2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import jalview.schemes.*;
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27 import java.awt.BorderLayout;
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32 public class GAlignFrame
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33 extends JInternalFrame
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35 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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36 protected JMenu fileMenu = new JMenu();
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37 protected JMenuItem closeMenuItem = new JMenuItem();
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38 protected JMenu editMenu = new JMenu();
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39 protected JMenu viewMenu = new JMenu();
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40 protected JMenu colourMenu = new JMenu();
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41 protected JMenu calculateMenu = new JMenu();
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42 protected JMenu webService = new JMenu();
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43 protected JMenuItem webServiceNoServices;
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44 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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45 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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46 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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47 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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48 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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49 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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50 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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51 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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52 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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53 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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54 protected JMenuItem sortIDMenuItem = new JMenuItem();
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55 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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56 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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57 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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58 protected JMenuItem PCAMenuItem = new JMenuItem();
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59 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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60 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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61 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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62 BorderLayout borderLayout1 = new BorderLayout();
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63 public JLabel statusBar = new JLabel();
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64 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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65 protected JMenu outputTextboxMenu = new JMenu();
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66 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem hydrophobicityColour = new
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70 JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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74 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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75 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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76 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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77 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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78 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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79 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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80 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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81 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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82 JMenuItem htmlMenuItem = new JMenuItem();
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83 JMenuItem overviewMenuItem = new JMenuItem();
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84 protected JMenuItem undoMenuItem = new JMenuItem();
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85 protected JMenuItem redoMenuItem = new JMenuItem();
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86 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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87 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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88 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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89 JMenuItem printMenuItem = new JMenuItem();
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90 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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91 JMenuItem findMenuItem = new JMenuItem();
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92 JMenu searchMenu = new JMenu();
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93 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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94 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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95 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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96 JMenuItem deleteGroups = new JMenuItem();
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97 JMenuItem delete = new JMenuItem();
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98 JMenuItem copy = new JMenuItem();
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99 JMenuItem cut = new JMenuItem();
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100 JMenu jMenu1 = new JMenu();
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101 JMenuItem pasteNew = new JMenuItem();
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102 JMenuItem pasteThis = new JMenuItem();
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103 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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104 JMenuItem createPNG = new JMenuItem();
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105 protected JMenuItem font = new JMenuItem();
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106 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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107 JMenuItem epsFile = new JMenuItem();
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108 JMenuItem LoadtreeMenuItem = new JMenuItem();
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109 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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110 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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111 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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112 protected JMenuItem modifyPID = new JMenuItem();
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113 protected JMenuItem modifyConservation = new JMenuItem();
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114 protected JMenu sortByTreeMenu = new JMenu();
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115 protected JMenu sort = new JMenu();
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116 JMenu calculate = new JMenu();
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117 JMenu jMenu2 = new JMenu();
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118 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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119 protected ButtonGroup colours = new ButtonGroup();
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120 JMenuItem vamsasStore = new JMenuItem();
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121 protected JMenuItem showTranslation = new JMenuItem();
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122 public JMenuItem featureSettings = new JMenuItem();
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123 JMenuItem fetchSequence = new JMenuItem();
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124 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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125 JMenuItem annotationColour = new JMenuItem();
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126 JMenuItem associatedData = new JMenuItem();
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127 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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128 JMenu addSequenceMenu = new JMenu();
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129 JMenuItem addFromFile = new JMenuItem();
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130 JMenuItem addFromText = new JMenuItem();
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131 JMenuItem addFromURL = new JMenuItem();
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132 JMenuItem exportAnnotations = new JMenuItem();
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133 JMenuItem exportFeatures = new JMenuItem();
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134 protected JPanel statusPanel = new JPanel();
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135 GridLayout gridLayout1 = new GridLayout();
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136 JMenu jMenu3 = new JMenu();
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137 JMenuItem showAllSeqs = new JMenuItem();
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138 JMenuItem showAllColumns = new JMenuItem();
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139 JMenu hideMenu = new JMenu();
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140 JMenuItem hideSelSequences = new JMenuItem();
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141 JMenuItem hideSelColumns = new JMenuItem();
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142 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
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143 JMenuItem invertColSel = new JMenuItem();
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144 protected JTabbedPane tabbedPane = new JTabbedPane();
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145 public GAlignFrame()
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150 setJMenuBar(alignFrameMenuBar);
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152 // dynamically fill save as menu with available formats
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153 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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155 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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157 item.addActionListener(new java.awt.event.ActionListener()
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159 public void actionPerformed(ActionEvent e)
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161 outputText_actionPerformed(e);
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165 outputTextboxMenu.add(item);
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168 catch (Exception e)
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173 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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175 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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176 getUserColourSchemes().keys();
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178 while (userColours.hasMoreElements())
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180 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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181 nextElement().toString());
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182 radioItem.setName("USER_DEFINED");
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183 radioItem.addMouseListener(new MouseAdapter()
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185 public void mousePressed(MouseEvent evt)
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187 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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189 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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191 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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192 "Remove from default list?",
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193 "Remove user defined colour",
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194 JOptionPane.YES_NO_OPTION);
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195 if(option == JOptionPane.YES_OPTION)
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197 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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198 colourMenu.remove(radioItem);
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201 radioItem.addActionListener(new ActionListener()
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203 public void actionPerformed(ActionEvent evt)
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205 userDefinedColour_actionPerformed(evt);
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211 radioItem.addActionListener(new ActionListener()
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213 public void actionPerformed(ActionEvent evt)
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215 userDefinedColour_actionPerformed(evt);
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218 colourMenu.insert(radioItem, 15);
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219 colours.add(radioItem);
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222 colours.add(noColourmenuItem);
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223 colours.add(clustalColour);
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224 colours.add(zappoColour);
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225 colours.add(taylorColour);
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226 colours.add(hydrophobicityColour);
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227 colours.add(helixColour);
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228 colours.add(strandColour);
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229 colours.add(turnColour);
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230 colours.add(buriedColour);
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231 colours.add(userDefinedColour);
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232 colours.add(PIDColour);
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233 colours.add(BLOSUM62Colour);
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234 colours.add(nucleotideColour);
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236 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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241 public void setColourSelected(String defaultColour)
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244 if (defaultColour != null)
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246 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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250 case ColourSchemeProperty.NONE:
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251 noColourmenuItem.setSelected(true);
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253 case ColourSchemeProperty.CLUSTAL:
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254 clustalColour.setSelected(true);
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258 case ColourSchemeProperty.BLOSUM:
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259 BLOSUM62Colour.setSelected(true);
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263 case ColourSchemeProperty.PID:
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264 PIDColour.setSelected(true);
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268 case ColourSchemeProperty.ZAPPO:
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269 zappoColour.setSelected(true);
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273 case ColourSchemeProperty.TAYLOR:
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274 taylorColour.setSelected(true);
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277 case ColourSchemeProperty.HYDROPHOBIC:
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278 hydrophobicityColour.setSelected(true);
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282 case ColourSchemeProperty.HELIX:
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283 helixColour.setSelected(true);
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287 case ColourSchemeProperty.STRAND:
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288 strandColour.setSelected(true);
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292 case ColourSchemeProperty.TURN:
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293 turnColour.setSelected(true);
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297 case ColourSchemeProperty.BURIED:
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298 buriedColour.setSelected(true);
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302 case ColourSchemeProperty.NUCLEOTIDE:
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303 nucleotideColour.setSelected(true);
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307 case ColourSchemeProperty.USER_DEFINED:
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308 userDefinedColour.setSelected(true);
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316 private void jbInit()
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319 fileMenu.setMnemonic('F');
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320 fileMenu.setText("File");
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321 saveAlignmentMenu.setMnemonic('L');
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322 saveAlignmentMenu.setText("Save As");
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323 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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324 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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325 saveAlignmentMenu.addActionListener(new ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 saveAlignmentMenu_actionPerformed(e);
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332 closeMenuItem.setMnemonic('C');
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333 closeMenuItem.setText("Close");
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334 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 closeMenuItem_actionPerformed(e);
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341 editMenu.setText("Edit");
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342 viewMenu.setText("View");
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343 colourMenu.setText("Colour");
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344 calculateMenu.setText("Calculate");
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345 webService.setText("Web Service");
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346 selectAllSequenceMenuItem.setText("Select all");
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347 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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348 java.awt.event.KeyEvent.VK_A,
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349 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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350 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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353 public void actionPerformed(ActionEvent e)
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355 selectAllSequenceMenuItem_actionPerformed(e);
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358 deselectAllSequenceMenuItem.setText("Deselect All");
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359 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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361 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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362 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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365 public void actionPerformed(ActionEvent e)
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367 deselectAllSequenceMenuItem_actionPerformed(e);
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370 invertSequenceMenuItem.setText("Invert Sequence Selection");
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371 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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373 public void actionPerformed(ActionEvent e)
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375 invertSequenceMenuItem_actionPerformed(e);
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378 remove2LeftMenuItem.setText("Remove Left");
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379 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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381 public void actionPerformed(ActionEvent e)
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383 remove2LeftMenuItem_actionPerformed(e);
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386 remove2RightMenuItem.setText("Remove Right");
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387 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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389 public void actionPerformed(ActionEvent e)
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391 remove2RightMenuItem_actionPerformed(e);
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394 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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395 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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398 public void actionPerformed(ActionEvent e)
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400 removeGappedColumnMenuItem_actionPerformed(e);
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403 removeAllGapsMenuItem.setText("Remove All Gaps");
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404 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 removeAllGapsMenuItem_actionPerformed(e);
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411 viewBoxesMenuItem.setText("Boxes");
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412 viewBoxesMenuItem.setState(true);
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413 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 viewBoxesMenuItem_actionPerformed(e);
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420 viewTextMenuItem.setText("Text");
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421 viewTextMenuItem.setState(true);
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422 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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424 public void actionPerformed(ActionEvent e)
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426 viewTextMenuItem_actionPerformed(e);
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429 sortPairwiseMenuItem.setText("by Pairwise Identity");
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430 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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432 public void actionPerformed(ActionEvent e)
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434 sortPairwiseMenuItem_actionPerformed(e);
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437 sortIDMenuItem.setText("by ID");
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438 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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440 public void actionPerformed(ActionEvent e)
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442 sortIDMenuItem_actionPerformed(e);
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445 sortGroupMenuItem.setText("by Group");
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446 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 sortGroupMenuItem_actionPerformed(e);
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453 removeRedundancyMenuItem.setText("Remove Redundancy...");
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454 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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457 public void actionPerformed(ActionEvent e)
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459 removeRedundancyMenuItem_actionPerformed(e);
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462 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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463 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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466 public void actionPerformed(ActionEvent e)
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468 pairwiseAlignmentMenuItem_actionPerformed(e);
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471 PCAMenuItem.setText("Principal Component Analysis");
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472 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 PCAMenuItem_actionPerformed(e);
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479 averageDistanceTreeMenuItem.setText(
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480 "Average Distance Using % Identity");
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481 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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484 public void actionPerformed(ActionEvent e)
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486 averageDistanceTreeMenuItem_actionPerformed(e);
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489 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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490 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 neighbourTreeMenuItem_actionPerformed(e);
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497 this.getContentPane().setLayout(borderLayout1);
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498 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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499 statusBar.setBackground(Color.white);
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500 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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501 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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502 statusBar.setText("Status bar");
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503 outputTextboxMenu.setMnemonic('T');
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504 outputTextboxMenu.setText("Output to Textbox");
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505 clustalColour.setText("Clustalx");
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507 clustalColour.addActionListener(new java.awt.event.ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 clustalColour_actionPerformed(e);
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514 zappoColour.setText("Zappo");
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515 zappoColour.addActionListener(new java.awt.event.ActionListener()
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517 public void actionPerformed(ActionEvent e)
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519 zappoColour_actionPerformed(e);
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522 taylorColour.setText("Taylor");
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523 taylorColour.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 taylorColour_actionPerformed(e);
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530 hydrophobicityColour.setText("Hydrophobicity");
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531 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 hydrophobicityColour_actionPerformed(e);
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538 helixColour.setText("Helix Propensity");
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539 helixColour.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 helixColour_actionPerformed(e);
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546 strandColour.setText("Strand Propensity");
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547 strandColour.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 strandColour_actionPerformed(e);
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554 turnColour.setText("Turn Propensity");
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555 turnColour.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 turnColour_actionPerformed(e);
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562 buriedColour.setText("Buried Index");
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563 buriedColour.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 buriedColour_actionPerformed(e);
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570 userDefinedColour.setText("User Defined...");
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571 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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573 public void actionPerformed(ActionEvent e)
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575 userDefinedColour_actionPerformed(e);
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578 PIDColour.setText("Percentage Identity");
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579 PIDColour.addActionListener(new java.awt.event.ActionListener()
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581 public void actionPerformed(ActionEvent e)
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583 PIDColour_actionPerformed(e);
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586 BLOSUM62Colour.setText("BLOSUM62 Score");
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587 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 BLOSUM62Colour_actionPerformed(e);
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594 avDistanceTreeBlosumMenuItem.setText(
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595 "Average Distance Using BLOSUM62");
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596 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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599 public void actionPerformed(ActionEvent e)
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601 avTreeBlosumMenuItem_actionPerformed(e);
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604 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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605 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 njTreeBlosumMenuItem_actionPerformed(e);
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612 annotationPanelMenuItem.setActionCommand("");
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613 annotationPanelMenuItem.setText("Show Annotations");
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614 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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615 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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617 public void actionPerformed(ActionEvent e)
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619 annotationPanelMenuItem_actionPerformed(e);
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622 colourTextMenuItem.setText("Colour Text");
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623 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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625 public void actionPerformed(ActionEvent e)
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627 colourTextMenuItem_actionPerformed(e);
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630 htmlMenuItem.setText("HTML");
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631 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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633 public void actionPerformed(ActionEvent e)
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635 htmlMenuItem_actionPerformed(e);
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638 overviewMenuItem.setText("Overview Window");
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639 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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641 public void actionPerformed(ActionEvent e)
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643 overviewMenuItem_actionPerformed(e);
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646 undoMenuItem.setEnabled(false);
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647 undoMenuItem.setMnemonic('Z');
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648 undoMenuItem.setText("Undo");
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649 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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650 java.awt.event.KeyEvent.VK_Z,
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651 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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652 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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654 public void actionPerformed(ActionEvent e)
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656 undoMenuItem_actionPerformed(e);
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659 redoMenuItem.setEnabled(false);
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660 redoMenuItem.setMnemonic('0');
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661 redoMenuItem.setText("Redo");
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662 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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664 public void actionPerformed(ActionEvent e)
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666 redoMenuItem_actionPerformed(e);
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669 conservationMenuItem.setText("By Conservation");
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670 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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672 public void actionPerformed(ActionEvent e)
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674 conservationMenuItem_actionPerformed(e);
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677 noColourmenuItem.setText("None");
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678 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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680 public void actionPerformed(ActionEvent e)
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682 noColourmenuItem_actionPerformed(e);
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685 wrapMenuItem.setText("Wrap");
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686 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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688 public void actionPerformed(ActionEvent e)
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690 wrapMenuItem_actionPerformed(e);
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693 printMenuItem.setText("Print");
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694 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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696 public void actionPerformed(ActionEvent e)
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698 printMenuItem_actionPerformed(e);
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701 renderGapsMenuItem.setText("Show Gaps");
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702 renderGapsMenuItem.setState(true);
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703 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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705 public void actionPerformed(ActionEvent e)
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707 renderGapsMenuItem_actionPerformed(e);
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710 findMenuItem.setText("Find...");
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711 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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712 java.awt.event.KeyEvent.VK_F,
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713 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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714 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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716 public void actionPerformed(ActionEvent e)
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718 findMenuItem_actionPerformed(e);
\r
721 searchMenu.setText("Search");
\r
723 abovePIDThreshold.setText("Above Identity Threshold");
\r
724 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
\r
726 public void actionPerformed(ActionEvent e)
\r
728 abovePIDThreshold_actionPerformed(e);
\r
731 showSeqFeatures.setText("Show Sequence Features");
\r
732 showSeqFeatures.addActionListener(new ActionListener()
\r
734 public void actionPerformed(ActionEvent actionEvent)
\r
736 showSeqFeatures_actionPerformed(actionEvent);
\r
739 nucleotideColour.setText("Nucleotide");
\r
740 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
742 public void actionPerformed(ActionEvent e)
\r
744 nucleotideColour_actionPerformed(e);
\r
747 deleteGroups.setText("Undefine groups");
\r
748 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
750 public void actionPerformed(ActionEvent e)
\r
752 deleteGroups_actionPerformed(e);
\r
755 copy.setText("Copy");
\r
756 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
757 java.awt.event.KeyEvent.VK_C,
\r
758 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
759 copy.setMnemonic(KeyEvent.VK_C);
\r
761 copy.addActionListener(new java.awt.event.ActionListener()
\r
763 public void actionPerformed(ActionEvent e)
\r
765 copy_actionPerformed(e);
\r
768 cut.setText("Cut");
\r
769 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
770 java.awt.event.KeyEvent.VK_X,
\r
771 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
772 cut.setMnemonic(KeyEvent.VK_X);
\r
773 cut.addActionListener(new java.awt.event.ActionListener()
\r
775 public void actionPerformed(ActionEvent e)
\r
777 cut_actionPerformed(e);
\r
780 delete.setText("Delete");
\r
781 delete.addActionListener(new java.awt.event.ActionListener()
\r
783 public void actionPerformed(ActionEvent e)
\r
785 delete_actionPerformed(e);
\r
788 jMenu1.setMnemonic('V');
\r
789 jMenu1.setText("Paste");
\r
790 pasteNew.setText("To New Alignment");
\r
791 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
792 java.awt.event.KeyEvent.VK_V,
\r
793 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
794 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
796 public void actionPerformed(ActionEvent e)
\r
798 pasteNew_actionPerformed(e);
\r
801 pasteThis.setText("Add To This Alignment");
\r
802 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
804 public void actionPerformed(ActionEvent e)
\r
806 pasteThis_actionPerformed(e);
\r
809 applyToAllGroups.setText("Apply Colour To All Groups");
\r
810 applyToAllGroups.setState(true);
\r
811 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
813 public void actionPerformed(ActionEvent e)
\r
815 applyToAllGroups_actionPerformed(e);
\r
818 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
820 public void actionPerformed(ActionEvent e)
\r
825 createPNG.setActionCommand("Save As PNG Image");
\r
826 createPNG.setText("PNG");
\r
827 font.setText("Font...");
\r
828 font.addActionListener(new java.awt.event.ActionListener()
\r
830 public void actionPerformed(ActionEvent e)
\r
832 font_actionPerformed(e);
\r
836 seqLimits.setText("Show Sequence Limits");
\r
837 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
838 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
840 public void actionPerformed(ActionEvent e)
\r
842 seqLimit_actionPerformed(e);
\r
845 epsFile.setText("EPS");
\r
846 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
848 public void actionPerformed(ActionEvent e)
\r
853 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
854 LoadtreeMenuItem.setText("Load Associated Tree");
\r
855 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
857 public void actionPerformed(ActionEvent e)
\r
859 LoadtreeMenuItem_actionPerformed(e);
\r
862 scaleAbove.setVisible(false);
\r
863 scaleAbove.setText("Scale Above");
\r
864 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
866 public void actionPerformed(ActionEvent e)
\r
868 scaleAbove_actionPerformed(e);
\r
871 scaleLeft.setVisible(false);
\r
872 scaleLeft.setSelected(true);
\r
873 scaleLeft.setText("Scale Left");
\r
874 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
876 public void actionPerformed(ActionEvent e)
\r
878 scaleLeft_actionPerformed(e);
\r
881 scaleRight.setVisible(false);
\r
882 scaleRight.setSelected(true);
\r
883 scaleRight.setText("Scale Right");
\r
884 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
886 public void actionPerformed(ActionEvent e)
\r
888 scaleRight_actionPerformed(e);
\r
891 modifyPID.setText("Modify Identity Threshold...");
\r
892 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
894 public void actionPerformed(ActionEvent e)
\r
896 modifyPID_actionPerformed(e);
\r
899 modifyConservation.setText("Modify Conservation Threshold...");
\r
900 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
902 public void actionPerformed(ActionEvent e)
\r
904 modifyConservation_actionPerformed(e);
\r
907 sortByTreeMenu.setText("By Tree Order");
\r
908 sort.setText("Sort");
\r
909 calculate.setText("Calculate Tree");
\r
911 jMenu2.setText("Export");
\r
912 padGapsMenuitem.setText("Pad Gaps");
\r
913 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
914 padGapsMenuitem.addActionListener(new ActionListener()
\r
916 public void actionPerformed(ActionEvent e)
\r
918 padGapsMenuitem_actionPerformed(e);
\r
921 vamsasStore.setVisible(false);
\r
922 vamsasStore.setText("VAMSAS store");
\r
923 vamsasStore.addActionListener(new ActionListener()
\r
925 public void actionPerformed(ActionEvent e)
\r
927 vamsasStore_actionPerformed(e);
\r
930 showTranslation.setText("Translate cDNA");
\r
931 showTranslation.addActionListener(new ActionListener()
\r
933 public void actionPerformed(ActionEvent e)
\r
935 showTranslation_actionPerformed(e);
\r
939 /* tabbedPane.addChangeListener(new ChangeListener()
\r
941 public void stateChanged(ChangeEvent ece)
\r
947 featureSettings.setText("Feature Settings...");
\r
948 featureSettings.addActionListener(new ActionListener()
\r
950 public void actionPerformed(ActionEvent e)
\r
952 featureSettings_actionPerformed(e);
\r
955 fetchSequence.setText("Fetch Sequence(s)...");
\r
956 fetchSequence.addActionListener(new ActionListener()
\r
958 public void actionPerformed(ActionEvent e)
\r
960 fetchSequence_actionPerformed(e);
\r
963 smoothFont.setText("Smooth Fonts");
\r
964 smoothFont.addActionListener(new ActionListener()
\r
966 public void actionPerformed(ActionEvent e)
\r
968 smoothFont_actionPerformed(e);
\r
971 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
972 annotationColour.setText("By Annotation...");
\r
973 annotationColour.addActionListener(new ActionListener()
\r
975 public void actionPerformed(ActionEvent e)
\r
977 annotationColour_actionPerformed(e);
\r
980 associatedData.setText("Load Features / Annotations");
\r
981 associatedData.addActionListener(new ActionListener()
\r
983 public void actionPerformed(ActionEvent e)
\r
985 associatedData_actionPerformed(e);
\r
988 autoCalculate.setText("Autocalculate Consensus");
\r
989 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
990 autoCalculate.addActionListener(new ActionListener()
\r
992 public void actionPerformed(ActionEvent e)
\r
994 autoCalculate_actionPerformed(e);
\r
997 addSequenceMenu.setText("Add Sequences");
\r
998 addFromFile.setText("From File");
\r
999 addFromFile.addActionListener(new ActionListener()
\r
1001 public void actionPerformed(ActionEvent e)
\r
1003 addFromFile_actionPerformed(e);
\r
1006 addFromText.setText("From Textbox");
\r
1007 addFromText.addActionListener(new ActionListener()
\r
1009 public void actionPerformed(ActionEvent e)
\r
1011 addFromText_actionPerformed(e);
\r
1014 addFromURL.setText("From URL");
\r
1015 addFromURL.addActionListener(new ActionListener()
\r
1017 public void actionPerformed(ActionEvent e)
\r
1019 addFromURL_actionPerformed(e);
\r
1022 exportFeatures.setText("Export Features...");
\r
1023 exportFeatures.addActionListener(new ActionListener()
\r
1025 public void actionPerformed(ActionEvent e)
\r
1027 exportFeatures_actionPerformed(e);
\r
1030 exportAnnotations.setText("Export Annotations...");
\r
1031 exportAnnotations.addActionListener(new ActionListener()
\r
1033 public void actionPerformed(ActionEvent e)
\r
1035 exportAnnotations_actionPerformed(e);
\r
1038 statusPanel.setLayout(gridLayout1);
\r
1039 jMenu3.setText("Show");
\r
1040 showAllSeqs.setText("All Sequences");
\r
1041 showAllSeqs.addActionListener(new ActionListener()
\r
1043 public void actionPerformed(ActionEvent e)
\r
1045 showAllSeqs_actionPerformed(e);
\r
1048 showAllColumns.setText("All Columns");
\r
1049 showAllColumns.addActionListener(new ActionListener()
\r
1051 public void actionPerformed(ActionEvent e)
\r
1053 showAllColumns_actionPerformed(e);
\r
1056 hideMenu.setText("Hide");
\r
1057 hideSelSequences.setText("Selected Sequences");
\r
1058 hideSelSequences.addActionListener(new ActionListener()
\r
1060 public void actionPerformed(ActionEvent e)
\r
1062 hideSelSequences_actionPerformed(e);
\r
1065 hideSelColumns.setText("Selected Columns");
\r
1066 hideSelColumns.addActionListener(new ActionListener()
\r
1068 public void actionPerformed(ActionEvent e)
\r
1070 hideSelColumns_actionPerformed(e);
\r
1073 hiddenMarkers.setText("Hidden Markers");
\r
1074 hiddenMarkers.setState(true);
\r
1075 hiddenMarkers.addActionListener(new ActionListener()
\r
1077 public void actionPerformed(ActionEvent e)
\r
1079 hiddenMarkers_actionPerformed(e);
\r
1082 invertColSel.setText("Invert Column Selection");
\r
1083 invertColSel.addActionListener(new ActionListener()
\r
1085 public void actionPerformed(ActionEvent e)
\r
1087 invertColSel_actionPerformed(e);
\r
1090 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
\r
1092 public void stateChanged(ChangeEvent evt)
\r
1094 JTabbedPane pane = (JTabbedPane)evt.getSource();
\r
1095 int sel = pane.getSelectedIndex();
\r
1096 tabSelectionChanged(sel);
\r
1099 tabbedPane.addMouseListener(new MouseAdapter()
\r
1101 public void mousePressed(MouseEvent e)
\r
1103 tabbedPane_mousePressed(e);
\r
1107 alignFrameMenuBar.add(fileMenu);
\r
1108 alignFrameMenuBar.add(editMenu);
\r
1109 alignFrameMenuBar.add(searchMenu);
\r
1110 alignFrameMenuBar.add(viewMenu);
\r
1111 alignFrameMenuBar.add(colourMenu);
\r
1112 alignFrameMenuBar.add(calculateMenu);
\r
1113 alignFrameMenuBar.add(webService);
\r
1114 fileMenu.add(addSequenceMenu);
\r
1115 fileMenu.add(fetchSequence);
\r
1116 fileMenu.addSeparator();
\r
1117 fileMenu.add(vamsasStore);
\r
1118 fileMenu.add(saveAlignmentMenu);
\r
1119 fileMenu.add(jMenu2);
\r
1120 fileMenu.add(outputTextboxMenu);
\r
1121 fileMenu.add(printMenuItem);
\r
1122 fileMenu.addSeparator();
\r
1123 fileMenu.add(exportFeatures);
\r
1124 fileMenu.add(exportAnnotations);
\r
1125 fileMenu.add(LoadtreeMenuItem);
\r
1126 fileMenu.add(associatedData);
\r
1127 fileMenu.addSeparator();
\r
1128 fileMenu.add(closeMenuItem);
\r
1129 editMenu.add(undoMenuItem);
\r
1130 editMenu.add(redoMenuItem);
\r
1131 editMenu.add(cut);
\r
1132 editMenu.add(copy);
\r
1133 editMenu.add(jMenu1);
\r
1134 editMenu.add(delete);
\r
1135 editMenu.addSeparator();
\r
1136 editMenu.add(selectAllSequenceMenuItem);
\r
1137 editMenu.add(deselectAllSequenceMenuItem);
\r
1138 editMenu.add(invertSequenceMenuItem);
\r
1139 editMenu.add(invertColSel);
\r
1140 editMenu.add(deleteGroups);
\r
1141 editMenu.addSeparator();
\r
1142 editMenu.add(remove2LeftMenuItem);
\r
1143 editMenu.add(remove2RightMenuItem);
\r
1144 editMenu.add(removeGappedColumnMenuItem);
\r
1145 editMenu.add(removeAllGapsMenuItem);
\r
1146 editMenu.add(removeRedundancyMenuItem);
\r
1147 editMenu.addSeparator();
\r
1148 editMenu.add(padGapsMenuitem);
\r
1149 searchMenu.add(findMenuItem);
\r
1150 viewMenu.add(font);
\r
1151 viewMenu.add(smoothFont);
\r
1152 viewMenu.addSeparator();
\r
1153 viewMenu.add(jMenu3);
\r
1154 viewMenu.add(hideMenu);
\r
1155 viewMenu.add(hiddenMarkers);
\r
1156 viewMenu.addSeparator();
\r
1157 viewMenu.add(wrapMenuItem);
\r
1158 viewMenu.add(seqLimits);
\r
1159 viewMenu.add(scaleAbove);
\r
1160 viewMenu.add(scaleLeft);
\r
1161 viewMenu.add(scaleRight);
\r
1162 viewMenu.add(viewBoxesMenuItem);
\r
1163 viewMenu.add(viewTextMenuItem);
\r
1164 viewMenu.add(colourTextMenuItem);
\r
1165 viewMenu.add(renderGapsMenuItem);
\r
1166 viewMenu.add(annotationPanelMenuItem);
\r
1167 viewMenu.addSeparator();
\r
1168 viewMenu.add(showSeqFeatures);
\r
1169 viewMenu.add(featureSettings);
\r
1170 viewMenu.addSeparator();
\r
1171 viewMenu.add(overviewMenuItem);
\r
1172 colourMenu.add(applyToAllGroups);
\r
1173 colourMenu.addSeparator();
\r
1174 colourMenu.add(noColourmenuItem);
\r
1175 colourMenu.add(clustalColour);
\r
1176 colourMenu.add(BLOSUM62Colour);
\r
1177 colourMenu.add(PIDColour);
\r
1178 colourMenu.add(zappoColour);
\r
1179 colourMenu.add(taylorColour);
\r
1180 colourMenu.add(hydrophobicityColour);
\r
1181 colourMenu.add(helixColour);
\r
1182 colourMenu.add(strandColour);
\r
1183 colourMenu.add(turnColour);
\r
1184 colourMenu.add(buriedColour);
\r
1185 colourMenu.add(nucleotideColour);
\r
1186 colourMenu.add(userDefinedColour);
\r
1187 colourMenu.addSeparator();
\r
1188 colourMenu.add(conservationMenuItem);
\r
1189 colourMenu.add(modifyConservation);
\r
1190 colourMenu.add(abovePIDThreshold);
\r
1191 colourMenu.add(modifyPID);
\r
1192 colourMenu.add(annotationColour);
\r
1193 calculateMenu.add(sort);
\r
1194 calculateMenu.add(calculate);
\r
1195 calculateMenu.addSeparator();
\r
1196 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1197 calculateMenu.add(PCAMenuItem);
\r
1198 calculateMenu.addSeparator();
\r
1199 calculateMenu.add(showTranslation);
\r
1200 calculateMenu.add(autoCalculate);
\r
1201 webServiceNoServices=new JMenuItem("<No Services>");
\r
1202 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1203 jMenu1.add(pasteThis);
\r
1204 sort.add(sortIDMenuItem);
\r
1205 sort.add(sortGroupMenuItem);
\r
1206 sort.add(sortPairwiseMenuItem);
\r
1207 calculate.add(averageDistanceTreeMenuItem);
\r
1208 calculate.add(neighbourTreeMenuItem);
\r
1209 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1210 calculate.add(njTreeBlosumMenuItem);
\r
1211 jMenu2.add(htmlMenuItem);
\r
1212 jMenu2.add(epsFile);
\r
1213 jMenu2.add(createPNG);
\r
1214 addSequenceMenu.add(addFromFile);
\r
1215 addSequenceMenu.add(addFromText);
\r
1216 addSequenceMenu.add(addFromURL);
\r
1217 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1218 statusPanel.add(statusBar, null);
\r
1219 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1220 jMenu3.add(showAllColumns);
\r
1221 jMenu3.add(showAllSeqs);
\r
1222 hideMenu.add(hideSelColumns);
\r
1223 hideMenu.add(hideSelSequences);
\r
1226 protected void outputText_actionPerformed(ActionEvent e)
\r
1230 public void addFromFile_actionPerformed(ActionEvent e)
\r
1235 public void addFromText_actionPerformed(ActionEvent e)
\r
1240 public void addFromURL_actionPerformed(ActionEvent e)
\r
1245 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1250 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1255 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1259 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1263 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1267 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1271 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1275 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1279 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1283 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1287 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1291 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1295 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1299 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1303 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1307 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1311 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1315 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1319 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1323 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1327 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1331 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1335 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1339 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1343 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1347 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1351 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1355 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1359 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1363 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1367 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1371 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1375 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1379 protected void helixColour_actionPerformed(ActionEvent e)
\r
1383 protected void strandColour_actionPerformed(ActionEvent e)
\r
1387 protected void turnColour_actionPerformed(ActionEvent e)
\r
1391 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1395 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1399 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1403 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1407 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1411 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1415 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1419 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1423 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1427 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1431 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1435 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1439 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1443 protected void copy_actionPerformed(ActionEvent e)
\r
1447 protected void cut_actionPerformed(ActionEvent e)
\r
1451 protected void delete_actionPerformed(ActionEvent e)
\r
1455 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1459 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1463 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1467 public void createPNG(java.io.File f)
\r
1471 protected void font_actionPerformed(ActionEvent e)
\r
1475 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1479 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1485 public void createEPS(java.io.File f)
\r
1489 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1493 protected void jpred_actionPerformed(ActionEvent e)
\r
1497 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1501 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1505 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1509 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1513 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1519 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1523 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1528 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1533 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1538 public void showTranslation_actionPerformed(ActionEvent e)
\r
1543 public void featureSettings_actionPerformed(ActionEvent e)
\r
1548 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1553 public void smoothFont_actionPerformed(ActionEvent e)
\r
1558 public void annotationColour_actionPerformed(ActionEvent e)
\r
1564 public void associatedData_actionPerformed(ActionEvent e)
\r
1569 public void autoCalculate_actionPerformed(ActionEvent e)
\r
1574 public void showAllSeqs_actionPerformed(ActionEvent e)
\r
1579 public void showAllColumns_actionPerformed(ActionEvent e)
\r
1584 public void hideSelSequences_actionPerformed(ActionEvent e)
\r
1589 public void hideSelColumns_actionPerformed(ActionEvent e)
\r
1594 public void hiddenMarkers_actionPerformed(ActionEvent e)
\r
1599 public void findPdbId_actionPerformed(ActionEvent e)
\r
1604 public void enterPdbId_actionPerformed(ActionEvent e)
\r
1609 public void pdbFile_actionPerformed(ActionEvent e)
\r
1614 public void invertColSel_actionPerformed(ActionEvent e)
\r
1619 public void tabSelectionChanged(int sel)
\r
1624 public void tabbedPane_mousePressed(MouseEvent e)
\r