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 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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62 BorderLayout borderLayout1 = new BorderLayout();
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63 public JLabel statusBar = new JLabel();
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64 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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65 protected JMenu outputTextboxMenu = new JMenu();
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66 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem hydrophobicityColour = new
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70 JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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75 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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76 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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77 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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78 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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79 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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80 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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81 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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82 JMenuItem htmlMenuItem = new JMenuItem();
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83 JMenuItem overviewMenuItem = new JMenuItem();
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84 protected JMenuItem undoMenuItem = new JMenuItem();
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85 protected JMenuItem redoMenuItem = new JMenuItem();
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86 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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87 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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88 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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89 JMenuItem printMenuItem = new JMenuItem();
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90 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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91 JMenuItem findMenuItem = new JMenuItem();
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92 JMenu searchMenu = new JMenu();
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93 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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94 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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95 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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96 JMenuItem deleteGroups = new JMenuItem();
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97 JMenuItem delete = new JMenuItem();
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98 JMenuItem copy = new JMenuItem();
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99 JMenuItem cut = new JMenuItem();
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100 JMenu jMenu1 = new JMenu();
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101 JMenuItem pasteNew = new JMenuItem();
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102 JMenuItem pasteThis = new JMenuItem();
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103 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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104 JMenuItem createPNG = new JMenuItem();
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105 protected JMenuItem font = new JMenuItem();
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106 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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107 JMenuItem epsFile = new JMenuItem();
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108 JMenuItem LoadtreeMenuItem = new JMenuItem();
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109 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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110 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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111 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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112 protected JMenuItem modifyPID = new JMenuItem();
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113 protected JMenuItem modifyConservation = new JMenuItem();
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114 protected JMenu sortByTreeMenu = new JMenu();
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115 protected JMenu sort = new JMenu();
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116 JMenu calculate = new JMenu();
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117 JMenu jMenu2 = new JMenu();
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118 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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119 protected ButtonGroup colours = new ButtonGroup();
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120 JMenuItem vamsasStore = new JMenuItem();
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121 protected JMenuItem showTranslation = new JMenuItem();
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122 public JMenuItem featureSettings = new JMenuItem();
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123 JMenuItem fetchSequence = new JMenuItem();
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124 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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125 JMenuItem annotationColour = new JMenuItem();
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126 JMenuItem associatedData = new JMenuItem();
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127 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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128 JMenu addSequenceMenu = new JMenu();
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129 JMenuItem addFromFile = new JMenuItem();
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130 JMenuItem addFromText = new JMenuItem();
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131 JMenuItem addFromURL = new JMenuItem();
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132 JMenuItem exportAnnotations = new JMenuItem();
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133 JMenuItem exportFeatures = new JMenuItem();
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134 protected JPanel statusPanel = new JPanel();
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135 GridLayout gridLayout1 = new GridLayout();
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136 JMenu jMenu3 = new JMenu();
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137 JMenuItem showAllSeqs = new JMenuItem();
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138 JMenuItem showAllColumns = new JMenuItem();
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139 JMenu hideMenu = new JMenu();
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140 JMenuItem hideSelSequences = new JMenuItem();
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141 JMenuItem hideSelColumns = new JMenuItem();
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142 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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143 JMenuItem invertColSel = new JMenuItem();
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144 protected JTabbedPane tabbedPane = new JTabbedPane();
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145 public GAlignFrame()
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150 setJMenuBar(alignFrameMenuBar);
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152 // dynamically fill save as menu with available formats
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153 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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155 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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157 item.addActionListener(new java.awt.event.ActionListener()
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159 public void actionPerformed(ActionEvent e)
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161 outputText_actionPerformed(e);
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165 outputTextboxMenu.add(item);
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168 catch (Exception e)
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173 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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175 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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176 getUserColourSchemes().keys();
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178 while (userColours.hasMoreElements())
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180 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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181 nextElement().toString());
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182 radioItem.setName("USER_DEFINED");
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183 radioItem.addMouseListener(new MouseAdapter()
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185 public void mousePressed(MouseEvent evt)
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187 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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189 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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191 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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192 "Remove from default list?",
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193 "Remove user defined colour",
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194 JOptionPane.YES_NO_OPTION);
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195 if(option == JOptionPane.YES_OPTION)
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197 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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198 colourMenu.remove(radioItem);
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201 radioItem.addActionListener(new ActionListener()
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203 public void actionPerformed(ActionEvent evt)
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205 userDefinedColour_actionPerformed(evt);
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211 radioItem.addActionListener(new ActionListener()
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213 public void actionPerformed(ActionEvent evt)
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215 userDefinedColour_actionPerformed(evt);
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218 colourMenu.insert(radioItem, 15);
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219 colours.add(radioItem);
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222 colours.add(noColourmenuItem);
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223 colours.add(clustalColour);
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224 colours.add(zappoColour);
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225 colours.add(taylorColour);
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226 colours.add(hydrophobicityColour);
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227 colours.add(helixColour);
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228 colours.add(strandColour);
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229 colours.add(turnColour);
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230 colours.add(buriedColour);
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231 colours.add(userDefinedColour);
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232 colours.add(PIDColour);
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233 colours.add(BLOSUM62Colour);
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234 colours.add(nucleotideColour);
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236 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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241 public void setColourSelected(String defaultColour)
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244 if (defaultColour != null)
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246 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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250 case ColourSchemeProperty.NONE:
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251 noColourmenuItem.setSelected(true);
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253 case ColourSchemeProperty.CLUSTAL:
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254 clustalColour.setSelected(true);
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258 case ColourSchemeProperty.BLOSUM:
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259 BLOSUM62Colour.setSelected(true);
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263 case ColourSchemeProperty.PID:
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264 PIDColour.setSelected(true);
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268 case ColourSchemeProperty.ZAPPO:
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269 zappoColour.setSelected(true);
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273 case ColourSchemeProperty.TAYLOR:
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274 taylorColour.setSelected(true);
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277 case ColourSchemeProperty.HYDROPHOBIC:
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278 hydrophobicityColour.setSelected(true);
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282 case ColourSchemeProperty.HELIX:
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283 helixColour.setSelected(true);
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287 case ColourSchemeProperty.STRAND:
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288 strandColour.setSelected(true);
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292 case ColourSchemeProperty.TURN:
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293 turnColour.setSelected(true);
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297 case ColourSchemeProperty.BURIED:
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298 buriedColour.setSelected(true);
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302 case ColourSchemeProperty.NUCLEOTIDE:
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303 nucleotideColour.setSelected(true);
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307 case ColourSchemeProperty.USER_DEFINED:
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308 userDefinedColour.setSelected(true);
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316 private void jbInit()
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319 fileMenu.setMnemonic('F');
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320 fileMenu.setText("File");
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321 saveAlignmentMenu.setMnemonic('L');
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322 saveAlignmentMenu.setText("Save As");
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323 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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324 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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325 saveAlignmentMenu.addActionListener(new ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 saveAlignmentMenu_actionPerformed(e);
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332 closeMenuItem.setMnemonic('C');
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333 closeMenuItem.setText("Close");
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334 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 closeMenuItem_actionPerformed(e);
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341 editMenu.setText("Edit");
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342 viewMenu.setText("View");
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343 colourMenu.setText("Colour");
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344 calculateMenu.setText("Calculate");
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345 webService.setText("Web Service");
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346 selectAllSequenceMenuItem.setText("Select all");
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347 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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348 java.awt.event.KeyEvent.VK_A,
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349 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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350 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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353 public void actionPerformed(ActionEvent e)
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355 selectAllSequenceMenuItem_actionPerformed(e);
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358 deselectAllSequenceMenuItem.setText("Deselect All");
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359 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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361 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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362 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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365 public void actionPerformed(ActionEvent e)
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367 deselectAllSequenceMenuItem_actionPerformed(e);
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370 invertSequenceMenuItem.setText("Invert Sequence Selection");
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371 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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372 java.awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.SHIFT_MASK, false));
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373 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 invertSequenceMenuItem_actionPerformed(e);
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380 remove2LeftMenuItem.setText("Remove Left");
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381 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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382 awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));
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383 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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385 public void actionPerformed(ActionEvent e)
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387 remove2LeftMenuItem_actionPerformed(e);
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390 remove2RightMenuItem.setText("Remove Right");
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391 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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392 awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));
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393 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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395 public void actionPerformed(ActionEvent e)
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397 remove2RightMenuItem_actionPerformed(e);
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400 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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401 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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402 getKeyStroke(java.awt.event.
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403 KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));
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404 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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407 public void actionPerformed(ActionEvent e)
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409 removeGappedColumnMenuItem_actionPerformed(e);
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412 removeAllGapsMenuItem.setText("Remove All Gaps");
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413 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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414 java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));
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415 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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417 public void actionPerformed(ActionEvent e)
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419 removeAllGapsMenuItem_actionPerformed(e);
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422 viewBoxesMenuItem.setText("Boxes");
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423 viewBoxesMenuItem.setState(true);
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424 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 viewBoxesMenuItem_actionPerformed(e);
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431 viewTextMenuItem.setText("Text");
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432 viewTextMenuItem.setState(true);
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433 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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435 public void actionPerformed(ActionEvent e)
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437 viewTextMenuItem_actionPerformed(e);
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440 sortPairwiseMenuItem.setText("by Pairwise Identity");
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441 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 sortPairwiseMenuItem_actionPerformed(e);
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448 sortIDMenuItem.setText("by ID");
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449 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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451 public void actionPerformed(ActionEvent e)
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453 sortIDMenuItem_actionPerformed(e);
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456 sortGroupMenuItem.setText("by Group");
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457 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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459 public void actionPerformed(ActionEvent e)
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461 sortGroupMenuItem_actionPerformed(e);
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464 removeRedundancyMenuItem.setText("Remove Redundancy...");
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465 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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468 public void actionPerformed(ActionEvent e)
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470 removeRedundancyMenuItem_actionPerformed(e);
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473 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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474 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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477 public void actionPerformed(ActionEvent e)
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479 pairwiseAlignmentMenuItem_actionPerformed(e);
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482 PCAMenuItem.setText("Principal Component Analysis");
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483 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 PCAMenuItem_actionPerformed(e);
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490 averageDistanceTreeMenuItem.setText(
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491 "Average Distance Using % Identity");
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492 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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495 public void actionPerformed(ActionEvent e)
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497 averageDistanceTreeMenuItem_actionPerformed(e);
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500 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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501 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 neighbourTreeMenuItem_actionPerformed(e);
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508 this.getContentPane().setLayout(borderLayout1);
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509 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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510 statusBar.setBackground(Color.white);
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511 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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512 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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513 statusBar.setText("Status bar");
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514 outputTextboxMenu.setMnemonic('T');
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515 outputTextboxMenu.setText("Output to Textbox");
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516 clustalColour.setText("Clustalx");
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518 clustalColour.addActionListener(new java.awt.event.ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 clustalColour_actionPerformed(e);
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525 zappoColour.setText("Zappo");
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526 zappoColour.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 zappoColour_actionPerformed(e);
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533 taylorColour.setText("Taylor");
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534 taylorColour.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 taylorColour_actionPerformed(e);
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541 hydrophobicityColour.setText("Hydrophobicity");
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542 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 hydrophobicityColour_actionPerformed(e);
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549 helixColour.setText("Helix Propensity");
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550 helixColour.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 helixColour_actionPerformed(e);
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557 strandColour.setText("Strand Propensity");
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558 strandColour.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 strandColour_actionPerformed(e);
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565 turnColour.setText("Turn Propensity");
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566 turnColour.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 turnColour_actionPerformed(e);
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573 buriedColour.setText("Buried Index");
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574 buriedColour.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 buriedColour_actionPerformed(e);
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581 userDefinedColour.setText("User Defined...");
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582 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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584 public void actionPerformed(ActionEvent e)
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586 userDefinedColour_actionPerformed(e);
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589 PIDColour.setText("Percentage Identity");
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590 PIDColour.addActionListener(new java.awt.event.ActionListener()
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592 public void actionPerformed(ActionEvent e)
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594 PIDColour_actionPerformed(e);
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597 BLOSUM62Colour.setText("BLOSUM62 Score");
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598 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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600 public void actionPerformed(ActionEvent e)
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602 BLOSUM62Colour_actionPerformed(e);
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605 avDistanceTreeBlosumMenuItem.setText(
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606 "Average Distance Using BLOSUM62");
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607 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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610 public void actionPerformed(ActionEvent e)
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612 avTreeBlosumMenuItem_actionPerformed(e);
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615 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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616 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 njTreeBlosumMenuItem_actionPerformed(e);
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623 annotationPanelMenuItem.setActionCommand("");
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624 annotationPanelMenuItem.setText("Show Annotations");
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625 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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626 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 annotationPanelMenuItem_actionPerformed(e);
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633 colourTextMenuItem.setText("Colour Text");
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634 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 colourTextMenuItem_actionPerformed(e);
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641 htmlMenuItem.setText("HTML");
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642 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 htmlMenuItem_actionPerformed(e);
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649 overviewMenuItem.setText("Overview Window");
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650 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 overviewMenuItem_actionPerformed(e);
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657 undoMenuItem.setEnabled(false);
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658 undoMenuItem.setMnemonic('Z');
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659 undoMenuItem.setText("Undo");
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660 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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661 java.awt.event.KeyEvent.VK_Z,
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662 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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663 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 undoMenuItem_actionPerformed(e);
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670 redoMenuItem.setEnabled(false);
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671 redoMenuItem.setMnemonic('0');
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672 redoMenuItem.setText("Redo");
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673 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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674 event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));
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675 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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677 public void actionPerformed(ActionEvent e)
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679 redoMenuItem_actionPerformed(e);
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682 conservationMenuItem.setText("By Conservation");
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683 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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685 public void actionPerformed(ActionEvent e)
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687 conservationMenuItem_actionPerformed(e);
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690 noColourmenuItem.setText("None");
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691 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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693 public void actionPerformed(ActionEvent e)
\r
695 noColourmenuItem_actionPerformed(e);
\r
698 wrapMenuItem.setText("Wrap");
\r
699 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
701 public void actionPerformed(ActionEvent e)
\r
703 wrapMenuItem_actionPerformed(e);
\r
706 printMenuItem.setText("Print");
\r
707 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
709 public void actionPerformed(ActionEvent e)
\r
711 printMenuItem_actionPerformed(e);
\r
714 renderGapsMenuItem.setText("Show Gaps");
\r
715 renderGapsMenuItem.setState(true);
\r
716 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
718 public void actionPerformed(ActionEvent e)
\r
720 renderGapsMenuItem_actionPerformed(e);
\r
723 findMenuItem.setText("Find...");
\r
724 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
725 java.awt.event.KeyEvent.VK_F,
\r
726 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
727 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
729 public void actionPerformed(ActionEvent e)
\r
731 findMenuItem_actionPerformed(e);
\r
734 searchMenu.setText("Search");
\r
736 abovePIDThreshold.setText("Above Identity Threshold");
\r
737 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
739 public void actionPerformed(ActionEvent e)
\r
741 abovePIDThreshold_actionPerformed(e);
\r
744 showSeqFeatures.setText("Show Sequence Features");
\r
745 showSeqFeatures.addActionListener(new ActionListener()
\r
747 public void actionPerformed(ActionEvent actionEvent)
\r
749 showSeqFeatures_actionPerformed(actionEvent);
\r
752 nucleotideColour.setText("Nucleotide");
\r
753 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
755 public void actionPerformed(ActionEvent e)
\r
757 nucleotideColour_actionPerformed(e);
\r
760 deleteGroups.setText("Undefine groups");
\r
761 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
763 public void actionPerformed(ActionEvent e)
\r
765 deleteGroups_actionPerformed(e);
\r
768 copy.setText("Copy");
\r
769 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
770 java.awt.event.KeyEvent.VK_C,
\r
771 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
772 copy.setMnemonic(KeyEvent.VK_C);
\r
774 copy.addActionListener(new java.awt.event.ActionListener()
\r
776 public void actionPerformed(ActionEvent e)
\r
778 copy_actionPerformed(e);
\r
781 cut.setText("Cut");
\r
782 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
783 java.awt.event.KeyEvent.VK_X,
\r
784 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
785 cut.setMnemonic(KeyEvent.VK_X);
\r
786 cut.addActionListener(new java.awt.event.ActionListener()
\r
788 public void actionPerformed(ActionEvent e)
\r
790 cut_actionPerformed(e);
\r
793 delete.setText("Delete");
\r
794 delete.addActionListener(new java.awt.event.ActionListener()
\r
796 public void actionPerformed(ActionEvent e)
\r
798 delete_actionPerformed(e);
\r
801 jMenu1.setMnemonic('V');
\r
802 jMenu1.setText("Paste");
\r
803 pasteNew.setText("To New Alignment");
\r
804 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
805 java.awt.event.KeyEvent.VK_V,
\r
806 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
807 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
809 public void actionPerformed(ActionEvent e)
\r
811 pasteNew_actionPerformed(e);
\r
814 pasteThis.setText("Add To This Alignment");
\r
815 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
817 public void actionPerformed(ActionEvent e)
\r
819 pasteThis_actionPerformed(e);
\r
822 applyToAllGroups.setText("Apply Colour To All Groups");
\r
823 applyToAllGroups.setState(true);
\r
824 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
826 public void actionPerformed(ActionEvent e)
\r
828 applyToAllGroups_actionPerformed(e);
\r
831 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
833 public void actionPerformed(ActionEvent e)
\r
838 createPNG.setActionCommand("Save As PNG Image");
\r
839 createPNG.setText("PNG");
\r
840 font.setText("Font...");
\r
841 font.addActionListener(new java.awt.event.ActionListener()
\r
843 public void actionPerformed(ActionEvent e)
\r
845 font_actionPerformed(e);
\r
849 seqLimits.setText("Show Sequence Limits");
\r
850 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
851 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
853 public void actionPerformed(ActionEvent e)
\r
855 seqLimit_actionPerformed(e);
\r
858 epsFile.setText("EPS");
\r
859 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
861 public void actionPerformed(ActionEvent e)
\r
866 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
867 LoadtreeMenuItem.setText("Load Associated Tree");
\r
868 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
870 public void actionPerformed(ActionEvent e)
\r
872 LoadtreeMenuItem_actionPerformed(e);
\r
875 scaleAbove.setVisible(false);
\r
876 scaleAbove.setText("Scale Above");
\r
877 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
879 public void actionPerformed(ActionEvent e)
\r
881 scaleAbove_actionPerformed(e);
\r
884 scaleLeft.setVisible(false);
\r
885 scaleLeft.setSelected(true);
\r
886 scaleLeft.setText("Scale Left");
\r
887 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
889 public void actionPerformed(ActionEvent e)
\r
891 scaleLeft_actionPerformed(e);
\r
894 scaleRight.setVisible(false);
\r
895 scaleRight.setSelected(true);
\r
896 scaleRight.setText("Scale Right");
\r
897 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
899 public void actionPerformed(ActionEvent e)
\r
901 scaleRight_actionPerformed(e);
\r
904 modifyPID.setText("Modify Identity Threshold...");
\r
905 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
907 public void actionPerformed(ActionEvent e)
\r
909 modifyPID_actionPerformed(e);
\r
912 modifyConservation.setText("Modify Conservation Threshold...");
\r
913 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
915 public void actionPerformed(ActionEvent e)
\r
917 modifyConservation_actionPerformed(e);
\r
920 sortByTreeMenu.setText("By Tree Order");
\r
921 sort.setText("Sort");
\r
922 calculate.setText("Calculate Tree");
\r
924 jMenu2.setText("Export");
\r
925 padGapsMenuitem.setText("Pad Gaps");
\r
926 padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
927 event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));
\r
928 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
929 padGapsMenuitem.addActionListener(new ActionListener()
\r
931 public void actionPerformed(ActionEvent e)
\r
933 padGapsMenuitem_actionPerformed(e);
\r
936 vamsasStore.setVisible(false);
\r
937 vamsasStore.setText("VAMSAS store");
\r
938 vamsasStore.addActionListener(new ActionListener()
\r
940 public void actionPerformed(ActionEvent e)
\r
942 vamsasStore_actionPerformed(e);
\r
945 showTranslation.setText("Translate cDNA");
\r
946 showTranslation.addActionListener(new ActionListener()
\r
948 public void actionPerformed(ActionEvent e)
\r
950 showTranslation_actionPerformed(e);
\r
954 /* tabbedPane.addChangeListener(new ChangeListener()
\r
956 public void stateChanged(ChangeEvent ece)
\r
962 featureSettings.setText("Feature Settings...");
\r
963 featureSettings.addActionListener(new ActionListener()
\r
965 public void actionPerformed(ActionEvent e)
\r
967 featureSettings_actionPerformed(e);
\r
970 fetchSequence.setText("Fetch Sequence(s)...");
\r
971 fetchSequence.addActionListener(new ActionListener()
\r
973 public void actionPerformed(ActionEvent e)
\r
975 fetchSequence_actionPerformed(e);
\r
978 smoothFont.setText("Smooth Fonts");
\r
979 smoothFont.addActionListener(new ActionListener()
\r
981 public void actionPerformed(ActionEvent e)
\r
983 smoothFont_actionPerformed(e);
\r
986 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
987 annotationColour.setText("By Annotation...");
\r
988 annotationColour.addActionListener(new ActionListener()
\r
990 public void actionPerformed(ActionEvent e)
\r
992 annotationColour_actionPerformed(e);
\r
995 associatedData.setText("Load Features / Annotations");
\r
996 associatedData.addActionListener(new ActionListener()
\r
998 public void actionPerformed(ActionEvent e)
\r
1000 associatedData_actionPerformed(e);
\r
1003 autoCalculate.setText("Autocalculate Consensus");
\r
1004 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1005 autoCalculate.addActionListener(new ActionListener()
\r
1007 public void actionPerformed(ActionEvent e)
\r
1009 autoCalculate_actionPerformed(e);
\r
1012 addSequenceMenu.setText("Add Sequences");
\r
1013 addFromFile.setText("From File");
\r
1014 addFromFile.addActionListener(new ActionListener()
\r
1016 public void actionPerformed(ActionEvent e)
\r
1018 addFromFile_actionPerformed(e);
\r
1021 addFromText.setText("From Textbox");
\r
1022 addFromText.addActionListener(new ActionListener()
\r
1024 public void actionPerformed(ActionEvent e)
\r
1026 addFromText_actionPerformed(e);
\r
1029 addFromURL.setText("From URL");
\r
1030 addFromURL.addActionListener(new ActionListener()
\r
1032 public void actionPerformed(ActionEvent e)
\r
1034 addFromURL_actionPerformed(e);
\r
1037 exportFeatures.setText("Export Features...");
\r
1038 exportFeatures.addActionListener(new ActionListener()
\r
1040 public void actionPerformed(ActionEvent e)
\r
1042 exportFeatures_actionPerformed(e);
\r
1045 exportAnnotations.setText("Export Annotations...");
\r
1046 exportAnnotations.addActionListener(new ActionListener()
\r
1048 public void actionPerformed(ActionEvent e)
\r
1050 exportAnnotations_actionPerformed(e);
\r
1053 statusPanel.setLayout(gridLayout1);
\r
1054 jMenu3.setText("Show");
\r
1055 showAllSeqs.setText("All Sequences");
\r
1056 showAllSeqs.addActionListener(new ActionListener()
\r
1058 public void actionPerformed(ActionEvent e)
\r
1060 showAllSeqs_actionPerformed(e);
\r
1063 showAllColumns.setText("All Columns");
\r
1064 showAllColumns.addActionListener(new ActionListener()
\r
1066 public void actionPerformed(ActionEvent e)
\r
1068 showAllColumns_actionPerformed(e);
\r
1071 hideMenu.setText("Hide");
\r
1072 hideSelSequences.setText("Selected Sequences");
\r
1073 hideSelSequences.addActionListener(new ActionListener()
\r
1075 public void actionPerformed(ActionEvent e)
\r
1077 hideSelSequences_actionPerformed(e);
\r
1080 hideSelColumns.setText("Selected Columns");
\r
1081 hideSelColumns.addActionListener(new ActionListener()
\r
1083 public void actionPerformed(ActionEvent e)
\r
1085 hideSelColumns_actionPerformed(e);
\r
1088 hiddenMarkers.setText("Hidden Markers");
\r
1089 hiddenMarkers.setState(true);
\r
1090 hiddenMarkers.addActionListener(new ActionListener()
\r
1092 public void actionPerformed(ActionEvent e)
\r
1094 hiddenMarkers_actionPerformed(e);
\r
1097 invertColSel.setText("Invert Column Selection");
\r
1098 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1099 event.KeyEvent.VK_C, java.awt.event.KeyEvent.SHIFT_MASK, false));
\r
1100 invertColSel.addActionListener(new ActionListener()
\r
1102 public void actionPerformed(ActionEvent e)
\r
1104 invertColSel_actionPerformed(e);
\r
1107 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1109 public void stateChanged(ChangeEvent evt)
\r
1111 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1112 int sel = pane.getSelectedIndex();
\r
1113 tabSelectionChanged(sel);
\r
1116 tabbedPane.addMouseListener(new MouseAdapter()
\r
1118 public void mousePressed(MouseEvent e)
\r
1120 tabbedPane_mousePressed(e);
\r
1124 alignFrameMenuBar.add(fileMenu);
\r
1125 alignFrameMenuBar.add(editMenu);
\r
1126 alignFrameMenuBar.add(searchMenu);
\r
1127 alignFrameMenuBar.add(viewMenu);
\r
1128 alignFrameMenuBar.add(colourMenu);
\r
1129 alignFrameMenuBar.add(calculateMenu);
\r
1130 alignFrameMenuBar.add(webService);
\r
1131 fileMenu.add(addSequenceMenu);
\r
1132 fileMenu.add(fetchSequence);
\r
1133 fileMenu.addSeparator();
\r
1134 fileMenu.add(vamsasStore);
\r
1135 fileMenu.add(saveAlignmentMenu);
\r
1136 fileMenu.add(jMenu2);
\r
1137 fileMenu.add(outputTextboxMenu);
\r
1138 fileMenu.add(printMenuItem);
\r
1139 fileMenu.addSeparator();
\r
1140 fileMenu.add(exportFeatures);
\r
1141 fileMenu.add(exportAnnotations);
\r
1142 fileMenu.add(LoadtreeMenuItem);
\r
1143 fileMenu.add(associatedData);
\r
1144 fileMenu.addSeparator();
\r
1145 fileMenu.add(closeMenuItem);
\r
1146 editMenu.add(undoMenuItem);
\r
1147 editMenu.add(redoMenuItem);
\r
1148 editMenu.add(cut);
\r
1149 editMenu.add(copy);
\r
1150 editMenu.add(jMenu1);
\r
1151 editMenu.add(delete);
\r
1152 editMenu.addSeparator();
\r
1153 editMenu.add(selectAllSequenceMenuItem);
\r
1154 editMenu.add(deselectAllSequenceMenuItem);
\r
1155 editMenu.add(invertSequenceMenuItem);
\r
1156 editMenu.add(invertColSel);
\r
1157 editMenu.add(deleteGroups);
\r
1158 editMenu.addSeparator();
\r
1159 editMenu.add(remove2LeftMenuItem);
\r
1160 editMenu.add(remove2RightMenuItem);
\r
1161 editMenu.add(removeGappedColumnMenuItem);
\r
1162 editMenu.add(removeAllGapsMenuItem);
\r
1163 editMenu.add(removeRedundancyMenuItem);
\r
1164 editMenu.addSeparator();
\r
1165 editMenu.add(padGapsMenuitem);
\r
1166 searchMenu.add(findMenuItem);
\r
1167 viewMenu.add(font);
\r
1168 viewMenu.add(smoothFont);
\r
1169 viewMenu.addSeparator();
\r
1170 viewMenu.add(jMenu3);
\r
1171 viewMenu.add(hideMenu);
\r
1172 viewMenu.add(hiddenMarkers);
\r
1173 viewMenu.addSeparator();
\r
1174 viewMenu.add(wrapMenuItem);
\r
1175 viewMenu.add(seqLimits);
\r
1176 viewMenu.add(scaleAbove);
\r
1177 viewMenu.add(scaleLeft);
\r
1178 viewMenu.add(scaleRight);
\r
1179 viewMenu.add(viewBoxesMenuItem);
\r
1180 viewMenu.add(viewTextMenuItem);
\r
1181 viewMenu.add(colourTextMenuItem);
\r
1182 viewMenu.add(renderGapsMenuItem);
\r
1183 viewMenu.add(annotationPanelMenuItem);
\r
1184 viewMenu.addSeparator();
\r
1185 viewMenu.add(showSeqFeatures);
\r
1186 viewMenu.add(featureSettings);
\r
1187 viewMenu.addSeparator();
\r
1188 viewMenu.add(overviewMenuItem);
\r
1189 colourMenu.add(applyToAllGroups);
\r
1190 colourMenu.addSeparator();
\r
1191 colourMenu.add(noColourmenuItem);
\r
1192 colourMenu.add(clustalColour);
\r
1193 colourMenu.add(BLOSUM62Colour);
\r
1194 colourMenu.add(PIDColour);
\r
1195 colourMenu.add(zappoColour);
\r
1196 colourMenu.add(taylorColour);
\r
1197 colourMenu.add(hydrophobicityColour);
\r
1198 colourMenu.add(helixColour);
\r
1199 colourMenu.add(strandColour);
\r
1200 colourMenu.add(turnColour);
\r
1201 colourMenu.add(buriedColour);
\r
1202 colourMenu.add(nucleotideColour);
\r
1203 colourMenu.add(userDefinedColour);
\r
1204 colourMenu.addSeparator();
\r
1205 colourMenu.add(conservationMenuItem);
\r
1206 colourMenu.add(modifyConservation);
\r
1207 colourMenu.add(abovePIDThreshold);
\r
1208 colourMenu.add(modifyPID);
\r
1209 colourMenu.add(annotationColour);
\r
1210 calculateMenu.add(sort);
\r
1211 calculateMenu.add(calculate);
\r
1212 calculateMenu.addSeparator();
\r
1213 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1214 calculateMenu.add(PCAMenuItem);
\r
1215 calculateMenu.addSeparator();
\r
1216 calculateMenu.add(showTranslation);
\r
1217 calculateMenu.add(autoCalculate);
\r
1218 webServiceNoServices=new JMenuItem("<No Services>");
\r
1219 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1220 jMenu1.add(pasteThis);
\r
1221 sort.add(sortIDMenuItem);
\r
1222 sort.add(sortGroupMenuItem);
\r
1223 sort.add(sortPairwiseMenuItem);
\r
1224 calculate.add(averageDistanceTreeMenuItem);
\r
1225 calculate.add(neighbourTreeMenuItem);
\r
1226 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1227 calculate.add(njTreeBlosumMenuItem);
\r
1228 jMenu2.add(htmlMenuItem);
\r
1229 jMenu2.add(epsFile);
\r
1230 jMenu2.add(createPNG);
\r
1231 addSequenceMenu.add(addFromFile);
\r
1232 addSequenceMenu.add(addFromText);
\r
1233 addSequenceMenu.add(addFromURL);
\r
1234 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1235 statusPanel.add(statusBar, null);
\r
1236 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1237 jMenu3.add(showAllColumns);
\r
1238 jMenu3.add(showAllSeqs);
\r
1239 hideMenu.add(hideSelColumns);
\r
1240 hideMenu.add(hideSelSequences);
\r
1243 protected void outputText_actionPerformed(ActionEvent e)
\r
1247 public void addFromFile_actionPerformed(ActionEvent e)
\r
1252 public void addFromText_actionPerformed(ActionEvent e)
\r
1257 public void addFromURL_actionPerformed(ActionEvent e)
\r
1262 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1267 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1272 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1276 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1280 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1284 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1288 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1292 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1296 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1300 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1304 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1308 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1312 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1316 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1320 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1324 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1328 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1332 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1336 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1340 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1344 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1348 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1352 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1356 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1360 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1364 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1368 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1372 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1376 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1380 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1384 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1388 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1392 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1396 protected void helixColour_actionPerformed(ActionEvent e)
\r
1400 protected void strandColour_actionPerformed(ActionEvent e)
\r
1404 protected void turnColour_actionPerformed(ActionEvent e)
\r
1408 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1412 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1416 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1420 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1424 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1428 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1432 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1436 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1440 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1444 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1448 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1452 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1456 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1460 protected void copy_actionPerformed(ActionEvent e)
\r
1464 protected void cut_actionPerformed(ActionEvent e)
\r
1468 protected void delete_actionPerformed(ActionEvent e)
\r
1472 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1476 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1480 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1484 public void createPNG(java.io.File f)
\r
1488 protected void font_actionPerformed(ActionEvent e)
\r
1492 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1496 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1502 public void createEPS(java.io.File f)
\r
1506 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1510 protected void jpred_actionPerformed(ActionEvent e)
\r
1514 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1518 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1522 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1526 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1530 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1536 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1540 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1545 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1550 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1555 public void showTranslation_actionPerformed(ActionEvent e)
\r
1560 public void featureSettings_actionPerformed(ActionEvent e)
\r
1565 public void fetchSequence_actionPerformed(ActionEvent e)
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1570 public void smoothFont_actionPerformed(ActionEvent e)
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1575 public void annotationColour_actionPerformed(ActionEvent e)
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1581 public void associatedData_actionPerformed(ActionEvent e)
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1586 public void autoCalculate_actionPerformed(ActionEvent e)
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1591 public void showAllSeqs_actionPerformed(ActionEvent e)
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1596 public void showAllColumns_actionPerformed(ActionEvent e)
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1601 public void hideSelSequences_actionPerformed(ActionEvent e)
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1606 public void hideSelColumns_actionPerformed(ActionEvent e)
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1611 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1616 public void findPdbId_actionPerformed(ActionEvent e)
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1621 public void enterPdbId_actionPerformed(ActionEvent e)
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1626 public void pdbFile_actionPerformed(ActionEvent e)
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1631 public void invertColSel_actionPerformed(ActionEvent e)
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1636 public void tabSelectionChanged(int sel)
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1641 public void tabbedPane_mousePressed(MouseEvent e)
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