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 showSeqFeatures = 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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120 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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121 JMenuItem annotationColour = new JMenuItem();
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122 JMenuItem fetchSeqFeatures = new JMenuItem();
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124 public GAlignFrame()
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131 setJMenuBar(alignFrameMenuBar);
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133 // dynamically fill save as menu with available formats
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134 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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136 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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139 item.addActionListener(new java.awt.event.ActionListener()
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141 public void actionPerformed(ActionEvent e)
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143 outputText_actionPerformed(e);
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147 outputTextboxMenu.add(item);
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150 catch (Exception e)
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155 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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157 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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158 getUserColourSchemes().keys();
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160 while (userColours.hasMoreElements())
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162 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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163 nextElement().toString());
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164 radioItem.setName("USER_DEFINED");
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165 radioItem.addMouseListener(new MouseAdapter()
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167 public void mousePressed(MouseEvent evt)
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169 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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171 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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173 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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174 "Remove from default list?",
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175 "Remove user defined colour",
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176 JOptionPane.YES_NO_OPTION);
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177 if(option == JOptionPane.YES_OPTION)
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179 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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180 colourMenu.remove(radioItem);
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183 radioItem.addActionListener(new ActionListener()
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185 public void actionPerformed(ActionEvent evt)
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187 userDefinedColour_actionPerformed(evt);
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193 radioItem.addActionListener(new ActionListener()
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195 public void actionPerformed(ActionEvent evt)
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197 userDefinedColour_actionPerformed(evt);
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200 colourMenu.insert(radioItem, 15);
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201 colours.add(radioItem);
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204 colours.add(noColourmenuItem);
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205 colours.add(clustalColour);
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206 colours.add(zappoColour);
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207 colours.add(taylorColour);
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208 colours.add(hydrophobicityColour);
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209 colours.add(helixColour);
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210 colours.add(strandColour);
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211 colours.add(turnColour);
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212 colours.add(buriedColour);
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213 colours.add(userDefinedColour);
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214 colours.add(PIDColour);
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215 colours.add(BLOSUM62Colour);
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216 colours.add(nucleotideColour);
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218 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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223 public void setColourSelected(String defaultColour)
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226 if (defaultColour != null)
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228 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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232 case ColourSchemeProperty.NONE:
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233 noColourmenuItem.setSelected(true);
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235 case ColourSchemeProperty.CLUSTAL:
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236 clustalColour.setSelected(true);
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240 case ColourSchemeProperty.BLOSUM:
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241 BLOSUM62Colour.setSelected(true);
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245 case ColourSchemeProperty.PID:
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246 PIDColour.setSelected(true);
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250 case ColourSchemeProperty.ZAPPO:
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251 zappoColour.setSelected(true);
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255 case ColourSchemeProperty.TAYLOR:
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256 taylorColour.setSelected(true);
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259 case ColourSchemeProperty.HYDROPHOBIC:
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260 hydrophobicityColour.setSelected(true);
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264 case ColourSchemeProperty.HELIX:
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265 helixColour.setSelected(true);
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269 case ColourSchemeProperty.STRAND:
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270 strandColour.setSelected(true);
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274 case ColourSchemeProperty.TURN:
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275 turnColour.setSelected(true);
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279 case ColourSchemeProperty.BURIED:
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280 buriedColour.setSelected(true);
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284 case ColourSchemeProperty.NUCLEOTIDE:
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285 nucleotideColour.setSelected(true);
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289 case ColourSchemeProperty.USER_DEFINED:
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290 userDefinedColour.setSelected(true);
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298 private void jbInit()
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301 fileMenu.setMnemonic('F');
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302 fileMenu.setText("File");
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303 saveAlignmentMenu.setMnemonic('L');
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304 saveAlignmentMenu.setText("Save As");
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305 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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306 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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307 saveAlignmentMenu.addActionListener(new ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 saveAlignmentMenu_actionPerformed(e);
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314 closeMenuItem.setMnemonic('C');
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315 closeMenuItem.setText("Close");
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316 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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318 public void actionPerformed(ActionEvent e)
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320 closeMenuItem_actionPerformed(e);
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323 editMenu.setText("Edit");
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324 viewMenu.setText("View");
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325 colourMenu.setText("Colour");
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326 calculateMenu.setText("Calculate");
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327 webService.setText("Web Service");
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328 selectAllSequenceMenuItem.setText("Select all");
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329 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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330 java.awt.event.KeyEvent.VK_A,
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331 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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332 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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335 public void actionPerformed(ActionEvent e)
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337 selectAllSequenceMenuItem_actionPerformed(e);
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340 deselectAllSequenceMenuItem.setText("Deselect All");
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341 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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343 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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344 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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347 public void actionPerformed(ActionEvent e)
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349 deselectAllSequenceMenuItem_actionPerformed(e);
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352 invertSequenceMenuItem.setText("Invert Selection");
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353 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 invertSequenceMenuItem_actionPerformed(e);
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360 remove2LeftMenuItem.setText("Remove Left");
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361 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 remove2LeftMenuItem_actionPerformed(e);
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368 remove2RightMenuItem.setText("Remove Right");
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369 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 remove2RightMenuItem_actionPerformed(e);
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376 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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377 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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380 public void actionPerformed(ActionEvent e)
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382 removeGappedColumnMenuItem_actionPerformed(e);
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385 removeAllGapsMenuItem.setText("Remove All Gaps");
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386 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 removeAllGapsMenuItem_actionPerformed(e);
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393 viewBoxesMenuItem.setText("Boxes");
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394 viewBoxesMenuItem.setState(true);
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395 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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397 public void actionPerformed(ActionEvent e)
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399 viewBoxesMenuItem_actionPerformed(e);
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402 viewTextMenuItem.setText("Text");
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403 viewTextMenuItem.setState(true);
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404 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 viewTextMenuItem_actionPerformed(e);
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411 sortPairwiseMenuItem.setText("by Pairwise Identity");
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412 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 sortPairwiseMenuItem_actionPerformed(e);
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419 sortIDMenuItem.setText("by ID");
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420 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 sortIDMenuItem_actionPerformed(e);
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427 sortGroupMenuItem.setText("by Group");
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428 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 sortGroupMenuItem_actionPerformed(e);
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435 removeRedundancyMenuItem.setText("Remove Redundancy...");
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436 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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439 public void actionPerformed(ActionEvent e)
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441 removeRedundancyMenuItem_actionPerformed(e);
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444 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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445 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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448 public void actionPerformed(ActionEvent e)
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450 pairwiseAlignmentMenuItem_actionPerformed(e);
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453 PCAMenuItem.setText("Principal Component Analysis");
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454 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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456 public void actionPerformed(ActionEvent e)
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458 PCAMenuItem_actionPerformed(e);
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461 averageDistanceTreeMenuItem.setText(
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462 "Average Distance Using % Identity");
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463 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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466 public void actionPerformed(ActionEvent e)
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468 averageDistanceTreeMenuItem_actionPerformed(e);
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471 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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472 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 neighbourTreeMenuItem_actionPerformed(e);
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479 this.getContentPane().setLayout(borderLayout1);
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480 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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481 statusBar.setBackground(Color.white);
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482 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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483 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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484 statusBar.setText("Status bar");
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485 outputTextboxMenu.setMnemonic('T');
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486 outputTextboxMenu.setText("Output to Textbox");
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487 clustalColour.setText("Clustalx");
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489 clustalColour.addActionListener(new java.awt.event.ActionListener()
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491 public void actionPerformed(ActionEvent e)
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493 clustalColour_actionPerformed(e);
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496 zappoColour.setText("Zappo");
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497 zappoColour.addActionListener(new java.awt.event.ActionListener()
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499 public void actionPerformed(ActionEvent e)
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501 zappoColour_actionPerformed(e);
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504 taylorColour.setText("Taylor");
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505 taylorColour.addActionListener(new java.awt.event.ActionListener()
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507 public void actionPerformed(ActionEvent e)
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509 taylorColour_actionPerformed(e);
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512 hydrophobicityColour.setText("Hydrophobicity");
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513 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 hydrophobicityColour_actionPerformed(e);
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520 helixColour.setText("Helix Propensity");
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521 helixColour.addActionListener(new java.awt.event.ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 helixColour_actionPerformed(e);
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528 strandColour.setText("Strand Propensity");
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529 strandColour.addActionListener(new java.awt.event.ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 strandColour_actionPerformed(e);
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536 turnColour.setText("Turn Propensity");
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537 turnColour.addActionListener(new java.awt.event.ActionListener()
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539 public void actionPerformed(ActionEvent e)
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541 turnColour_actionPerformed(e);
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544 buriedColour.setText("Buried Index");
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545 buriedColour.addActionListener(new java.awt.event.ActionListener()
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547 public void actionPerformed(ActionEvent e)
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549 buriedColour_actionPerformed(e);
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552 userDefinedColour.setText("User Defined...");
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553 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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555 public void actionPerformed(ActionEvent e)
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557 userDefinedColour_actionPerformed(e);
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560 PIDColour.setText("Percentage Identity");
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561 PIDColour.addActionListener(new java.awt.event.ActionListener()
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563 public void actionPerformed(ActionEvent e)
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565 PIDColour_actionPerformed(e);
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568 BLOSUM62Colour.setText("BLOSUM62 Score");
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569 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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571 public void actionPerformed(ActionEvent e)
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573 BLOSUM62Colour_actionPerformed(e);
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576 avDistanceTreeBlosumMenuItem.setText(
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577 "Average Distance Using BLOSUM62");
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578 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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581 public void actionPerformed(ActionEvent e)
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583 avTreeBlosumMenuItem_actionPerformed(e);
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586 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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587 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 njTreeBlosumMenuItem_actionPerformed(e);
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594 annotationPanelMenuItem.setActionCommand("");
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595 annotationPanelMenuItem.setText("Show Annotations");
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596 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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597 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 annotationPanelMenuItem_actionPerformed(e);
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604 colourTextMenuItem.setText("Colour Text");
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605 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 colourTextMenuItem_actionPerformed(e);
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612 htmlMenuItem.setText("HTML");
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613 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 htmlMenuItem_actionPerformed(e);
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620 overviewMenuItem.setText("Overview Window");
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621 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 overviewMenuItem_actionPerformed(e);
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628 undoMenuItem.setEnabled(false);
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629 undoMenuItem.setMnemonic('Z');
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630 undoMenuItem.setText("Undo");
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631 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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632 java.awt.event.KeyEvent.VK_Z,
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633 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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634 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 undoMenuItem_actionPerformed(e);
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641 redoMenuItem.setEnabled(false);
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642 redoMenuItem.setMnemonic('0');
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643 redoMenuItem.setText("Redo");
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644 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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646 public void actionPerformed(ActionEvent e)
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648 redoMenuItem_actionPerformed(e);
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651 conservationMenuItem.setText("By Conservation");
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652 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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654 public void actionPerformed(ActionEvent e)
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656 conservationMenuItem_actionPerformed(e);
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659 noColourmenuItem.setText("None");
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660 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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662 public void actionPerformed(ActionEvent e)
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664 noColourmenuItem_actionPerformed(e);
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667 wrapMenuItem.setText("Wrap");
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668 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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670 public void actionPerformed(ActionEvent e)
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672 wrapMenuItem_actionPerformed(e);
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675 printMenuItem.setText("Print");
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676 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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678 public void actionPerformed(ActionEvent e)
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680 printMenuItem_actionPerformed(e);
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683 renderGapsMenuItem.setText("Show Gaps");
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684 renderGapsMenuItem.setState(true);
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685 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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687 public void actionPerformed(ActionEvent e)
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689 renderGapsMenuItem_actionPerformed(e);
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692 findMenuItem.setText("Find...");
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693 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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694 java.awt.event.KeyEvent.VK_F,
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695 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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696 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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698 public void actionPerformed(ActionEvent e)
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700 findMenuItem_actionPerformed(e);
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703 searchMenu.setText("Search");
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705 abovePIDThreshold.setText("Above Identity Threshold");
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706 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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708 public void actionPerformed(ActionEvent e)
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710 abovePIDThreshold_actionPerformed(e);
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713 showSeqFeatures.setText("Show Sequence Features");
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714 showSeqFeatures.addActionListener(new ActionListener()
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716 public void actionPerformed(ActionEvent actionEvent)
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718 showSeqFeatures_actionPerformed(actionEvent);
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721 nucleotideColour.setText("Nucleotide");
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722 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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724 public void actionPerformed(ActionEvent e)
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726 nucleotideColour_actionPerformed(e);
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729 deleteGroups.setText("Undefine groups");
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730 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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732 public void actionPerformed(ActionEvent e)
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734 deleteGroups_actionPerformed(e);
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737 copy.setText("Copy");
\r
738 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
739 java.awt.event.KeyEvent.VK_C,
\r
740 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
741 copy.setMnemonic(KeyEvent.VK_C);
\r
743 copy.addActionListener(new java.awt.event.ActionListener()
\r
745 public void actionPerformed(ActionEvent e)
\r
747 copy_actionPerformed(e);
\r
750 cut.setText("Cut");
\r
751 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
752 java.awt.event.KeyEvent.VK_X,
\r
753 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
754 cut.setMnemonic(KeyEvent.VK_X);
\r
755 cut.addActionListener(new java.awt.event.ActionListener()
\r
757 public void actionPerformed(ActionEvent e)
\r
759 cut_actionPerformed(e);
\r
762 delete.setText("Delete");
\r
763 delete.addActionListener(new java.awt.event.ActionListener()
\r
765 public void actionPerformed(ActionEvent e)
\r
767 delete_actionPerformed(e);
\r
770 jMenu1.setMnemonic('V');
\r
771 jMenu1.setText("Paste");
\r
772 pasteNew.setText("To New Alignment");
\r
773 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
774 java.awt.event.KeyEvent.VK_V,
\r
775 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
776 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
778 public void actionPerformed(ActionEvent e)
\r
780 pasteNew_actionPerformed(e);
\r
783 pasteThis.setText("Add To This Alignment");
\r
784 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
786 public void actionPerformed(ActionEvent e)
\r
788 pasteThis_actionPerformed(e);
\r
791 applyToAllGroups.setText("Apply Colour To All Groups");
\r
792 applyToAllGroups.setState(true);
\r
793 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
795 public void actionPerformed(ActionEvent e)
\r
797 applyToAllGroups_actionPerformed(e);
\r
800 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
802 public void actionPerformed(ActionEvent e)
\r
807 createPNG.setActionCommand("Save As PNG Image");
\r
808 createPNG.setText("PNG");
\r
809 font.setText("Font...");
\r
810 font.addActionListener(new java.awt.event.ActionListener()
\r
812 public void actionPerformed(ActionEvent e)
\r
814 font_actionPerformed(e);
\r
818 seqLimits.setText("Show Sequence Limits");
\r
819 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
820 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
822 public void actionPerformed(ActionEvent e)
\r
824 seqLimit_actionPerformed(e);
\r
827 epsFile.setText("EPS");
\r
828 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
830 public void actionPerformed(ActionEvent e)
\r
835 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
836 LoadtreeMenuItem.setText("Load Associated Tree");
\r
837 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
839 public void actionPerformed(ActionEvent e)
\r
841 LoadtreeMenuItem_actionPerformed(e);
\r
844 scaleAbove.setVisible(false);
\r
845 scaleAbove.setText("Scale Above");
\r
846 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
848 public void actionPerformed(ActionEvent e)
\r
850 scaleAbove_actionPerformed(e);
\r
853 scaleLeft.setVisible(false);
\r
854 scaleLeft.setSelected(true);
\r
855 scaleLeft.setText("Scale Left");
\r
856 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
858 public void actionPerformed(ActionEvent e)
\r
860 scaleLeft_actionPerformed(e);
\r
863 scaleRight.setVisible(false);
\r
864 scaleRight.setSelected(true);
\r
865 scaleRight.setText("Scale Right");
\r
866 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
868 public void actionPerformed(ActionEvent e)
\r
870 scaleRight_actionPerformed(e);
\r
873 modifyPID.setText("Modify Identity Threshold...");
\r
874 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
876 public void actionPerformed(ActionEvent e)
\r
878 modifyPID_actionPerformed(e);
\r
881 modifyConservation.setText("Modify Conservation Threshold...");
\r
882 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
884 public void actionPerformed(ActionEvent e)
\r
886 modifyConservation_actionPerformed(e);
\r
889 sortByTreeMenu.setText("By Tree Order");
\r
890 sort.setText("Sort");
\r
891 calculate.setText("Calculate Tree");
\r
893 jMenu2.setText("Export");
\r
894 padGapsMenuitem.setText("Pad Gaps");
\r
895 padGapsMenuitem.addActionListener(new ActionListener()
\r
897 public void actionPerformed(ActionEvent e)
\r
899 padGapsMenuitem_actionPerformed(e);
\r
902 vamsasStore.setVisible(false);
\r
903 vamsasStore.setText("VAMSAS store");
\r
904 vamsasStore.addActionListener(new ActionListener()
\r
906 public void actionPerformed(ActionEvent e)
\r
908 vamsasStore_actionPerformed(e);
\r
911 showTranslation.setText("Translate cDNA");
\r
912 showTranslation.addActionListener(new ActionListener()
\r
914 public void actionPerformed(ActionEvent e)
\r
916 showTranslation_actionPerformed(e);
\r
920 /* tabbedPane.addChangeListener(new ChangeListener()
\r
922 public void stateChanged(ChangeEvent ece)
\r
928 featureSettings.setText("Feature Settings...");
\r
929 featureSettings.addActionListener(new ActionListener()
\r
931 public void actionPerformed(ActionEvent e)
\r
933 featureSettings_actionPerformed(e);
\r
936 fetchSequence.setText("Fetch Sequence(s)...");
\r
937 fetchSequence.addActionListener(new ActionListener()
\r
939 public void actionPerformed(ActionEvent e)
\r
941 fetchSequence_actionPerformed(e);
\r
944 smoothFont.setText("Smooth Fonts");
\r
945 smoothFont.addActionListener(new ActionListener()
\r
947 public void actionPerformed(ActionEvent e)
\r
949 smoothFont_actionPerformed(e);
\r
952 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
953 annotationColour.setText("By Annotation...");
\r
954 annotationColour.addActionListener(new ActionListener()
\r
956 public void actionPerformed(ActionEvent e)
\r
958 annotationColour_actionPerformed(e);
\r
961 fetchSeqFeatures.setText("Fetch Sequence Features");
\r
962 fetchSeqFeatures.addActionListener(new ActionListener()
\r
964 public void actionPerformed(ActionEvent e)
\r
966 fetchSeqFeatures_actionPerformed(e);
\r
969 alignFrameMenuBar.add(fileMenu);
\r
970 alignFrameMenuBar.add(editMenu);
\r
971 alignFrameMenuBar.add(searchMenu);
\r
972 alignFrameMenuBar.add(viewMenu);
\r
973 alignFrameMenuBar.add(colourMenu);
\r
974 alignFrameMenuBar.add(calculateMenu);
\r
975 alignFrameMenuBar.add(webService);
\r
976 fileMenu.add(fetchSequence);
\r
977 fileMenu.add(vamsasStore);
\r
978 fileMenu.add(saveAlignmentMenu);
\r
979 fileMenu.add(jMenu2);
\r
980 fileMenu.add(outputTextboxMenu);
\r
981 fileMenu.add(printMenuItem);
\r
982 fileMenu.addSeparator();
\r
983 fileMenu.add(LoadtreeMenuItem);
\r
984 fileMenu.addSeparator();
\r
985 fileMenu.add(closeMenuItem);
\r
986 editMenu.add(undoMenuItem);
\r
987 editMenu.add(redoMenuItem);
\r
989 editMenu.add(copy);
\r
990 editMenu.add(jMenu1);
\r
991 editMenu.add(delete);
\r
992 editMenu.addSeparator();
\r
993 editMenu.add(selectAllSequenceMenuItem);
\r
994 editMenu.add(deselectAllSequenceMenuItem);
\r
995 editMenu.add(invertSequenceMenuItem);
\r
996 editMenu.add(deleteGroups);
\r
997 editMenu.addSeparator();
\r
998 editMenu.add(remove2LeftMenuItem);
\r
999 editMenu.add(remove2RightMenuItem);
\r
1000 editMenu.add(removeGappedColumnMenuItem);
\r
1001 editMenu.add(removeAllGapsMenuItem);
\r
1002 editMenu.add(removeRedundancyMenuItem);
\r
1003 editMenu.addSeparator();
\r
1004 editMenu.add(padGapsMenuitem);
\r
1005 searchMenu.add(findMenuItem);
\r
1006 viewMenu.add(font);
\r
1007 viewMenu.add(smoothFont);
\r
1008 viewMenu.addSeparator();
\r
1009 viewMenu.add(wrapMenuItem);
\r
1010 viewMenu.add(seqLimits);
\r
1011 viewMenu.add(scaleAbove);
\r
1012 viewMenu.add(scaleLeft);
\r
1013 viewMenu.add(scaleRight);
\r
1014 viewMenu.add(viewBoxesMenuItem);
\r
1015 viewMenu.add(viewTextMenuItem);
\r
1016 viewMenu.add(colourTextMenuItem);
\r
1017 viewMenu.add(renderGapsMenuItem);
\r
1018 viewMenu.add(annotationPanelMenuItem);
\r
1019 viewMenu.addSeparator();
\r
1020 viewMenu.add(fetchSeqFeatures);
\r
1021 viewMenu.add(showSeqFeatures);
\r
1022 viewMenu.add(featureSettings);
\r
1023 viewMenu.addSeparator();
\r
1024 viewMenu.add(overviewMenuItem);
\r
1025 colourMenu.add(applyToAllGroups);
\r
1026 colourMenu.addSeparator();
\r
1027 colourMenu.add(noColourmenuItem);
\r
1028 colourMenu.add(clustalColour);
\r
1029 colourMenu.add(BLOSUM62Colour);
\r
1030 colourMenu.add(PIDColour);
\r
1031 colourMenu.add(zappoColour);
\r
1032 colourMenu.add(taylorColour);
\r
1033 colourMenu.add(hydrophobicityColour);
\r
1034 colourMenu.add(helixColour);
\r
1035 colourMenu.add(strandColour);
\r
1036 colourMenu.add(turnColour);
\r
1037 colourMenu.add(buriedColour);
\r
1038 colourMenu.add(nucleotideColour);
\r
1039 colourMenu.add(userDefinedColour);
\r
1040 colourMenu.addSeparator();
\r
1041 colourMenu.add(annotationColour);
\r
1042 colourMenu.add(conservationMenuItem);
\r
1043 colourMenu.add(modifyConservation);
\r
1044 colourMenu.add(abovePIDThreshold);
\r
1045 colourMenu.add(modifyPID);
\r
1046 calculateMenu.add(sort);
\r
1047 calculateMenu.add(calculate);
\r
1048 calculateMenu.addSeparator();
\r
1049 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1050 calculateMenu.add(PCAMenuItem);
\r
1051 calculateMenu.addSeparator();
\r
1052 calculateMenu.add(showTranslation);
\r
1053 webServiceNoServices=new JMenuItem("<No Services>");
\r
1054 webService.add(webServiceNoServices);
\r
1055 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
1056 // this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1057 jMenu1.add(pasteNew);
\r
1058 jMenu1.add(pasteThis);
\r
1059 sort.add(sortIDMenuItem);
\r
1060 sort.add(sortGroupMenuItem);
\r
1061 sort.add(sortPairwiseMenuItem);
\r
1062 calculate.add(averageDistanceTreeMenuItem);
\r
1063 calculate.add(neighbourTreeMenuItem);
\r
1064 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1065 calculate.add(njTreeBlosumMenuItem);
\r
1066 jMenu2.add(htmlMenuItem);
\r
1067 jMenu2.add(epsFile);
\r
1068 jMenu2.add(createPNG);
\r
1071 protected void outputText_actionPerformed(ActionEvent e)
\r
1075 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1079 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1083 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1087 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1091 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1095 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1099 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1103 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1107 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1111 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1115 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1119 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1123 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1127 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1131 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1135 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1139 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1143 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1147 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1151 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1155 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1159 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1163 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1167 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1171 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1175 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1179 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1183 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1187 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1191 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1195 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1199 protected void helixColour_actionPerformed(ActionEvent e)
\r
1203 protected void strandColour_actionPerformed(ActionEvent e)
\r
1207 protected void turnColour_actionPerformed(ActionEvent e)
\r
1211 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1215 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1219 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1223 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1227 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1231 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1235 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1239 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1243 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1247 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1251 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1255 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1259 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1263 protected void copy_actionPerformed(ActionEvent e)
\r
1267 protected void cut_actionPerformed(ActionEvent e)
\r
1271 protected void delete_actionPerformed(ActionEvent e)
\r
1275 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1279 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1283 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1287 public void createPNG(java.io.File f)
\r
1291 protected void font_actionPerformed(ActionEvent e)
\r
1295 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1299 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1305 public void createEPS(java.io.File f)
\r
1309 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1313 protected void jpred_actionPerformed(ActionEvent e)
\r
1317 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1321 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1325 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1329 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1333 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1339 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1343 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1348 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1353 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1358 public void showTranslation_actionPerformed(ActionEvent e)
\r
1363 public void tabSelected()
\r
1368 public void featureSettings_actionPerformed(ActionEvent e)
\r
1373 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1378 public void smoothFont_actionPerformed(ActionEvent e)
\r
1383 public void annotationColour_actionPerformed(ActionEvent e)
\r
1388 public void fetchSeqFeatures_actionPerformed(ActionEvent e)
\r