src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.border.*;
  26 import javax.swing.event.*;
  27 import java.awt.Rectangle;
  28
  29 /**
  30  * DOCUMENT ME!
  31  *
  32  * @author $author$
  33  * @version $Revision$
  34  */
  35 public class GPreferences extends JPanel
  36 {
  37   JTabbedPane tabbedPane = new JTabbedPane();
  38
  39   JButton ok = new JButton();
  40
  41   JButton cancel = new JButton();
  42
  43   JPanel okCancelPanel = new JPanel();
  44
  45   BorderLayout borderLayout1 = new BorderLayout();
  46
  47   protected JCheckBox quality = new JCheckBox();
  48
  49   JPanel visualTab = new JPanel();
  50
  51   protected JCheckBox fullScreen = new JCheckBox();
  52
  53   protected JCheckBox conservation = new JCheckBox();
  54
  55   protected JCheckBox identity = new JCheckBox();
  56
  57   protected JCheckBox annotations = new JCheckBox();
  58
  59   JLabel gapLabel = new JLabel();
  60
  61   protected JComboBox colour = new JComboBox();
  62
  63   JLabel colourLabel = new JLabel();
  64
  65   JLabel fontLabel = new JLabel();
  66
  67   protected JComboBox fontSizeCB = new JComboBox();
  68
  69   protected JComboBox fontStyleCB = new JComboBox();
  70
  71   protected JComboBox fontNameCB = new JComboBox();
  72
  73   protected JComboBox gapSymbolCB = new JComboBox();
  74
  75   protected JCheckBox startupCheckbox = new JCheckBox();
  76
  77   protected JTextField startupFileTextfield = new JTextField();
  78
  79   JPanel connectTab = new JPanel();
  80
  81   JLabel serverLabel = new JLabel();
  82
  83   protected JList linkURLList = new JList();
  84
  85   protected JTextField proxyServerTB = new JTextField();
  86
  87   protected JTextField proxyPortTB = new JTextField();
  88
  89   JLabel portLabel = new JLabel();
  90
  91   JLabel browserLabel = new JLabel();
  92
  93   protected JTextField defaultBrowser = new JTextField();
  94
  95   JButton newLink = new JButton();
  96
  97   JButton editLink = new JButton();
  98
  99   JButton deleteLink = new JButton();
 100
 101   JScrollPane linkScrollPane = new JScrollPane();
 102
 103   JPanel linkPanel = new JPanel();
 104
 105   BorderLayout borderLayout2 = new BorderLayout();
 106
 107   JPanel editLinkButtons = new JPanel();
 108
 109   GridLayout gridLayout1 = new GridLayout();
 110
 111   protected JList linkNameList = new JList();
 112
 113   JPanel linkPanel2 = new JPanel();
 114
 115   BorderLayout borderLayout3 = new BorderLayout();
 116
 117   protected JCheckBox useProxy = new JCheckBox();
 118
 119   JPanel jPanel1 = new JPanel();
 120
 121   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
 122
 123   TitledBorder titledBorder2 = new TitledBorder("File Output");
 124
 125   GridBagLayout gridBagLayout2 = new GridBagLayout();
 126
 127   GridBagLayout gridBagLayout1 = new GridBagLayout();
 128
 129   GridBagLayout gridBagLayout3 = new GridBagLayout();
 130
 131   protected JComboBox sortby = new JComboBox();
 132
 133   JLabel sortLabel = new JLabel();
 134
 135   JPanel jPanel2 = new JPanel();
 136
 137   GridLayout gridLayout2 = new GridLayout();
 138
 139   JPanel jPanel3 = new JPanel();
 140
 141   JPanel autoAnnotSettings1 = new JPanel();
 142
 143   JPanel autoAnnotSettings2 = new JPanel();
 144
 145   JPanel exportTab = new JPanel();
 146
 147   JLabel epsLabel = new JLabel();
 148
 149   protected JComboBox epsRendering = new JComboBox();
 150
 151   JLabel jLabel1 = new JLabel();
 152
 153   protected JCheckBox blcjv = new JCheckBox();
 154
 155   protected JCheckBox pileupjv = new JCheckBox();
 156
 157   protected JCheckBox clustaljv = new JCheckBox();
 158
 159   protected JCheckBox msfjv = new JCheckBox();
 160
 161   protected JCheckBox fastajv = new JCheckBox();
 162
 163   protected JCheckBox pfamjv = new JCheckBox();
 164
 165   FlowLayout flowLayout1 = new FlowLayout();
 166
 167   protected JCheckBox pirjv = new JCheckBox();
 168
 169   JPanel jPanel11 = new JPanel();
 170
 171   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
 172
 173   protected JCheckBox seqLimit = new JCheckBox();
 174
 175   GridLayout gridLayout3 = new GridLayout();
 176
 177   protected JCheckBox smoothFont = new JCheckBox();
 178
 179   JPanel calcTab = new JPanel();
 180
 181   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 182
 183   protected JCheckBox padGaps = new JCheckBox();
 184
 185   protected JCheckBox modellerOutput = new JCheckBox();
 186
 187   protected JPanel dasPanel = new JPanel();
 188
 189   BorderLayout borderLayout4 = new BorderLayout();
 190
 191   protected JCheckBox wrap = new JCheckBox();
 192
 193   protected JCheckBox rightAlign = new JCheckBox();
 194
 195   protected JCheckBox showUnconserved = new JCheckBox();
 196
 197   protected JCheckBox idItalics = new JCheckBox();
 198
 199   protected JCheckBox openoverv = new JCheckBox();
 200   protected JCheckBox usagestats = new JCheckBox();
 201   protected JCheckBox questionnaire = new JCheckBox();
 202   protected JCheckBox versioncheck = new JCheckBox();
 203   protected JLabel showGroupbits = new JLabel();
 204   protected JLabel showConsensbits = new JLabel();
 205   protected JCheckBox showConsensProfile = new JCheckBox();
 206   protected JCheckBox showConsensHistogram = new JCheckBox();
 207   protected JCheckBox showGroupConsensus = new JCheckBox();
 208   protected JCheckBox showGroupConservation = new JCheckBox();
 209
 210   /**
 211    * Creates a new GPreferences object.
 212    */
 213   public GPreferences()
 214   {
 215     try
 216     {
 217       jbInit();
 218     } catch (Exception ex)
 219     {
 220       ex.printStackTrace();
 221     }
 222   }
 223
 224   /**
 225    * DOCUMENT ME!
 226    *
 227    * @throws Exception
 228    *                 DOCUMENT ME!
 229    */
 230   private void jbInit() throws Exception
 231   {
 232     this.setLayout(borderLayout1);
 233     ok.setText("OK");
 234     ok.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         ok_actionPerformed(e);
 239       }
 240     });
 241     cancel.setText("Cancel");
 242     cancel.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         cancel_actionPerformed(e);
 247       }
 248     });
 249     quality.setEnabled(false);
 250     quality.setFont(verdana11);
 251     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 252     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 253     quality.setSelected(true);
 254     quality.setText("Quality");
 255     visualTab.setBorder(new TitledBorder("Open new alignment"));
 256     visualTab.setLayout(null);
 257     fullScreen.setFont(verdana11);
 258     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 259     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 260     fullScreen.setText("Maximise Window");
 261     conservation.setEnabled(false);
 262     conservation.setFont(verdana11);
 263     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 264     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 265     conservation.setSelected(true);
 266     conservation.setText("Conservation");
 267     identity.setEnabled(false);
 268     identity.setFont(verdana11);
 269     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 270     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 271     identity.setSelected(true);
 272     identity.setText("Consensus");
 273     showGroupbits.setFont(verdana11);
 274     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 275     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 276     showGroupbits.setText("Group:");
 277     showConsensbits.setFont(verdana11);
 278     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 279     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 280     showConsensbits.setText("Consensus:");
 281     showConsensHistogram.setEnabled(false);
 282     showConsensHistogram.setFont(verdana11);
 283     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 284     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 285     showConsensHistogram.setSelected(true);
 286     showConsensHistogram.setText("Histogram");
 287     showConsensProfile.setEnabled(false);
 288     showConsensProfile.setFont(verdana11);
 289     showConsensProfile.setHorizontalAlignment(SwingConstants.RIGHT);
 290     showConsensProfile.setHorizontalTextPosition(SwingConstants.LEFT);
 291     showConsensProfile.setSelected(true);
 292     showConsensProfile.setText("Profile");
 293     showGroupConsensus.setEnabled(false);
 294     showGroupConsensus.setFont(verdana11);
 295     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 296     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 297     showGroupConsensus.setSelected(true);
 298     showGroupConsensus.setText("Consensus");
 299     showGroupConservation.setEnabled(false);
 300     showGroupConservation.setFont(verdana11);
 301     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 302     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 303     showGroupConservation.setSelected(true);
 304     showGroupConservation.setText("Conservation");
 305     annotations.setFont(verdana11);
 306     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 307     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
 308     annotations.setSelected(true);
 309     annotations.setText("Show Annotations");
 310     annotations.addActionListener(new ActionListener()
 311     {
 312       public void actionPerformed(ActionEvent e)
 313       {
 314         annotations_actionPerformed(e);
 315       }
 316     });
 317     showUnconserved.setFont(verdana11);
 318     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 319     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 320     //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 321     showUnconserved.setSelected(true);
 322     showUnconserved.setText("Show Unconserved");
 323     showUnconserved.addActionListener(new ActionListener()
 324     {
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         showunconserved_actionPerformed(e);
 328       }
 329     });
 330
 331     gapLabel.setFont(verdana11);
 332     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 333     gapLabel.setText("Gap Symbol ");
 334     colour.setFont(verdana11);
 335     colour.setBounds(new Rectangle(172, 225, 155, 21));
 336     colourLabel.setFont(verdana11);
 337     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 338     colourLabel.setText("Colour ");
 339     fontLabel.setFont(verdana11);
 340     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 341     fontLabel.setText("Font ");
 342     fontSizeCB.setFont(verdana11);
 343     fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
 344     fontStyleCB.setFont(verdana11);
 345     fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
 346     fontNameCB.setFont(verdana11);
 347     fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
 348     gapSymbolCB.setFont(verdana11);
 349     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
 350     startupCheckbox.setText("Open file");
 351     startupCheckbox.setFont(verdana11);
 352     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 353     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 354     startupCheckbox.setSelected(true);
 355     startupFileTextfield.setFont(verdana11);
 356     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 357     startupFileTextfield.addMouseListener(new MouseAdapter()
 358     {
 359       public void mouseClicked(MouseEvent e)
 360       {
 361         if (e.getClickCount() > 1)
 362         {
 363           startupFileTextfield_mouseClicked();
 364         }
 365       }
 366     });
 367
 368     connectTab.setLayout(gridBagLayout3);
 369     serverLabel.setText("Address");
 370     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 371     serverLabel.setFont(verdana11);
 372     proxyServerTB.setFont(verdana11);
 373     proxyPortTB.setFont(verdana11);
 374     portLabel.setFont(verdana11);
 375     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 376     portLabel.setText("Port");
 377     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 378     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 379     browserLabel.setText("Default Browser (Unix)");
 380     defaultBrowser.setFont(verdana11);
 381     defaultBrowser.setText("");
 382     usagestats.setText("Send usage statistics");
 383     usagestats.setFont(verdana11);
 384     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 385     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 386     questionnaire.setText("Check for questionnaires");
 387     questionnaire.setFont(verdana11);
 388     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 389     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 390     versioncheck.setText("Check for latest version");
 391     versioncheck.setFont(verdana11);
 392     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 393     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 394     newLink.setText("New");
 395     newLink.addActionListener(new java.awt.event.ActionListener()
 396     {
 397       public void actionPerformed(ActionEvent e)
 398       {
 399         newLink_actionPerformed(e);
 400       }
 401     });
 402     editLink.setText("Edit");
 403     editLink.addActionListener(new java.awt.event.ActionListener()
 404     {
 405       public void actionPerformed(ActionEvent e)
 406       {
 407         editLink_actionPerformed(e);
 408       }
 409     });
 410     deleteLink.setText("Delete");
 411     deleteLink.addActionListener(new java.awt.event.ActionListener()
 412     {
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         deleteLink_actionPerformed(e);
 416       }
 417     });
 418
 419     linkURLList.addListSelectionListener(new ListSelectionListener()
 420     {
 421       public void valueChanged(ListSelectionEvent e)
 422       {
 423         int index = linkURLList.getSelectedIndex();
 424         linkNameList.setSelectedIndex(index);
 425       }
 426     });
 427
 428     linkNameList.addListSelectionListener(new ListSelectionListener()
 429     {
 430       public void valueChanged(ListSelectionEvent e)
 431       {
 432         int index = linkNameList.getSelectedIndex();
 433         linkURLList.setSelectedIndex(index);
 434       }
 435     });
 436
 437     linkScrollPane.setBorder(null);
 438     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 439     linkPanel.setLayout(borderLayout2);
 440     editLinkButtons.setLayout(gridLayout1);
 441     gridLayout1.setRows(3);
 442     linkNameList.setFont(verdana11);
 443     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 444     linkPanel2.setLayout(borderLayout3);
 445     linkURLList.setFont(verdana11);
 446     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 447
 448     defaultBrowser.addMouseListener(new MouseAdapter()
 449     {
 450       public void mouseClicked(MouseEvent e)
 451       {
 452         if (e.getClickCount() > 1)
 453         {
 454           defaultBrowser_mouseClicked(e);
 455         }
 456       }
 457     });
 458     useProxy.setFont(verdana11);
 459     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 460     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 461     useProxy.setText("Use a proxy server");
 462     useProxy.addActionListener(new ActionListener()
 463     {
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         useProxy_actionPerformed();
 467       }
 468     });
 469     jPanel1.setBorder(titledBorder1);
 470     jPanel1.setLayout(gridBagLayout1);
 471     sortby.setFont(verdana11);
 472     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 473     sortLabel.setFont(verdana11);
 474     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 475     sortLabel.setText("Sort by ");
 476     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 477     jPanel2.setLayout(gridLayout2);
 478     gridLayout2.setRows(13);
 479     jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
 480     autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
 481     autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
 482     exportTab.setLayout(null);
 483     epsLabel.setFont(verdana11);
 484     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 485     epsLabel.setText("EPS Rendering Style");
 486     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 487     epsRendering.setFont(verdana11);
 488     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 489     jLabel1.setFont(verdana11);
 490     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 491     jLabel1.setText("Append /start-end (/15-380)");
 492     jLabel1.setFont(verdana11);
 493     fastajv.setFont(verdana11);
 494     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 495     clustaljv.setText("Clustal     ");
 496     blcjv.setText("BLC     ");
 497     fastajv.setText("Fasta     ");
 498     msfjv.setText("MSF     ");
 499     pfamjv.setText("PFAM     ");
 500     pileupjv.setText("Pileup     ");
 501     msfjv.setFont(verdana11);
 502     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 503     pirjv.setText("PIR     ");
 504     jPanel11.setFont(verdana11);
 505     jPanel11.setBorder(titledBorder2);
 506     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 507     jPanel11.setLayout(gridLayout3);
 508     blcjv.setFont(verdana11);
 509     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 510     clustaljv.setFont(verdana11);
 511     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 512     pfamjv.setFont(verdana11);
 513     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 514     pileupjv.setFont(verdana11);
 515     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 516     pirjv.setFont(verdana11);
 517     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 518     seqLimit.setFont(verdana11);
 519     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 520     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 521     seqLimit.setText("Full Sequence Id");
 522     gridLayout3.setRows(8);
 523     smoothFont.setFont(verdana11);
 524     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 525     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 526     smoothFont.setText("Smooth Font");
 527     calcTab.setLayout(null);
 528     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 529             11));
 530     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 531     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 532     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 533     padGaps.setText("Pad gaps when editing");
 534     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 535     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 536     modellerOutput.setText("Use Modeller Output");
 537     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 538     dasPanel.setLayout(borderLayout4);
 539     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 540     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 541     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 542     wrap.setText("Wrap Alignment");
 543     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 544     rightAlign.setForeground(Color.black);
 545     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 546     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 547     rightAlign.setText("Right Align Ids");
 548     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 549     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 550     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 551     idItalics.setText("Sequence Name Italics");
 552     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 553     openoverv.setActionCommand("Open Overview");
 554     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 555     openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
 556     openoverv.setText("Open Overview Window");
 557     openoverv.setBounds(new Rectangle(169, 17, 200, 23));
 558     jPanel2.add(fullScreen);
 559     jPanel2.add(annotations);
 560     jPanel2.add(seqLimit);
 561     jPanel2.add(rightAlign);
 562     jPanel2.add(fontLabel);
 563     jPanel2.add(showUnconserved);
 564     jPanel2.add(idItalics);
 565     jPanel2.add(smoothFont);
 566     jPanel2.add(wrap);
 567     jPanel2.add(gapLabel);
 568     jPanel2.add(colourLabel);
 569     jPanel2.add(sortLabel);
 570     jPanel2.add(startupCheckbox);
 571     visualTab.add(openoverv);
 572     visualTab.add(startupFileTextfield);
 573     visualTab.add(sortby);
 574     visualTab.add(colour);
 575     visualTab.add(gapSymbolCB);
 576     visualTab.add(jPanel3);
 577     visualTab.add(fontNameCB);
 578     visualTab.add(fontSizeCB);
 579     visualTab.add(fontStyleCB);
 580     visualTab.add(autoAnnotSettings1);
 581     visualTab.add(autoAnnotSettings2);
 582     jPanel3.add(conservation);
 583     jPanel3.add(identity);
 584     jPanel3.add(quality);
 585     autoAnnotSettings1.setLayout(new FlowLayout());
 586     autoAnnotSettings2.setLayout(new FlowLayout());
 587     autoAnnotSettings1.add(showConsensbits);
 588     autoAnnotSettings1.add(showConsensHistogram);
 589     autoAnnotSettings1.add(showConsensProfile);
 590     autoAnnotSettings2.add(showGroupbits);
 591     autoAnnotSettings2.add(showGroupConsensus);
 592     autoAnnotSettings2.add(showGroupConservation);
 593     visualTab.add(jPanel2);
 594
 595     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 596     editLinkButtons.add(newLink, null);
 597     editLinkButtons.add(editLink, null);
 598     editLinkButtons.add(deleteLink, null);
 599     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 600     linkScrollPane.getViewport().add(linkPanel2, null);
 601     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 602     linkPanel2.add(linkNameList, BorderLayout.WEST);
 603     okCancelPanel.add(ok);
 604     okCancelPanel.add(cancel);
 605     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 606
 607     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 608     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 609             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 610                     2, 4, 0), 5, 0));
 611     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 612             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 613                     0, 4, 0), 11, 6));
 614     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 615             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 616                     16, 0, 0, 12), 359, -17));
 617     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 618             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 619                     21, 0, 35, 12), 4, 6));
 620     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 621             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 622             new Insets(16, 0, 0, 0), 5, 1));
 623     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 624             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 625             new Insets(0, 2, 4, 2), 54, 1));
 626     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 627             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 628             new Insets(0, 2, 4, 0), 263, 1));
 629     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 630             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 631             new Insets(15, 0, 0, 15), 307, 1));
 632     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
 633             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 634             new Insets(0, 2, 4,2), 70, 1));
 635     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 636             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 637             new Insets(0, 2, 4,2), 70, 1));
 638     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 639             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 640             new Insets(0, 2, 4,2), 70, 1));
 641
 642     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 643             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 644                     2, 5, 185), 2, -4));
 645     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 646     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 647     gapSymbolCB.setRenderer(dlcr);
 648
 649     tabbedPane.add(visualTab, "Visual");
 650     tabbedPane.add(connectTab, "Connections");
 651     tabbedPane.add(exportTab, "Output");
 652     jPanel11.add(jLabel1);
 653     jPanel11.add(blcjv);
 654     jPanel11.add(clustaljv);
 655     jPanel11.add(fastajv);
 656     jPanel11.add(msfjv);
 657     jPanel11.add(pfamjv);
 658     jPanel11.add(pileupjv);
 659     jPanel11.add(pirjv);
 660     exportTab.add(modellerOutput);
 661     tabbedPane.add(calcTab, "Editing");
 662     calcTab.add(autoCalculateConsCheck);
 663     calcTab.add(padGaps);
 664     tabbedPane.add(dasPanel, "DAS Settings");
 665
 666     exportTab.add(epsLabel);
 667     exportTab.add(epsRendering);
 668     exportTab.add(jPanel11);
 669   }
 670
 671   protected void showunconserved_actionPerformed(ActionEvent e)
 672   {
 673     // TODO Auto-generated method stub
 674
 675   }
 676
 677   /**
 678    * DOCUMENT ME!
 679    *
 680    * @param e
 681    *                DOCUMENT ME!
 682    */
 683   public void ok_actionPerformed(ActionEvent e)
 684   {
 685   }
 686
 687   /**
 688    * DOCUMENT ME!
 689    *
 690    * @param e
 691    *                DOCUMENT ME!
 692    */
 693   public void cancel_actionPerformed(ActionEvent e)
 694   {
 695   }
 696
 697   /**
 698    * DOCUMENT ME!
 699    *
 700    * @param e
 701    *                DOCUMENT ME!
 702    */
 703   public void annotations_actionPerformed(ActionEvent e)
 704   {
 705   }
 706
 707   /**
 708    * DOCUMENT ME!
 709    */
 710   public void startupFileTextfield_mouseClicked()
 711   {
 712   }
 713
 714   public void newLink_actionPerformed(ActionEvent e)
 715   {
 716
 717   }
 718
 719   public void editLink_actionPerformed(ActionEvent e)
 720   {
 721
 722   }
 723
 724   public void deleteLink_actionPerformed(ActionEvent e)
 725   {
 726
 727   }
 728
 729   public void defaultBrowser_mouseClicked(MouseEvent e)
 730   {
 731
 732   }
 733
 734   public void linkURLList_keyTyped(KeyEvent e)
 735   {
 736
 737   }
 738
 739   public void useProxy_actionPerformed()
 740   {
 741     proxyServerTB.setEnabled(useProxy.isSelected());
 742     proxyPortTB.setEnabled(useProxy.isSelected());
 743   }
 744
 745 }