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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126 JMenuItem associatedData = new JMenuItem();
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127 public GAlignFrame()
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134 setJMenuBar(alignFrameMenuBar);
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136 // dynamically fill save as menu with available formats
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137 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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139 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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142 item.addActionListener(new java.awt.event.ActionListener()
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144 public void actionPerformed(ActionEvent e)
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146 outputText_actionPerformed(e);
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150 outputTextboxMenu.add(item);
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153 catch (Exception e)
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158 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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160 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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161 getUserColourSchemes().keys();
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163 while (userColours.hasMoreElements())
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165 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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166 nextElement().toString());
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167 radioItem.setName("USER_DEFINED");
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168 radioItem.addMouseListener(new MouseAdapter()
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170 public void mousePressed(MouseEvent evt)
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172 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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174 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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176 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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177 "Remove from default list?",
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178 "Remove user defined colour",
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179 JOptionPane.YES_NO_OPTION);
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180 if(option == JOptionPane.YES_OPTION)
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182 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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183 colourMenu.remove(radioItem);
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186 radioItem.addActionListener(new ActionListener()
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188 public void actionPerformed(ActionEvent evt)
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190 userDefinedColour_actionPerformed(evt);
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196 radioItem.addActionListener(new ActionListener()
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198 public void actionPerformed(ActionEvent evt)
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200 userDefinedColour_actionPerformed(evt);
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203 colourMenu.insert(radioItem, 15);
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204 colours.add(radioItem);
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207 colours.add(noColourmenuItem);
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208 colours.add(clustalColour);
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209 colours.add(zappoColour);
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210 colours.add(taylorColour);
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211 colours.add(hydrophobicityColour);
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212 colours.add(helixColour);
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213 colours.add(strandColour);
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214 colours.add(turnColour);
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215 colours.add(buriedColour);
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216 colours.add(userDefinedColour);
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217 colours.add(PIDColour);
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218 colours.add(BLOSUM62Colour);
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219 colours.add(nucleotideColour);
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221 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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226 public void setColourSelected(String defaultColour)
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229 if (defaultColour != null)
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231 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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235 case ColourSchemeProperty.NONE:
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236 noColourmenuItem.setSelected(true);
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238 case ColourSchemeProperty.CLUSTAL:
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239 clustalColour.setSelected(true);
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243 case ColourSchemeProperty.BLOSUM:
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244 BLOSUM62Colour.setSelected(true);
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248 case ColourSchemeProperty.PID:
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249 PIDColour.setSelected(true);
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253 case ColourSchemeProperty.ZAPPO:
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254 zappoColour.setSelected(true);
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258 case ColourSchemeProperty.TAYLOR:
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259 taylorColour.setSelected(true);
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262 case ColourSchemeProperty.HYDROPHOBIC:
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263 hydrophobicityColour.setSelected(true);
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267 case ColourSchemeProperty.HELIX:
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268 helixColour.setSelected(true);
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272 case ColourSchemeProperty.STRAND:
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273 strandColour.setSelected(true);
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277 case ColourSchemeProperty.TURN:
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278 turnColour.setSelected(true);
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282 case ColourSchemeProperty.BURIED:
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283 buriedColour.setSelected(true);
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287 case ColourSchemeProperty.NUCLEOTIDE:
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288 nucleotideColour.setSelected(true);
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292 case ColourSchemeProperty.USER_DEFINED:
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293 userDefinedColour.setSelected(true);
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301 private void jbInit()
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304 fileMenu.setMnemonic('F');
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305 fileMenu.setText("File");
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306 saveAlignmentMenu.setMnemonic('L');
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307 saveAlignmentMenu.setText("Save As");
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308 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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309 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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310 saveAlignmentMenu.addActionListener(new ActionListener()
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312 public void actionPerformed(ActionEvent e)
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314 saveAlignmentMenu_actionPerformed(e);
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317 closeMenuItem.setMnemonic('C');
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318 closeMenuItem.setText("Close");
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319 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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321 public void actionPerformed(ActionEvent e)
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323 closeMenuItem_actionPerformed(e);
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326 editMenu.setText("Edit");
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327 viewMenu.setText("View");
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328 colourMenu.setText("Colour");
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329 calculateMenu.setText("Calculate");
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330 webService.setText("Web Service");
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331 selectAllSequenceMenuItem.setText("Select all");
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332 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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333 java.awt.event.KeyEvent.VK_A,
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334 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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335 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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338 public void actionPerformed(ActionEvent e)
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340 selectAllSequenceMenuItem_actionPerformed(e);
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343 deselectAllSequenceMenuItem.setText("Deselect All");
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344 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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346 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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347 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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350 public void actionPerformed(ActionEvent e)
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352 deselectAllSequenceMenuItem_actionPerformed(e);
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355 invertSequenceMenuItem.setText("Invert Selection");
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356 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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358 public void actionPerformed(ActionEvent e)
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360 invertSequenceMenuItem_actionPerformed(e);
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363 remove2LeftMenuItem.setText("Remove Left");
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364 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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366 public void actionPerformed(ActionEvent e)
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368 remove2LeftMenuItem_actionPerformed(e);
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371 remove2RightMenuItem.setText("Remove Right");
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372 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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374 public void actionPerformed(ActionEvent e)
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376 remove2RightMenuItem_actionPerformed(e);
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379 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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380 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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383 public void actionPerformed(ActionEvent e)
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385 removeGappedColumnMenuItem_actionPerformed(e);
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388 removeAllGapsMenuItem.setText("Remove All Gaps");
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389 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 removeAllGapsMenuItem_actionPerformed(e);
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396 viewBoxesMenuItem.setText("Boxes");
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397 viewBoxesMenuItem.setState(true);
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398 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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400 public void actionPerformed(ActionEvent e)
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402 viewBoxesMenuItem_actionPerformed(e);
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405 viewTextMenuItem.setText("Text");
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406 viewTextMenuItem.setState(true);
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407 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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409 public void actionPerformed(ActionEvent e)
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411 viewTextMenuItem_actionPerformed(e);
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414 sortPairwiseMenuItem.setText("by Pairwise Identity");
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415 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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417 public void actionPerformed(ActionEvent e)
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419 sortPairwiseMenuItem_actionPerformed(e);
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422 sortIDMenuItem.setText("by ID");
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423 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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425 public void actionPerformed(ActionEvent e)
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427 sortIDMenuItem_actionPerformed(e);
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430 sortGroupMenuItem.setText("by Group");
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431 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 sortGroupMenuItem_actionPerformed(e);
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438 removeRedundancyMenuItem.setText("Remove Redundancy...");
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439 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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442 public void actionPerformed(ActionEvent e)
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444 removeRedundancyMenuItem_actionPerformed(e);
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447 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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448 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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451 public void actionPerformed(ActionEvent e)
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453 pairwiseAlignmentMenuItem_actionPerformed(e);
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456 PCAMenuItem.setText("Principal Component Analysis");
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457 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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459 public void actionPerformed(ActionEvent e)
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461 PCAMenuItem_actionPerformed(e);
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464 averageDistanceTreeMenuItem.setText(
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465 "Average Distance Using % Identity");
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466 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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469 public void actionPerformed(ActionEvent e)
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471 averageDistanceTreeMenuItem_actionPerformed(e);
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474 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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475 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 neighbourTreeMenuItem_actionPerformed(e);
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482 this.getContentPane().setLayout(borderLayout1);
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483 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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484 statusBar.setBackground(Color.white);
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485 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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486 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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487 statusBar.setText("Status bar");
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488 outputTextboxMenu.setMnemonic('T');
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489 outputTextboxMenu.setText("Output to Textbox");
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490 clustalColour.setText("Clustalx");
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492 clustalColour.addActionListener(new java.awt.event.ActionListener()
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494 public void actionPerformed(ActionEvent e)
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496 clustalColour_actionPerformed(e);
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499 zappoColour.setText("Zappo");
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500 zappoColour.addActionListener(new java.awt.event.ActionListener()
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502 public void actionPerformed(ActionEvent e)
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504 zappoColour_actionPerformed(e);
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507 taylorColour.setText("Taylor");
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508 taylorColour.addActionListener(new java.awt.event.ActionListener()
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510 public void actionPerformed(ActionEvent e)
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512 taylorColour_actionPerformed(e);
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515 hydrophobicityColour.setText("Hydrophobicity");
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516 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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518 public void actionPerformed(ActionEvent e)
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520 hydrophobicityColour_actionPerformed(e);
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523 helixColour.setText("Helix Propensity");
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524 helixColour.addActionListener(new java.awt.event.ActionListener()
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526 public void actionPerformed(ActionEvent e)
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528 helixColour_actionPerformed(e);
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531 strandColour.setText("Strand Propensity");
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532 strandColour.addActionListener(new java.awt.event.ActionListener()
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534 public void actionPerformed(ActionEvent e)
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536 strandColour_actionPerformed(e);
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539 turnColour.setText("Turn Propensity");
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540 turnColour.addActionListener(new java.awt.event.ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 turnColour_actionPerformed(e);
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547 buriedColour.setText("Buried Index");
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548 buriedColour.addActionListener(new java.awt.event.ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 buriedColour_actionPerformed(e);
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555 userDefinedColour.setText("User Defined...");
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556 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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558 public void actionPerformed(ActionEvent e)
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560 userDefinedColour_actionPerformed(e);
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563 PIDColour.setText("Percentage Identity");
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564 PIDColour.addActionListener(new java.awt.event.ActionListener()
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566 public void actionPerformed(ActionEvent e)
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568 PIDColour_actionPerformed(e);
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571 BLOSUM62Colour.setText("BLOSUM62 Score");
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572 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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574 public void actionPerformed(ActionEvent e)
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576 BLOSUM62Colour_actionPerformed(e);
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579 avDistanceTreeBlosumMenuItem.setText(
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580 "Average Distance Using BLOSUM62");
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581 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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584 public void actionPerformed(ActionEvent e)
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586 avTreeBlosumMenuItem_actionPerformed(e);
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589 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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590 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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592 public void actionPerformed(ActionEvent e)
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594 njTreeBlosumMenuItem_actionPerformed(e);
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597 annotationPanelMenuItem.setActionCommand("");
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598 annotationPanelMenuItem.setText("Show Annotations");
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599 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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600 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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602 public void actionPerformed(ActionEvent e)
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604 annotationPanelMenuItem_actionPerformed(e);
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607 colourTextMenuItem.setText("Colour Text");
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608 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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610 public void actionPerformed(ActionEvent e)
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612 colourTextMenuItem_actionPerformed(e);
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615 htmlMenuItem.setText("HTML");
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616 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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618 public void actionPerformed(ActionEvent e)
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620 htmlMenuItem_actionPerformed(e);
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623 overviewMenuItem.setText("Overview Window");
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624 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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626 public void actionPerformed(ActionEvent e)
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628 overviewMenuItem_actionPerformed(e);
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631 undoMenuItem.setEnabled(false);
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632 undoMenuItem.setMnemonic('Z');
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633 undoMenuItem.setText("Undo");
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634 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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635 java.awt.event.KeyEvent.VK_Z,
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636 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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637 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 undoMenuItem_actionPerformed(e);
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644 redoMenuItem.setEnabled(false);
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645 redoMenuItem.setMnemonic('0');
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646 redoMenuItem.setText("Redo");
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647 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 redoMenuItem_actionPerformed(e);
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654 conservationMenuItem.setText("By Conservation");
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655 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 conservationMenuItem_actionPerformed(e);
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662 noColourmenuItem.setText("None");
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663 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 noColourmenuItem_actionPerformed(e);
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670 wrapMenuItem.setText("Wrap");
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671 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 wrapMenuItem_actionPerformed(e);
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678 printMenuItem.setText("Print");
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679 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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681 public void actionPerformed(ActionEvent e)
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683 printMenuItem_actionPerformed(e);
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686 renderGapsMenuItem.setText("Show Gaps");
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687 renderGapsMenuItem.setState(true);
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688 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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690 public void actionPerformed(ActionEvent e)
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692 renderGapsMenuItem_actionPerformed(e);
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695 findMenuItem.setText("Find...");
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696 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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697 java.awt.event.KeyEvent.VK_F,
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698 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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699 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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701 public void actionPerformed(ActionEvent e)
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703 findMenuItem_actionPerformed(e);
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706 searchMenu.setText("Search");
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708 abovePIDThreshold.setText("Above Identity Threshold");
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709 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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711 public void actionPerformed(ActionEvent e)
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713 abovePIDThreshold_actionPerformed(e);
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716 showSeqFeatures.setText("Show Sequence Features");
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717 showSeqFeatures.addActionListener(new ActionListener()
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719 public void actionPerformed(ActionEvent actionEvent)
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721 showSeqFeatures_actionPerformed(actionEvent);
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724 nucleotideColour.setText("Nucleotide");
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725 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
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727 public void actionPerformed(ActionEvent e)
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729 nucleotideColour_actionPerformed(e);
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732 deleteGroups.setText("Undefine groups");
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733 deleteGroups.addActionListener(new java.awt.event.ActionListener()
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735 public void actionPerformed(ActionEvent e)
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737 deleteGroups_actionPerformed(e);
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740 copy.setText("Copy");
\r
741 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
742 java.awt.event.KeyEvent.VK_C,
\r
743 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
744 copy.setMnemonic(KeyEvent.VK_C);
\r
746 copy.addActionListener(new java.awt.event.ActionListener()
\r
748 public void actionPerformed(ActionEvent e)
\r
750 copy_actionPerformed(e);
\r
753 cut.setText("Cut");
\r
754 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
755 java.awt.event.KeyEvent.VK_X,
\r
756 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
757 cut.setMnemonic(KeyEvent.VK_X);
\r
758 cut.addActionListener(new java.awt.event.ActionListener()
\r
760 public void actionPerformed(ActionEvent e)
\r
762 cut_actionPerformed(e);
\r
765 delete.setText("Delete");
\r
766 delete.addActionListener(new java.awt.event.ActionListener()
\r
768 public void actionPerformed(ActionEvent e)
\r
770 delete_actionPerformed(e);
\r
773 jMenu1.setMnemonic('V');
\r
774 jMenu1.setText("Paste");
\r
775 pasteNew.setText("To New Alignment");
\r
776 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
777 java.awt.event.KeyEvent.VK_V,
\r
778 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
779 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
781 public void actionPerformed(ActionEvent e)
\r
783 pasteNew_actionPerformed(e);
\r
786 pasteThis.setText("Add To This Alignment");
\r
787 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
789 public void actionPerformed(ActionEvent e)
\r
791 pasteThis_actionPerformed(e);
\r
794 applyToAllGroups.setText("Apply Colour To All Groups");
\r
795 applyToAllGroups.setState(true);
\r
796 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
798 public void actionPerformed(ActionEvent e)
\r
800 applyToAllGroups_actionPerformed(e);
\r
803 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
805 public void actionPerformed(ActionEvent e)
\r
810 createPNG.setActionCommand("Save As PNG Image");
\r
811 createPNG.setText("PNG");
\r
812 font.setText("Font...");
\r
813 font.addActionListener(new java.awt.event.ActionListener()
\r
815 public void actionPerformed(ActionEvent e)
\r
817 font_actionPerformed(e);
\r
821 seqLimits.setText("Show Sequence Limits");
\r
822 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
823 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
825 public void actionPerformed(ActionEvent e)
\r
827 seqLimit_actionPerformed(e);
\r
830 epsFile.setText("EPS");
\r
831 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
833 public void actionPerformed(ActionEvent e)
\r
838 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
839 LoadtreeMenuItem.setText("Load Associated Tree");
\r
840 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
842 public void actionPerformed(ActionEvent e)
\r
844 LoadtreeMenuItem_actionPerformed(e);
\r
847 scaleAbove.setVisible(false);
\r
848 scaleAbove.setText("Scale Above");
\r
849 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
851 public void actionPerformed(ActionEvent e)
\r
853 scaleAbove_actionPerformed(e);
\r
856 scaleLeft.setVisible(false);
\r
857 scaleLeft.setSelected(true);
\r
858 scaleLeft.setText("Scale Left");
\r
859 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
861 public void actionPerformed(ActionEvent e)
\r
863 scaleLeft_actionPerformed(e);
\r
866 scaleRight.setVisible(false);
\r
867 scaleRight.setSelected(true);
\r
868 scaleRight.setText("Scale Right");
\r
869 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
871 public void actionPerformed(ActionEvent e)
\r
873 scaleRight_actionPerformed(e);
\r
876 modifyPID.setText("Modify Identity Threshold...");
\r
877 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
879 public void actionPerformed(ActionEvent e)
\r
881 modifyPID_actionPerformed(e);
\r
884 modifyConservation.setText("Modify Conservation Threshold...");
\r
885 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
887 public void actionPerformed(ActionEvent e)
\r
889 modifyConservation_actionPerformed(e);
\r
892 sortByTreeMenu.setText("By Tree Order");
\r
893 sort.setText("Sort");
\r
894 calculate.setText("Calculate Tree");
\r
896 jMenu2.setText("Export");
\r
897 padGapsMenuitem.setText("Pad Gaps");
\r
898 padGapsMenuitem.addActionListener(new ActionListener()
\r
900 public void actionPerformed(ActionEvent e)
\r
902 padGapsMenuitem_actionPerformed(e);
\r
905 vamsasStore.setVisible(false);
\r
906 vamsasStore.setText("VAMSAS store");
\r
907 vamsasStore.addActionListener(new ActionListener()
\r
909 public void actionPerformed(ActionEvent e)
\r
911 vamsasStore_actionPerformed(e);
\r
914 showTranslation.setText("Translate cDNA");
\r
915 showTranslation.addActionListener(new ActionListener()
\r
917 public void actionPerformed(ActionEvent e)
\r
919 showTranslation_actionPerformed(e);
\r
923 /* tabbedPane.addChangeListener(new ChangeListener()
\r
925 public void stateChanged(ChangeEvent ece)
\r
931 featureSettings.setText("Feature Settings...");
\r
932 featureSettings.addActionListener(new ActionListener()
\r
934 public void actionPerformed(ActionEvent e)
\r
936 featureSettings_actionPerformed(e);
\r
939 fetchSequence.setText("Fetch Sequence(s)...");
\r
940 fetchSequence.addActionListener(new ActionListener()
\r
942 public void actionPerformed(ActionEvent e)
\r
944 fetchSequence_actionPerformed(e);
\r
947 smoothFont.setText("Smooth Fonts");
\r
948 smoothFont.addActionListener(new ActionListener()
\r
950 public void actionPerformed(ActionEvent e)
\r
952 smoothFont_actionPerformed(e);
\r
955 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
956 annotationColour.setText("By Annotation...");
\r
957 annotationColour.addActionListener(new ActionListener()
\r
959 public void actionPerformed(ActionEvent e)
\r
961 annotationColour_actionPerformed(e);
\r
964 fetchSeqFeatures.setText("Fetch Sequence Features");
\r
965 fetchSeqFeatures.addActionListener(new ActionListener()
\r
967 public void actionPerformed(ActionEvent e)
\r
969 fetchSeqFeatures_actionPerformed(e);
\r
972 associatedData.setText("Load Features / Annotations");
\r
973 associatedData.addActionListener(new ActionListener()
\r
975 public void actionPerformed(ActionEvent e)
\r
977 associatedData_actionPerformed(e);
\r
980 alignFrameMenuBar.add(fileMenu);
\r
981 alignFrameMenuBar.add(editMenu);
\r
982 alignFrameMenuBar.add(searchMenu);
\r
983 alignFrameMenuBar.add(viewMenu);
\r
984 alignFrameMenuBar.add(colourMenu);
\r
985 alignFrameMenuBar.add(calculateMenu);
\r
986 alignFrameMenuBar.add(webService);
\r
987 fileMenu.add(fetchSequence);
\r
988 fileMenu.addSeparator();
\r
989 fileMenu.add(vamsasStore);
\r
990 fileMenu.add(saveAlignmentMenu);
\r
991 fileMenu.add(jMenu2);
\r
992 fileMenu.add(outputTextboxMenu);
\r
993 fileMenu.add(printMenuItem);
\r
994 fileMenu.addSeparator();
\r
995 fileMenu.add(LoadtreeMenuItem);
\r
996 fileMenu.add(associatedData);
\r
997 fileMenu.addSeparator();
\r
998 fileMenu.add(closeMenuItem);
\r
999 editMenu.add(undoMenuItem);
\r
1000 editMenu.add(redoMenuItem);
\r
1001 editMenu.add(cut);
\r
1002 editMenu.add(copy);
\r
1003 editMenu.add(jMenu1);
\r
1004 editMenu.add(delete);
\r
1005 editMenu.addSeparator();
\r
1006 editMenu.add(selectAllSequenceMenuItem);
\r
1007 editMenu.add(deselectAllSequenceMenuItem);
\r
1008 editMenu.add(invertSequenceMenuItem);
\r
1009 editMenu.add(deleteGroups);
\r
1010 editMenu.addSeparator();
\r
1011 editMenu.add(remove2LeftMenuItem);
\r
1012 editMenu.add(remove2RightMenuItem);
\r
1013 editMenu.add(removeGappedColumnMenuItem);
\r
1014 editMenu.add(removeAllGapsMenuItem);
\r
1015 editMenu.add(removeRedundancyMenuItem);
\r
1016 editMenu.addSeparator();
\r
1017 editMenu.add(padGapsMenuitem);
\r
1018 searchMenu.add(findMenuItem);
\r
1019 viewMenu.add(font);
\r
1020 viewMenu.add(smoothFont);
\r
1021 viewMenu.addSeparator();
\r
1022 viewMenu.add(wrapMenuItem);
\r
1023 viewMenu.add(seqLimits);
\r
1024 viewMenu.add(scaleAbove);
\r
1025 viewMenu.add(scaleLeft);
\r
1026 viewMenu.add(scaleRight);
\r
1027 viewMenu.add(viewBoxesMenuItem);
\r
1028 viewMenu.add(viewTextMenuItem);
\r
1029 viewMenu.add(colourTextMenuItem);
\r
1030 viewMenu.add(renderGapsMenuItem);
\r
1031 viewMenu.add(annotationPanelMenuItem);
\r
1032 viewMenu.addSeparator();
\r
1033 viewMenu.add(fetchSeqFeatures);
\r
1034 viewMenu.add(showSeqFeatures);
\r
1035 viewMenu.add(featureSettings);
\r
1036 viewMenu.addSeparator();
\r
1037 viewMenu.add(overviewMenuItem);
\r
1038 colourMenu.add(applyToAllGroups);
\r
1039 colourMenu.addSeparator();
\r
1040 colourMenu.add(noColourmenuItem);
\r
1041 colourMenu.add(clustalColour);
\r
1042 colourMenu.add(BLOSUM62Colour);
\r
1043 colourMenu.add(PIDColour);
\r
1044 colourMenu.add(zappoColour);
\r
1045 colourMenu.add(taylorColour);
\r
1046 colourMenu.add(hydrophobicityColour);
\r
1047 colourMenu.add(helixColour);
\r
1048 colourMenu.add(strandColour);
\r
1049 colourMenu.add(turnColour);
\r
1050 colourMenu.add(buriedColour);
\r
1051 colourMenu.add(nucleotideColour);
\r
1052 colourMenu.add(userDefinedColour);
\r
1053 colourMenu.addSeparator();
\r
1054 colourMenu.add(annotationColour);
\r
1055 colourMenu.add(conservationMenuItem);
\r
1056 colourMenu.add(modifyConservation);
\r
1057 colourMenu.add(abovePIDThreshold);
\r
1058 colourMenu.add(modifyPID);
\r
1059 calculateMenu.add(sort);
\r
1060 calculateMenu.add(calculate);
\r
1061 calculateMenu.addSeparator();
\r
1062 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1063 calculateMenu.add(PCAMenuItem);
\r
1064 calculateMenu.addSeparator();
\r
1065 calculateMenu.add(showTranslation);
\r
1066 webServiceNoServices=new JMenuItem("<No Services>");
\r
1067 webService.add(webServiceNoServices);
\r
1068 this.getContentPane().add(statusBar, BorderLayout.SOUTH);
\r
1069 // this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
\r
1070 jMenu1.add(pasteNew);
\r
1071 jMenu1.add(pasteThis);
\r
1072 sort.add(sortIDMenuItem);
\r
1073 sort.add(sortGroupMenuItem);
\r
1074 sort.add(sortPairwiseMenuItem);
\r
1075 calculate.add(averageDistanceTreeMenuItem);
\r
1076 calculate.add(neighbourTreeMenuItem);
\r
1077 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1078 calculate.add(njTreeBlosumMenuItem);
\r
1079 jMenu2.add(htmlMenuItem);
\r
1080 jMenu2.add(epsFile);
\r
1081 jMenu2.add(createPNG);
\r
1084 protected void outputText_actionPerformed(ActionEvent e)
\r
1088 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1092 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1096 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1100 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1104 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1108 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1112 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1116 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1120 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1124 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1128 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1132 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1136 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1140 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1144 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1148 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1152 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1156 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1160 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1164 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1168 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1172 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1176 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1180 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1184 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1188 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1192 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1196 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1200 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1204 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1208 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1212 protected void helixColour_actionPerformed(ActionEvent e)
\r
1216 protected void strandColour_actionPerformed(ActionEvent e)
\r
1220 protected void turnColour_actionPerformed(ActionEvent e)
\r
1224 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1228 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1232 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1236 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1240 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1244 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1248 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1252 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1256 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1260 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1264 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1268 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1272 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1276 protected void copy_actionPerformed(ActionEvent e)
\r
1280 protected void cut_actionPerformed(ActionEvent e)
\r
1284 protected void delete_actionPerformed(ActionEvent e)
\r
1288 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1292 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1296 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1300 public void createPNG(java.io.File f)
\r
1304 protected void font_actionPerformed(ActionEvent e)
\r
1308 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1312 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1318 public void createEPS(java.io.File f)
\r
1322 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1326 protected void jpred_actionPerformed(ActionEvent e)
\r
1330 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1334 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1338 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1342 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1346 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1352 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1356 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1361 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1366 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1371 public void showTranslation_actionPerformed(ActionEvent e)
\r
1376 public void tabSelected()
\r
1381 public void featureSettings_actionPerformed(ActionEvent e)
\r
1386 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1391 public void smoothFont_actionPerformed(ActionEvent e)
\r
1396 public void annotationColour_actionPerformed(ActionEvent e)
\r
1401 public void fetchSeqFeatures_actionPerformed(ActionEvent e)
\r
1406 public void associatedData_actionPerformed(ActionEvent e)
\r