed(e);
\r
1016 associatedData.setText("Load Features / Annotations");
\r
1017 associatedData.addActionListener(new ActionListener()
\r
1019 public void actionPerformed(ActionEvent e)
\r
1021 associatedData_actionPerformed(e);
\r
1024 autoCalculate.setText("Autocalculate Consensus");
\r
1025 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1026 autoCalculate.addActionListener(new ActionListener()
\r
1028 public void actionPerformed(ActionEvent e)
\r
1030 autoCalculate_actionPerformed(e);
\r
1033 addSequenceMenu.setText("Add Sequences");
\r
1034 addFromFile.setText("From File");
\r
1035 addFromFile.addActionListener(new ActionListener()
\r
1037 public void actionPerformed(ActionEvent e)
\r
1039 addFromFile_actionPerformed(e);
\r
1042 addFromText.setText("From Textbox");
\r
1043 addFromText.addActionListener(new ActionListener()
\r
1045 public void actionPerformed(ActionEvent e)
\r
1047 addFromText_actionPerformed(e);
\r
1050 addFromURL.setText("From URL");
\r
1051 addFromURL.addActionListener(new ActionListener()
\r
1053 public void actionPerformed(ActionEvent e)
\r
1055 addFromURL_actionPerformed(e);
\r
1058 exportFeatures.setText("Export Features...");
\r
1059 exportFeatures.addActionListener(new ActionListener()
\r
1061 public void actionPerformed(ActionEvent e)
\r
1063 exportFeatures_actionPerformed(e);
\r
1066 exportAnnotations.setText("Export Annotations...");
\r
1067 exportAnnotations.addActionListener(new ActionListener()
\r
1069 public void actionPerformed(ActionEvent e)
\r
1071 exportAnnotations_actionPerformed(e);
\r
1074 statusPanel.setLayout(gridLayout1);
\r
1075 jMenu3.setText("Show");
\r
1076 showAllSeqs.setText("All Sequences");
\r
1077 showAllSeqs.addActionListener(new ActionListener()
\r
1079 public void actionPerformed(ActionEvent e)
\r
1081 showAllSeqs_actionPerformed(e);
\r
1084 showAllColumns.setText("All Columns");
\r
1085 showAllColumns.addActionListener(new ActionListener()
\r
1087 public void actionPerformed(ActionEvent e)
\r
1089 showAllColumns_actionPerformed(e);
\r
1092 hideMenu.setText("Hide");
\r
1093 hideSelSequences.setText("Selected Sequences");
\r
1094 hideSelSequences.addActionListener(new ActionListener()
\r
1096 public void actionPerformed(ActionEvent e)
\r
1098 hideSelSequences_actionPerformed(e);
\r
1101 hideSelColumns.setText("Selected Columns");
\r
1102 hideSelColumns.addActionListener(new ActionListener()
\r
1104 public void actionPerformed(ActionEvent e)
\r
1106 hideSelColumns_actionPerformed(e);
\r
1109 hiddenMarkers.setText("Show Hidden Markers");
\r
1110 hiddenMarkers.addActionListener(new ActionListener()
\r
1112 public void actionPerformed(ActionEvent e)
\r
1114 hiddenMarkers_actionPerformed(e);
\r
1117 invertColSel.setText("Invert Column Selection");
\r
1118 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1119 event.KeyEvent.VK_I,
\r
1120 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
\r
1121 |java.awt.event.KeyEvent.ALT_MASK,
\r
1123 invertColSel.addActionListener(new ActionListener()
\r
1125 public void actionPerformed(ActionEvent e)
\r
1127 invertColSel_actionPerformed(e);
\r
1130 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1132 public void stateChanged(ChangeEvent evt)
\r
1134 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1135 int sel = pane.getSelectedIndex();
\r
1136 tabSelectionChanged(sel);
\r
1139 tabbedPane.addMouseListener(new MouseAdapter()
\r
1141 public void mousePressed(MouseEvent e)
\r
1143 tabbedPane_mousePressed(e);
\r
1146 tabbedPane.addFocusListener(new FocusAdapter()
\r
1148 public void focusGained(FocusEvent e)
\r
1150 tabbedPane_focusGained(e);
\r
1153 save.setText("Save");
\r
1154 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1155 KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1156 save.addActionListener(new ActionListener()
\r
1158 public void actionPerformed(ActionEvent e)
\r
1160 save_actionPerformed(e);
\r
1163 reload.setEnabled(false);
\r
1164 reload.setText("Reload");
\r
1165 reload.addActionListener(new ActionListener()
\r
1167 public void actionPerformed(ActionEvent e)
\r
1169 reload_actionPerformed(e);
\r
1172 newView.setText("New View");
\r
1173 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
\r
1174 KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
1175 newView.addActionListener(new ActionListener()
\r
1177 public void actionPerformed(ActionEvent e)
\r
1179 newView_actionPerformed(e);
\r
1182 tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
\r
1183 +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
\r
1184 textColour.setText("Text Colour");
\r
1185 textColour.addActionListener(new ActionListener()
\r
1187 public void actionPerformed(ActionEvent e)
\r
1189 textColour_actionPerformed(e);
\r
1192 formatMenu.setText("Format");
\r
1193 selectMenu.setText("Select");
\r
1194 idRightAlign.setText("Right Align Sequence Id");
\r
1195 idRightAlign.addActionListener(new ActionListener()
\r
1197 public void actionPerformed(ActionEvent e)
\r
1199 idRightAlign_actionPerformed(e);
\r
1202 gatherViews.setEnabled(false);
\r
1203 gatherViews.setText("Gather Views");
\r
1204 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1205 event.KeyEvent.VK_G, 0, false));
\r
1206 gatherViews.addActionListener(new ActionListener()
\r
1208 public void actionPerformed(ActionEvent e)
\r
1210 gatherViews_actionPerformed(e);
\r
1213 expandViews.setEnabled(false);
\r
1214 expandViews.setText("Expand Views");
\r
1215 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1216 event.KeyEvent.VK_X, 0, false));
\r
1217 expandViews.addActionListener(new ActionListener()
\r
1219 public void actionPerformed(ActionEvent e)
\r
1221 expandViews_actionPerformed(e);
\r
1224 pageSetup.setText("Page Setup ...");
\r
1225 pageSetup.addActionListener(new ActionListener()
\r
1227 public void actionPerformed(ActionEvent e)
\r
1229 pageSetup_actionPerformed(e);
\r
1233 alignFrameMenuBar.add(fileMenu);
\r
1234 alignFrameMenuBar.add(editMenu);
\r
1235 alignFrameMenuBar.add(selectMenu);
\r
1236 alignFrameMenuBar.add(viewMenu);
\r
1237 alignFrameMenuBar.add(formatMenu);
\r
1238 alignFrameMenuBar.add(colourMenu);
\r
1239 alignFrameMenuBar.add(calculateMenu);
\r
1240 alignFrameMenuBar.add(webService);
\r
1241 fileMenu.add(fetchSequence);
\r
1242 fileMenu.add(addSequenceMenu);
\r
1243 fileMenu.add(reload);
\r
1244 fileMenu.addSeparator();
\r
1245 fileMenu.add(vamsasStore);
\r
1246 fileMenu.add(save);
\r
1247 fileMenu.add(saveAs);
\r
1248 fileMenu.add(outputTextboxMenu);
\r
1249 fileMenu.add(pageSetup);
\r
1250 fileMenu.add(printMenuItem);
\r
1251 fileMenu.addSeparator();
\r
1252 fileMenu.add(jMenu2);
\r
1253 fileMenu.add(exportFeatures);
\r
1254 fileMenu.add(exportAnnotations);
\r
1255 fileMenu.add(LoadtreeMenuItem);
\r
1256 fileMenu.add(associatedData);
\r
1257 fileMenu.addSeparator();
\r
1258 fileMenu.add(closeMenuItem);
\r
1259 editMenu.add(undoMenuItem);
\r
1260 editMenu.add(redoMenuItem);
\r
1261 editMenu.add(cut);
\r
1262 editMenu.add(copy);
\r
1263 editMenu.add(pasteMenu);
\r
1264 editMenu.add(delete);
\r
1265 editMenu.addSeparator();
\r
1266 editMenu.add(remove2LeftMenuItem);
\r
1267 editMenu.add(remove2RightMenuItem);
\r
1268 editMenu.add(removeGappedColumnMenuItem);
\r
1269 editMenu.add(removeAllGapsMenuItem);
\r
1270 editMenu.add(removeRedundancyMenuItem);
\r
1271 editMenu.addSeparator();
\r
1272 editMenu.add(padGapsMenuitem);
\r
1273 viewMenu.add(newView);
\r
1274 viewMenu.add(expandViews);
\r
1275 viewMenu.add(gatherViews);
\r
1276 viewMenu.addSeparator();
\r
1277 viewMenu.add(jMenu3);
\r
1278 viewMenu.add(hideMenu);
\r
1279 viewMenu.addSeparator();
\r
1280 viewMenu.add(annotationPanelMenuItem);
\r
1281 viewMenu.addSeparator();
\r
1282 viewMenu.add(showSeqFeatures);
\r
1283 viewMenu.add(featureSettings);
\r
1284 viewMenu.addSeparator();
\r
1285 viewMenu.add(overviewMenuItem);
\r
1286 colourMenu.add(applyToAllGroups);
\r
1287 colourMenu.add(textColour);
\r
1288 colourMenu.addSeparator();
\r
1289 colourMenu.add(noColourmenuItem);
\r
1290 colourMenu.add(clustalColour);
\r
1291 colourMenu.add(BLOSUM62Colour);
\r
1292 colourMenu.add(PIDColour);
\r
1293 colourMenu.add(zappoColour);
\r
1294 colourMenu.add(taylorColour);
\r
1295 colourMenu.add(hydrophobicityColour);
\r
1296 colourMenu.add(helixColour);
\r
1297 colourMenu.add(strandColour);
\r
1298 colourMenu.add(turnColour);
\r
1299 colourMenu.add(buriedColour);
\r
1300 colourMenu.add(nucleotideColour);
\r
1301 colourMenu.add(userDefinedColour);
\r
1302 colourMenu.addSeparator();
\r
1303 colourMenu.add(conservationMenuItem);
\r
1304 colourMenu.add(modifyConservation);
\r
1305 colourMenu.add(abovePIDThreshold);
\r
1306 colourMenu.add(modifyPID);
\r
1307 colourMenu.add(annotationColour);
\r
1308 calculateMenu.add(sort);
\r
1309 calculateMenu.add(calculate);
\r
1310 calculateMenu.addSeparator();
\r
1311 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1312 calculateMenu.add(PCAMenuItem);
\r
1313 calculateMenu.addSeparator();
\r
1314 calculateMenu.add(showTranslation);
\r
1315 calculateMenu.add(autoCalculate);
\r
1316 webServiceNoServices=new JMenuItem("<No Services>");
\r
1317 webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
\r
1318 pasteMenu.add(pasteThis);
\r
1319 sort.add(sortIDMenuItem);
\r
1320 sort.add(sortGroupMenuItem);
\r
1321 sort.add(sortPairwiseMenuItem);
\r
1322 sort.add(sortByTreeMenu);
\r
1323 calculate.add(averageDistanceTreeMenuItem);
\r
1324 calculate.add(neighbourTreeMenuItem);
\r
1325 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1326 calculate.add(njTreeBlosumMenuItem);
\r
1327 jMenu2.add(htmlMenuItem);
\r
1328 jMenu2.add(epsFile);
\r
1329 jMenu2.add(createPNG);
\r
1330 addSequenceMenu.add(addFromFile);
\r
1331 addSequenceMenu.add(addFromText);
\r
1332 addSequenceMenu.add(addFromURL);
\r
1333 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1334 statusPanel.add(statusBar, null);
\r
1335 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1336 jMenu3.add(showAllColumns);
\r
1337 jMenu3.add(showAllSeqs);
\r
1338 hideMenu.add(hideSelColumns);
\r
1339 hideMenu.add(hideSelSequences);
\r
1340 formatMenu.add(font);
\r
1341 formatMenu.addSeparator();
\r
1342 formatMenu.add(wrapMenuItem);
\r
1343 formatMenu.add(scaleAbove);
\r
1344 formatMenu.add(scaleLeft);
\r
1345 formatMenu.add(scaleRight);
\r
1346 formatMenu.add(seqLimits);
\r
1347 formatMenu.add(idRightAlign);
\r
1348 formatMenu.add(hiddenMarkers);
\r
1349 formatMenu.add(viewBoxesMenuItem);
\r
1350 formatMenu.add(viewTextMenuItem);
\r
1351 formatMenu.add(colourTextMenuItem);
\r
1352 formatMenu.add(renderGapsMenuItem);
\r
1353 selectMenu.add(findMenuItem);
\r
1354 selectMenu.addSeparator();
\r
1355 selectMenu.add(selectAllSequenceMenuItem);
\r
1356 selectMenu.add(deselectAllSequenceMenuItem);
\r
1357 selectMenu.add(invertSequenceMenuItem);
\r
1358 selectMenu.add(invertColSel);
\r
1359 selectMenu.add(deleteGroups);
\r
1362 protected void outputText_actionPerformed(ActionEvent e)
\r
1366 public void addFromFile_actionPerformed(ActionEvent e)
\r
1371 public void addFromText_actionPerformed(ActionEvent e)
\r
1376 public void addFromURL_actionPerformed(ActionEvent e)
\r
1381 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1386 public void exportAnnotations_actionPerformed(ActionEvent e)
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1391 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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1395 protected void closeMenuItem_actionPerformed(boolean b)
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1399 protected void redoMenuItem_actionPerformed(ActionEvent e)
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1403 protected void undoMenuItem_actionPerformed(ActionEvent e)
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1407 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1411 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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1415 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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1419 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1423 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1427 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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1431 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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1435 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1439 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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1443 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
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1447 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1451 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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1455 protected void overviewMenuItem_actionPerformed(ActionEvent e)
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1459 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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1463 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
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1467 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
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1471 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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1475 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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1479 protected void PCAMenuItem_actionPerformed(ActionEvent e)
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1483 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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1487 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1491 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1495 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1499 protected void clustalColour_actionPerformed(ActionEvent e)
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1503 protected void zappoColour_actionPerformed(ActionEvent e)
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1507 protected void taylorColour_actionPerformed(ActionEvent e)
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1511 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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1515 protected void helixColour_actionPerformed(ActionEvent e)
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1519 protected void strandColour_actionPerformed(ActionEvent e)
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1523 protected void turnColour_actionPerformed(ActionEvent e)
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1527 protected void buriedColour_actionPerformed(ActionEvent e)
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1531 protected void userDefinedColour_actionPerformed(ActionEvent e)
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1535 protected void PIDColour_actionPerformed(ActionEvent e)
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1539 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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1543 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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1547 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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1551 protected void printMenuItem_actionPerformed(ActionEvent e)
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1555 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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1559 protected void findMenuItem_actionPerformed(ActionEvent e)
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1563 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
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1567 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
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1571 protected void nucleotideColour_actionPerformed(ActionEvent e)
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1575 protected void deleteGroups_actionPerformed(ActionEvent e)
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1579 protected void copy_actionPerformed(ActionEvent e)
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1583 protected void cut_actionPerformed(ActionEvent e)
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1587 protected void delete_actionPerformed(ActionEvent e)
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1591 protected void pasteNew_actionPerformed(ActionEvent e)
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1595 protected void pasteThis_actionPerformed(ActionEvent e)
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1599 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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1603 public void createPNG(java.io.File f)
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1607 protected void font_actionPerformed(ActionEvent e)
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1611 protected void seqLimit_actionPerformed(ActionEvent e)
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1615 public void seqDBRef_actionPerformed(ActionEvent e)
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1621 public void createEPS(java.io.File f)
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1625 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
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1629 protected void jpred_actionPerformed(ActionEvent e)
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1633 protected void scaleAbove_actionPerformed(ActionEvent e)
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1637 protected void scaleLeft_actionPerformed(ActionEvent e)
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1641 protected void scaleRight_actionPerformed(ActionEvent e)
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1645 protected void modifyPID_actionPerformed(ActionEvent e)
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1649 protected void modifyConservation_actionPerformed(ActionEvent e)
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1655 protected void saveAs_actionPerformed(ActionEvent e)
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1659 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1664 public void vamsasStore_actionPerformed(ActionEvent e)
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1669 public void vamsasLoad_actionPerformed(ActionEvent e)
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1674 public void showTranslation_actionPerformed(ActionEvent e)
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1679 public void featureSettings_actionPerformed(ActionEvent e)
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1684 public void fetchSequence_actionPerformed(ActionEvent e)
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1689 public void smoothFont_actionPerformed(ActionEvent e)
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1694 public void annotationColour_actionPerformed(ActionEvent e)
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1700 public void associatedData_actionPerformed(ActionEvent e)
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1705 public void autoCalculate_actionPerformed(ActionEvent e)
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1710 public void showAllSeqs_actionPerformed(ActionEvent e)
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1715 public void showAllColumns_actionPerformed(ActionEvent e)
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1720 public void hideSelSequences_actionPerformed(ActionEvent e)
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1725 public void hideSelColumns_actionPerformed(ActionEvent e)
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1730 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1735 public void findPdbId_actionPerformed(ActionEvent e)
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1740 public void enterPdbId_actionPerformed(ActionEvent e)
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1745 public void pdbFile_actionPerformed(ActionEvent e)
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1750 public void invertColSel_actionPerformed(ActionEvent e)
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1755 public void tabSelectionChanged(int sel)
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1760 public void tabbedPane_mousePressed(MouseEvent e)
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1765 public void tabbedPane_focusGained(FocusEvent e)
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1770 public void save_actionPerformed(ActionEvent e)
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1775 public void reload_actionPerformed(ActionEvent e)
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1780 public void newView_actionPerformed(ActionEvent e)
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1785 public void textColour_actionPerformed(ActionEvent e)
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1790 public void idRightAlign_actionPerformed(ActionEvent e)
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1795 public void expandViews_actionPerformed(ActionEvent e)
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1800 public void gatherViews_actionPerformed(ActionEvent e)
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1805 public void buildTreeMenu()
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1810 public void pageSetup_actionPerformed(ActionEvent e)
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