2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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25 import jalview.schemes.*;
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26 import java.awt.BorderLayout;
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28 public class GAlignFrame
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29 extends JInternalFrame
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31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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32 protected JMenu fileMenu = new JMenu();
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33 protected JMenuItem closeMenuItem = new JMenuItem();
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34 protected JMenu editMenu = new JMenu();
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35 protected JMenu viewMenu = new JMenu();
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36 protected JMenu colourMenu = new JMenu();
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37 protected JMenu calculateMenu = new JMenu();
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38 protected JMenu webService = new JMenu();
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39 protected JMenuItem webServiceNoServices;
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40 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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41 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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42 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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43 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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44 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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45 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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46 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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47 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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48 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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49 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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50 protected JMenuItem sortIDMenuItem = new JMenuItem();
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51 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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52 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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53 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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54 protected JMenuItem PCAMenuItem = new JMenuItem();
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55 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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56 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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57 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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58 BorderLayout borderLayout1 = new BorderLayout();
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59 public JLabel statusBar = new JLabel();
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60 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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61 protected JMenu outputTextboxMenu = new JMenu();
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62 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem hydrophobicityColour = new
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66 JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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74 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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75 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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76 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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77 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem htmlMenuItem = new JMenuItem();
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79 JMenuItem overviewMenuItem = new JMenuItem();
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80 protected JMenuItem undoMenuItem = new JMenuItem();
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81 protected JMenuItem redoMenuItem = new JMenuItem();
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82 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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83 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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84 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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85 JMenuItem printMenuItem = new JMenuItem();
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86 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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87 JMenuItem findMenuItem = new JMenuItem();
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88 JMenu searchMenu = new JMenu();
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89 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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90 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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91 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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92 JMenuItem deleteGroups = new JMenuItem();
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93 JMenuItem delete = new JMenuItem();
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94 JMenuItem copy = new JMenuItem();
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95 JMenuItem cut = new JMenuItem();
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96 JMenu jMenu1 = new JMenu();
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97 JMenuItem pasteNew = new JMenuItem();
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98 JMenuItem pasteThis = new JMenuItem();
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99 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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100 JMenuItem createPNG = new JMenuItem();
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101 protected JMenuItem font = new JMenuItem();
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102 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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103 JMenuItem epsFile = new JMenuItem();
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104 JMenuItem LoadtreeMenuItem = new JMenuItem();
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105 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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106 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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107 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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108 protected JMenuItem modifyPID = new JMenuItem();
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109 protected JMenuItem modifyConservation = new JMenuItem();
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110 protected JMenu sortByTreeMenu = new JMenu();
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111 protected JMenu sort = new JMenu();
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112 JMenu calculate = new JMenu();
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113 JMenu jMenu2 = new JMenu();
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114 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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115 protected ButtonGroup colours = new ButtonGroup();
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116 JMenuItem vamsasStore = new JMenuItem();
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117 protected JMenuItem showTranslation = new JMenuItem();
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118 public JMenuItem featureSettings = new JMenuItem();
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119 JMenuItem fetchSequence = new JMenuItem();
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120 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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121 JMenuItem annotationColour = new JMenuItem();
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122 JMenuItem associatedData = new JMenuItem();
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123 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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124 JMenu addSequenceMenu = new JMenu();
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125 JMenuItem addFromFile = new JMenuItem();
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126 JMenuItem addFromText = new JMenuItem();
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127 JMenuItem addFromURL = new JMenuItem();
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128 JMenuItem exportAnnotations = new JMenuItem();
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129 JMenuItem exportFeatures = new JMenuItem();
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130 protected JPanel statusPanel = new JPanel();
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131 GridLayout gridLayout1 = new GridLayout();
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132 JMenu jMenu3 = new JMenu();
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133 JMenuItem showAllSeqs = new JMenuItem();
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134 JMenuItem showAllColumns = new JMenuItem();
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135 JMenu jMenu4 = new JMenu();
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136 JMenuItem hideSelSequences = new JMenuItem();
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137 JMenuItem hideSelColumns = new JMenuItem();
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138 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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140 public GAlignFrame()
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147 setJMenuBar(alignFrameMenuBar);
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149 // dynamically fill save as menu with available formats
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150 for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
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152 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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155 item.addActionListener(new java.awt.event.ActionListener()
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157 public void actionPerformed(ActionEvent e)
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159 outputText_actionPerformed(e);
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163 outputTextboxMenu.add(item);
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166 catch (Exception e)
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171 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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173 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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174 getUserColourSchemes().keys();
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176 while (userColours.hasMoreElements())
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178 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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179 nextElement().toString());
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180 radioItem.setName("USER_DEFINED");
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181 radioItem.addMouseListener(new MouseAdapter()
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183 public void mousePressed(MouseEvent evt)
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185 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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187 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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189 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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190 "Remove from default list?",
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191 "Remove user defined colour",
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192 JOptionPane.YES_NO_OPTION);
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193 if(option == JOptionPane.YES_OPTION)
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195 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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196 colourMenu.remove(radioItem);
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199 radioItem.addActionListener(new ActionListener()
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201 public void actionPerformed(ActionEvent evt)
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203 userDefinedColour_actionPerformed(evt);
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209 radioItem.addActionListener(new ActionListener()
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211 public void actionPerformed(ActionEvent evt)
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213 userDefinedColour_actionPerformed(evt);
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216 colourMenu.insert(radioItem, 15);
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217 colours.add(radioItem);
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220 colours.add(noColourmenuItem);
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221 colours.add(clustalColour);
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222 colours.add(zappoColour);
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223 colours.add(taylorColour);
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224 colours.add(hydrophobicityColour);
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225 colours.add(helixColour);
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226 colours.add(strandColour);
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227 colours.add(turnColour);
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228 colours.add(buriedColour);
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229 colours.add(userDefinedColour);
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230 colours.add(PIDColour);
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231 colours.add(BLOSUM62Colour);
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232 colours.add(nucleotideColour);
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234 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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239 public void setColourSelected(String defaultColour)
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242 if (defaultColour != null)
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244 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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248 case ColourSchemeProperty.NONE:
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249 noColourmenuItem.setSelected(true);
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251 case ColourSchemeProperty.CLUSTAL:
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252 clustalColour.setSelected(true);
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256 case ColourSchemeProperty.BLOSUM:
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257 BLOSUM62Colour.setSelected(true);
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261 case ColourSchemeProperty.PID:
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262 PIDColour.setSelected(true);
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266 case ColourSchemeProperty.ZAPPO:
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267 zappoColour.setSelected(true);
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271 case ColourSchemeProperty.TAYLOR:
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272 taylorColour.setSelected(true);
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275 case ColourSchemeProperty.HYDROPHOBIC:
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276 hydrophobicityColour.setSelected(true);
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280 case ColourSchemeProperty.HELIX:
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281 helixColour.setSelected(true);
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285 case ColourSchemeProperty.STRAND:
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286 strandColour.setSelected(true);
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290 case ColourSchemeProperty.TURN:
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291 turnColour.setSelected(true);
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295 case ColourSchemeProperty.BURIED:
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296 buriedColour.setSelected(true);
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300 case ColourSchemeProperty.NUCLEOTIDE:
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301 nucleotideColour.setSelected(true);
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305 case ColourSchemeProperty.USER_DEFINED:
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306 userDefinedColour.setSelected(true);
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314 private void jbInit()
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317 fileMenu.setMnemonic('F');
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318 fileMenu.setText("File");
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319 saveAlignmentMenu.setMnemonic('L');
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320 saveAlignmentMenu.setText("Save As");
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321 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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322 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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323 saveAlignmentMenu.addActionListener(new ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 saveAlignmentMenu_actionPerformed(e);
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330 closeMenuItem.setMnemonic('C');
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331 closeMenuItem.setText("Close");
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332 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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334 public void actionPerformed(ActionEvent e)
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336 closeMenuItem_actionPerformed(e);
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339 editMenu.setText("Edit");
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340 viewMenu.setText("View");
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341 colourMenu.setText("Colour");
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342 calculateMenu.setText("Calculate");
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343 webService.setText("Web Service");
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344 selectAllSequenceMenuItem.setText("Select all");
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345 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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346 java.awt.event.KeyEvent.VK_A,
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347 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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348 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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351 public void actionPerformed(ActionEvent e)
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353 selectAllSequenceMenuItem_actionPerformed(e);
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356 deselectAllSequenceMenuItem.setText("Deselect All");
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357 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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359 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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360 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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363 public void actionPerformed(ActionEvent e)
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365 deselectAllSequenceMenuItem_actionPerformed(e);
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368 invertSequenceMenuItem.setText("Invert Selection");
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369 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 invertSequenceMenuItem_actionPerformed(e);
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376 remove2LeftMenuItem.setText("Remove Left");
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377 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 remove2LeftMenuItem_actionPerformed(e);
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384 remove2RightMenuItem.setText("Remove Right");
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385 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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387 public void actionPerformed(ActionEvent e)
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389 remove2RightMenuItem_actionPerformed(e);
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392 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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393 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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396 public void actionPerformed(ActionEvent e)
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398 removeGappedColumnMenuItem_actionPerformed(e);
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401 removeAllGapsMenuItem.setText("Remove All Gaps");
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402 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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404 public void actionPerformed(ActionEvent e)
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406 removeAllGapsMenuItem_actionPerformed(e);
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409 viewBoxesMenuItem.setText("Boxes");
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410 viewBoxesMenuItem.setState(true);
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411 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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413 public void actionPerformed(ActionEvent e)
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415 viewBoxesMenuItem_actionPerformed(e);
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418 viewTextMenuItem.setText("Text");
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419 viewTextMenuItem.setState(true);
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420 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 viewTextMenuItem_actionPerformed(e);
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427 sortPairwiseMenuItem.setText("by Pairwise Identity");
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428 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 sortPairwiseMenuItem_actionPerformed(e);
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435 sortIDMenuItem.setText("by ID");
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436 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 sortIDMenuItem_actionPerformed(e);
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443 sortGroupMenuItem.setText("by Group");
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444 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 sortGroupMenuItem_actionPerformed(e);
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451 removeRedundancyMenuItem.setText("Remove Redundancy...");
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452 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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455 public void actionPerformed(ActionEvent e)
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457 removeRedundancyMenuItem_actionPerformed(e);
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460 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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461 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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464 public void actionPerformed(ActionEvent e)
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466 pairwiseAlignmentMenuItem_actionPerformed(e);
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469 PCAMenuItem.setText("Principal Component Analysis");
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470 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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472 public void actionPerformed(ActionEvent e)
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474 PCAMenuItem_actionPerformed(e);
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477 averageDistanceTreeMenuItem.setText(
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478 "Average Distance Using % Identity");
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479 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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482 public void actionPerformed(ActionEvent e)
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484 averageDistanceTreeMenuItem_actionPerformed(e);
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487 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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488 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 neighbourTreeMenuItem_actionPerformed(e);
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495 this.getContentPane().setLayout(borderLayout1);
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496 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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497 statusBar.setBackground(Color.white);
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498 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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499 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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500 statusBar.setText("Status bar");
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501 outputTextboxMenu.setMnemonic('T');
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502 outputTextboxMenu.setText("Output to Textbox");
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503 clustalColour.setText("Clustalx");
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505 clustalColour.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 clustalColour_actionPerformed(e);
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512 zappoColour.setText("Zappo");
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513 zappoColour.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 zappoColour_actionPerformed(e);
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520 taylorColour.setText("Taylor");
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521 taylorColour.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 taylorColour_actionPerformed(e);
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528 hydrophobicityColour.setText("Hydrophobicity");
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529 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 hydrophobicityColour_actionPerformed(e);
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536 helixColour.setText("Helix Propensity");
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537 helixColour.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 helixColour_actionPerformed(e);
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544 strandColour.setText("Strand Propensity");
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545 strandColour.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 strandColour_actionPerformed(e);
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552 turnColour.setText("Turn Propensity");
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553 turnColour.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 turnColour_actionPerformed(e);
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560 buriedColour.setText("Buried Index");
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561 buriedColour.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 buriedColour_actionPerformed(e);
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568 userDefinedColour.setText("User Defined...");
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569 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 userDefinedColour_actionPerformed(e);
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576 PIDColour.setText("Percentage Identity");
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577 PIDColour.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 PIDColour_actionPerformed(e);
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584 BLOSUM62Colour.setText("BLOSUM62 Score");
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585 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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587 public void actionPerformed(ActionEvent e)
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589 BLOSUM62Colour_actionPerformed(e);
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592 avDistanceTreeBlosumMenuItem.setText(
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593 "Average Distance Using BLOSUM62");
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594 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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597 public void actionPerformed(ActionEvent e)
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599 avTreeBlosumMenuItem_actionPerformed(e);
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602 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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603 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 njTreeBlosumMenuItem_actionPerformed(e);
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610 annotationPanelMenuItem.setActionCommand("");
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611 annotationPanelMenuItem.setText("Show Annotations");
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612 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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613 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 annotationPanelMenuItem_actionPerformed(e);
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620 colourTextMenuItem.setText("Colour Text");
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621 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 colourTextMenuItem_actionPerformed(e);
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628 htmlMenuItem.setText("HTML");
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629 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 htmlMenuItem_actionPerformed(e);
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636 overviewMenuItem.setText("Overview Window");
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637 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 overviewMenuItem_actionPerformed(e);
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644 undoMenuItem.setEnabled(false);
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645 undoMenuItem.setMnemonic('Z');
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646 undoMenuItem.setText("Undo");
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647 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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648 java.awt.event.KeyEvent.VK_Z,
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649 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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650 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 undoMenuItem_actionPerformed(e);
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657 redoMenuItem.setEnabled(false);
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658 redoMenuItem.setMnemonic('0');
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659 redoMenuItem.setText("Redo");
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660 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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662 public void actionPerformed(ActionEvent e)
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664 redoMenuItem_actionPerformed(e);
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667 conservationMenuItem.setText("By Conservation");
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668 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 conservationMenuItem_actionPerformed(e);
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675 noColourmenuItem.setText("None");
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676 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 noColourmenuItem_actionPerformed(e);
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683 wrapMenuItem.setText("Wrap");
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684 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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686 public void actionPerformed(ActionEvent e)
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688 wrapMenuItem_actionPerformed(e);
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691 printMenuItem.setText("Print");
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692 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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694 public void actionPerformed(ActionEvent e)
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696 printMenuItem_actionPerformed(e);
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699 renderGapsMenuItem.setText("Show Gaps");
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700 renderGapsMenuItem.setState(true);
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701 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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703 public void actionPerformed(ActionEvent e)
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705 renderGapsMenuItem_actionPerformed(e);
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708 findMenuItem.setText("Find...");
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709 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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710 java.awt.event.KeyEvent.VK_F,
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711 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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712 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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714 public void actionPerformed(ActionEvent e)
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716 findMenuItem_actionPerformed(e);
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719 searchMenu.setText("Search");
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721 abovePIDThreshold.setText("Above Identity Threshold");
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722 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
724 public void actionPerformed(ActionEvent e)
\r
726 abovePIDThreshold_actionPerformed(e);
\r
729 showSeqFeatures.setText("Show Sequence Features");
\r
730 showSeqFeatures.addActionListener(new ActionListener()
\r
732 public void actionPerformed(ActionEvent actionEvent)
\r
734 showSeqFeatures_actionPerformed(actionEvent);
\r
737 nucleotideColour.setText("Nucleotide");
\r
738 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
740 public void actionPerformed(ActionEvent e)
\r
742 nucleotideColour_actionPerformed(e);
\r
745 deleteGroups.setText("Undefine groups");
\r
746 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
748 public void actionPerformed(ActionEvent e)
\r
750 deleteGroups_actionPerformed(e);
\r
753 copy.setText("Copy");
\r
754 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
755 java.awt.event.KeyEvent.VK_C,
\r
756 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
757 copy.setMnemonic(KeyEvent.VK_C);
\r
759 copy.addActionListener(new java.awt.event.ActionListener()
\r
761 public void actionPerformed(ActionEvent e)
\r
763 copy_actionPerformed(e);
\r
766 cut.setText("Cut");
\r
767 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
768 java.awt.event.KeyEvent.VK_X,
\r
769 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
770 cut.setMnemonic(KeyEvent.VK_X);
\r
771 cut.addActionListener(new java.awt.event.ActionListener()
\r
773 public void actionPerformed(ActionEvent e)
\r
775 cut_actionPerformed(e);
\r
778 delete.setText("Delete");
\r
779 delete.addActionListener(new java.awt.event.ActionListener()
\r
781 public void actionPerformed(ActionEvent e)
\r
783 delete_actionPerformed(e);
\r
786 jMenu1.setMnemonic('V');
\r
787 jMenu1.setText("Paste");
\r
788 pasteNew.setText("To New Alignment");
\r
789 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
790 java.awt.event.KeyEvent.VK_V,
\r
791 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
792 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
794 public void actionPerformed(ActionEvent e)
\r
796 pasteNew_actionPerformed(e);
\r
799 pasteThis.setText("Add To This Alignment");
\r
800 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
802 public void actionPerformed(ActionEvent e)
\r
804 pasteThis_actionPerformed(e);
\r
807 applyToAllGroups.setText("Apply Colour To All Groups");
\r
808 applyToAllGroups.setState(true);
\r
809 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
811 public void actionPerformed(ActionEvent e)
\r
813 applyToAllGroups_actionPerformed(e);
\r
816 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
818 public void actionPerformed(ActionEvent e)
\r
823 createPNG.setActionCommand("Save As PNG Image");
\r
824 createPNG.setText("PNG");
\r
825 font.setText("Font...");
\r
826 font.addActionListener(new java.awt.event.ActionListener()
\r
828 public void actionPerformed(ActionEvent e)
\r
830 font_actionPerformed(e);
\r
834 seqLimits.setText("Show Sequence Limits");
\r
835 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
836 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
838 public void actionPerformed(ActionEvent e)
\r
840 seqLimit_actionPerformed(e);
\r
843 epsFile.setText("EPS");
\r
844 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
846 public void actionPerformed(ActionEvent e)
\r
851 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
852 LoadtreeMenuItem.setText("Load Associated Tree");
\r
853 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
855 public void actionPerformed(ActionEvent e)
\r
857 LoadtreeMenuItem_actionPerformed(e);
\r
860 scaleAbove.setVisible(false);
\r
861 scaleAbove.setText("Scale Above");
\r
862 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
864 public void actionPerformed(ActionEvent e)
\r
866 scaleAbove_actionPerformed(e);
\r
869 scaleLeft.setVisible(false);
\r
870 scaleLeft.setSelected(true);
\r
871 scaleLeft.setText("Scale Left");
\r
872 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
874 public void actionPerformed(ActionEvent e)
\r
876 scaleLeft_actionPerformed(e);
\r
879 scaleRight.setVisible(false);
\r
880 scaleRight.setSelected(true);
\r
881 scaleRight.setText("Scale Right");
\r
882 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
884 public void actionPerformed(ActionEvent e)
\r
886 scaleRight_actionPerformed(e);
\r
889 modifyPID.setText("Modify Identity Threshold...");
\r
890 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
892 public void actionPerformed(ActionEvent e)
\r
894 modifyPID_actionPerformed(e);
\r
897 modifyConservation.setText("Modify Conservation Threshold...");
\r
898 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
900 public void actionPerformed(ActionEvent e)
\r
902 modifyConservation_actionPerformed(e);
\r
905 sortByTreeMenu.setText("By Tree Order");
\r
906 sort.setText("Sort");
\r
907 calculate.setText("Calculate Tree");
\r
909 jMenu2.setText("Export");
\r
910 padGapsMenuitem.setText("Pad Gaps");
\r
911 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
912 padGapsMenuitem.addActionListener(new ActionListener()
\r
914 public void actionPerformed(ActionEvent e)
\r
916 padGapsMenuitem_actionPerformed(e);
\r
919 vamsasStore.setVisible(false);
\r
920 vamsasStore.setText("VAMSAS store");
\r
921 vamsasStore.addActionListener(new ActionListener()
\r
923 public void actionPerformed(ActionEvent e)
\r
925 vamsasStore_actionPerformed(e);
\r
928 showTranslation.setText("Translate cDNA");
\r
929 showTranslation.addActionListener(new ActionListener()
\r
931 public void actionPerformed(ActionEvent e)
\r
933 showTranslation_actionPerformed(e);
\r
937 /* tabbedPane.addChangeListener(new ChangeListener()
\r
939 public void stateChanged(ChangeEvent ece)
\r
945 featureSettings.setText("Feature Settings...");
\r
946 featureSettings.addActionListener(new ActionListener()
\r
948 public void actionPerformed(ActionEvent e)
\r
950 featureSettings_actionPerformed(e);
\r
953 fetchSequence.setText("Fetch Sequence(s)...");
\r
954 fetchSequence.addActionListener(new ActionListener()
\r
956 public void actionPerformed(ActionEvent e)
\r
958 fetchSequence_actionPerformed(e);
\r
961 smoothFont.setText("Smooth Fonts");
\r
962 smoothFont.addActionListener(new ActionListener()
\r
964 public void actionPerformed(ActionEvent e)
\r
966 smoothFont_actionPerformed(e);
\r
969 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
970 annotationColour.setText("By Annotation...");
\r
971 annotationColour.addActionListener(new ActionListener()
\r
973 public void actionPerformed(ActionEvent e)
\r
975 annotationColour_actionPerformed(e);
\r
978 associatedData.setText("Load Features / Annotations");
\r
979 associatedData.addActionListener(new ActionListener()
\r
981 public void actionPerformed(ActionEvent e)
\r
983 associatedData_actionPerformed(e);
\r
986 autoCalculate.setText("Autocalculate Consensus");
\r
987 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
988 autoCalculate.addActionListener(new ActionListener()
\r
990 public void actionPerformed(ActionEvent e)
\r
992 autoCalculate_actionPerformed(e);
\r
995 addSequenceMenu.setText("Add Sequences");
\r
996 addFromFile.setText("From File");
\r
997 addFromFile.addActionListener(new ActionListener()
\r
999 public void actionPerformed(ActionEvent e)
\r
1001 addFromFile_actionPerformed(e);
\r
1004 addFromText.setText("From Textbox");
\r
1005 addFromText.addActionListener(new ActionListener()
\r
1007 public void actionPerformed(ActionEvent e)
\r
1009 addFromText_actionPerformed(e);
\r
1012 addFromURL.setText("From URL");
\r
1013 addFromURL.addActionListener(new ActionListener()
\r
1015 public void actionPerformed(ActionEvent e)
\r
1017 addFromURL_actionPerformed(e);
\r
1020 exportFeatures.setText("Export Features...");
\r
1021 exportFeatures.addActionListener(new ActionListener()
\r
1023 public void actionPerformed(ActionEvent e)
\r
1025 exportFeatures_actionPerformed(e);
\r
1028 exportAnnotations.setText("Export Annotations...");
\r
1029 exportAnnotations.addActionListener(new ActionListener()
\r
1031 public void actionPerformed(ActionEvent e)
\r
1033 exportAnnotations_actionPerformed(e);
\r
1036 statusPanel.setLayout(gridLayout1);
\r
1037 jMenu3.setText("Show");
\r
1038 showAllSeqs.setText("All Sequences");
\r
1039 showAllSeqs.addActionListener(new ActionListener()
\r
1041 public void actionPerformed(ActionEvent e)
\r
1043 showAllSeqs_actionPerformed(e);
\r
1046 showAllColumns.setText("All Columns");
\r
1047 showAllColumns.addActionListener(new ActionListener()
\r
1049 public void actionPerformed(ActionEvent e)
\r
1051 showAllColumns_actionPerformed(e);
\r
1054 jMenu4.setText("Hide");
\r
1055 hideSelSequences.setText("Selected Sequences");
\r
1056 hideSelSequences.addActionListener(new ActionListener()
\r
1058 public void actionPerformed(ActionEvent e)
\r
1060 hideSelSequences_actionPerformed(e);
\r
1063 hideSelColumns.setText("Selected Columns");
\r
1064 hideSelColumns.addActionListener(new ActionListener()
\r
1066 public void actionPerformed(ActionEvent e)
\r
1068 hideSelColumns_actionPerformed(e);
\r
1071 hiddenMarkers.setText("Hidden Markers");
\r
1072 hiddenMarkers.setState(true);
\r
1073 hiddenMarkers.addActionListener(new ActionListener()
\r
1075 public void actionPerformed(ActionEvent e)
\r
1077 hiddenMarkers_actionPerformed(e);
\r
1081 alignFrameMenuBar.add(fileMenu);
\r
1082 alignFrameMenuBar.add(editMenu);
\r
1083 alignFrameMenuBar.add(searchMenu);
\r
1084 alignFrameMenuBar.add(viewMenu);
\r
1085 alignFrameMenuBar.add(colourMenu);
\r
1086 alignFrameMenuBar.add(calculateMenu);
\r
1087 alignFrameMenuBar.add(webService);
\r
1088 fileMenu.add(addSequenceMenu);
\r
1089 fileMenu.add(fetchSequence);
\r
1090 fileMenu.addSeparator();
\r
1091 fileMenu.add(vamsasStore);
\r
1092 fileMenu.add(saveAlignmentMenu);
\r
1093 fileMenu.add(jMenu2);
\r
1094 fileMenu.add(outputTextboxMenu);
\r
1095 fileMenu.add(printMenuItem);
\r
1096 fileMenu.addSeparator();
\r
1097 fileMenu.add(exportFeatures);
\r
1098 fileMenu.add(exportAnnotations);
\r
1099 fileMenu.add(LoadtreeMenuItem);
\r
1100 fileMenu.add(associatedData);
\r
1101 fileMenu.addSeparator();
\r
1102 fileMenu.add(closeMenuItem);
\r
1103 editMenu.add(undoMenuItem);
\r
1104 editMenu.add(redoMenuItem);
\r
1105 editMenu.add(cut);
\r
1106 editMenu.add(copy);
\r
1107 editMenu.add(jMenu1);
\r
1108 editMenu.add(delete);
\r
1109 editMenu.addSeparator();
\r
1110 editMenu.add(selectAllSequenceMenuItem);
\r
1111 editMenu.add(deselectAllSequenceMenuItem);
\r
1112 editMenu.add(invertSequenceMenuItem);
\r
1113 editMenu.add(deleteGroups);
\r
1114 editMenu.addSeparator();
\r
1115 editMenu.add(remove2LeftMenuItem);
\r
1116 editMenu.add(remove2RightMenuItem);
\r
1117 editMenu.add(removeGappedColumnMenuItem);
\r
1118 editMenu.add(removeAllGapsMenuItem);
\r
1119 editMenu.add(removeRedundancyMenuItem);
\r
1120 editMenu.addSeparator();
\r
1121 editMenu.add(padGapsMenuitem);
\r
1122 searchMenu.add(findMenuItem);
\r
1123 viewMenu.add(font);
\r
1124 viewMenu.add(smoothFont);
\r
1125 viewMenu.addSeparator();
\r
1126 viewMenu.add(jMenu3);
\r
1127 viewMenu.add(jMenu4);
\r
1128 viewMenu.add(hiddenMarkers);
\r
1129 viewMenu.addSeparator();
\r
1130 viewMenu.add(wrapMenuItem);
\r
1131 viewMenu.add(seqLimits);
\r
1132 viewMenu.add(scaleAbove);
\r
1133 viewMenu.add(scaleLeft);
\r
1134 viewMenu.add(scaleRight);
\r
1135 viewMenu.add(viewBoxesMenuItem);
\r
1136 viewMenu.add(viewTextMenuItem);
\r
1137 viewMenu.add(colourTextMenuItem);
\r
1138 viewMenu.add(renderGapsMenuItem);
\r
1139 viewMenu.add(annotationPanelMenuItem);
\r
1140 viewMenu.addSeparator();
\r
1141 viewMenu.add(showSeqFeatures);
\r
1142 viewMenu.add(featureSettings);
\r
1143 viewMenu.addSeparator();
\r
1144 viewMenu.add(overviewMenuItem);
\r
1145 colourMenu.add(applyToAllGroups);
\r
1146 colourMenu.addSeparator();
\r
1147 colourMenu.add(noColourmenuItem);
\r
1148 colourMenu.add(clustalColour);
\r
1149 colourMenu.add(BLOSUM62Colour);
\r
1150 colourMenu.add(PIDColour);
\r
1151 colourMenu.add(zappoColour);
\r
1152 colourMenu.add(taylorColour);
\r
1153 colourMenu.add(hydrophobicityColour);
\r
1154 colourMenu.add(helixColour);
\r
1155 colourMenu.add(strandColour);
\r
1156 colourMenu.add(turnColour);
\r
1157 colourMenu.add(buriedColour);
\r
1158 colourMenu.add(nucleotideColour);
\r
1159 colourMenu.add(userDefinedColour);
\r
1160 colourMenu.addSeparator();
\r
1161 colourMenu.add(conservationMenuItem);
\r
1162 colourMenu.add(modifyConservation);
\r
1163 colourMenu.add(abovePIDThreshold);
\r
1164 colourMenu.add(modifyPID);
\r
1165 colourMenu.add(annotationColour);
\r
1166 calculateMenu.add(sort);
\r
1167 calculateMenu.add(calculate);
\r
1168 calculateMenu.addSeparator();
\r
1169 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1170 calculateMenu.add(PCAMenuItem);
\r
1171 calculateMenu.addSeparator();
\r
1172 calculateMenu.add(showTranslation);
\r
1173 calculateMenu.add(autoCalculate);
\r
1174 webServiceNoServices=new JMenuItem("<No Services>");
\r
1175 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1176 jMenu1.add(pasteThis);
\r
1177 sort.add(sortIDMenuItem);
\r
1178 sort.add(sortGroupMenuItem);
\r
1179 sort.add(sortPairwiseMenuItem);
\r
1180 calculate.add(averageDistanceTreeMenuItem);
\r
1181 calculate.add(neighbourTreeMenuItem);
\r
1182 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1183 calculate.add(njTreeBlosumMenuItem);
\r
1184 jMenu2.add(htmlMenuItem);
\r
1185 jMenu2.add(epsFile);
\r
1186 jMenu2.add(createPNG);
\r
1187 addSequenceMenu.add(addFromFile);
\r
1188 addSequenceMenu.add(addFromText);
\r
1189 addSequenceMenu.add(addFromURL);
\r
1190 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1191 statusPanel.add(statusBar, null);
\r
1192 jMenu3.add(showAllColumns);
\r
1193 jMenu3.add(showAllSeqs);
\r
1194 jMenu4.add(hideSelColumns);
\r
1195 jMenu4.add(hideSelSequences);
\r
1198 protected void outputText_actionPerformed(ActionEvent e)
\r
1202 public void addFromFile_actionPerformed(ActionEvent e)
\r
1207 public void addFromText_actionPerformed(ActionEvent e)
\r
1212 public void addFromURL_actionPerformed(ActionEvent e)
\r
1217 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1222 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1227 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1231 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1235 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1239 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1243 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1247 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1251 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1255 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1259 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1263 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1267 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1271 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1275 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1279 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1283 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1287 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1291 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1295 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1299 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1303 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1307 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1311 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1315 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1319 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1323 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1327 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1331 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1335 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1339 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1343 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1347 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1351 protected void helixColour_actionPerformed(ActionEvent e)
\r
1355 protected void strandColour_actionPerformed(ActionEvent e)
\r
1359 protected void turnColour_actionPerformed(ActionEvent e)
\r
1363 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1367 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1371 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1375 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1379 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1383 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1387 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1391 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1395 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1399 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1403 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1407 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1411 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1415 protected void copy_actionPerformed(ActionEvent e)
\r
1419 protected void cut_actionPerformed(ActionEvent e)
\r
1423 protected void delete_actionPerformed(ActionEvent e)
\r
1427 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1431 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1435 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1439 public void createPNG(java.io.File f)
\r
1443 protected void font_actionPerformed(ActionEvent e)
\r
1447 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1451 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1457 public void createEPS(java.io.File f)
\r
1461 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1465 protected void jpred_actionPerformed(ActionEvent e)
\r
1469 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1473 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1477 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1481 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1485 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1491 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1495 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1500 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1505 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1510 public void showTranslation_actionPerformed(ActionEvent e)
\r
1515 public void featureSettings_actionPerformed(ActionEvent e)
\r
1520 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1525 public void smoothFont_actionPerformed(ActionEvent e)
\r
1530 public void annotationColour_actionPerformed(ActionEvent e)
\r
1536 public void associatedData_actionPerformed(ActionEvent e)
\r
1541 public void autoCalculate_actionPerformed(ActionEvent e)
\r
1546 public void showAllSeqs_actionPerformed(ActionEvent e)
\r
1551 public void showAllColumns_actionPerformed(ActionEvent e)
\r
1556 public void hideSelSequences_actionPerformed(ActionEvent e)
\r
1561 public void hideSelColumns_actionPerformed(ActionEvent e)
\r
1566 public void hiddenMarkers_actionPerformed(ActionEvent e)
\r
1571 public void findPdbId_actionPerformed(ActionEvent e)
\r
1576 public void enterPdbId_actionPerformed(ActionEvent e)
\r
1581 public void pdbFile_actionPerformed(ActionEvent e)
\r