src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.gui.JvSwingUtils;
  24 import jalview.gui.StructureViewer.ViewerType;
  25 import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.Color;
  30 import java.awt.Component;
  31 import java.awt.Dimension;
  32 import java.awt.FlowLayout;
  33 import java.awt.Font;
  34 import java.awt.GridBagConstraints;
  35 import java.awt.GridBagLayout;
  36 import java.awt.GridLayout;
  37 import java.awt.Insets;
  38 import java.awt.Rectangle;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.FocusEvent;
  42 import java.awt.event.KeyEvent;
  43 import java.awt.event.MouseAdapter;
  44 import java.awt.event.MouseEvent;
  45
  46 import javax.swing.BorderFactory;
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.DefaultListCellRenderer;
  49 import javax.swing.JButton;
  50 import javax.swing.JCheckBox;
  51 import javax.swing.JComboBox;
  52 import javax.swing.JFileChooser;
  53 import javax.swing.JLabel;
  54 import javax.swing.JList;
  55 import javax.swing.JPanel;
  56 import javax.swing.JRadioButton;
  57 import javax.swing.JScrollPane;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.JTextField;
  60 import javax.swing.ListSelectionModel;
  61 import javax.swing.SwingConstants;
  62 import javax.swing.border.Border;
  63 import javax.swing.border.EmptyBorder;
  64 import javax.swing.border.EtchedBorder;
  65 import javax.swing.border.TitledBorder;
  66 import javax.swing.event.ChangeEvent;
  67 import javax.swing.event.ChangeListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70
  71 /**
  72  * Base class for the Preferences panel.
  73  *
  74  * @author $author$
  75  * @version $Revision$
  76  */
  77 public class GPreferences extends JPanel
  78 {
  79   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  80
  81   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  82           false, true);
  83
  84   /*
  85    * Visual tab components
  86    */
  87   protected JCheckBox fullScreen = new JCheckBox();
  88
  89   protected JCheckBox openoverv = new JCheckBox();
  90
  91   protected JCheckBox seqLimit = new JCheckBox();
  92
  93   protected JCheckBox rightAlign = new JCheckBox();
  94
  95   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  96
  97   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  98
  99   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 100
 101   protected JCheckBox showUnconserved = new JCheckBox();
 102
 103   protected JCheckBox idItalics = new JCheckBox();
 104
 105   protected JCheckBox smoothFont = new JCheckBox();
 106
 107   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 108
 109   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 110
 111   protected JCheckBox wrap = new JCheckBox();
 112
 113   protected JComboBox<String> sortby = new JComboBox<String>();
 114
 115   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 116
 117   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 118
 119   protected JCheckBox startupCheckbox = new JCheckBox();
 120
 121   protected JTextField startupFileTextfield = new JTextField();
 122
 123   // below are in the 'second column'
 124   protected JCheckBox annotations = new JCheckBox();
 125
 126   protected JCheckBox quality = new JCheckBox();
 127
 128   protected JCheckBox conservation = new JCheckBox();
 129
 130   protected JCheckBox identity = new JCheckBox();
 131
 132   protected JCheckBox showGroupConsensus = new JCheckBox();
 133
 134   protected JCheckBox showGroupConservation = new JCheckBox();
 135
 136   protected JCheckBox showConsensHistogram = new JCheckBox();
 137
 138   protected JCheckBox showConsensLogo = new JCheckBox();
 139
 140   protected JCheckBox showDbRefTooltip = new JCheckBox();
 141
 142   protected JCheckBox showNpTooltip = new JCheckBox();
 143
 144   /*
 145    * Structure tab and components
 146    */
 147   protected JPanel structureTab;
 148
 149   protected JCheckBox structFromPdb = new JCheckBox();
 150
 151   protected JCheckBox useRnaView = new JCheckBox();
 152
 153   protected JCheckBox addSecondaryStructure = new JCheckBox();
 154
 155   protected JCheckBox addTempFactor = new JCheckBox();
 156
 157   protected JComboBox<String> structViewer = new JComboBox<String>();
 158
 159   protected JTextField chimeraPath = new JTextField();
 160
 161   protected ButtonGroup mappingMethod = new ButtonGroup();
 162
 163   protected JRadioButton siftsMapping = new JRadioButton();
 164
 165   protected JRadioButton nwMapping = new JRadioButton();
 166
 167   /*
 168    * Colours tab components
 169    */
 170   protected JPanel minColour = new JPanel();
 171
 172   protected JPanel maxColour = new JPanel();
 173
 174   protected JComboBox<String> protColour = new JComboBox<String>();
 175
 176   protected JComboBox<String> nucColour = new JComboBox<String>();
 177
 178   /*
 179    * Connections tab components
 180    */
 181   protected JList linkURLList = new JList();
 182
 183   protected JTextField proxyServerTB = new JTextField();
 184
 185   protected JTextField proxyPortTB = new JTextField();
 186
 187   protected JTextField defaultBrowser = new JTextField();
 188
 189   protected JList linkNameList = new JList();
 190
 191   protected JCheckBox useProxy = new JCheckBox();
 192
 193   protected JCheckBox usagestats = new JCheckBox();
 194
 195   protected JCheckBox questionnaire = new JCheckBox();
 196
 197   protected JCheckBox versioncheck = new JCheckBox();
 198
 199   /*
 200    * Output tab components
 201    */
 202   protected JComboBox<String> epsRendering = new JComboBox<String>();
 203
 204   protected JLabel userIdWidthlabel = new JLabel();
 205
 206   protected JCheckBox autoIdWidth = new JCheckBox();
 207
 208   protected JTextField userIdWidth = new JTextField();
 209
 210   protected JCheckBox blcjv = new JCheckBox();
 211
 212   protected JCheckBox pileupjv = new JCheckBox();
 213
 214   protected JCheckBox clustaljv = new JCheckBox();
 215
 216   protected JCheckBox msfjv = new JCheckBox();
 217
 218   protected JCheckBox fastajv = new JCheckBox();
 219
 220   protected JCheckBox pfamjv = new JCheckBox();
 221
 222   protected JCheckBox pirjv = new JCheckBox();
 223
 224   protected JCheckBox modellerOutput = new JCheckBox();
 225
 226   protected JCheckBox embbedBioJSON = new JCheckBox();
 227
 228   /*
 229    * Editing tab components
 230    */
 231   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 232
 233   protected JCheckBox padGaps = new JCheckBox();
 234
 235   protected JCheckBox sortByTree = new JCheckBox();
 236
 237   /*
 238    * DAS Settings tab
 239    */
 240   protected JPanel dasTab = new JPanel();
 241
 242   /*
 243    * Web Services tab
 244    */
 245   protected JPanel wsTab = new JPanel();
 246
 247   /**
 248    * Creates a new GPreferences object.
 249    */
 250   public GPreferences()
 251   {
 252     try
 253     {
 254       jbInit();
 255     } catch (Exception ex)
 256     {
 257       ex.printStackTrace();
 258     }
 259   }
 260
 261   /**
 262    * Construct the panel and its tabbed sub-panels.
 263    *
 264    * @throws Exception
 265    */
 266   private void jbInit() throws Exception
 267   {
 268     final JTabbedPane tabbedPane = new JTabbedPane();
 269     this.setLayout(new BorderLayout());
 270     JPanel okCancelPanel = initOkCancelPanel();
 271     this.add(tabbedPane, BorderLayout.CENTER);
 272     this.add(okCancelPanel, BorderLayout.SOUTH);
 273
 274     tabbedPane.add(initVisualTab(),
 275             MessageManager.getString("label.visual"));
 276
 277     tabbedPane.add(initColoursTab(),
 278             MessageManager.getString("label.colours"));
 279
 280     tabbedPane.add(initStructureTab(),
 281             MessageManager.getString("label.structure"));
 282
 283     tabbedPane.add(initConnectionsTab(),
 284             MessageManager.getString("label.connections"));
 285
 286     tabbedPane.add(initOutputTab(),
 287             MessageManager.getString("label.output"));
 288
 289     tabbedPane.add(initEditingTab(),
 290             MessageManager.getString("label.editing"));
 291
 292     /*
 293      * See DasSourceBrowser for the real work of configuring this tab.
 294      */
 295     dasTab.setLayout(new BorderLayout());
 296     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 297
 298     /*
 299      * See WsPreferences for the real work of configuring this tab.
 300      */
 301     wsTab.setLayout(new BorderLayout());
 302     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 303
 304     /*
 305      * Handler to validate a tab before leaving it - currently only for
 306      * Structure.
 307      */
 308     tabbedPane.addChangeListener(new ChangeListener()
 309     {
 310       private Component lastTab;
 311
 312       @Override
 313       public void stateChanged(ChangeEvent e)
 314       {
 315         if (lastTab == structureTab
 316                 && tabbedPane.getSelectedComponent() != structureTab)
 317         {
 318           if (!validateStructure())
 319           {
 320             tabbedPane.setSelectedComponent(structureTab);
 321             return;
 322           }
 323         }
 324         lastTab = tabbedPane.getSelectedComponent();
 325       }
 326
 327     });
 328   }
 329
 330   /**
 331    * Initialises the Editing tabbed panel.
 332    *
 333    * @return
 334    */
 335   private JPanel initEditingTab()
 336   {
 337     JPanel editingTab = new JPanel();
 338     editingTab.setLayout(null);
 339     autoCalculateConsCheck.setFont(LABEL_FONT);
 340     autoCalculateConsCheck.setText(MessageManager
 341             .getString("label.autocalculate_consensus"));
 342     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 343     padGaps.setFont(LABEL_FONT);
 344     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 345     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 346     sortByTree.setFont(LABEL_FONT);
 347     sortByTree
 348             .setText(MessageManager.getString("label.sort_with_new_tree"));
 349     sortByTree
 350             .setToolTipText(MessageManager
 351                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 352     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 353     editingTab.add(autoCalculateConsCheck);
 354     editingTab.add(padGaps);
 355     editingTab.add(sortByTree);
 356     return editingTab;
 357   }
 358
 359   /**
 360    * Initialises the Output tabbed panel.
 361    *
 362    * @return
 363    */
 364   private JPanel initOutputTab()
 365   {
 366     JPanel outputTab = new JPanel();
 367     outputTab.setLayout(null);
 368     JLabel epsLabel = new JLabel();
 369     epsLabel.setFont(LABEL_FONT);
 370     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 371     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 372     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 373     epsRendering.setFont(LABEL_FONT);
 374     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 375     JLabel jLabel1 = new JLabel();
 376     jLabel1.setFont(LABEL_FONT);
 377     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 378     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 379     jLabel1.setFont(LABEL_FONT);
 380     fastajv.setFont(LABEL_FONT);
 381     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 382     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 383     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 384     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 385     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 386     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 387     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 388     msfjv.setFont(LABEL_FONT);
 389     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 390     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 391     JPanel jPanel11 = new JPanel();
 392     jPanel11.setFont(LABEL_FONT);
 393     TitledBorder titledBorder2 = new TitledBorder(
 394             MessageManager.getString("label.file_output"));
 395     jPanel11.setBorder(titledBorder2);
 396     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 397     GridLayout gridLayout3 = new GridLayout();
 398     jPanel11.setLayout(gridLayout3);
 399     gridLayout3.setRows(8);
 400     blcjv.setFont(LABEL_FONT);
 401     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 402     clustaljv.setFont(LABEL_FONT);
 403     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 404     pfamjv.setFont(LABEL_FONT);
 405     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 406     pileupjv.setFont(LABEL_FONT);
 407     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 408     pirjv.setFont(LABEL_FONT);
 409     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 410     autoIdWidth.setFont(LABEL_FONT);
 411     autoIdWidth.setText(MessageManager
 412             .getString("label.automatically_set_id_width"));
 413     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 414             MessageManager
 415                     .getString("label.adjusts_width_generated_eps_png")));
 416     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 417     autoIdWidth.addActionListener(new ActionListener()
 418     {
 419
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         autoIdWidth_actionPerformed();
 424       }
 425     });
 426     userIdWidthlabel.setFont(LABEL_FONT);
 427     userIdWidthlabel.setText(MessageManager
 428             .getString("label.figure_id_column_width"));
 429     userIdWidth
 430             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 431                     .getString("label.manually_specify_width_left_column")));
 432     userIdWidthlabel
 433             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 434                     .getString("label.manually_specify_width_left_column")));
 435     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 436     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 437     userIdWidth.setText("");
 438     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 439     userIdWidth.addActionListener(new ActionListener()
 440     {
 441
 442       @Override
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         userIdWidth_actionPerformed();
 446       }
 447     });
 448     modellerOutput.setFont(LABEL_FONT);
 449     modellerOutput.setText(MessageManager
 450             .getString("label.use_modeller_output"));
 451     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 452     embbedBioJSON.setFont(LABEL_FONT);
 453     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 454     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 455
 456     jPanel11.add(jLabel1);
 457     jPanel11.add(blcjv);
 458     jPanel11.add(clustaljv);
 459     jPanel11.add(fastajv);
 460     jPanel11.add(msfjv);
 461     jPanel11.add(pfamjv);
 462     jPanel11.add(pileupjv);
 463     jPanel11.add(pirjv);
 464     outputTab.add(autoIdWidth);
 465     outputTab.add(userIdWidth);
 466     outputTab.add(userIdWidthlabel);
 467     outputTab.add(modellerOutput);
 468     outputTab.add(embbedBioJSON);
 469     outputTab.add(epsLabel);
 470     outputTab.add(epsRendering);
 471     outputTab.add(jPanel11);
 472     return outputTab;
 473   }
 474
 475   /**
 476    * Initialises the Connections tabbed panel.
 477    *
 478    * @return
 479    */
 480   private JPanel initConnectionsTab()
 481   {
 482     JPanel connectTab = new JPanel();
 483     connectTab.setLayout(new GridBagLayout());
 484     JLabel serverLabel = new JLabel();
 485     serverLabel.setText(MessageManager.getString("label.address"));
 486     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 487     serverLabel.setFont(LABEL_FONT);
 488     proxyServerTB.setFont(LABEL_FONT);
 489     proxyPortTB.setFont(LABEL_FONT);
 490     JLabel portLabel = new JLabel();
 491     portLabel.setFont(LABEL_FONT);
 492     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 493     portLabel.setText(MessageManager.getString("label.port"));
 494     JLabel browserLabel = new JLabel();
 495     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 496     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 497     browserLabel.setText(MessageManager
 498             .getString("label.default_browser_unix"));
 499     defaultBrowser.setFont(LABEL_FONT);
 500     defaultBrowser.setText("");
 501     usagestats.setText(MessageManager
 502             .getString("label.send_usage_statistics"));
 503     usagestats.setFont(LABEL_FONT);
 504     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 505     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 506     questionnaire.setText(MessageManager
 507             .getString("label.check_for_questionnaires"));
 508     questionnaire.setFont(LABEL_FONT);
 509     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 510     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 511     versioncheck.setText(MessageManager
 512             .getString("label.check_for_latest_version"));
 513     versioncheck.setFont(LABEL_FONT);
 514     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 515     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 516     JButton newLink = new JButton();
 517     newLink.setText(MessageManager.getString("action.new"));
 518     newLink.addActionListener(new java.awt.event.ActionListener()
 519     {
 520       @Override
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         newLink_actionPerformed(e);
 524       }
 525     });
 526     JButton editLink = new JButton();
 527     editLink.setText(MessageManager.getString("action.edit"));
 528     editLink.addActionListener(new java.awt.event.ActionListener()
 529     {
 530       @Override
 531       public void actionPerformed(ActionEvent e)
 532       {
 533         editLink_actionPerformed(e);
 534       }
 535     });
 536     JButton deleteLink = new JButton();
 537     deleteLink.setText(MessageManager.getString("action.delete"));
 538     deleteLink.addActionListener(new java.awt.event.ActionListener()
 539     {
 540       @Override
 541       public void actionPerformed(ActionEvent e)
 542       {
 543         deleteLink_actionPerformed(e);
 544       }
 545     });
 546
 547     linkURLList.addListSelectionListener(new ListSelectionListener()
 548     {
 549       @Override
 550       public void valueChanged(ListSelectionEvent e)
 551       {
 552         int index = linkURLList.getSelectedIndex();
 553         linkNameList.setSelectedIndex(index);
 554       }
 555     });
 556
 557     linkNameList.addListSelectionListener(new ListSelectionListener()
 558     {
 559       @Override
 560       public void valueChanged(ListSelectionEvent e)
 561       {
 562         int index = linkNameList.getSelectedIndex();
 563         linkURLList.setSelectedIndex(index);
 564       }
 565     });
 566
 567     JScrollPane linkScrollPane = new JScrollPane();
 568     linkScrollPane.setBorder(null);
 569     JPanel linkPanel = new JPanel();
 570     linkPanel.setBorder(new TitledBorder(MessageManager
 571             .getString("label.url_linkfrom_sequence_id")));
 572     linkPanel.setLayout(new BorderLayout());
 573     GridLayout gridLayout1 = new GridLayout();
 574     JPanel editLinkButtons = new JPanel();
 575     editLinkButtons.setLayout(gridLayout1);
 576     gridLayout1.setRows(3);
 577     linkNameList.setFont(LABEL_FONT);
 578     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 579     BorderLayout borderLayout3 = new BorderLayout();
 580     JPanel linkPanel2 = new JPanel();
 581     linkPanel2.setLayout(borderLayout3);
 582     linkURLList.setFont(LABEL_FONT);
 583     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 584
 585     defaultBrowser.addMouseListener(new MouseAdapter()
 586     {
 587       @Override
 588       public void mouseClicked(MouseEvent e)
 589       {
 590         if (e.getClickCount() > 1)
 591         {
 592           defaultBrowser_mouseClicked(e);
 593         }
 594       }
 595     });
 596     useProxy.setFont(LABEL_FONT);
 597     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 598     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 599     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 600     useProxy.addActionListener(new ActionListener()
 601     {
 602       @Override
 603       public void actionPerformed(ActionEvent e)
 604       {
 605         useProxy_actionPerformed();
 606       }
 607     });
 608     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 609     editLinkButtons.add(newLink, null);
 610     editLinkButtons.add(editLink, null);
 611     editLinkButtons.add(deleteLink, null);
 612     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 613     linkScrollPane.getViewport().add(linkPanel2, null);
 614     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 615     linkPanel2.add(linkNameList, BorderLayout.WEST);
 616     JPanel jPanel1 = new JPanel();
 617     TitledBorder titledBorder1 = new TitledBorder(
 618             MessageManager.getString("label.proxy_server"));
 619     jPanel1.setBorder(titledBorder1);
 620     jPanel1.setLayout(new GridBagLayout());
 621     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 622             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 623                     2, 4, 0), 5, 0));
 624     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 625             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 626                     0, 4, 0), 11, 6));
 627     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 628             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 629                     16, 0, 0, 12), 359, -17));
 630     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 631             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 632                     21, 0, 35, 12), 4, 6));
 633     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 634             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 635             new Insets(16, 0, 0, 0), 5, 1));
 636     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 637             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 638                     2, 5, 185), 2, -4));
 639     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 640             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 641             new Insets(0, 2, 4, 2), 54, 1));
 642     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 643             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 644             new Insets(0, 2, 4, 0), 263, 1));
 645     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 646             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 647             new Insets(15, 0, 0, 15), 307, 1));
 648     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 649             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 650             new Insets(0, 2, 4, 2), 70, 1));
 651     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 652             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 653             new Insets(0, 2, 4, 2), 70, 1));
 654     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 655             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 656             new Insets(0, 2, 4, 2), 70, 1));
 657     return connectTab;
 658   }
 659
 660   /**
 661    * Initialises the parent panel which contains the tabbed sections.
 662    *
 663    * @return
 664    */
 665   private JPanel initOkCancelPanel()
 666   {
 667     JButton ok = new JButton();
 668     ok.setText(MessageManager.getString("action.ok"));
 669     ok.addActionListener(new ActionListener()
 670     {
 671       @Override
 672       public void actionPerformed(ActionEvent e)
 673       {
 674         ok_actionPerformed(e);
 675       }
 676     });
 677     JButton cancel = new JButton();
 678     cancel.setText(MessageManager.getString("action.cancel"));
 679     cancel.addActionListener(new ActionListener()
 680     {
 681       @Override
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         cancel_actionPerformed(e);
 685       }
 686     });
 687     JPanel okCancelPanel = new JPanel();
 688     okCancelPanel.add(ok);
 689     okCancelPanel.add(cancel);
 690     return okCancelPanel;
 691   }
 692
 693   /**
 694    * Initialises the Colours tabbed panel.
 695    *
 696    * @return
 697    */
 698   private JPanel initColoursTab()
 699   {
 700     JPanel coloursTab = new JPanel();
 701     coloursTab.setBorder(new TitledBorder(MessageManager
 702             .getString("action.open_new_alignment")));
 703     coloursTab.setLayout(new FlowLayout());
 704     JLabel mincolourLabel = new JLabel();
 705     mincolourLabel.setFont(LABEL_FONT);
 706     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 707     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 708     minColour.setFont(LABEL_FONT);
 709     minColour.setBorder(BorderFactory.createEtchedBorder());
 710     minColour.setPreferredSize(new Dimension(40, 20));
 711     minColour.addMouseListener(new MouseAdapter()
 712     {
 713       @Override
 714       public void mousePressed(MouseEvent e)
 715       {
 716         minColour_actionPerformed(minColour);
 717       }
 718     });
 719     JLabel maxcolourLabel = new JLabel();
 720     maxcolourLabel.setFont(LABEL_FONT);
 721     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 722     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 723     maxColour.setFont(LABEL_FONT);
 724     maxColour.setBorder(BorderFactory.createEtchedBorder());
 725     maxColour.setPreferredSize(new Dimension(40, 20));
 726     maxColour.addMouseListener(new MouseAdapter()
 727     {
 728       @Override
 729       public void mousePressed(MouseEvent e)
 730       {
 731         maxColour_actionPerformed(maxColour);
 732       }
 733     });
 734
 735     protColour.setFont(LABEL_FONT);
 736     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 737     JLabel protColourLabel = new JLabel();
 738     protColourLabel.setFont(LABEL_FONT);
 739     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 740     protColourLabel.setText(MessageManager
 741             .getString("label.prot_alignment_colour") + " ");
 742     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 743             .getString("label.default_colour_scheme_for_alignment"),
 744             protColourLabel, protColour);
 745
 746     nucColour.setFont(LABEL_FONT);
 747     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 748     JLabel nucColourLabel = new JLabel();
 749     nucColourLabel.setFont(LABEL_FONT);
 750     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 751     nucColourLabel.setText(MessageManager
 752             .getString("label.nuc_alignment_colour") + " ");
 753     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 754             .getString("label.default_colour_scheme_for_alignment"),
 755             nucColourLabel, nucColour);
 756
 757     JPanel annotationShding = new JPanel();
 758     annotationShding.setBorder(new TitledBorder(MessageManager
 759             .getString("label.annotation_shading_default")));
 760     annotationShding.setLayout(new GridLayout(1, 2));
 761     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 762             .getString("label.default_minimum_colour_annotation_shading"),
 763             mincolourLabel, minColour);
 764     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 765             .getString("label.default_maximum_colour_annotation_shading"),
 766             maxcolourLabel, maxColour);
 767     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 768     return coloursTab;
 769   }
 770
 771   /**
 772    * Initialises the Structure tabbed panel.
 773    *
 774    * @return
 775    */
 776   private JPanel initStructureTab()
 777   {
 778     structureTab = new JPanel();
 779
 780     structureTab.setBorder(new TitledBorder(MessageManager
 781             .getString("label.structure_options")));
 782     structureTab.setLayout(null);
 783     final int width = 400;
 784     final int height = 22;
 785     final int lineSpacing = 25;
 786     int ypos = 15;
 787
 788     structFromPdb.setFont(LABEL_FONT);
 789     structFromPdb
 790             .setText(MessageManager.getString("label.struct_from_pdb"));
 791     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 792     structFromPdb.addActionListener(new ActionListener()
 793     {
 794       @Override
 795       public void actionPerformed(ActionEvent e)
 796       {
 797         boolean selected = structFromPdb.isSelected();
 798         // enable other options only when the first is checked
 799         useRnaView.setEnabled(selected);
 800         addSecondaryStructure.setEnabled(selected);
 801         addTempFactor.setEnabled(selected);
 802       }
 803     });
 804     structureTab.add(structFromPdb);
 805
 806     // indent checkboxes that are conditional on the first one
 807     ypos += lineSpacing;
 808     useRnaView.setFont(LABEL_FONT);
 809     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 810     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 811     structureTab.add(useRnaView);
 812
 813     ypos += lineSpacing;
 814     addSecondaryStructure.setFont(LABEL_FONT);
 815     addSecondaryStructure.setText(MessageManager
 816             .getString("label.autoadd_secstr"));
 817     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 818     structureTab.add(addSecondaryStructure);
 819
 820     ypos += lineSpacing;
 821     addTempFactor.setFont(LABEL_FONT);
 822     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 823     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 824     structureTab.add(addTempFactor);
 825
 826     ypos += lineSpacing;
 827     JLabel viewerLabel = new JLabel();
 828     viewerLabel.setFont(LABEL_FONT);
 829     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 830     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 831     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 832     structureTab.add(viewerLabel);
 833
 834     structViewer.setFont(LABEL_FONT);
 835     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 836     structViewer.addItem(ViewerType.JMOL.name());
 837     structViewer.addItem(ViewerType.CHIMERA.name());
 838     structViewer.addActionListener(new ActionListener()
 839     {
 840       @Override
 841       public void actionPerformed(ActionEvent e)
 842       {
 843         structureViewer_actionPerformed((String) structViewer
 844                 .getSelectedItem());
 845       }
 846     });
 847     structureTab.add(structViewer);
 848
 849     ypos += lineSpacing;
 850     JLabel pathLabel = new JLabel();
 851     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 852     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 853     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 854     final String tooltip = JvSwingUtils.wrapTooltip(true,
 855             MessageManager.getString("label.chimera_path_tip"));
 856     pathLabel.setToolTipText(tooltip);
 857     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 858     structureTab.add(pathLabel);
 859
 860     chimeraPath.setFont(LABEL_FONT);
 861     chimeraPath.setText("");
 862     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 863     chimeraPath.addMouseListener(new MouseAdapter()
 864     {
 865       @Override
 866       public void mouseClicked(MouseEvent e)
 867       {
 868         if (e.getClickCount() == 2)
 869         {
 870           String chosen = openFileChooser();
 871           if (chosen != null)
 872           {
 873             chimeraPath.setText(chosen);
 874           }
 875         }
 876       }
 877     });
 878     structureTab.add(chimeraPath);
 879
 880     ypos += lineSpacing;
 881     nwMapping.setFont(LABEL_FONT);
 882     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
 883     siftsMapping.setFont(LABEL_FONT);
 884     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
 885     mappingMethod.add(nwMapping);
 886     mappingMethod.add(siftsMapping);
 887     JPanel mappingPanel = new JPanel();
 888     mappingPanel.setFont(LABEL_FONT);
 889     TitledBorder mmTitledBorder = new TitledBorder(
 890             MessageManager.getString("label.mapping_method"));
 891     mmTitledBorder.setTitleFont(LABEL_FONT);
 892     mappingPanel.setBorder(mmTitledBorder);
 893     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
 894     // GridLayout mappingLayout = new GridLayout();
 895     mappingPanel.setLayout(new GridLayout());
 896     mappingPanel.add(nwMapping);
 897     mappingPanel.add(siftsMapping);
 898     structureTab.add(mappingPanel);
 899
 900     ypos += lineSpacing;
 901     ypos += lineSpacing;
 902     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 903             PreferenceSource.PREFERENCES);
 904     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
 905     structureTab.add(docFieldPref);
 906
 907     return structureTab;
 908   }
 909
 910   /**
 911    * Action on choosing a structure viewer from combobox options.
 912    *
 913    * @param selectedItem
 914    */
 915   protected void structureViewer_actionPerformed(String selectedItem)
 916   {
 917   }
 918
 919   /**
 920    * Show a dialog for the user to choose a file. Returns the chosen path, or
 921    * null on Cancel.
 922    *
 923    * @return
 924    */
 925   protected String openFileChooser()
 926   {
 927     String choice = null;
 928     JFileChooser chooser = new JFileChooser();
 929
 930     // chooser.setFileView(new JalviewFileView());
 931     chooser.setDialogTitle(MessageManager
 932             .getString("label.open_local_file"));
 933     chooser.setToolTipText(MessageManager.getString("action.open"));
 934
 935     int value = chooser.showOpenDialog(this);
 936
 937     if (value == JFileChooser.APPROVE_OPTION)
 938     {
 939       choice = chooser.getSelectedFile().getPath();
 940     }
 941     return choice;
 942   }
 943
 944   /**
 945    * Validate the structure tab preferences; if invalid, set focus on this tab.
 946    *
 947    * @param e
 948    */
 949   protected boolean validateStructure(FocusEvent e)
 950   {
 951     if (!validateStructure())
 952     {
 953       e.getComponent().requestFocusInWindow();
 954       return false;
 955     }
 956     return true;
 957   }
 958
 959   protected boolean validateStructure()
 960   {
 961     return false;
 962   }
 963
 964   /**
 965    * Initialises the Visual tabbed panel.
 966    *
 967    * @return
 968    */
 969   private JPanel initVisualTab()
 970   {
 971     JPanel visualTab = new JPanel();
 972     visualTab.setBorder(new TitledBorder(MessageManager
 973             .getString("action.open_new_alignment")));
 974     visualTab.setLayout(null);
 975     fullScreen.setFont(LABEL_FONT);
 976     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 977     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 978     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 979     quality.setEnabled(false);
 980     quality.setFont(LABEL_FONT);
 981     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 982     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 983     quality.setSelected(true);
 984     quality.setText(MessageManager.getString("label.quality"));
 985     conservation.setEnabled(false);
 986     conservation.setFont(LABEL_FONT);
 987     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 988     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 989     conservation.setSelected(true);
 990     conservation.setText(MessageManager.getString("label.conservation"));
 991     identity.setEnabled(false);
 992     identity.setFont(LABEL_FONT);
 993     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 994     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 995     identity.setSelected(true);
 996     identity.setText(MessageManager.getString("label.consensus"));
 997     JLabel showGroupbits = new JLabel();
 998     showGroupbits.setFont(LABEL_FONT);
 999     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1000     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1001     showGroupbits.setText(MessageManager.getString("action.show_group")
1002             + ":");
1003     JLabel showConsensbits = new JLabel();
1004     showConsensbits.setFont(LABEL_FONT);
1005     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1006     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1007     showConsensbits.setText(MessageManager.getString("label.consensus")
1008             + ":");
1009     showConsensHistogram.setEnabled(false);
1010     showConsensHistogram.setFont(LABEL_FONT);
1011     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1012     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1013     showConsensHistogram.setSelected(true);
1014     showConsensHistogram.setText(MessageManager
1015             .getString("label.histogram"));
1016     showConsensLogo.setEnabled(false);
1017     showConsensLogo.setFont(LABEL_FONT);
1018     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1019     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1020     showConsensLogo.setSelected(true);
1021     showConsensLogo.setText(MessageManager.getString("label.logo"));
1022     showGroupConsensus.setEnabled(false);
1023     showGroupConsensus.setFont(LABEL_FONT);
1024     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1025     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1026     showGroupConsensus.setSelected(true);
1027     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1028     showGroupConservation.setEnabled(false);
1029     showGroupConservation.setFont(LABEL_FONT);
1030     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1031     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1032     showGroupConservation.setSelected(true);
1033     showGroupConservation.setText(MessageManager
1034             .getString("label.conservation"));
1035     showNpTooltip.setEnabled(true);
1036     showNpTooltip.setFont(LABEL_FONT);
1037     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1038     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1039     showNpTooltip.setSelected(true);
1040     showNpTooltip.setText(MessageManager
1041             .getString("label.non_positional_features"));
1042     showDbRefTooltip.setEnabled(true);
1043     showDbRefTooltip.setFont(LABEL_FONT);
1044     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1045     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1046     showDbRefTooltip.setSelected(true);
1047     showDbRefTooltip.setText(MessageManager
1048             .getString("label.database_references"));
1049     annotations.setFont(LABEL_FONT);
1050     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1051     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1052     annotations.setSelected(true);
1053     annotations.setText(MessageManager.getString("label.show_annotations"));
1054     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1055     annotations.addActionListener(new ActionListener()
1056     {
1057       @Override
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         annotations_actionPerformed(e);
1061       }
1062     });
1063     identity.addActionListener(new ActionListener()
1064     {
1065       @Override
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         annotations_actionPerformed(e);
1069       }
1070     });
1071     showGroupConsensus.addActionListener(new ActionListener()
1072     {
1073       @Override
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         annotations_actionPerformed(e);
1077       }
1078     });
1079     showUnconserved.setFont(LABEL_FONT);
1080     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1081     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1082     showUnconserved.setSelected(true);
1083     showUnconserved.setText(MessageManager
1084             .getString("action.show_unconserved"));
1085     showUnconserved.addActionListener(new ActionListener()
1086     {
1087       @Override
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         showunconserved_actionPerformed(e);
1091       }
1092     });
1093
1094     // TODO these are not yet added to / action from Preferences
1095     // JCheckBox shareSelections = new JCheckBox();
1096     // shareSelections.setFont(verdana11);
1097     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1098     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1099     // shareSelections.setSelected(true);
1100     // shareSelections.setText(MessageManager
1101     // .getString("label.share_selection_across_views"));
1102     // JCheckBox followHighlight = new JCheckBox();
1103     // followHighlight.setFont(verdana11);
1104     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1105     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1106     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1107     // followHighlight.setSelected(true);
1108     // followHighlight.setText(MessageManager
1109     // .getString("label.scroll_highlighted_regions"));
1110
1111     seqLimit.setFont(LABEL_FONT);
1112     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1113     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1114     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1115     smoothFont.setFont(LABEL_FONT);
1116     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1117     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1118     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1119     scaleProteinToCdna.setFont(LABEL_FONT);
1120     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1121     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1122     scaleProteinToCdna.setText(MessageManager
1123             .getString("label.scale_protein_to_cdna"));
1124     scaleProteinToCdna.setToolTipText(MessageManager
1125             .getString("label.scale_protein_to_cdna_tip"));
1126     JLabel gapLabel = new JLabel();
1127     gapLabel.setFont(LABEL_FONT);
1128     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1129     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1130     JLabel fontLabel = new JLabel();
1131     fontLabel.setFont(LABEL_FONT);
1132     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1133     fontLabel.setText(MessageManager.getString("label.font"));
1134     fontSizeCB.setFont(LABEL_FONT);
1135     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1136     fontStyleCB.setFont(LABEL_FONT);
1137     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1138     fontNameCB.setFont(LABEL_FONT);
1139     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1140     gapSymbolCB.setFont(LABEL_FONT);
1141     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1142     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1143     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1144     gapSymbolCB.setRenderer(dlcr);
1145
1146     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1147     startupCheckbox.setFont(LABEL_FONT);
1148     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1149     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1150     startupCheckbox.setSelected(true);
1151     startupFileTextfield.setFont(LABEL_FONT);
1152     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1153     startupFileTextfield.addMouseListener(new MouseAdapter()
1154     {
1155       @Override
1156       public void mouseClicked(MouseEvent e)
1157       {
1158         if (e.getClickCount() > 1)
1159         {
1160           startupFileTextfield_mouseClicked();
1161         }
1162       }
1163     });
1164
1165     sortby.setFont(LABEL_FONT);
1166     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1167     JLabel sortLabel = new JLabel();
1168     sortLabel.setFont(LABEL_FONT);
1169     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1170     sortLabel.setText(MessageManager.getString("label.sort_by"));
1171     sortAnnBy.setFont(LABEL_FONT);
1172     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1173     JLabel sortAnnLabel = new JLabel();
1174     sortAnnLabel.setFont(LABEL_FONT);
1175     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1176     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1177     sortAutocalc.setFont(LABEL_FONT);
1178     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1179
1180     JPanel annsettingsPanel = new JPanel();
1181     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1182     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1183     annsettingsPanel.setBorder(new EtchedBorder());
1184     visualTab.add(annsettingsPanel);
1185     Border jb = new EmptyBorder(1, 1, 4, 5);
1186     quality.setBorder(jb);
1187     conservation.setBorder(jb);
1188     identity.setBorder(jb);
1189     showConsensbits.setBorder(jb);
1190     showGroupbits.setBorder(jb);
1191     showGroupConsensus.setBorder(jb);
1192     showGroupConservation.setBorder(jb);
1193     showConsensHistogram.setBorder(jb);
1194     showConsensLogo.setBorder(jb);
1195
1196     JPanel autoAnnotSettings = new JPanel();
1197     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1198     annsettingsPanel.add(autoAnnotSettings);
1199     autoAnnotSettings.add(quality);
1200     autoAnnotSettings.add(conservation);
1201     autoAnnotSettings.add(identity);
1202     autoAnnotSettings.add(showGroupbits);
1203     autoAnnotSettings.add(showGroupConservation);
1204     autoAnnotSettings.add(showGroupConsensus);
1205     autoAnnotSettings.add(showConsensbits);
1206     autoAnnotSettings.add(showConsensHistogram);
1207     autoAnnotSettings.add(showConsensLogo);
1208
1209     JPanel tooltipSettings = new JPanel();
1210     tooltipSettings.setBorder(new TitledBorder(MessageManager
1211             .getString("label.sequence_id_tooltip")));
1212     tooltipSettings.setBounds(173, 140, 220, 62);
1213     tooltipSettings.setLayout(new GridLayout(2, 1));
1214     tooltipSettings.add(showDbRefTooltip);
1215     tooltipSettings.add(showNpTooltip);
1216     visualTab.add(tooltipSettings);
1217
1218     wrap.setFont(LABEL_FONT);
1219     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1220     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1221     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1222     rightAlign.setFont(LABEL_FONT);
1223     rightAlign.setForeground(Color.black);
1224     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1225     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1226     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1227     idItalics.setFont(LABEL_FONT_ITALIC);
1228     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1229     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1230     idItalics.setText(MessageManager
1231             .getString("label.sequence_name_italics"));
1232     openoverv.setFont(LABEL_FONT);
1233     openoverv.setActionCommand(MessageManager
1234             .getString("label.open_overview"));
1235     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1236     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1237     openoverv.setText(MessageManager.getString(("label.open_overview")));
1238     JPanel jPanel2 = new JPanel();
1239     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1240     jPanel2.setLayout(new GridLayout(14, 1));
1241     jPanel2.add(fullScreen);
1242     jPanel2.add(openoverv);
1243     jPanel2.add(seqLimit);
1244     jPanel2.add(rightAlign);
1245     jPanel2.add(fontLabel);
1246     jPanel2.add(showUnconserved);
1247     jPanel2.add(idItalics);
1248     jPanel2.add(smoothFont);
1249     jPanel2.add(scaleProteinToCdna);
1250     jPanel2.add(gapLabel);
1251     jPanel2.add(wrap);
1252     jPanel2.add(sortLabel);
1253     jPanel2.add(sortAnnLabel);
1254     jPanel2.add(startupCheckbox);
1255     visualTab.add(jPanel2);
1256     visualTab.add(annotations);
1257     visualTab.add(startupFileTextfield);
1258     visualTab.add(sortby);
1259     visualTab.add(sortAnnBy);
1260     visualTab.add(sortAutocalc);
1261     visualTab.add(gapSymbolCB);
1262     visualTab.add(fontNameCB);
1263     visualTab.add(fontSizeCB);
1264     visualTab.add(fontStyleCB);
1265     return visualTab;
1266   }
1267
1268   protected void autoIdWidth_actionPerformed()
1269   {
1270     // TODO Auto-generated method stub
1271
1272   }
1273
1274   protected void userIdWidth_actionPerformed()
1275   {
1276     // TODO Auto-generated method stub
1277
1278   }
1279
1280   protected void maxColour_actionPerformed(JPanel panel)
1281   {
1282   }
1283
1284   protected void minColour_actionPerformed(JPanel panel)
1285   {
1286   }
1287
1288   protected void showunconserved_actionPerformed(ActionEvent e)
1289   {
1290     // TODO Auto-generated method stub
1291
1292   }
1293
1294   /**
1295    * DOCUMENT ME!
1296    *
1297    * @param e
1298    *          DOCUMENT ME!
1299    */
1300   public void ok_actionPerformed(ActionEvent e)
1301   {
1302   }
1303
1304   /**
1305    * DOCUMENT ME!
1306    *
1307    * @param e
1308    *          DOCUMENT ME!
1309    */
1310   public void cancel_actionPerformed(ActionEvent e)
1311   {
1312   }
1313
1314   /**
1315    * DOCUMENT ME!
1316    *
1317    * @param e
1318    *          DOCUMENT ME!
1319    */
1320   public void annotations_actionPerformed(ActionEvent e)
1321   {
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    */
1327   public void startupFileTextfield_mouseClicked()
1328   {
1329   }
1330
1331   public void newLink_actionPerformed(ActionEvent e)
1332   {
1333
1334   }
1335
1336   public void editLink_actionPerformed(ActionEvent e)
1337   {
1338
1339   }
1340
1341   public void deleteLink_actionPerformed(ActionEvent e)
1342   {
1343
1344   }
1345
1346   public void defaultBrowser_mouseClicked(MouseEvent e)
1347   {
1348
1349   }
1350
1351   public void linkURLList_keyTyped(KeyEvent e)
1352   {
1353
1354   }
1355
1356   public void useProxy_actionPerformed()
1357   {
1358     proxyServerTB.setEnabled(useProxy.isSelected());
1359     proxyPortTB.setEnabled(useProxy.isSelected());
1360   }
1361
1362 }