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
 140   JPanel annsettingsPanel = new JPanel();
 141   JPanel autoAnnotSettings1 = new JPanel();
 142   JPanel autoAnnotSettings2 = new JPanel();
 143   JPanel autoAnnotSettings3 = 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   protected JCheckBox showDbRefTooltip = new JCheckBox();
 197   protected JCheckBox showNpTooltip = new JCheckBox();
 198
 199   protected JCheckBox idItalics = new JCheckBox();
 200
 201   protected JCheckBox openoverv = new JCheckBox();
 202   protected JCheckBox usagestats = new JCheckBox();
 203   protected JCheckBox questionnaire = new JCheckBox();
 204   protected JCheckBox versioncheck = new JCheckBox();
 205   protected JLabel showGroupbits = new JLabel();
 206   protected JLabel showConsensbits = new JLabel();
 207   protected JCheckBox showConsensLogo = new JCheckBox();
 208   protected JCheckBox showConsensHistogram = new JCheckBox();
 209   protected JCheckBox showGroupConsensus = new JCheckBox();
 210   protected JCheckBox showGroupConservation = new JCheckBox();
 211   protected JCheckBox shareSelections = new JCheckBox();
 212   protected JCheckBox followHighlight = new JCheckBox();
 213
 214
 215   /**
 216    * Creates a new GPreferences object.
 217    */
 218   public GPreferences()
 219   {
 220     try
 221     {
 222       jbInit();
 223     } catch (Exception ex)
 224     {
 225       ex.printStackTrace();
 226     }
 227   }
 228
 229   /**
 230    * DOCUMENT ME!
 231    *
 232    * @throws Exception
 233    *                 DOCUMENT ME!
 234    */
 235   private void jbInit() throws Exception
 236   {
 237     this.setLayout(borderLayout1);
 238     ok.setText("OK");
 239     ok.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         ok_actionPerformed(e);
 244       }
 245     });
 246     cancel.setText("Cancel");
 247     cancel.addActionListener(new ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         cancel_actionPerformed(e);
 252       }
 253     });
 254     quality.setEnabled(false);
 255     quality.setFont(verdana11);
 256     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 257     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 258     quality.setSelected(true);
 259     quality.setText("Quality");
 260     visualTab.setBorder(new TitledBorder("Open new alignment"));
 261     visualTab.setLayout(null);
 262     fullScreen.setFont(verdana11);
 263     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 264     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 265     fullScreen.setText("Maximise Window");
 266     conservation.setEnabled(false);
 267     conservation.setFont(verdana11);
 268     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 269     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 270     conservation.setSelected(true);
 271     conservation.setText("Conservation");
 272     identity.setEnabled(false);
 273     identity.setFont(verdana11);
 274     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 275     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 276     identity.setSelected(true);
 277     identity.setText("Consensus");
 278     showGroupbits.setFont(verdana11);
 279     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 280     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 281     showGroupbits.setText("Show group:");
 282     showConsensbits.setFont(verdana11);
 283     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 284     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 285     showConsensbits.setText("Consensus:");
 286     showConsensHistogram.setEnabled(false);
 287     showConsensHistogram.setFont(verdana11);
 288     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 289     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 290     showConsensHistogram.setSelected(true);
 291     showConsensHistogram.setText("Histogram");
 292     showConsensLogo.setEnabled(false);
 293     showConsensLogo.setFont(verdana11);
 294     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 295     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 296     showConsensLogo.setSelected(true);
 297     showConsensLogo.setText("Logo");
 298     showGroupConsensus.setEnabled(false);
 299     showGroupConsensus.setFont(verdana11);
 300     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 301     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 302     showGroupConsensus.setSelected(true);
 303     showGroupConsensus.setText("Consensus");
 304     showGroupConservation.setEnabled(false);
 305     showGroupConservation.setFont(verdana11);
 306     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 307     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 308     showGroupConservation.setSelected(true);
 309     showGroupConservation.setText("Conservation");
 310     showNpTooltip.setEnabled(true);
 311     showNpTooltip.setFont(verdana11);
 312     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 313     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 314     showNpTooltip.setSelected(true);
 315     showNpTooltip.setText("Non-positional Features");
 316     showDbRefTooltip.setEnabled(true);
 317     showDbRefTooltip.setFont(verdana11);
 318     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 319     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 320     showDbRefTooltip.setSelected(true);
 321     showDbRefTooltip.setText("Database References");
 322     annotations.setFont(verdana11);
 323     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 324     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 325     annotations.setSelected(true);
 326     annotations.setText("Show Annotations");
 327     annotations.setBounds(new Rectangle(169, 16, 200, 23));
 328     annotations.addActionListener(new ActionListener()
 329     {
 330       public void actionPerformed(ActionEvent e)
 331       {
 332         annotations_actionPerformed(e);
 333       }
 334     });
 335     identity.addActionListener(new ActionListener()
 336       {
 337         public void actionPerformed(ActionEvent e)
 338         {
 339           annotations_actionPerformed(e);
 340         }
 341       });
 342     showGroupConsensus.addActionListener(new ActionListener()
 343       {
 344         public void actionPerformed(ActionEvent e)
 345         {
 346           annotations_actionPerformed(e);
 347         }
 348       });
 349     showUnconserved.setFont(verdana11);
 350     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 351     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 352     showUnconserved.setSelected(true);
 353     showUnconserved.setText("Show Unconserved");
 354     showUnconserved.addActionListener(new ActionListener()
 355     {
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         showunconserved_actionPerformed(e);
 359       }
 360     });
 361     shareSelections.setFont(verdana11);
 362     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 363     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 364     shareSelections.setSelected(true);
 365     shareSelections.setText("Share selection across views");
 366     followHighlight.setFont(verdana11);
 367     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 368     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 369     //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 370     followHighlight.setSelected(true);
 371     followHighlight.setText("Scroll to highlighted regions");
 372
 373     gapLabel.setFont(verdana11);
 374     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 375     gapLabel.setText("Gap Symbol ");
 376     colour.setFont(verdana11);
 377     colour.setBounds(new Rectangle(172, 225, 155, 21));
 378     colourLabel.setFont(verdana11);
 379     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 380     colourLabel.setText("Colour ");
 381     fontLabel.setFont(verdana11);
 382     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 383     fontLabel.setText("Font ");
 384     fontSizeCB.setFont(verdana11);
 385     fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
 386     fontStyleCB.setFont(verdana11);
 387     fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
 388     fontNameCB.setFont(verdana11);
 389     fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
 390     gapSymbolCB.setFont(verdana11);
 391     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
 392     startupCheckbox.setText("Open file");
 393     startupCheckbox.setFont(verdana11);
 394     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 395     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 396     startupCheckbox.setSelected(true);
 397     startupFileTextfield.setFont(verdana11);
 398     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 399     startupFileTextfield.addMouseListener(new MouseAdapter()
 400     {
 401       public void mouseClicked(MouseEvent e)
 402       {
 403         if (e.getClickCount() > 1)
 404         {
 405           startupFileTextfield_mouseClicked();
 406         }
 407       }
 408     });
 409
 410     connectTab.setLayout(gridBagLayout3);
 411     serverLabel.setText("Address");
 412     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 413     serverLabel.setFont(verdana11);
 414     proxyServerTB.setFont(verdana11);
 415     proxyPortTB.setFont(verdana11);
 416     portLabel.setFont(verdana11);
 417     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 418     portLabel.setText("Port");
 419     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 420     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 421     browserLabel.setText("Default Browser (Unix)");
 422     defaultBrowser.setFont(verdana11);
 423     defaultBrowser.setText("");
 424     usagestats.setText("Send usage statistics");
 425     usagestats.setFont(verdana11);
 426     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 427     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 428     questionnaire.setText("Check for questionnaires");
 429     questionnaire.setFont(verdana11);
 430     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 431     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 432     versioncheck.setText("Check for latest version");
 433     versioncheck.setFont(verdana11);
 434     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 435     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 436     newLink.setText("New");
 437     newLink.addActionListener(new java.awt.event.ActionListener()
 438     {
 439       public void actionPerformed(ActionEvent e)
 440       {
 441         newLink_actionPerformed(e);
 442       }
 443     });
 444     editLink.setText("Edit");
 445     editLink.addActionListener(new java.awt.event.ActionListener()
 446     {
 447       public void actionPerformed(ActionEvent e)
 448       {
 449         editLink_actionPerformed(e);
 450       }
 451     });
 452     deleteLink.setText("Delete");
 453     deleteLink.addActionListener(new java.awt.event.ActionListener()
 454     {
 455       public void actionPerformed(ActionEvent e)
 456       {
 457         deleteLink_actionPerformed(e);
 458       }
 459     });
 460
 461     linkURLList.addListSelectionListener(new ListSelectionListener()
 462     {
 463       public void valueChanged(ListSelectionEvent e)
 464       {
 465         int index = linkURLList.getSelectedIndex();
 466         linkNameList.setSelectedIndex(index);
 467       }
 468     });
 469
 470     linkNameList.addListSelectionListener(new ListSelectionListener()
 471     {
 472       public void valueChanged(ListSelectionEvent e)
 473       {
 474         int index = linkNameList.getSelectedIndex();
 475         linkURLList.setSelectedIndex(index);
 476       }
 477     });
 478
 479     linkScrollPane.setBorder(null);
 480     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 481     linkPanel.setLayout(borderLayout2);
 482     editLinkButtons.setLayout(gridLayout1);
 483     gridLayout1.setRows(3);
 484     linkNameList.setFont(verdana11);
 485     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 486     linkPanel2.setLayout(borderLayout3);
 487     linkURLList.setFont(verdana11);
 488     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 489
 490     defaultBrowser.addMouseListener(new MouseAdapter()
 491     {
 492       public void mouseClicked(MouseEvent e)
 493       {
 494         if (e.getClickCount() > 1)
 495         {
 496           defaultBrowser_mouseClicked(e);
 497         }
 498       }
 499     });
 500     useProxy.setFont(verdana11);
 501     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 502     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 503     useProxy.setText("Use a proxy server");
 504     useProxy.addActionListener(new ActionListener()
 505     {
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         useProxy_actionPerformed();
 509       }
 510     });
 511     jPanel1.setBorder(titledBorder1);
 512     jPanel1.setLayout(gridBagLayout1);
 513     sortby.setFont(verdana11);
 514     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 515     sortLabel.setFont(verdana11);
 516     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 517     sortLabel.setText("Sort by ");
 518     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 519     jPanel2.setLayout(gridLayout2);
 520     gridLayout2.setRows(13);
 521     exportTab.setLayout(null);
 522     epsLabel.setFont(verdana11);
 523     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 524     epsLabel.setText("EPS Rendering Style");
 525     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 526     epsRendering.setFont(verdana11);
 527     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 528     jLabel1.setFont(verdana11);
 529     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 530     jLabel1.setText("Append /start-end (/15-380)");
 531     jLabel1.setFont(verdana11);
 532     fastajv.setFont(verdana11);
 533     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 534     clustaljv.setText("Clustal     ");
 535     blcjv.setText("BLC     ");
 536     fastajv.setText("Fasta     ");
 537     msfjv.setText("MSF     ");
 538     pfamjv.setText("PFAM     ");
 539     pileupjv.setText("Pileup     ");
 540     msfjv.setFont(verdana11);
 541     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 542     pirjv.setText("PIR     ");
 543     jPanel11.setFont(verdana11);
 544     jPanel11.setBorder(titledBorder2);
 545     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 546     jPanel11.setLayout(gridLayout3);
 547     blcjv.setFont(verdana11);
 548     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 549     clustaljv.setFont(verdana11);
 550     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 551     pfamjv.setFont(verdana11);
 552     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 553     pileupjv.setFont(verdana11);
 554     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 555     pirjv.setFont(verdana11);
 556     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 557     seqLimit.setFont(verdana11);
 558     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 559     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 560     seqLimit.setText("Full Sequence Id");
 561     gridLayout3.setRows(8);
 562     smoothFont.setFont(verdana11);
 563     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 564     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 565     smoothFont.setText("Smooth Font");
 566     calcTab.setLayout(null);
 567     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 568             11));
 569     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 570     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 571     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 572     padGaps.setText("Pad gaps when editing");
 573     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 574     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 575     modellerOutput.setText("Use Modeller Output");
 576     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 577     dasPanel.setLayout(borderLayout4);
 578     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 579     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 580     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 581     wrap.setText("Wrap Alignment");
 582     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 583     rightAlign.setForeground(Color.black);
 584     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 585     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 586     rightAlign.setText("Right Align Ids");
 587     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 588     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 589     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 590     idItalics.setText("Sequence Name Italics");
 591     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 592     openoverv.setActionCommand("Open Overview");
 593     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 594     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 595     openoverv.setText("Open Overview");
 596     jPanel2.add(fullScreen);
 597     jPanel2.add(openoverv);
 598     jPanel2.add(seqLimit);
 599     jPanel2.add(rightAlign);
 600     jPanel2.add(fontLabel);
 601     jPanel2.add(showUnconserved);
 602     jPanel2.add(idItalics);
 603     jPanel2.add(smoothFont);
 604     jPanel2.add(wrap);
 605     jPanel2.add(gapLabel);
 606     jPanel2.add(colourLabel);
 607     jPanel2.add(sortLabel);
 608     jPanel2.add(startupCheckbox);
 609     visualTab.add(annotations);
 610     visualTab.add(startupFileTextfield);
 611     visualTab.add(sortby);
 612     visualTab.add(colour);
 613     visualTab.add(gapSymbolCB);
 614     visualTab.add(fontNameCB);
 615     visualTab.add(fontSizeCB);
 616     visualTab.add(fontStyleCB);
 617     annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
 618     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
 619     annsettingsPanel.add(autoAnnotSettings1);
 620     annsettingsPanel.add(autoAnnotSettings2);
 621     annsettingsPanel.add(autoAnnotSettings3);
 622     autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
 623   autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
 624   autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
 625     visualTab.add(annsettingsPanel);
 626     Border jb = new EmptyBorder(1,1,4,5);
 627     quality.setBorder(jb);
 628     conservation.setBorder(jb);
 629     identity.setBorder(jb);
 630     showConsensbits.setBorder(jb);
 631     showGroupbits.setBorder(jb);
 632     showGroupConsensus.setBorder(jb);
 633     showGroupConservation.setBorder(jb);
 634     showConsensHistogram.setBorder(jb);
 635     showConsensLogo.setBorder(jb);
 636
 637     autoAnnotSettings2.add(conservation);
 638     autoAnnotSettings1.add(quality);
 639     autoAnnotSettings3.add(identity);
 640 autoAnnotSettings1.add(showGroupbits);
 641     autoAnnotSettings3.add(showGroupConsensus);
 642     autoAnnotSettings2.add(showGroupConservation);
 643     autoAnnotSettings1.add(showConsensbits);
 644     autoAnnotSettings2.add(showConsensHistogram);
 645     autoAnnotSettings3.add(showConsensLogo);
 646
 647     JPanel tooltipSettings = new JPanel();
 648     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 649     tooltipSettings.setBounds(173, 130, 200,62);
 650     tooltipSettings.setLayout(new GridLayout(2,1));
 651     tooltipSettings.add(showDbRefTooltip);
 652     tooltipSettings.add(showNpTooltip);
 653     visualTab.add(tooltipSettings);
 654     visualTab.add(jPanel2);
 655
 656     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 657     editLinkButtons.add(newLink, null);
 658     editLinkButtons.add(editLink, null);
 659     editLinkButtons.add(deleteLink, null);
 660     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 661     linkScrollPane.getViewport().add(linkPanel2, null);
 662     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 663     linkPanel2.add(linkNameList, BorderLayout.WEST);
 664     okCancelPanel.add(ok);
 665     okCancelPanel.add(cancel);
 666     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 667
 668     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 669     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 670             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 671                     2, 4, 0), 5, 0));
 672     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 673             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 674                     0, 4, 0), 11, 6));
 675     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 676             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 677                     16, 0, 0, 12), 359, -17));
 678     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 679             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 680                     21, 0, 35, 12), 4, 6));
 681     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 682             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 683             new Insets(16, 0, 0, 0), 5, 1));
 684     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 685             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 686             new Insets(0, 2, 4, 2), 54, 1));
 687     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 688             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 689             new Insets(0, 2, 4, 0), 263, 1));
 690     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 691             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 692             new Insets(15, 0, 0, 15), 307, 1));
 693     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
 694             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 695             new Insets(0, 2, 4,2), 70, 1));
 696     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 697             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 698             new Insets(0, 2, 4,2), 70, 1));
 699     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 700             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 701             new Insets(0, 2, 4,2), 70, 1));
 702
 703     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 704             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 705                     2, 5, 185), 2, -4));
 706     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 707     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 708     gapSymbolCB.setRenderer(dlcr);
 709
 710     tabbedPane.add(visualTab, "Visual");
 711     tabbedPane.add(connectTab, "Connections");
 712     tabbedPane.add(exportTab, "Output");
 713     jPanel11.add(jLabel1);
 714     jPanel11.add(blcjv);
 715     jPanel11.add(clustaljv);
 716     jPanel11.add(fastajv);
 717     jPanel11.add(msfjv);
 718     jPanel11.add(pfamjv);
 719     jPanel11.add(pileupjv);
 720     jPanel11.add(pirjv);
 721     exportTab.add(modellerOutput);
 722     tabbedPane.add(calcTab, "Editing");
 723     calcTab.add(autoCalculateConsCheck);
 724     calcTab.add(padGaps);
 725     tabbedPane.add(dasPanel, "DAS Settings");
 726
 727     exportTab.add(epsLabel);
 728     exportTab.add(epsRendering);
 729     exportTab.add(jPanel11);
 730   }
 731
 732   protected void showunconserved_actionPerformed(ActionEvent e)
 733   {
 734     // TODO Auto-generated method stub
 735
 736   }
 737
 738   /**
 739    * DOCUMENT ME!
 740    *
 741    * @param e
 742    *                DOCUMENT ME!
 743    */
 744   public void ok_actionPerformed(ActionEvent e)
 745   {
 746   }
 747
 748   /**
 749    * DOCUMENT ME!
 750    *
 751    * @param e
 752    *                DOCUMENT ME!
 753    */
 754   public void cancel_actionPerformed(ActionEvent e)
 755   {
 756   }
 757
 758   /**
 759    * DOCUMENT ME!
 760    *
 761    * @param e
 762    *                DOCUMENT ME!
 763    */
 764   public void annotations_actionPerformed(ActionEvent e)
 765   {
 766   }
 767
 768   /**
 769    * DOCUMENT ME!
 770    */
 771   public void startupFileTextfield_mouseClicked()
 772   {
 773   }
 774
 775   public void newLink_actionPerformed(ActionEvent e)
 776   {
 777
 778   }
 779
 780   public void editLink_actionPerformed(ActionEvent e)
 781   {
 782
 783   }
 784
 785   public void deleteLink_actionPerformed(ActionEvent e)
 786   {
 787
 788   }
 789
 790   public void defaultBrowser_mouseClicked(MouseEvent e)
 791   {
 792
 793   }
 794
 795   public void linkURLList_keyTyped(KeyEvent e)
 796   {
 797
 798   }
 799
 800   public void useProxy_actionPerformed()
 801   {
 802     proxyServerTB.setEnabled(useProxy.isSelected());
 803     proxyPortTB.setEnabled(useProxy.isSelected());
 804   }
 805
 806 }