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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27 public class GAlignFrame
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28 extends JInternalFrame
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30 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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31 protected JMenu fileMenu = new JMenu();
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32 protected JMenuItem closeMenuItem = new JMenuItem();
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33 protected JMenu editMenu = new JMenu();
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34 protected JMenu viewMenu = new JMenu();
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35 protected JMenu colourMenu = new JMenu();
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36 protected JMenu calculateMenu = new JMenu();
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37 protected JMenu webService = new JMenu();
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38 protected JMenuItem webServiceNoServices;
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39 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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40 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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41 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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42 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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43 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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44 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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45 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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46 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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47 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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48 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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49 protected JMenuItem sortIDMenuItem = new JMenuItem();
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50 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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51 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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52 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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53 protected JMenuItem PCAMenuItem = new JMenuItem();
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54 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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55 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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56 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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57 BorderLayout borderLayout1 = new BorderLayout();
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58 public JLabel statusBar = new JLabel();
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59 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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60 protected JMenu outputTextboxMenu = new JMenu();
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61 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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62 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem hydrophobicityColour = new
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65 JRadioButtonMenuItem();
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66 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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73 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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74 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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75 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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76 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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77 JMenuItem htmlMenuItem = new JMenuItem();
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78 JMenuItem overviewMenuItem = new JMenuItem();
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79 protected JMenuItem undoMenuItem = new JMenuItem();
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80 protected JMenuItem redoMenuItem = new JMenuItem();
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81 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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82 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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83 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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84 JMenuItem printMenuItem = new JMenuItem();
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85 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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86 JMenuItem findMenuItem = new JMenuItem();
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87 JMenu searchMenu = new JMenu();
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88 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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89 public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
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90 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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91 JMenuItem deleteGroups = new JMenuItem();
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92 JMenuItem delete = new JMenuItem();
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93 JMenuItem copy = new JMenuItem();
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94 JMenuItem cut = new JMenuItem();
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95 JMenu jMenu1 = new JMenu();
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96 JMenuItem pasteNew = new JMenuItem();
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97 JMenuItem pasteThis = new JMenuItem();
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98 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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99 JMenuItem createPNG = new JMenuItem();
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100 protected JMenuItem font = new JMenuItem();
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101 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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102 JMenuItem epsFile = new JMenuItem();
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103 JMenuItem LoadtreeMenuItem = new JMenuItem();
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104 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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105 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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106 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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107 protected JMenuItem modifyPID = new JMenuItem();
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108 protected JMenuItem modifyConservation = new JMenuItem();
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109 protected JMenu sortByTreeMenu = new JMenu();
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110 protected JMenu sort = new JMenu();
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111 JMenu calculate = new JMenu();
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112 JMenu jMenu2 = new JMenu();
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113 JMenuItem padGapsMenuitem = new JMenuItem();
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114 protected ButtonGroup colours = new ButtonGroup();
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115 JMenuItem vamsasStore = new JMenuItem();
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116 protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
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117 //protected JTabbedPane tabbedPane = new JTabbedPane();
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118 public JMenuItem featureSettings = new JMenuItem();
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119 JMenuItem fetchSequence = new JMenuItem();
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121 public GAlignFrame()
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128 setJMenuBar(alignFrameMenuBar);
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130 // dynamically fill save as menu with available formats
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131 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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133 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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136 item.addActionListener(new java.awt.event.ActionListener()
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138 public void actionPerformed(ActionEvent e)
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140 outputText_actionPerformed(e);
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144 outputTextboxMenu.add(item);
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147 catch (Exception e)
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152 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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154 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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155 getUserColourSchemes().keys();
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157 while (userColours.hasMoreElements())
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159 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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160 nextElement().toString());
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161 radioItem.setName("USER_DEFINED");
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162 radioItem.addMouseListener(new MouseAdapter()
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164 public void mousePressed(MouseEvent evt)
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166 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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168 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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170 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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171 "Remove from default list?",
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172 "Remove user defined colour",
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173 JOptionPane.YES_NO_OPTION);
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174 if(option == JOptionPane.YES_OPTION)
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176 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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177 colourMenu.remove(radioItem);
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180 radioItem.addActionListener(new ActionListener()
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182 public void actionPerformed(ActionEvent evt)
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184 userDefinedColour_actionPerformed(evt);
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190 radioItem.addActionListener(new ActionListener()
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192 public void actionPerformed(ActionEvent evt)
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194 userDefinedColour_actionPerformed(evt);
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197 colourMenu.insert(radioItem, 15);
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198 colours.add(radioItem);
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201 colours.add(noColourmenuItem);
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202 colours.add(clustalColour);
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203 colours.add(zappoColour);
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204 colours.add(taylorColour);
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205 colours.add(hydrophobicityColour);
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206 colours.add(helixColour);
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207 colours.add(strandColour);
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208 colours.add(turnColour);
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209 colours.add(buriedColour);
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210 colours.add(userDefinedColour);
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211 colours.add(PIDColour);
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212 colours.add(BLOSUM62Colour);
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213 colours.add(nucleotideColour);
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215 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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220 public void setColourSelected(String defaultColour)
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223 if (defaultColour != null)
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225 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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229 case ColourSchemeProperty.NONE:
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230 noColourmenuItem.setSelected(true);
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232 case ColourSchemeProperty.CLUSTAL:
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233 clustalColour.setSelected(true);
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237 case ColourSchemeProperty.BLOSUM:
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238 BLOSUM62Colour.setSelected(true);
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242 case ColourSchemeProperty.PID:
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243 PIDColour.setSelected(true);
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247 case ColourSchemeProperty.ZAPPO:
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248 zappoColour.setSelected(true);
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252 case ColourSchemeProperty.TAYLOR:
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253 taylorColour.setSelected(true);
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256 case ColourSchemeProperty.HYDROPHOBIC:
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257 hydrophobicityColour.setSelected(true);
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261 case ColourSchemeProperty.HELIX:
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262 helixColour.setSelected(true);
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266 case ColourSchemeProperty.STRAND:
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267 strandColour.setSelected(true);
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271 case ColourSchemeProperty.TURN:
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272 turnColour.setSelected(true);
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276 case ColourSchemeProperty.BURIED:
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277 buriedColour.setSelected(true);
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281 case ColourSchemeProperty.NUCLEOTIDE:
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282 nucleotideColour.setSelected(true);
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286 case ColourSchemeProperty.USER_DEFINED:
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287 userDefinedColour.setSelected(true);
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295 private void jbInit()
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298 fileMenu.setMnemonic('F');
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299 fileMenu.setText("File");
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300 saveAlignmentMenu.setMnemonic('L');
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301 saveAlignmentMenu.setText("Save As");
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302 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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303 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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304 saveAlignmentMenu.addActionListener(new ActionListener()
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306 public void actionPerformed(ActionEvent e)
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308 saveAlignmentMenu_actionPerformed(e);
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311 closeMenuItem.setMnemonic('C');
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312 closeMenuItem.setText("Close");
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313 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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315 public void actionPerformed(ActionEvent e)
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317 closeMenuItem_actionPerformed(e);
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320 editMenu.setText("Edit");
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321 viewMenu.setText("View");
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322 colourMenu.setText("Colour");
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323 calculateMenu.setText("Calculate");
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324 webService.setText("Web Service");
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325 selectAllSequenceMenuItem.setText("Select all");
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326 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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327 java.awt.event.KeyEvent.VK_A,
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328 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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329 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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332 public void actionPerformed(ActionEvent e)
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334 selectAllSequenceMenuItem_actionPerformed(e);
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337 deselectAllSequenceMenuItem.setText("Deselect All");
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338 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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340 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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341 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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344 public void actionPerformed(ActionEvent e)
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346 deselectAllSequenceMenuItem_actionPerformed(e);
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349 invertSequenceMenuItem.setText("Invert Selection");
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350 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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352 public void actionPerformed(ActionEvent e)
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354 invertSequenceMenuItem_actionPerformed(e);
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357 remove2LeftMenuItem.setText("Remove Left");
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358 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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360 public void actionPerformed(ActionEvent e)
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362 remove2LeftMenuItem_actionPerformed(e);
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365 remove2RightMenuItem.setText("Remove Right");
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366 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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368 public void actionPerformed(ActionEvent e)
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370 remove2RightMenuItem_actionPerformed(e);
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373 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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374 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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377 public void actionPerformed(ActionEvent e)
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379 removeGappedColumnMenuItem_actionPerformed(e);
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382 removeAllGapsMenuItem.setText("Remove All Gaps");
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383 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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385 public void actionPerformed(ActionEvent e)
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387 removeAllGapsMenuItem_actionPerformed(e);
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390 viewBoxesMenuItem.setText("Boxes");
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391 viewBoxesMenuItem.setState(true);
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392 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 viewBoxesMenuItem_actionPerformed(e);
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399 viewTextMenuItem.setText("Text");
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400 viewTextMenuItem.setState(true);
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401 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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403 public void actionPerformed(ActionEvent e)
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405 viewTextMenuItem_actionPerformed(e);
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408 sortPairwiseMenuItem.setText("by Pairwise Identity");
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409 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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411 public void actionPerformed(ActionEvent e)
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413 sortPairwiseMenuItem_actionPerformed(e);
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416 sortIDMenuItem.setText("by ID");
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417 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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419 public void actionPerformed(ActionEvent e)
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421 sortIDMenuItem_actionPerformed(e);
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424 sortGroupMenuItem.setText("by Group");
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425 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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427 public void actionPerformed(ActionEvent e)
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429 sortGroupMenuItem_actionPerformed(e);
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432 removeRedundancyMenuItem.setText("Remove Redundancy...");
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433 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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436 public void actionPerformed(ActionEvent e)
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438 removeRedundancyMenuItem_actionPerformed(e);
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441 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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442 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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445 public void actionPerformed(ActionEvent e)
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447 pairwiseAlignmentMenuItem_actionPerformed(e);
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450 PCAMenuItem.setText("Principal Component Analysis");
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451 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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453 public void actionPerformed(ActionEvent e)
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455 PCAMenuItem_actionPerformed(e);
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458 averageDistanceTreeMenuItem.setText(
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459 "Average Distance Using % Identity");
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460 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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463 public void actionPerformed(ActionEvent e)
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465 averageDistanceTreeMenuItem_actionPerformed(e);
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468 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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469 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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471 public void actionPerformed(ActionEvent e)
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473 neighbourTreeMenuItem_actionPerformed(e);
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476 this.getContentPane().setLayout(borderLayout1);
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477 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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478 statusBar.setBackground(Color.white);
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479 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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480 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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481 statusBar.setText("Status bar");
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482 outputTextboxMenu.setMnemonic('T');
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483 outputTextboxMenu.setText("Output to Textbox");
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484 clustalColour.setText("Clustalx");
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486 clustalColour.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 clustalColour_actionPerformed(e);
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493 zappoColour.setText("Zappo");
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494 zappoColour.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 zappoColour_actionPerformed(e);
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501 taylorColour.setText("Taylor");
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502 taylorColour.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 taylorColour_actionPerformed(e);
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509 hydrophobicityColour.setText("Hydrophobicity");
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510 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 hydrophobicityColour_actionPerformed(e);
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517 helixColour.setText("Helix Propensity");
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518 helixColour.addActionListener(new java.awt.event.ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 helixColour_actionPerformed(e);
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525 strandColour.setText("Strand Propensity");
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526 strandColour.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 strandColour_actionPerformed(e);
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533 turnColour.setText("Turn Propensity");
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534 turnColour.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 turnColour_actionPerformed(e);
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541 buriedColour.setText("Buried Index");
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542 buriedColour.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 buriedColour_actionPerformed(e);
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549 userDefinedColour.setText("User Defined...");
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550 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 userDefinedColour_actionPerformed(e);
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557 PIDColour.setText("Percentage Identity");
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558 PIDColour.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 PIDColour_actionPerformed(e);
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565 BLOSUM62Colour.setText("BLOSUM62 Score");
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566 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 BLOSUM62Colour_actionPerformed(e);
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573 avDistanceTreeBlosumMenuItem.setText(
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574 "Average Distance Using BLOSUM62");
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575 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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578 public void actionPerformed(ActionEvent e)
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580 avTreeBlosumMenuItem_actionPerformed(e);
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583 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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584 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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586 public void actionPerformed(ActionEvent e)
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588 njTreeBlosumMenuItem_actionPerformed(e);
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591 annotationPanelMenuItem.setActionCommand("");
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592 annotationPanelMenuItem.setText("Show Annotations");
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593 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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594 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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596 public void actionPerformed(ActionEvent e)
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598 annotationPanelMenuItem_actionPerformed(e);
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601 colourTextMenuItem.setText("Colour Text");
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602 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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604 public void actionPerformed(ActionEvent e)
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606 colourTextMenuItem_actionPerformed(e);
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609 htmlMenuItem.setText("HTML");
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610 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 htmlMenuItem_actionPerformed(e);
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617 overviewMenuItem.setText("Overview Window");
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618 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 overviewMenuItem_actionPerformed(e);
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625 undoMenuItem.setEnabled(false);
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626 undoMenuItem.setMnemonic('Z');
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627 undoMenuItem.setText("Undo");
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628 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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629 java.awt.event.KeyEvent.VK_Z,
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630 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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631 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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633 public void actionPerformed(ActionEvent e)
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635 undoMenuItem_actionPerformed(e);
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638 redoMenuItem.setEnabled(false);
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639 redoMenuItem.setMnemonic('0');
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640 redoMenuItem.setText("Redo");
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641 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 redoMenuItem_actionPerformed(e);
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648 conservationMenuItem.setText("By Conservation");
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649 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 conservationMenuItem_actionPerformed(e);
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656 noColourmenuItem.setText("None");
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657 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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659 public void actionPerformed(ActionEvent e)
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661 noColourmenuItem_actionPerformed(e);
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664 wrapMenuItem.setText("Wrap");
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665 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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667 public void actionPerformed(ActionEvent e)
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669 wrapMenuItem_actionPerformed(e);
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672 printMenuItem.setText("Print");
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673 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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675 public void actionPerformed(ActionEvent e)
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677 printMenuItem_actionPerformed(e);
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680 renderGapsMenuItem.setText("Show Gaps");
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681 renderGapsMenuItem.setState(true);
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682 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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684 public void actionPerformed(ActionEvent e)
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686 renderGapsMenuItem_actionPerformed(e);
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689 findMenuItem.setText("Find...");
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690 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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691 java.awt.event.KeyEvent.VK_F,
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692 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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693 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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695 public void actionPerformed(ActionEvent e)
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697 findMenuItem_actionPerformed(e);
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700 searchMenu.setText("Search");
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702 abovePIDThreshold.setText("Above Identity Threshold");
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703 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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705 public void actionPerformed(ActionEvent e)
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707 abovePIDThreshold_actionPerformed(e);
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710 sequenceFeatures.setText("Sequence Features");
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711 sequenceFeatures.addActionListener(new ActionListener()
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713 public void actionPerformed(ActionEvent actionEvent)
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715 sequenceFeatures_actionPerformed(actionEvent);
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718 nucleotideColour.setText("Nucleotide");
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719 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 nucleotideColour_actionPerformed(e);
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726 deleteGroups.setText("Undefine groups");
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727 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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729 public void actionPerformed(ActionEvent e)
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731 deleteGroups_actionPerformed(e);
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734 copy.setText("Copy");
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735 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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736 java.awt.event.KeyEvent.VK_C,
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737 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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738 copy.setMnemonic(KeyEvent.VK_C);
\r
740 copy.addActionListener(new java.awt.event.ActionListener()
\r
742 public void actionPerformed(ActionEvent e)
\r
744 copy_actionPerformed(e);
\r
747 cut.setText("Cut");
\r
748 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
749 java.awt.event.KeyEvent.VK_X,
\r
750 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
751 cut.setMnemonic(KeyEvent.VK_X);
\r
752 cut.addActionListener(new java.awt.event.ActionListener()
\r
754 public void actionPerformed(ActionEvent e)
\r
756 cut_actionPerformed(e);
\r
759 delete.setText("Delete");
\r
760 delete.addActionListener(new java.awt.event.ActionListener()
\r
762 public void actionPerformed(ActionEvent e)
\r
764 delete_actionPerformed(e);
\r
767 jMenu1.setMnemonic('V');
\r
768 jMenu1.setText("Paste");
\r
769 pasteNew.setText("To New Alignment");
\r
770 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
771 java.awt.event.KeyEvent.VK_V,
\r
772 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
773 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
775 public void actionPerformed(ActionEvent e)
\r
777 pasteNew_actionPerformed(e);
\r
780 pasteThis.setText("Add To This Alignment");
\r
781 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
783 public void actionPerformed(ActionEvent e)
\r
785 pasteThis_actionPerformed(e);
\r
788 applyToAllGroups.setText("Apply Colour To All Groups");
\r
789 applyToAllGroups.setState(true);
\r
790 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
792 public void actionPerformed(ActionEvent e)
\r
794 applyToAllGroups_actionPerformed(e);
\r
797 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
799 public void actionPerformed(ActionEvent e)
\r
804 createPNG.setActionCommand("Save As PNG Image");
\r
805 createPNG.setText("PNG");
\r
806 font.setText("Font...");
\r
807 font.addActionListener(new java.awt.event.ActionListener()
\r
809 public void actionPerformed(ActionEvent e)
\r
811 font_actionPerformed(e);
\r
815 seqLimits.setText("Show Sequence Limits");
\r
816 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
817 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
819 public void actionPerformed(ActionEvent e)
\r
821 seqLimit_actionPerformed(e);
\r
824 epsFile.setText("EPS");
\r
825 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
827 public void actionPerformed(ActionEvent e)
\r
832 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
833 LoadtreeMenuItem.setText("Load Assocated Tree");
\r
834 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
836 public void actionPerformed(ActionEvent e)
\r
838 LoadtreeMenuItem_actionPerformed(e);
\r
841 scaleAbove.setVisible(false);
\r
842 scaleAbove.setText("Scale Above");
\r
843 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
845 public void actionPerformed(ActionEvent e)
\r
847 scaleAbove_actionPerformed(e);
\r
850 scaleLeft.setVisible(false);
\r
851 scaleLeft.setSelected(true);
\r
852 scaleLeft.setText("Scale Left");
\r
853 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
855 public void actionPerformed(ActionEvent e)
\r
857 scaleLeft_actionPerformed(e);
\r
860 scaleRight.setVisible(false);
\r
861 scaleRight.setSelected(true);
\r
862 scaleRight.setText("Scale Right");
\r
863 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
865 public void actionPerformed(ActionEvent e)
\r
867 scaleRight_actionPerformed(e);
\r
870 modifyPID.setText("Modify Identity Threshold...");
\r
871 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
873 public void actionPerformed(ActionEvent e)
\r
875 modifyPID_actionPerformed(e);
\r
878 modifyConservation.setText("Modify Conservation Threshold...");
\r
879 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
881 public void actionPerformed(ActionEvent e)
\r
883 modifyConservation_actionPerformed(e);
\r
886 sortByTreeMenu.setText("By Tree Order");
\r
887 sort.setText("Sort");
\r
888 calculate.setText("Calculate Tree");
\r
890 jMenu2.setText("Export");
\r
891 padGapsMenuitem.setText("Pad Gaps");
\r
892 padGapsMenuitem.addActionListener(new ActionListener()
\r
894 public void actionPerformed(ActionEvent e)
\r
896 padGapsMenuitem_actionPerformed(e);
\r
899 vamsasStore.setVisible(false);
\r
900 vamsasStore.setText("VAMSAS store");
\r
901 vamsasStore.addActionListener(new ActionListener()
\r
903 public void actionPerformed(ActionEvent e)
\r
905 vamsasStore_actionPerformed(e);
\r
908 showTranslation.setText("Translate cDNA");
\r
909 showTranslation.addActionListener(new ActionListener()
\r
911 public void actionPerformed(ActionEvent e)
\r
913 showTranslation_actionPerformed(e);
\r
917 /* tabbedPane.addChangeListener(new ChangeListener()
\r
919 public void stateChanged(ChangeEvent ece)
\r
925 featureSettings.setEnabled(false);
\r
926 featureSettings.setText("Feature Settings...");
\r
927 featureSettings.addActionListener(new ActionListener()
\r
929 public void actionPerformed(ActionEvent e)
\r
931 featureSettings_actionPerformed(e);
\r
934 fetchSequence.setText("Fetch Sequence...");
\r
935 fetchSequence.addActionListener(new ActionListener()
\r
937 public void actionPerformed(ActionEvent e)
\r
939 fetchSequence_actionPerformed(e);
\r
942 alignFrameMenuBar.add(fileMenu);
\r
943 alignFrameMenuBar.add(editMenu);
\r
944 alignFrameMenuBar.add(searchMenu);
\r
945 alignFrameMenuBar.add(viewMenu);
\r
946 alignFrameMenuBar.add(colourMenu);
\r
947 alignFrameMenuBar.add(calculateMenu);
\r
948 alignFrameMenuBar.add(webService);
\r
949 fileMenu.add(fetchSequence);
\r
950 fileMenu.add(vamsasStore);
\r
951 fileMenu.add(saveAlignmentMenu);
\r
952 fileMenu.add(jMenu2);
\r
953 fileMenu.add(outputTextboxMenu);
\r
954 fileMenu.add(printMenuItem);
\r
955 fileMenu.addSeparator();
\r
956 fileMenu.add(LoadtreeMenuItem);
\r
957 fileMenu.addSeparator();
\r
958 fileMenu.add(closeMenuItem);
\r
959 editMenu.add(undoMenuItem);
\r
960 editMenu.add(redoMenuItem);
\r
962 editMenu.add(copy);
\r
963 editMenu.add(jMenu1);
\r
964 editMenu.add(delete);
\r
965 editMenu.addSeparator();
\r
966 editMenu.add(selectAllSequenceMenuItem);
\r
967 editMenu.add(deselectAllSequenceMenuItem);
\r
968 editMenu.add(invertSequenceMenuItem);
\r
969 editMenu.add(deleteGroups);
\r
970 editMenu.addSeparator();
\r
971 editMenu.add(remove2LeftMenuItem);
\r
972 editMenu.add(remove2RightMenuItem);
\r
973 editMenu.add(removeGappedColumnMenuItem);
\r
974 editMenu.add(removeAllGapsMenuItem);
\r
975 editMenu.add(removeRedundancyMenuItem);
\r
976 editMenu.addSeparator();
\r
977 editMenu.add(padGapsMenuitem);
\r
978 searchMenu.add(findMenuItem);
\r
979 viewMenu.add(font);
\r
980 viewMenu.addSeparator();
\r
981 viewMenu.add(wrapMenuItem);
\r
982 viewMenu.add(seqLimits);
\r
983 viewMenu.add(scaleAbove);
\r
984 viewMenu.add(scaleLeft);
\r
985 viewMenu.add(scaleRight);
\r
986 viewMenu.add(viewBoxesMenuItem);
\r
987 viewMenu.add(viewTextMenuItem);
\r
988 viewMenu.add(colourTextMenuItem);
\r
989 viewMenu.add(renderGapsMenuItem);
\r
990 viewMenu.add(annotationPanelMenuItem);
\r
991 viewMenu.addSeparator();
\r
992 viewMenu.add(sequenceFeatures);
\r
993 viewMenu.add(featureSettings);
\r
994 viewMenu.addSeparator();
\r
995 viewMenu.add(overviewMenuItem);
\r
996 colourMenu.add(applyToAllGroups);
\r
997 colourMenu.addSeparator();
\r
998 colourMenu.add(noColourmenuItem);
\r
999 colourMenu.add(clustalColour);
\r
1000 colourMenu.add(BLOSUM62Colour);
\r
1001 colourMenu.add(PIDColour);
\r
1002 colourMenu.add(zappoColour);
\r
1003 colourMenu.add(taylorColour);
\r
1004 colourMenu.add(hydrophobicityColour);
\r
1005 colourMenu.add(helixColour);
\r
1006 colourMenu.add(strandColour);
\r
1007 colourMenu.add(turnColour);
\r
1008 colourMenu.add(buriedColour);
\r
1009 colourMenu.add(nucleotideColour);
\r
1010 colourMenu.add(userDefinedColour);
\r
1011 colourMenu.addSeparator();
\r
1012 colourMenu.add(conservationMenuItem);
\r
1013 colourMenu.add(modifyConservation);
\r
1014 colourMenu.add(abovePIDThreshold);
\r
1015 colourMenu.add(modifyPID);
\r
1016 calculateMenu.add(sort);
\r
1017 calculateMenu.add(calculate);
\r
1018 calculateMenu.addSeparator();
\r
1019 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1020 calculateMenu.add(PCAMenuItem);
\r
1021 calculateMenu.addSeparator();
\r
1022 calculateMenu.add(showTranslation);
\r
1023 webServiceNoServices=new JMenuItem("<No Services>");
\r
1024 webService.add(webServiceNoServices);
\r
1025 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
1026 // this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1027 jMenu1.add(pasteNew);
\r
1028 jMenu1.add(pasteThis);
\r
1029 sort.add(sortIDMenuItem);
\r
1030 sort.add(sortGroupMenuItem);
\r
1031 sort.add(sortPairwiseMenuItem);
\r
1032 calculate.add(averageDistanceTreeMenuItem);
\r
1033 calculate.add(neighbourTreeMenuItem);
\r
1034 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1035 calculate.add(njTreeBlosumMenuItem);
\r
1036 jMenu2.add(htmlMenuItem);
\r
1037 jMenu2.add(epsFile);
\r
1038 jMenu2.add(createPNG);
\r
1041 protected void outputText_actionPerformed(ActionEvent e)
\r
1045 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1049 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1053 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1057 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1061 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1065 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1069 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1073 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1077 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1081 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1085 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1089 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1093 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1097 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1101 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1105 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1109 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1113 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1117 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1121 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1125 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1129 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1133 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1137 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1141 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1145 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1149 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1153 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1157 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1161 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1165 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1169 protected void helixColour_actionPerformed(ActionEvent e)
\r
1173 protected void strandColour_actionPerformed(ActionEvent e)
\r
1177 protected void turnColour_actionPerformed(ActionEvent e)
\r
1181 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1185 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1189 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1193 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1197 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1201 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1205 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1209 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1213 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1217 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1221 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
\r
1225 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1229 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1233 protected void copy_actionPerformed(ActionEvent e)
\r
1237 protected void cut_actionPerformed(ActionEvent e)
\r
1241 protected void delete_actionPerformed(ActionEvent e)
\r
1245 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1249 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1253 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1257 public void createPNG(java.io.File f)
\r
1261 protected void font_actionPerformed(ActionEvent e)
\r
1265 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1269 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1275 public void createEPS(java.io.File f)
\r
1279 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1283 protected void jpred_actionPerformed(ActionEvent e)
\r
1287 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1291 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1295 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1299 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1303 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1309 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1313 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1318 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1323 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1328 public void showTranslation_actionPerformed(ActionEvent e)
\r
1333 public void tabSelected()
\r
1338 public void featureSettings_actionPerformed(ActionEvent e)
\r
1343 public void fetchSequence_actionPerformed(ActionEvent e)
\r