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
 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 showConsensLogo = new JCheckBox();
 206   protected JCheckBox showConsensHistogram = new JCheckBox();
 207   protected JCheckBox showGroupConsensus = new JCheckBox();
 208   protected JCheckBox showGroupConservation = new JCheckBox();
 209   protected JCheckBox shareSelections = new JCheckBox();
 210   protected JCheckBox followHighlight = new JCheckBox();
 211
 212
 213   /**
 214    * Creates a new GPreferences object.
 215    */
 216   public GPreferences()
 217   {
 218     try
 219     {
 220       jbInit();
 221     } catch (Exception ex)
 222     {
 223       ex.printStackTrace();
 224     }
 225   }
 226
 227   /**
 228    * DOCUMENT ME!
 229    *
 230    * @throws Exception
 231    *                 DOCUMENT ME!
 232    */
 233   private void jbInit() throws Exception
 234   {
 235     this.setLayout(borderLayout1);
 236     ok.setText("OK");
 237     ok.addActionListener(new ActionListener()
 238     {
 239       public void actionPerformed(ActionEvent e)
 240       {
 241         ok_actionPerformed(e);
 242       }
 243     });
 244     cancel.setText("Cancel");
 245     cancel.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         cancel_actionPerformed(e);
 250       }
 251     });
 252     quality.setEnabled(false);
 253     quality.setFont(verdana11);
 254     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 255     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 256     quality.setSelected(true);
 257     quality.setText("Quality");
 258     visualTab.setBorder(new TitledBorder("Open new alignment"));
 259     visualTab.setLayout(null);
 260     fullScreen.setFont(verdana11);
 261     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 262     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 263     fullScreen.setText("Maximise Window");
 264     conservation.setEnabled(false);
 265     conservation.setFont(verdana11);
 266     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 267     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 268     conservation.setSelected(true);
 269     conservation.setText("Conservation");
 270     identity.setEnabled(false);
 271     identity.setFont(verdana11);
 272     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 273     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 274     identity.setSelected(true);
 275     identity.setText("Consensus");
 276     showGroupbits.setFont(verdana11);
 277     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 278     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 279     showGroupbits.setText("Show group:");
 280     showConsensbits.setFont(verdana11);
 281     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 282     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 283     showConsensbits.setText("Consensus:");
 284     showConsensHistogram.setEnabled(false);
 285     showConsensHistogram.setFont(verdana11);
 286     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 287     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 288     showConsensHistogram.setSelected(true);
 289     showConsensHistogram.setText("Histogram");
 290     showConsensLogo.setEnabled(false);
 291     showConsensLogo.setFont(verdana11);
 292     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 293     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 294     showConsensLogo.setSelected(true);
 295     showConsensLogo.setText("Logo");
 296     showGroupConsensus.setEnabled(false);
 297     showGroupConsensus.setFont(verdana11);
 298     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 299     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 300     showGroupConsensus.setSelected(true);
 301     showGroupConsensus.setText("Consensus");
 302     showGroupConservation.setEnabled(false);
 303     showGroupConservation.setFont(verdana11);
 304     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 305     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 306     showGroupConservation.setSelected(true);
 307     showGroupConservation.setText("Conservation");
 308     annotations.setFont(verdana11);
 309     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 310     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 311     annotations.setSelected(true);
 312     annotations.setText("Show Annotations");
 313     annotations.setBounds(new Rectangle(169, 16, 200, 23));
 314     annotations.addActionListener(new ActionListener()
 315     {
 316       public void actionPerformed(ActionEvent e)
 317       {
 318         annotations_actionPerformed(e);
 319       }
 320     });
 321     identity.addActionListener(new ActionListener()
 322       {
 323         public void actionPerformed(ActionEvent e)
 324         {
 325           annotations_actionPerformed(e);
 326         }
 327       });
 328     showGroupConsensus.addActionListener(new ActionListener()
 329       {
 330         public void actionPerformed(ActionEvent e)
 331         {
 332           annotations_actionPerformed(e);
 333         }
 334       });
 335     showUnconserved.setFont(verdana11);
 336     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 337     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 338     //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 339     showUnconserved.setSelected(true);
 340     showUnconserved.setText("Show Unconserved");
 341     showUnconserved.addActionListener(new ActionListener()
 342     {
 343       public void actionPerformed(ActionEvent e)
 344       {
 345         showunconserved_actionPerformed(e);
 346       }
 347     });
 348     shareSelections.setFont(verdana11);
 349     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 350     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 351     //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 352     shareSelections.setSelected(true);
 353     shareSelections.setText("Share selection across views");
 354     followHighlight.setFont(verdana11);
 355     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 356     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 357     //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 358     followHighlight.setSelected(true);
 359     followHighlight.setText("Scroll to highlighted regions");
 360
 361     gapLabel.setFont(verdana11);
 362     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 363     gapLabel.setText("Gap Symbol ");
 364     colour.setFont(verdana11);
 365     colour.setBounds(new Rectangle(172, 225, 155, 21));
 366     colourLabel.setFont(verdana11);
 367     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 368     colourLabel.setText("Colour ");
 369     fontLabel.setFont(verdana11);
 370     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 371     fontLabel.setText("Font ");
 372     fontSizeCB.setFont(verdana11);
 373     fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
 374     fontStyleCB.setFont(verdana11);
 375     fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
 376     fontNameCB.setFont(verdana11);
 377     fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
 378     gapSymbolCB.setFont(verdana11);
 379     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
 380     startupCheckbox.setText("Open file");
 381     startupCheckbox.setFont(verdana11);
 382     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 383     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 384     startupCheckbox.setSelected(true);
 385     startupFileTextfield.setFont(verdana11);
 386     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 387     startupFileTextfield.addMouseListener(new MouseAdapter()
 388     {
 389       public void mouseClicked(MouseEvent e)
 390       {
 391         if (e.getClickCount() > 1)
 392         {
 393           startupFileTextfield_mouseClicked();
 394         }
 395       }
 396     });
 397
 398     connectTab.setLayout(gridBagLayout3);
 399     serverLabel.setText("Address");
 400     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 401     serverLabel.setFont(verdana11);
 402     proxyServerTB.setFont(verdana11);
 403     proxyPortTB.setFont(verdana11);
 404     portLabel.setFont(verdana11);
 405     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 406     portLabel.setText("Port");
 407     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 408     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 409     browserLabel.setText("Default Browser (Unix)");
 410     defaultBrowser.setFont(verdana11);
 411     defaultBrowser.setText("");
 412     usagestats.setText("Send usage statistics");
 413     usagestats.setFont(verdana11);
 414     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 415     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 416     questionnaire.setText("Check for questionnaires");
 417     questionnaire.setFont(verdana11);
 418     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 419     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 420     versioncheck.setText("Check for latest version");
 421     versioncheck.setFont(verdana11);
 422     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 423     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 424     newLink.setText("New");
 425     newLink.addActionListener(new java.awt.event.ActionListener()
 426     {
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         newLink_actionPerformed(e);
 430       }
 431     });
 432     editLink.setText("Edit");
 433     editLink.addActionListener(new java.awt.event.ActionListener()
 434     {
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         editLink_actionPerformed(e);
 438       }
 439     });
 440     deleteLink.setText("Delete");
 441     deleteLink.addActionListener(new java.awt.event.ActionListener()
 442     {
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         deleteLink_actionPerformed(e);
 446       }
 447     });
 448
 449     linkURLList.addListSelectionListener(new ListSelectionListener()
 450     {
 451       public void valueChanged(ListSelectionEvent e)
 452       {
 453         int index = linkURLList.getSelectedIndex();
 454         linkNameList.setSelectedIndex(index);
 455       }
 456     });
 457
 458     linkNameList.addListSelectionListener(new ListSelectionListener()
 459     {
 460       public void valueChanged(ListSelectionEvent e)
 461       {
 462         int index = linkNameList.getSelectedIndex();
 463         linkURLList.setSelectedIndex(index);
 464       }
 465     });
 466
 467     linkScrollPane.setBorder(null);
 468     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 469     linkPanel.setLayout(borderLayout2);
 470     editLinkButtons.setLayout(gridLayout1);
 471     gridLayout1.setRows(3);
 472     linkNameList.setFont(verdana11);
 473     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 474     linkPanel2.setLayout(borderLayout3);
 475     linkURLList.setFont(verdana11);
 476     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 477
 478     defaultBrowser.addMouseListener(new MouseAdapter()
 479     {
 480       public void mouseClicked(MouseEvent e)
 481       {
 482         if (e.getClickCount() > 1)
 483         {
 484           defaultBrowser_mouseClicked(e);
 485         }
 486       }
 487     });
 488     useProxy.setFont(verdana11);
 489     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 490     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 491     useProxy.setText("Use a proxy server");
 492     useProxy.addActionListener(new ActionListener()
 493     {
 494       public void actionPerformed(ActionEvent e)
 495       {
 496         useProxy_actionPerformed();
 497       }
 498     });
 499     jPanel1.setBorder(titledBorder1);
 500     jPanel1.setLayout(gridBagLayout1);
 501     sortby.setFont(verdana11);
 502     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 503     sortLabel.setFont(verdana11);
 504     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 505     sortLabel.setText("Sort by ");
 506     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 507     jPanel2.setLayout(gridLayout2);
 508     gridLayout2.setRows(13);
 509   //  jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
 510     //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
 511     //jPanel3.setLayout(new GridLayout(3,3));
 512 //    autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
 513 //    autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
 514     exportTab.setLayout(null);
 515     epsLabel.setFont(verdana11);
 516     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 517     epsLabel.setText("EPS Rendering Style");
 518     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 519     epsRendering.setFont(verdana11);
 520     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 521     jLabel1.setFont(verdana11);
 522     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 523     jLabel1.setText("Append /start-end (/15-380)");
 524     jLabel1.setFont(verdana11);
 525     fastajv.setFont(verdana11);
 526     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 527     clustaljv.setText("Clustal     ");
 528     blcjv.setText("BLC     ");
 529     fastajv.setText("Fasta     ");
 530     msfjv.setText("MSF     ");
 531     pfamjv.setText("PFAM     ");
 532     pileupjv.setText("Pileup     ");
 533     msfjv.setFont(verdana11);
 534     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 535     pirjv.setText("PIR     ");
 536     jPanel11.setFont(verdana11);
 537     jPanel11.setBorder(titledBorder2);
 538     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 539     jPanel11.setLayout(gridLayout3);
 540     blcjv.setFont(verdana11);
 541     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 542     clustaljv.setFont(verdana11);
 543     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 544     pfamjv.setFont(verdana11);
 545     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 546     pileupjv.setFont(verdana11);
 547     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 548     pirjv.setFont(verdana11);
 549     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 550     seqLimit.setFont(verdana11);
 551     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 552     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 553     seqLimit.setText("Full Sequence Id");
 554     gridLayout3.setRows(8);
 555     smoothFont.setFont(verdana11);
 556     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 557     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 558     smoothFont.setText("Smooth Font");
 559     calcTab.setLayout(null);
 560     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 561             11));
 562     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 563     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 564     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 565     padGaps.setText("Pad gaps when editing");
 566     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 567     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 568     modellerOutput.setText("Use Modeller Output");
 569     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 570     dasPanel.setLayout(borderLayout4);
 571     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 572     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 573     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 574     wrap.setText("Wrap Alignment");
 575     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 576     rightAlign.setForeground(Color.black);
 577     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 578     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 579     rightAlign.setText("Right Align Ids");
 580     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 581     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 582     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 583     idItalics.setText("Sequence Name Italics");
 584     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 585     openoverv.setActionCommand("Open Overview");
 586     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 587     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 588     openoverv.setText("Open Overview");
 589     jPanel2.add(fullScreen);
 590     jPanel2.add(openoverv);
 591     jPanel2.add(seqLimit);
 592     jPanel2.add(rightAlign);
 593     jPanel2.add(fontLabel);
 594     jPanel2.add(showUnconserved);
 595     jPanel2.add(idItalics);
 596     jPanel2.add(smoothFont);
 597     jPanel2.add(wrap);
 598     jPanel2.add(gapLabel);
 599     jPanel2.add(colourLabel);
 600     jPanel2.add(sortLabel);
 601     jPanel2.add(startupCheckbox);
 602     visualTab.add(annotations);
 603     visualTab.add(startupFileTextfield);
 604     visualTab.add(sortby);
 605     visualTab.add(colour);
 606     visualTab.add(gapSymbolCB);
 607     visualTab.add(fontNameCB);
 608     visualTab.add(fontSizeCB);
 609     visualTab.add(fontStyleCB);
 610     annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
 611     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
 612     annsettingsPanel.add(autoAnnotSettings1);
 613     annsettingsPanel.add(autoAnnotSettings2);
 614     annsettingsPanel.add(autoAnnotSettings3);
 615     autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
 616 //  autoAnnotSettings1.setPreferredSize(new Dimensions())
 617   autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
 618   autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
 619     visualTab.add(annsettingsPanel);
 620     //visualTab.add(autoAnnotSettings1);
 621     //visualTab.add(autoAnnotSettings2);
 622     Border jb = new EmptyBorder(1,1,4,5);
 623     quality.setBorder(jb);
 624     conservation.setBorder(jb);
 625     identity.setBorder(jb);
 626     showConsensbits.setBorder(jb);
 627     showGroupbits.setBorder(jb);
 628     showGroupConsensus.setBorder(jb);
 629     showGroupConservation.setBorder(jb);
 630     showConsensHistogram.setBorder(jb);
 631     showConsensLogo.setBorder(jb);
 632
 633     autoAnnotSettings2.add(conservation);
 634     autoAnnotSettings1.add(quality);
 635     autoAnnotSettings3.add(identity);
 636
 637     /*FlowLayout fl = new FlowLayout();
 638     fl.setAlignment(FlowLayout.LEFT);
 639     autoAnnotSettings1.setLayout(fl);
 640     fl = new FlowLayout();
 641     fl.setAlignment(FlowLayout.LEFT);
 642     autoAnnotSettings2.setLayout(fl); */
 643     autoAnnotSettings1.add(showGroupbits);
 644     autoAnnotSettings3.add(showGroupConsensus);
 645     autoAnnotSettings2.add(showGroupConservation);
 646     autoAnnotSettings1.add(showConsensbits);
 647     autoAnnotSettings2.add(showConsensHistogram);
 648     autoAnnotSettings3.add(showConsensLogo);
 649     visualTab.add(jPanel2);
 650
 651     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 652     editLinkButtons.add(newLink, null);
 653     editLinkButtons.add(editLink, null);
 654     editLinkButtons.add(deleteLink, null);
 655     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 656     linkScrollPane.getViewport().add(linkPanel2, null);
 657     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 658     linkPanel2.add(linkNameList, BorderLayout.WEST);
 659     okCancelPanel.add(ok);
 660     okCancelPanel.add(cancel);
 661     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 662
 663     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 664     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 665             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 666                     2, 4, 0), 5, 0));
 667     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 668             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 669                     0, 4, 0), 11, 6));
 670     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 671             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 672                     16, 0, 0, 12), 359, -17));
 673     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 674             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 675                     21, 0, 35, 12), 4, 6));
 676     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 677             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 678             new Insets(16, 0, 0, 0), 5, 1));
 679     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 680             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 681             new Insets(0, 2, 4, 2), 54, 1));
 682     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 683             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 684             new Insets(0, 2, 4, 0), 263, 1));
 685     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 686             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 687             new Insets(15, 0, 0, 15), 307, 1));
 688     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
 689             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 690             new Insets(0, 2, 4,2), 70, 1));
 691     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 692             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 693             new Insets(0, 2, 4,2), 70, 1));
 694     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 695             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 696             new Insets(0, 2, 4,2), 70, 1));
 697
 698     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 699             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 700                     2, 5, 185), 2, -4));
 701     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 702     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 703     gapSymbolCB.setRenderer(dlcr);
 704
 705     tabbedPane.add(visualTab, "Visual");
 706     tabbedPane.add(connectTab, "Connections");
 707     tabbedPane.add(exportTab, "Output");
 708     jPanel11.add(jLabel1);
 709     jPanel11.add(blcjv);
 710     jPanel11.add(clustaljv);
 711     jPanel11.add(fastajv);
 712     jPanel11.add(msfjv);
 713     jPanel11.add(pfamjv);
 714     jPanel11.add(pileupjv);
 715     jPanel11.add(pirjv);
 716     exportTab.add(modellerOutput);
 717     tabbedPane.add(calcTab, "Editing");
 718     calcTab.add(autoCalculateConsCheck);
 719     calcTab.add(padGaps);
 720     tabbedPane.add(dasPanel, "DAS Settings");
 721
 722     exportTab.add(epsLabel);
 723     exportTab.add(epsRendering);
 724     exportTab.add(jPanel11);
 725   }
 726
 727   protected void showunconserved_actionPerformed(ActionEvent e)
 728   {
 729     // TODO Auto-generated method stub
 730
 731   }
 732
 733   /**
 734    * DOCUMENT ME!
 735    *
 736    * @param e
 737    *                DOCUMENT ME!
 738    */
 739   public void ok_actionPerformed(ActionEvent e)
 740   {
 741   }
 742
 743   /**
 744    * DOCUMENT ME!
 745    *
 746    * @param e
 747    *                DOCUMENT ME!
 748    */
 749   public void cancel_actionPerformed(ActionEvent e)
 750   {
 751   }
 752
 753   /**
 754    * DOCUMENT ME!
 755    *
 756    * @param e
 757    *                DOCUMENT ME!
 758    */
 759   public void annotations_actionPerformed(ActionEvent e)
 760   {
 761   }
 762
 763   /**
 764    * DOCUMENT ME!
 765    */
 766   public void startupFileTextfield_mouseClicked()
 767   {
 768   }
 769
 770   public void newLink_actionPerformed(ActionEvent e)
 771   {
 772
 773   }
 774
 775   public void editLink_actionPerformed(ActionEvent e)
 776   {
 777
 778   }
 779
 780   public void deleteLink_actionPerformed(ActionEvent e)
 781   {
 782
 783   }
 784
 785   public void defaultBrowser_mouseClicked(MouseEvent e)
 786   {
 787
 788   }
 789
 790   public void linkURLList_keyTyped(KeyEvent e)
 791   {
 792
 793   }
 794
 795   public void useProxy_actionPerformed()
 796   {
 797     proxyServerTB.setEnabled(useProxy.isSelected());
 798     proxyPortTB.setEnabled(useProxy.isSelected());
 799   }
 800
 801 }