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
 234
 235   /**
 236    * Creates a new GPreferences object.
 237    */
 238   public GPreferences()
 239   {
 240     try
 241     {
 242       jbInit();
 243     } catch (Exception ex)
 244     {
 245       ex.printStackTrace();
 246     }
 247   }
 248
 249   /**
 250    * DOCUMENT ME!
 251    *
 252    * @throws Exception
 253    *           DOCUMENT ME!
 254    */
 255   private void jbInit() throws Exception
 256   {
 257     this.setLayout(borderLayout1);
 258     ok.setText("OK");
 259     ok.addActionListener(new ActionListener()
 260     {
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         ok_actionPerformed(e);
 264       }
 265     });
 266     cancel.setText("Cancel");
 267     cancel.addActionListener(new ActionListener()
 268     {
 269       public void actionPerformed(ActionEvent e)
 270       {
 271         cancel_actionPerformed(e);
 272       }
 273     });
 274     quality.setEnabled(false);
 275     quality.setFont(verdana11);
 276     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 277     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 278     quality.setSelected(true);
 279     quality.setText("Quality");
 280     visualTab.setBorder(new TitledBorder("Open new alignment"));
 281     visualTab.setLayout(null);
 282     fullScreen.setFont(verdana11);
 283     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 284     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 285     fullScreen.setText("Maximise Window");
 286     conservation.setEnabled(false);
 287     conservation.setFont(verdana11);
 288     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 289     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 290     conservation.setSelected(true);
 291     conservation.setText("Conservation");
 292     identity.setEnabled(false);
 293     identity.setFont(verdana11);
 294     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 295     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 296     identity.setSelected(true);
 297     identity.setText("Consensus");
 298     showGroupbits.setFont(verdana11);
 299     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 300     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 301     showGroupbits.setText("Show group:");
 302     showConsensbits.setFont(verdana11);
 303     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 304     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 305     showConsensbits.setText("Consensus:");
 306     showConsensHistogram.setEnabled(false);
 307     showConsensHistogram.setFont(verdana11);
 308     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 309     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 310     showConsensHistogram.setSelected(true);
 311     showConsensHistogram.setText("Histogram");
 312     showConsensLogo.setEnabled(false);
 313     showConsensLogo.setFont(verdana11);
 314     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 315     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 316     showConsensLogo.setSelected(true);
 317     showConsensLogo.setText("Logo");
 318     showGroupConsensus.setEnabled(false);
 319     showGroupConsensus.setFont(verdana11);
 320     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 321     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 322     showGroupConsensus.setSelected(true);
 323     showGroupConsensus.setText("Consensus");
 324     showGroupConservation.setEnabled(false);
 325     showGroupConservation.setFont(verdana11);
 326     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 327     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 328     showGroupConservation.setSelected(true);
 329     showGroupConservation.setText("Conservation");
 330     showNpTooltip.setEnabled(true);
 331     showNpTooltip.setFont(verdana11);
 332     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 333     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 334     showNpTooltip.setSelected(true);
 335     showNpTooltip.setText("Non-positional Features");
 336     showDbRefTooltip.setEnabled(true);
 337     showDbRefTooltip.setFont(verdana11);
 338     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 339     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 340     showDbRefTooltip.setSelected(true);
 341     showDbRefTooltip.setText("Database References");
 342     annotations.setFont(verdana11);
 343     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 344     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 345     annotations.setSelected(true);
 346     annotations.setText("Show Annotations");
 347     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 348     annotations.addActionListener(new ActionListener()
 349     {
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         annotations_actionPerformed(e);
 353       }
 354     });
 355     identity.addActionListener(new ActionListener()
 356     {
 357       public void actionPerformed(ActionEvent e)
 358       {
 359         annotations_actionPerformed(e);
 360       }
 361     });
 362     showGroupConsensus.addActionListener(new ActionListener()
 363     {
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         annotations_actionPerformed(e);
 367       }
 368     });
 369     showUnconserved.setFont(verdana11);
 370     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 371     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 372     showUnconserved.setSelected(true);
 373     showUnconserved.setText("Show Unconserved");
 374     showUnconserved.addActionListener(new ActionListener()
 375     {
 376       public void actionPerformed(ActionEvent e)
 377       {
 378         showunconserved_actionPerformed(e);
 379       }
 380     });
 381     // / TODO: fit these in to preferences panel!!!!!
 382     shareSelections.setFont(verdana11);
 383     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
 384     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
 385     shareSelections.setSelected(true);
 386     shareSelections.setText("Share selection across views");
 387     followHighlight.setFont(verdana11);
 388     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
 389     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
 390     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
 391     followHighlight.setSelected(true);
 392     followHighlight.setText("Scroll to highlighted regions");
 393
 394     gapLabel.setFont(verdana11);
 395     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 396     gapLabel.setText("Gap Symbol ");
 397     colour.setFont(verdana11);
 398     colour.setBounds(new Rectangle(172, 225, 155, 21));
 399     colourLabel.setFont(verdana11);
 400     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 401     colourLabel.setText("Colour ");
 402     fontLabel.setFont(verdana11);
 403     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 404     fontLabel.setText("Font ");
 405     fontSizeCB.setFont(verdana11);
 406     fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
 407     fontStyleCB.setFont(verdana11);
 408     fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
 409     fontNameCB.setFont(verdana11);
 410     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
 411     gapSymbolCB.setFont(verdana11);
 412     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
 413     startupCheckbox.setText("Open file");
 414     startupCheckbox.setFont(verdana11);
 415     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
 416     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
 417     startupCheckbox.setSelected(true);
 418     startupFileTextfield.setFont(verdana11);
 419     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
 420     startupFileTextfield.addMouseListener(new MouseAdapter()
 421     {
 422       public void mouseClicked(MouseEvent e)
 423       {
 424         if (e.getClickCount() > 1)
 425         {
 426           startupFileTextfield_mouseClicked();
 427         }
 428       }
 429     });
 430
 431     connectTab.setLayout(gridBagLayout3);
 432     serverLabel.setText("Address");
 433     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 434     serverLabel.setFont(verdana11);
 435     proxyServerTB.setFont(verdana11);
 436     proxyPortTB.setFont(verdana11);
 437     portLabel.setFont(verdana11);
 438     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 439     portLabel.setText("Port");
 440     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 441     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 442     browserLabel.setText("Default Browser (Unix)");
 443     defaultBrowser.setFont(verdana11);
 444     defaultBrowser.setText("");
 445     usagestats.setText("Send usage statistics");
 446     usagestats.setFont(verdana11);
 447     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 448     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 449     questionnaire.setText("Check for questionnaires");
 450     questionnaire.setFont(verdana11);
 451     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 452     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 453     versioncheck.setText("Check for latest version");
 454     versioncheck.setFont(verdana11);
 455     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 456     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 457     newLink.setText("New");
 458     newLink.addActionListener(new java.awt.event.ActionListener()
 459     {
 460       public void actionPerformed(ActionEvent e)
 461       {
 462         newLink_actionPerformed(e);
 463       }
 464     });
 465     editLink.setText("Edit");
 466     editLink.addActionListener(new java.awt.event.ActionListener()
 467     {
 468       public void actionPerformed(ActionEvent e)
 469       {
 470         editLink_actionPerformed(e);
 471       }
 472     });
 473     deleteLink.setText("Delete");
 474     deleteLink.addActionListener(new java.awt.event.ActionListener()
 475     {
 476       public void actionPerformed(ActionEvent e)
 477       {
 478         deleteLink_actionPerformed(e);
 479       }
 480     });
 481
 482     linkURLList.addListSelectionListener(new ListSelectionListener()
 483     {
 484       public void valueChanged(ListSelectionEvent e)
 485       {
 486         int index = linkURLList.getSelectedIndex();
 487         linkNameList.setSelectedIndex(index);
 488       }
 489     });
 490
 491     linkNameList.addListSelectionListener(new ListSelectionListener()
 492     {
 493       public void valueChanged(ListSelectionEvent e)
 494       {
 495         int index = linkNameList.getSelectedIndex();
 496         linkURLList.setSelectedIndex(index);
 497       }
 498     });
 499
 500     linkScrollPane.setBorder(null);
 501     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
 502     linkPanel.setLayout(borderLayout2);
 503     editLinkButtons.setLayout(gridLayout1);
 504     gridLayout1.setRows(3);
 505     linkNameList.setFont(verdana11);
 506     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 507     linkPanel2.setLayout(borderLayout3);
 508     linkURLList.setFont(verdana11);
 509     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 510
 511     defaultBrowser.addMouseListener(new MouseAdapter()
 512     {
 513       public void mouseClicked(MouseEvent e)
 514       {
 515         if (e.getClickCount() > 1)
 516         {
 517           defaultBrowser_mouseClicked(e);
 518         }
 519       }
 520     });
 521     useProxy.setFont(verdana11);
 522     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 523     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 524     useProxy.setText("Use a proxy server");
 525     useProxy.addActionListener(new ActionListener()
 526     {
 527       public void actionPerformed(ActionEvent e)
 528       {
 529         useProxy_actionPerformed();
 530       }
 531     });
 532     jPanel1.setBorder(titledBorder1);
 533     jPanel1.setLayout(gridBagLayout1);
 534     sortby.setFont(verdana11);
 535     sortby.setBounds(new Rectangle(172, 249, 155, 21));
 536     sortLabel.setFont(verdana11);
 537     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 538     sortLabel.setText("Sort by ");
 539     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
 540     jPanel2.setLayout(gridLayout2);
 541     gridLayout2.setRows(13);
 542     exportTab.setLayout(null);
 543     epsLabel.setFont(verdana11);
 544     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 545     epsLabel.setText("EPS Rendering Style");
 546     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 547     epsRendering.setFont(verdana11);
 548     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 549     jLabel1.setFont(verdana11);
 550     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 551     jLabel1.setText("Append /start-end (/15-380)");
 552     jLabel1.setFont(verdana11);
 553     fastajv.setFont(verdana11);
 554     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 555     clustaljv.setText("Clustal     ");
 556     blcjv.setText("BLC     ");
 557     fastajv.setText("Fasta     ");
 558     msfjv.setText("MSF     ");
 559     pfamjv.setText("PFAM     ");
 560     pileupjv.setText("Pileup     ");
 561     msfjv.setFont(verdana11);
 562     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 563     pirjv.setText("PIR     ");
 564     jPanel11.setFont(verdana11);
 565     jPanel11.setBorder(titledBorder2);
 566     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 567     jPanel11.setLayout(gridLayout3);
 568     blcjv.setFont(verdana11);
 569     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 570     clustaljv.setFont(verdana11);
 571     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 572     pfamjv.setFont(verdana11);
 573     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 574     pileupjv.setFont(verdana11);
 575     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 576     pirjv.setFont(verdana11);
 577     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 578     seqLimit.setFont(verdana11);
 579     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
 580     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
 581     seqLimit.setText("Full Sequence Id");
 582     gridLayout3.setRows(8);
 583     smoothFont.setFont(verdana11);
 584     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
 585     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
 586     smoothFont.setText("Smooth Font");
 587     calcTab.setLayout(null);
 588     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
 589             11));
 590     autoCalculateConsCheck.setText("AutoCalculate Consensus");
 591     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 592     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 593     padGaps.setText("Pad gaps when editing");
 594     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 595     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 596     modellerOutput.setText("Use Modeller Output");
 597     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 598     dasPanel.setLayout(borderLayout4);
 599     wsPanel.setLayout(borderLayout5);
 600     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 601     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
 602     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
 603     wrap.setText("Wrap Alignment");
 604     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 605     rightAlign.setForeground(Color.black);
 606     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
 607     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
 608     rightAlign.setText("Right Align Ids");
 609     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 610     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
 611     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
 612     idItalics.setText("Sequence Name Italics");
 613     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 614     openoverv.setActionCommand("Open Overview");
 615     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
 616     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
 617     openoverv.setText("Open Overview");
 618     jPanel2.add(fullScreen);
 619     jPanel2.add(openoverv);
 620     jPanel2.add(seqLimit);
 621     jPanel2.add(rightAlign);
 622     jPanel2.add(fontLabel);
 623     jPanel2.add(showUnconserved);
 624     jPanel2.add(idItalics);
 625     jPanel2.add(smoothFont);
 626     jPanel2.add(wrap);
 627     jPanel2.add(gapLabel);
 628     jPanel2.add(colourLabel);
 629     jPanel2.add(sortLabel);
 630     jPanel2.add(startupCheckbox);
 631     visualTab.add(annotations);
 632     visualTab.add(startupFileTextfield);
 633     visualTab.add(sortby);
 634     visualTab.add(colour);
 635     visualTab.add(gapSymbolCB);
 636     visualTab.add(fontNameCB);
 637     visualTab.add(fontSizeCB);
 638     visualTab.add(fontStyleCB);
 639     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
 640     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
 641     annsettingsPanel.add(autoAnnotSettings1);
 642     annsettingsPanel.add(autoAnnotSettings2);
 643     annsettingsPanel.add(autoAnnotSettings3);
 644     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
 645     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
 646     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
 647     visualTab.add(annsettingsPanel);
 648     Border jb = new EmptyBorder(1, 1, 4, 5);
 649     quality.setBorder(jb);
 650     conservation.setBorder(jb);
 651     identity.setBorder(jb);
 652     showConsensbits.setBorder(jb);
 653     showGroupbits.setBorder(jb);
 654     showGroupConsensus.setBorder(jb);
 655     showGroupConservation.setBorder(jb);
 656     showConsensHistogram.setBorder(jb);
 657     showConsensLogo.setBorder(jb);
 658
 659     autoAnnotSettings2.add(conservation);
 660     autoAnnotSettings1.add(quality);
 661     autoAnnotSettings3.add(identity);
 662     autoAnnotSettings1.add(showGroupbits);
 663     autoAnnotSettings3.add(showGroupConsensus);
 664     autoAnnotSettings2.add(showGroupConservation);
 665     autoAnnotSettings1.add(showConsensbits);
 666     autoAnnotSettings2.add(showConsensHistogram);
 667     autoAnnotSettings3.add(showConsensLogo);
 668
 669     JPanel tooltipSettings = new JPanel();
 670     tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
 671     tooltipSettings.setBounds(173, 130, 200, 62);
 672     tooltipSettings.setLayout(new GridLayout(2, 1));
 673     tooltipSettings.add(showDbRefTooltip);
 674     tooltipSettings.add(showNpTooltip);
 675     visualTab.add(tooltipSettings);
 676     visualTab.add(jPanel2);
 677
 678     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 679     editLinkButtons.add(newLink, null);
 680     editLinkButtons.add(editLink, null);
 681     editLinkButtons.add(deleteLink, null);
 682     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 683     linkScrollPane.getViewport().add(linkPanel2, null);
 684     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 685     linkPanel2.add(linkNameList, BorderLayout.WEST);
 686     okCancelPanel.add(ok);
 687     okCancelPanel.add(cancel);
 688     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 689
 690     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 691     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 692             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 693                     2, 4, 0), 5, 0));
 694     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 695             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 696                     0, 4, 0), 11, 6));
 697     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 698             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 699                     16, 0, 0, 12), 359, -17));
 700     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 701             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 702                     21, 0, 35, 12), 4, 6));
 703     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 704             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 705             new Insets(16, 0, 0, 0), 5, 1));
 706     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 707             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 708             new Insets(0, 2, 4, 2), 54, 1));
 709     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 710             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 711             new Insets(0, 2, 4, 0), 263, 1));
 712     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 713             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 714             new Insets(15, 0, 0, 15), 307, 1));
 715     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 716             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 717             new Insets(0, 2, 4, 2), 70, 1));
 718     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 719             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 720             new Insets(0, 2, 4, 2), 70, 1));
 721     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 722             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 723             new Insets(0, 2, 4, 2), 70, 1));
 724
 725     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 726             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 727                     2, 5, 185), 2, -4));
 728     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
 729     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
 730     gapSymbolCB.setRenderer(dlcr);
 731
 732     tabbedPane.add(visualTab, "Visual");
 733     tabbedPane.add(connectTab, "Connections");
 734     tabbedPane.add(exportTab, "Output");
 735     jPanel11.add(jLabel1);
 736     jPanel11.add(blcjv);
 737     jPanel11.add(clustaljv);
 738     jPanel11.add(fastajv);
 739     jPanel11.add(msfjv);
 740     jPanel11.add(pfamjv);
 741     jPanel11.add(pileupjv);
 742     jPanel11.add(pirjv);
 743     exportTab.add(modellerOutput);
 744     tabbedPane.add(calcTab, "Editing");
 745     calcTab.add(autoCalculateConsCheck);
 746     calcTab.add(padGaps);
 747     tabbedPane.add(dasPanel, "DAS Settings");
 748     tabbedPane.add(wsPanel, "Web Services");
 749
 750     exportTab.add(epsLabel);
 751     exportTab.add(epsRendering);
 752     exportTab.add(jPanel11);
 753   }
 754
 755   protected void showunconserved_actionPerformed(ActionEvent e)
 756   {
 757     // TODO Auto-generated method stub
 758
 759   }
 760
 761   /**
 762    * DOCUMENT ME!
 763    *
 764    * @param e
 765    *          DOCUMENT ME!
 766    */
 767   public void ok_actionPerformed(ActionEvent e)
 768   {
 769   }
 770
 771   /**
 772    * DOCUMENT ME!
 773    *
 774    * @param e
 775    *          DOCUMENT ME!
 776    */
 777   public void cancel_actionPerformed(ActionEvent e)
 778   {
 779   }
 780
 781   /**
 782    * DOCUMENT ME!
 783    *
 784    * @param e
 785    *          DOCUMENT ME!
 786    */
 787   public void annotations_actionPerformed(ActionEvent e)
 788   {
 789   }
 790
 791   /**
 792    * DOCUMENT ME!
 793    */
 794   public void startupFileTextfield_mouseClicked()
 795   {
 796   }
 797
 798   public void newLink_actionPerformed(ActionEvent e)
 799   {
 800
 801   }
 802
 803   public void editLink_actionPerformed(ActionEvent e)
 804   {
 805
 806   }
 807
 808   public void deleteLink_actionPerformed(ActionEvent e)
 809   {
 810
 811   }
 812
 813   public void defaultBrowser_mouseClicked(MouseEvent e)
 814   {
 815
 816   }
 817
 818   public void linkURLList_keyTyped(KeyEvent e)
 819   {
 820
 821   }
 822
 823   public void useProxy_actionPerformed()
 824   {
 825     proxyServerTB.setEnabled(useProxy.isSelected());
 826     proxyPortTB.setEnabled(useProxy.isSelected());
 827   }
 828
 829 }