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_I,
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373 java.awt.event.KeyEvent.CTRL_MASK | java.awt.event.KeyEvent.SHIFT_MASK, false));
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374 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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376 public void actionPerformed(ActionEvent e)
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378 invertSequenceMenuItem_actionPerformed(e);
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381 remove2LeftMenuItem.setText("Remove Left");
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382 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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383 awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));
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384 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 remove2LeftMenuItem_actionPerformed(e);
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391 remove2RightMenuItem.setText("Remove Right");
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392 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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393 awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));
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394 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 remove2RightMenuItem_actionPerformed(e);
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401 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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402 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
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403 getKeyStroke(java.awt.event.
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404 KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));
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405 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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408 public void actionPerformed(ActionEvent e)
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410 removeGappedColumnMenuItem_actionPerformed(e);
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413 removeAllGapsMenuItem.setText("Remove All Gaps");
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414 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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415 java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));
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416 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 removeAllGapsMenuItem_actionPerformed(e);
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423 viewBoxesMenuItem.setText("Boxes");
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424 viewBoxesMenuItem.setState(true);
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425 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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427 public void actionPerformed(ActionEvent e)
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429 viewBoxesMenuItem_actionPerformed(e);
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432 viewTextMenuItem.setText("Text");
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433 viewTextMenuItem.setState(true);
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434 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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436 public void actionPerformed(ActionEvent e)
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438 viewTextMenuItem_actionPerformed(e);
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441 sortPairwiseMenuItem.setText("by Pairwise Identity");
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442 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 sortPairwiseMenuItem_actionPerformed(e);
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449 sortIDMenuItem.setText("by ID");
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450 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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452 public void actionPerformed(ActionEvent e)
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454 sortIDMenuItem_actionPerformed(e);
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457 sortGroupMenuItem.setText("by Group");
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458 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 sortGroupMenuItem_actionPerformed(e);
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465 removeRedundancyMenuItem.setText("Remove Redundancy...");
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466 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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467 java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));
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468 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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471 public void actionPerformed(ActionEvent e)
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473 removeRedundancyMenuItem_actionPerformed(e);
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476 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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477 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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480 public void actionPerformed(ActionEvent e)
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482 pairwiseAlignmentMenuItem_actionPerformed(e);
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485 PCAMenuItem.setText("Principal Component Analysis");
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486 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 PCAMenuItem_actionPerformed(e);
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493 averageDistanceTreeMenuItem.setText(
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494 "Average Distance Using % Identity");
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495 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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498 public void actionPerformed(ActionEvent e)
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500 averageDistanceTreeMenuItem_actionPerformed(e);
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503 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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504 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 neighbourTreeMenuItem_actionPerformed(e);
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511 this.getContentPane().setLayout(borderLayout1);
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512 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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513 statusBar.setBackground(Color.white);
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514 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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515 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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516 statusBar.setText("Status bar");
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517 outputTextboxMenu.setMnemonic('T');
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518 outputTextboxMenu.setText("Output to Textbox");
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519 clustalColour.setText("Clustalx");
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521 clustalColour.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 clustalColour_actionPerformed(e);
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528 zappoColour.setText("Zappo");
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529 zappoColour.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 zappoColour_actionPerformed(e);
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536 taylorColour.setText("Taylor");
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537 taylorColour.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 taylorColour_actionPerformed(e);
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544 hydrophobicityColour.setText("Hydrophobicity");
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545 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 hydrophobicityColour_actionPerformed(e);
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552 helixColour.setText("Helix Propensity");
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553 helixColour.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 helixColour_actionPerformed(e);
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560 strandColour.setText("Strand Propensity");
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561 strandColour.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 strandColour_actionPerformed(e);
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568 turnColour.setText("Turn Propensity");
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569 turnColour.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 turnColour_actionPerformed(e);
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576 buriedColour.setText("Buried Index");
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577 buriedColour.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 buriedColour_actionPerformed(e);
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584 userDefinedColour.setText("User Defined...");
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585 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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587 public void actionPerformed(ActionEvent e)
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589 userDefinedColour_actionPerformed(e);
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592 PIDColour.setText("Percentage Identity");
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593 PIDColour.addActionListener(new java.awt.event.ActionListener()
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595 public void actionPerformed(ActionEvent e)
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597 PIDColour_actionPerformed(e);
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600 BLOSUM62Colour.setText("BLOSUM62 Score");
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601 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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603 public void actionPerformed(ActionEvent e)
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605 BLOSUM62Colour_actionPerformed(e);
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608 avDistanceTreeBlosumMenuItem.setText(
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609 "Average Distance Using BLOSUM62");
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610 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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613 public void actionPerformed(ActionEvent e)
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615 avTreeBlosumMenuItem_actionPerformed(e);
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618 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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619 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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621 public void actionPerformed(ActionEvent e)
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623 njTreeBlosumMenuItem_actionPerformed(e);
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626 annotationPanelMenuItem.setActionCommand("");
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627 annotationPanelMenuItem.setText("Show Annotations");
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628 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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629 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 annotationPanelMenuItem_actionPerformed(e);
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636 colourTextMenuItem.setText("Colour Text");
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637 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 colourTextMenuItem_actionPerformed(e);
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644 htmlMenuItem.setText("HTML");
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645 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 htmlMenuItem_actionPerformed(e);
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652 overviewMenuItem.setText("Overview Window");
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653 overviewMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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654 event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));
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655 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 overviewMenuItem_actionPerformed(e);
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662 undoMenuItem.setEnabled(false);
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663 undoMenuItem.setMnemonic('Z');
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664 undoMenuItem.setText("Undo");
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665 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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666 java.awt.event.KeyEvent.VK_Z,
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667 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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668 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 undoMenuItem_actionPerformed(e);
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675 redoMenuItem.setEnabled(false);
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676 redoMenuItem.setMnemonic('0');
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677 redoMenuItem.setText("Redo");
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678 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
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679 event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));
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680 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
682 public void actionPerformed(ActionEvent e)
\r
684 redoMenuItem_actionPerformed(e);
\r
687 conservationMenuItem.setText("By Conservation");
\r
688 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
690 public void actionPerformed(ActionEvent e)
\r
692 conservationMenuItem_actionPerformed(e);
\r
695 noColourmenuItem.setText("None");
\r
696 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
698 public void actionPerformed(ActionEvent e)
\r
700 noColourmenuItem_actionPerformed(e);
\r
703 wrapMenuItem.setText("Wrap");
\r
704 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
706 public void actionPerformed(ActionEvent e)
\r
708 wrapMenuItem_actionPerformed(e);
\r
711 printMenuItem.setText("Print");
\r
712 printMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
714 public void actionPerformed(ActionEvent e)
\r
716 printMenuItem_actionPerformed(e);
\r
719 renderGapsMenuItem.setText("Show Gaps");
\r
720 renderGapsMenuItem.setState(true);
\r
721 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
723 public void actionPerformed(ActionEvent e)
\r
725 renderGapsMenuItem_actionPerformed(e);
\r
728 findMenuItem.setText("Find...");
\r
729 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
730 java.awt.event.KeyEvent.VK_F,
\r
731 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
732 findMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
734 public void actionPerformed(ActionEvent e)
\r
736 findMenuItem_actionPerformed(e);
\r
739 searchMenu.setText("Search");
\r
741 abovePIDThreshold.setText("Above Identity Threshold");
\r
742 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
744 public void actionPerformed(ActionEvent e)
\r
746 abovePIDThreshold_actionPerformed(e);
\r
749 showSeqFeatures.setText("Show Sequence Features");
\r
750 showSeqFeatures.addActionListener(new ActionListener()
\r
752 public void actionPerformed(ActionEvent actionEvent)
\r
754 showSeqFeatures_actionPerformed(actionEvent);
\r
757 nucleotideColour.setText("Nucleotide");
\r
758 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
760 public void actionPerformed(ActionEvent e)
\r
762 nucleotideColour_actionPerformed(e);
\r
765 deleteGroups.setText("Undefine groups");
\r
766 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
767 event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));
\r
768 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
770 public void actionPerformed(ActionEvent e)
\r
772 deleteGroups_actionPerformed(e);
\r
775 copy.setText("Copy");
\r
776 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
777 java.awt.event.KeyEvent.VK_C,
\r
778 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
779 copy.setMnemonic(KeyEvent.VK_C);
\r
781 copy.addActionListener(new java.awt.event.ActionListener()
\r
783 public void actionPerformed(ActionEvent e)
\r
785 copy_actionPerformed(e);
\r
788 cut.setText("Cut");
\r
789 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
790 java.awt.event.KeyEvent.VK_X,
\r
791 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
792 cut.setMnemonic(KeyEvent.VK_X);
\r
793 cut.addActionListener(new java.awt.event.ActionListener()
\r
795 public void actionPerformed(ActionEvent e)
\r
797 cut_actionPerformed(e);
\r
800 delete.setText("Delete");
\r
801 delete.addActionListener(new java.awt.event.ActionListener()
\r
803 public void actionPerformed(ActionEvent e)
\r
805 delete_actionPerformed(e);
\r
808 jMenu1.setMnemonic('V');
\r
809 jMenu1.setText("Paste");
\r
810 pasteNew.setText("To New Alignment");
\r
811 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
812 java.awt.event.KeyEvent.VK_V,
\r
813 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
814 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
816 public void actionPerformed(ActionEvent e)
\r
818 pasteNew_actionPerformed(e);
\r
821 pasteThis.setText("Add To This Alignment");
\r
822 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
824 public void actionPerformed(ActionEvent e)
\r
826 pasteThis_actionPerformed(e);
\r
829 applyToAllGroups.setText("Apply Colour To All Groups");
\r
830 applyToAllGroups.setState(true);
\r
831 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
833 public void actionPerformed(ActionEvent e)
\r
835 applyToAllGroups_actionPerformed(e);
\r
838 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
840 public void actionPerformed(ActionEvent e)
\r
845 createPNG.setActionCommand("Save As PNG Image");
\r
846 createPNG.setText("PNG");
\r
847 font.setText("Font...");
\r
848 font.addActionListener(new java.awt.event.ActionListener()
\r
850 public void actionPerformed(ActionEvent e)
\r
852 font_actionPerformed(e);
\r
856 seqLimits.setText("Show Sequence Limits");
\r
857 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
858 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
860 public void actionPerformed(ActionEvent e)
\r
862 seqLimit_actionPerformed(e);
\r
865 epsFile.setText("EPS");
\r
866 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
868 public void actionPerformed(ActionEvent e)
\r
873 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
874 LoadtreeMenuItem.setText("Load Associated Tree");
\r
875 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
877 public void actionPerformed(ActionEvent e)
\r
879 LoadtreeMenuItem_actionPerformed(e);
\r
882 scaleAbove.setVisible(false);
\r
883 scaleAbove.setText("Scale Above");
\r
884 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
886 public void actionPerformed(ActionEvent e)
\r
888 scaleAbove_actionPerformed(e);
\r
891 scaleLeft.setVisible(false);
\r
892 scaleLeft.setSelected(true);
\r
893 scaleLeft.setText("Scale Left");
\r
894 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
896 public void actionPerformed(ActionEvent e)
\r
898 scaleLeft_actionPerformed(e);
\r
901 scaleRight.setVisible(false);
\r
902 scaleRight.setSelected(true);
\r
903 scaleRight.setText("Scale Right");
\r
904 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
906 public void actionPerformed(ActionEvent e)
\r
908 scaleRight_actionPerformed(e);
\r
911 modifyPID.setText("Modify Identity Threshold...");
\r
912 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
914 public void actionPerformed(ActionEvent e)
\r
916 modifyPID_actionPerformed(e);
\r
919 modifyConservation.setText("Modify Conservation Threshold...");
\r
920 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
922 public void actionPerformed(ActionEvent e)
\r
924 modifyConservation_actionPerformed(e);
\r
927 sortByTreeMenu.setText("By Tree Order");
\r
928 sort.setText("Sort");
\r
929 calculate.setText("Calculate Tree");
\r
931 jMenu2.setText("Export");
\r
932 padGapsMenuitem.setText("Pad Gaps");
\r
933 padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
934 event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));
\r
935 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
936 padGapsMenuitem.addActionListener(new ActionListener()
\r
938 public void actionPerformed(ActionEvent e)
\r
940 padGapsMenuitem_actionPerformed(e);
\r
943 vamsasStore.setVisible(false);
\r
944 vamsasStore.setText("VAMSAS store");
\r
945 vamsasStore.addActionListener(new ActionListener()
\r
947 public void actionPerformed(ActionEvent e)
\r
949 vamsasStore_actionPerformed(e);
\r
952 showTranslation.setText("Translate cDNA");
\r
953 showTranslation.addActionListener(new ActionListener()
\r
955 public void actionPerformed(ActionEvent e)
\r
957 showTranslation_actionPerformed(e);
\r
961 /* tabbedPane.addChangeListener(new ChangeListener()
\r
963 public void stateChanged(ChangeEvent ece)
\r
969 featureSettings.setText("Feature Settings...");
\r
970 featureSettings.addActionListener(new ActionListener()
\r
972 public void actionPerformed(ActionEvent e)
\r
974 featureSettings_actionPerformed(e);
\r
977 fetchSequence.setText("Fetch Sequence(s)...");
\r
978 fetchSequence.addActionListener(new ActionListener()
\r
980 public void actionPerformed(ActionEvent e)
\r
982 fetchSequence_actionPerformed(e);
\r
985 smoothFont.setText("Smooth Fonts");
\r
986 smoothFont.addActionListener(new ActionListener()
\r
988 public void actionPerformed(ActionEvent e)
\r
990 smoothFont_actionPerformed(e);
\r
993 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
994 annotationColour.setText("By Annotation...");
\r
995 annotationColour.addActionListener(new ActionListener()
\r
997 public void actionPerformed(ActionEvent e)
\r
999 annotationColour_actionPerformed(e);
\r
1002 associatedData.setText("Load Features / Annotations");
\r
1003 associatedData.addActionListener(new ActionListener()
\r
1005 public void actionPerformed(ActionEvent e)
\r
1007 associatedData_actionPerformed(e);
\r
1010 autoCalculate.setText("Autocalculate Consensus");
\r
1011 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
1012 autoCalculate.addActionListener(new ActionListener()
\r
1014 public void actionPerformed(ActionEvent e)
\r
1016 autoCalculate_actionPerformed(e);
\r
1019 addSequenceMenu.setText("Add Sequences");
\r
1020 addFromFile.setText("From File");
\r
1021 addFromFile.addActionListener(new ActionListener()
\r
1023 public void actionPerformed(ActionEvent e)
\r
1025 addFromFile_actionPerformed(e);
\r
1028 addFromText.setText("From Textbox");
\r
1029 addFromText.addActionListener(new ActionListener()
\r
1031 public void actionPerformed(ActionEvent e)
\r
1033 addFromText_actionPerformed(e);
\r
1036 addFromURL.setText("From URL");
\r
1037 addFromURL.addActionListener(new ActionListener()
\r
1039 public void actionPerformed(ActionEvent e)
\r
1041 addFromURL_actionPerformed(e);
\r
1044 exportFeatures.setText("Export Features...");
\r
1045 exportFeatures.addActionListener(new ActionListener()
\r
1047 public void actionPerformed(ActionEvent e)
\r
1049 exportFeatures_actionPerformed(e);
\r
1052 exportAnnotations.setText("Export Annotations...");
\r
1053 exportAnnotations.addActionListener(new ActionListener()
\r
1055 public void actionPerformed(ActionEvent e)
\r
1057 exportAnnotations_actionPerformed(e);
\r
1060 statusPanel.setLayout(gridLayout1);
\r
1061 jMenu3.setText("Show");
\r
1062 showAllSeqs.setText("All Sequences");
\r
1063 showAllSeqs.addActionListener(new ActionListener()
\r
1065 public void actionPerformed(ActionEvent e)
\r
1067 showAllSeqs_actionPerformed(e);
\r
1070 showAllColumns.setText("All Columns");
\r
1071 showAllColumns.addActionListener(new ActionListener()
\r
1073 public void actionPerformed(ActionEvent e)
\r
1075 showAllColumns_actionPerformed(e);
\r
1078 hideMenu.setText("Hide");
\r
1079 hideSelSequences.setText("Selected Sequences");
\r
1080 hideSelSequences.addActionListener(new ActionListener()
\r
1082 public void actionPerformed(ActionEvent e)
\r
1084 hideSelSequences_actionPerformed(e);
\r
1087 hideSelColumns.setText("Selected Columns");
\r
1088 hideSelColumns.addActionListener(new ActionListener()
\r
1090 public void actionPerformed(ActionEvent e)
\r
1092 hideSelColumns_actionPerformed(e);
\r
1095 hiddenMarkers.setText("Hidden Markers");
\r
1096 hiddenMarkers.setState(true);
\r
1097 hiddenMarkers.addActionListener(new ActionListener()
\r
1099 public void actionPerformed(ActionEvent e)
\r
1101 hiddenMarkers_actionPerformed(e);
\r
1104 invertColSel.setText("Invert Column Selection");
\r
1105 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
\r
1106 event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false));
\r
1107 invertColSel.addActionListener(new ActionListener()
\r
1109 public void actionPerformed(ActionEvent e)
\r
1111 invertColSel_actionPerformed(e);
\r
1114 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1116 public void stateChanged(ChangeEvent evt)
\r
1118 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1119 int sel = pane.getSelectedIndex();
\r
1120 tabSelectionChanged(sel);
\r
1123 tabbedPane.addMouseListener(new MouseAdapter()
\r
1125 public void mousePressed(MouseEvent e)
\r
1127 tabbedPane_mousePressed(e);
\r
1131 alignFrameMenuBar.add(fileMenu);
\r
1132 alignFrameMenuBar.add(editMenu);
\r
1133 alignFrameMenuBar.add(searchMenu);
\r
1134 alignFrameMenuBar.add(viewMenu);
\r
1135 alignFrameMenuBar.add(colourMenu);
\r
1136 alignFrameMenuBar.add(calculateMenu);
\r
1137 alignFrameMenuBar.add(webService);
\r
1138 fileMenu.add(addSequenceMenu);
\r
1139 fileMenu.add(fetchSequence);
\r
1140 fileMenu.addSeparator();
\r
1141 fileMenu.add(vamsasStore);
\r
1142 fileMenu.add(saveAlignmentMenu);
\r
1143 fileMenu.add(jMenu2);
\r
1144 fileMenu.add(outputTextboxMenu);
\r
1145 fileMenu.add(printMenuItem);
\r
1146 fileMenu.addSeparator();
\r
1147 fileMenu.add(exportFeatures);
\r
1148 fileMenu.add(exportAnnotations);
\r
1149 fileMenu.add(LoadtreeMenuItem);
\r
1150 fileMenu.add(associatedData);
\r
1151 fileMenu.addSeparator();
\r
1152 fileMenu.add(closeMenuItem);
\r
1153 editMenu.add(undoMenuItem);
\r
1154 editMenu.add(redoMenuItem);
\r
1155 editMenu.add(cut);
\r
1156 editMenu.add(copy);
\r
1157 editMenu.add(jMenu1);
\r
1158 editMenu.add(delete);
\r
1159 editMenu.addSeparator();
\r
1160 editMenu.add(selectAllSequenceMenuItem);
\r
1161 editMenu.add(deselectAllSequenceMenuItem);
\r
1162 editMenu.add(invertSequenceMenuItem);
\r
1163 editMenu.add(invertColSel);
\r
1164 editMenu.add(deleteGroups);
\r
1165 editMenu.addSeparator();
\r
1166 editMenu.add(remove2LeftMenuItem);
\r
1167 editMenu.add(remove2RightMenuItem);
\r
1168 editMenu.add(removeGappedColumnMenuItem);
\r
1169 editMenu.add(removeAllGapsMenuItem);
\r
1170 editMenu.add(removeRedundancyMenuItem);
\r
1171 editMenu.addSeparator();
\r
1172 editMenu.add(padGapsMenuitem);
\r
1173 searchMenu.add(findMenuItem);
\r
1174 viewMenu.add(font);
\r
1175 viewMenu.add(smoothFont);
\r
1176 viewMenu.addSeparator();
\r
1177 viewMenu.add(jMenu3);
\r
1178 viewMenu.add(hideMenu);
\r
1179 viewMenu.add(hiddenMarkers);
\r
1180 viewMenu.addSeparator();
\r
1181 viewMenu.add(wrapMenuItem);
\r
1182 viewMenu.add(seqLimits);
\r
1183 viewMenu.add(scaleAbove);
\r
1184 viewMenu.add(scaleLeft);
\r
1185 viewMenu.add(scaleRight);
\r
1186 viewMenu.add(viewBoxesMenuItem);
\r
1187 viewMenu.add(viewTextMenuItem);
\r
1188 viewMenu.add(colourTextMenuItem);
\r
1189 viewMenu.add(renderGapsMenuItem);
\r
1190 viewMenu.add(annotationPanelMenuItem);
\r
1191 viewMenu.addSeparator();
\r
1192 viewMenu.add(showSeqFeatures);
\r
1193 viewMenu.add(featureSettings);
\r
1194 viewMenu.addSeparator();
\r
1195 viewMenu.add(overviewMenuItem);
\r
1196 colourMenu.add(applyToAllGroups);
\r
1197 colourMenu.addSeparator();
\r
1198 colourMenu.add(noColourmenuItem);
\r
1199 colourMenu.add(clustalColour);
\r
1200 colourMenu.add(BLOSUM62Colour);
\r
1201 colourMenu.add(PIDColour);
\r
1202 colourMenu.add(zappoColour);
\r
1203 colourMenu.add(taylorColour);
\r
1204 colourMenu.add(hydrophobicityColour);
\r
1205 colourMenu.add(helixColour);
\r
1206 colourMenu.add(strandColour);
\r
1207 colourMenu.add(turnColour);
\r
1208 colourMenu.add(buriedColour);
\r
1209 colourMenu.add(nucleotideColour);
\r
1210 colourMenu.add(userDefinedColour);
\r
1211 colourMenu.addSeparator();
\r
1212 colourMenu.add(conservationMenuItem);
\r
1213 colourMenu.add(modifyConservation);
\r
1214 colourMenu.add(abovePIDThreshold);
\r
1215 colourMenu.add(modifyPID);
\r
1216 colourMenu.add(annotationColour);
\r
1217 calculateMenu.add(sort);
\r
1218 calculateMenu.add(calculate);
\r
1219 calculateMenu.addSeparator();
\r
1220 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1221 calculateMenu.add(PCAMenuItem);
\r
1222 calculateMenu.addSeparator();
\r
1223 calculateMenu.add(showTranslation);
\r
1224 calculateMenu.add(autoCalculate);
\r
1225 webServiceNoServices=new JMenuItem("<No Services>");
\r
1226 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1227 jMenu1.add(pasteThis);
\r
1228 sort.add(sortIDMenuItem);
\r
1229 sort.add(sortGroupMenuItem);
\r
1230 sort.add(sortPairwiseMenuItem);
\r
1231 calculate.add(averageDistanceTreeMenuItem);
\r
1232 calculate.add(neighbourTreeMenuItem);
\r
1233 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1234 calculate.add(njTreeBlosumMenuItem);
\r
1235 jMenu2.add(htmlMenuItem);
\r
1236 jMenu2.add(epsFile);
\r
1237 jMenu2.add(createPNG);
\r
1238 addSequenceMenu.add(addFromFile);
\r
1239 addSequenceMenu.add(addFromText);
\r
1240 addSequenceMenu.add(addFromURL);
\r
1241 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1242 statusPanel.add(statusBar, null);
\r
1243 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1244 jMenu3.add(showAllColumns);
\r
1245 jMenu3.add(showAllSeqs);
\r
1246 hideMenu.add(hideSelColumns);
\r
1247 hideMenu.add(hideSelSequences);
\r
1250 protected void outputText_actionPerformed(ActionEvent e)
\r
1254 public void addFromFile_actionPerformed(ActionEvent e)
\r
1259 public void addFromText_actionPerformed(ActionEvent e)
\r
1264 public void addFromURL_actionPerformed(ActionEvent e)
\r
1269 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1274 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1279 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1283 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1287 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1291 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1295 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1299 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1303 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1307 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1311 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1315 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1319 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1323 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1327 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1331 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1335 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1339 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1343 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1347 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1351 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1355 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1359 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1363 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1367 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1371 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1375 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1379 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1383 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1387 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1391 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1395 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1399 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1403 protected void helixColour_actionPerformed(ActionEvent e)
\r
1407 protected void strandColour_actionPerformed(ActionEvent e)
\r
1411 protected void turnColour_actionPerformed(ActionEvent e)
\r
1415 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1419 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1423 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1427 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1431 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1435 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1439 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1443 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1447 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1451 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1455 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1459 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1463 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1467 protected void copy_actionPerformed(ActionEvent e)
\r
1471 protected void cut_actionPerformed(ActionEvent e)
\r
1475 protected void delete_actionPerformed(ActionEvent e)
\r
1479 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1483 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1487 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1491 public void createPNG(java.io.File f)
\r
1495 protected void font_actionPerformed(ActionEvent e)
\r
1499 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1503 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1509 public void createEPS(java.io.File f)
\r
1513 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1517 protected void jpred_actionPerformed(ActionEvent e)
\r
1521 protected void scaleAbove_actionPerformed(ActionEvent e)
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1525 protected void scaleLeft_actionPerformed(ActionEvent e)
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1529 protected void scaleRight_actionPerformed(ActionEvent e)
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1533 protected void modifyPID_actionPerformed(ActionEvent e)
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1537 protected void modifyConservation_actionPerformed(ActionEvent e)
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1543 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
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1547 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
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1552 public void vamsasStore_actionPerformed(ActionEvent e)
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1557 public void vamsasLoad_actionPerformed(ActionEvent e)
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1562 public void showTranslation_actionPerformed(ActionEvent e)
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1567 public void featureSettings_actionPerformed(ActionEvent e)
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1572 public void fetchSequence_actionPerformed(ActionEvent e)
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1577 public void smoothFont_actionPerformed(ActionEvent e)
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1582 public void annotationColour_actionPerformed(ActionEvent e)
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1588 public void associatedData_actionPerformed(ActionEvent e)
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1593 public void autoCalculate_actionPerformed(ActionEvent e)
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1598 public void showAllSeqs_actionPerformed(ActionEvent e)
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1603 public void showAllColumns_actionPerformed(ActionEvent e)
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1608 public void hideSelSequences_actionPerformed(ActionEvent e)
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1613 public void hideSelColumns_actionPerformed(ActionEvent e)
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1618 public void hiddenMarkers_actionPerformed(ActionEvent e)
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1623 public void findPdbId_actionPerformed(ActionEvent e)
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1628 public void enterPdbId_actionPerformed(ActionEvent e)
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1633 public void pdbFile_actionPerformed(ActionEvent e)
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1638 public void invertColSel_actionPerformed(ActionEvent e)
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1643 public void tabSelectionChanged(int sel)
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1648 public void tabbedPane_mousePressed(MouseEvent e)
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