2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbgui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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25 import jalview.schemes.*;
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26 import java.awt.BorderLayout;
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28 public class GAlignFrame
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29 extends JInternalFrame
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31 protected JMenuBar alignFrameMenuBar = new JMenuBar();
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32 protected JMenu fileMenu = new JMenu();
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33 protected JMenuItem closeMenuItem = new JMenuItem();
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34 protected JMenu editMenu = new JMenu();
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35 protected JMenu viewMenu = new JMenu();
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36 protected JMenu colourMenu = new JMenu();
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37 protected JMenu calculateMenu = new JMenu();
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38 protected JMenu webService = new JMenu();
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39 protected JMenuItem webServiceNoServices;
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40 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
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41 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
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42 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
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43 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
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44 protected JMenuItem remove2RightMenuItem = new JMenuItem();
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45 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
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46 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
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47 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
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48 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
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49 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
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50 protected JMenuItem sortIDMenuItem = new JMenuItem();
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51 protected JMenuItem sortGroupMenuItem = new JMenuItem();
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52 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
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53 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
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54 protected JMenuItem PCAMenuItem = new JMenuItem();
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55 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
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56 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
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57 protected JMenuItem clustalAlignMenuItem = new JMenuItem();
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58 BorderLayout borderLayout1 = new BorderLayout();
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59 public JLabel statusBar = new JLabel();
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60 protected JMenuItem saveAlignmentMenu = new JMenuItem();
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61 protected JMenu outputTextboxMenu = new JMenu();
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62 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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63 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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64 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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65 protected JRadioButtonMenuItem hydrophobicityColour = new
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66 JRadioButtonMenuItem();
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67 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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68 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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69 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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70 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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71 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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72 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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73 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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74 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
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75 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
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76 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
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77 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
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78 JMenuItem htmlMenuItem = new JMenuItem();
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79 JMenuItem overviewMenuItem = new JMenuItem();
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80 protected JMenuItem undoMenuItem = new JMenuItem();
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81 protected JMenuItem redoMenuItem = new JMenuItem();
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82 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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83 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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84 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
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85 JMenuItem printMenuItem = new JMenuItem();
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86 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
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87 JMenuItem findMenuItem = new JMenuItem();
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88 JMenu searchMenu = new JMenu();
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89 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
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90 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
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91 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
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92 JMenuItem deleteGroups = new JMenuItem();
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93 JMenuItem delete = new JMenuItem();
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94 JMenuItem copy = new JMenuItem();
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95 JMenuItem cut = new JMenuItem();
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96 JMenu jMenu1 = new JMenu();
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97 JMenuItem pasteNew = new JMenuItem();
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98 JMenuItem pasteThis = new JMenuItem();
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99 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
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100 JMenuItem createPNG = new JMenuItem();
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101 protected JMenuItem font = new JMenuItem();
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102 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
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103 JMenuItem epsFile = new JMenuItem();
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104 JMenuItem LoadtreeMenuItem = new JMenuItem();
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105 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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106 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
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107 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
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108 protected JMenuItem modifyPID = new JMenuItem();
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109 protected JMenuItem modifyConservation = new JMenuItem();
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110 protected JMenu sortByTreeMenu = new JMenu();
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111 protected JMenu sort = new JMenu();
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112 JMenu calculate = new JMenu();
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113 JMenu jMenu2 = new JMenu();
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114 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
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115 protected ButtonGroup colours = new ButtonGroup();
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116 JMenuItem vamsasStore = new JMenuItem();
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117 protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
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118 public JMenuItem featureSettings = new JMenuItem();
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119 JMenuItem fetchSequence = new JMenuItem();
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120 protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
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121 JMenuItem annotationColour = new JMenuItem();
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122 JMenuItem fetchSeqFeatures = new JMenuItem();
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126 JMenuItem associatedData = new JMenuItem();
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127 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
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128 JMenu addSequenceMenu = new JMenu();
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129 JMenuItem addFromFile = new JMenuItem();
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130 JMenuItem addFromText = new JMenuItem();
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131 JMenuItem addFromURL = new JMenuItem();
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132 JMenuItem exportAnnotations = new JMenuItem();
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133 JMenuItem exportFeatures = new JMenuItem();
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134 JMenuItem dbRefs = new JMenuItem();
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135 protected JPanel statusPanel = new JPanel();
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136 GridLayout gridLayout1 = new GridLayout();
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137 public GAlignFrame()
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144 setJMenuBar(alignFrameMenuBar);
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146 // dynamically fill save as menu with available formats
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147 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
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149 JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
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152 item.addActionListener(new java.awt.event.ActionListener()
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154 public void actionPerformed(ActionEvent e)
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156 outputText_actionPerformed(e);
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160 outputTextboxMenu.add(item);
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163 catch (Exception e)
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168 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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170 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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171 getUserColourSchemes().keys();
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173 while (userColours.hasMoreElements())
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175 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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176 nextElement().toString());
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177 radioItem.setName("USER_DEFINED");
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178 radioItem.addMouseListener(new MouseAdapter()
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180 public void mousePressed(MouseEvent evt)
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182 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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184 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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186 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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187 "Remove from default list?",
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188 "Remove user defined colour",
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189 JOptionPane.YES_NO_OPTION);
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190 if(option == JOptionPane.YES_OPTION)
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192 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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193 colourMenu.remove(radioItem);
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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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206 radioItem.addActionListener(new ActionListener()
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208 public void actionPerformed(ActionEvent evt)
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210 userDefinedColour_actionPerformed(evt);
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213 colourMenu.insert(radioItem, 15);
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214 colours.add(radioItem);
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217 colours.add(noColourmenuItem);
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218 colours.add(clustalColour);
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219 colours.add(zappoColour);
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220 colours.add(taylorColour);
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221 colours.add(hydrophobicityColour);
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222 colours.add(helixColour);
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223 colours.add(strandColour);
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224 colours.add(turnColour);
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225 colours.add(buriedColour);
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226 colours.add(userDefinedColour);
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227 colours.add(PIDColour);
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228 colours.add(BLOSUM62Colour);
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229 colours.add(nucleotideColour);
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231 setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
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236 public void setColourSelected(String defaultColour)
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239 if (defaultColour != null)
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241 int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
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245 case ColourSchemeProperty.NONE:
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246 noColourmenuItem.setSelected(true);
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248 case ColourSchemeProperty.CLUSTAL:
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249 clustalColour.setSelected(true);
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253 case ColourSchemeProperty.BLOSUM:
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254 BLOSUM62Colour.setSelected(true);
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258 case ColourSchemeProperty.PID:
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259 PIDColour.setSelected(true);
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263 case ColourSchemeProperty.ZAPPO:
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264 zappoColour.setSelected(true);
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268 case ColourSchemeProperty.TAYLOR:
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269 taylorColour.setSelected(true);
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272 case ColourSchemeProperty.HYDROPHOBIC:
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273 hydrophobicityColour.setSelected(true);
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277 case ColourSchemeProperty.HELIX:
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278 helixColour.setSelected(true);
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282 case ColourSchemeProperty.STRAND:
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283 strandColour.setSelected(true);
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287 case ColourSchemeProperty.TURN:
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288 turnColour.setSelected(true);
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292 case ColourSchemeProperty.BURIED:
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293 buriedColour.setSelected(true);
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297 case ColourSchemeProperty.NUCLEOTIDE:
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298 nucleotideColour.setSelected(true);
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302 case ColourSchemeProperty.USER_DEFINED:
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303 userDefinedColour.setSelected(true);
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311 private void jbInit()
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314 fileMenu.setMnemonic('F');
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315 fileMenu.setText("File");
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316 saveAlignmentMenu.setMnemonic('L');
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317 saveAlignmentMenu.setText("Save As");
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318 saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
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319 awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
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320 saveAlignmentMenu.addActionListener(new ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 saveAlignmentMenu_actionPerformed(e);
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327 closeMenuItem.setMnemonic('C');
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328 closeMenuItem.setText("Close");
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329 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
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331 public void actionPerformed(ActionEvent e)
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333 closeMenuItem_actionPerformed(e);
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336 editMenu.setText("Edit");
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337 viewMenu.setText("View");
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338 colourMenu.setText("Colour");
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339 calculateMenu.setText("Calculate");
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340 webService.setText("Web Service");
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341 selectAllSequenceMenuItem.setText("Select all");
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342 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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343 java.awt.event.KeyEvent.VK_A,
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344 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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345 selectAllSequenceMenuItem.addActionListener(new java.awt.event.
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348 public void actionPerformed(ActionEvent e)
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350 selectAllSequenceMenuItem_actionPerformed(e);
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353 deselectAllSequenceMenuItem.setText("Deselect All");
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354 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
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356 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
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357 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
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360 public void actionPerformed(ActionEvent e)
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362 deselectAllSequenceMenuItem_actionPerformed(e);
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365 invertSequenceMenuItem.setText("Invert Selection");
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366 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
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368 public void actionPerformed(ActionEvent e)
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370 invertSequenceMenuItem_actionPerformed(e);
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373 remove2LeftMenuItem.setText("Remove Left");
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374 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
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376 public void actionPerformed(ActionEvent e)
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378 remove2LeftMenuItem_actionPerformed(e);
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381 remove2RightMenuItem.setText("Remove Right");
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382 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
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384 public void actionPerformed(ActionEvent e)
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386 remove2RightMenuItem_actionPerformed(e);
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389 removeGappedColumnMenuItem.setText("Remove Empty Columns");
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390 removeGappedColumnMenuItem.addActionListener(new java.awt.event.
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393 public void actionPerformed(ActionEvent e)
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395 removeGappedColumnMenuItem_actionPerformed(e);
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398 removeAllGapsMenuItem.setText("Remove All Gaps");
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399 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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401 public void actionPerformed(ActionEvent e)
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403 removeAllGapsMenuItem_actionPerformed(e);
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406 viewBoxesMenuItem.setText("Boxes");
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407 viewBoxesMenuItem.setState(true);
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408 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 viewBoxesMenuItem_actionPerformed(e);
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415 viewTextMenuItem.setText("Text");
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416 viewTextMenuItem.setState(true);
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417 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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419 public void actionPerformed(ActionEvent e)
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421 viewTextMenuItem_actionPerformed(e);
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424 sortPairwiseMenuItem.setText("by Pairwise Identity");
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425 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
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427 public void actionPerformed(ActionEvent e)
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429 sortPairwiseMenuItem_actionPerformed(e);
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432 sortIDMenuItem.setText("by ID");
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433 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
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435 public void actionPerformed(ActionEvent e)
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437 sortIDMenuItem_actionPerformed(e);
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440 sortGroupMenuItem.setText("by Group");
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441 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 sortGroupMenuItem_actionPerformed(e);
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448 removeRedundancyMenuItem.setText("Remove Redundancy...");
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449 removeRedundancyMenuItem.addActionListener(new java.awt.event.
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452 public void actionPerformed(ActionEvent e)
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454 removeRedundancyMenuItem_actionPerformed(e);
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457 pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
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458 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
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461 public void actionPerformed(ActionEvent e)
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463 pairwiseAlignmentMenuItem_actionPerformed(e);
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466 PCAMenuItem.setText("Principal Component Analysis");
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467 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 PCAMenuItem_actionPerformed(e);
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474 averageDistanceTreeMenuItem.setText(
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475 "Average Distance Using % Identity");
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476 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
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479 public void actionPerformed(ActionEvent e)
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481 averageDistanceTreeMenuItem_actionPerformed(e);
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484 neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
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485 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 neighbourTreeMenuItem_actionPerformed(e);
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492 this.getContentPane().setLayout(borderLayout1);
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493 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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494 statusBar.setBackground(Color.white);
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495 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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496 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
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497 statusBar.setText("Status bar");
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498 outputTextboxMenu.setMnemonic('T');
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499 outputTextboxMenu.setText("Output to Textbox");
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500 clustalColour.setText("Clustalx");
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502 clustalColour.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 clustalColour_actionPerformed(e);
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509 zappoColour.setText("Zappo");
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510 zappoColour.addActionListener(new java.awt.event.ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 zappoColour_actionPerformed(e);
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517 taylorColour.setText("Taylor");
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518 taylorColour.addActionListener(new java.awt.event.ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 taylorColour_actionPerformed(e);
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525 hydrophobicityColour.setText("Hydrophobicity");
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526 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 hydrophobicityColour_actionPerformed(e);
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533 helixColour.setText("Helix Propensity");
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534 helixColour.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 helixColour_actionPerformed(e);
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541 strandColour.setText("Strand Propensity");
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542 strandColour.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 strandColour_actionPerformed(e);
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549 turnColour.setText("Turn Propensity");
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550 turnColour.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 turnColour_actionPerformed(e);
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557 buriedColour.setText("Buried Index");
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558 buriedColour.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 buriedColour_actionPerformed(e);
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565 userDefinedColour.setText("User Defined...");
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566 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 userDefinedColour_actionPerformed(e);
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573 PIDColour.setText("Percentage Identity");
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574 PIDColour.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 PIDColour_actionPerformed(e);
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581 BLOSUM62Colour.setText("BLOSUM62 Score");
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582 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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584 public void actionPerformed(ActionEvent e)
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586 BLOSUM62Colour_actionPerformed(e);
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589 avDistanceTreeBlosumMenuItem.setText(
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590 "Average Distance Using BLOSUM62");
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591 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
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594 public void actionPerformed(ActionEvent e)
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596 avTreeBlosumMenuItem_actionPerformed(e);
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599 njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
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600 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
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602 public void actionPerformed(ActionEvent e)
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604 njTreeBlosumMenuItem_actionPerformed(e);
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607 annotationPanelMenuItem.setActionCommand("");
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608 annotationPanelMenuItem.setText("Show Annotations");
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609 annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
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610 annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 annotationPanelMenuItem_actionPerformed(e);
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617 colourTextMenuItem.setText("Colour Text");
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618 colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 colourTextMenuItem_actionPerformed(e);
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625 htmlMenuItem.setText("HTML");
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626 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 htmlMenuItem_actionPerformed(e);
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633 overviewMenuItem.setText("Overview Window");
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634 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 overviewMenuItem_actionPerformed(e);
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641 undoMenuItem.setEnabled(false);
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642 undoMenuItem.setMnemonic('Z');
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643 undoMenuItem.setText("Undo");
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644 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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645 java.awt.event.KeyEvent.VK_Z,
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646 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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647 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 undoMenuItem_actionPerformed(e);
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654 redoMenuItem.setEnabled(false);
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655 redoMenuItem.setMnemonic('0');
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656 redoMenuItem.setText("Redo");
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657 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
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659 public void actionPerformed(ActionEvent e)
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661 redoMenuItem_actionPerformed(e);
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664 conservationMenuItem.setText("By Conservation");
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665 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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667 public void actionPerformed(ActionEvent e)
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669 conservationMenuItem_actionPerformed(e);
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672 noColourmenuItem.setText("None");
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673 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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675 public void actionPerformed(ActionEvent e)
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677 noColourmenuItem_actionPerformed(e);
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680 wrapMenuItem.setText("Wrap");
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681 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
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683 public void actionPerformed(ActionEvent e)
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685 wrapMenuItem_actionPerformed(e);
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688 printMenuItem.setText("Print");
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689 printMenuItem.addActionListener(new java.awt.event.ActionListener()
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691 public void actionPerformed(ActionEvent e)
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693 printMenuItem_actionPerformed(e);
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696 renderGapsMenuItem.setText("Show Gaps");
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697 renderGapsMenuItem.setState(true);
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698 renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
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700 public void actionPerformed(ActionEvent e)
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702 renderGapsMenuItem_actionPerformed(e);
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705 findMenuItem.setText("Find...");
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706 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
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707 java.awt.event.KeyEvent.VK_F,
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708 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
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709 findMenuItem.addActionListener(new java.awt.event.ActionListener()
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711 public void actionPerformed(ActionEvent e)
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713 findMenuItem_actionPerformed(e);
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716 searchMenu.setText("Search");
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718 abovePIDThreshold.setText("Above Identity Threshold");
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719 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 abovePIDThreshold_actionPerformed(e);
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726 showSeqFeatures.setText("Show Sequence Features");
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727 showSeqFeatures.addActionListener(new ActionListener()
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729 public void actionPerformed(ActionEvent actionEvent)
\r
731 showSeqFeatures_actionPerformed(actionEvent);
\r
734 nucleotideColour.setText("Nucleotide");
\r
735 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
\r
737 public void actionPerformed(ActionEvent e)
\r
739 nucleotideColour_actionPerformed(e);
\r
742 deleteGroups.setText("Undefine groups");
\r
743 deleteGroups.addActionListener(new java.awt.event.ActionListener()
\r
745 public void actionPerformed(ActionEvent e)
\r
747 deleteGroups_actionPerformed(e);
\r
750 copy.setText("Copy");
\r
751 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
752 java.awt.event.KeyEvent.VK_C,
\r
753 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
754 copy.setMnemonic(KeyEvent.VK_C);
\r
756 copy.addActionListener(new java.awt.event.ActionListener()
\r
758 public void actionPerformed(ActionEvent e)
\r
760 copy_actionPerformed(e);
\r
763 cut.setText("Cut");
\r
764 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
765 java.awt.event.KeyEvent.VK_X,
\r
766 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
767 cut.setMnemonic(KeyEvent.VK_X);
\r
768 cut.addActionListener(new java.awt.event.ActionListener()
\r
770 public void actionPerformed(ActionEvent e)
\r
772 cut_actionPerformed(e);
\r
775 delete.setText("Delete");
\r
776 delete.addActionListener(new java.awt.event.ActionListener()
\r
778 public void actionPerformed(ActionEvent e)
\r
780 delete_actionPerformed(e);
\r
783 jMenu1.setMnemonic('V');
\r
784 jMenu1.setText("Paste");
\r
785 pasteNew.setText("To New Alignment");
\r
786 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
\r
787 java.awt.event.KeyEvent.VK_V,
\r
788 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
\r
789 pasteNew.addActionListener(new java.awt.event.ActionListener()
\r
791 public void actionPerformed(ActionEvent e)
\r
793 pasteNew_actionPerformed(e);
\r
796 pasteThis.setText("Add To This Alignment");
\r
797 pasteThis.addActionListener(new java.awt.event.ActionListener()
\r
799 public void actionPerformed(ActionEvent e)
\r
801 pasteThis_actionPerformed(e);
\r
804 applyToAllGroups.setText("Apply Colour To All Groups");
\r
805 applyToAllGroups.setState(true);
\r
806 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
\r
808 public void actionPerformed(ActionEvent e)
\r
810 applyToAllGroups_actionPerformed(e);
\r
813 createPNG.addActionListener(new java.awt.event.ActionListener()
\r
815 public void actionPerformed(ActionEvent e)
\r
820 createPNG.setActionCommand("Save As PNG Image");
\r
821 createPNG.setText("PNG");
\r
822 font.setText("Font...");
\r
823 font.addActionListener(new java.awt.event.ActionListener()
\r
825 public void actionPerformed(ActionEvent e)
\r
827 font_actionPerformed(e);
\r
831 seqLimits.setText("Show Sequence Limits");
\r
832 seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
\r
833 seqLimits.addActionListener(new java.awt.event.ActionListener()
\r
835 public void actionPerformed(ActionEvent e)
\r
837 seqLimit_actionPerformed(e);
\r
840 epsFile.setText("EPS");
\r
841 epsFile.addActionListener(new java.awt.event.ActionListener()
\r
843 public void actionPerformed(ActionEvent e)
\r
848 LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
\r
849 LoadtreeMenuItem.setText("Load Associated Tree");
\r
850 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
852 public void actionPerformed(ActionEvent e)
\r
854 LoadtreeMenuItem_actionPerformed(e);
\r
857 scaleAbove.setVisible(false);
\r
858 scaleAbove.setText("Scale Above");
\r
859 scaleAbove.addActionListener(new java.awt.event.ActionListener()
\r
861 public void actionPerformed(ActionEvent e)
\r
863 scaleAbove_actionPerformed(e);
\r
866 scaleLeft.setVisible(false);
\r
867 scaleLeft.setSelected(true);
\r
868 scaleLeft.setText("Scale Left");
\r
869 scaleLeft.addActionListener(new java.awt.event.ActionListener()
\r
871 public void actionPerformed(ActionEvent e)
\r
873 scaleLeft_actionPerformed(e);
\r
876 scaleRight.setVisible(false);
\r
877 scaleRight.setSelected(true);
\r
878 scaleRight.setText("Scale Right");
\r
879 scaleRight.addActionListener(new java.awt.event.ActionListener()
\r
881 public void actionPerformed(ActionEvent e)
\r
883 scaleRight_actionPerformed(e);
\r
886 modifyPID.setText("Modify Identity Threshold...");
\r
887 modifyPID.addActionListener(new java.awt.event.ActionListener()
\r
889 public void actionPerformed(ActionEvent e)
\r
891 modifyPID_actionPerformed(e);
\r
894 modifyConservation.setText("Modify Conservation Threshold...");
\r
895 modifyConservation.addActionListener(new java.awt.event.ActionListener()
\r
897 public void actionPerformed(ActionEvent e)
\r
899 modifyConservation_actionPerformed(e);
\r
902 sortByTreeMenu.setText("By Tree Order");
\r
903 sort.setText("Sort");
\r
904 calculate.setText("Calculate Tree");
\r
906 jMenu2.setText("Export");
\r
907 padGapsMenuitem.setText("Pad Gaps");
\r
908 padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
\r
909 padGapsMenuitem.addActionListener(new ActionListener()
\r
911 public void actionPerformed(ActionEvent e)
\r
913 padGapsMenuitem_actionPerformed(e);
\r
916 vamsasStore.setVisible(false);
\r
917 vamsasStore.setText("VAMSAS store");
\r
918 vamsasStore.addActionListener(new ActionListener()
\r
920 public void actionPerformed(ActionEvent e)
\r
922 vamsasStore_actionPerformed(e);
\r
925 showTranslation.setText("Translate cDNA");
\r
926 showTranslation.addActionListener(new ActionListener()
\r
928 public void actionPerformed(ActionEvent e)
\r
930 showTranslation_actionPerformed(e);
\r
934 /* tabbedPane.addChangeListener(new ChangeListener()
\r
936 public void stateChanged(ChangeEvent ece)
\r
942 featureSettings.setText("Feature Settings...");
\r
943 featureSettings.addActionListener(new ActionListener()
\r
945 public void actionPerformed(ActionEvent e)
\r
947 featureSettings_actionPerformed(e);
\r
950 fetchSequence.setText("Fetch Sequence(s)...");
\r
951 fetchSequence.addActionListener(new ActionListener()
\r
953 public void actionPerformed(ActionEvent e)
\r
955 fetchSequence_actionPerformed(e);
\r
958 smoothFont.setText("Smooth Fonts");
\r
959 smoothFont.addActionListener(new ActionListener()
\r
961 public void actionPerformed(ActionEvent e)
\r
963 smoothFont_actionPerformed(e);
\r
966 smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
\r
967 annotationColour.setText("By Annotation...");
\r
968 annotationColour.addActionListener(new ActionListener()
\r
970 public void actionPerformed(ActionEvent e)
\r
972 annotationColour_actionPerformed(e);
\r
975 fetchSeqFeatures.setText("Fetch Sequence Features");
\r
976 fetchSeqFeatures.addActionListener(new ActionListener()
\r
978 public void actionPerformed(ActionEvent e)
\r
980 fetchSeqFeatures_actionPerformed(e);
\r
983 associatedData.setText("Load Features / Annotations");
\r
984 associatedData.addActionListener(new ActionListener()
\r
986 public void actionPerformed(ActionEvent e)
\r
988 associatedData_actionPerformed(e);
\r
991 autoCalculate.setText("Autocalculate Consensus");
\r
992 autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
\r
993 autoCalculate.addActionListener(new ActionListener()
\r
995 public void actionPerformed(ActionEvent e)
\r
997 autoCalculate_actionPerformed(e);
\r
1000 addSequenceMenu.setText("Add Sequences");
\r
1001 addFromFile.setText("From File");
\r
1002 addFromFile.addActionListener(new ActionListener()
\r
1004 public void actionPerformed(ActionEvent e)
\r
1006 addFromFile_actionPerformed(e);
\r
1009 addFromText.setText("From Textbox");
\r
1010 addFromText.addActionListener(new ActionListener()
\r
1012 public void actionPerformed(ActionEvent e)
\r
1014 addFromText_actionPerformed(e);
\r
1017 addFromURL.setText("From URL");
\r
1018 addFromURL.addActionListener(new ActionListener()
\r
1020 public void actionPerformed(ActionEvent e)
\r
1022 addFromURL_actionPerformed(e);
\r
1025 exportFeatures.setText("Export Features...");
\r
1026 exportFeatures.addActionListener(new ActionListener()
\r
1028 public void actionPerformed(ActionEvent e)
\r
1030 exportFeatures_actionPerformed(e);
\r
1033 exportAnnotations.setText("Export Annotations...");
\r
1034 exportAnnotations.addActionListener(new ActionListener()
\r
1036 public void actionPerformed(ActionEvent e)
\r
1038 exportAnnotations_actionPerformed(e);
\r
1041 dbRefs.setText("Fetch DB Refs");
\r
1042 dbRefs.addActionListener(new ActionListener()
\r
1044 public void actionPerformed(ActionEvent e)
\r
1046 dbRefs_actionPerformed(e);
\r
1049 statusPanel.setLayout(gridLayout1);
\r
1050 alignFrameMenuBar.add(fileMenu);
\r
1051 alignFrameMenuBar.add(editMenu);
\r
1052 alignFrameMenuBar.add(searchMenu);
\r
1053 alignFrameMenuBar.add(viewMenu);
\r
1054 alignFrameMenuBar.add(colourMenu);
\r
1055 alignFrameMenuBar.add(calculateMenu);
\r
1056 alignFrameMenuBar.add(webService);
\r
1057 fileMenu.add(addSequenceMenu);
\r
1058 fileMenu.add(fetchSequence);
\r
1059 fileMenu.addSeparator();
\r
1060 fileMenu.add(vamsasStore);
\r
1061 fileMenu.add(saveAlignmentMenu);
\r
1062 fileMenu.add(jMenu2);
\r
1063 fileMenu.add(outputTextboxMenu);
\r
1064 fileMenu.add(printMenuItem);
\r
1065 fileMenu.addSeparator();
\r
1066 fileMenu.add(exportFeatures);
\r
1067 fileMenu.add(exportAnnotations);
\r
1068 fileMenu.add(LoadtreeMenuItem);
\r
1069 fileMenu.add(associatedData);
\r
1070 fileMenu.addSeparator();
\r
1071 fileMenu.add(closeMenuItem);
\r
1072 editMenu.add(undoMenuItem);
\r
1073 editMenu.add(redoMenuItem);
\r
1074 editMenu.add(cut);
\r
1075 editMenu.add(copy);
\r
1076 editMenu.add(jMenu1);
\r
1077 editMenu.add(delete);
\r
1078 editMenu.addSeparator();
\r
1079 editMenu.add(selectAllSequenceMenuItem);
\r
1080 editMenu.add(deselectAllSequenceMenuItem);
\r
1081 editMenu.add(invertSequenceMenuItem);
\r
1082 editMenu.add(deleteGroups);
\r
1083 editMenu.addSeparator();
\r
1084 editMenu.add(remove2LeftMenuItem);
\r
1085 editMenu.add(remove2RightMenuItem);
\r
1086 editMenu.add(removeGappedColumnMenuItem);
\r
1087 editMenu.add(removeAllGapsMenuItem);
\r
1088 editMenu.add(removeRedundancyMenuItem);
\r
1089 editMenu.addSeparator();
\r
1090 editMenu.add(padGapsMenuitem);
\r
1091 searchMenu.add(findMenuItem);
\r
1092 viewMenu.add(font);
\r
1093 viewMenu.add(smoothFont);
\r
1094 viewMenu.addSeparator();
\r
1095 viewMenu.add(wrapMenuItem);
\r
1096 viewMenu.add(seqLimits);
\r
1097 viewMenu.add(scaleAbove);
\r
1098 viewMenu.add(scaleLeft);
\r
1099 viewMenu.add(scaleRight);
\r
1100 viewMenu.add(viewBoxesMenuItem);
\r
1101 viewMenu.add(viewTextMenuItem);
\r
1102 viewMenu.add(colourTextMenuItem);
\r
1103 viewMenu.add(renderGapsMenuItem);
\r
1104 viewMenu.add(annotationPanelMenuItem);
\r
1105 viewMenu.addSeparator();
\r
1106 viewMenu.add(dbRefs);
\r
1107 viewMenu.add(fetchSeqFeatures);
\r
1108 viewMenu.add(showSeqFeatures);
\r
1109 viewMenu.add(featureSettings);
\r
1110 viewMenu.addSeparator();
\r
1111 viewMenu.add(overviewMenuItem);
\r
1112 colourMenu.add(applyToAllGroups);
\r
1113 colourMenu.addSeparator();
\r
1114 colourMenu.add(noColourmenuItem);
\r
1115 colourMenu.add(clustalColour);
\r
1116 colourMenu.add(BLOSUM62Colour);
\r
1117 colourMenu.add(PIDColour);
\r
1118 colourMenu.add(zappoColour);
\r
1119 colourMenu.add(taylorColour);
\r
1120 colourMenu.add(hydrophobicityColour);
\r
1121 colourMenu.add(helixColour);
\r
1122 colourMenu.add(strandColour);
\r
1123 colourMenu.add(turnColour);
\r
1124 colourMenu.add(buriedColour);
\r
1125 colourMenu.add(nucleotideColour);
\r
1126 colourMenu.add(userDefinedColour);
\r
1127 colourMenu.addSeparator();
\r
1128 colourMenu.add(conservationMenuItem);
\r
1129 colourMenu.add(modifyConservation);
\r
1130 colourMenu.add(abovePIDThreshold);
\r
1131 colourMenu.add(modifyPID);
\r
1132 colourMenu.add(annotationColour);
\r
1133 calculateMenu.add(sort);
\r
1134 calculateMenu.add(calculate);
\r
1135 calculateMenu.addSeparator();
\r
1136 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1137 calculateMenu.add(PCAMenuItem);
\r
1138 calculateMenu.addSeparator();
\r
1139 calculateMenu.add(showTranslation);
\r
1140 calculateMenu.add(autoCalculate);
\r
1141 webServiceNoServices=new JMenuItem("<No Services>");
\r
1142 webService.add(webServiceNoServices);jMenu1.add(pasteNew);
\r
1143 jMenu1.add(pasteThis);
\r
1144 sort.add(sortIDMenuItem);
\r
1145 sort.add(sortGroupMenuItem);
\r
1146 sort.add(sortPairwiseMenuItem);
\r
1147 calculate.add(averageDistanceTreeMenuItem);
\r
1148 calculate.add(neighbourTreeMenuItem);
\r
1149 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1150 calculate.add(njTreeBlosumMenuItem);
\r
1151 jMenu2.add(htmlMenuItem);
\r
1152 jMenu2.add(epsFile);
\r
1153 jMenu2.add(createPNG);
\r
1154 addSequenceMenu.add(addFromFile);
\r
1155 addSequenceMenu.add(addFromText);
\r
1156 addSequenceMenu.add(addFromURL);
\r
1157 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
\r
1158 statusPanel.add(statusBar, null);
\r
1161 protected void outputText_actionPerformed(ActionEvent e)
\r
1165 public void addFromFile_actionPerformed(ActionEvent e)
\r
1170 public void addFromText_actionPerformed(ActionEvent e)
\r
1175 public void addFromURL_actionPerformed(ActionEvent e)
\r
1180 public void exportFeatures_actionPerformed(ActionEvent e)
\r
1185 public void exportAnnotations_actionPerformed(ActionEvent e)
\r
1190 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
1194 protected void closeMenuItem_actionPerformed(ActionEvent e)
\r
1198 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
1202 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
1206 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1210 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1214 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
1218 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
1222 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1226 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1230 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1234 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1238 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1242 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1246 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1250 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1254 protected void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1258 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1262 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1266 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1270 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1274 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1278 protected void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1282 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1286 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1290 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1294 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1298 protected void clustalColour_actionPerformed(ActionEvent e)
\r
1302 protected void zappoColour_actionPerformed(ActionEvent e)
\r
1306 protected void taylorColour_actionPerformed(ActionEvent e)
\r
1310 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1314 protected void helixColour_actionPerformed(ActionEvent e)
\r
1318 protected void strandColour_actionPerformed(ActionEvent e)
\r
1322 protected void turnColour_actionPerformed(ActionEvent e)
\r
1326 protected void buriedColour_actionPerformed(ActionEvent e)
\r
1330 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
1334 protected void PIDColour_actionPerformed(ActionEvent e)
\r
1338 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1342 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1346 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1350 protected void printMenuItem_actionPerformed(ActionEvent e)
\r
1354 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1358 protected void findMenuItem_actionPerformed(ActionEvent e)
\r
1362 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1366 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
\r
1370 protected void nucleotideColour_actionPerformed(ActionEvent e)
\r
1374 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
1378 protected void copy_actionPerformed(ActionEvent e)
\r
1382 protected void cut_actionPerformed(ActionEvent e)
\r
1386 protected void delete_actionPerformed(ActionEvent e)
\r
1390 protected void pasteNew_actionPerformed(ActionEvent e)
\r
1394 protected void pasteThis_actionPerformed(ActionEvent e)
\r
1398 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1402 public void createPNG(java.io.File f)
\r
1406 protected void font_actionPerformed(ActionEvent e)
\r
1410 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1414 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1420 public void createEPS(java.io.File f)
\r
1424 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1428 protected void jpred_actionPerformed(ActionEvent e)
\r
1432 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1436 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1440 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1444 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1448 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1454 protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
1458 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1463 public void vamsasStore_actionPerformed(ActionEvent e)
\r
1468 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
1473 public void showTranslation_actionPerformed(ActionEvent e)
\r
1478 public void featureSettings_actionPerformed(ActionEvent e)
\r
1483 public void fetchSequence_actionPerformed(ActionEvent e)
\r
1488 public void smoothFont_actionPerformed(ActionEvent e)
\r
1493 public void annotationColour_actionPerformed(ActionEvent e)
\r
1498 public void fetchSeqFeatures_actionPerformed(ActionEvent e)
\r
1503 public void associatedData_actionPerformed(ActionEvent e)
\r
1508 public void autoCalculate_actionPerformed(ActionEvent e)
\r
1513 public void dbRefs_actionPerformed(ActionEvent e)
\r