src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.fts.core.FTSDataColumnPreferences;
  24 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  25 import jalview.fts.service.pdb.PDBFTSRestClient;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.Component;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.Font;
  36 import java.awt.GridBagConstraints;
  37 import java.awt.GridBagLayout;
  38 import java.awt.GridLayout;
  39 import java.awt.Insets;
  40 import java.awt.Rectangle;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.FocusEvent;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseAdapter;
  46 import java.awt.event.MouseEvent;
  47
  48 import javax.swing.BorderFactory;
  49 import javax.swing.ButtonGroup;
  50 import javax.swing.DefaultListCellRenderer;
  51 import javax.swing.JButton;
  52 import javax.swing.JCheckBox;
  53 import javax.swing.JComboBox;
  54 import javax.swing.JFileChooser;
  55 import javax.swing.JLabel;
  56 import javax.swing.JList;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButton;
  59 import javax.swing.JScrollPane;
  60 import javax.swing.JTabbedPane;
  61 import javax.swing.JTextField;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.SwingConstants;
  64 import javax.swing.border.Border;
  65 import javax.swing.border.EmptyBorder;
  66 import javax.swing.border.EtchedBorder;
  67 import javax.swing.border.TitledBorder;
  68 import javax.swing.event.ChangeEvent;
  69 import javax.swing.event.ChangeListener;
  70 import javax.swing.event.ListSelectionEvent;
  71 import javax.swing.event.ListSelectionListener;
  72
  73 /**
  74  * Base class for the Preferences panel.
  75  *
  76  * @author $author$
  77  * @version $Revision$
  78  */
  79 public class GPreferences extends JPanel
  80 {
  81   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  82
  83   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  84           false, true);
  85
  86   /*
  87    * Visual tab components
  88    */
  89   protected JCheckBox fullScreen = new JCheckBox();
  90
  91   protected JCheckBox openoverv = new JCheckBox();
  92
  93   protected JCheckBox seqLimit = new JCheckBox();
  94
  95   protected JCheckBox rightAlign = new JCheckBox();
  96
  97   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  98
  99   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
 100
 101   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 102
 103   protected JCheckBox showUnconserved = new JCheckBox();
 104
 105   protected JCheckBox idItalics = new JCheckBox();
 106
 107   protected JCheckBox smoothFont = new JCheckBox();
 108
 109   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 110
 111   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 112
 113   protected JCheckBox wrap = new JCheckBox();
 114
 115   protected JComboBox<String> sortby = new JComboBox<String>();
 116
 117   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 118
 119   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 120
 121   protected JCheckBox startupCheckbox = new JCheckBox();
 122
 123   protected JTextField startupFileTextfield = new JTextField();
 124
 125   // below are in the 'second column'
 126   protected JCheckBox annotations = new JCheckBox();
 127
 128   protected JCheckBox quality = new JCheckBox();
 129
 130   protected JCheckBox conservation = new JCheckBox();
 131
 132   protected JCheckBox identity = new JCheckBox();
 133
 134   protected JCheckBox showGroupConsensus = new JCheckBox();
 135
 136   protected JCheckBox showGroupConservation = new JCheckBox();
 137
 138   protected JCheckBox showConsensHistogram = new JCheckBox();
 139
 140   protected JCheckBox showConsensLogo = new JCheckBox();
 141
 142   protected JCheckBox showDbRefTooltip = new JCheckBox();
 143
 144   protected JCheckBox showNpTooltip = new JCheckBox();
 145
 146   /*
 147    * Structure tab and components
 148    */
 149   protected JPanel structureTab;
 150
 151   protected JCheckBox structFromPdb = new JCheckBox();
 152
 153   protected JCheckBox useRnaView = new JCheckBox();
 154
 155   protected JCheckBox addSecondaryStructure = new JCheckBox();
 156
 157   protected JCheckBox addTempFactor = new JCheckBox();
 158
 159   protected JComboBox<String> structViewer = new JComboBox<String>();
 160
 161   protected JTextField chimeraPath = new JTextField();
 162
 163   protected ButtonGroup mappingMethod = new ButtonGroup();
 164
 165   protected JRadioButton siftsMapping = new JRadioButton();
 166
 167   protected JRadioButton nwMapping = new JRadioButton();
 168
 169   /*
 170    * Colours tab components
 171    */
 172   protected JPanel minColour = new JPanel();
 173
 174   protected JPanel maxColour = new JPanel();
 175
 176   protected JComboBox<String> protColour = new JComboBox<String>();
 177
 178   protected JComboBox<String> nucColour = new JComboBox<String>();
 179
 180   /*
 181    * Connections tab components
 182    */
 183   protected JList linkURLList = new JList();
 184
 185   protected JTextField proxyServerTB = new JTextField();
 186
 187   protected JTextField proxyPortTB = new JTextField();
 188
 189   protected JTextField defaultBrowser = new JTextField();
 190
 191   protected JList linkNameList = new JList();
 192
 193   protected JCheckBox useProxy = new JCheckBox();
 194
 195   protected JCheckBox usagestats = new JCheckBox();
 196
 197   protected JCheckBox questionnaire = new JCheckBox();
 198
 199   protected JCheckBox versioncheck = new JCheckBox();
 200
 201   /*
 202    * Output tab components
 203    */
 204   protected JComboBox<Object> epsRendering = new JComboBox<Object>();
 205
 206   protected JLabel userIdWidthlabel = new JLabel();
 207
 208   protected JCheckBox autoIdWidth = new JCheckBox();
 209
 210   protected JTextField userIdWidth = new JTextField();
 211
 212   protected JCheckBox blcjv = new JCheckBox();
 213
 214   protected JCheckBox pileupjv = new JCheckBox();
 215
 216   protected JCheckBox clustaljv = new JCheckBox();
 217
 218   protected JCheckBox msfjv = new JCheckBox();
 219
 220   protected JCheckBox fastajv = new JCheckBox();
 221
 222   protected JCheckBox pfamjv = new JCheckBox();
 223
 224   protected JCheckBox pirjv = new JCheckBox();
 225
 226   protected JCheckBox modellerOutput = new JCheckBox();
 227
 228   protected JCheckBox embbedBioJSON = new JCheckBox();
 229
 230   /*
 231    * Editing tab components
 232    */
 233   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 234
 235   protected JCheckBox padGaps = new JCheckBox();
 236
 237   protected JCheckBox sortByTree = new JCheckBox();
 238
 239   /*
 240    * DAS Settings tab
 241    */
 242   protected JPanel dasTab = new JPanel();
 243
 244   /*
 245    * Web Services tab
 246    */
 247   protected JPanel wsTab = new JPanel();
 248
 249   /**
 250    * Creates a new GPreferences object.
 251    */
 252   public GPreferences()
 253   {
 254     try
 255     {
 256       jbInit();
 257     } catch (Exception ex)
 258     {
 259       ex.printStackTrace();
 260     }
 261   }
 262
 263   /**
 264    * Construct the panel and its tabbed sub-panels.
 265    *
 266    * @throws Exception
 267    */
 268   private void jbInit() throws Exception
 269   {
 270     final JTabbedPane tabbedPane = new JTabbedPane();
 271     this.setLayout(new BorderLayout());
 272     JPanel okCancelPanel = initOkCancelPanel();
 273     this.add(tabbedPane, BorderLayout.CENTER);
 274     this.add(okCancelPanel, BorderLayout.SOUTH);
 275
 276     tabbedPane.add(initVisualTab(),
 277             MessageManager.getString("label.visual"));
 278
 279     tabbedPane.add(initColoursTab(),
 280             MessageManager.getString("label.colours"));
 281
 282     tabbedPane.add(initStructureTab(),
 283             MessageManager.getString("label.structure"));
 284
 285     tabbedPane.add(initConnectionsTab(),
 286             MessageManager.getString("label.connections"));
 287
 288     tabbedPane.add(initOutputTab(),
 289             MessageManager.getString("label.output"));
 290
 291     tabbedPane.add(initEditingTab(),
 292             MessageManager.getString("label.editing"));
 293
 294     /*
 295      * See DasSourceBrowser for the real work of configuring this tab.
 296      */
 297     dasTab.setLayout(new BorderLayout());
 298     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 299
 300     /*
 301      * See WsPreferences for the real work of configuring this tab.
 302      */
 303     wsTab.setLayout(new BorderLayout());
 304     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 305
 306     /*
 307      * Handler to validate a tab before leaving it - currently only for
 308      * Structure.
 309      */
 310     tabbedPane.addChangeListener(new ChangeListener()
 311     {
 312       private Component lastTab;
 313
 314       @Override
 315       public void stateChanged(ChangeEvent e)
 316       {
 317         if (lastTab == structureTab
 318                 && tabbedPane.getSelectedComponent() != structureTab)
 319         {
 320           if (!validateStructure())
 321           {
 322             tabbedPane.setSelectedComponent(structureTab);
 323             return;
 324           }
 325         }
 326         lastTab = tabbedPane.getSelectedComponent();
 327       }
 328
 329     });
 330   }
 331
 332   /**
 333    * Initialises the Editing tabbed panel.
 334    *
 335    * @return
 336    */
 337   private JPanel initEditingTab()
 338   {
 339     JPanel editingTab = new JPanel();
 340     editingTab.setLayout(null);
 341     autoCalculateConsCheck.setFont(LABEL_FONT);
 342     autoCalculateConsCheck.setText(MessageManager
 343             .getString("label.autocalculate_consensus"));
 344     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 345     padGaps.setFont(LABEL_FONT);
 346     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 347     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 348     sortByTree.setFont(LABEL_FONT);
 349     sortByTree
 350             .setText(MessageManager.getString("label.sort_with_new_tree"));
 351     sortByTree
 352             .setToolTipText(MessageManager
 353                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 354     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 355     editingTab.add(autoCalculateConsCheck);
 356     editingTab.add(padGaps);
 357     editingTab.add(sortByTree);
 358     return editingTab;
 359   }
 360
 361   /**
 362    * Initialises the Output tabbed panel.
 363    *
 364    * @return
 365    */
 366   private JPanel initOutputTab()
 367   {
 368     JPanel outputTab = new JPanel();
 369     outputTab.setLayout(null);
 370     JLabel epsLabel = new JLabel();
 371     epsLabel.setFont(LABEL_FONT);
 372     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 373     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 374     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 375     epsRendering.setFont(LABEL_FONT);
 376     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 377     JLabel jLabel1 = new JLabel();
 378     jLabel1.setFont(LABEL_FONT);
 379     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 380     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 381     jLabel1.setFont(LABEL_FONT);
 382     fastajv.setFont(LABEL_FONT);
 383     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 384     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 385     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 386     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 387     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 388     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 389     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 390     msfjv.setFont(LABEL_FONT);
 391     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 392     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 393     JPanel jPanel11 = new JPanel();
 394     jPanel11.setFont(LABEL_FONT);
 395     TitledBorder titledBorder2 = new TitledBorder(
 396             MessageManager.getString("label.file_output"));
 397     jPanel11.setBorder(titledBorder2);
 398     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 399     GridLayout gridLayout3 = new GridLayout();
 400     jPanel11.setLayout(gridLayout3);
 401     gridLayout3.setRows(8);
 402     blcjv.setFont(LABEL_FONT);
 403     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 404     clustaljv.setFont(LABEL_FONT);
 405     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 406     pfamjv.setFont(LABEL_FONT);
 407     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 408     pileupjv.setFont(LABEL_FONT);
 409     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 410     pirjv.setFont(LABEL_FONT);
 411     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 412     autoIdWidth.setFont(LABEL_FONT);
 413     autoIdWidth.setText(MessageManager
 414             .getString("label.automatically_set_id_width"));
 415     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 416             MessageManager
 417                     .getString("label.adjusts_width_generated_eps_png")));
 418     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 419     autoIdWidth.addActionListener(new ActionListener()
 420     {
 421
 422       @Override
 423       public void actionPerformed(ActionEvent e)
 424       {
 425         autoIdWidth_actionPerformed();
 426       }
 427     });
 428     userIdWidthlabel.setFont(LABEL_FONT);
 429     userIdWidthlabel.setText(MessageManager
 430             .getString("label.figure_id_column_width"));
 431     userIdWidth
 432             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 433                     .getString("label.manually_specify_width_left_column")));
 434     userIdWidthlabel
 435             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 436                     .getString("label.manually_specify_width_left_column")));
 437     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 438     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 439     userIdWidth.setText("");
 440     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 441     userIdWidth.addActionListener(new ActionListener()
 442     {
 443
 444       @Override
 445       public void actionPerformed(ActionEvent e)
 446       {
 447         userIdWidth_actionPerformed();
 448       }
 449     });
 450     modellerOutput.setFont(LABEL_FONT);
 451     modellerOutput.setText(MessageManager
 452             .getString("label.use_modeller_output"));
 453     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 454     embbedBioJSON.setFont(LABEL_FONT);
 455     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 456     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 457
 458     jPanel11.add(jLabel1);
 459     jPanel11.add(blcjv);
 460     jPanel11.add(clustaljv);
 461     jPanel11.add(fastajv);
 462     jPanel11.add(msfjv);
 463     jPanel11.add(pfamjv);
 464     jPanel11.add(pileupjv);
 465     jPanel11.add(pirjv);
 466     outputTab.add(autoIdWidth);
 467     outputTab.add(userIdWidth);
 468     outputTab.add(userIdWidthlabel);
 469     outputTab.add(modellerOutput);
 470     outputTab.add(embbedBioJSON);
 471     outputTab.add(epsLabel);
 472     outputTab.add(epsRendering);
 473     outputTab.add(jPanel11);
 474     return outputTab;
 475   }
 476
 477   /**
 478    * Initialises the Connections tabbed panel.
 479    *
 480    * @return
 481    */
 482   private JPanel initConnectionsTab()
 483   {
 484     JPanel connectTab = new JPanel();
 485     connectTab.setLayout(new GridBagLayout());
 486     JLabel serverLabel = new JLabel();
 487     serverLabel.setText(MessageManager.getString("label.address"));
 488     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 489     serverLabel.setFont(LABEL_FONT);
 490     proxyServerTB.setFont(LABEL_FONT);
 491     proxyPortTB.setFont(LABEL_FONT);
 492     JLabel portLabel = new JLabel();
 493     portLabel.setFont(LABEL_FONT);
 494     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 495     portLabel.setText(MessageManager.getString("label.port"));
 496     JLabel browserLabel = new JLabel();
 497     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 498     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 499     browserLabel.setText(MessageManager
 500             .getString("label.default_browser_unix"));
 501     defaultBrowser.setFont(LABEL_FONT);
 502     defaultBrowser.setText("");
 503     usagestats.setText(MessageManager
 504             .getString("label.send_usage_statistics"));
 505     usagestats.setFont(LABEL_FONT);
 506     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 507     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 508     questionnaire.setText(MessageManager
 509             .getString("label.check_for_questionnaires"));
 510     questionnaire.setFont(LABEL_FONT);
 511     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 512     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 513     versioncheck.setText(MessageManager
 514             .getString("label.check_for_latest_version"));
 515     versioncheck.setFont(LABEL_FONT);
 516     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 517     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 518     JButton newLink = new JButton();
 519     newLink.setText(MessageManager.getString("action.new"));
 520     newLink.addActionListener(new java.awt.event.ActionListener()
 521     {
 522       @Override
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         newLink_actionPerformed(e);
 526       }
 527     });
 528     JButton editLink = new JButton();
 529     editLink.setText(MessageManager.getString("action.edit"));
 530     editLink.addActionListener(new java.awt.event.ActionListener()
 531     {
 532       @Override
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         editLink_actionPerformed(e);
 536       }
 537     });
 538     JButton deleteLink = new JButton();
 539     deleteLink.setText(MessageManager.getString("action.delete"));
 540     deleteLink.addActionListener(new java.awt.event.ActionListener()
 541     {
 542       @Override
 543       public void actionPerformed(ActionEvent e)
 544       {
 545         deleteLink_actionPerformed(e);
 546       }
 547     });
 548
 549     linkURLList.addListSelectionListener(new ListSelectionListener()
 550     {
 551       @Override
 552       public void valueChanged(ListSelectionEvent e)
 553       {
 554         int index = linkURLList.getSelectedIndex();
 555         linkNameList.setSelectedIndex(index);
 556       }
 557     });
 558
 559     linkNameList.addListSelectionListener(new ListSelectionListener()
 560     {
 561       @Override
 562       public void valueChanged(ListSelectionEvent e)
 563       {
 564         int index = linkNameList.getSelectedIndex();
 565         linkURLList.setSelectedIndex(index);
 566       }
 567     });
 568
 569     JScrollPane linkScrollPane = new JScrollPane();
 570     linkScrollPane.setBorder(null);
 571     JPanel linkPanel = new JPanel();
 572     linkPanel.setBorder(new TitledBorder(MessageManager
 573             .getString("label.url_linkfrom_sequence_id")));
 574     linkPanel.setLayout(new BorderLayout());
 575     GridLayout gridLayout1 = new GridLayout();
 576     JPanel editLinkButtons = new JPanel();
 577     editLinkButtons.setLayout(gridLayout1);
 578     gridLayout1.setRows(3);
 579     linkNameList.setFont(LABEL_FONT);
 580     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 581     BorderLayout borderLayout3 = new BorderLayout();
 582     JPanel linkPanel2 = new JPanel();
 583     linkPanel2.setLayout(borderLayout3);
 584     linkURLList.setFont(LABEL_FONT);
 585     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 586
 587     defaultBrowser.addMouseListener(new MouseAdapter()
 588     {
 589       @Override
 590       public void mouseClicked(MouseEvent e)
 591       {
 592         if (e.getClickCount() > 1)
 593         {
 594           defaultBrowser_mouseClicked(e);
 595         }
 596       }
 597     });
 598     useProxy.setFont(LABEL_FONT);
 599     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 600     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 601     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 602     useProxy.addActionListener(new ActionListener()
 603     {
 604       @Override
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         useProxy_actionPerformed();
 608       }
 609     });
 610     linkPanel.add(editLinkButtons, BorderLayout.EAST);
 611     editLinkButtons.add(newLink, null);
 612     editLinkButtons.add(editLink, null);
 613     editLinkButtons.add(deleteLink, null);
 614     linkPanel.add(linkScrollPane, BorderLayout.CENTER);
 615     linkScrollPane.getViewport().add(linkPanel2, null);
 616     linkPanel2.add(linkURLList, BorderLayout.CENTER);
 617     linkPanel2.add(linkNameList, BorderLayout.WEST);
 618     JPanel jPanel1 = new JPanel();
 619     TitledBorder titledBorder1 = new TitledBorder(
 620             MessageManager.getString("label.proxy_server"));
 621     jPanel1.setBorder(titledBorder1);
 622     jPanel1.setLayout(new GridBagLayout());
 623     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 624             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 625                     2, 4, 0), 5, 0));
 626     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 627             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 628                     0, 4, 0), 11, 6));
 629     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
 630             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 631                     16, 0, 0, 12), 359, -17));
 632     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
 633             GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
 634                     21, 0, 35, 12), 4, 6));
 635     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 636             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 637             new Insets(16, 0, 0, 0), 5, 1));
 638     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 639             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 640                     2, 5, 185), 2, -4));
 641     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 642             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 643             new Insets(0, 2, 4, 2), 54, 1));
 644     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 645             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 646             new Insets(0, 2, 4, 0), 263, 1));
 647     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 648             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 649             new Insets(15, 0, 0, 15), 307, 1));
 650     connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
 651             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 652             new Insets(0, 2, 4, 2), 70, 1));
 653     connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
 654             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 655             new Insets(0, 2, 4, 2), 70, 1));
 656     connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
 657             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 658             new Insets(0, 2, 4, 2), 70, 1));
 659     return connectTab;
 660   }
 661
 662   /**
 663    * Initialises the parent panel which contains the tabbed sections.
 664    *
 665    * @return
 666    */
 667   private JPanel initOkCancelPanel()
 668   {
 669     JButton ok = new JButton();
 670     ok.setText(MessageManager.getString("action.ok"));
 671     ok.addActionListener(new ActionListener()
 672     {
 673       @Override
 674       public void actionPerformed(ActionEvent e)
 675       {
 676         ok_actionPerformed(e);
 677       }
 678     });
 679     JButton cancel = new JButton();
 680     cancel.setText(MessageManager.getString("action.cancel"));
 681     cancel.addActionListener(new ActionListener()
 682     {
 683       @Override
 684       public void actionPerformed(ActionEvent e)
 685       {
 686         cancel_actionPerformed(e);
 687       }
 688     });
 689     JPanel okCancelPanel = new JPanel();
 690     okCancelPanel.add(ok);
 691     okCancelPanel.add(cancel);
 692     return okCancelPanel;
 693   }
 694
 695   /**
 696    * Initialises the Colours tabbed panel.
 697    *
 698    * @return
 699    */
 700   private JPanel initColoursTab()
 701   {
 702     JPanel coloursTab = new JPanel();
 703     coloursTab.setBorder(new TitledBorder(MessageManager
 704             .getString("action.open_new_alignment")));
 705     coloursTab.setLayout(new FlowLayout());
 706     JLabel mincolourLabel = new JLabel();
 707     mincolourLabel.setFont(LABEL_FONT);
 708     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 709     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 710     minColour.setFont(LABEL_FONT);
 711     minColour.setBorder(BorderFactory.createEtchedBorder());
 712     minColour.setPreferredSize(new Dimension(40, 20));
 713     minColour.addMouseListener(new MouseAdapter()
 714     {
 715       @Override
 716       public void mousePressed(MouseEvent e)
 717       {
 718         minColour_actionPerformed(minColour);
 719       }
 720     });
 721     JLabel maxcolourLabel = new JLabel();
 722     maxcolourLabel.setFont(LABEL_FONT);
 723     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 724     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 725     maxColour.setFont(LABEL_FONT);
 726     maxColour.setBorder(BorderFactory.createEtchedBorder());
 727     maxColour.setPreferredSize(new Dimension(40, 20));
 728     maxColour.addMouseListener(new MouseAdapter()
 729     {
 730       @Override
 731       public void mousePressed(MouseEvent e)
 732       {
 733         maxColour_actionPerformed(maxColour);
 734       }
 735     });
 736
 737     protColour.setFont(LABEL_FONT);
 738     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 739     JLabel protColourLabel = new JLabel();
 740     protColourLabel.setFont(LABEL_FONT);
 741     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 742     protColourLabel.setText(MessageManager
 743             .getString("label.prot_alignment_colour") + " ");
 744     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 745             .getString("label.default_colour_scheme_for_alignment"),
 746             protColourLabel, protColour);
 747
 748     nucColour.setFont(LABEL_FONT);
 749     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 750     JLabel nucColourLabel = new JLabel();
 751     nucColourLabel.setFont(LABEL_FONT);
 752     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 753     nucColourLabel.setText(MessageManager
 754             .getString("label.nuc_alignment_colour") + " ");
 755     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 756             .getString("label.default_colour_scheme_for_alignment"),
 757             nucColourLabel, nucColour);
 758
 759     JPanel annotationShding = new JPanel();
 760     annotationShding.setBorder(new TitledBorder(MessageManager
 761             .getString("label.annotation_shading_default")));
 762     annotationShding.setLayout(new GridLayout(1, 2));
 763     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 764             .getString("label.default_minimum_colour_annotation_shading"),
 765             mincolourLabel, minColour);
 766     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 767             .getString("label.default_maximum_colour_annotation_shading"),
 768             maxcolourLabel, maxColour);
 769     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 770     return coloursTab;
 771   }
 772
 773   /**
 774    * Initialises the Structure tabbed panel.
 775    *
 776    * @return
 777    */
 778   private JPanel initStructureTab()
 779   {
 780     structureTab = new JPanel();
 781
 782     structureTab.setBorder(new TitledBorder(MessageManager
 783             .getString("label.structure_options")));
 784     structureTab.setLayout(null);
 785     final int width = 400;
 786     final int height = 22;
 787     final int lineSpacing = 25;
 788     int ypos = 15;
 789
 790     structFromPdb.setFont(LABEL_FONT);
 791     structFromPdb
 792             .setText(MessageManager.getString("label.struct_from_pdb"));
 793     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 794     structFromPdb.addActionListener(new ActionListener()
 795     {
 796       @Override
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         boolean selected = structFromPdb.isSelected();
 800         // enable other options only when the first is checked
 801         useRnaView.setEnabled(selected);
 802         addSecondaryStructure.setEnabled(selected);
 803         addTempFactor.setEnabled(selected);
 804       }
 805     });
 806     structureTab.add(structFromPdb);
 807
 808     // indent checkboxes that are conditional on the first one
 809     ypos += lineSpacing;
 810     useRnaView.setFont(LABEL_FONT);
 811     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 812     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 813     structureTab.add(useRnaView);
 814
 815     ypos += lineSpacing;
 816     addSecondaryStructure.setFont(LABEL_FONT);
 817     addSecondaryStructure.setText(MessageManager
 818             .getString("label.autoadd_secstr"));
 819     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 820     structureTab.add(addSecondaryStructure);
 821
 822     ypos += lineSpacing;
 823     addTempFactor.setFont(LABEL_FONT);
 824     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 825     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 826     structureTab.add(addTempFactor);
 827
 828     ypos += lineSpacing;
 829     JLabel viewerLabel = new JLabel();
 830     viewerLabel.setFont(LABEL_FONT);
 831     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 832     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 833     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 834     structureTab.add(viewerLabel);
 835
 836     structViewer.setFont(LABEL_FONT);
 837     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 838     structViewer.addItem(ViewerType.JMOL.name());
 839     structViewer.addItem(ViewerType.CHIMERA.name());
 840     structViewer.addActionListener(new ActionListener()
 841     {
 842       @Override
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         structureViewer_actionPerformed((String) structViewer
 846                 .getSelectedItem());
 847       }
 848     });
 849     structureTab.add(structViewer);
 850
 851     ypos += lineSpacing;
 852     JLabel pathLabel = new JLabel();
 853     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 854     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 855     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 856     final String tooltip = JvSwingUtils.wrapTooltip(true,
 857             MessageManager.getString("label.chimera_path_tip"));
 858     pathLabel.setToolTipText(tooltip);
 859     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 860     structureTab.add(pathLabel);
 861
 862     chimeraPath.setFont(LABEL_FONT);
 863     chimeraPath.setText("");
 864     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 865     chimeraPath.addMouseListener(new MouseAdapter()
 866     {
 867       @Override
 868       public void mouseClicked(MouseEvent e)
 869       {
 870         if (e.getClickCount() == 2)
 871         {
 872           String chosen = openFileChooser();
 873           if (chosen != null)
 874           {
 875             chimeraPath.setText(chosen);
 876           }
 877         }
 878       }
 879     });
 880     structureTab.add(chimeraPath);
 881
 882     ypos += lineSpacing;
 883     nwMapping.setFont(LABEL_FONT);
 884     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
 885     siftsMapping.setFont(LABEL_FONT);
 886     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
 887     mappingMethod.add(nwMapping);
 888     mappingMethod.add(siftsMapping);
 889     JPanel mappingPanel = new JPanel();
 890     mappingPanel.setFont(LABEL_FONT);
 891     TitledBorder mmTitledBorder = new TitledBorder(
 892             MessageManager.getString("label.mapping_method"));
 893     mmTitledBorder.setTitleFont(LABEL_FONT);
 894     mappingPanel.setBorder(mmTitledBorder);
 895     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
 896     // GridLayout mappingLayout = new GridLayout();
 897     mappingPanel.setLayout(new GridLayout());
 898     mappingPanel.add(nwMapping);
 899     mappingPanel.add(siftsMapping);
 900     structureTab.add(mappingPanel);
 901
 902     ypos += lineSpacing;
 903     ypos += lineSpacing;
 904     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
 905             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
 906     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
 907     structureTab.add(docFieldPref);
 908
 909     return structureTab;
 910   }
 911
 912   /**
 913    * Action on choosing a structure viewer from combobox options.
 914    *
 915    * @param selectedItem
 916    */
 917   protected void structureViewer_actionPerformed(String selectedItem)
 918   {
 919   }
 920
 921   /**
 922    * Show a dialog for the user to choose a file. Returns the chosen path, or
 923    * null on Cancel.
 924    *
 925    * @return
 926    */
 927   protected String openFileChooser()
 928   {
 929     String choice = null;
 930     JFileChooser chooser = new JFileChooser();
 931
 932     // chooser.setFileView(new JalviewFileView());
 933     chooser.setDialogTitle(MessageManager
 934             .getString("label.open_local_file"));
 935     chooser.setToolTipText(MessageManager.getString("action.open"));
 936
 937     int value = chooser.showOpenDialog(this);
 938
 939     if (value == JFileChooser.APPROVE_OPTION)
 940     {
 941       choice = chooser.getSelectedFile().getPath();
 942     }
 943     return choice;
 944   }
 945
 946   /**
 947    * Validate the structure tab preferences; if invalid, set focus on this tab.
 948    *
 949    * @param e
 950    */
 951   protected boolean validateStructure(FocusEvent e)
 952   {
 953     if (!validateStructure())
 954     {
 955       e.getComponent().requestFocusInWindow();
 956       return false;
 957     }
 958     return true;
 959   }
 960
 961   protected boolean validateStructure()
 962   {
 963     return false;
 964   }
 965
 966   /**
 967    * Initialises the Visual tabbed panel.
 968    *
 969    * @return
 970    */
 971   private JPanel initVisualTab()
 972   {
 973     JPanel visualTab = new JPanel();
 974     visualTab.setBorder(new TitledBorder(MessageManager
 975             .getString("action.open_new_alignment")));
 976     visualTab.setLayout(null);
 977     fullScreen.setFont(LABEL_FONT);
 978     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
 979     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
 980     fullScreen.setText(MessageManager.getString("label.maximize_window"));
 981     quality.setEnabled(false);
 982     quality.setFont(LABEL_FONT);
 983     quality.setHorizontalAlignment(SwingConstants.RIGHT);
 984     quality.setHorizontalTextPosition(SwingConstants.LEFT);
 985     quality.setSelected(true);
 986     quality.setText(MessageManager.getString("label.quality"));
 987     conservation.setEnabled(false);
 988     conservation.setFont(LABEL_FONT);
 989     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
 990     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
 991     conservation.setSelected(true);
 992     conservation.setText(MessageManager.getString("label.conservation"));
 993     identity.setEnabled(false);
 994     identity.setFont(LABEL_FONT);
 995     identity.setHorizontalAlignment(SwingConstants.RIGHT);
 996     identity.setHorizontalTextPosition(SwingConstants.LEFT);
 997     identity.setSelected(true);
 998     identity.setText(MessageManager.getString("label.consensus"));
 999     JLabel showGroupbits = new JLabel();
1000     showGroupbits.setFont(LABEL_FONT);
1001     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1002     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1003     showGroupbits.setText(MessageManager.getString("action.show_group")
1004             + ":");
1005     JLabel showConsensbits = new JLabel();
1006     showConsensbits.setFont(LABEL_FONT);
1007     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1008     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1009     showConsensbits.setText(MessageManager.getString("label.consensus")
1010             + ":");
1011     showConsensHistogram.setEnabled(false);
1012     showConsensHistogram.setFont(LABEL_FONT);
1013     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1014     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1015     showConsensHistogram.setSelected(true);
1016     showConsensHistogram.setText(MessageManager
1017             .getString("label.histogram"));
1018     showConsensLogo.setEnabled(false);
1019     showConsensLogo.setFont(LABEL_FONT);
1020     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1021     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1022     showConsensLogo.setSelected(true);
1023     showConsensLogo.setText(MessageManager.getString("label.logo"));
1024     showGroupConsensus.setEnabled(false);
1025     showGroupConsensus.setFont(LABEL_FONT);
1026     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1027     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1028     showGroupConsensus.setSelected(true);
1029     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1030     showGroupConservation.setEnabled(false);
1031     showGroupConservation.setFont(LABEL_FONT);
1032     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1033     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1034     showGroupConservation.setSelected(true);
1035     showGroupConservation.setText(MessageManager
1036             .getString("label.conservation"));
1037     showNpTooltip.setEnabled(true);
1038     showNpTooltip.setFont(LABEL_FONT);
1039     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1040     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1041     showNpTooltip.setSelected(true);
1042     showNpTooltip.setText(MessageManager
1043             .getString("label.non_positional_features"));
1044     showDbRefTooltip.setEnabled(true);
1045     showDbRefTooltip.setFont(LABEL_FONT);
1046     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1047     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1048     showDbRefTooltip.setSelected(true);
1049     showDbRefTooltip.setText(MessageManager
1050             .getString("label.database_references"));
1051     annotations.setFont(LABEL_FONT);
1052     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1053     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1054     annotations.setSelected(true);
1055     annotations.setText(MessageManager.getString("label.show_annotations"));
1056     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1057     annotations.addActionListener(new ActionListener()
1058     {
1059       @Override
1060       public void actionPerformed(ActionEvent e)
1061       {
1062         annotations_actionPerformed(e);
1063       }
1064     });
1065     identity.addActionListener(new ActionListener()
1066     {
1067       @Override
1068       public void actionPerformed(ActionEvent e)
1069       {
1070         annotations_actionPerformed(e);
1071       }
1072     });
1073     showGroupConsensus.addActionListener(new ActionListener()
1074     {
1075       @Override
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         annotations_actionPerformed(e);
1079       }
1080     });
1081     showUnconserved.setFont(LABEL_FONT);
1082     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1083     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1084     showUnconserved.setSelected(true);
1085     showUnconserved.setText(MessageManager
1086             .getString("action.show_unconserved"));
1087     showUnconserved.addActionListener(new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         showunconserved_actionPerformed(e);
1093       }
1094     });
1095
1096     // TODO these are not yet added to / action from Preferences
1097     // JCheckBox shareSelections = new JCheckBox();
1098     // shareSelections.setFont(verdana11);
1099     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1100     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1101     // shareSelections.setSelected(true);
1102     // shareSelections.setText(MessageManager
1103     // .getString("label.share_selection_across_views"));
1104     // JCheckBox followHighlight = new JCheckBox();
1105     // followHighlight.setFont(verdana11);
1106     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1107     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1108     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1109     // followHighlight.setSelected(true);
1110     // followHighlight.setText(MessageManager
1111     // .getString("label.scroll_highlighted_regions"));
1112
1113     seqLimit.setFont(LABEL_FONT);
1114     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1115     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1116     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1117     smoothFont.setFont(LABEL_FONT);
1118     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1119     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1120     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1121     scaleProteinToCdna.setFont(LABEL_FONT);
1122     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1123     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1124     scaleProteinToCdna.setText(MessageManager
1125             .getString("label.scale_protein_to_cdna"));
1126     scaleProteinToCdna.setToolTipText(MessageManager
1127             .getString("label.scale_protein_to_cdna_tip"));
1128     JLabel gapLabel = new JLabel();
1129     gapLabel.setFont(LABEL_FONT);
1130     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1131     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1132     JLabel fontLabel = new JLabel();
1133     fontLabel.setFont(LABEL_FONT);
1134     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1135     fontLabel.setText(MessageManager.getString("label.font"));
1136     fontSizeCB.setFont(LABEL_FONT);
1137     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1138     fontStyleCB.setFont(LABEL_FONT);
1139     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1140     fontNameCB.setFont(LABEL_FONT);
1141     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1142     gapSymbolCB.setFont(LABEL_FONT);
1143     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1144     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1145     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1146     gapSymbolCB.setRenderer(dlcr);
1147
1148     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1149     startupCheckbox.setFont(LABEL_FONT);
1150     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1151     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1152     startupCheckbox.setSelected(true);
1153     startupFileTextfield.setFont(LABEL_FONT);
1154     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1155     startupFileTextfield.addMouseListener(new MouseAdapter()
1156     {
1157       @Override
1158       public void mouseClicked(MouseEvent e)
1159       {
1160         if (e.getClickCount() > 1)
1161         {
1162           startupFileTextfield_mouseClicked();
1163         }
1164       }
1165     });
1166
1167     sortby.setFont(LABEL_FONT);
1168     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1169     JLabel sortLabel = new JLabel();
1170     sortLabel.setFont(LABEL_FONT);
1171     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1172     sortLabel.setText(MessageManager.getString("label.sort_by"));
1173     sortAnnBy.setFont(LABEL_FONT);
1174     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1175     JLabel sortAnnLabel = new JLabel();
1176     sortAnnLabel.setFont(LABEL_FONT);
1177     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1178     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1179     sortAutocalc.setFont(LABEL_FONT);
1180     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1181
1182     JPanel annsettingsPanel = new JPanel();
1183     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1184     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1185     annsettingsPanel.setBorder(new EtchedBorder());
1186     visualTab.add(annsettingsPanel);
1187     Border jb = new EmptyBorder(1, 1, 4, 5);
1188     quality.setBorder(jb);
1189     conservation.setBorder(jb);
1190     identity.setBorder(jb);
1191     showConsensbits.setBorder(jb);
1192     showGroupbits.setBorder(jb);
1193     showGroupConsensus.setBorder(jb);
1194     showGroupConservation.setBorder(jb);
1195     showConsensHistogram.setBorder(jb);
1196     showConsensLogo.setBorder(jb);
1197
1198     JPanel autoAnnotSettings = new JPanel();
1199     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1200     annsettingsPanel.add(autoAnnotSettings);
1201     autoAnnotSettings.add(quality);
1202     autoAnnotSettings.add(conservation);
1203     autoAnnotSettings.add(identity);
1204     autoAnnotSettings.add(showGroupbits);
1205     autoAnnotSettings.add(showGroupConservation);
1206     autoAnnotSettings.add(showGroupConsensus);
1207     autoAnnotSettings.add(showConsensbits);
1208     autoAnnotSettings.add(showConsensHistogram);
1209     autoAnnotSettings.add(showConsensLogo);
1210
1211     JPanel tooltipSettings = new JPanel();
1212     tooltipSettings.setBorder(new TitledBorder(MessageManager
1213             .getString("label.sequence_id_tooltip")));
1214     tooltipSettings.setBounds(173, 140, 220, 62);
1215     tooltipSettings.setLayout(new GridLayout(2, 1));
1216     tooltipSettings.add(showDbRefTooltip);
1217     tooltipSettings.add(showNpTooltip);
1218     visualTab.add(tooltipSettings);
1219
1220     wrap.setFont(LABEL_FONT);
1221     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1222     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1223     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1224     rightAlign.setFont(LABEL_FONT);
1225     rightAlign.setForeground(Color.black);
1226     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1227     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1228     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1229     idItalics.setFont(LABEL_FONT_ITALIC);
1230     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1231     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1232     idItalics.setText(MessageManager
1233             .getString("label.sequence_name_italics"));
1234     openoverv.setFont(LABEL_FONT);
1235     openoverv.setActionCommand(MessageManager
1236             .getString("label.open_overview"));
1237     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1238     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1239     openoverv.setText(MessageManager.getString("label.open_overview"));
1240     JPanel jPanel2 = new JPanel();
1241     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1242     jPanel2.setLayout(new GridLayout(14, 1));
1243     jPanel2.add(fullScreen);
1244     jPanel2.add(openoverv);
1245     jPanel2.add(seqLimit);
1246     jPanel2.add(rightAlign);
1247     jPanel2.add(fontLabel);
1248     jPanel2.add(showUnconserved);
1249     jPanel2.add(idItalics);
1250     jPanel2.add(smoothFont);
1251     jPanel2.add(scaleProteinToCdna);
1252     jPanel2.add(gapLabel);
1253     jPanel2.add(wrap);
1254     jPanel2.add(sortLabel);
1255     jPanel2.add(sortAnnLabel);
1256     jPanel2.add(startupCheckbox);
1257     visualTab.add(jPanel2);
1258     visualTab.add(annotations);
1259     visualTab.add(startupFileTextfield);
1260     visualTab.add(sortby);
1261     visualTab.add(sortAnnBy);
1262     visualTab.add(sortAutocalc);
1263     visualTab.add(gapSymbolCB);
1264     visualTab.add(fontNameCB);
1265     visualTab.add(fontSizeCB);
1266     visualTab.add(fontStyleCB);
1267     return visualTab;
1268   }
1269
1270   protected void autoIdWidth_actionPerformed()
1271   {
1272     // TODO Auto-generated method stub
1273
1274   }
1275
1276   protected void userIdWidth_actionPerformed()
1277   {
1278     // TODO Auto-generated method stub
1279
1280   }
1281
1282   protected void maxColour_actionPerformed(JPanel panel)
1283   {
1284   }
1285
1286   protected void minColour_actionPerformed(JPanel panel)
1287   {
1288   }
1289
1290   protected void showunconserved_actionPerformed(ActionEvent e)
1291   {
1292     // TODO Auto-generated method stub
1293
1294   }
1295
1296   /**
1297    * DOCUMENT ME!
1298    *
1299    * @param e
1300    *          DOCUMENT ME!
1301    */
1302   public void ok_actionPerformed(ActionEvent e)
1303   {
1304   }
1305
1306   /**
1307    * DOCUMENT ME!
1308    *
1309    * @param e
1310    *          DOCUMENT ME!
1311    */
1312   public void cancel_actionPerformed(ActionEvent e)
1313   {
1314   }
1315
1316   /**
1317    * DOCUMENT ME!
1318    *
1319    * @param e
1320    *          DOCUMENT ME!
1321    */
1322   public void annotations_actionPerformed(ActionEvent e)
1323   {
1324   }
1325
1326   /**
1327    * DOCUMENT ME!
1328    */
1329   public void startupFileTextfield_mouseClicked()
1330   {
1331   }
1332
1333   public void newLink_actionPerformed(ActionEvent e)
1334   {
1335
1336   }
1337
1338   public void editLink_actionPerformed(ActionEvent e)
1339   {
1340
1341   }
1342
1343   public void deleteLink_actionPerformed(ActionEvent e)
1344   {
1345
1346   }
1347
1348   public void defaultBrowser_mouseClicked(MouseEvent e)
1349   {
1350
1351   }
1352
1353   public void linkURLList_keyTyped(KeyEvent e)
1354   {
1355
1356   }
1357
1358   public void useProxy_actionPerformed()
1359   {
1360     proxyServerTB.setEnabled(useProxy.isSelected());
1361     proxyPortTB.setEnabled(useProxy.isSelected());
1362   }
1363
1364 }