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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23 import javax.swing.*;
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24 import javax.swing.border.TitledBorder;
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25 import java.awt.event.*;
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26 import javax.swing.event.*;
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33 * @version $Revision$
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35 public class GPreferences extends JPanel
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37 JTabbedPane tabbedPane = new JTabbedPane();
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39 JButton ok = new JButton();
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40 JButton cancel = new JButton();
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41 JPanel okCancelPanel = new JPanel();
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42 BorderLayout borderLayout1 = new BorderLayout();
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43 protected JCheckBox quality = new JCheckBox();
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44 JPanel visualTab = new JPanel();
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45 protected JCheckBox fullID = new JCheckBox();
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46 protected JCheckBox fullScreen = new JCheckBox();
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47 protected JCheckBox conservation = new JCheckBox();
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48 protected JCheckBox identity = new JCheckBox();
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49 protected JCheckBox annotations = new JCheckBox();
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50 JLabel gapLabel = new JLabel();
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51 protected JComboBox colour = new JComboBox();
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52 JLabel colourLabel = new JLabel();
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53 JLabel fontLabel = new JLabel();
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54 protected JComboBox fontSizeCB = new JComboBox();
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55 protected JComboBox fontStyleCB = new JComboBox();
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56 protected JComboBox fontNameCB = new JComboBox();
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57 protected JComboBox gapSymbolCB = new JComboBox();
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58 protected JCheckBox startupCheckbox = new JCheckBox();
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59 protected JTextField startupFileTextfield = new JTextField();
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60 JPanel connectTab = new JPanel();
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61 JLabel serverLabel = new JLabel();
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62 protected JList linkURLList = new JList();
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63 protected JTextField proxyServerTB = new JTextField();
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64 protected JTextField proxyPortTB = new JTextField();
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65 JLabel portLabel = new JLabel();
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66 JLabel browserLabel = new JLabel();
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67 protected JTextField defaultBrowser = new JTextField();
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68 JButton newLink = new JButton();
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69 JButton editLink = new JButton();
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70 JButton deleteLink = new JButton();
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71 JScrollPane linkScrollPane = new JScrollPane();
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72 JPanel linkPanel = new JPanel();
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73 BorderLayout borderLayout2 = new BorderLayout();
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74 JPanel editLinkButtons = new JPanel();
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75 GridLayout gridLayout1 = new GridLayout();
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76 protected JList linkNameList = new JList();
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77 JPanel linkPanel2 = new JPanel();
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78 BorderLayout borderLayout3 = new BorderLayout();
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79 protected JCheckBox useProxy = new JCheckBox();
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80 JPanel jPanel1 = new JPanel();
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81 TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
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82 TitledBorder titledBorder2 = new TitledBorder("File Output");
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83 GridBagLayout gridBagLayout2 = new GridBagLayout();
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84 GridBagLayout gridBagLayout1 = new GridBagLayout();
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85 GridBagLayout gridBagLayout3 = new GridBagLayout();
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86 protected JComboBox sortby = new JComboBox();
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87 JLabel sortLabel = new JLabel();
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88 JPanel jPanel2 = new JPanel();
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89 GridLayout gridLayout2 = new GridLayout();
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90 JPanel jPanel3 = new JPanel();
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91 JPanel exportTab = new JPanel();
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92 JLabel epsLabel = new JLabel();
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93 protected JComboBox epsRendering = new JComboBox();
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94 JLabel jLabel1 = new JLabel();
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95 JLabel jLabel2 = new JLabel();
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96 protected JCheckBox pileupdb = new JCheckBox();
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97 protected JCheckBox fastadb = new JCheckBox();
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98 protected JCheckBox blcjv = new JCheckBox();
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99 protected JCheckBox pileupjv = new JCheckBox();
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100 protected JCheckBox msfdb = new JCheckBox();
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101 protected JCheckBox pfamdb = new JCheckBox();
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102 protected JCheckBox clustaljv = new JCheckBox();
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103 protected JCheckBox msfjv = new JCheckBox();
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104 protected JCheckBox blcdb = new JCheckBox();
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105 protected JCheckBox clustaldb = new JCheckBox();
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106 protected JCheckBox fastajv = new JCheckBox();
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107 protected JCheckBox pfamjv = new JCheckBox();
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108 JLabel jLabel10 = new JLabel();
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109 JLabel jLabel11 = new JLabel();
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110 FlowLayout flowLayout1 = new FlowLayout();
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111 protected JCheckBox pirdb = new JCheckBox();
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112 protected JCheckBox pirjv = new JCheckBox();
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113 JPanel jPanel11 = new JPanel();
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114 GridLayout gridLayout3 = new GridLayout();
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115 Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
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117 * Creates a new GPreferences object.
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119 public GPreferences()
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125 catch (Exception ex)
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127 ex.printStackTrace();
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134 * @throws Exception DOCUMENT ME!
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136 private void jbInit() throws Exception
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138 this.setLayout(borderLayout1);
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140 ok.addActionListener(new ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 ok_actionPerformed(e);
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147 cancel.setText("Cancel");
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148 cancel.addActionListener(new ActionListener()
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150 public void actionPerformed(ActionEvent e)
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152 cancel_actionPerformed(e);
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155 quality.setEnabled(false);
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156 quality.setFont(verdana11);
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157 quality.setHorizontalAlignment(SwingConstants.RIGHT);
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158 quality.setHorizontalTextPosition(SwingConstants.LEFT);
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159 quality.setSelected(true);
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160 quality.setText("Quality");
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161 visualTab.setBorder(new TitledBorder("Open new alignment"));
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162 visualTab.setLayout(null);
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163 fullID.setFont(verdana11);
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164 fullID.setHorizontalAlignment(SwingConstants.RIGHT);
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165 fullID.setHorizontalTextPosition(SwingConstants.LEFT);
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166 fullID.setMargin(new Insets(4, 2, 2, 0));
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167 fullID.setText("Full Sequence ID");
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168 fullScreen.setFont(verdana11);
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169 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
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170 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
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171 fullScreen.setMargin(new Insets(2, 2, 2, 0));
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172 fullScreen.setText("Maximise Window");
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173 conservation.setEnabled(false);
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174 conservation.setFont(verdana11);
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175 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
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176 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
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177 conservation.setSelected(true);
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178 conservation.setText("Conservation");
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179 identity.setEnabled(false);
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180 identity.setFont(verdana11);
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181 identity.setHorizontalAlignment(SwingConstants.RIGHT);
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182 identity.setHorizontalTextPosition(SwingConstants.LEFT);
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183 identity.setSelected(true);
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184 identity.setText("Consensus");
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185 annotations.setFont(verdana11);
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186 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
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187 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
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188 annotations.setMargin(new Insets(2, 4, 2, 0));
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189 annotations.setSelected(true);
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190 annotations.setText("Show Annotations");
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191 annotations.addActionListener(new ActionListener()
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193 public void actionPerformed(ActionEvent e)
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195 annotations_actionPerformed(e);
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198 gapLabel.setFont(verdana11);
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199 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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200 gapLabel.setText("Gap Symbol ");
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201 colour.setFont(verdana11);
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202 colour.setBounds(new Rectangle(148, 171, 154, 21));
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203 colourLabel.setFont(verdana11);
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204 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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205 colourLabel.setText("Colour ");
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206 fontLabel.setFont(verdana11);
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207 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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208 fontLabel.setText("Font ");
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209 fontSizeCB.setFont(verdana11);
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210 fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));
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211 fontStyleCB.setFont(verdana11);
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212 fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));
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213 fontNameCB.setFont(verdana11);
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214 fontNameCB.setBounds(new Rectangle(148, 111, 169, 21));
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215 gapSymbolCB.setFont(verdana11);
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216 gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21));
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217 startupCheckbox.setText("Open file");
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218 startupCheckbox.setFont(verdana11);
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219 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
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220 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
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221 startupCheckbox.setSelected(true);
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222 startupFileTextfield.setFont(verdana11);
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223 startupFileTextfield.setBounds(new Rectangle(148, 232, 302, 20));
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224 startupFileTextfield.addMouseListener(new MouseAdapter()
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226 public void mouseClicked(MouseEvent e)
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228 if (e.getClickCount() > 1)
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230 startupFileTextfield_mouseClicked();
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235 connectTab.setLayout(gridBagLayout3);
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236 serverLabel.setText("Address");
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237 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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238 serverLabel.setFont(verdana11);
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239 proxyServerTB.setFont(verdana11);
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240 proxyPortTB.setFont(verdana11);
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241 portLabel.setFont(verdana11);
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242 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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243 portLabel.setText("Port");
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244 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
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245 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
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246 browserLabel.setText("Default Browser (Unix)");
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247 defaultBrowser.setFont(verdana11);
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248 defaultBrowser.setText("");
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249 newLink.setText("New");
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250 newLink.addActionListener(new java.awt.event.ActionListener() {
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251 public void actionPerformed(ActionEvent e) {
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252 newLink_actionPerformed(e);
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255 editLink.setText("Edit");
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256 editLink.addActionListener(new java.awt.event.ActionListener() {
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257 public void actionPerformed(ActionEvent e) {
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258 editLink_actionPerformed(e);
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261 deleteLink.setText("Delete");
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262 deleteLink.addActionListener(new java.awt.event.ActionListener() {
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263 public void actionPerformed(ActionEvent e) {
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264 deleteLink_actionPerformed(e);
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268 linkURLList.addListSelectionListener(new ListSelectionListener()
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270 public void valueChanged(ListSelectionEvent e)
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272 int index = linkURLList.getSelectedIndex();
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273 linkNameList.setSelectedIndex(index);
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277 linkNameList.addListSelectionListener(new ListSelectionListener()
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279 public void valueChanged(ListSelectionEvent e)
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281 int index = linkNameList.getSelectedIndex();
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282 linkURLList.setSelectedIndex(index);
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286 linkScrollPane.setBorder(null);
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287 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
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288 linkPanel.setLayout(borderLayout2);
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289 editLinkButtons.setLayout(gridLayout1);
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290 gridLayout1.setRows(3);
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291 linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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292 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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293 linkPanel2.setLayout(borderLayout3);
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294 linkURLList.setFont(verdana11);
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295 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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297 defaultBrowser.addMouseListener(new MouseAdapter()
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299 public void mouseClicked(MouseEvent e)
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301 if (e.getClickCount() > 1)
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303 defaultBrowser_mouseClicked(e);
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307 useProxy.setFont(verdana11);
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308 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
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309 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
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310 useProxy.setText("Use a proxy server");
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311 useProxy.addActionListener(new ActionListener()
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313 public void actionPerformed(ActionEvent e)
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315 useProxy_actionPerformed();
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318 jPanel1.setBorder(titledBorder1);
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319 jPanel1.setLayout(gridBagLayout1);
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320 sortby.setFont(verdana11);
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321 sortby.setBounds(new Rectangle(148, 200, 302, 21));
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322 sortLabel.setFont(verdana11);
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323 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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324 sortLabel.setText("Sort by ");
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325 jPanel2.setBounds(new Rectangle(7, 17, 138, 242));
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326 jPanel2.setLayout(gridLayout2);
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327 gridLayout2.setRows(8);
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328 jPanel3.setBounds(new Rectangle(147, 46, 274, 26));
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329 exportTab.setLayout(null);
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330 epsLabel.setFont(verdana11);
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331 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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332 epsLabel.setText("EPS Rendering Style");
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333 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
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334 epsRendering.setFont(verdana11);
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335 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
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336 jLabel1.setFont(verdana11);
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337 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
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338 jLabel1.setText("/start-end suffix");
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339 jLabel2.setFont(verdana11);
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340 jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
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341 jLabel2.setHorizontalTextPosition(SwingConstants.RIGHT);
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342 jLabel2.setText("Database ref prefix");
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343 jLabel1.setFont(verdana11);
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344 jLabel2.setFont(verdana11);
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345 fastajv.setFont(verdana11);
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346 fastajv.setHorizontalAlignment(SwingConstants.CENTER);
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347 jLabel10.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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348 jLabel10.setHorizontalAlignment(SwingConstants.RIGHT);
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349 jLabel10.setText("(Uniprot|P02055)");
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350 jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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351 jLabel11.setHorizontalAlignment(SwingConstants.CENTER);
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352 jLabel11.setText("(/15-380)");
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353 clustaldb.setFont(verdana11);
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354 clustaldb.setHorizontalAlignment(SwingConstants.RIGHT);
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355 clustaldb.setHorizontalTextPosition(SwingConstants.LEFT);
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356 clustaldb.setText("Clustal ");
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357 blcdb.setFont(verdana11);
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358 blcdb.setHorizontalAlignment(SwingConstants.RIGHT);
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359 blcdb.setHorizontalTextPosition(SwingConstants.LEFT);
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360 blcdb.setText("BLC ");
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361 fastadb.setFont(verdana11);
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362 fastadb.setHorizontalAlignment(SwingConstants.RIGHT);
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363 fastadb.setHorizontalTextPosition(SwingConstants.LEFT);
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364 fastadb.setText("Fasta ");
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365 msfdb.setFont(verdana11);
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366 msfdb.setHorizontalTextPosition(SwingConstants.LEFT);
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367 msfdb.setHorizontalAlignment(SwingConstants.RIGHT);
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368 msfdb.setText("MSF ");
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369 pfamdb.setFont(verdana11);
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370 pfamdb.setHorizontalAlignment(SwingConstants.RIGHT);
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371 pfamdb.setHorizontalTextPosition(SwingConstants.LEFT);
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372 pfamdb.setText("PFAM ");
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373 pileupdb.setFont(verdana11);
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374 pileupdb.setHorizontalAlignment(SwingConstants.RIGHT);
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375 pileupdb.setHorizontalTextPosition(SwingConstants.LEFT);
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376 pileupdb.setText("Pileup ");
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377 msfjv.setFont(verdana11);
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378 msfjv.setHorizontalAlignment(SwingConstants.CENTER);
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379 pirdb.setFont(verdana11);
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380 pirdb.setHorizontalAlignment(SwingConstants.RIGHT);
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381 pirdb.setHorizontalTextPosition(SwingConstants.LEFT);
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382 pirdb.setText("PIR ");
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383 jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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384 jPanel11.setBorder(titledBorder2);
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385 jPanel11.setBounds(new Rectangle(18, 72, 325, 182));
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386 jPanel11.setLayout(gridLayout3);
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387 gridLayout3.setColumns(2);
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388 gridLayout3.setRows(9);
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389 blcjv.setFont(verdana11);
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390 blcjv.setHorizontalAlignment(SwingConstants.CENTER);
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391 clustaljv.setFont(verdana11);
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392 clustaljv.setHorizontalAlignment(SwingConstants.CENTER);
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393 pfamjv.setFont(verdana11);
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394 pfamjv.setHorizontalAlignment(SwingConstants.CENTER);
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395 pileupjv.setFont(verdana11);
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396 pileupjv.setHorizontalAlignment(SwingConstants.CENTER);
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397 pirjv.setFont(verdana11);
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398 pirjv.setHorizontalAlignment(SwingConstants.CENTER);
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399 jPanel2.add(fullScreen);
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400 jPanel2.add(annotations);
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401 jPanel2.add(fullID);
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402 jPanel2.add(fontLabel);
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403 jPanel2.add(gapLabel);
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404 jPanel2.add(colourLabel);
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405 jPanel2.add(sortLabel);
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406 jPanel2.add(startupCheckbox);
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407 visualTab.add(jPanel3);
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408 jPanel3.add(conservation);
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409 jPanel3.add(quality);
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410 jPanel3.add(identity);
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411 visualTab.add(sortby);
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412 visualTab.add(colour);
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413 visualTab.add(startupFileTextfield);
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414 visualTab.add(fontNameCB);
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415 visualTab.add(fontSizeCB);
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416 visualTab.add(fontStyleCB);
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417 visualTab.add(gapSymbolCB);
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418 visualTab.add(jPanel2);
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420 linkPanel.add(editLinkButtons, BorderLayout.EAST);
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421 editLinkButtons.add(newLink, null);
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422 editLinkButtons.add(editLink, null);
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423 editLinkButtons.add(deleteLink, null);
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424 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
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425 linkScrollPane.getViewport().add(linkPanel2, null);
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426 linkPanel2.add(linkURLList, BorderLayout.CENTER);
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427 linkPanel2.add(linkNameList, BorderLayout.WEST);
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428 okCancelPanel.add(ok);
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429 okCancelPanel.add(cancel);
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430 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
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432 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
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433 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
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434 , GridBagConstraints.WEST, GridBagConstraints.NONE,
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435 new Insets(0, 2, 4, 0), 5, 0));
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436 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
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437 , GridBagConstraints.WEST,
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438 GridBagConstraints.NONE,
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439 new Insets(0, 0, 4, 0), 11, 6));
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440 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
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441 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
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442 new Insets(16, 0, 0, 12), 359, -17));
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443 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
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444 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
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445 new Insets(21, 0, 35, 12), 4, 6));
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446 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
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447 , GridBagConstraints.WEST, GridBagConstraints.NONE,
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448 new Insets(16, 0, 0, 0), 5, 1));
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449 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
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450 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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451 new Insets(0, 2, 4, 2), 54, 1));
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452 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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453 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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454 new Insets(0, 2, 4, 0), 263, 1));
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455 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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456 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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457 new Insets(15, 0, 0, 15), 307, 1));
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460 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
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461 , GridBagConstraints.WEST,
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462 GridBagConstraints.NONE,
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463 new Insets(0, 2, 5, 185), 2,
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465 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
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466 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
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467 gapSymbolCB.setRenderer(dlcr);
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469 tabbedPane.add(visualTab, "Visual");
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470 tabbedPane.add(connectTab,"Connections");
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471 tabbedPane.add(exportTab, "File");
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472 jPanel11.add(jLabel2);
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473 jPanel11.add(jLabel1);
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474 jPanel11.add(jLabel10);
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475 jPanel11.add(jLabel11);
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476 jPanel11.add(blcdb);
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477 jPanel11.add(blcjv);
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478 jPanel11.add(clustaldb);
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479 jPanel11.add(clustaljv);
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480 jPanel11.add(fastadb);
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481 jPanel11.add(fastajv);
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482 jPanel11.add(msfdb);
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483 jPanel11.add(msfjv);
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484 jPanel11.add(pfamdb);
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485 jPanel11.add(pfamjv);
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486 jPanel11.add(pileupdb);
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487 jPanel11.add(pileupjv);
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488 jPanel11.add(pirdb);
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489 jPanel11.add(pirjv);
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490 exportTab.add(epsLabel);
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491 exportTab.add(epsRendering);
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492 exportTab.add(jPanel11);
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498 * @param e DOCUMENT ME!
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500 public void ok_actionPerformed(ActionEvent e)
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507 * @param e DOCUMENT ME!
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509 public void cancel_actionPerformed(ActionEvent e)
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516 * @param e DOCUMENT ME!
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518 public void annotations_actionPerformed(ActionEvent e)
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526 public void startupFileTextfield_mouseClicked()
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531 public void newLink_actionPerformed(ActionEvent e) {
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535 public void editLink_actionPerformed(ActionEvent e) {
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539 public void deleteLink_actionPerformed(ActionEvent e) {
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543 public void defaultBrowser_mouseClicked(MouseEvent e)
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548 public void linkURLList_keyTyped(KeyEvent e)
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553 public void useProxy_actionPerformed()
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555 proxyServerTB.setEnabled(useProxy.isSelected());
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556 proxyPortTB.setEnabled(useProxy.isSelected());
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