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