src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.DefaultListCellRenderer;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JLabel;
  53 import javax.swing.JList;
  54 import javax.swing.JPanel;
  55 import javax.swing.JScrollPane;
  56 import javax.swing.JTabbedPane;
  57 import javax.swing.JTextField;
  58 import javax.swing.ListSelectionModel;
  59 import javax.swing.SwingConstants;
  60 import javax.swing.border.Border;
  61 import javax.swing.border.EmptyBorder;
  62 import javax.swing.border.TitledBorder;
  63 import javax.swing.event.ChangeEvent;
  64 import javax.swing.event.ChangeListener;
  65 import javax.swing.event.ListSelectionEvent;
  66 import javax.swing.event.ListSelectionListener;
  67
  68 /**
  69  * Base class for the Preferences panel.
  70  *
  71  * @author $author$
  72  * @version $Revision$
  73  */
  74 public class GPreferences extends JPanel
  75 {
  76   private static final Font verdana11 = JvSwingUtils.getLabelFont();
  77
  78   /*
  79    * Visual tab components
  80    */
  81   protected JCheckBox fullScreen = new JCheckBox();
  82
  83   protected JCheckBox openoverv = new JCheckBox();
  84
  85   protected JCheckBox seqLimit = new JCheckBox();
  86
  87   protected JCheckBox rightAlign = new JCheckBox();
  88
  89   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  90
  91   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  92
  93   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  94
  95   protected JCheckBox showUnconserved = new JCheckBox();
  96
  97   protected JCheckBox idItalics = new JCheckBox();
  98
  99   protected JCheckBox smoothFont = new JCheckBox();
 100
 101   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 102
 103   protected JCheckBox wrap = new JCheckBox();
 104
 105   protected JComboBox<String> sortby = new JComboBox<String>();
 106
 107   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 108
 109   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 110
 111   protected JCheckBox startupCheckbox = new JCheckBox();
 112
 113   protected JTextField startupFileTextfield = new JTextField();
 114
 115   // below are in the 'second column'
 116   protected JCheckBox annotations = new JCheckBox();
 117
 118   protected JCheckBox quality = new JCheckBox();
 119
 120   protected JCheckBox conservation = new JCheckBox();
 121
 122   protected JCheckBox identity = new JCheckBox();
 123
 124   protected JCheckBox showGroupConsensus = new JCheckBox();
 125
 126   protected JCheckBox showGroupConservation = new JCheckBox();
 127
 128   protected JCheckBox showConsensHistogram = new JCheckBox();
 129
 130   protected JCheckBox showConsensLogo = new JCheckBox();
 131
 132   protected JCheckBox showDbRefTooltip = new JCheckBox();
 133
 134   protected JCheckBox showNpTooltip = new JCheckBox();
 135
 136   /*
 137    * Structure tab and components
 138    */
 139   protected JPanel structureTab;
 140
 141   protected JCheckBox structFromPdb = new JCheckBox();
 142
 143   protected JCheckBox useRnaView = new JCheckBox();
 144
 145   protected JCheckBox addSecondaryStructure = new JCheckBox();
 146
 147   protected JCheckBox addTempFactor = new JCheckBox();
 148
 149   protected JComboBox<String> structViewer = new JComboBox<String>();
 150
 151   protected JTextField chimeraPath = new JTextField();
 152
 153
 154   /*
 155    * Colours tab components
 156    */
 157   protected JPanel minColour = new JPanel();
 158
 159   protected JPanel maxColour = new JPanel();
 160
 161   protected JComboBox<String> colour = new JComboBox<String>();
 162
 163   /*
 164    * Connections tab components
 165    */
 166   protected JList linkURLList = new JList();
 167
 168   protected JTextField proxyServerTB = new JTextField();
 169
 170   protected JTextField proxyPortTB = new JTextField();
 171
 172   protected JTextField defaultBrowser = new JTextField();
 173
 174   protected JList linkNameList = new JList();
 175
 176   protected JCheckBox useProxy = new JCheckBox();
 177
 178   protected JCheckBox usagestats = new JCheckBox();
 179
 180   protected JCheckBox questionnaire = new JCheckBox();
 181
 182   protected JCheckBox versioncheck = new JCheckBox();
 183
 184   /*
 185    * Output tab components
 186    */
 187   protected JComboBox<String> epsRendering = new JComboBox<String>();
 188
 189   protected JLabel userIdWidthlabel = new JLabel();
 190
 191   protected JCheckBox autoIdWidth = new JCheckBox();
 192
 193   protected JTextField userIdWidth = new JTextField();
 194
 195   protected JCheckBox blcjv = new JCheckBox();
 196
 197   protected JCheckBox pileupjv = new JCheckBox();
 198
 199   protected JCheckBox clustaljv = new JCheckBox();
 200
 201   protected JCheckBox msfjv = new JCheckBox();
 202
 203   protected JCheckBox fastajv = new JCheckBox();
 204
 205   protected JCheckBox pfamjv = new JCheckBox();
 206
 207   protected JCheckBox pirjv = new JCheckBox();
 208
 209   protected JCheckBox modellerOutput = new JCheckBox();
 210
 211   /*
 212    * Editing tab components
 213    */
 214   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 215
 216   protected JCheckBox padGaps = new JCheckBox();
 217
 218   protected JCheckBox sortByTree = new JCheckBox();
 219
 220   /*
 221    * DAS Settings tab
 222    */
 223   protected JPanel dasTab = new JPanel();
 224
 225   /*
 226    * Web Services tab
 227    */
 228   protected JPanel wsTab = new JPanel();
 229
 230   /**
 231    * Creates a new GPreferences object.
 232    */
 233   public GPreferences()
 234   {
 235     try
 236     {
 237       jbInit();
 238     } catch (Exception ex)
 239     {
 240       ex.printStackTrace();
 241     }
 242   }
 243
 244   /**
 245    * Construct the panel and its tabbed sub-panels.
 246    *
 247    * @throws Exception
 248    */
 249   private void jbInit() throws Exception
 250   {
 251     final JTabbedPane tabbedPane = new JTabbedPane();
 252     this.setLayout(new BorderLayout());
 253     JPanel okCancelPanel = initOkCancelPanel();
 254     this.add(tabbedPane, BorderLayout.CENTER);
 255     this.add(okCancelPanel, BorderLayout.SOUTH);
 256
 257     tabbedPane.add(initVisualTab(),
 258             MessageManager.getString("label.visual"));
 259
 260     tabbedPane.add(initColoursTab(),
 261             MessageManager.getString("label.colours"));
 262
 263     tabbedPane.add(initStructureTab(),
 264             MessageManager.getString("label.structure"));
 265
 266     tabbedPane.add(initConnectionsTab(),
 267             MessageManager.getString("label.connections"));
 268
 269     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 270
 271     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 272
 273     /*
 274      * See DasSourceBrowser for the real work of configuring this tab.
 275      */
 276     dasTab.setLayout(new BorderLayout());
 277     tabbedPane
 278             .add(dasTab, MessageManager.getString("label.das_settings"));
 279
 280     /*
 281      * See WsPreferences for the real work of configuring this tab.
 282      */
 283     wsTab.setLayout(new BorderLayout());
 284     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 285
 286     /*
 287      * Handler to validate a tab before leaving it - currently only for
 288      * Structure.
 289      */
 290     tabbedPane.addChangeListener(new ChangeListener()
 291     {
 292       private Component lastTab;
 293
 294       @Override
 295       public void stateChanged(ChangeEvent e)
 296       {
 297         if (lastTab == structureTab
 298                 && tabbedPane.getSelectedComponent() != structureTab)
 299         {
 300           if (!validateStructure())
 301           {
 302             tabbedPane.setSelectedComponent(structureTab);
 303             return;
 304           }
 305         }
 306         lastTab = tabbedPane.getSelectedComponent();
 307       }
 308
 309     });
 310   }
 311
 312   /**
 313    * Initialises the Editing tabbed panel.
 314    *
 315    * @return
 316    */
 317   private JPanel initEditingTab()
 318   {
 319     JPanel editingTab = new JPanel();
 320     editingTab.setLayout(null);
 321     autoCalculateConsCheck.setFont(verdana11);
 322     autoCalculateConsCheck.setText(MessageManager
 323             .getString("label.autocalculate_consensus"));
 324     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 325     padGaps.setFont(verdana11);
 326     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 327     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 328     sortByTree.setFont(verdana11);
 329     sortByTree
 330             .setText(MessageManager.getString("label.sort_with_new_tree"));
 331     sortByTree
 332             .setToolTipText(MessageManager
 333                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 334     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 335     editingTab.add(autoCalculateConsCheck);
 336     editingTab.add(padGaps);
 337     editingTab.add(sortByTree);
 338     return editingTab;
 339   }
 340
 341   /**
 342    * Initialises the Output tabbed panel.
 343    *
 344    * @return
 345    */
 346   private JPanel initOutputTab()
 347   {
 348     JPanel outputTab = new JPanel();
 349     outputTab.setLayout(null);
 350     JLabel epsLabel = new JLabel();
 351     epsLabel.setFont(verdana11);
 352     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 353     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 354     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 355     epsRendering.setFont(verdana11);
 356     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 357     JLabel jLabel1 = new JLabel();
 358     jLabel1.setFont(verdana11);
 359     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 360     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 361     jLabel1.setFont(verdana11);
 362     fastajv.setFont(verdana11);
 363     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 364     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 365     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 366     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 367     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 368     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 369     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 370     msfjv.setFont(verdana11);
 371     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 372     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 373     JPanel jPanel11 = new JPanel();
 374     jPanel11.setFont(verdana11);
 375     TitledBorder titledBorder2 = new TitledBorder(
 376             MessageManager.getString("label.file_output"));
 377     jPanel11.setBorder(titledBorder2);
 378     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 379     GridLayout gridLayout3 = new GridLayout();
 380     jPanel11.setLayout(gridLayout3);
 381     gridLayout3.setRows(8);
 382     blcjv.setFont(verdana11);
 383     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 384     clustaljv.setFont(verdana11);
 385     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 386     pfamjv.setFont(verdana11);
 387     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 388     pileupjv.setFont(verdana11);
 389     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 390     pirjv.setFont(verdana11);
 391     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 392     autoIdWidth.setFont(verdana11);
 393     autoIdWidth.setText(MessageManager
 394             .getString("label.automatically_set_id_width"));
 395     autoIdWidth
 396             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 397     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 398     autoIdWidth.addActionListener(new ActionListener()
 399     {
 400
 401       @Override
 402       public void actionPerformed(ActionEvent e)
 403       {
 404         autoIdWidth_actionPerformed();
 405       }
 406     });
 407     userIdWidthlabel.setFont(verdana11);
 408     userIdWidthlabel.setText(MessageManager
 409             .getString("label.figure_id_column_width"));
 410     userIdWidth
 411             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 412     userIdWidthlabel
 413             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 414     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 415     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 416     userIdWidth.setText("");
 417     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 418     userIdWidth.addActionListener(new ActionListener()
 419     {
 420
 421       @Override
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         userIdWidth_actionPerformed();
 425       }
 426     });
 427     jPanel11.add(jLabel1);
 428     jPanel11.add(blcjv);
 429     jPanel11.add(clustaljv);
 430     jPanel11.add(fastajv);
 431     jPanel11.add(msfjv);
 432     jPanel11.add(pfamjv);
 433     jPanel11.add(pileupjv);
 434     jPanel11.add(pirjv);
 435     outputTab.add(autoIdWidth);
 436     outputTab.add(userIdWidth);
 437     outputTab.add(userIdWidthlabel);
 438     outputTab.add(modellerOutput);
 439     outputTab.add(epsLabel);
 440     outputTab.add(epsRendering);
 441     outputTab.add(jPanel11);
 442     modellerOutput.setFont(verdana11);
 443     modellerOutput.setText(MessageManager
 444             .getString("label.use_modeller_output"));
 445     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 446     return outputTab;
 447   }
 448
 449   /**
 450    * Initialises the Connections tabbed panel.
 451    *
 452    * @return
 453    */
 454   private JPanel initConnectionsTab()
 455   {
 456     JPanel connectTab = new JPanel();
 457     connectTab.setLayout(new GridBagLayout());
 458     JLabel serverLabel = new JLabel();
 459     serverLabel.setText(MessageManager.getString("label.address"));
 460     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 461     serverLabel.setFont(verdana11);
 462     proxyServerTB.setFont(verdana11);
 463     proxyPortTB.setFont(verdana11);
 464     JLabel portLabel = new JLabel();
 465     portLabel.setFont(verdana11);
 466     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 467     portLabel.setText(MessageManager.getString("label.port"));
 468     JLabel browserLabel = new JLabel();
 469     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 470     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 471     browserLabel.setText(MessageManager
 472             .getString("label.default_browser_unix"));
 473     defaultBrowser.setFont(verdana11);
 474     defaultBrowser.setText("");
 475     usagestats.setText(MessageManager
 476             .getString("label.send_usage_statistics"));
 477     usagestats.setFont(verdana11);
 478     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 479     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 480     questionnaire.setText(MessageManager
 481             .getString("label.check_for_questionnaires"));
 482     questionnaire.setFont(verdana11);
 483     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 484     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 485     versioncheck.setText(MessageManager
 486             .getString("label.check_for_latest_version"));
 487     versioncheck.setFont(verdana11);
 488     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 489     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 490     JButton newLink = new JButton();
 491     newLink.setText(MessageManager.getString("action.new"));
 492     newLink.addActionListener(new java.awt.event.ActionListener()
 493     {
 494       public void actionPerformed(ActionEvent e)
 495       {
 496         newLink_actionPerformed(e);
 497       }
 498     });
 499     JButton editLink = new JButton();
 500     editLink.setText(MessageManager.getString("action.edit"));
 501     editLink.addActionListener(new java.awt.event.ActionListener()
 502     {
 503       public void actionPerformed(ActionEvent e)
 504       {
 505         editLink_actionPerformed(e);
 506       }
 507     });
 508     JButton deleteLink = new JButton();
 509     deleteLink.setText(MessageManager.getString("action.delete"));
 510     deleteLink.addActionListener(new java.awt.event.ActionListener()
 511     {
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         deleteLink_actionPerformed(e);
 515       }
 516     });
 517
 518     linkURLList.addListSelectionListener(new ListSelectionListener()
 519     {
 520       public void valueChanged(ListSelectionEvent e)
 521       {
 522         int index = linkURLList.getSelectedIndex();
 523         linkNameList.setSelectedIndex(index);
 524       }
 525     });
 526
 527     linkNameList.addListSelectionListener(new ListSelectionListener()
 528     {
 529       public void valueChanged(ListSelectionEvent e)
 530       {
 531         int index = linkNameList.getSelectedIndex();
 532         linkURLList.setSelectedIndex(index);
 533       }
 534     });
 535
 536     JScrollPane linkScrollPane = new JScrollPane();
 537     linkScrollPane.setBorder(null);
 538     JPanel linkPanel = new JPanel();
 539     linkPanel.setBorder(new TitledBorder(MessageManager
 540             .getString("label.url_linkfrom_sequence_id")));
 541     linkPanel.setLayout(new BorderLayout());
 542     GridLayout gridLayout1 = new GridLayout();
 543     JPanel editLinkButtons = new JPanel();
 544     editLinkButtons.setLayout(gridLayout1);
 545     gridLayout1.setRows(3);
 546     linkNameList.setFont(verdana11);
 547     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 548     BorderLayout borderLayout3 = new BorderLayout();
 549     JPanel linkPanel2 = new JPanel();
 550     linkPanel2.setLayout(borderLayout3);
 551     linkURLList.setFont(verdana11);
 552     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 553
 554     defaultBrowser.addMouseListener(new MouseAdapter()
 555     {
 556       public void mouseClicked(MouseEvent e)
 557       {
 558         if (e.getClickCount() > 1)
 559         {
 560           defaultBrowser_mouseClicked(e);
 561         }
 562       }
 563     });
 564     useProxy.setFont(verdana11);
 565     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 566     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 567     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 568     useProxy.addActionListener(new ActionListener()
 569     {
 570       public void actionPerformed(ActionEvent e)
 571       {
 572         useProxy_actionPerformed();
 573       }
 574     });
 575     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 576     editLinkButtons.add(newLink, null);
 577     editLinkButtons.add(editLink, null);
 578     editLinkButtons.add(deleteLink, null);
 579     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 580     linkScrollPane.getViewport().add(linkPanel2, null);
 581     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 582     linkPanel2.add(linkNameList, BorderLayout.WEST);
 583     JPanel jPanel1 = new JPanel();
 584     TitledBorder titledBorder1 = new TitledBorder(
 585             MessageManager.getString("label.proxy_server"));
 586     jPanel1.setBorder(titledBorder1);
 587     jPanel1.setLayout(new GridBagLayout());
 588     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 589             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 590                     2, 4, 0), 5, 0));
 591     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 592             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 593                     0, 4, 0), 11, 6));
 594     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 595             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 596                     16, 0, 0, 12), 359, -17));
 597     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 598             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 599                     21, 0, 35, 12), 4, 6));
 600     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 601             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 602             new Insets(16, 0, 0, 0), 5, 1));
 603     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 604             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 605                     2, 5, 185), 2, -4));
 606     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 607             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 608             new Insets(0, 2, 4, 2), 54, 1));
 609     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 610             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 611             new Insets(0, 2, 4, 0), 263, 1));
 612     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 613             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 614             new Insets(15, 0, 0, 15), 307, 1));
 615     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 616             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 617             new Insets(0, 2, 4, 2), 70, 1));
 618     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 619             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 620             new Insets(0, 2, 4, 2), 70, 1));
 621     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 622             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 623             new Insets(0, 2, 4, 2), 70, 1));
 624     return connectTab;
 625   }
 626
 627   /**
 628    * Initialises the parent panel which contains the tabbed sections.
 629    *
 630    * @return
 631    */
 632   private JPanel initOkCancelPanel()
 633   {
 634     JButton ok = new JButton();
 635     ok.setText(MessageManager.getString("action.ok"));
 636     ok.addActionListener(new ActionListener()
 637     {
 638       public void actionPerformed(ActionEvent e)
 639       {
 640         ok_actionPerformed(e);
 641       }
 642     });
 643     JButton cancel = new JButton();
 644     cancel.setText(MessageManager.getString("action.cancel"));
 645     cancel.addActionListener(new ActionListener()
 646     {
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         cancel_actionPerformed(e);
 650       }
 651     });
 652     JPanel okCancelPanel = new JPanel();
 653     okCancelPanel.add(ok);
 654     okCancelPanel.add(cancel);
 655     return okCancelPanel;
 656   }
 657
 658   /**
 659    * Initialises the Colours tabbed panel.
 660    *
 661    * @return
 662    */
 663   private JPanel initColoursTab()
 664   {
 665     JPanel coloursTab = new JPanel();
 666     coloursTab.setBorder(new TitledBorder(MessageManager
 667             .getString("action.open_new_alignment")));
 668     coloursTab.setLayout(new FlowLayout());
 669     JLabel mincolourLabel = new JLabel();
 670     mincolourLabel.setFont(verdana11);
 671     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 672     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 673     minColour.setFont(verdana11);
 674     minColour.setBorder(BorderFactory.createEtchedBorder());
 675     minColour.setPreferredSize(new Dimension(40, 20));
 676     minColour.addMouseListener(new MouseAdapter()
 677     {
 678       public void mousePressed(MouseEvent e)
 679       {
 680         minColour_actionPerformed(minColour);
 681       }
 682     });
 683     JLabel maxcolourLabel = new JLabel();
 684     maxcolourLabel.setFont(verdana11);
 685     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 686     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 687     maxColour.setFont(verdana11);
 688     maxColour.setBorder(BorderFactory.createEtchedBorder());
 689     maxColour.setPreferredSize(new Dimension(40, 20));
 690     maxColour.addMouseListener(new MouseAdapter()
 691     {
 692       public void mousePressed(MouseEvent e)
 693       {
 694         maxColour_actionPerformed(maxColour);
 695       }
 696     });
 697     colour.setFont(verdana11);
 698     colour.setBounds(new Rectangle(172, 225, 155, 21));
 699     JLabel colourLabel = new JLabel();
 700     colourLabel.setFont(verdana11);
 701     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 702     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 703             + " ");
 704     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 705             .getString("label.default_colour_scheme_for_alignment"),
 706             colourLabel, colour);
 707     JPanel annotationShding = new JPanel();
 708     annotationShding.setBorder(new TitledBorder(MessageManager
 709             .getString("label.annotation_shading_default")));
 710     annotationShding.setLayout(new GridLayout(1, 2));
 711     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 712             .getString("label.default_minimum_colour_annotation_shading"),
 713             mincolourLabel, minColour);
 714     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 715             .getString("label.default_maximum_colour_annotation_shading"),
 716             maxcolourLabel, maxColour);
 717     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 718     return coloursTab;
 719   }
 720
 721   /**
 722    * Initialises the Structure tabbed panel.
 723    *
 724    * @return
 725    */
 726   private JPanel initStructureTab()
 727   {
 728     structureTab = new JPanel();
 729
 730     structureTab.setBorder(new TitledBorder(MessageManager
 731             .getString("label.structure_options")));
 732     structureTab.setLayout(null);
 733     final int width = 400;
 734     final int height = 22;
 735     final int lineSpacing = 25;
 736     int ypos = 30;
 737
 738     structFromPdb.setFont(verdana11);
 739     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 740     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 741     structFromPdb.addActionListener(new ActionListener()
 742     {
 743       @Override
 744       public void actionPerformed(ActionEvent e)
 745       {
 746         boolean selected = structFromPdb.isSelected();
 747         // enable other options only when the first is checked
 748         useRnaView.setEnabled(selected);
 749         addSecondaryStructure.setEnabled(selected);
 750         addTempFactor.setEnabled(selected);
 751       }
 752     });
 753     structureTab.add(structFromPdb);
 754
 755     // indent checkboxes that are conditional on the first one
 756     ypos += lineSpacing;
 757     useRnaView.setFont(verdana11);
 758     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 759     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 760     structureTab.add(useRnaView);
 761
 762     ypos += lineSpacing;
 763     addSecondaryStructure.setFont(verdana11);
 764     addSecondaryStructure.setText(MessageManager
 765             .getString("label.autoadd_secstr"));
 766     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 767     structureTab.add(addSecondaryStructure);
 768
 769     ypos += lineSpacing;
 770     addTempFactor.setFont(verdana11);
 771     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 772     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 773     structureTab.add(addTempFactor);
 774
 775     ypos += lineSpacing;
 776     JLabel viewerLabel = new JLabel();
 777     viewerLabel.setFont(verdana11);
 778     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 779     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 780     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 781     structureTab.add(viewerLabel);
 782
 783     structViewer.setFont(verdana11);
 784     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 785     structViewer.addItem(ViewerType.JMOL.name());
 786     structViewer.addItem(ViewerType.CHIMERA.name());
 787     structViewer.addActionListener(new ActionListener()
 788     {
 789       @Override
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         structureViewer_actionPerformed((String) structViewer
 793                 .getSelectedItem());
 794       }
 795     });
 796     structureTab.add(structViewer);
 797
 798     ypos += lineSpacing;
 799     JLabel pathLabel = new JLabel();
 800     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 801     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 802     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 803     final String tooltip = JvSwingUtils.wrapTooltip(true,
 804             MessageManager.getString("label.chimera_path_tip"));
 805     pathLabel.setToolTipText(tooltip);
 806     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 807     structureTab.add(pathLabel);
 808
 809     chimeraPath.setFont(verdana11);
 810     chimeraPath.setText("");
 811     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 812     chimeraPath.addMouseListener(new MouseAdapter()
 813     {
 814       @Override
 815       public void mouseClicked(MouseEvent e)
 816       {
 817         if (e.getClickCount() == 2)
 818         {
 819           String chosen = openFileChooser();
 820           if (chosen != null)
 821           {
 822             chimeraPath.setText(chosen);
 823           }
 824         }
 825       }
 826     });
 827     structureTab.add(chimeraPath);
 828
 829     ypos += lineSpacing;
 830     // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
 831     // scrl_pdbDocFieldConfig
 832     // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 833     // scrl_pdbDocFieldConfig.setBounds();
 834     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
 835             PreferenceSource.PREFERENCES);
 836     docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
 837     structureTab.add(docFieldPref);
 838
 839
 840
 841
 842     return structureTab;
 843   }
 844
 845
 846   /**
 847    * Action on choosing a structure viewer from combobox options.
 848    *
 849    * @param selectedItem
 850    */
 851   protected void structureViewer_actionPerformed(String selectedItem)
 852   {
 853   }
 854
 855   /**
 856    * Show a dialog for the user to choose a file. Returns the chosen path, or
 857    * null on Cancel.
 858    *
 859    * @return
 860    */
 861   protected String openFileChooser()
 862   {
 863     String choice = null;
 864     JFileChooser chooser = new JFileChooser();
 865
 866     // chooser.setFileView(new JalviewFileView());
 867     chooser.setDialogTitle(MessageManager
 868             .getString("label.open_local_file"));
 869     chooser.setToolTipText(MessageManager.getString("action.open"));
 870
 871     int value = chooser.showOpenDialog(this);
 872
 873     if (value == JFileChooser.APPROVE_OPTION)
 874     {
 875       choice = chooser.getSelectedFile().getPath();
 876     }
 877     return choice;
 878   }
 879
 880   /**
 881    * Validate the structure tab preferences; if invalid, set focus on this tab.
 882    *
 883    * @param e
 884    */
 885   protected boolean validateStructure(FocusEvent e)
 886   {
 887     if (!validateStructure())
 888     {
 889       e.getComponent().requestFocusInWindow();
 890       return false;
 891     }
 892     return true;
 893   }
 894
 895   protected boolean validateStructure()
 896   {
 897     return false;
 898   }
 899
 900   /**
 901    * Initialises the Visual tabbed panel.
 902    *
 903    * @return
 904    */
 905   private JPanel initVisualTab()
 906   {
 907     JPanel visualTab = new JPanel();
 908     visualTab.setBorder(new TitledBorder(MessageManager
 909             .getString("action.open_new_alignment")));
 910     visualTab.setLayout(null);
 911     fullScreen.setFont(verdana11);
 912     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 913     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 914     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 915     quality.setEnabled(false);
 916     quality.setFont(verdana11);
 917     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 918     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 919     quality.setSelected(true);
 920     quality.setText(MessageManager.getString("label.quality"));
 921     conservation.setEnabled(false);
 922     conservation.setFont(verdana11);
 923     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 924     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 925     conservation.setSelected(true);
 926     conservation.setText(MessageManager.getString("label.conservation"));
 927     identity.setEnabled(false);
 928     identity.setFont(verdana11);
 929     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 930     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 931     identity.setSelected(true);
 932     identity.setText(MessageManager.getString("label.consensus"));
 933     JLabel showGroupbits = new JLabel();
 934     showGroupbits.setFont(verdana11);
 935     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 936     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 937     showGroupbits.setText(MessageManager.getString("action.show_group")
 938             + ":");
 939     JLabel showConsensbits = new JLabel();
 940     showConsensbits.setFont(verdana11);
 941     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 942     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 943     showConsensbits.setText(MessageManager.getString("label.consensus")
 944             + ":");
 945     showConsensHistogram.setEnabled(false);
 946     showConsensHistogram.setFont(verdana11);
 947     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 948     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 949     showConsensHistogram.setSelected(true);
 950     showConsensHistogram.setText(MessageManager
 951             .getString("label.histogram"));
 952     showConsensLogo.setEnabled(false);
 953     showConsensLogo.setFont(verdana11);
 954     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 955     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 956     showConsensLogo.setSelected(true);
 957     showConsensLogo.setText(MessageManager.getString("label.logo"));
 958     showGroupConsensus.setEnabled(false);
 959     showGroupConsensus.setFont(verdana11);
 960     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 961     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 962     showGroupConsensus.setSelected(true);
 963     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 964     showGroupConservation.setEnabled(false);
 965     showGroupConservation.setFont(verdana11);
 966     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 967     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 968     showGroupConservation.setSelected(true);
 969     showGroupConservation.setText(MessageManager
 970             .getString("label.conservation"));
 971     showNpTooltip.setEnabled(true);
 972     showNpTooltip.setFont(verdana11);
 973     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 974     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 975     showNpTooltip.setSelected(true);
 976     showNpTooltip.setText(MessageManager
 977             .getString("label.non_positional_features"));
 978     showDbRefTooltip.setEnabled(true);
 979     showDbRefTooltip.setFont(verdana11);
 980     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 981     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 982     showDbRefTooltip.setSelected(true);
 983     showDbRefTooltip.setText(MessageManager
 984             .getString("label.database_references"));
 985     annotations.setFont(verdana11);
 986     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 987     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 988     annotations.setSelected(true);
 989     annotations.setText(MessageManager.getString("label.show_annotations"));
 990     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 991     annotations.addActionListener(new ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         annotations_actionPerformed(e);
 996       }
 997     });
 998     identity.addActionListener(new ActionListener()
 999     {
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         annotations_actionPerformed(e);
1003       }
1004     });
1005     showGroupConsensus.addActionListener(new ActionListener()
1006     {
1007       public void actionPerformed(ActionEvent e)
1008       {
1009         annotations_actionPerformed(e);
1010       }
1011     });
1012     showUnconserved.setFont(verdana11);
1013     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1014     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1015     showUnconserved.setSelected(true);
1016     showUnconserved.setText(MessageManager
1017             .getString("action.show_unconserved"));
1018     showUnconserved.addActionListener(new ActionListener()
1019     {
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         showunconserved_actionPerformed(e);
1023       }
1024     });
1025
1026     // TODO these are not yet added to / action from Preferences
1027     // JCheckBox shareSelections = new JCheckBox();
1028     // shareSelections.setFont(verdana11);
1029     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1030     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1031     // shareSelections.setSelected(true);
1032     // shareSelections.setText(MessageManager
1033     // .getString("label.share_selection_across_views"));
1034     // JCheckBox followHighlight = new JCheckBox();
1035     // followHighlight.setFont(verdana11);
1036     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1037     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1038     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1039     // followHighlight.setSelected(true);
1040     // followHighlight.setText(MessageManager
1041     // .getString("label.scroll_highlighted_regions"));
1042
1043     seqLimit.setFont(verdana11);
1044     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1045     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1046     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1047     smoothFont.setFont(verdana11);
1048     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1049     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1050     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1051     JLabel gapLabel = new JLabel();
1052     gapLabel.setFont(verdana11);
1053     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1054     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1055     JLabel fontLabel = new JLabel();
1056     fontLabel.setFont(verdana11);
1057     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1058     fontLabel.setText(MessageManager.getString("label.font"));
1059     fontSizeCB.setFont(verdana11);
1060     fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
1061     fontStyleCB.setFont(verdana11);
1062     fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
1063     fontNameCB.setFont(verdana11);
1064     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
1065     gapSymbolCB.setFont(verdana11);
1066     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
1067     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1068     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1069     gapSymbolCB.setRenderer(dlcr);
1070
1071     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1072     startupCheckbox.setFont(verdana11);
1073     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1074     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1075     startupCheckbox.setSelected(true);
1076     startupFileTextfield.setFont(verdana11);
1077     startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
1078     startupFileTextfield.addMouseListener(new MouseAdapter()
1079     {
1080       public void mouseClicked(MouseEvent e)
1081       {
1082         if (e.getClickCount() > 1)
1083         {
1084           startupFileTextfield_mouseClicked();
1085         }
1086       }
1087     });
1088
1089     sortby.setFont(verdana11);
1090     sortby.setBounds(new Rectangle(172, 240, 155, 21));
1091     JLabel sortLabel = new JLabel();
1092     sortLabel.setFont(verdana11);
1093     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1094     sortLabel.setText(MessageManager.getString("label.sort_by"));
1095     sortAnnBy.setFont(verdana11);
1096     sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
1097     JLabel sortAnnLabel = new JLabel();
1098     sortAnnLabel.setFont(verdana11);
1099     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1100     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1101     sortAutocalc.setFont(verdana11);
1102     sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
1103     JPanel annsettingsPanel = new JPanel();
1104     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
1105     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1106     JPanel autoAnnotSettings1 = new JPanel();
1107     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
1108     annsettingsPanel.add(autoAnnotSettings1);
1109     JPanel autoAnnotSettings2 = new JPanel();
1110     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
1111     annsettingsPanel.add(autoAnnotSettings2);
1112     JPanel autoAnnotSettings3 = new JPanel();
1113     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
1114     annsettingsPanel.add(autoAnnotSettings3);
1115     visualTab.add(annsettingsPanel);
1116     Border jb = new EmptyBorder(1, 1, 4, 5);
1117     quality.setBorder(jb);
1118     conservation.setBorder(jb);
1119     identity.setBorder(jb);
1120     showConsensbits.setBorder(jb);
1121     showGroupbits.setBorder(jb);
1122     showGroupConsensus.setBorder(jb);
1123     showGroupConservation.setBorder(jb);
1124     showConsensHistogram.setBorder(jb);
1125     showConsensLogo.setBorder(jb);
1126
1127     autoAnnotSettings2.add(conservation);
1128     autoAnnotSettings1.add(quality);
1129     autoAnnotSettings3.add(identity);
1130     autoAnnotSettings1.add(showGroupbits);
1131     autoAnnotSettings3.add(showGroupConsensus);
1132     autoAnnotSettings2.add(showGroupConservation);
1133     autoAnnotSettings1.add(showConsensbits);
1134     autoAnnotSettings2.add(showConsensHistogram);
1135     autoAnnotSettings3.add(showConsensLogo);
1136
1137     JPanel tooltipSettings = new JPanel();
1138     tooltipSettings.setBorder(new TitledBorder(MessageManager
1139             .getString("label.sequence_id_tooltip")));
1140     tooltipSettings.setBounds(173, 130, 200, 62);
1141     tooltipSettings.setLayout(new GridLayout(2, 1));
1142     tooltipSettings.add(showDbRefTooltip);
1143     tooltipSettings.add(showNpTooltip);
1144     visualTab.add(tooltipSettings);
1145
1146     wrap.setFont(verdana11);
1147     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1148     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1149     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1150     rightAlign.setFont(verdana11);
1151     rightAlign.setForeground(Color.black);
1152     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1153     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1154     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1155     idItalics.setFont(verdana11);
1156     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1157     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1158     idItalics.setText(MessageManager
1159             .getString("label.sequence_name_italics"));
1160     openoverv.setFont(verdana11);
1161     openoverv.setActionCommand(MessageManager
1162             .getString("label.open_overview"));
1163     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1164     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1165     openoverv.setText(MessageManager.getString(("label.open_overview")));
1166     JPanel jPanel2 = new JPanel();
1167     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
1168     GridLayout gridLayout2 = new GridLayout();
1169     jPanel2.setLayout(gridLayout2);
1170     gridLayout2.setRows(13);
1171     jPanel2.add(fullScreen);
1172     jPanel2.add(openoverv);
1173     jPanel2.add(seqLimit);
1174     jPanel2.add(rightAlign);
1175     jPanel2.add(fontLabel);
1176     jPanel2.add(showUnconserved);
1177     jPanel2.add(idItalics);
1178     jPanel2.add(smoothFont);
1179     jPanel2.add(gapLabel);
1180     jPanel2.add(wrap);
1181     jPanel2.add(sortLabel);
1182     jPanel2.add(sortAnnLabel);
1183     jPanel2.add(startupCheckbox);
1184     visualTab.add(jPanel2);
1185     visualTab.add(annotations);
1186     visualTab.add(startupFileTextfield);
1187     visualTab.add(sortby);
1188     visualTab.add(sortAnnBy);
1189     visualTab.add(sortAutocalc);
1190     visualTab.add(gapSymbolCB);
1191     visualTab.add(fontNameCB);
1192     visualTab.add(fontSizeCB);
1193     visualTab.add(fontStyleCB);
1194     return visualTab;
1195   }
1196
1197   protected void autoIdWidth_actionPerformed()
1198   {
1199     // TODO Auto-generated method stub
1200
1201   }
1202
1203   protected void userIdWidth_actionPerformed()
1204   {
1205     // TODO Auto-generated method stub
1206
1207   }
1208
1209   protected void maxColour_actionPerformed(JPanel panel)
1210   {
1211   }
1212
1213   protected void minColour_actionPerformed(JPanel panel)
1214   {
1215   }
1216
1217   protected void showunconserved_actionPerformed(ActionEvent e)
1218   {
1219     // TODO Auto-generated method stub
1220
1221   }
1222
1223   /**
1224    * DOCUMENT ME!
1225    *
1226    * @param e
1227    *          DOCUMENT ME!
1228    */
1229   public void ok_actionPerformed(ActionEvent e)
1230   {
1231   }
1232
1233   /**
1234    * DOCUMENT ME!
1235    *
1236    * @param e
1237    *          DOCUMENT ME!
1238    */
1239   public void cancel_actionPerformed(ActionEvent e)
1240   {
1241   }
1242
1243   /**
1244    * DOCUMENT ME!
1245    *
1246    * @param e
1247    *          DOCUMENT ME!
1248    */
1249   public void annotations_actionPerformed(ActionEvent e)
1250   {
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    */
1256   public void startupFileTextfield_mouseClicked()
1257   {
1258   }
1259
1260   public void newLink_actionPerformed(ActionEvent e)
1261   {
1262
1263   }
1264
1265   public void editLink_actionPerformed(ActionEvent e)
1266   {
1267
1268   }
1269
1270   public void deleteLink_actionPerformed(ActionEvent e)
1271   {
1272
1273   }
1274
1275   public void defaultBrowser_mouseClicked(MouseEvent e)
1276   {
1277
1278   }
1279
1280   public void linkURLList_keyTyped(KeyEvent e)
1281   {
1282
1283   }
1284
1285   public void useProxy_actionPerformed()
1286   {
1287     proxyServerTB.setEnabled(useProxy.isSelected());
1288     proxyPortTB.setEnabled(useProxy.isSelected());
1289   }
1290
1291 }