src/jalview/jbgui/GPreferences.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.jbgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.border.*;\r
  25 import javax.swing.event.*;\r
  26 import java.awt.Rectangle;\r
  27 \r
  28 /**\r
  29  * DOCUMENT ME!\r
  30  *\r
  31  * @author $author$\r
  32  * @version $Revision$\r
  33  */\r
  34 public class GPreferences\r
  35     extends JPanel\r
  36 {\r
  37   JTabbedPane tabbedPane = new JTabbedPane();\r
  38 \r
  39   JButton ok = new JButton();\r
  40   JButton cancel = new JButton();\r
  41   JPanel okCancelPanel = new JPanel();\r
  42   BorderLayout borderLayout1 = new BorderLayout();\r
  43   protected JCheckBox quality = new JCheckBox();\r
  44   JPanel visualTab = new JPanel();\r
  45   protected JCheckBox fullScreen = new JCheckBox();\r
  46   protected JCheckBox conservation = new JCheckBox();\r
  47   protected JCheckBox identity = new JCheckBox();\r
  48   protected JCheckBox annotations = new JCheckBox();\r
  49   JLabel gapLabel = new JLabel();\r
  50   protected JComboBox colour = new JComboBox();\r
  51   JLabel colourLabel = new JLabel();\r
  52   JLabel fontLabel = new JLabel();\r
  53   protected JComboBox fontSizeCB = new JComboBox();\r
  54   protected JComboBox fontStyleCB = new JComboBox();\r
  55   protected JComboBox fontNameCB = new JComboBox();\r
  56   protected JComboBox gapSymbolCB = new JComboBox();\r
  57   protected JCheckBox startupCheckbox = new JCheckBox();\r
  58   protected JTextField startupFileTextfield = new JTextField();\r
  59   JPanel connectTab = new JPanel();\r
  60   JLabel serverLabel = new JLabel();\r
  61   protected JList linkURLList = new JList();\r
  62   protected JTextField proxyServerTB = new JTextField();\r
  63   protected JTextField proxyPortTB = new JTextField();\r
  64   JLabel portLabel = new JLabel();\r
  65   JLabel browserLabel = new JLabel();\r
  66   protected JTextField defaultBrowser = new JTextField();\r
  67   JButton newLink = new JButton();\r
  68   JButton editLink = new JButton();\r
  69   JButton deleteLink = new JButton();\r
  70   JScrollPane linkScrollPane = new JScrollPane();\r
  71   JPanel linkPanel = new JPanel();\r
  72   BorderLayout borderLayout2 = new BorderLayout();\r
  73   JPanel editLinkButtons = new JPanel();\r
  74   GridLayout gridLayout1 = new GridLayout();\r
  75   protected JList linkNameList = new JList();\r
  76   JPanel linkPanel2 = new JPanel();\r
  77   BorderLayout borderLayout3 = new BorderLayout();\r
  78   protected JCheckBox useProxy = new JCheckBox();\r
  79   JPanel jPanel1 = new JPanel();\r
  80   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
  81   TitledBorder titledBorder2 = new TitledBorder("File Output");\r
  82   GridBagLayout gridBagLayout2 = new GridBagLayout();\r
  83   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
  84   GridBagLayout gridBagLayout3 = new GridBagLayout();\r
  85   protected JComboBox sortby = new JComboBox();\r
  86   JLabel sortLabel = new JLabel();\r
  87   JPanel jPanel2 = new JPanel();\r
  88   GridLayout gridLayout2 = new GridLayout();\r
  89   JPanel jPanel3 = new JPanel();\r
  90   JPanel exportTab = new JPanel();\r
  91   JLabel epsLabel = new JLabel();\r
  92   protected JComboBox epsRendering = new JComboBox();\r
  93   JLabel jLabel1 = new JLabel();\r
  94   protected JCheckBox blcjv = new JCheckBox();\r
  95   protected JCheckBox pileupjv = new JCheckBox();\r
  96   protected JCheckBox clustaljv = new JCheckBox();\r
  97   protected JCheckBox msfjv = new JCheckBox();\r
  98   protected JCheckBox fastajv = new JCheckBox();\r
  99   protected JCheckBox pfamjv = new JCheckBox();\r
 100   FlowLayout flowLayout1 = new FlowLayout();\r
 101   protected JCheckBox pirjv = new JCheckBox();\r
 102   JPanel jPanel11 = new JPanel();\r
 103   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
 104   protected JCheckBox seqLimit = new JCheckBox();\r
 105   GridLayout gridLayout3 = new GridLayout();\r
 106   protected JCheckBox smoothFont = new JCheckBox();\r
 107   JPanel calcTab = new JPanel();\r
 108   protected JCheckBox autoCalculateConsCheck = new JCheckBox();\r
 109   protected JCheckBox padGaps = new JCheckBox();\r
 110   protected JCheckBox modellerOutput = new JCheckBox();\r
 111   protected JPanel dasPanel = new JPanel();\r
 112   BorderLayout borderLayout4 = new BorderLayout();\r
 113   protected JCheckBox wrap = new JCheckBox();\r
 114   protected JCheckBox rightAlign = new JCheckBox();\r
 115   protected JCheckBox idItalics = new JCheckBox();\r
 116   protected JCheckBox openoverv = new JCheckBox();\r
 117   /**\r
 118    * Creates a new GPreferences object.\r
 119    */\r
 120   public GPreferences()\r
 121   {\r
 122     try\r
 123     {\r
 124       jbInit();\r
 125     }\r
 126     catch (Exception ex)\r
 127     {\r
 128       ex.printStackTrace();\r
 129     }\r
 130   }\r
 131 \r
 132   /**\r
 133    * DOCUMENT ME!\r
 134    *\r
 135    * @throws Exception DOCUMENT ME!\r
 136    */\r
 137   private void jbInit()\r
 138       throws Exception\r
 139   {\r
 140     this.setLayout(borderLayout1);\r
 141     ok.setText("OK");\r
 142     ok.addActionListener(new ActionListener()\r
 143     {\r
 144       public void actionPerformed(ActionEvent e)\r
 145       {\r
 146         ok_actionPerformed(e);\r
 147       }\r
 148     });\r
 149     cancel.setText("Cancel");\r
 150     cancel.addActionListener(new ActionListener()\r
 151     {\r
 152       public void actionPerformed(ActionEvent e)\r
 153       {\r
 154         cancel_actionPerformed(e);\r
 155       }\r
 156     });\r
 157     quality.setEnabled(false);\r
 158     quality.setFont(verdana11);\r
 159     quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
 160     quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
 161     quality.setSelected(true);\r
 162     quality.setText("Quality");\r
 163     visualTab.setBorder(new TitledBorder("Open new alignment"));\r
 164     visualTab.setLayout(null);\r
 165     fullScreen.setFont(verdana11);\r
 166     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
 167     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
 168     fullScreen.setText("Maximise Window");\r
 169     conservation.setEnabled(false);\r
 170     conservation.setFont(verdana11);\r
 171     conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
 172     conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
 173     conservation.setSelected(true);\r
 174     conservation.setText("Conservation");\r
 175     identity.setEnabled(false);\r
 176     identity.setFont(verdana11);\r
 177     identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
 178     identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
 179     identity.setSelected(true);\r
 180     identity.setText("Consensus");\r
 181     annotations.setFont(verdana11);\r
 182     annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
 183     annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
 184     annotations.setSelected(true);\r
 185     annotations.setText("Show Annotations");\r
 186     annotations.addActionListener(new ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         annotations_actionPerformed(e);\r
 191       }\r
 192     });\r
 193     gapLabel.setFont(verdana11);\r
 194     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 195     gapLabel.setText("Gap Symbol ");\r
 196     colour.setFont(verdana11);\r
 197     colour.setBounds(new Rectangle(172, 225, 155, 21));\r
 198     colourLabel.setFont(verdana11);\r
 199     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 200     colourLabel.setText("Colour ");\r
 201     fontLabel.setFont(verdana11);\r
 202     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 203     fontLabel.setText("Font ");\r
 204     fontSizeCB.setFont(verdana11);\r
 205     fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));\r
 206     fontStyleCB.setFont(verdana11);\r
 207     fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));\r
 208     fontNameCB.setFont(verdana11);\r
 209     fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));\r
 210     gapSymbolCB.setFont(verdana11);\r
 211     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));\r
 212     startupCheckbox.setText("Open file");\r
 213     startupCheckbox.setFont(verdana11);\r
 214     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
 215     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
 216     startupCheckbox.setSelected(true);\r
 217     startupFileTextfield.setFont(verdana11);\r
 218     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));\r
 219     startupFileTextfield.addMouseListener(new MouseAdapter()\r
 220     {\r
 221       public void mouseClicked(MouseEvent e)\r
 222       {\r
 223         if (e.getClickCount() > 1)\r
 224         {\r
 225           startupFileTextfield_mouseClicked();\r
 226         }\r
 227       }\r
 228     });\r
 229 \r
 230     connectTab.setLayout(gridBagLayout3);\r
 231     serverLabel.setText("Address");\r
 232     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 233     serverLabel.setFont(verdana11);\r
 234     proxyServerTB.setFont(verdana11);\r
 235     proxyPortTB.setFont(verdana11);\r
 236     portLabel.setFont(verdana11);\r
 237     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 238     portLabel.setText("Port");\r
 239     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
 240     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
 241     browserLabel.setText("Default Browser (Unix)");\r
 242     defaultBrowser.setFont(verdana11);\r
 243     defaultBrowser.setText("");\r
 244     newLink.setText("New");\r
 245     newLink.addActionListener(new java.awt.event.ActionListener()\r
 246     {\r
 247       public void actionPerformed(ActionEvent e)\r
 248       {\r
 249         newLink_actionPerformed(e);\r
 250       }\r
 251     });\r
 252     editLink.setText("Edit");\r
 253     editLink.addActionListener(new java.awt.event.ActionListener()\r
 254     {\r
 255       public void actionPerformed(ActionEvent e)\r
 256       {\r
 257         editLink_actionPerformed(e);\r
 258       }\r
 259     });\r
 260     deleteLink.setText("Delete");\r
 261     deleteLink.addActionListener(new java.awt.event.ActionListener()\r
 262     {\r
 263       public void actionPerformed(ActionEvent e)\r
 264       {\r
 265         deleteLink_actionPerformed(e);\r
 266       }\r
 267     });\r
 268 \r
 269     linkURLList.addListSelectionListener(new ListSelectionListener()\r
 270     {\r
 271       public void valueChanged(ListSelectionEvent e)\r
 272       {\r
 273         int index = linkURLList.getSelectedIndex();\r
 274         linkNameList.setSelectedIndex(index);\r
 275       }\r
 276     });\r
 277 \r
 278     linkNameList.addListSelectionListener(new ListSelectionListener()\r
 279     {\r
 280       public void valueChanged(ListSelectionEvent e)\r
 281       {\r
 282         int index = linkNameList.getSelectedIndex();\r
 283         linkURLList.setSelectedIndex(index);\r
 284       }\r
 285     });\r
 286 \r
 287     linkScrollPane.setBorder(null);\r
 288     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));\r
 289     linkPanel.setLayout(borderLayout2);\r
 290     editLinkButtons.setLayout(gridLayout1);\r
 291     gridLayout1.setRows(3);\r
 292     linkNameList.setFont(verdana11);\r
 293     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 294     linkPanel2.setLayout(borderLayout3);\r
 295     linkURLList.setFont(verdana11);\r
 296     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 297 \r
 298     defaultBrowser.addMouseListener(new MouseAdapter()\r
 299     {\r
 300       public void mouseClicked(MouseEvent e)\r
 301       {\r
 302         if (e.getClickCount() > 1)\r
 303         {\r
 304           defaultBrowser_mouseClicked(e);\r
 305         }\r
 306       }\r
 307     });\r
 308     useProxy.setFont(verdana11);\r
 309     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
 310     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
 311     useProxy.setText("Use a proxy server");\r
 312     useProxy.addActionListener(new ActionListener()\r
 313     {\r
 314       public void actionPerformed(ActionEvent e)\r
 315       {\r
 316         useProxy_actionPerformed();\r
 317       }\r
 318     });\r
 319     jPanel1.setBorder(titledBorder1);\r
 320     jPanel1.setLayout(gridBagLayout1);\r
 321     sortby.setFont(verdana11);\r
 322     sortby.setBounds(new Rectangle(172, 249, 155, 21));\r
 323     sortLabel.setFont(verdana11);\r
 324     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 325     sortLabel.setText("Sort by ");\r
 326     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));\r
 327     jPanel2.setLayout(gridLayout2);\r
 328     gridLayout2.setRows(12);\r
 329     jPanel3.setBounds(new Rectangle(173, 35, 274, 26));\r
 330     exportTab.setLayout(null);\r
 331     epsLabel.setFont(verdana11);\r
 332     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
 333     epsLabel.setText("EPS Rendering Style");\r
 334     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));\r
 335     epsRendering.setFont(verdana11);\r
 336     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
 337     jLabel1.setFont(verdana11);\r
 338     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
 339     jLabel1.setText("Append /start-end (/15-380)");\r
 340     jLabel1.setFont(verdana11);\r
 341     fastajv.setFont(verdana11);\r
 342     fastajv.setHorizontalAlignment(SwingConstants.LEFT);\r
 343     clustaljv.setText("Clustal     ");\r
 344     blcjv.setText("BLC     ");\r
 345     fastajv.setText("Fasta     ");\r
 346     msfjv.setText("MSF     ");\r
 347     pfamjv.setText("PFAM     ");\r
 348     pileupjv.setText("Pileup     ");\r
 349     msfjv.setFont(verdana11);\r
 350     msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
 351     pirjv.setText("PIR     ");\r
 352     jPanel11.setFont(verdana11);\r
 353     jPanel11.setBorder(titledBorder2);\r
 354     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
 355     jPanel11.setLayout(gridLayout3);\r
 356     blcjv.setFont(verdana11);\r
 357     blcjv.setHorizontalAlignment(SwingConstants.LEFT);\r
 358     clustaljv.setFont(verdana11);\r
 359     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);\r
 360     pfamjv.setFont(verdana11);\r
 361     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);\r
 362     pileupjv.setFont(verdana11);\r
 363     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
 364     pirjv.setFont(verdana11);\r
 365     pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
 366     seqLimit.setFont(verdana11);\r
 367     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
 368     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);\r
 369     seqLimit.setText("Full Sequence Id");\r
 370     gridLayout3.setRows(8);\r
 371     smoothFont.setFont(verdana11);\r
 372     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);\r
 373     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);\r
 374     smoothFont.setText("Smooth Font");\r
 375     calcTab.setLayout(null);\r
 376     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 377     autoCalculateConsCheck.setText("AutoCalculate Consensus");\r
 378     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));\r
 379     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 380     padGaps.setText("Pad gaps when editing");\r
 381     padGaps.setBounds(new Rectangle(22, 94, 168, 23));\r
 382     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 383     modellerOutput.setText("Use Modeller Output");\r
 384     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
 385     dasPanel.setLayout(borderLayout4);\r
 386     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 387     wrap.setHorizontalAlignment(SwingConstants.TRAILING);\r
 388     wrap.setHorizontalTextPosition(SwingConstants.LEADING);\r
 389     wrap.setText("Wrap Alignment");\r
 390     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 391     rightAlign.setForeground(Color.black);\r
 392     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);\r
 393     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);\r
 394     rightAlign.setText("Right Align Ids");\r
 395     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 396     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);\r
 397     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);\r
 398     idItalics.setText("Sequence Name Italics");\r
 399     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 400     openoverv.setActionCommand("Open Overview");\r
 401     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);\r
 402     openoverv.setHorizontalTextPosition(SwingConstants.LEADING);\r
 403     openoverv.setText("Open Overview Window");\r
 404     openoverv.setBounds(new Rectangle(169, 17, 200, 23));\r
 405     jPanel2.add(fullScreen);\r
 406     jPanel2.add(annotations);\r
 407     jPanel2.add(seqLimit);\r
 408     jPanel2.add(rightAlign);\r
 409     jPanel2.add(fontLabel);\r
 410     jPanel2.add(idItalics);\r
 411     jPanel2.add(smoothFont);\r
 412     jPanel2.add(wrap);\r
 413     jPanel2.add(gapLabel);\r
 414     jPanel2.add(colourLabel);\r
 415     jPanel2.add(sortLabel);\r
 416     jPanel2.add(startupCheckbox);\r
 417     visualTab.add(openoverv);\r
 418     visualTab.add(startupFileTextfield);\r
 419     visualTab.add(sortby);\r
 420     visualTab.add(colour);\r
 421     visualTab.add(gapSymbolCB);\r
 422     visualTab.add(jPanel3);\r
 423     visualTab.add(fontNameCB);\r
 424     visualTab.add(fontSizeCB);\r
 425     visualTab.add(fontStyleCB);\r
 426     jPanel3.add(conservation);\r
 427     jPanel3.add(identity);\r
 428     jPanel3.add(quality);\r
 429     visualTab.add(jPanel2);\r
 430     linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
 431     editLinkButtons.add(newLink, null);\r
 432     editLinkButtons.add(editLink, null);\r
 433     editLinkButtons.add(deleteLink, null);\r
 434     linkPanel.add(linkScrollPane, BorderLayout.CENTER);\r
 435     linkScrollPane.getViewport().add(linkPanel2, null);\r
 436     linkPanel2.add(linkURLList, BorderLayout.CENTER);\r
 437     linkPanel2.add(linkNameList, BorderLayout.WEST);\r
 438     okCancelPanel.add(ok);\r
 439     okCancelPanel.add(cancel);\r
 440     this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
 441 \r
 442     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);\r
 443     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
 444         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
 445         new Insets(0, 2, 4, 0), 5, 0));\r
 446     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0\r
 447                                                   , GridBagConstraints.WEST,\r
 448                                                   GridBagConstraints.NONE,\r
 449                                                   new Insets(0, 0, 4, 0), 11, 6));\r
 450     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0\r
 451         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
 452         new Insets(16, 0, 0, 12), 359, -17));\r
 453     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
 454         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
 455         new Insets(21, 0, 35, 12), 4, 6));\r
 456     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
 457         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
 458         new Insets(16, 0, 0, 0), 5, 1));\r
 459     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0\r
 460         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
 461         new Insets(0, 2, 4, 2), 54, 1));\r
 462     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
 463         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
 464         new Insets(0, 2, 4, 0), 263, 1));\r
 465     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
 466         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
 467         new Insets(15, 0, 0, 15), 307, 1));\r
 468 \r
 469     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
 470                                                  , GridBagConstraints.WEST,\r
 471                                                  GridBagConstraints.NONE,\r
 472                                                  new Insets(0, 2, 5, 185), 2,\r
 473                                                  -4));\r
 474     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
 475     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
 476     gapSymbolCB.setRenderer(dlcr);\r
 477 \r
 478     tabbedPane.add(visualTab, "Visual");\r
 479     tabbedPane.add(connectTab, "Connections");\r
 480     tabbedPane.add(exportTab, "Output");\r
 481     jPanel11.add(jLabel1);\r
 482     jPanel11.add(blcjv);\r
 483     jPanel11.add(clustaljv);\r
 484     jPanel11.add(fastajv);\r
 485     jPanel11.add(msfjv);\r
 486     jPanel11.add(pfamjv);\r
 487     jPanel11.add(pileupjv);\r
 488     jPanel11.add(pirjv);\r
 489     exportTab.add(modellerOutput);\r
 490     tabbedPane.add(calcTab, "Editing");\r
 491     calcTab.add(autoCalculateConsCheck);\r
 492     calcTab.add(padGaps);\r
 493     tabbedPane.add(dasPanel, "DAS Settings");\r
 494 \r
 495     exportTab.add(epsLabel);\r
 496     exportTab.add(epsRendering);\r
 497     exportTab.add(jPanel11);\r
 498   }\r
 499 \r
 500   /**\r
 501    * DOCUMENT ME!\r
 502    *\r
 503    * @param e DOCUMENT ME!\r
 504    */\r
 505   public void ok_actionPerformed(ActionEvent e)\r
 506   {\r
 507   }\r
 508 \r
 509   /**\r
 510    * DOCUMENT ME!\r
 511    *\r
 512    * @param e DOCUMENT ME!\r
 513    */\r
 514   public void cancel_actionPerformed(ActionEvent e)\r
 515   {\r
 516   }\r
 517 \r
 518   /**\r
 519    * DOCUMENT ME!\r
 520    *\r
 521    * @param e DOCUMENT ME!\r
 522    */\r
 523   public void annotations_actionPerformed(ActionEvent e)\r
 524   {\r
 525   }\r
 526 \r
 527   /**\r
 528    * DOCUMENT ME!\r
 529    */\r
 530   public void startupFileTextfield_mouseClicked()\r
 531   {\r
 532   }\r
 533 \r
 534   public void newLink_actionPerformed(ActionEvent e)\r
 535   {\r
 536 \r
 537   }\r
 538 \r
 539   public void editLink_actionPerformed(ActionEvent e)\r
 540   {\r
 541 \r
 542   }\r
 543 \r
 544   public void deleteLink_actionPerformed(ActionEvent e)\r
 545   {\r
 546 \r
 547   }\r
 548 \r
 549   public void defaultBrowser_mouseClicked(MouseEvent e)\r
 550   {\r
 551 \r
 552   }\r
 553 \r
 554   public void linkURLList_keyTyped(KeyEvent e)\r
 555   {\r
 556 \r
 557   }\r
 558 \r
 559   public void useProxy_actionPerformed()\r
 560   {\r
 561     proxyServerTB.setEnabled(useProxy.isSelected());\r
 562     proxyPortTB.setEnabled(useProxy.isSelected());\r
 563   }\r
 564 \r
 565 }\r