src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.border.*;
  25 import javax.swing.event.*;
  26 import java.awt.Rectangle;
  27
  28 /**
  29  * DOCUMENT ME!
  30  *
  31  * @author $author$
  32  * @version $Revision$
  33  */
  34 public class GPreferences extends JPanel
  35 {
  36   JTabbedPane tabbedPane = new JTabbedPane();
  37
  38   JButton ok = new JButton();
  39
  40   JButton cancel = new JButton();
  41
  42   JPanel okCancelPanel = new JPanel();
  43
  44   BorderLayout borderLayout1 = new BorderLayout();
  45
  46   protected JCheckBox quality = new JCheckBox();
  47
  48   JPanel visualTab = new JPanel();
  49
  50   protected JCheckBox fullScreen = new JCheckBox();
  51
  52   protected JCheckBox conservation = new JCheckBox();
  53
  54   protected JCheckBox identity = new JCheckBox();
  55
  56   protected JCheckBox annotations = new JCheckBox();
  57
  58   JLabel gapLabel = new JLabel();
  59
  60   protected JComboBox colour = new JComboBox();
  61
  62   JLabel colourLabel = new JLabel();
  63
  64   JLabel fontLabel = new JLabel();
  65
  66   protected JComboBox fontSizeCB = new JComboBox();
  67
  68   protected JComboBox fontStyleCB = new JComboBox();
  69
  70   protected JComboBox fontNameCB = new JComboBox();
  71
  72   protected JComboBox gapSymbolCB = new JComboBox();
  73
  74   protected JCheckBox startupCheckbox = new JCheckBox();
  75
  76   protected JTextField startupFileTextfield = new JTextField();
  77
  78   JPanel connectTab = new JPanel();
  79
  80   JLabel serverLabel = new JLabel();
  81
  82   protected JList linkURLList = new JList();
  83
  84   protected JTextField proxyServerTB = new JTextField();
  85
  86   protected JTextField proxyPortTB = new JTextField();
  87
  88   JLabel portLabel = new JLabel();
  89
  90   JLabel browserLabel = new JLabel();
  91
  92   protected JTextField defaultBrowser = new JTextField();
  93
  94   JButton newLink = new JButton();
  95
  96   JButton editLink = new JButton();
  97
  98   JButton deleteLink = new JButton();
  99
 100   JScrollPane linkScrollPane = new JScrollPane();
 101
 102   JPanel linkPanel = new JPanel();
 103
 104   BorderLayout borderLayout2 = new BorderLayout();
 105
 106   JPanel editLinkButtons = new JPanel();
 107
 108   GridLayout gridLayout1 = new GridLayout();
 109
 110   protected JList linkNameList = new JList();
 111
 112   JPanel linkPanel2 = new JPanel();
 113
 114   BorderLayout borderLayout3 = new BorderLayout();
 115
 116   protected JCheckBox useProxy = new JCheckBox();
 117
 118   JPanel jPanel1 = new JPanel();
 119
 120   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
 121
 122   TitledBorder titledBorder2 = new TitledBorder("File Output");
 123
 124   GridBagLayout gridBagLayout2 = new GridBagLayout();
 125
 126   GridBagLayout gridBagLayout1 = new GridBagLayout();
 127
 128   GridBagLayout gridBagLayout3 = new GridBagLayout();
 129
 130   protected JComboBox sortby = new JComboBox();
 131
 132   JLabel sortLabel = new JLabel();
 133
 134   JPanel jPanel2 = new JPanel();
 135
 136   GridLayout gridLayout2 = new GridLayout();
 137
 138   JPanel annsettingsPanel = new JPanel();
 139
 140   JPanel autoAnnotSettings1 = new JPanel();
 141
 142   JPanel autoAnnotSettings2 = new JPanel();
 143
 144   JPanel autoAnnotSettings3 = new JPanel();
 145
 146   JPanel exportTab = new JPanel();
 147
 148   JLabel epsLabel = new JLabel();
 149
 150   protected JComboBox epsRendering = new JComboBox();
 151
 152   JLabel jLabel1 = new JLabel();
 153
 154   protected JCheckBox blcjv = new JCheckBox();
 155
 156   protected JCheckBox pileupjv = new JCheckBox();
 157
 158   protected JCheckBox clustaljv = new JCheckBox();
 159
 160   protected JCheckBox msfjv = new JCheckBox();
 161
 162   protected JCheckBox fastajv = new JCheckBox();
 163
 164   protected JCheckBox pfamjv = new JCheckBox();
 165
 166   FlowLayout flowLayout1 = new FlowLayout();
 167
 168   protected JCheckBox pirjv = new JCheckBox();
 169
 170   JPanel jPanel11 = new JPanel();
 171
 172   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
 173
 174   protected JCheckBox seqLimit = new JCheckBox();
 175
 176   GridLayout gridLayout3 = new GridLayout();
 177
 178   protected JCheckBox smoothFont = new JCheckBox();
 179
 180   JPanel calcTab = new JPanel();
 181
 182   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 183
 184   protected JCheckBox padGaps = new JCheckBox();
 185
 186   protected JCheckBox modellerOutput = new JCheckBox();
 187
 188   protected JPanel dasPanel = new JPanel();
 189
 190   BorderLayout borderLayout4 = new BorderLayout();
 191
 192   protected JPanel wsPanel = new JPanel();
 193
 194   BorderLayout borderLayout5 = new BorderLayout();
 195
 196   protected JCheckBox wrap = new JCheckBox();
 197
 198   protected JCheckBox rightAlign = new JCheckBox();
 199
 200   protected JCheckBox showUnconserved = new JCheckBox();
 201
 202   protected JCheckBox showDbRefTooltip = new JCheckBox();
 203
 204   protected JCheckBox showNpTooltip = new JCheckBox();
 205
 206   protected JCheckBox idItalics = new JCheckBox();
 207
 208   protected JCheckBox openoverv = new JCheckBox();
 209
 210   protected JCheckBox usagestats = new JCheckBox();
 211
 212   protected JCheckBox questionnaire = new JCheckBox();
 213
 214   protected JCheckBox versioncheck = new JCheckBox();
 215
 216   protected JLabel showGroupbits = new JLabel();
 217
 218   protected JLabel showConsensbits = new JLabel();
 219
 220   protected JCheckBox showConsensLogo = new JCheckBox();
 221
 222   protected JCheckBox showConsensHistogram = new JCheckBox();
 223
 224   protected JCheckBox showGroupConsensus = new JCheckBox();
 225
 226   protected JCheckBox showGroupConservation = new JCheckBox();
 227
 228   protected JCheckBox shareSelections = new JCheckBox();
 229
 230   protected JCheckBox followHighlight = new JCheckBox();
 231
 232   /**
 233    * Creates a new GPreferences object.
 234    */
 235   public GPreferences()
 236   {
 237     try
 238     {
 239       jbInit();
 240     } catch (Exception ex)
 241     {
 242       ex.printStackTrace();
 243     }
 244   }
 245
 246   /**
 247    * DOCUMENT ME!
 248    *
 249    * @throws Exception
 250    *           DOCUMENT ME!
 251    */
 252   private void jbInit() throws Exception
 253   {
 254     this.setLayout(borderLayout1);
 255     ok.setText("OK");
 256     ok.addActionListener(new ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         ok_actionPerformed(e);
 261       }
 262     });
 263     cancel.setText("Cancel");
 264     cancel.addActionListener(new ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent e)
 267       {
 268         cancel_actionPerformed(e);
 269       }
 270     });
 271     quality.setEnabled(false);
 272     quality.setFont(verdana11);
 273     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 274     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 275     quality.setSelected(true);
 276     quality.setText("Quality");
 277     visualTab.setBorder(new TitledBorder("Open new alignment"));
 278     visualTab.setLayout(null);
 279     fullScreen.setFont(verdana11);
 280     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 281     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 282     fullScreen.setText("Maximise Window");
 283     conservation.setEnabled(false);
 284     conservation.setFont(verdana11);
 285     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 286     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 287     conservation.setSelected(true);
 288     conservation.setText("Conservation");
 289     identity.setEnabled(false);
 290     identity.setFont(verdana11);
 291     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 292     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 293     identity.setSelected(true);
 294     identity.setText("Consensus");
 295     showGroupbits.setFont(verdana11);
 296     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 297     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 298     showGroupbits.setText("Show group:");
 299     showConsensbits.setFont(verdana11);
 300     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 301     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 302     showConsensbits.setText("Consensus:");
 303     showConsensHistogram.setEnabled(false);
 304     showConsensHistogram.setFont(verdana11);
 305     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 306     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 307     showConsensHistogram.setSelected(true);
 308     showConsensHistogram.setText("Histogram");
 309     showConsensLogo.setEnabled(false);
 310     showConsensLogo.setFont(verdana11);
 311     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 312     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 313     showConsensLogo.setSelected(true);
 314     showConsensLogo.setText("Logo");
 315     showGroupConsensus.setEnabled(false);
 316     showGroupConsensus.setFont(verdana11);
 317     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 318     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 319     showGroupConsensus.setSelected(true);
 320     showGroupConsensus.setText("Consensus");
 321     showGroupConservation.setEnabled(false);
 322     showGroupConservation.setFont(verdana11);
 323     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 324     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 325     showGroupConservation.setSelected(true);
 326     showGroupConservation.setText("Conservation");
 327     showNpTooltip.setEnabled(true);
 328     showNpTooltip.setFont(verdana11);
 329     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 330     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 331     showNpTooltip.setSelected(true);
 332     showNpTooltip.setText("Non-positional Features");
 333     showDbRefTooltip.setEnabled(true);
 334     showDbRefTooltip.setFont(verdana11);
 335     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 336     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 337     showDbRefTooltip.setSelected(true);
 338     showDbRefTooltip.setText("Database References");
 339     annotations.setFont(verdana11);
 340     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 341     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 342     annotations.setSelected(true);
 343     annotations.setText("Show Annotations");
 344     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 345     annotations.addActionListener(new ActionListener()
 346     {
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         annotations_actionPerformed(e);
 350       }
 351     });
 352     identity.addActionListener(new ActionListener()
 353     {
 354       public void actionPerformed(ActionEvent e)
 355       {
 356         annotations_actionPerformed(e);
 357       }
 358     });
 359     showGroupConsensus.addActionListener(new ActionListener()
 360     {
 361       public void actionPerformed(ActionEvent e)
 362       {
 363         annotations_actionPerformed(e);
 364       }
 365     });
 366     showUnconserved.setFont(verdana11);
 367     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 368     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 369     showUnconserved.setSelected(true);
 370     showUnconserved.setText("Show Unconserved");
 371     showUnconserved.addActionListener(new ActionListener()
 372     {
 373       public void actionPerformed(ActionEvent e)
 374       {
 375         showunconserved_actionPerformed(e);
 376       }
 377     });
 378     // / TODO: fit these in to preferences panel!!!!!
 379     shareSelections.setFont(verdana11);
 380     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 381     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 382     shareSelections.setSelected(true);
 383     shareSelections.setText("Share selection across views");
 384     followHighlight.setFont(verdana11);
 385     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 386     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 387     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 388     followHighlight.setSelected(true);
 389     followHighlight.setText("Scroll to highlighted regions");
 390
 391     gapLabel.setFont(verdana11);
 392     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 393     gapLabel.setText("Gap Symbol ");
 394     colour.setFont(verdana11);
 395     colour.setBounds(new Rectangle(172, 225, 155, 21));
 396     colourLabel.setFont(verdana11);
 397     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 398     colourLabel.setText("Colour ");
 399     fontLabel.setFont(verdana11);
 400     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 401     fontLabel.setText("Font ");
 402     fontSizeCB.setFont(verdana11);
 403     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 404     fontStyleCB.setFont(verdana11);
 405     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 406     fontNameCB.setFont(verdana11);
 407     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 408     gapSymbolCB.setFont(verdana11);
 409     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 410     startupCheckbox.setText("Open file");
 411     startupCheckbox.setFont(verdana11);
 412     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 413     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 414     startupCheckbox.setSelected(true);
 415     startupFileTextfield.setFont(verdana11);
 416     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 417     startupFileTextfield.addMouseListener(new MouseAdapter()
 418     {
 419       public void mouseClicked(MouseEvent e)
 420       {
 421         if (e.getClickCount() > 1)
 422         {
 423           startupFileTextfield_mouseClicked();
 424         }
 425       }
 426     });
 427
 428     connectTab.setLayout(gridBagLayout3);
 429     serverLabel.setText("Address");
 430     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 431     serverLabel.setFont(verdana11);
 432     proxyServerTB.setFont(verdana11);
 433     proxyPortTB.setFont(verdana11);
 434     portLabel.setFont(verdana11);
 435     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 436     portLabel.setText("Port");
 437     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 438     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 439     browserLabel.setText("Default Browser (Unix)");
 440     defaultBrowser.setFont(verdana11);
 441     defaultBrowser.setText("");
 442     usagestats.setText("Send usage statistics");
 443     usagestats.setFont(verdana11);
 444     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 445     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 446     questionnaire.setText("Check for questionnaires");
 447     questionnaire.setFont(verdana11);
 448     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 449     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 450     versioncheck.setText("Check for latest version");
 451     versioncheck.setFont(verdana11);
 452     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 453     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 454     newLink.setText("New");
 455     newLink.addActionListener(new java.awt.event.ActionListener()
 456     {
 457       public void actionPerformed(ActionEvent e)
 458       {
 459         newLink_actionPerformed(e);
 460       }
 461     });
 462     editLink.setText("Edit");
 463     editLink.addActionListener(new java.awt.event.ActionListener()
 464     {
 465       public void actionPerformed(ActionEvent e)
 466       {
 467         editLink_actionPerformed(e);
 468       }
 469     });
 470     deleteLink.setText("Delete");
 471     deleteLink.addActionListener(new java.awt.event.ActionListener()
 472     {
 473       public void actionPerformed(ActionEvent e)
 474       {
 475         deleteLink_actionPerformed(e);
 476       }
 477     });
 478
 479     linkURLList.addListSelectionListener(new ListSelectionListener()
 480     {
 481       public void valueChanged(ListSelectionEvent e)
 482       {
 483         int index = linkURLList.getSelectedIndex();
 484         linkNameList.setSelectedIndex(index);
 485       }
 486     });
 487
 488     linkNameList.addListSelectionListener(new ListSelectionListener()
 489     {
 490       public void valueChanged(ListSelectionEvent e)
 491       {
 492         int index = linkNameList.getSelectedIndex();
 493         linkURLList.setSelectedIndex(index);
 494       }
 495     });
 496
 497     linkScrollPane.setBorder(null);
 498     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 499     linkPanel.setLayout(borderLayout2);
 500     editLinkButtons.setLayout(gridLayout1);
 501     gridLayout1.setRows(3);
 502     linkNameList.setFont(verdana11);
 503     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 504     linkPanel2.setLayout(borderLayout3);
 505     linkURLList.setFont(verdana11);
 506     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 507
 508     defaultBrowser.addMouseListener(new MouseAdapter()
 509     {
 510       public void mouseClicked(MouseEvent e)
 511       {
 512         if (e.getClickCount() > 1)
 513         {
 514           defaultBrowser_mouseClicked(e);
 515         }
 516       }
 517     });
 518     useProxy.setFont(verdana11);
 519     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 520     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 521     useProxy.setText("Use a proxy server");
 522     useProxy.addActionListener(new ActionListener()
 523     {
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         useProxy_actionPerformed();
 527       }
 528     });
 529     jPanel1.setBorder(titledBorder1);
 530     jPanel1.setLayout(gridBagLayout1);
 531     sortby.setFont(verdana11);
 532     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 533     sortLabel.setFont(verdana11);
 534     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 535     sortLabel.setText("Sort by ");
 536     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 537     jPanel2.setLayout(gridLayout2);
 538     gridLayout2.setRows(13);
 539     exportTab.setLayout(null);
 540     epsLabel.setFont(verdana11);
 541     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 542     epsLabel.setText("EPS Rendering Style");
 543     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 544     epsRendering.setFont(verdana11);
 545     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 546     jLabel1.setFont(verdana11);
 547     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 548     jLabel1.setText("Append /start-end (/15-380)");
 549     jLabel1.setFont(verdana11);
 550     fastajv.setFont(verdana11);
 551     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 552     clustaljv.setText("Clustal     ");
 553     blcjv.setText("BLC     ");
 554     fastajv.setText("Fasta     ");
 555     msfjv.setText("MSF     ");
 556     pfamjv.setText("PFAM     ");
 557     pileupjv.setText("Pileup     ");
 558     msfjv.setFont(verdana11);
 559     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 560     pirjv.setText("PIR     ");
 561     jPanel11.setFont(verdana11);
 562     jPanel11.setBorder(titledBorder2);
 563     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 564     jPanel11.setLayout(gridLayout3);
 565     blcjv.setFont(verdana11);
 566     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 567     clustaljv.setFont(verdana11);
 568     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 569     pfamjv.setFont(verdana11);
 570     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 571     pileupjv.setFont(verdana11);
 572     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 573     pirjv.setFont(verdana11);
 574     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 575     seqLimit.setFont(verdana11);
 576     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 577     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 578     seqLimit.setText("Full Sequence Id");
 579     gridLayout3.setRows(8);
 580     smoothFont.setFont(verdana11);
 581     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 582     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 583     smoothFont.setText("Smooth Font");
 584     calcTab.setLayout(null);
 585     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 586             11));
 587     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 588     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 589     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 590     padGaps.setText("Pad gaps when editing");
 591     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 592     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 593     modellerOutput.setText("Use Modeller Output");
 594     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 595     dasPanel.setLayout(borderLayout4);
 596     wsPanel.setLayout(borderLayout5);
 597     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 598     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 599     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 600     wrap.setText("Wrap Alignment");
 601     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 602     rightAlign.setForeground(Color.black);
 603     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 604     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 605     rightAlign.setText("Right Align Ids");
 606     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 607     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 608     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 609     idItalics.setText("Sequence Name Italics");
 610     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 611     openoverv.setActionCommand("Open Overview");
 612     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 613     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 614     openoverv.setText("Open Overview");
 615     jPanel2.add(fullScreen);
 616     jPanel2.add(openoverv);
 617     jPanel2.add(seqLimit);
 618     jPanel2.add(rightAlign);
 619     jPanel2.add(fontLabel);
 620     jPanel2.add(showUnconserved);
 621     jPanel2.add(idItalics);
 622     jPanel2.add(smoothFont);
 623     jPanel2.add(wrap);
 624     jPanel2.add(gapLabel);
 625     jPanel2.add(colourLabel);
 626     jPanel2.add(sortLabel);
 627     jPanel2.add(startupCheckbox);
 628     visualTab.add(annotations);
 629     visualTab.add(startupFileTextfield);
 630     visualTab.add(sortby);
 631     visualTab.add(colour);
 632     visualTab.add(gapSymbolCB);
 633     visualTab.add(fontNameCB);
 634     visualTab.add(fontSizeCB);
 635     visualTab.add(fontStyleCB);
 636     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 637     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 638     annsettingsPanel.add(autoAnnotSettings1);
 639     annsettingsPanel.add(autoAnnotSettings2);
 640     annsettingsPanel.add(autoAnnotSettings3);
 641     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 642     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 643     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 644     visualTab.add(annsettingsPanel);
 645     Border jb = new EmptyBorder(1, 1, 4, 5);
 646     quality.setBorder(jb);
 647     conservation.setBorder(jb);
 648     identity.setBorder(jb);
 649     showConsensbits.setBorder(jb);
 650     showGroupbits.setBorder(jb);
 651     showGroupConsensus.setBorder(jb);
 652     showGroupConservation.setBorder(jb);
 653     showConsensHistogram.setBorder(jb);
 654     showConsensLogo.setBorder(jb);
 655
 656     autoAnnotSettings2.add(conservation);
 657     autoAnnotSettings1.add(quality);
 658     autoAnnotSettings3.add(identity);
 659     autoAnnotSettings1.add(showGroupbits);
 660     autoAnnotSettings3.add(showGroupConsensus);
 661     autoAnnotSettings2.add(showGroupConservation);
 662     autoAnnotSettings1.add(showConsensbits);
 663     autoAnnotSettings2.add(showConsensHistogram);
 664     autoAnnotSettings3.add(showConsensLogo);
 665
 666     JPanel tooltipSettings = new JPanel();
 667     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 668     tooltipSettings.setBounds(173, 130, 200, 62);
 669     tooltipSettings.setLayout(new GridLayout(2, 1));
 670     tooltipSettings.add(showDbRefTooltip);
 671     tooltipSettings.add(showNpTooltip);
 672     visualTab.add(tooltipSettings);
 673     visualTab.add(jPanel2);
 674
 675     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 676     editLinkButtons.add(newLink, null);
 677     editLinkButtons.add(editLink, null);
 678     editLinkButtons.add(deleteLink, null);
 679     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 680     linkScrollPane.getViewport().add(linkPanel2, null);
 681     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 682     linkPanel2.add(linkNameList, BorderLayout.WEST);
 683     okCancelPanel.add(ok);
 684     okCancelPanel.add(cancel);
 685     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 686
 687     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 688     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 689             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 690                     2, 4, 0), 5, 0));
 691     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 692             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 693                     0, 4, 0), 11, 6));
 694     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 695             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 696                     16, 0, 0, 12), 359, -17));
 697     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 698             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 699                     21, 0, 35, 12), 4, 6));
 700     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 701             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 702             new Insets(16, 0, 0, 0), 5, 1));
 703     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 704             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 705             new Insets(0, 2, 4, 2), 54, 1));
 706     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 707             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 708             new Insets(0, 2, 4, 0), 263, 1));
 709     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 710             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 711             new Insets(15, 0, 0, 15), 307, 1));
 712     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 713             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 714             new Insets(0, 2, 4, 2), 70, 1));
 715     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 716             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 717             new Insets(0, 2, 4, 2), 70, 1));
 718     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 719             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 720             new Insets(0, 2, 4, 2), 70, 1));
 721
 722     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 723             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 724                     2, 5, 185), 2, -4));
 725     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 726     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 727     gapSymbolCB.setRenderer(dlcr);
 728
 729     tabbedPane.add(visualTab, "Visual");
 730     tabbedPane.add(connectTab, "Connections");
 731     tabbedPane.add(exportTab, "Output");
 732     jPanel11.add(jLabel1);
 733     jPanel11.add(blcjv);
 734     jPanel11.add(clustaljv);
 735     jPanel11.add(fastajv);
 736     jPanel11.add(msfjv);
 737     jPanel11.add(pfamjv);
 738     jPanel11.add(pileupjv);
 739     jPanel11.add(pirjv);
 740     exportTab.add(modellerOutput);
 741     tabbedPane.add(calcTab, "Editing");
 742     calcTab.add(autoCalculateConsCheck);
 743     calcTab.add(padGaps);
 744     tabbedPane.add(dasPanel, "DAS Settings");
 745     tabbedPane.add(wsPanel, "Web Services");
 746
 747     exportTab.add(epsLabel);
 748     exportTab.add(epsRendering);
 749     exportTab.add(jPanel11);
 750   }
 751
 752   protected void showunconserved_actionPerformed(ActionEvent e)
 753   {
 754     // TODO Auto-generated method stub
 755
 756   }
 757
 758   /**
 759    * DOCUMENT ME!
 760    *
 761    * @param e
 762    *          DOCUMENT ME!
 763    */
 764   public void ok_actionPerformed(ActionEvent e)
 765   {
 766   }
 767
 768   /**
 769    * DOCUMENT ME!
 770    *
 771    * @param e
 772    *          DOCUMENT ME!
 773    */
 774   public void cancel_actionPerformed(ActionEvent e)
 775   {
 776   }
 777
 778   /**
 779    * DOCUMENT ME!
 780    *
 781    * @param e
 782    *          DOCUMENT ME!
 783    */
 784   public void annotations_actionPerformed(ActionEvent e)
 785   {
 786   }
 787
 788   /**
 789    * DOCUMENT ME!
 790    */
 791   public void startupFileTextfield_mouseClicked()
 792   {
 793   }
 794
 795   public void newLink_actionPerformed(ActionEvent e)
 796   {
 797
 798   }
 799
 800   public void editLink_actionPerformed(ActionEvent e)
 801   {
 802
 803   }
 804
 805   public void deleteLink_actionPerformed(ActionEvent e)
 806   {
 807
 808   }
 809
 810   public void defaultBrowser_mouseClicked(MouseEvent e)
 811   {
 812
 813   }
 814
 815   public void linkURLList_keyTyped(KeyEvent e)
 816   {
 817
 818   }
 819
 820   public void useProxy_actionPerformed()
 821   {
 822     proxyServerTB.setEnabled(useProxy.isSelected());
 823     proxyPortTB.setEnabled(useProxy.isSelected());
 824   }
 825
 826 }