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 public GAlignFrame()
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139 setJMenuBar(alignFrameMenuBar);
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141 // dynamically fill save as menu with available formats
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142 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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144 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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147 item.addActionListener(new java.awt.event.ActionListener()
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149 public void actionPerformed(ActionEvent e)
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151 outputText_actionPerformed(e);
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155 outputTextboxMenu.add(item);
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158 catch (Exception e)
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163 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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165 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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166 getUserColourSchemes().keys();
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168 while (userColours.hasMoreElements())
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170 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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171 nextElement().toString());
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172 radioItem.setName("USER_DEFINED");
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173 radioItem.addMouseListener(new MouseAdapter()
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175 public void mousePressed(MouseEvent evt)
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177 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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179 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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181 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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182 "Remove from default list?",
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183 "Remove user defined colour",
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184 JOptionPane.YES_NO_OPTION);
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185 if(option == JOptionPane.YES_OPTION)
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187 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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188 colourMenu.remove(radioItem);
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191 radioItem.addActionListener(new ActionListener()
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193 public void actionPerformed(ActionEvent evt)
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195 userDefinedColour_actionPerformed(evt);
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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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208 colourMenu.insert(radioItem, 15);
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209 colours.add(radioItem);
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212 colours.add(noColourmenuItem);
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213 colours.add(clustalColour);
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214 colours.add(zappoColour);
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215 colours.add(taylorColour);
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216 colours.add(hydrophobicityColour);
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217 colours.add(helixColour);
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218 colours.add(strandColour);
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219 colours.add(turnColour);
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220 colours.add(buriedColour);
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221 colours.add(userDefinedColour);
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222 colours.add(PIDColour);
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223 colours.add(BLOSUM62Colour);
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224 colours.add(nucleotideColour);
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226 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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231 public void setColourSelected(String defaultColour)
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234 if (defaultColour != null)
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236 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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240 case ColourSchemeProperty.NONE:
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241 noColourmenuItem.setSelected(true);
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243 case ColourSchemeProperty.CLUSTAL:
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244 clustalColour.setSelected(true);
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248 case ColourSchemeProperty.BLOSUM:
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249 BLOSUM62Colour.setSelected(true);
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253 case ColourSchemeProperty.PID:
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254 PIDColour.setSelected(true);
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258 case ColourSchemeProperty.ZAPPO:
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259 zappoColour.setSelected(true);
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263 case ColourSchemeProperty.TAYLOR:
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264 taylorColour.setSelected(true);
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267 case ColourSchemeProperty.HYDROPHOBIC:
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268 hydrophobicityColour.setSelected(true);
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272 case ColourSchemeProperty.HELIX:
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273 helixColour.setSelected(true);
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277 case ColourSchemeProperty.STRAND:
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278 strandColour.setSelected(true);
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282 case ColourSchemeProperty.TURN:
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283 turnColour.setSelected(true);
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287 case ColourSchemeProperty.BURIED:
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288 buriedColour.setSelected(true);
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292 case ColourSchemeProperty.NUCLEOTIDE:
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293 nucleotideColour.setSelected(true);
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297 case ColourSchemeProperty.USER_DEFINED:
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298 userDefinedColour.setSelected(true);
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306 private void jbInit()
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309 fileMenu.setMnemonic('F');
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310 fileMenu.setText("File");
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311 saveAlignmentMenu.setMnemonic('L');
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312 saveAlignmentMenu.setText("Save As");
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313 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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314 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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315 saveAlignmentMenu.addActionListener(new ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 saveAlignmentMenu_actionPerformed(e);
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322 closeMenuItem.setMnemonic('C');
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323 closeMenuItem.setText("Close");
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324 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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326 public void actionPerformed(ActionEvent e)
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328 closeMenuItem_actionPerformed(e);
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331 editMenu.setText("Edit");
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332 viewMenu.setText("View");
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333 colourMenu.setText("Colour");
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334 calculateMenu.setText("Calculate");
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335 webService.setText("Web Service");
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336 selectAllSequenceMenuItem.setText("Select all");
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337 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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338 java.awt.event.KeyEvent.VK_A,
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339 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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340 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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343 public void actionPerformed(ActionEvent e)
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345 selectAllSequenceMenuItem_actionPerformed(e);
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348 deselectAllSequenceMenuItem.setText("Deselect All");
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349 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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351 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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352 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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355 public void actionPerformed(ActionEvent e)
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357 deselectAllSequenceMenuItem_actionPerformed(e);
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360 invertSequenceMenuItem.setText("Invert Selection");
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361 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 invertSequenceMenuItem_actionPerformed(e);
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368 remove2LeftMenuItem.setText("Remove Left");
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369 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 remove2LeftMenuItem_actionPerformed(e);
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376 remove2RightMenuItem.setText("Remove Right");
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377 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 remove2RightMenuItem_actionPerformed(e);
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384 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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385 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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388 public void actionPerformed(ActionEvent e)
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390 removeGappedColumnMenuItem_actionPerformed(e);
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393 removeAllGapsMenuItem.setText("Remove All Gaps");
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394 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 removeAllGapsMenuItem_actionPerformed(e);
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401 viewBoxesMenuItem.setText("Boxes");
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402 viewBoxesMenuItem.setState(true);
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403 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 viewBoxesMenuItem_actionPerformed(e);
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410 viewTextMenuItem.setText("Text");
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411 viewTextMenuItem.setState(true);
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412 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 viewTextMenuItem_actionPerformed(e);
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419 sortPairwiseMenuItem.setText("by Pairwise Identity");
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420 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 sortPairwiseMenuItem_actionPerformed(e);
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427 sortIDMenuItem.setText("by ID");
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428 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 sortIDMenuItem_actionPerformed(e);
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435 sortGroupMenuItem.setText("by Group");
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436 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 sortGroupMenuItem_actionPerformed(e);
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443 removeRedundancyMenuItem.setText("Remove Redundancy...");
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444 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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447 public void actionPerformed(ActionEvent e)
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449 removeRedundancyMenuItem_actionPerformed(e);
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452 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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453 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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456 public void actionPerformed(ActionEvent e)
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458 pairwiseAlignmentMenuItem_actionPerformed(e);
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461 PCAMenuItem.setText("Principal Component Analysis");
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462 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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464 public void actionPerformed(ActionEvent e)
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466 PCAMenuItem_actionPerformed(e);
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469 averageDistanceTreeMenuItem.setText(
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470 "Average Distance Using % Identity");
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471 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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474 public void actionPerformed(ActionEvent e)
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476 averageDistanceTreeMenuItem_actionPerformed(e);
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479 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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480 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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482 public void actionPerformed(ActionEvent e)
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484 neighbourTreeMenuItem_actionPerformed(e);
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487 this.getContentPane().setLayout(borderLayout1);
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488 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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489 statusBar.setBackground(Color.white);
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490 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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491 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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492 statusBar.setText("Status bar");
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493 outputTextboxMenu.setMnemonic('T');
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494 outputTextboxMenu.setText("Output to Textbox");
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495 clustalColour.setText("Clustalx");
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497 clustalColour.addActionListener(new java.awt.event.ActionListener()
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499 public void actionPerformed(ActionEvent e)
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501 clustalColour_actionPerformed(e);
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504 zappoColour.setText("Zappo");
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505 zappoColour.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 zappoColour_actionPerformed(e);
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512 taylorColour.setText("Taylor");
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513 taylorColour.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 taylorColour_actionPerformed(e);
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520 hydrophobicityColour.setText("Hydrophobicity");
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521 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 hydrophobicityColour_actionPerformed(e);
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528 helixColour.setText("Helix Propensity");
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529 helixColour.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 helixColour_actionPerformed(e);
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536 strandColour.setText("Strand Propensity");
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537 strandColour.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 strandColour_actionPerformed(e);
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544 turnColour.setText("Turn Propensity");
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545 turnColour.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 turnColour_actionPerformed(e);
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552 buriedColour.setText("Buried Index");
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553 buriedColour.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 buriedColour_actionPerformed(e);
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560 userDefinedColour.setText("User Defined...");
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561 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 userDefinedColour_actionPerformed(e);
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568 PIDColour.setText("Percentage Identity");
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569 PIDColour.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 PIDColour_actionPerformed(e);
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576 BLOSUM62Colour.setText("BLOSUM62 Score");
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577 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 BLOSUM62Colour_actionPerformed(e);
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584 avDistanceTreeBlosumMenuItem.setText(
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585 "Average Distance Using BLOSUM62");
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586 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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589 public void actionPerformed(ActionEvent e)
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591 avTreeBlosumMenuItem_actionPerformed(e);
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594 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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595 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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597 public void actionPerformed(ActionEvent e)
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599 njTreeBlosumMenuItem_actionPerformed(e);
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602 annotationPanelMenuItem.setActionCommand("");
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603 annotationPanelMenuItem.setText("Show Annotations");
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604 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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605 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 annotationPanelMenuItem_actionPerformed(e);
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612 colourTextMenuItem.setText("Colour Text");
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613 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 colourTextMenuItem_actionPerformed(e);
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620 htmlMenuItem.setText("HTML");
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621 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 htmlMenuItem_actionPerformed(e);
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628 overviewMenuItem.setText("Overview Window");
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629 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 overviewMenuItem_actionPerformed(e);
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636 undoMenuItem.setEnabled(false);
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637 undoMenuItem.setMnemonic('Z');
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638 undoMenuItem.setText("Undo");
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639 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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640 java.awt.event.KeyEvent.VK_Z,
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641 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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642 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 undoMenuItem_actionPerformed(e);
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649 redoMenuItem.setEnabled(false);
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650 redoMenuItem.setMnemonic('0');
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651 redoMenuItem.setText("Redo");
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652 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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654 public void actionPerformed(ActionEvent e)
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656 redoMenuItem_actionPerformed(e);
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659 conservationMenuItem.setText("By Conservation");
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660 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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662 public void actionPerformed(ActionEvent e)
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664 conservationMenuItem_actionPerformed(e);
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667 noColourmenuItem.setText("None");
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668 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 noColourmenuItem_actionPerformed(e);
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675 wrapMenuItem.setText("Wrap");
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676 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 wrapMenuItem_actionPerformed(e);
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683 printMenuItem.setText("Print");
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684 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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686 public void actionPerformed(ActionEvent e)
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688 printMenuItem_actionPerformed(e);
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691 renderGapsMenuItem.setText("Show Gaps");
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692 renderGapsMenuItem.setState(true);
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693 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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695 public void actionPerformed(ActionEvent e)
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697 renderGapsMenuItem_actionPerformed(e);
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700 findMenuItem.setText("Find...");
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701 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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702 java.awt.event.KeyEvent.VK_F,
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703 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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704 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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706 public void actionPerformed(ActionEvent e)
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708 findMenuItem_actionPerformed(e);
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711 searchMenu.setText("Search");
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713 abovePIDThreshold.setText("Above Identity Threshold");
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714 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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716 public void actionPerformed(ActionEvent e)
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718 abovePIDThreshold_actionPerformed(e);
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721 showSeqFeatures.setText("Show Sequence Features");
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722 showSeqFeatures.addActionListener(new ActionListener()
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724 public void actionPerformed(ActionEvent actionEvent)
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726 showSeqFeatures_actionPerformed(actionEvent);
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729 nucleotideColour.setText("Nucleotide");
\r
730 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
732 public void actionPerformed(ActionEvent e)
\r
734 nucleotideColour_actionPerformed(e);
\r
737 deleteGroups.setText("Undefine groups");
\r
738 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
740 public void actionPerformed(ActionEvent e)
\r
742 deleteGroups_actionPerformed(e);
\r
745 copy.setText("Copy");
\r
746 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
747 java.awt.event.KeyEvent.VK_C,
\r
748 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
749 copy.setMnemonic(KeyEvent.VK_C);
\r
751 copy.addActionListener(new java.awt.event.ActionListener()
\r
753 public void actionPerformed(ActionEvent e)
\r
755 copy_actionPerformed(e);
\r
758 cut.setText("Cut");
\r
759 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
760 java.awt.event.KeyEvent.VK_X,
\r
761 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
762 cut.setMnemonic(KeyEvent.VK_X);
\r
763 cut.addActionListener(new java.awt.event.ActionListener()
\r
765 public void actionPerformed(ActionEvent e)
\r
767 cut_actionPerformed(e);
\r
770 delete.setText("Delete");
\r
771 delete.addActionListener(new java.awt.event.ActionListener()
\r
773 public void actionPerformed(ActionEvent e)
\r
775 delete_actionPerformed(e);
\r
778 jMenu1.setMnemonic('V');
\r
779 jMenu1.setText("Paste");
\r
780 pasteNew.setText("To New Alignment");
\r
781 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
782 java.awt.event.KeyEvent.VK_V,
\r
783 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
784 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
786 public void actionPerformed(ActionEvent e)
\r
788 pasteNew_actionPerformed(e);
\r
791 pasteThis.setText("Add To This Alignment");
\r
792 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
794 public void actionPerformed(ActionEvent e)
\r
796 pasteThis_actionPerformed(e);
\r
799 applyToAllGroups.setText("Apply Colour To All Groups");
\r
800 applyToAllGroups.setState(true);
\r
801 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
803 public void actionPerformed(ActionEvent e)
\r
805 applyToAllGroups_actionPerformed(e);
\r
808 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
810 public void actionPerformed(ActionEvent e)
\r
815 createPNG.setActionCommand("Save As PNG Image");
\r
816 createPNG.setText("PNG");
\r
817 font.setText("Font...");
\r
818 font.addActionListener(new java.awt.event.ActionListener()
\r
820 public void actionPerformed(ActionEvent e)
\r
822 font_actionPerformed(e);
\r
826 seqLimits.setText("Show Sequence Limits");
\r
827 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
828 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
830 public void actionPerformed(ActionEvent e)
\r
832 seqLimit_actionPerformed(e);
\r
835 epsFile.setText("EPS");
\r
836 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
838 public void actionPerformed(ActionEvent e)
\r
843 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
844 LoadtreeMenuItem.setText("Load Associated Tree");
\r
845 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
847 public void actionPerformed(ActionEvent e)
\r
849 LoadtreeMenuItem_actionPerformed(e);
\r
852 scaleAbove.setVisible(false);
\r
853 scaleAbove.setText("Scale Above");
\r
854 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
856 public void actionPerformed(ActionEvent e)
\r
858 scaleAbove_actionPerformed(e);
\r
861 scaleLeft.setVisible(false);
\r
862 scaleLeft.setSelected(true);
\r
863 scaleLeft.setText("Scale Left");
\r
864 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
866 public void actionPerformed(ActionEvent e)
\r
868 scaleLeft_actionPerformed(e);
\r
871 scaleRight.setVisible(false);
\r
872 scaleRight.setSelected(true);
\r
873 scaleRight.setText("Scale Right");
\r
874 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
876 public void actionPerformed(ActionEvent e)
\r
878 scaleRight_actionPerformed(e);
\r
881 modifyPID.setText("Modify Identity Threshold...");
\r
882 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
884 public void actionPerformed(ActionEvent e)
\r
886 modifyPID_actionPerformed(e);
\r
889 modifyConservation.setText("Modify Conservation Threshold...");
\r
890 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
892 public void actionPerformed(ActionEvent e)
\r
894 modifyConservation_actionPerformed(e);
\r
897 sortByTreeMenu.setText("By Tree Order");
\r
898 sort.setText("Sort");
\r
899 calculate.setText("Calculate Tree");
\r
901 jMenu2.setText("Export");
\r
902 padGapsMenuitem.setText("Pad Gaps");
\r
903 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
904 padGapsMenuitem.addActionListener(new ActionListener()
\r
906 public void actionPerformed(ActionEvent e)
\r
908 padGapsMenuitem_actionPerformed(e);
\r
911 vamsasStore.setVisible(false);
\r
912 vamsasStore.setText("VAMSAS store");
\r
913 vamsasStore.addActionListener(new ActionListener()
\r
915 public void actionPerformed(ActionEvent e)
\r
917 vamsasStore_actionPerformed(e);
\r
920 showTranslation.setText("Translate cDNA");
\r
921 showTranslation.addActionListener(new ActionListener()
\r
923 public void actionPerformed(ActionEvent e)
\r
925 showTranslation_actionPerformed(e);
\r
929 /* tabbedPane.addChangeListener(new ChangeListener()
\r
931 public void stateChanged(ChangeEvent ece)
\r
937 featureSettings.setText("Feature Settings...");
\r
938 featureSettings.addActionListener(new ActionListener()
\r
940 public void actionPerformed(ActionEvent e)
\r
942 featureSettings_actionPerformed(e);
\r
945 fetchSequence.setText("Fetch Sequence(s)...");
\r
946 fetchSequence.addActionListener(new ActionListener()
\r
948 public void actionPerformed(ActionEvent e)
\r
950 fetchSequence_actionPerformed(e);
\r
953 smoothFont.setText("Smooth Fonts");
\r
954 smoothFont.addActionListener(new ActionListener()
\r
956 public void actionPerformed(ActionEvent e)
\r
958 smoothFont_actionPerformed(e);
\r
961 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
962 annotationColour.setText("By Annotation...");
\r
963 annotationColour.addActionListener(new ActionListener()
\r
965 public void actionPerformed(ActionEvent e)
\r
967 annotationColour_actionPerformed(e);
\r
970 associatedData.setText("Load Features / Annotations");
\r
971 associatedData.addActionListener(new ActionListener()
\r
973 public void actionPerformed(ActionEvent e)
\r
975 associatedData_actionPerformed(e);
\r
978 autoCalculate.setText("Autocalculate Consensus");
\r
979 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
980 autoCalculate.addActionListener(new ActionListener()
\r
982 public void actionPerformed(ActionEvent e)
\r
984 autoCalculate_actionPerformed(e);
\r
987 addSequenceMenu.setText("Add Sequences");
\r
988 addFromFile.setText("From File");
\r
989 addFromFile.addActionListener(new ActionListener()
\r
991 public void actionPerformed(ActionEvent e)
\r
993 addFromFile_actionPerformed(e);
\r
996 addFromText.setText("From Textbox");
\r
997 addFromText.addActionListener(new ActionListener()
\r
999 public void actionPerformed(ActionEvent e)
\r
1001 addFromText_actionPerformed(e);
\r
1004 addFromURL.setText("From URL");
\r
1005 addFromURL.addActionListener(new ActionListener()
\r
1007 public void actionPerformed(ActionEvent e)
\r
1009 addFromURL_actionPerformed(e);
\r
1012 exportFeatures.setText("Export Features...");
\r
1013 exportFeatures.addActionListener(new ActionListener()
\r
1015 public void actionPerformed(ActionEvent e)
\r
1017 exportFeatures_actionPerformed(e);
\r
1020 exportAnnotations.setText("Export Annotations...");
\r
1021 exportAnnotations.addActionListener(new ActionListener()
\r
1023 public void actionPerformed(ActionEvent e)
\r
1025 exportAnnotations_actionPerformed(e);
\r
1028 statusPanel.setLayout(gridLayout1);
\r
1029 alignFrameMenuBar.add(fileMenu);
\r
1030 alignFrameMenuBar.add(editMenu);
\r
1031 alignFrameMenuBar.add(searchMenu);
\r
1032 alignFrameMenuBar.add(viewMenu);
\r
1033 alignFrameMenuBar.add(colourMenu);
\r
1034 alignFrameMenuBar.add(calculateMenu);
\r
1035 alignFrameMenuBar.add(webService);
\r
1036 fileMenu.add(addSequenceMenu);
\r
1037 fileMenu.add(fetchSequence);
\r
1038 fileMenu.addSeparator();
\r
1039 fileMenu.add(vamsasStore);
\r
1040 fileMenu.add(saveAlignmentMenu);
\r
1041 fileMenu.add(jMenu2);
\r
1042 fileMenu.add(outputTextboxMenu);
\r
1043 fileMenu.add(printMenuItem);
\r
1044 fileMenu.addSeparator();
\r
1045 fileMenu.add(exportFeatures);
\r
1046 fileMenu.add(exportAnnotations);
\r
1047 fileMenu.add(LoadtreeMenuItem);
\r
1048 fileMenu.add(associatedData);
\r
1049 fileMenu.addSeparator();
\r
1050 fileMenu.add(closeMenuItem);
\r
1051 editMenu.add(undoMenuItem);
\r
1052 editMenu.add(redoMenuItem);
\r
1053 editMenu.add(cut);
\r
1054 editMenu.add(copy);
\r
1055 editMenu.add(jMenu1);
\r
1056 editMenu.add(delete);
\r
1057 editMenu.addSeparator();
\r
1058 editMenu.add(selectAllSequenceMenuItem);
\r
1059 editMenu.add(deselectAllSequenceMenuItem);
\r
1060 editMenu.add(invertSequenceMenuItem);
\r
1061 editMenu.add(deleteGroups);
\r
1062 editMenu.addSeparator();
\r
1063 editMenu.add(remove2LeftMenuItem);
\r
1064 editMenu.add(remove2RightMenuItem);
\r
1065 editMenu.add(removeGappedColumnMenuItem);
\r
1066 editMenu.add(removeAllGapsMenuItem);
\r
1067 editMenu.add(removeRedundancyMenuItem);
\r
1068 editMenu.addSeparator();
\r
1069 editMenu.add(padGapsMenuitem);
\r
1070 searchMenu.add(findMenuItem);
\r
1071 viewMenu.add(font);
\r
1072 viewMenu.add(smoothFont);
\r
1073 viewMenu.addSeparator();
\r
1074 viewMenu.add(wrapMenuItem);
\r
1075 viewMenu.add(seqLimits);
\r
1076 viewMenu.add(scaleAbove);
\r
1077 viewMenu.add(scaleLeft);
\r
1078 viewMenu.add(scaleRight);
\r
1079 viewMenu.add(viewBoxesMenuItem);
\r
1080 viewMenu.add(viewTextMenuItem);
\r
1081 viewMenu.add(colourTextMenuItem);
\r
1082 viewMenu.add(renderGapsMenuItem);
\r
1083 viewMenu.add(annotationPanelMenuItem);
\r
1084 viewMenu.addSeparator();
\r
1085 viewMenu.add(showSeqFeatures);
\r
1086 viewMenu.add(featureSettings);
\r
1087 viewMenu.addSeparator();
\r
1088 viewMenu.add(overviewMenuItem);
\r
1089 colourMenu.add(applyToAllGroups);
\r
1090 colourMenu.addSeparator();
\r
1091 colourMenu.add(noColourmenuItem);
\r
1092 colourMenu.add(clustalColour);
\r
1093 colourMenu.add(BLOSUM62Colour);
\r
1094 colourMenu.add(PIDColour);
\r
1095 colourMenu.add(zappoColour);
\r
1096 colourMenu.add(taylorColour);
\r
1097 colourMenu.add(hydrophobicityColour);
\r
1098 colourMenu.add(helixColour);
\r
1099 colourMenu.add(strandColour);
\r
1100 colourMenu.add(turnColour);
\r
1101 colourMenu.add(buriedColour);
\r
1102 colourMenu.add(nucleotideColour);
\r
1103 colourMenu.add(userDefinedColour);
\r
1104 colourMenu.addSeparator();
\r
1105 colourMenu.add(conservationMenuItem);
\r
1106 colourMenu.add(modifyConservation);
\r
1107 colourMenu.add(abovePIDThreshold);
\r
1108 colourMenu.add(modifyPID);
\r
1109 colourMenu.add(annotationColour);
\r
1110 calculateMenu.add(sort);
\r
1111 calculateMenu.add(calculate);
\r
1112 calculateMenu.addSeparator();
\r
1113 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1114 calculateMenu.add(PCAMenuItem);
\r
1115 calculateMenu.addSeparator();
\r
1116 calculateMenu.add(showTranslation);
\r
1117 calculateMenu.add(autoCalculate);
\r
1118 webServiceNoServices=new JMenuItem("<No Services>");
\r
1119 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1120 jMenu1.add(pasteThis);
\r
1121 sort.add(sortIDMenuItem);
\r
1122 sort.add(sortGroupMenuItem);
\r
1123 sort.add(sortPairwiseMenuItem);
\r
1124 calculate.add(averageDistanceTreeMenuItem);
\r
1125 calculate.add(neighbourTreeMenuItem);
\r
1126 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1127 calculate.add(njTreeBlosumMenuItem);
\r
1128 jMenu2.add(htmlMenuItem);
\r
1129 jMenu2.add(epsFile);
\r
1130 jMenu2.add(createPNG);
\r
1131 addSequenceMenu.add(addFromFile);
\r
1132 addSequenceMenu.add(addFromText);
\r
1133 addSequenceMenu.add(addFromURL);
\r
1134 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1135 statusPanel.add(statusBar, null);
\r
1138 protected void outputText_actionPerformed(ActionEvent e)
\r
1142 public void addFromFile_actionPerformed(ActionEvent e)
\r
1147 public void addFromText_actionPerformed(ActionEvent e)
\r
1152 public void addFromURL_actionPerformed(ActionEvent e)
\r
1157 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1162 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1167 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1171 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1175 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1179 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1183 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1187 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1191 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1195 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1199 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1203 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1207 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1211 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1215 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1219 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1223 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1227 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1231 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1235 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1239 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1243 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1247 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1251 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1255 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1259 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1263 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1267 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1271 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1275 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1279 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1283 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1287 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1291 protected void helixColour_actionPerformed(ActionEvent e)
\r
1295 protected void strandColour_actionPerformed(ActionEvent e)
\r
1299 protected void turnColour_actionPerformed(ActionEvent e)
\r
1303 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1307 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1311 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1315 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1319 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1323 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1327 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1331 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1335 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1339 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1343 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1347 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1351 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1355 protected void copy_actionPerformed(ActionEvent e)
\r
1359 protected void cut_actionPerformed(ActionEvent e)
\r
1363 protected void delete_actionPerformed(ActionEvent e)
\r
1367 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1371 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1375 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1379 public void createPNG(java.io.File f)
\r
1383 protected void font_actionPerformed(ActionEvent e)
\r
1387 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1391 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1397 public void createEPS(java.io.File f)
\r
1401 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1405 protected void jpred_actionPerformed(ActionEvent e)
\r
1409 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1413 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1417 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1421 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1425 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1431 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1435 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1440 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1445 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1450 public void showTranslation_actionPerformed(ActionEvent e)
\r
1455 public void featureSettings_actionPerformed(ActionEvent e)
\r
1460 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1465 public void smoothFont_actionPerformed(ActionEvent e)
\r
1470 public void annotationColour_actionPerformed(ActionEvent e)
\r
1476 public void associatedData_actionPerformed(ActionEvent e)
\r
1481 public void autoCalculate_actionPerformed(ActionEvent e)
\r