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 JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
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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 JMenuItem dbRefs = new JMenuItem();
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131 protected JPanel statusPanel = new JPanel();
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132 GridLayout gridLayout1 = new GridLayout();
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133 JMenu jMenu3 = new JMenu();
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134 JMenuItem defaultDASSource = new JMenuItem();
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135 JMenuItem modifyDASSource = new JMenuItem();
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136 public GAlignFrame()
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143 setJMenuBar(alignFrameMenuBar);
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145 // dynamically fill save as menu with available formats
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146 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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148 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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151 item.addActionListener(new java.awt.event.ActionListener()
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153 public void actionPerformed(ActionEvent e)
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155 outputText_actionPerformed(e);
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159 outputTextboxMenu.add(item);
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162 catch (Exception e)
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167 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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169 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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170 getUserColourSchemes().keys();
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172 while (userColours.hasMoreElements())
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174 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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175 nextElement().toString());
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176 radioItem.setName("USER_DEFINED");
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177 radioItem.addMouseListener(new MouseAdapter()
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179 public void mousePressed(MouseEvent evt)
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181 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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183 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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185 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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186 "Remove from default list?",
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187 "Remove user defined colour",
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188 JOptionPane.YES_NO_OPTION);
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189 if(option == JOptionPane.YES_OPTION)
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191 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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192 colourMenu.remove(radioItem);
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195 radioItem.addActionListener(new ActionListener()
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197 public void actionPerformed(ActionEvent evt)
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199 userDefinedColour_actionPerformed(evt);
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205 radioItem.addActionListener(new ActionListener()
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207 public void actionPerformed(ActionEvent evt)
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209 userDefinedColour_actionPerformed(evt);
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212 colourMenu.insert(radioItem, 15);
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213 colours.add(radioItem);
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216 colours.add(noColourmenuItem);
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217 colours.add(clustalColour);
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218 colours.add(zappoColour);
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219 colours.add(taylorColour);
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220 colours.add(hydrophobicityColour);
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221 colours.add(helixColour);
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222 colours.add(strandColour);
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223 colours.add(turnColour);
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224 colours.add(buriedColour);
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225 colours.add(userDefinedColour);
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226 colours.add(PIDColour);
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227 colours.add(BLOSUM62Colour);
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228 colours.add(nucleotideColour);
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230 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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235 public void setColourSelected(String defaultColour)
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238 if (defaultColour != null)
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240 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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244 case ColourSchemeProperty.NONE:
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245 noColourmenuItem.setSelected(true);
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247 case ColourSchemeProperty.CLUSTAL:
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248 clustalColour.setSelected(true);
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252 case ColourSchemeProperty.BLOSUM:
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253 BLOSUM62Colour.setSelected(true);
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257 case ColourSchemeProperty.PID:
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258 PIDColour.setSelected(true);
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262 case ColourSchemeProperty.ZAPPO:
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263 zappoColour.setSelected(true);
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267 case ColourSchemeProperty.TAYLOR:
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268 taylorColour.setSelected(true);
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271 case ColourSchemeProperty.HYDROPHOBIC:
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272 hydrophobicityColour.setSelected(true);
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276 case ColourSchemeProperty.HELIX:
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277 helixColour.setSelected(true);
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281 case ColourSchemeProperty.STRAND:
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282 strandColour.setSelected(true);
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286 case ColourSchemeProperty.TURN:
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287 turnColour.setSelected(true);
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291 case ColourSchemeProperty.BURIED:
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292 buriedColour.setSelected(true);
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296 case ColourSchemeProperty.NUCLEOTIDE:
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297 nucleotideColour.setSelected(true);
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301 case ColourSchemeProperty.USER_DEFINED:
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302 userDefinedColour.setSelected(true);
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310 private void jbInit()
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313 fileMenu.setMnemonic('F');
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314 fileMenu.setText("File");
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315 saveAlignmentMenu.setMnemonic('L');
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316 saveAlignmentMenu.setText("Save As");
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317 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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318 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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319 saveAlignmentMenu.addActionListener(new ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 saveAlignmentMenu_actionPerformed(e);
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326 closeMenuItem.setMnemonic('C');
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327 closeMenuItem.setText("Close");
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328 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 closeMenuItem_actionPerformed(e);
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335 editMenu.setText("Edit");
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336 viewMenu.setText("View");
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337 colourMenu.setText("Colour");
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338 calculateMenu.setText("Calculate");
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339 webService.setText("Web Service");
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340 selectAllSequenceMenuItem.setText("Select all");
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341 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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342 java.awt.event.KeyEvent.VK_A,
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343 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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344 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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347 public void actionPerformed(ActionEvent e)
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349 selectAllSequenceMenuItem_actionPerformed(e);
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352 deselectAllSequenceMenuItem.setText("Deselect All");
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353 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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355 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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356 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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359 public void actionPerformed(ActionEvent e)
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361 deselectAllSequenceMenuItem_actionPerformed(e);
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364 invertSequenceMenuItem.setText("Invert Selection");
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365 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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367 public void actionPerformed(ActionEvent e)
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369 invertSequenceMenuItem_actionPerformed(e);
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372 remove2LeftMenuItem.setText("Remove Left");
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373 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 remove2LeftMenuItem_actionPerformed(e);
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380 remove2RightMenuItem.setText("Remove Right");
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381 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 remove2RightMenuItem_actionPerformed(e);
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388 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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389 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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392 public void actionPerformed(ActionEvent e)
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394 removeGappedColumnMenuItem_actionPerformed(e);
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397 removeAllGapsMenuItem.setText("Remove All Gaps");
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398 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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400 public void actionPerformed(ActionEvent e)
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402 removeAllGapsMenuItem_actionPerformed(e);
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405 viewBoxesMenuItem.setText("Boxes");
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406 viewBoxesMenuItem.setState(true);
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407 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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409 public void actionPerformed(ActionEvent e)
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411 viewBoxesMenuItem_actionPerformed(e);
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414 viewTextMenuItem.setText("Text");
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415 viewTextMenuItem.setState(true);
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416 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 viewTextMenuItem_actionPerformed(e);
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423 sortPairwiseMenuItem.setText("by Pairwise Identity");
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424 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 sortPairwiseMenuItem_actionPerformed(e);
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431 sortIDMenuItem.setText("by ID");
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432 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 sortIDMenuItem_actionPerformed(e);
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439 sortGroupMenuItem.setText("by Group");
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440 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 sortGroupMenuItem_actionPerformed(e);
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447 removeRedundancyMenuItem.setText("Remove Redundancy...");
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448 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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451 public void actionPerformed(ActionEvent e)
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453 removeRedundancyMenuItem_actionPerformed(e);
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456 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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457 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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460 public void actionPerformed(ActionEvent e)
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462 pairwiseAlignmentMenuItem_actionPerformed(e);
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465 PCAMenuItem.setText("Principal Component Analysis");
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466 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 PCAMenuItem_actionPerformed(e);
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473 averageDistanceTreeMenuItem.setText(
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474 "Average Distance Using % Identity");
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475 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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478 public void actionPerformed(ActionEvent e)
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480 averageDistanceTreeMenuItem_actionPerformed(e);
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483 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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484 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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486 public void actionPerformed(ActionEvent e)
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488 neighbourTreeMenuItem_actionPerformed(e);
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491 this.getContentPane().setLayout(borderLayout1);
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492 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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493 statusBar.setBackground(Color.white);
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494 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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495 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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496 statusBar.setText("Status bar");
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497 outputTextboxMenu.setMnemonic('T');
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498 outputTextboxMenu.setText("Output to Textbox");
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499 clustalColour.setText("Clustalx");
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501 clustalColour.addActionListener(new java.awt.event.ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 clustalColour_actionPerformed(e);
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508 zappoColour.setText("Zappo");
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509 zappoColour.addActionListener(new java.awt.event.ActionListener()
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511 public void actionPerformed(ActionEvent e)
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513 zappoColour_actionPerformed(e);
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516 taylorColour.setText("Taylor");
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517 taylorColour.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 taylorColour_actionPerformed(e);
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524 hydrophobicityColour.setText("Hydrophobicity");
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525 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 hydrophobicityColour_actionPerformed(e);
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532 helixColour.setText("Helix Propensity");
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533 helixColour.addActionListener(new java.awt.event.ActionListener()
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535 public void actionPerformed(ActionEvent e)
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537 helixColour_actionPerformed(e);
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540 strandColour.setText("Strand Propensity");
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541 strandColour.addActionListener(new java.awt.event.ActionListener()
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543 public void actionPerformed(ActionEvent e)
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545 strandColour_actionPerformed(e);
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548 turnColour.setText("Turn Propensity");
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549 turnColour.addActionListener(new java.awt.event.ActionListener()
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551 public void actionPerformed(ActionEvent e)
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553 turnColour_actionPerformed(e);
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556 buriedColour.setText("Buried Index");
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557 buriedColour.addActionListener(new java.awt.event.ActionListener()
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559 public void actionPerformed(ActionEvent e)
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561 buriedColour_actionPerformed(e);
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564 userDefinedColour.setText("User Defined...");
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565 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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567 public void actionPerformed(ActionEvent e)
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569 userDefinedColour_actionPerformed(e);
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572 PIDColour.setText("Percentage Identity");
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573 PIDColour.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 PIDColour_actionPerformed(e);
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580 BLOSUM62Colour.setText("BLOSUM62 Score");
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581 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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583 public void actionPerformed(ActionEvent e)
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585 BLOSUM62Colour_actionPerformed(e);
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588 avDistanceTreeBlosumMenuItem.setText(
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589 "Average Distance Using BLOSUM62");
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590 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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593 public void actionPerformed(ActionEvent e)
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595 avTreeBlosumMenuItem_actionPerformed(e);
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598 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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599 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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601 public void actionPerformed(ActionEvent e)
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603 njTreeBlosumMenuItem_actionPerformed(e);
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606 annotationPanelMenuItem.setActionCommand("");
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607 annotationPanelMenuItem.setText("Show Annotations");
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608 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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609 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 annotationPanelMenuItem_actionPerformed(e);
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616 colourTextMenuItem.setText("Colour Text");
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617 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 colourTextMenuItem_actionPerformed(e);
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624 htmlMenuItem.setText("HTML");
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625 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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627 public void actionPerformed(ActionEvent e)
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629 htmlMenuItem_actionPerformed(e);
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632 overviewMenuItem.setText("Overview Window");
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633 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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635 public void actionPerformed(ActionEvent e)
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637 overviewMenuItem_actionPerformed(e);
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640 undoMenuItem.setEnabled(false);
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641 undoMenuItem.setMnemonic('Z');
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642 undoMenuItem.setText("Undo");
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643 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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644 java.awt.event.KeyEvent.VK_Z,
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645 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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646 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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648 public void actionPerformed(ActionEvent e)
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650 undoMenuItem_actionPerformed(e);
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653 redoMenuItem.setEnabled(false);
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654 redoMenuItem.setMnemonic('0');
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655 redoMenuItem.setText("Redo");
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656 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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658 public void actionPerformed(ActionEvent e)
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660 redoMenuItem_actionPerformed(e);
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663 conservationMenuItem.setText("By Conservation");
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664 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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666 public void actionPerformed(ActionEvent e)
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668 conservationMenuItem_actionPerformed(e);
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671 noColourmenuItem.setText("None");
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672 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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674 public void actionPerformed(ActionEvent e)
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676 noColourmenuItem_actionPerformed(e);
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679 wrapMenuItem.setText("Wrap");
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680 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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682 public void actionPerformed(ActionEvent e)
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684 wrapMenuItem_actionPerformed(e);
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687 printMenuItem.setText("Print");
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688 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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690 public void actionPerformed(ActionEvent e)
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692 printMenuItem_actionPerformed(e);
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695 renderGapsMenuItem.setText("Show Gaps");
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696 renderGapsMenuItem.setState(true);
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697 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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699 public void actionPerformed(ActionEvent e)
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701 renderGapsMenuItem_actionPerformed(e);
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704 findMenuItem.setText("Find...");
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705 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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706 java.awt.event.KeyEvent.VK_F,
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707 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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708 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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710 public void actionPerformed(ActionEvent e)
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712 findMenuItem_actionPerformed(e);
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715 searchMenu.setText("Search");
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717 abovePIDThreshold.setText("Above Identity Threshold");
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718 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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720 public void actionPerformed(ActionEvent e)
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722 abovePIDThreshold_actionPerformed(e);
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725 showSeqFeatures.setText("Show Sequence Features");
\r
726 showSeqFeatures.addActionListener(new ActionListener()
\r
728 public void actionPerformed(ActionEvent actionEvent)
\r
730 showSeqFeatures_actionPerformed(actionEvent);
\r
733 nucleotideColour.setText("Nucleotide");
\r
734 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
736 public void actionPerformed(ActionEvent e)
\r
738 nucleotideColour_actionPerformed(e);
\r
741 deleteGroups.setText("Undefine groups");
\r
742 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
744 public void actionPerformed(ActionEvent e)
\r
746 deleteGroups_actionPerformed(e);
\r
749 copy.setText("Copy");
\r
750 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
751 java.awt.event.KeyEvent.VK_C,
\r
752 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
753 copy.setMnemonic(KeyEvent.VK_C);
\r
755 copy.addActionListener(new java.awt.event.ActionListener()
\r
757 public void actionPerformed(ActionEvent e)
\r
759 copy_actionPerformed(e);
\r
762 cut.setText("Cut");
\r
763 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
764 java.awt.event.KeyEvent.VK_X,
\r
765 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
766 cut.setMnemonic(KeyEvent.VK_X);
\r
767 cut.addActionListener(new java.awt.event.ActionListener()
\r
769 public void actionPerformed(ActionEvent e)
\r
771 cut_actionPerformed(e);
\r
774 delete.setText("Delete");
\r
775 delete.addActionListener(new java.awt.event.ActionListener()
\r
777 public void actionPerformed(ActionEvent e)
\r
779 delete_actionPerformed(e);
\r
782 jMenu1.setMnemonic('V');
\r
783 jMenu1.setText("Paste");
\r
784 pasteNew.setText("To New Alignment");
\r
785 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
786 java.awt.event.KeyEvent.VK_V,
\r
787 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
788 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
790 public void actionPerformed(ActionEvent e)
\r
792 pasteNew_actionPerformed(e);
\r
795 pasteThis.setText("Add To This Alignment");
\r
796 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
798 public void actionPerformed(ActionEvent e)
\r
800 pasteThis_actionPerformed(e);
\r
803 applyToAllGroups.setText("Apply Colour To All Groups");
\r
804 applyToAllGroups.setState(true);
\r
805 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
807 public void actionPerformed(ActionEvent e)
\r
809 applyToAllGroups_actionPerformed(e);
\r
812 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
814 public void actionPerformed(ActionEvent e)
\r
819 createPNG.setActionCommand("Save As PNG Image");
\r
820 createPNG.setText("PNG");
\r
821 font.setText("Font...");
\r
822 font.addActionListener(new java.awt.event.ActionListener()
\r
824 public void actionPerformed(ActionEvent e)
\r
826 font_actionPerformed(e);
\r
830 seqLimits.setText("Show Sequence Limits");
\r
831 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
832 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
834 public void actionPerformed(ActionEvent e)
\r
836 seqLimit_actionPerformed(e);
\r
839 epsFile.setText("EPS");
\r
840 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
842 public void actionPerformed(ActionEvent e)
\r
847 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
848 LoadtreeMenuItem.setText("Load Associated Tree");
\r
849 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
851 public void actionPerformed(ActionEvent e)
\r
853 LoadtreeMenuItem_actionPerformed(e);
\r
856 scaleAbove.setVisible(false);
\r
857 scaleAbove.setText("Scale Above");
\r
858 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
860 public void actionPerformed(ActionEvent e)
\r
862 scaleAbove_actionPerformed(e);
\r
865 scaleLeft.setVisible(false);
\r
866 scaleLeft.setSelected(true);
\r
867 scaleLeft.setText("Scale Left");
\r
868 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
870 public void actionPerformed(ActionEvent e)
\r
872 scaleLeft_actionPerformed(e);
\r
875 scaleRight.setVisible(false);
\r
876 scaleRight.setSelected(true);
\r
877 scaleRight.setText("Scale Right");
\r
878 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
880 public void actionPerformed(ActionEvent e)
\r
882 scaleRight_actionPerformed(e);
\r
885 modifyPID.setText("Modify Identity Threshold...");
\r
886 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
888 public void actionPerformed(ActionEvent e)
\r
890 modifyPID_actionPerformed(e);
\r
893 modifyConservation.setText("Modify Conservation Threshold...");
\r
894 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
896 public void actionPerformed(ActionEvent e)
\r
898 modifyConservation_actionPerformed(e);
\r
901 sortByTreeMenu.setText("By Tree Order");
\r
902 sort.setText("Sort");
\r
903 calculate.setText("Calculate Tree");
\r
905 jMenu2.setText("Export");
\r
906 padGapsMenuitem.setText("Pad Gaps");
\r
907 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
908 padGapsMenuitem.addActionListener(new ActionListener()
\r
910 public void actionPerformed(ActionEvent e)
\r
912 padGapsMenuitem_actionPerformed(e);
\r
915 vamsasStore.setVisible(false);
\r
916 vamsasStore.setText("VAMSAS store");
\r
917 vamsasStore.addActionListener(new ActionListener()
\r
919 public void actionPerformed(ActionEvent e)
\r
921 vamsasStore_actionPerformed(e);
\r
924 showTranslation.setText("Translate cDNA");
\r
925 showTranslation.addActionListener(new ActionListener()
\r
927 public void actionPerformed(ActionEvent e)
\r
929 showTranslation_actionPerformed(e);
\r
933 /* tabbedPane.addChangeListener(new ChangeListener()
\r
935 public void stateChanged(ChangeEvent ece)
\r
941 featureSettings.setText("Feature Settings...");
\r
942 featureSettings.addActionListener(new ActionListener()
\r
944 public void actionPerformed(ActionEvent e)
\r
946 featureSettings_actionPerformed(e);
\r
949 fetchSequence.setText("Fetch Sequence(s)...");
\r
950 fetchSequence.addActionListener(new ActionListener()
\r
952 public void actionPerformed(ActionEvent e)
\r
954 fetchSequence_actionPerformed(e);
\r
957 smoothFont.setText("Smooth Fonts");
\r
958 smoothFont.addActionListener(new ActionListener()
\r
960 public void actionPerformed(ActionEvent e)
\r
962 smoothFont_actionPerformed(e);
\r
965 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
966 annotationColour.setText("By Annotation...");
\r
967 annotationColour.addActionListener(new ActionListener()
\r
969 public void actionPerformed(ActionEvent e)
\r
971 annotationColour_actionPerformed(e);
\r
974 associatedData.setText("Load Features / Annotations");
\r
975 associatedData.addActionListener(new ActionListener()
\r
977 public void actionPerformed(ActionEvent e)
\r
979 associatedData_actionPerformed(e);
\r
982 autoCalculate.setText("Autocalculate Consensus");
\r
983 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
984 autoCalculate.addActionListener(new ActionListener()
\r
986 public void actionPerformed(ActionEvent e)
\r
988 autoCalculate_actionPerformed(e);
\r
991 addSequenceMenu.setText("Add Sequences");
\r
992 addFromFile.setText("From File");
\r
993 addFromFile.addActionListener(new ActionListener()
\r
995 public void actionPerformed(ActionEvent e)
\r
997 addFromFile_actionPerformed(e);
\r
1000 addFromText.setText("From Textbox");
\r
1001 addFromText.addActionListener(new ActionListener()
\r
1003 public void actionPerformed(ActionEvent e)
\r
1005 addFromText_actionPerformed(e);
\r
1008 addFromURL.setText("From URL");
\r
1009 addFromURL.addActionListener(new ActionListener()
\r
1011 public void actionPerformed(ActionEvent e)
\r
1013 addFromURL_actionPerformed(e);
\r
1016 exportFeatures.setText("Export Features...");
\r
1017 exportFeatures.addActionListener(new ActionListener()
\r
1019 public void actionPerformed(ActionEvent e)
\r
1021 exportFeatures_actionPerformed(e);
\r
1024 exportAnnotations.setText("Export Annotations...");
\r
1025 exportAnnotations.addActionListener(new ActionListener()
\r
1027 public void actionPerformed(ActionEvent e)
\r
1029 exportAnnotations_actionPerformed(e);
\r
1032 dbRefs.setText("Fetch DB Refs");
\r
1033 dbRefs.addActionListener(new ActionListener()
\r
1035 public void actionPerformed(ActionEvent e)
\r
1037 dbRefs_actionPerformed(e);
\r
1040 statusPanel.setLayout(gridLayout1);
\r
1041 jMenu3.setText("Fetch Sequence Features");
\r
1042 defaultDASSource.setText("Use Default DAS Source");
\r
1043 defaultDASSource.addActionListener(new ActionListener()
\r
1045 public void actionPerformed(ActionEvent e)
\r
1047 defaultDASSource_actionPerformed(e);
\r
1050 modifyDASSource.setText("Modify DAS Source...");
\r
1051 modifyDASSource.addActionListener(new ActionListener()
\r
1053 public void actionPerformed(ActionEvent e)
\r
1055 modifyDASSource_actionPerformed(e);
\r
1058 alignFrameMenuBar.add(fileMenu);
\r
1059 alignFrameMenuBar.add(editMenu);
\r
1060 alignFrameMenuBar.add(searchMenu);
\r
1061 alignFrameMenuBar.add(viewMenu);
\r
1062 alignFrameMenuBar.add(colourMenu);
\r
1063 alignFrameMenuBar.add(calculateMenu);
\r
1064 alignFrameMenuBar.add(webService);
\r
1065 fileMenu.add(addSequenceMenu);
\r
1066 fileMenu.add(fetchSequence);
\r
1067 fileMenu.addSeparator();
\r
1068 fileMenu.add(vamsasStore);
\r
1069 fileMenu.add(saveAlignmentMenu);
\r
1070 fileMenu.add(jMenu2);
\r
1071 fileMenu.add(outputTextboxMenu);
\r
1072 fileMenu.add(printMenuItem);
\r
1073 fileMenu.addSeparator();
\r
1074 fileMenu.add(exportFeatures);
\r
1075 fileMenu.add(exportAnnotations);
\r
1076 fileMenu.add(LoadtreeMenuItem);
\r
1077 fileMenu.add(associatedData);
\r
1078 fileMenu.addSeparator();
\r
1079 fileMenu.add(closeMenuItem);
\r
1080 editMenu.add(undoMenuItem);
\r
1081 editMenu.add(redoMenuItem);
\r
1082 editMenu.add(cut);
\r
1083 editMenu.add(copy);
\r
1084 editMenu.add(jMenu1);
\r
1085 editMenu.add(delete);
\r
1086 editMenu.addSeparator();
\r
1087 editMenu.add(selectAllSequenceMenuItem);
\r
1088 editMenu.add(deselectAllSequenceMenuItem);
\r
1089 editMenu.add(invertSequenceMenuItem);
\r
1090 editMenu.add(deleteGroups);
\r
1091 editMenu.addSeparator();
\r
1092 editMenu.add(remove2LeftMenuItem);
\r
1093 editMenu.add(remove2RightMenuItem);
\r
1094 editMenu.add(removeGappedColumnMenuItem);
\r
1095 editMenu.add(removeAllGapsMenuItem);
\r
1096 editMenu.add(removeRedundancyMenuItem);
\r
1097 editMenu.addSeparator();
\r
1098 editMenu.add(padGapsMenuitem);
\r
1099 searchMenu.add(findMenuItem);
\r
1100 viewMenu.add(font);
\r
1101 viewMenu.add(smoothFont);
\r
1102 viewMenu.addSeparator();
\r
1103 viewMenu.add(wrapMenuItem);
\r
1104 viewMenu.add(seqLimits);
\r
1105 viewMenu.add(scaleAbove);
\r
1106 viewMenu.add(scaleLeft);
\r
1107 viewMenu.add(scaleRight);
\r
1108 viewMenu.add(viewBoxesMenuItem);
\r
1109 viewMenu.add(viewTextMenuItem);
\r
1110 viewMenu.add(colourTextMenuItem);
\r
1111 viewMenu.add(renderGapsMenuItem);
\r
1112 viewMenu.add(annotationPanelMenuItem);
\r
1113 viewMenu.addSeparator();
\r
1114 viewMenu.add(dbRefs);
\r
1115 viewMenu.add(jMenu3);
\r
1116 viewMenu.add(showSeqFeatures);
\r
1117 viewMenu.add(featureSettings);
\r
1118 viewMenu.addSeparator();
\r
1119 viewMenu.add(overviewMenuItem);
\r
1120 colourMenu.add(applyToAllGroups);
\r
1121 colourMenu.addSeparator();
\r
1122 colourMenu.add(noColourmenuItem);
\r
1123 colourMenu.add(clustalColour);
\r
1124 colourMenu.add(BLOSUM62Colour);
\r
1125 colourMenu.add(PIDColour);
\r
1126 colourMenu.add(zappoColour);
\r
1127 colourMenu.add(taylorColour);
\r
1128 colourMenu.add(hydrophobicityColour);
\r
1129 colourMenu.add(helixColour);
\r
1130 colourMenu.add(strandColour);
\r
1131 colourMenu.add(turnColour);
\r
1132 colourMenu.add(buriedColour);
\r
1133 colourMenu.add(nucleotideColour);
\r
1134 colourMenu.add(userDefinedColour);
\r
1135 colourMenu.addSeparator();
\r
1136 colourMenu.add(conservationMenuItem);
\r
1137 colourMenu.add(modifyConservation);
\r
1138 colourMenu.add(abovePIDThreshold);
\r
1139 colourMenu.add(modifyPID);
\r
1140 colourMenu.add(annotationColour);
\r
1141 calculateMenu.add(sort);
\r
1142 calculateMenu.add(calculate);
\r
1143 calculateMenu.addSeparator();
\r
1144 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1145 calculateMenu.add(PCAMenuItem);
\r
1146 calculateMenu.addSeparator();
\r
1147 calculateMenu.add(showTranslation);
\r
1148 calculateMenu.add(autoCalculate);
\r
1149 webServiceNoServices=new JMenuItem("<No Services>");
\r
1150 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1151 jMenu1.add(pasteThis);
\r
1152 sort.add(sortIDMenuItem);
\r
1153 sort.add(sortGroupMenuItem);
\r
1154 sort.add(sortPairwiseMenuItem);
\r
1155 calculate.add(averageDistanceTreeMenuItem);
\r
1156 calculate.add(neighbourTreeMenuItem);
\r
1157 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1158 calculate.add(njTreeBlosumMenuItem);
\r
1159 jMenu2.add(htmlMenuItem);
\r
1160 jMenu2.add(epsFile);
\r
1161 jMenu2.add(createPNG);
\r
1162 addSequenceMenu.add(addFromFile);
\r
1163 addSequenceMenu.add(addFromText);
\r
1164 addSequenceMenu.add(addFromURL);
\r
1165 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1166 statusPanel.add(statusBar, null);
\r
1167 jMenu3.add(defaultDASSource);
\r
1168 jMenu3.add(modifyDASSource);
\r
1171 protected void outputText_actionPerformed(ActionEvent e)
\r
1175 public void addFromFile_actionPerformed(ActionEvent e)
\r
1180 public void addFromText_actionPerformed(ActionEvent e)
\r
1185 public void addFromURL_actionPerformed(ActionEvent e)
\r
1190 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1195 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1200 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1204 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1208 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1212 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1216 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1220 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1224 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1228 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1232 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1236 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1240 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1244 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1248 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1252 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1256 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1260 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1264 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1268 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1272 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1276 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1280 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1284 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1288 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1292 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1296 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1300 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1304 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1308 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1312 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1316 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1320 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1324 protected void helixColour_actionPerformed(ActionEvent e)
\r
1328 protected void strandColour_actionPerformed(ActionEvent e)
\r
1332 protected void turnColour_actionPerformed(ActionEvent e)
\r
1336 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1340 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1344 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1348 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1352 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1356 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1360 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1364 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1368 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1372 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1376 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1380 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1384 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1388 protected void copy_actionPerformed(ActionEvent e)
\r
1392 protected void cut_actionPerformed(ActionEvent e)
\r
1396 protected void delete_actionPerformed(ActionEvent e)
\r
1400 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1404 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1408 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1412 public void createPNG(java.io.File f)
\r
1416 protected void font_actionPerformed(ActionEvent e)
\r
1420 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1424 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1430 public void createEPS(java.io.File f)
\r
1434 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1438 protected void jpred_actionPerformed(ActionEvent e)
\r
1442 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1446 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1450 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1454 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1458 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1464 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1468 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1473 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1478 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1483 public void showTranslation_actionPerformed(ActionEvent e)
\r
1488 public void featureSettings_actionPerformed(ActionEvent e)
\r
1493 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1498 public void smoothFont_actionPerformed(ActionEvent e)
\r
1503 public void annotationColour_actionPerformed(ActionEvent e)
\r
1509 public void associatedData_actionPerformed(ActionEvent e)
\r
1514 public void autoCalculate_actionPerformed(ActionEvent e)
\r
1519 public void dbRefs_actionPerformed(ActionEvent e)
\r
1524 public void defaultDASSource_actionPerformed(ActionEvent e)
\r
1529 public void modifyDASSource_actionPerformed(ActionEvent e)
\r