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 dbRef = 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 protected JCheckBox blcjv = new JCheckBox();
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96 protected JCheckBox pileupjv = new JCheckBox();
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97 protected JCheckBox clustaljv = new JCheckBox();
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98 protected JCheckBox msfjv = new JCheckBox();
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99 protected JCheckBox fastajv = new JCheckBox();
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100 protected JCheckBox pfamjv = new JCheckBox();
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101 JLabel jLabel11 = new JLabel();
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102 FlowLayout flowLayout1 = new FlowLayout();
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103 protected JCheckBox pirjv = new JCheckBox();
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104 JPanel jPanel11 = new JPanel();
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105 Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
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106 protected JCheckBox seqLimit = new JCheckBox();
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107 GridLayout gridLayout3 = new GridLayout();
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109 * Creates a new GPreferences object.
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111 public GPreferences()
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117 catch (Exception ex)
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119 ex.printStackTrace();
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126 * @throws Exception DOCUMENT ME!
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128 private void jbInit() throws Exception
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130 this.setLayout(borderLayout1);
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132 ok.addActionListener(new ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 ok_actionPerformed(e);
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139 cancel.setText("Cancel");
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140 cancel.addActionListener(new ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 cancel_actionPerformed(e);
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147 quality.setEnabled(false);
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148 quality.setFont(verdana11);
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149 quality.setHorizontalAlignment(SwingConstants.RIGHT);
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150 quality.setHorizontalTextPosition(SwingConstants.LEFT);
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151 quality.setSelected(true);
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152 quality.setText("Quality");
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153 visualTab.setBorder(new TitledBorder("Open new alignment"));
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154 visualTab.setLayout(null);
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155 dbRef.setFont(verdana11);
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156 dbRef.setHorizontalAlignment(SwingConstants.RIGHT);
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157 dbRef.setHorizontalTextPosition(SwingConstants.LEFT);
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158 dbRef.setMargin(new Insets(4, 2, 2, 0));
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159 dbRef.setText("DB prefix (DB|AccNo)");
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160 fullScreen.setFont(verdana11);
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161 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
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162 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
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163 fullScreen.setMargin(new Insets(2, 2, 2, 0));
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164 fullScreen.setText("Maximise Window");
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165 conservation.setEnabled(false);
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166 conservation.setFont(verdana11);
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167 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
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168 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
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169 conservation.setSelected(true);
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170 conservation.setText("Conservation");
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171 identity.setEnabled(false);
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172 identity.setFont(verdana11);
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173 identity.setHorizontalAlignment(SwingConstants.RIGHT);
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174 identity.setHorizontalTextPosition(SwingConstants.LEFT);
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175 identity.setSelected(true);
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176 identity.setText("Consensus");
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177 annotations.setFont(verdana11);
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178 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
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179 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
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180 annotations.setMargin(new Insets(2, 4, 2, 0));
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181 annotations.setSelected(true);
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182 annotations.setText("Show Annotations");
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183 annotations.addActionListener(new ActionListener()
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185 public void actionPerformed(ActionEvent e)
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187 annotations_actionPerformed(e);
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190 gapLabel.setFont(verdana11);
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191 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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192 gapLabel.setText("Gap Symbol ");
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193 colour.setFont(verdana11);
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194 colour.setBounds(new Rectangle(170, 170, 155, 21));
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195 colourLabel.setFont(verdana11);
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196 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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197 colourLabel.setText("Colour ");
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198 fontLabel.setFont(verdana11);
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199 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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200 fontLabel.setText("Font ");
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201 fontSizeCB.setFont(verdana11);
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202 fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));
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203 fontStyleCB.setFont(verdana11);
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204 fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));
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205 fontNameCB.setFont(verdana11);
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206 fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));
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207 gapSymbolCB.setFont(verdana11);
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208 gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21));
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209 startupCheckbox.setText("Open file");
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210 startupCheckbox.setFont(verdana11);
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211 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
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212 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
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213 startupCheckbox.setSelected(true);
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214 startupFileTextfield.setFont(verdana11);
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215 startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));
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216 startupFileTextfield.addMouseListener(new MouseAdapter()
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218 public void mouseClicked(MouseEvent e)
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220 if (e.getClickCount() > 1)
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222 startupFileTextfield_mouseClicked();
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227 connectTab.setLayout(gridBagLayout3);
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228 serverLabel.setText("Address");
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229 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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230 serverLabel.setFont(verdana11);
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231 proxyServerTB.setFont(verdana11);
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232 proxyPortTB.setFont(verdana11);
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233 portLabel.setFont(verdana11);
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234 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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235 portLabel.setText("Port");
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236 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
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237 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
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238 browserLabel.setText("Default Browser (Unix)");
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239 defaultBrowser.setFont(verdana11);
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240 defaultBrowser.setText("");
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241 newLink.setText("New");
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242 newLink.addActionListener(new java.awt.event.ActionListener() {
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243 public void actionPerformed(ActionEvent e) {
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244 newLink_actionPerformed(e);
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247 editLink.setText("Edit");
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248 editLink.addActionListener(new java.awt.event.ActionListener() {
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249 public void actionPerformed(ActionEvent e) {
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250 editLink_actionPerformed(e);
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253 deleteLink.setText("Delete");
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254 deleteLink.addActionListener(new java.awt.event.ActionListener() {
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255 public void actionPerformed(ActionEvent e) {
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256 deleteLink_actionPerformed(e);
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260 linkURLList.addListSelectionListener(new ListSelectionListener()
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262 public void valueChanged(ListSelectionEvent e)
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264 int index = linkURLList.getSelectedIndex();
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265 linkNameList.setSelectedIndex(index);
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269 linkNameList.addListSelectionListener(new ListSelectionListener()
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271 public void valueChanged(ListSelectionEvent e)
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273 int index = linkNameList.getSelectedIndex();
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274 linkURLList.setSelectedIndex(index);
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278 linkScrollPane.setBorder(null);
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279 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
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280 linkPanel.setLayout(borderLayout2);
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281 editLinkButtons.setLayout(gridLayout1);
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282 gridLayout1.setRows(3);
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283 linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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284 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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285 linkPanel2.setLayout(borderLayout3);
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286 linkURLList.setFont(verdana11);
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287 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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289 defaultBrowser.addMouseListener(new MouseAdapter()
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291 public void mouseClicked(MouseEvent e)
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293 if (e.getClickCount() > 1)
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295 defaultBrowser_mouseClicked(e);
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299 useProxy.setFont(verdana11);
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300 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
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301 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
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302 useProxy.setText("Use a proxy server");
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303 useProxy.addActionListener(new ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 useProxy_actionPerformed();
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310 jPanel1.setBorder(titledBorder1);
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311 jPanel1.setLayout(gridBagLayout1);
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312 sortby.setFont(verdana11);
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313 sortby.setBounds(new Rectangle(170, 200, 155, 21));
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314 sortLabel.setFont(verdana11);
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315 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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316 sortLabel.setText("Sort by ");
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317 jPanel2.setBounds(new Rectangle(7, 17, 158, 242));
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318 jPanel2.setLayout(gridLayout2);
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319 gridLayout2.setRows(8);
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320 jPanel3.setBounds(new Rectangle(168, 47, 274, 26));
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321 exportTab.setLayout(null);
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322 epsLabel.setFont(verdana11);
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323 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
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324 epsLabel.setText("EPS Rendering Style");
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325 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
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326 epsRendering.setFont(verdana11);
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327 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
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328 jLabel1.setFont(verdana11);
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329 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
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330 jLabel1.setText("/start-end suffix");
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331 jLabel1.setFont(verdana11);
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332 fastajv.setFont(verdana11);
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333 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
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334 jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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335 jLabel11.setHorizontalAlignment(SwingConstants.CENTER);
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336 jLabel11.setText("(/15-380)");
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337 clustaljv.setText("Clustal ");
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338 blcjv.setText("BLC ");
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339 fastajv.setText("Fasta ");
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340 msfjv.setText("MSF ");
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341 pfamjv.setText("PFAM ");
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342 pileupjv.setText("Pileup ");
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343 msfjv.setFont(verdana11);
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344 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
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345 pirjv.setText("PIR ");
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346 jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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347 jPanel11.setBorder(titledBorder2);
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348 jPanel11.setBounds(new Rectangle(63, 70, 137, 182));
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349 jPanel11.setLayout(gridLayout3);
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350 blcjv.setFont(verdana11);
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351 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
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352 clustaljv.setFont(verdana11);
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353 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
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354 pfamjv.setFont(verdana11);
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355 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
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356 pileupjv.setFont(verdana11);
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357 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
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358 pirjv.setFont(verdana11);
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359 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
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360 seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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361 seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);
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362 seqLimit.setText("Sequence Limits (/1-350)");
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363 seqLimit.setBounds(new Rectangle(172, 82, 195, 23));
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364 gridLayout3.setRows(9);
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365 jPanel2.add(fullScreen);
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366 jPanel2.add(annotations);
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367 jPanel2.add(dbRef);
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368 jPanel2.add(fontLabel);
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369 jPanel2.add(gapLabel);
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370 jPanel2.add(colourLabel);
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371 jPanel2.add(sortLabel);
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372 jPanel2.add(startupCheckbox);
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373 visualTab.add(gapSymbolCB);
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374 visualTab.add(colour);
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375 visualTab.add(seqLimit);
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376 visualTab.add(jPanel3);
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377 jPanel3.add(conservation);
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378 jPanel3.add(identity);
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379 jPanel3.add(quality);
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380 visualTab.add(sortby);
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381 visualTab.add(startupFileTextfield);
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382 visualTab.add(fontNameCB);
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383 visualTab.add(fontSizeCB);
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384 visualTab.add(fontStyleCB);
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385 visualTab.add(jPanel2);
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386 linkPanel.add(editLinkButtons, BorderLayout.EAST);
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387 editLinkButtons.add(newLink, null);
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388 editLinkButtons.add(editLink, null);
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389 editLinkButtons.add(deleteLink, null);
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390 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
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391 linkScrollPane.getViewport().add(linkPanel2, null);
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392 linkPanel2.add(linkURLList, BorderLayout.CENTER);
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393 linkPanel2.add(linkNameList, BorderLayout.WEST);
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394 okCancelPanel.add(ok);
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395 okCancelPanel.add(cancel);
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396 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
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398 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
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399 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
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400 , GridBagConstraints.WEST, GridBagConstraints.NONE,
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401 new Insets(0, 2, 4, 0), 5, 0));
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402 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
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403 , GridBagConstraints.WEST,
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404 GridBagConstraints.NONE,
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405 new Insets(0, 0, 4, 0), 11, 6));
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406 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
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407 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
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408 new Insets(16, 0, 0, 12), 359, -17));
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409 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
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410 , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
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411 new Insets(21, 0, 35, 12), 4, 6));
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412 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
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413 , GridBagConstraints.WEST, GridBagConstraints.NONE,
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414 new Insets(16, 0, 0, 0), 5, 1));
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415 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
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416 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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417 new Insets(0, 2, 4, 2), 54, 1));
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418 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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419 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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420 new Insets(0, 2, 4, 0), 263, 1));
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421 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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422 , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
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423 new Insets(15, 0, 0, 15), 307, 1));
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426 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
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427 , GridBagConstraints.WEST,
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428 GridBagConstraints.NONE,
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429 new Insets(0, 2, 5, 185), 2,
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431 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
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432 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
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433 gapSymbolCB.setRenderer(dlcr);
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435 tabbedPane.add(visualTab, "Visual");
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436 tabbedPane.add(connectTab,"Connections");
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437 tabbedPane.add(exportTab, "Output");
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438 jPanel11.add(jLabel1);
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439 jPanel11.add(jLabel11);
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440 jPanel11.add(blcjv);
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441 jPanel11.add(clustaljv);
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442 jPanel11.add(fastajv);
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443 jPanel11.add(msfjv);
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444 jPanel11.add(pfamjv);
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445 jPanel11.add(pileupjv);
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446 jPanel11.add(pirjv);
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447 exportTab.add(epsLabel);
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448 exportTab.add(epsRendering);
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449 exportTab.add(jPanel11);
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455 * @param e DOCUMENT ME!
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457 public void ok_actionPerformed(ActionEvent e)
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464 * @param e DOCUMENT ME!
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466 public void cancel_actionPerformed(ActionEvent e)
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473 * @param e DOCUMENT ME!
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475 public void annotations_actionPerformed(ActionEvent e)
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483 public void startupFileTextfield_mouseClicked()
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488 public void newLink_actionPerformed(ActionEvent e) {
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492 public void editLink_actionPerformed(ActionEvent e) {
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496 public void deleteLink_actionPerformed(ActionEvent e) {
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500 public void defaultBrowser_mouseClicked(MouseEvent e)
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505 public void linkURLList_keyTyped(KeyEvent e)
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510 public void useProxy_actionPerformed()
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512 proxyServerTB.setEnabled(useProxy.isSelected());
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513 proxyPortTB.setEnabled(useProxy.isSelected());
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