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.Viewer;
  25 import jalview.util.MessageManager;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.Color;
  29 import java.awt.Component;
  30 import java.awt.Dimension;
  31 import java.awt.FlowLayout;
  32 import java.awt.Font;
  33 import java.awt.GridBagConstraints;
  34 import java.awt.GridBagLayout;
  35 import java.awt.GridLayout;
  36 import java.awt.Insets;
  37 import java.awt.Rectangle;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.KeyEvent;
  42 import java.awt.event.MouseAdapter;
  43 import java.awt.event.MouseEvent;
  44
  45 import javax.swing.BorderFactory;
  46 import javax.swing.DefaultListCellRenderer;
  47 import javax.swing.JButton;
  48 import javax.swing.JCheckBox;
  49 import javax.swing.JComboBox;
  50 import javax.swing.JFileChooser;
  51 import javax.swing.JLabel;
  52 import javax.swing.JList;
  53 import javax.swing.JPanel;
  54 import javax.swing.JScrollPane;
  55 import javax.swing.JTabbedPane;
  56 import javax.swing.JTextField;
  57 import javax.swing.ListSelectionModel;
  58 import javax.swing.SwingConstants;
  59 import javax.swing.border.Border;
  60 import javax.swing.border.EmptyBorder;
  61 import javax.swing.border.TitledBorder;
  62 import javax.swing.event.ChangeEvent;
  63 import javax.swing.event.ChangeListener;
  64 import javax.swing.event.ListSelectionEvent;
  65 import javax.swing.event.ListSelectionListener;
  66
  67 /**
  68  * Base class for the Preferences panel.
  69  *
  70  * @author $author$
  71  * @version $Revision$
  72  */
  73 public class GPreferences extends JPanel
  74 {
  75   private static final Font verdana11 = JvSwingUtils.getLabelFont();
  76
  77   /*
  78    * Visual tab components
  79    */
  80   protected JCheckBox fullScreen = new JCheckBox();
  81
  82   protected JCheckBox openoverv = new JCheckBox();
  83
  84   protected JCheckBox seqLimit = new JCheckBox();
  85
  86   protected JCheckBox rightAlign = new JCheckBox();
  87
  88   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  89
  90   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
  91
  92   protected JComboBox<String> fontNameCB = new JComboBox<String>();
  93
  94   protected JCheckBox showUnconserved = new JCheckBox();
  95
  96   protected JCheckBox idItalics = new JCheckBox();
  97
  98   protected JCheckBox smoothFont = new JCheckBox();
  99
 100   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 101
 102   protected JCheckBox wrap = new JCheckBox();
 103
 104   protected JComboBox<String> sortby = new JComboBox<String>();
 105
 106   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 107
 108   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 109
 110   protected JCheckBox startupCheckbox = new JCheckBox();
 111
 112   protected JTextField startupFileTextfield = new JTextField();
 113
 114   // below are in the 'second column'
 115   protected JCheckBox annotations = new JCheckBox();
 116
 117   protected JCheckBox quality = new JCheckBox();
 118
 119   protected JCheckBox conservation = new JCheckBox();
 120
 121   protected JCheckBox identity = new JCheckBox();
 122
 123   protected JCheckBox showGroupConsensus = new JCheckBox();
 124
 125   protected JCheckBox showGroupConservation = new JCheckBox();
 126
 127   protected JCheckBox showConsensHistogram = new JCheckBox();
 128
 129   protected JCheckBox showConsensLogo = new JCheckBox();
 130
 131   protected JCheckBox showDbRefTooltip = new JCheckBox();
 132
 133   protected JCheckBox showNpTooltip = new JCheckBox();
 134
 135   /*
 136    * Structure tab and components
 137    */
 138   protected JPanel structureTab;
 139
 140   protected JCheckBox structFromPdb = new JCheckBox();
 141
 142   protected JCheckBox useRnaView = new JCheckBox();
 143
 144   protected JCheckBox addSecondaryStructure = new JCheckBox();
 145
 146   protected JCheckBox addTempFactor = new JCheckBox();
 147
 148   protected JComboBox<String> structViewer = new JComboBox<String>();
 149
 150   protected JTextField chimeraPath = new JTextField();
 151
 152   /*
 153    * Colours tab components
 154    */
 155   protected JPanel minColour = new JPanel();
 156
 157   protected JPanel maxColour = new JPanel();
 158
 159   protected JComboBox<String> colour = new JComboBox<String>();
 160
 161   /*
 162    * Connections tab components
 163    */
 164   protected JList linkURLList = new JList();
 165
 166   protected JTextField proxyServerTB = new JTextField();
 167
 168   protected JTextField proxyPortTB = new JTextField();
 169
 170   protected JTextField defaultBrowser = new JTextField();
 171
 172   protected JList linkNameList = new JList();
 173
 174   protected JCheckBox useProxy = new JCheckBox();
 175
 176   protected JCheckBox usagestats = new JCheckBox();
 177
 178   protected JCheckBox questionnaire = new JCheckBox();
 179
 180   protected JCheckBox versioncheck = new JCheckBox();
 181
 182   /*
 183    * Output tab components
 184    */
 185   protected JComboBox<String> epsRendering = new JComboBox<String>();
 186
 187   protected JLabel userIdWidthlabel = new JLabel();
 188
 189   protected JCheckBox autoIdWidth = new JCheckBox();
 190
 191   protected JTextField userIdWidth = new JTextField();
 192
 193   protected JCheckBox blcjv = new JCheckBox();
 194
 195   protected JCheckBox pileupjv = new JCheckBox();
 196
 197   protected JCheckBox clustaljv = new JCheckBox();
 198
 199   protected JCheckBox msfjv = new JCheckBox();
 200
 201   protected JCheckBox fastajv = new JCheckBox();
 202
 203   protected JCheckBox pfamjv = new JCheckBox();
 204
 205   protected JCheckBox pirjv = new JCheckBox();
 206
 207   protected JCheckBox modellerOutput = new JCheckBox();
 208
 209   /*
 210    * Editing tab components
 211    */
 212   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 213
 214   protected JCheckBox padGaps = new JCheckBox();
 215
 216   protected JCheckBox sortByTree = new JCheckBox();
 217
 218   /*
 219    * DAS Settings tab
 220    */
 221   protected JPanel dasTab = new JPanel();
 222
 223   /*
 224    * Web Services tab
 225    */
 226   protected JPanel wsTab = new JPanel();
 227
 228   /**
 229    * Creates a new GPreferences object.
 230    */
 231   public GPreferences()
 232   {
 233     try
 234     {
 235       jbInit();
 236     } catch (Exception ex)
 237     {
 238       ex.printStackTrace();
 239     }
 240   }
 241
 242   /**
 243    * Construct the panel and its tabbed sub-panels.
 244    *
 245    * @throws Exception
 246    */
 247   private void jbInit() throws Exception
 248   {
 249     final JTabbedPane tabbedPane = new JTabbedPane();
 250     this.setLayout(new BorderLayout());
 251     JPanel okCancelPanel = initOkCancelPanel();
 252     this.add(tabbedPane, BorderLayout.CENTER);
 253     this.add(okCancelPanel, BorderLayout.SOUTH);
 254
 255     tabbedPane.add(initVisualTab(),
 256             MessageManager.getString("label.visual"));
 257
 258     tabbedPane.add(initColoursTab(),
 259             MessageManager.getString("label.colours"));
 260
 261     tabbedPane.add(initStructureTab(),
 262             MessageManager.getString("label.structure"));
 263
 264     tabbedPane.add(initConnectionsTab(),
 265             MessageManager.getString("label.connections"));
 266
 267     tabbedPane.add(initOutputTab(), MessageManager.getString("label.output"));
 268
 269     tabbedPane.add(initEditingTab(), MessageManager.getString("label.editing"));
 270
 271     /*
 272      * See DasSourceBrowser for the real work of configuring this tab.
 273      */
 274     dasTab.setLayout(new BorderLayout());
 275     tabbedPane
 276             .add(dasTab, MessageManager.getString("label.das_settings"));
 277
 278     /*
 279      * See WsPreferences for the real work of configuring this tab.
 280      */
 281     wsTab.setLayout(new BorderLayout());
 282     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 283
 284     /*
 285      * Handler to validate a tab before leaving it - currently only for
 286      * Structure.
 287      */
 288     tabbedPane.addChangeListener(new ChangeListener()
 289     {
 290       private Component lastTab;
 291
 292       @Override
 293       public void stateChanged(ChangeEvent e)
 294       {
 295         if (lastTab == structureTab
 296                 && tabbedPane.getSelectedComponent() != structureTab)
 297         {
 298           if (!validateStructure())
 299           {
 300             tabbedPane.setSelectedComponent(structureTab);
 301             return;
 302           }
 303         }
 304         lastTab = tabbedPane.getSelectedComponent();
 305       }
 306
 307     });
 308   }
 309
 310   /**
 311    * Initialises the Editing tabbed panel.
 312    *
 313    * @return
 314    */
 315   private JPanel initEditingTab()
 316   {
 317     JPanel editingTab = new JPanel();
 318     editingTab.setLayout(null);
 319     autoCalculateConsCheck.setFont(verdana11);
 320     autoCalculateConsCheck.setText(MessageManager
 321             .getString("label.autocalculate_consensus"));
 322     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 323     padGaps.setFont(verdana11);
 324     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 325     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 326     sortByTree.setFont(verdana11);
 327     sortByTree
 328             .setText(MessageManager.getString("label.sort_with_new_tree"));
 329     sortByTree
 330             .setToolTipText(MessageManager
 331                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 332     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 333     editingTab.add(autoCalculateConsCheck);
 334     editingTab.add(padGaps);
 335     editingTab.add(sortByTree);
 336     return editingTab;
 337   }
 338
 339   /**
 340    * Initialises the Output tabbed panel.
 341    *
 342    * @return
 343    */
 344   private JPanel initOutputTab()
 345   {
 346     JPanel outputTab = new JPanel();
 347     outputTab.setLayout(null);
 348     JLabel epsLabel = new JLabel();
 349     epsLabel.setFont(verdana11);
 350     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 351     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 352     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 353     epsRendering.setFont(verdana11);
 354     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 355     JLabel jLabel1 = new JLabel();
 356     jLabel1.setFont(verdana11);
 357     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 358     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 359     jLabel1.setFont(verdana11);
 360     fastajv.setFont(verdana11);
 361     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 362     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 363     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 364     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 365     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 366     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 367     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 368     msfjv.setFont(verdana11);
 369     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 370     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 371     JPanel jPanel11 = new JPanel();
 372     jPanel11.setFont(verdana11);
 373     TitledBorder titledBorder2 = new TitledBorder(
 374             MessageManager.getString("label.file_output"));
 375     jPanel11.setBorder(titledBorder2);
 376     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 377     GridLayout gridLayout3 = new GridLayout();
 378     jPanel11.setLayout(gridLayout3);
 379     gridLayout3.setRows(8);
 380     blcjv.setFont(verdana11);
 381     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 382     clustaljv.setFont(verdana11);
 383     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 384     pfamjv.setFont(verdana11);
 385     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 386     pileupjv.setFont(verdana11);
 387     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 388     pirjv.setFont(verdana11);
 389     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 390     autoIdWidth.setFont(verdana11);
 391     autoIdWidth.setText(MessageManager
 392             .getString("label.automatically_set_id_width"));
 393     autoIdWidth
 394             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.adjusts_width_generated_eps_png")));
 395     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 396     autoIdWidth.addActionListener(new ActionListener()
 397     {
 398
 399       @Override
 400       public void actionPerformed(ActionEvent e)
 401       {
 402         autoIdWidth_actionPerformed();
 403       }
 404     });
 405     userIdWidthlabel.setFont(verdana11);
 406     userIdWidthlabel.setText(MessageManager
 407             .getString("label.figure_id_column_width"));
 408     userIdWidth
 409             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 410     userIdWidthlabel
 411             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.manually_specify_width_left_column")));
 412     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 413     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 414     userIdWidth.setText("");
 415     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 416     userIdWidth.addActionListener(new ActionListener()
 417     {
 418
 419       @Override
 420       public void actionPerformed(ActionEvent e)
 421       {
 422         userIdWidth_actionPerformed();
 423       }
 424     });
 425     jPanel11.add(jLabel1);
 426     jPanel11.add(blcjv);
 427     jPanel11.add(clustaljv);
 428     jPanel11.add(fastajv);
 429     jPanel11.add(msfjv);
 430     jPanel11.add(pfamjv);
 431     jPanel11.add(pileupjv);
 432     jPanel11.add(pirjv);
 433     outputTab.add(autoIdWidth);
 434     outputTab.add(userIdWidth);
 435     outputTab.add(userIdWidthlabel);
 436     outputTab.add(modellerOutput);
 437     outputTab.add(epsLabel);
 438     outputTab.add(epsRendering);
 439     outputTab.add(jPanel11);
 440     modellerOutput.setFont(verdana11);
 441     modellerOutput.setText(MessageManager
 442             .getString("label.use_modeller_output"));
 443     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 444     return outputTab;
 445   }
 446
 447   /**
 448    * Initialises the Connections tabbed panel.
 449    *
 450    * @return
 451    */
 452   private JPanel initConnectionsTab()
 453   {
 454     JPanel connectTab = new JPanel();
 455     connectTab.setLayout(new GridBagLayout());
 456     JLabel serverLabel = new JLabel();
 457     serverLabel.setText(MessageManager.getString("label.address"));
 458     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 459     serverLabel.setFont(verdana11);
 460     proxyServerTB.setFont(verdana11);
 461     proxyPortTB.setFont(verdana11);
 462     JLabel portLabel = new JLabel();
 463     portLabel.setFont(verdana11);
 464     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 465     portLabel.setText(MessageManager.getString("label.port"));
 466     JLabel browserLabel = new JLabel();
 467     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 468     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 469     browserLabel.setText(MessageManager
 470             .getString("label.default_browser_unix"));
 471     defaultBrowser.setFont(verdana11);
 472     defaultBrowser.setText("");
 473     usagestats.setText(MessageManager
 474             .getString("label.send_usage_statistics"));
 475     usagestats.setFont(verdana11);
 476     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 477     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 478     questionnaire.setText(MessageManager
 479             .getString("label.check_for_questionnaires"));
 480     questionnaire.setFont(verdana11);
 481     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 482     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 483     versioncheck.setText(MessageManager
 484             .getString("label.check_for_latest_version"));
 485     versioncheck.setFont(verdana11);
 486     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 487     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 488     JButton newLink = new JButton();
 489     newLink.setText(MessageManager.getString("action.new"));
 490     newLink.addActionListener(new java.awt.event.ActionListener()
 491     {
 492       public void actionPerformed(ActionEvent e)
 493       {
 494         newLink_actionPerformed(e);
 495       }
 496     });
 497     JButton editLink = new JButton();
 498     editLink.setText(MessageManager.getString("action.edit"));
 499     editLink.addActionListener(new java.awt.event.ActionListener()
 500     {
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         editLink_actionPerformed(e);
 504       }
 505     });
 506     JButton deleteLink = new JButton();
 507     deleteLink.setText(MessageManager.getString("action.delete"));
 508     deleteLink.addActionListener(new java.awt.event.ActionListener()
 509     {
 510       public void actionPerformed(ActionEvent e)
 511       {
 512         deleteLink_actionPerformed(e);
 513       }
 514     });
 515
 516     linkURLList.addListSelectionListener(new ListSelectionListener()
 517     {
 518       public void valueChanged(ListSelectionEvent e)
 519       {
 520         int index = linkURLList.getSelectedIndex();
 521         linkNameList.setSelectedIndex(index);
 522       }
 523     });
 524
 525     linkNameList.addListSelectionListener(new ListSelectionListener()
 526     {
 527       public void valueChanged(ListSelectionEvent e)
 528       {
 529         int index = linkNameList.getSelectedIndex();
 530         linkURLList.setSelectedIndex(index);
 531       }
 532     });
 533
 534     JScrollPane linkScrollPane = new JScrollPane();
 535     linkScrollPane.setBorder(null);
 536     JPanel linkPanel = new JPanel();
 537     linkPanel.setBorder(new TitledBorder(MessageManager
 538             .getString("label.url_linkfrom_sequence_id")));
 539     linkPanel.setLayout(new BorderLayout());
 540     GridLayout gridLayout1 = new GridLayout();
 541     JPanel editLinkButtons = new JPanel();
 542     editLinkButtons.setLayout(gridLayout1);
 543     gridLayout1.setRows(3);
 544     linkNameList.setFont(verdana11);
 545     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 546     BorderLayout borderLayout3 = new BorderLayout();
 547     JPanel linkPanel2 = new JPanel();
 548     linkPanel2.setLayout(borderLayout3);
 549     linkURLList.setFont(verdana11);
 550     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 551
 552     defaultBrowser.addMouseListener(new MouseAdapter()
 553     {
 554       public void mouseClicked(MouseEvent e)
 555       {
 556         if (e.getClickCount() > 1)
 557         {
 558           defaultBrowser_mouseClicked(e);
 559         }
 560       }
 561     });
 562     useProxy.setFont(verdana11);
 563     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 564     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 565     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 566     useProxy.addActionListener(new ActionListener()
 567     {
 568       public void actionPerformed(ActionEvent e)
 569       {
 570         useProxy_actionPerformed();
 571       }
 572     });
 573     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 574     editLinkButtons.add(newLink, null);
 575     editLinkButtons.add(editLink, null);
 576     editLinkButtons.add(deleteLink, null);
 577     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 578     linkScrollPane.getViewport().add(linkPanel2, null);
 579     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 580     linkPanel2.add(linkNameList, BorderLayout.WEST);
 581     JPanel jPanel1 = new JPanel();
 582     TitledBorder titledBorder1 = new TitledBorder(
 583             MessageManager.getString("label.proxy_server"));
 584     jPanel1.setBorder(titledBorder1);
 585     jPanel1.setLayout(new GridBagLayout());
 586     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 587             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 588                     2, 4, 0), 5, 0));
 589     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 590             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 591                     0, 4, 0), 11, 6));
 592     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 593             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 594                     16, 0, 0, 12), 359, -17));
 595     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 596             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 597                     21, 0, 35, 12), 4, 6));
 598     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 599             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 600             new Insets(16, 0, 0, 0), 5, 1));
 601     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 602             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 603                     2, 5, 185), 2, -4));
 604     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 605             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 606             new Insets(0, 2, 4, 2), 54, 1));
 607     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 608             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 609             new Insets(0, 2, 4, 0), 263, 1));
 610     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 611             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 612             new Insets(15, 0, 0, 15), 307, 1));
 613     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 614             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 615             new Insets(0, 2, 4, 2), 70, 1));
 616     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 617             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 618             new Insets(0, 2, 4, 2), 70, 1));
 619     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 620             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 621             new Insets(0, 2, 4, 2), 70, 1));
 622     return connectTab;
 623   }
 624
 625   /**
 626    * Initialises the parent panel which contains the tabbed sections.
 627    *
 628    * @return
 629    */
 630   private JPanel initOkCancelPanel()
 631   {
 632     JButton ok = new JButton();
 633     ok.setText(MessageManager.getString("action.ok"));
 634     ok.addActionListener(new ActionListener()
 635     {
 636       public void actionPerformed(ActionEvent e)
 637       {
 638         ok_actionPerformed(e);
 639       }
 640     });
 641     JButton cancel = new JButton();
 642     cancel.setText(MessageManager.getString("action.cancel"));
 643     cancel.addActionListener(new ActionListener()
 644     {
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         cancel_actionPerformed(e);
 648       }
 649     });
 650     JPanel okCancelPanel = new JPanel();
 651     okCancelPanel.add(ok);
 652     okCancelPanel.add(cancel);
 653     return okCancelPanel;
 654   }
 655
 656   /**
 657    * Initialises the Colours tabbed panel.
 658    *
 659    * @return
 660    */
 661   private JPanel initColoursTab()
 662   {
 663     JPanel coloursTab = new JPanel();
 664     coloursTab.setBorder(new TitledBorder(MessageManager
 665             .getString("action.open_new_alignment")));
 666     coloursTab.setLayout(new FlowLayout());
 667     JLabel mincolourLabel = new JLabel();
 668     mincolourLabel.setFont(verdana11);
 669     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 670     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 671     minColour.setFont(verdana11);
 672     minColour.setBorder(BorderFactory.createEtchedBorder());
 673     minColour.setPreferredSize(new Dimension(40, 20));
 674     minColour.addMouseListener(new MouseAdapter()
 675     {
 676       public void mousePressed(MouseEvent e)
 677       {
 678         minColour_actionPerformed(minColour);
 679       }
 680     });
 681     JLabel maxcolourLabel = new JLabel();
 682     maxcolourLabel.setFont(verdana11);
 683     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 684     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 685     maxColour.setFont(verdana11);
 686     maxColour.setBorder(BorderFactory.createEtchedBorder());
 687     maxColour.setPreferredSize(new Dimension(40, 20));
 688     maxColour.addMouseListener(new MouseAdapter()
 689     {
 690       public void mousePressed(MouseEvent e)
 691       {
 692         maxColour_actionPerformed(maxColour);
 693       }
 694     });
 695     colour.setFont(verdana11);
 696     colour.setBounds(new Rectangle(172, 225, 155, 21));
 697     JLabel colourLabel = new JLabel();
 698     colourLabel.setFont(verdana11);
 699     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 700     colourLabel.setText(MessageManager.getString("label.alignment_colour")
 701             + " ");
 702     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 703             .getString("label.default_colour_scheme_for_alignment"),
 704             colourLabel, colour);
 705     JPanel annotationShding = new JPanel();
 706     annotationShding.setBorder(new TitledBorder(MessageManager
 707             .getString("label.annotation_shading_default")));
 708     annotationShding.setLayout(new GridLayout(1, 2));
 709     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 710             .getString("label.default_minimum_colour_annotation_shading"),
 711             mincolourLabel, minColour);
 712     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 713             .getString("label.default_maximum_colour_annotation_shading"),
 714             maxcolourLabel, maxColour);
 715     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 716     return coloursTab;
 717   }
 718
 719   /**
 720    * Initialises the Structure tabbed panel.
 721    *
 722    * @return
 723    */
 724   private JPanel initStructureTab()
 725   {
 726     structureTab = new JPanel();
 727
 728     structureTab.setBorder(new TitledBorder(MessageManager
 729             .getString("label.structure_options")));
 730     structureTab.setLayout(null);
 731     final int width = 400;
 732     final int height = 23;
 733     final int lineSpacing = 30;
 734     int ypos = 30;
 735
 736     structFromPdb.setFont(verdana11);
 737     structFromPdb.setText(MessageManager.getString("label.struct_from_pdb"));
 738     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 739     structFromPdb.addActionListener(new ActionListener()
 740     {
 741       @Override
 742       public void actionPerformed(ActionEvent e)
 743       {
 744         boolean selected = structFromPdb.isSelected();
 745         // enable other options only when the first is checked
 746         useRnaView.setEnabled(selected);
 747         addSecondaryStructure.setEnabled(selected);
 748         addTempFactor.setEnabled(selected);
 749       }
 750     });
 751     structureTab.add(structFromPdb);
 752
 753     // indent checkboxes that are conditional on the first one
 754     ypos += lineSpacing;
 755     useRnaView.setFont(verdana11);
 756     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 757     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 758     structureTab.add(useRnaView);
 759
 760     ypos += lineSpacing;
 761     addSecondaryStructure.setFont(verdana11);
 762     addSecondaryStructure.setText(MessageManager
 763             .getString("label.autoadd_secstr"));
 764     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 765     structureTab.add(addSecondaryStructure);
 766
 767     ypos += lineSpacing;
 768     addTempFactor.setFont(verdana11);
 769     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 770     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 771     structureTab.add(addTempFactor);
 772
 773     ypos += lineSpacing;
 774     JLabel viewerLabel = new JLabel();
 775     viewerLabel.setFont(verdana11);
 776     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 777     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 778     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 779     structureTab.add(viewerLabel);
 780
 781     structViewer.setFont(verdana11);
 782     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 783     structViewer.addItem(Viewer.JMOL.name());
 784     structViewer.addItem(Viewer.CHIMERA.name());
 785     structViewer.addActionListener(new ActionListener()
 786     {
 787       @Override
 788       public void actionPerformed(ActionEvent e)
 789       {
 790         structureViewer_actionPerformed((String) structViewer
 791                 .getSelectedItem());
 792       }
 793     });
 794     structureTab.add(structViewer);
 795
 796     ypos += lineSpacing;
 797     JLabel pathLabel = new JLabel();
 798     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 799     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 800     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 801     final String tooltip = JvSwingUtils.wrapTooltip(true,
 802             MessageManager.getString("label.chimera_path_tip"));
 803     pathLabel.setToolTipText(tooltip);
 804     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 805     structureTab.add(pathLabel);
 806
 807     chimeraPath.setFont(verdana11);
 808     chimeraPath.setText("");
 809     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 810     chimeraPath.addMouseListener(new MouseAdapter()
 811     {
 812       @Override
 813       public void mouseClicked(MouseEvent e)
 814       {
 815         if (e.getClickCount() == 2)
 816         {
 817           String chosen = openFileChooser();
 818           if (chosen != null)
 819           {
 820             chimeraPath.setText(chosen);
 821           }
 822         }
 823       }
 824     });
 825     structureTab.add(chimeraPath);
 826
 827     return structureTab;
 828   }
 829
 830   /**
 831    * Action on choosing a structure viewer from combobox options.
 832    *
 833    * @param selectedItem
 834    */
 835   protected void structureViewer_actionPerformed(String selectedItem)
 836   {
 837   }
 838
 839   /**
 840    * Show a dialog for the user to choose a file. Returns the chosen path, or
 841    * null on Cancel.
 842    *
 843    * @return
 844    */
 845   protected String openFileChooser()
 846   {
 847     String choice = null;
 848     JFileChooser chooser = new JFileChooser();
 849
 850     // chooser.setFileView(new JalviewFileView());
 851     chooser.setDialogTitle(MessageManager
 852             .getString("label.open_local_file"));
 853     chooser.setToolTipText(MessageManager.getString("action.open"));
 854
 855     int value = chooser.showOpenDialog(this);
 856
 857     if (value == JFileChooser.APPROVE_OPTION)
 858     {
 859       choice = chooser.getSelectedFile().getPath();
 860     }
 861     return choice;
 862   }
 863
 864   /**
 865    * Validate the structure tab preferences; if invalid, set focus on this tab.
 866    *
 867    * @param e
 868    */
 869   protected boolean validateStructure(FocusEvent e)
 870   {
 871     if (!validateStructure())
 872     {
 873       e.getComponent().requestFocusInWindow();
 874       return false;
 875     }
 876     return true;
 877   }
 878
 879   protected boolean validateStructure()
 880   {
 881     return false;
 882   }
 883
 884   /**
 885    * Initialises the Visual tabbed panel.
 886    *
 887    * @return
 888    */
 889   private JPanel initVisualTab()
 890   {
 891     JPanel visualTab = new JPanel();
 892     visualTab.setBorder(new TitledBorder(MessageManager
 893             .getString("action.open_new_alignment")));
 894     visualTab.setLayout(null);
 895     fullScreen.setFont(verdana11);
 896     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 897     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 898     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 899     quality.setEnabled(false);
 900     quality.setFont(verdana11);
 901     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 902     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 903     quality.setSelected(true);
 904     quality.setText(MessageManager.getString("label.quality"));
 905     conservation.setEnabled(false);
 906     conservation.setFont(verdana11);
 907     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 908     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 909     conservation.setSelected(true);
 910     conservation.setText(MessageManager.getString("label.conservation"));
 911     identity.setEnabled(false);
 912     identity.setFont(verdana11);
 913     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 914     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 915     identity.setSelected(true);
 916     identity.setText(MessageManager.getString("label.consensus"));
 917     JLabel showGroupbits = new JLabel();
 918     showGroupbits.setFont(verdana11);
 919     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
 920     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
 921     showGroupbits.setText(MessageManager.getString("action.show_group")
 922             + ":");
 923     JLabel showConsensbits = new JLabel();
 924     showConsensbits.setFont(verdana11);
 925     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
 926     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
 927     showConsensbits.setText(MessageManager.getString("label.consensus")
 928             + ":");
 929     showConsensHistogram.setEnabled(false);
 930     showConsensHistogram.setFont(verdana11);
 931     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
 932     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
 933     showConsensHistogram.setSelected(true);
 934     showConsensHistogram.setText(MessageManager
 935             .getString("label.histogram"));
 936     showConsensLogo.setEnabled(false);
 937     showConsensLogo.setFont(verdana11);
 938     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
 939     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
 940     showConsensLogo.setSelected(true);
 941     showConsensLogo.setText(MessageManager.getString("label.logo"));
 942     showGroupConsensus.setEnabled(false);
 943     showGroupConsensus.setFont(verdana11);
 944     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
 945     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
 946     showGroupConsensus.setSelected(true);
 947     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
 948     showGroupConservation.setEnabled(false);
 949     showGroupConservation.setFont(verdana11);
 950     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
 951     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
 952     showGroupConservation.setSelected(true);
 953     showGroupConservation.setText(MessageManager
 954             .getString("label.conservation"));
 955     showNpTooltip.setEnabled(true);
 956     showNpTooltip.setFont(verdana11);
 957     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 958     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 959     showNpTooltip.setSelected(true);
 960     showNpTooltip.setText(MessageManager
 961             .getString("label.non_positional_features"));
 962     showDbRefTooltip.setEnabled(true);
 963     showDbRefTooltip.setFont(verdana11);
 964     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
 965     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
 966     showDbRefTooltip.setSelected(true);
 967     showDbRefTooltip.setText(MessageManager
 968             .getString("label.database_references"));
 969     annotations.setFont(verdana11);
 970     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
 971     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
 972     annotations.setSelected(true);
 973     annotations.setText(MessageManager.getString("label.show_annotations"));
 974     annotations.setBounds(new Rectangle(169, 12, 200, 23));
 975     annotations.addActionListener(new ActionListener()
 976     {
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         annotations_actionPerformed(e);
 980       }
 981     });
 982     identity.addActionListener(new ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         annotations_actionPerformed(e);
 987       }
 988     });
 989     showGroupConsensus.addActionListener(new ActionListener()
 990     {
 991       public void actionPerformed(ActionEvent e)
 992       {
 993         annotations_actionPerformed(e);
 994       }
 995     });
 996     showUnconserved.setFont(verdana11);
 997     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
 998     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
 999     showUnconserved.setSelected(true);
1000     showUnconserved.setText(MessageManager
1001             .getString("action.show_unconserved"));
1002     showUnconserved.addActionListener(new ActionListener()
1003     {
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         showunconserved_actionPerformed(e);
1007       }
1008     });
1009
1010     // TODO these are not yet added to / action from Preferences
1011     // JCheckBox shareSelections = new JCheckBox();
1012     // shareSelections.setFont(verdana11);
1013     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1014     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1015     // shareSelections.setSelected(true);
1016     // shareSelections.setText(MessageManager
1017     // .getString("label.share_selection_across_views"));
1018     // JCheckBox followHighlight = new JCheckBox();
1019     // followHighlight.setFont(verdana11);
1020     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1021     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1022     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1023     // followHighlight.setSelected(true);
1024     // followHighlight.setText(MessageManager
1025     // .getString("label.scroll_highlighted_regions"));
1026
1027     seqLimit.setFont(verdana11);
1028     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1029     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1030     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1031     smoothFont.setFont(verdana11);
1032     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1033     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1034     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1035     JLabel gapLabel = new JLabel();
1036     gapLabel.setFont(verdana11);
1037     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1038     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1039     JLabel fontLabel = new JLabel();
1040     fontLabel.setFont(verdana11);
1041     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1042     fontLabel.setText(MessageManager.getString("label.font"));
1043     fontSizeCB.setFont(verdana11);
1044     fontSizeCB.setBounds(new Rectangle(320, 104, 65, 23));
1045     fontStyleCB.setFont(verdana11);
1046     fontStyleCB.setBounds(new Rectangle(382, 104, 80, 23));
1047     fontNameCB.setFont(verdana11);
1048     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
1049     gapSymbolCB.setFont(verdana11);
1050     gapSymbolCB.setBounds(new Rectangle(172, 196, 69, 23));
1051     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1052     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1053     gapSymbolCB.setRenderer(dlcr);
1054
1055     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1056     startupCheckbox.setFont(verdana11);
1057     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1058     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1059     startupCheckbox.setSelected(true);
1060     startupFileTextfield.setFont(verdana11);
1061     startupFileTextfield.setBounds(new Rectangle(172, 290, 270, 20));
1062     startupFileTextfield.addMouseListener(new MouseAdapter()
1063     {
1064       public void mouseClicked(MouseEvent e)
1065       {
1066         if (e.getClickCount() > 1)
1067         {
1068           startupFileTextfield_mouseClicked();
1069         }
1070       }
1071     });
1072
1073     sortby.setFont(verdana11);
1074     sortby.setBounds(new Rectangle(172, 240, 155, 21));
1075     JLabel sortLabel = new JLabel();
1076     sortLabel.setFont(verdana11);
1077     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1078     sortLabel.setText(MessageManager.getString("label.sort_by"));
1079     sortAnnBy.setFont(verdana11);
1080     sortAnnBy.setBounds(new Rectangle(172, 265, 110, 21));
1081     JLabel sortAnnLabel = new JLabel();
1082     sortAnnLabel.setFont(verdana11);
1083     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1084     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1085     sortAutocalc.setFont(verdana11);
1086     sortAutocalc.setBounds(new Rectangle(290, 265, 165, 21));
1087     JPanel annsettingsPanel = new JPanel();
1088     annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
1089     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1090     JPanel autoAnnotSettings1 = new JPanel();
1091     autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
1092     annsettingsPanel.add(autoAnnotSettings1);
1093     JPanel autoAnnotSettings2 = new JPanel();
1094     autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
1095     annsettingsPanel.add(autoAnnotSettings2);
1096     JPanel autoAnnotSettings3 = new JPanel();
1097     autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
1098     annsettingsPanel.add(autoAnnotSettings3);
1099     visualTab.add(annsettingsPanel);
1100     Border jb = new EmptyBorder(1, 1, 4, 5);
1101     quality.setBorder(jb);
1102     conservation.setBorder(jb);
1103     identity.setBorder(jb);
1104     showConsensbits.setBorder(jb);
1105     showGroupbits.setBorder(jb);
1106     showGroupConsensus.setBorder(jb);
1107     showGroupConservation.setBorder(jb);
1108     showConsensHistogram.setBorder(jb);
1109     showConsensLogo.setBorder(jb);
1110
1111     autoAnnotSettings2.add(conservation);
1112     autoAnnotSettings1.add(quality);
1113     autoAnnotSettings3.add(identity);
1114     autoAnnotSettings1.add(showGroupbits);
1115     autoAnnotSettings3.add(showGroupConsensus);
1116     autoAnnotSettings2.add(showGroupConservation);
1117     autoAnnotSettings1.add(showConsensbits);
1118     autoAnnotSettings2.add(showConsensHistogram);
1119     autoAnnotSettings3.add(showConsensLogo);
1120
1121     JPanel tooltipSettings = new JPanel();
1122     tooltipSettings.setBorder(new TitledBorder(MessageManager
1123             .getString("label.sequence_id_tooltip")));
1124     tooltipSettings.setBounds(173, 130, 200, 62);
1125     tooltipSettings.setLayout(new GridLayout(2, 1));
1126     tooltipSettings.add(showDbRefTooltip);
1127     tooltipSettings.add(showNpTooltip);
1128     visualTab.add(tooltipSettings);
1129
1130     wrap.setFont(verdana11);
1131     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1132     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1133     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1134     rightAlign.setFont(verdana11);
1135     rightAlign.setForeground(Color.black);
1136     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1137     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1138     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1139     idItalics.setFont(verdana11);
1140     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1141     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1142     idItalics.setText(MessageManager
1143             .getString("label.sequence_name_italics"));
1144     openoverv.setFont(verdana11);
1145     openoverv.setActionCommand(MessageManager
1146             .getString("label.open_overview"));
1147     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1148     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1149     openoverv.setText(MessageManager.getString(("label.open_overview")));
1150     JPanel jPanel2 = new JPanel();
1151     jPanel2.setBounds(new Rectangle(7, 17, 158, 297));
1152     GridLayout gridLayout2 = new GridLayout();
1153     jPanel2.setLayout(gridLayout2);
1154     gridLayout2.setRows(13);
1155     jPanel2.add(fullScreen);
1156     jPanel2.add(openoverv);
1157     jPanel2.add(seqLimit);
1158     jPanel2.add(rightAlign);
1159     jPanel2.add(fontLabel);
1160     jPanel2.add(showUnconserved);
1161     jPanel2.add(idItalics);
1162     jPanel2.add(smoothFont);
1163     jPanel2.add(gapLabel);
1164     jPanel2.add(wrap);
1165     jPanel2.add(sortLabel);
1166     jPanel2.add(sortAnnLabel);
1167     jPanel2.add(startupCheckbox);
1168     visualTab.add(jPanel2);
1169     visualTab.add(annotations);
1170     visualTab.add(startupFileTextfield);
1171     visualTab.add(sortby);
1172     visualTab.add(sortAnnBy);
1173     visualTab.add(sortAutocalc);
1174     visualTab.add(gapSymbolCB);
1175     visualTab.add(fontNameCB);
1176     visualTab.add(fontSizeCB);
1177     visualTab.add(fontStyleCB);
1178     return visualTab;
1179   }
1180
1181   protected void autoIdWidth_actionPerformed()
1182   {
1183     // TODO Auto-generated method stub
1184
1185   }
1186
1187   protected void userIdWidth_actionPerformed()
1188   {
1189     // TODO Auto-generated method stub
1190
1191   }
1192
1193   protected void maxColour_actionPerformed(JPanel panel)
1194   {
1195   }
1196
1197   protected void minColour_actionPerformed(JPanel panel)
1198   {
1199   }
1200
1201   protected void showunconserved_actionPerformed(ActionEvent e)
1202   {
1203     // TODO Auto-generated method stub
1204
1205   }
1206
1207   /**
1208    * DOCUMENT ME!
1209    *
1210    * @param e
1211    *          DOCUMENT ME!
1212    */
1213   public void ok_actionPerformed(ActionEvent e)
1214   {
1215   }
1216
1217   /**
1218    * DOCUMENT ME!
1219    *
1220    * @param e
1221    *          DOCUMENT ME!
1222    */
1223   public void cancel_actionPerformed(ActionEvent e)
1224   {
1225   }
1226
1227   /**
1228    * DOCUMENT ME!
1229    *
1230    * @param e
1231    *          DOCUMENT ME!
1232    */
1233   public void annotations_actionPerformed(ActionEvent e)
1234   {
1235   }
1236
1237   /**
1238    * DOCUMENT ME!
1239    */
1240   public void startupFileTextfield_mouseClicked()
1241   {
1242   }
1243
1244   public void newLink_actionPerformed(ActionEvent e)
1245   {
1246
1247   }
1248
1249   public void editLink_actionPerformed(ActionEvent e)
1250   {
1251
1252   }
1253
1254   public void deleteLink_actionPerformed(ActionEvent e)
1255   {
1256
1257   }
1258
1259   public void defaultBrowser_mouseClicked(MouseEvent e)
1260   {
1261
1262   }
1263
1264   public void linkURLList_keyTyped(KeyEvent e)
1265   {
1266
1267   }
1268
1269   public void useProxy_actionPerformed()
1270   {
1271     proxyServerTB.setEnabled(useProxy.isSelected());
1272     proxyPortTB.setEnabled(useProxy.isSelected());
1273   }
1274
1275 }