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.AbstractCellEditor;
  49 import javax.swing.BorderFactory;
  50 import javax.swing.ButtonGroup;
  51 import javax.swing.DefaultListCellRenderer;
  52 import javax.swing.JButton;
  53 import javax.swing.JCheckBox;
  54 import javax.swing.JComboBox;
  55 import javax.swing.JFileChooser;
  56 import javax.swing.JLabel;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButton;
  59 import javax.swing.JScrollPane;
  60 import javax.swing.JTabbedPane;
  61 import javax.swing.JTable;
  62 import javax.swing.JTextField;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.SwingConstants;
  65 import javax.swing.border.Border;
  66 import javax.swing.border.EmptyBorder;
  67 import javax.swing.border.EtchedBorder;
  68 import javax.swing.border.TitledBorder;
  69 import javax.swing.event.ChangeEvent;
  70 import javax.swing.event.ChangeListener;
  71 import javax.swing.table.TableCellEditor;
  72 import javax.swing.table.TableCellRenderer;
  73
  74 /**
  75  * Base class for the Preferences panel.
  76  *
  77  * @author $author$
  78  * @version $Revision$
  79  */
  80 public class GPreferences extends JPanel
  81 {
  82   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  83
  84   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  85           false, true);
  86
  87   /*
  88    * Visual tab components
  89    */
  90   protected JCheckBox fullScreen = new JCheckBox();
  91
  92   protected JCheckBox openoverv = new JCheckBox();
  93
  94   protected JCheckBox seqLimit = new JCheckBox();
  95
  96   protected JCheckBox rightAlign = new JCheckBox();
  97
  98   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 103
 104   protected JCheckBox showUnconserved = new JCheckBox();
 105
 106   protected JCheckBox idItalics = new JCheckBox();
 107
 108   protected JCheckBox smoothFont = new JCheckBox();
 109
 110   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 111
 112   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 113
 114   protected JCheckBox wrap = new JCheckBox();
 115
 116   protected JComboBox<String> sortby = new JComboBox<String>();
 117
 118   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 119
 120   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 121
 122   protected JCheckBox startupCheckbox = new JCheckBox();
 123
 124   protected JTextField startupFileTextfield = new JTextField();
 125
 126   // below are in the 'second column'
 127   protected JCheckBox annotations = new JCheckBox();
 128
 129   protected JCheckBox quality = new JCheckBox();
 130
 131   protected JCheckBox conservation = new JCheckBox();
 132
 133   protected JCheckBox identity = new JCheckBox();
 134
 135   protected JCheckBox showGroupConsensus = new JCheckBox();
 136
 137   protected JCheckBox showGroupConservation = new JCheckBox();
 138
 139   protected JCheckBox showConsensHistogram = new JCheckBox();
 140
 141   protected JCheckBox showConsensLogo = new JCheckBox();
 142
 143   protected JCheckBox showDbRefTooltip = new JCheckBox();
 144
 145   protected JCheckBox showNpTooltip = new JCheckBox();
 146
 147   /*
 148    * Structure tab and components
 149    */
 150   protected JPanel structureTab;
 151
 152   protected JCheckBox structFromPdb = new JCheckBox();
 153
 154   protected JCheckBox useRnaView = new JCheckBox();
 155
 156   protected JCheckBox addSecondaryStructure = new JCheckBox();
 157
 158   protected JCheckBox addTempFactor = new JCheckBox();
 159
 160   protected JComboBox<String> structViewer = new JComboBox<String>();
 161
 162   protected JTextField chimeraPath = new JTextField();
 163
 164   protected ButtonGroup mappingMethod = new ButtonGroup();
 165
 166   protected JRadioButton siftsMapping = new JRadioButton();
 167
 168   protected JRadioButton nwMapping = new JRadioButton();
 169
 170   /*
 171    * Colours tab components
 172    */
 173   protected JPanel minColour = new JPanel();
 174
 175   protected JPanel maxColour = new JPanel();
 176
 177   protected JComboBox<String> protColour = new JComboBox<String>();
 178
 179   protected JComboBox<String> nucColour = new JComboBox<String>();
 180
 181   /*
 182    * Connections tab components
 183    */
 184   protected JTable linkUrlTable = new JTable();
 185
 186   protected JButton editLink = new JButton();
 187
 188   protected JButton deleteLink = new JButton();
 189
 190   protected JTextField filterTB = new JTextField();
 191
 192   protected JButton doReset = new JButton();
 193
 194   protected JButton userOnly = new JButton();
 195
 196   protected JLabel portLabel = new JLabel();
 197
 198   protected JLabel serverLabel = new JLabel();
 199
 200   protected JTextField proxyServerTB = new JTextField();
 201
 202   protected JTextField proxyPortTB = new JTextField();
 203
 204   protected JTextField defaultBrowser = new JTextField();
 205
 206   protected JCheckBox useProxy = new JCheckBox();
 207
 208   protected JCheckBox usagestats = new JCheckBox();
 209
 210   protected JCheckBox questionnaire = new JCheckBox();
 211
 212   protected JCheckBox versioncheck = new JCheckBox();
 213
 214   /*
 215    * Output tab components
 216    */
 217   protected JComboBox<Object> epsRendering = new JComboBox<Object>();
 218
 219   protected JLabel userIdWidthlabel = new JLabel();
 220
 221   protected JCheckBox autoIdWidth = new JCheckBox();
 222
 223   protected JTextField userIdWidth = new JTextField();
 224
 225   protected JCheckBox blcjv = new JCheckBox();
 226
 227   protected JCheckBox pileupjv = new JCheckBox();
 228
 229   protected JCheckBox clustaljv = new JCheckBox();
 230
 231   protected JCheckBox msfjv = new JCheckBox();
 232
 233   protected JCheckBox fastajv = new JCheckBox();
 234
 235   protected JCheckBox pfamjv = new JCheckBox();
 236
 237   protected JCheckBox pirjv = new JCheckBox();
 238
 239   protected JCheckBox modellerOutput = new JCheckBox();
 240
 241   protected JCheckBox embbedBioJSON = new JCheckBox();
 242
 243   /*
 244    * Editing tab components
 245    */
 246   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 247
 248   protected JCheckBox padGaps = new JCheckBox();
 249
 250   protected JCheckBox sortByTree = new JCheckBox();
 251
 252   /*
 253    * DAS Settings tab
 254    */
 255   protected JPanel dasTab = new JPanel();
 256
 257   /*
 258    * Web Services tab
 259    */
 260   protected JPanel wsTab = new JPanel();
 261
 262   /**
 263    * Creates a new GPreferences object.
 264    */
 265   public GPreferences()
 266   {
 267     try
 268     {
 269       jbInit();
 270     } catch (Exception ex)
 271     {
 272       ex.printStackTrace();
 273     }
 274   }
 275
 276   /**
 277    * Construct the panel and its tabbed sub-panels.
 278    *
 279    * @throws Exception
 280    */
 281   private void jbInit() throws Exception
 282   {
 283     final JTabbedPane tabbedPane = new JTabbedPane();
 284     this.setLayout(new BorderLayout());
 285     JPanel okCancelPanel = initOkCancelPanel();
 286     this.add(tabbedPane, BorderLayout.CENTER);
 287     this.add(okCancelPanel, BorderLayout.SOUTH);
 288
 289     tabbedPane.add(initVisualTab(),
 290             MessageManager.getString("label.visual"));
 291
 292     tabbedPane.add(initColoursTab(),
 293             MessageManager.getString("label.colours"));
 294
 295     tabbedPane.add(initStructureTab(),
 296             MessageManager.getString("label.structure"));
 297
 298     tabbedPane.add(initConnectionsTab(),
 299             MessageManager.getString("label.connections"));
 300
 301     tabbedPane.add(initOutputTab(),
 302             MessageManager.getString("label.output"));
 303
 304     tabbedPane.add(initEditingTab(),
 305             MessageManager.getString("label.editing"));
 306
 307     /*
 308      * See DasSourceBrowser for the real work of configuring this tab.
 309      */
 310     dasTab.setLayout(new BorderLayout());
 311     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 312
 313     /*
 314      * See WsPreferences for the real work of configuring this tab.
 315      */
 316     wsTab.setLayout(new BorderLayout());
 317     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 318
 319     /*
 320      * Handler to validate a tab before leaving it - currently only for
 321      * Structure.
 322      */
 323     tabbedPane.addChangeListener(new ChangeListener()
 324     {
 325       private Component lastTab;
 326
 327       @Override
 328       public void stateChanged(ChangeEvent e)
 329       {
 330         if (lastTab == structureTab
 331                 && tabbedPane.getSelectedComponent() != structureTab)
 332         {
 333           if (!validateStructure())
 334           {
 335             tabbedPane.setSelectedComponent(structureTab);
 336             return;
 337           }
 338         }
 339         lastTab = tabbedPane.getSelectedComponent();
 340       }
 341
 342     });
 343   }
 344
 345   /**
 346    * Initialises the Editing tabbed panel.
 347    *
 348    * @return
 349    */
 350   private JPanel initEditingTab()
 351   {
 352     JPanel editingTab = new JPanel();
 353     editingTab.setLayout(null);
 354     autoCalculateConsCheck.setFont(LABEL_FONT);
 355     autoCalculateConsCheck.setText(MessageManager
 356             .getString("label.autocalculate_consensus"));
 357     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 358     padGaps.setFont(LABEL_FONT);
 359     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 360     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 361     sortByTree.setFont(LABEL_FONT);
 362     sortByTree
 363             .setText(MessageManager.getString("label.sort_with_new_tree"));
 364     sortByTree
 365             .setToolTipText(MessageManager
 366                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 367     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 368     editingTab.add(autoCalculateConsCheck);
 369     editingTab.add(padGaps);
 370     editingTab.add(sortByTree);
 371     return editingTab;
 372   }
 373
 374   /**
 375    * Initialises the Output tabbed panel.
 376    *
 377    * @return
 378    */
 379   private JPanel initOutputTab()
 380   {
 381     JPanel outputTab = new JPanel();
 382     outputTab.setLayout(null);
 383     JLabel epsLabel = new JLabel();
 384     epsLabel.setFont(LABEL_FONT);
 385     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 386     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 387     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 388     epsRendering.setFont(LABEL_FONT);
 389     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 390     JLabel jLabel1 = new JLabel();
 391     jLabel1.setFont(LABEL_FONT);
 392     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 393     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 394     jLabel1.setFont(LABEL_FONT);
 395     fastajv.setFont(LABEL_FONT);
 396     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 397     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 398     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 399     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 400     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 401     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 402     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 403     msfjv.setFont(LABEL_FONT);
 404     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 405     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 406     JPanel jPanel11 = new JPanel();
 407     jPanel11.setFont(LABEL_FONT);
 408     TitledBorder titledBorder2 = new TitledBorder(
 409             MessageManager.getString("label.file_output"));
 410     jPanel11.setBorder(titledBorder2);
 411     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 412     GridLayout gridLayout3 = new GridLayout();
 413     jPanel11.setLayout(gridLayout3);
 414     gridLayout3.setRows(8);
 415     blcjv.setFont(LABEL_FONT);
 416     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 417     clustaljv.setFont(LABEL_FONT);
 418     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 419     pfamjv.setFont(LABEL_FONT);
 420     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 421     pileupjv.setFont(LABEL_FONT);
 422     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 423     pirjv.setFont(LABEL_FONT);
 424     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 425     autoIdWidth.setFont(LABEL_FONT);
 426     autoIdWidth.setText(MessageManager
 427             .getString("label.automatically_set_id_width"));
 428     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 429             MessageManager
 430                     .getString("label.adjusts_width_generated_eps_png")));
 431     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 432     autoIdWidth.addActionListener(new ActionListener()
 433     {
 434
 435       @Override
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         autoIdWidth_actionPerformed();
 439       }
 440     });
 441     userIdWidthlabel.setFont(LABEL_FONT);
 442     userIdWidthlabel.setText(MessageManager
 443             .getString("label.figure_id_column_width"));
 444     userIdWidth
 445             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 446                     .getString("label.manually_specify_width_left_column")));
 447     userIdWidthlabel
 448             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 449                     .getString("label.manually_specify_width_left_column")));
 450     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 451     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 452     userIdWidth.setText("");
 453     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 454     userIdWidth.addActionListener(new ActionListener()
 455     {
 456
 457       @Override
 458       public void actionPerformed(ActionEvent e)
 459       {
 460         userIdWidth_actionPerformed();
 461       }
 462     });
 463     modellerOutput.setFont(LABEL_FONT);
 464     modellerOutput.setText(MessageManager
 465             .getString("label.use_modeller_output"));
 466     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 467     embbedBioJSON.setFont(LABEL_FONT);
 468     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 469     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 470
 471     jPanel11.add(jLabel1);
 472     jPanel11.add(blcjv);
 473     jPanel11.add(clustaljv);
 474     jPanel11.add(fastajv);
 475     jPanel11.add(msfjv);
 476     jPanel11.add(pfamjv);
 477     jPanel11.add(pileupjv);
 478     jPanel11.add(pirjv);
 479     outputTab.add(autoIdWidth);
 480     outputTab.add(userIdWidth);
 481     outputTab.add(userIdWidthlabel);
 482     outputTab.add(modellerOutput);
 483     outputTab.add(embbedBioJSON);
 484     outputTab.add(epsLabel);
 485     outputTab.add(epsRendering);
 486     outputTab.add(jPanel11);
 487     return outputTab;
 488   }
 489
 490   /**
 491    * Initialises the Connections tabbed panel.
 492    *
 493    * @return
 494    */
 495   private JPanel initConnectionsTab()
 496   {
 497     JPanel connectTab = new JPanel();
 498     connectTab.setLayout(new GridBagLayout());
 499
 500     // Label for browser text box
 501     JLabel browserLabel = new JLabel();
 502     browserLabel.setFont(LABEL_FONT);
 503     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 504     browserLabel.setText(MessageManager
 505             .getString("label.default_browser_unix"));
 506     defaultBrowser.setFont(LABEL_FONT);
 507     defaultBrowser.setText("");
 508
 509     defaultBrowser.addMouseListener(new MouseAdapter()
 510     {
 511       @Override
 512       public void mouseClicked(MouseEvent e)
 513       {
 514         if (e.getClickCount() > 1)
 515         {
 516           defaultBrowser_mouseClicked(e);
 517         }
 518       }
 519     });
 520
 521     JPanel proxyPanel = initConnTabProxyPanel();
 522     JPanel linkPanel = initConnTabUrlLinks();
 523     initConnTabCheckboxes();
 524
 525     // Add URL link panel
 526     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 2.0, 2.0,
 527             GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(
 528                     16, 0, 0, 12), 359, 32));
 529
 530     // Add default Browser text box
 531     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 532             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 533             new Insets(10, 0, 0, 0), 5, 1));
 534
 535     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
 536             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 537             new Insets(10, 0, 0, 10), 307, 1));
 538
 539     // Add proxy server panel
 540     connectTab.add(proxyPanel, new GridBagConstraints(0, 2, 2, 1, 1.0, 0.0,
 541             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 542             new Insets(10, 0, 0, 12), 4, 10));
 543
 544     // Add usage stats, version check and questionnaire checkboxes
 545     connectTab.add(usagestats, new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 546             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 547             new Insets(0, 2, 4, 2), 70, 1));
 548     connectTab.add(questionnaire, new GridBagConstraints(1, 3, 1, 1, 1.0,
 549             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 550             new Insets(0, 2, 4, 10), 70, 1));
 551     connectTab.add(versioncheck, new GridBagConstraints(0, 4, 1, 1, 1.0,
 552             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 553             new Insets(0, 2, 4, 2), 70, 1));
 554     return connectTab;
 555   }
 556
 557   /**
 558    * Initialises the proxy server panel in the Connections tab
 559    *
 560    * @return the proxy server panel
 561    */
 562   private JPanel initConnTabProxyPanel()
 563   {
 564     // Label for server text box
 565     serverLabel.setText(MessageManager.getString("label.address"));
 566     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 567     serverLabel.setFont(LABEL_FONT);
 568
 569     // Proxy server and port text boxes
 570     proxyServerTB.setFont(LABEL_FONT);
 571     proxyPortTB.setFont(LABEL_FONT);
 572
 573     // Label for Port text box
 574     portLabel.setFont(LABEL_FONT);
 575     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 576     portLabel.setText(MessageManager.getString("label.port"));
 577
 578     // Use proxy server checkbox
 579     useProxy.setFont(LABEL_FONT);
 580     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 581     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 582     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 583     useProxy.addActionListener(new ActionListener()
 584     {
 585       @Override
 586       public void actionPerformed(ActionEvent e)
 587       {
 588         useProxy_actionPerformed();
 589       }
 590     });
 591
 592     // Make proxy server panel
 593     JPanel proxyPanel = new JPanel();
 594     TitledBorder titledBorder1 = new TitledBorder(
 595             MessageManager.getString("label.proxy_server"));
 596     proxyPanel.setBorder(titledBorder1);
 597     proxyPanel.setLayout(new GridBagLayout());
 598     proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 599             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 600             new Insets(0, 2, 2, 0), 5, 0));
 601     proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 602             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 603                     0, 2, 0), 11, 0));
 604     proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 605             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 606                     2, 5, 185), 2, -4));
 607     proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
 608             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 609             new Insets(0, 2, 2, 2), 54, 1));
 610     proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
 611             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 612             new Insets(0, 2, 2, 0), 263, 1));
 613
 614     return proxyPanel;
 615   }
 616
 617   /**
 618    * Initialises the checkboxes in the Connections tab
 619    */
 620   private void initConnTabCheckboxes()
 621   {
 622     // Usage stats checkbox label
 623     usagestats.setText(MessageManager
 624             .getString("label.send_usage_statistics"));
 625     usagestats.setFont(LABEL_FONT);
 626     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 627     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 628
 629     // Questionnaire checkbox label
 630     questionnaire.setText(MessageManager
 631             .getString("label.check_for_questionnaires"));
 632     questionnaire.setFont(LABEL_FONT);
 633     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 634     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 635
 636     // Check for latest version checkbox label
 637     versioncheck.setText(MessageManager
 638             .getString("label.check_for_latest_version"));
 639     versioncheck.setFont(LABEL_FONT);
 640     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 641     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 642   }
 643
 644   /**
 645    * Initialises the URL links panel in the Connection tab
 646    *
 647    * @return the URL links panel
 648    */
 649   private JPanel initConnTabUrlLinks()
 650   {
 651     // Set up table for Url links
 652     linkUrlTable.setFillsViewportHeight(true);
 653     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 654     linkUrlTable.setAutoCreateRowSorter(true);
 655     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 656
 657     // Table in scrollpane so that the table is given a scrollbar
 658     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 659     linkScrollPane.setBorder(null);
 660
 661     // Panel for links functionality
 662     JPanel linkPanel = new JPanel(new GridBagLayout());
 663     linkPanel.setBorder(new TitledBorder(MessageManager
 664             .getString("label.url_linkfrom_sequence_id")));
 665
 666     // Put the Url links panel together
 667
 668     // Buttons go at top right, resizing only resizes the blank space vertically
 669     JPanel buttonPanel = initConnTabUrlButtons();
 670     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 671     linkConstraints1.gridx = 1;
 672     linkConstraints1.gridy = 0;
 673     linkConstraints1.fill = GridBagConstraints.VERTICAL;
 674     linkPanel.add(buttonPanel, linkConstraints1);
 675
 676     // Links table goes at top left, resizing resizes the table
 677     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 678     linkConstraints2.gridx = 0;
 679     linkConstraints2.gridy = 0;
 680     linkConstraints2.weightx = 1.0;
 681     linkConstraints2.weighty = 1.0;
 682     linkConstraints2.fill = GridBagConstraints.BOTH;
 683     linkPanel.add(linkScrollPane, linkConstraints2);
 684
 685     // Filter box and buttons goes at bottom left, resizing resizes the text box
 686     JPanel filterPanel = initConnTabFilterPanel();
 687     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 688     linkConstraints3.gridx = 0;
 689     linkConstraints3.gridy = 1;
 690     linkConstraints3.weightx = 1.0;
 691     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 692     linkPanel.add(filterPanel, linkConstraints3);
 693
 694     return linkPanel;
 695   }
 696
 697   private JPanel initConnTabFilterPanel()
 698   {
 699     // Filter textbox and reset button
 700     JLabel filterLabel = new JLabel(
 701             MessageManager.getString("label.filter"));
 702     filterLabel.setFont(LABEL_FONT);
 703     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 704     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 705
 706     filterTB.setFont(LABEL_FONT);
 707     filterTB.setText("");
 708
 709     doReset.setText(MessageManager.getString("action.reset"));
 710     userOnly.setText(MessageManager.getString("action.customfilter"));
 711
 712     // Panel for filter functionality
 713     JPanel filterPanel = new JPanel(new GridBagLayout());
 714     GridBagConstraints gbc = new GridBagConstraints();
 715     gbc.gridx = 0;
 716     gbc.gridy = 0;
 717     gbc.fill = GridBagConstraints.NONE;
 718     gbc.anchor = GridBagConstraints.WEST;
 719
 720     filterPanel.add(filterLabel, gbc);
 721
 722     GridBagConstraints gbc1 = new GridBagConstraints();
 723     gbc1.gridx = 0;
 724     gbc1.gridx = 1;
 725     gbc1.fill = GridBagConstraints.HORIZONTAL;
 726     gbc1.anchor = GridBagConstraints.WEST;
 727     gbc1.weightx = 1.0;
 728     filterPanel.add(filterTB, gbc1);
 729
 730     GridBagConstraints gbc2 = new GridBagConstraints();
 731     gbc2.gridx = 2;
 732     gbc2.fill = GridBagConstraints.NONE;
 733     gbc2.anchor = GridBagConstraints.WEST;
 734     filterPanel.add(doReset, gbc2);
 735
 736     GridBagConstraints gbc3 = new GridBagConstraints();
 737     gbc3.gridx = 3;
 738     gbc3.fill = GridBagConstraints.NONE;
 739     gbc3.anchor = GridBagConstraints.WEST;
 740     filterPanel.add(userOnly, gbc3);
 741
 742     return filterPanel;
 743   }
 744
 745   private JPanel initConnTabUrlButtons()
 746   {
 747     // Buttons for new / edit / delete Url links
 748     JButton newLink = new JButton();
 749     newLink.setText(MessageManager.getString("action.new"));
 750     newLink.addActionListener(new java.awt.event.ActionListener()
 751     {
 752       @Override
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         newLink_actionPerformed(e);
 756       }
 757     });
 758
 759     editLink.setText(MessageManager.getString("action.edit"));
 760     editLink.addActionListener(new java.awt.event.ActionListener()
 761     {
 762       @Override
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         editLink_actionPerformed(e);
 766       }
 767     });
 768
 769     deleteLink.setText(MessageManager.getString("action.delete"));
 770     deleteLink.addActionListener(new java.awt.event.ActionListener()
 771     {
 772       @Override
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         deleteLink_actionPerformed(e);
 776       }
 777     });
 778
 779     // no current selection, so initially disable delete/edit buttons
 780     editLink.setEnabled(false);
 781     deleteLink.setEnabled(false);
 782
 783     // Panels for new/edit/delete link buttons
 784     // buttonContent prevents the buttons from being resized when the window is
 785     JPanel buttonContent = new JPanel(new GridLayout(0, 1, 0, 0));
 786     JPanel buttonPanel = new JPanel(new BorderLayout());
 787
 788     buttonContent.add(newLink, null);
 789     buttonContent.add(editLink, null);
 790     buttonContent.add(deleteLink, null);
 791     buttonPanel.add(buttonContent, BorderLayout.NORTH);
 792
 793     return buttonPanel;
 794   }
 795
 796   /**
 797    * Initialises the parent panel which contains the tabbed sections.
 798    *
 799    * @return
 800    */
 801   private JPanel initOkCancelPanel()
 802   {
 803     JButton ok = new JButton();
 804     ok.setText(MessageManager.getString("action.ok"));
 805     ok.addActionListener(new ActionListener()
 806     {
 807       @Override
 808       public void actionPerformed(ActionEvent e)
 809       {
 810         ok_actionPerformed(e);
 811       }
 812     });
 813     JButton cancel = new JButton();
 814     cancel.setText(MessageManager.getString("action.cancel"));
 815     cancel.addActionListener(new ActionListener()
 816     {
 817       @Override
 818       public void actionPerformed(ActionEvent e)
 819       {
 820         cancel_actionPerformed(e);
 821       }
 822     });
 823     JPanel okCancelPanel = new JPanel();
 824     okCancelPanel.add(ok);
 825     okCancelPanel.add(cancel);
 826     return okCancelPanel;
 827   }
 828
 829   /**
 830    * Initialises the Colours tabbed panel.
 831    *
 832    * @return
 833    */
 834   private JPanel initColoursTab()
 835   {
 836     JPanel coloursTab = new JPanel();
 837     coloursTab.setBorder(new TitledBorder(MessageManager
 838             .getString("action.open_new_alignment")));
 839     coloursTab.setLayout(new FlowLayout());
 840     JLabel mincolourLabel = new JLabel();
 841     mincolourLabel.setFont(LABEL_FONT);
 842     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 843     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 844     minColour.setFont(LABEL_FONT);
 845     minColour.setBorder(BorderFactory.createEtchedBorder());
 846     minColour.setPreferredSize(new Dimension(40, 20));
 847     minColour.addMouseListener(new MouseAdapter()
 848     {
 849       @Override
 850       public void mousePressed(MouseEvent e)
 851       {
 852         minColour_actionPerformed(minColour);
 853       }
 854     });
 855     JLabel maxcolourLabel = new JLabel();
 856     maxcolourLabel.setFont(LABEL_FONT);
 857     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 858     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 859     maxColour.setFont(LABEL_FONT);
 860     maxColour.setBorder(BorderFactory.createEtchedBorder());
 861     maxColour.setPreferredSize(new Dimension(40, 20));
 862     maxColour.addMouseListener(new MouseAdapter()
 863     {
 864       @Override
 865       public void mousePressed(MouseEvent e)
 866       {
 867         maxColour_actionPerformed(maxColour);
 868       }
 869     });
 870
 871     protColour.setFont(LABEL_FONT);
 872     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 873     JLabel protColourLabel = new JLabel();
 874     protColourLabel.setFont(LABEL_FONT);
 875     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 876     protColourLabel.setText(MessageManager
 877             .getString("label.prot_alignment_colour") + " ");
 878     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 879             .getString("label.default_colour_scheme_for_alignment"),
 880             protColourLabel, protColour);
 881
 882     nucColour.setFont(LABEL_FONT);
 883     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 884     JLabel nucColourLabel = new JLabel();
 885     nucColourLabel.setFont(LABEL_FONT);
 886     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 887     nucColourLabel.setText(MessageManager
 888             .getString("label.nuc_alignment_colour") + " ");
 889     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 890             .getString("label.default_colour_scheme_for_alignment"),
 891             nucColourLabel, nucColour);
 892
 893     JPanel annotationShding = new JPanel();
 894     annotationShding.setBorder(new TitledBorder(MessageManager
 895             .getString("label.annotation_shading_default")));
 896     annotationShding.setLayout(new GridLayout(1, 2));
 897     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 898             .getString("label.default_minimum_colour_annotation_shading"),
 899             mincolourLabel, minColour);
 900     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 901             .getString("label.default_maximum_colour_annotation_shading"),
 902             maxcolourLabel, maxColour);
 903     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 904     return coloursTab;
 905   }
 906
 907   /**
 908    * Initialises the Structure tabbed panel.
 909    *
 910    * @return
 911    */
 912   private JPanel initStructureTab()
 913   {
 914     structureTab = new JPanel();
 915
 916     structureTab.setBorder(new TitledBorder(MessageManager
 917             .getString("label.structure_options")));
 918     structureTab.setLayout(null);
 919     final int width = 400;
 920     final int height = 22;
 921     final int lineSpacing = 25;
 922     int ypos = 15;
 923
 924     structFromPdb.setFont(LABEL_FONT);
 925     structFromPdb
 926             .setText(MessageManager.getString("label.struct_from_pdb"));
 927     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 928     structFromPdb.addActionListener(new ActionListener()
 929     {
 930       @Override
 931       public void actionPerformed(ActionEvent e)
 932       {
 933         boolean selected = structFromPdb.isSelected();
 934         // enable other options only when the first is checked
 935         useRnaView.setEnabled(selected);
 936         addSecondaryStructure.setEnabled(selected);
 937         addTempFactor.setEnabled(selected);
 938       }
 939     });
 940     structureTab.add(structFromPdb);
 941
 942     // indent checkboxes that are conditional on the first one
 943     ypos += lineSpacing;
 944     useRnaView.setFont(LABEL_FONT);
 945     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 946     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 947     structureTab.add(useRnaView);
 948
 949     ypos += lineSpacing;
 950     addSecondaryStructure.setFont(LABEL_FONT);
 951     addSecondaryStructure.setText(MessageManager
 952             .getString("label.autoadd_secstr"));
 953     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
 954     structureTab.add(addSecondaryStructure);
 955
 956     ypos += lineSpacing;
 957     addTempFactor.setFont(LABEL_FONT);
 958     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
 959     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
 960     structureTab.add(addTempFactor);
 961
 962     ypos += lineSpacing;
 963     JLabel viewerLabel = new JLabel();
 964     viewerLabel.setFont(LABEL_FONT);
 965     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
 966     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
 967     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
 968     structureTab.add(viewerLabel);
 969
 970     structViewer.setFont(LABEL_FONT);
 971     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
 972     structViewer.addItem(ViewerType.JMOL.name());
 973     structViewer.addItem(ViewerType.CHIMERA.name());
 974     structViewer.addActionListener(new ActionListener()
 975     {
 976       @Override
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         structureViewer_actionPerformed((String) structViewer
 980                 .getSelectedItem());
 981       }
 982     });
 983     structureTab.add(structViewer);
 984
 985     ypos += lineSpacing;
 986     JLabel pathLabel = new JLabel();
 987     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
 988     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
 989     pathLabel.setText(MessageManager.getString("label.chimera_path"));
 990     final String tooltip = JvSwingUtils.wrapTooltip(true,
 991             MessageManager.getString("label.chimera_path_tip"));
 992     pathLabel.setToolTipText(tooltip);
 993     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
 994     structureTab.add(pathLabel);
 995
 996     chimeraPath.setFont(LABEL_FONT);
 997     chimeraPath.setText("");
 998     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
 999     chimeraPath.addMouseListener(new MouseAdapter()
1000     {
1001       @Override
1002       public void mouseClicked(MouseEvent e)
1003       {
1004         if (e.getClickCount() == 2)
1005         {
1006           String chosen = openFileChooser();
1007           if (chosen != null)
1008           {
1009             chimeraPath.setText(chosen);
1010           }
1011         }
1012       }
1013     });
1014     structureTab.add(chimeraPath);
1015
1016     ypos += lineSpacing;
1017     nwMapping.setFont(LABEL_FONT);
1018     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1019     siftsMapping.setFont(LABEL_FONT);
1020     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1021     mappingMethod.add(nwMapping);
1022     mappingMethod.add(siftsMapping);
1023     JPanel mappingPanel = new JPanel();
1024     mappingPanel.setFont(LABEL_FONT);
1025     TitledBorder mmTitledBorder = new TitledBorder(
1026             MessageManager.getString("label.mapping_method"));
1027     mmTitledBorder.setTitleFont(LABEL_FONT);
1028     mappingPanel.setBorder(mmTitledBorder);
1029     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1030     // GridLayout mappingLayout = new GridLayout();
1031     mappingPanel.setLayout(new GridLayout());
1032     mappingPanel.add(nwMapping);
1033     mappingPanel.add(siftsMapping);
1034     structureTab.add(mappingPanel);
1035
1036     ypos += lineSpacing;
1037     ypos += lineSpacing;
1038     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1039             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1040     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1041     structureTab.add(docFieldPref);
1042
1043     return structureTab;
1044   }
1045
1046   /**
1047    * Action on choosing a structure viewer from combobox options.
1048    *
1049    * @param selectedItem
1050    */
1051   protected void structureViewer_actionPerformed(String selectedItem)
1052   {
1053   }
1054
1055   /**
1056    * Show a dialog for the user to choose a file. Returns the chosen path, or
1057    * null on Cancel.
1058    *
1059    * @return
1060    */
1061   protected String openFileChooser()
1062   {
1063     String choice = null;
1064     JFileChooser chooser = new JFileChooser();
1065
1066     // chooser.setFileView(new JalviewFileView());
1067     chooser.setDialogTitle(MessageManager
1068             .getString("label.open_local_file"));
1069     chooser.setToolTipText(MessageManager.getString("action.open"));
1070
1071     int value = chooser.showOpenDialog(this);
1072
1073     if (value == JFileChooser.APPROVE_OPTION)
1074     {
1075       choice = chooser.getSelectedFile().getPath();
1076     }
1077     return choice;
1078   }
1079
1080   /**
1081    * Validate the structure tab preferences; if invalid, set focus on this tab.
1082    *
1083    * @param e
1084    */
1085   protected boolean validateStructure(FocusEvent e)
1086   {
1087     if (!validateStructure())
1088     {
1089       e.getComponent().requestFocusInWindow();
1090       return false;
1091     }
1092     return true;
1093   }
1094
1095   protected boolean validateStructure()
1096   {
1097     return false;
1098   }
1099
1100   /**
1101    * Initialises the Visual tabbed panel.
1102    *
1103    * @return
1104    */
1105   private JPanel initVisualTab()
1106   {
1107     JPanel visualTab = new JPanel();
1108     visualTab.setBorder(new TitledBorder(MessageManager
1109             .getString("action.open_new_alignment")));
1110     visualTab.setLayout(null);
1111     fullScreen.setFont(LABEL_FONT);
1112     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1113     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1114     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1115     quality.setEnabled(false);
1116     quality.setFont(LABEL_FONT);
1117     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1118     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1119     quality.setSelected(true);
1120     quality.setText(MessageManager.getString("label.quality"));
1121     conservation.setEnabled(false);
1122     conservation.setFont(LABEL_FONT);
1123     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1124     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1125     conservation.setSelected(true);
1126     conservation.setText(MessageManager.getString("label.conservation"));
1127     identity.setEnabled(false);
1128     identity.setFont(LABEL_FONT);
1129     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1130     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1131     identity.setSelected(true);
1132     identity.setText(MessageManager.getString("label.consensus"));
1133     JLabel showGroupbits = new JLabel();
1134     showGroupbits.setFont(LABEL_FONT);
1135     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1136     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1137     showGroupbits.setText(MessageManager.getString("action.show_group")
1138             + ":");
1139     JLabel showConsensbits = new JLabel();
1140     showConsensbits.setFont(LABEL_FONT);
1141     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1142     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1143     showConsensbits.setText(MessageManager.getString("label.consensus")
1144             + ":");
1145     showConsensHistogram.setEnabled(false);
1146     showConsensHistogram.setFont(LABEL_FONT);
1147     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1148     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1149     showConsensHistogram.setSelected(true);
1150     showConsensHistogram.setText(MessageManager
1151             .getString("label.histogram"));
1152     showConsensLogo.setEnabled(false);
1153     showConsensLogo.setFont(LABEL_FONT);
1154     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1155     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1156     showConsensLogo.setSelected(true);
1157     showConsensLogo.setText(MessageManager.getString("label.logo"));
1158     showGroupConsensus.setEnabled(false);
1159     showGroupConsensus.setFont(LABEL_FONT);
1160     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1161     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1162     showGroupConsensus.setSelected(true);
1163     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1164     showGroupConservation.setEnabled(false);
1165     showGroupConservation.setFont(LABEL_FONT);
1166     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1167     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1168     showGroupConservation.setSelected(true);
1169     showGroupConservation.setText(MessageManager
1170             .getString("label.conservation"));
1171     showNpTooltip.setEnabled(true);
1172     showNpTooltip.setFont(LABEL_FONT);
1173     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1174     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1175     showNpTooltip.setSelected(true);
1176     showNpTooltip.setText(MessageManager
1177             .getString("label.non_positional_features"));
1178     showDbRefTooltip.setEnabled(true);
1179     showDbRefTooltip.setFont(LABEL_FONT);
1180     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1181     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1182     showDbRefTooltip.setSelected(true);
1183     showDbRefTooltip.setText(MessageManager
1184             .getString("label.database_references"));
1185     annotations.setFont(LABEL_FONT);
1186     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1187     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
1188     annotations.setSelected(true);
1189     annotations.setText(MessageManager.getString("label.show_annotations"));
1190     annotations.setBounds(new Rectangle(169, 12, 200, 23));
1191     annotations.addActionListener(new ActionListener()
1192     {
1193       @Override
1194       public void actionPerformed(ActionEvent e)
1195       {
1196         annotations_actionPerformed(e);
1197       }
1198     });
1199     identity.addActionListener(new ActionListener()
1200     {
1201       @Override
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         annotations_actionPerformed(e);
1205       }
1206     });
1207     showGroupConsensus.addActionListener(new ActionListener()
1208     {
1209       @Override
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         annotations_actionPerformed(e);
1213       }
1214     });
1215     showUnconserved.setFont(LABEL_FONT);
1216     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1217     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1218     showUnconserved.setSelected(true);
1219     showUnconserved.setText(MessageManager
1220             .getString("action.show_unconserved"));
1221     showUnconserved.addActionListener(new ActionListener()
1222     {
1223       @Override
1224       public void actionPerformed(ActionEvent e)
1225       {
1226         showunconserved_actionPerformed(e);
1227       }
1228     });
1229
1230     // TODO these are not yet added to / action from Preferences
1231     // JCheckBox shareSelections = new JCheckBox();
1232     // shareSelections.setFont(verdana11);
1233     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1234     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1235     // shareSelections.setSelected(true);
1236     // shareSelections.setText(MessageManager
1237     // .getString("label.share_selection_across_views"));
1238     // JCheckBox followHighlight = new JCheckBox();
1239     // followHighlight.setFont(verdana11);
1240     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1241     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1242     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1243     // followHighlight.setSelected(true);
1244     // followHighlight.setText(MessageManager
1245     // .getString("label.scroll_highlighted_regions"));
1246
1247     seqLimit.setFont(LABEL_FONT);
1248     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1249     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1250     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1251     smoothFont.setFont(LABEL_FONT);
1252     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1253     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1254     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1255     scaleProteinToCdna.setFont(LABEL_FONT);
1256     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1257     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1258     scaleProteinToCdna.setText(MessageManager
1259             .getString("label.scale_protein_to_cdna"));
1260     scaleProteinToCdna.setToolTipText(MessageManager
1261             .getString("label.scale_protein_to_cdna_tip"));
1262     JLabel gapLabel = new JLabel();
1263     gapLabel.setFont(LABEL_FONT);
1264     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1265     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1266     JLabel fontLabel = new JLabel();
1267     fontLabel.setFont(LABEL_FONT);
1268     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1269     fontLabel.setText(MessageManager.getString("label.font"));
1270     fontSizeCB.setFont(LABEL_FONT);
1271     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1272     fontStyleCB.setFont(LABEL_FONT);
1273     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1274     fontNameCB.setFont(LABEL_FONT);
1275     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1276     gapSymbolCB.setFont(LABEL_FONT);
1277     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1278     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1279     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1280     gapSymbolCB.setRenderer(dlcr);
1281
1282     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1283     startupCheckbox.setFont(LABEL_FONT);
1284     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1285     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1286     startupCheckbox.setSelected(true);
1287     startupFileTextfield.setFont(LABEL_FONT);
1288     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1289     startupFileTextfield.addMouseListener(new MouseAdapter()
1290     {
1291       @Override
1292       public void mouseClicked(MouseEvent e)
1293       {
1294         if (e.getClickCount() > 1)
1295         {
1296           startupFileTextfield_mouseClicked();
1297         }
1298       }
1299     });
1300
1301     sortby.setFont(LABEL_FONT);
1302     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1303     JLabel sortLabel = new JLabel();
1304     sortLabel.setFont(LABEL_FONT);
1305     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1306     sortLabel.setText(MessageManager.getString("label.sort_by"));
1307     sortAnnBy.setFont(LABEL_FONT);
1308     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1309     JLabel sortAnnLabel = new JLabel();
1310     sortAnnLabel.setFont(LABEL_FONT);
1311     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1312     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1313     sortAutocalc.setFont(LABEL_FONT);
1314     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1315
1316     JPanel annsettingsPanel = new JPanel();
1317     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
1318     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1319     annsettingsPanel.setBorder(new EtchedBorder());
1320     visualTab.add(annsettingsPanel);
1321     Border jb = new EmptyBorder(1, 1, 4, 5);
1322     quality.setBorder(jb);
1323     conservation.setBorder(jb);
1324     identity.setBorder(jb);
1325     showConsensbits.setBorder(jb);
1326     showGroupbits.setBorder(jb);
1327     showGroupConsensus.setBorder(jb);
1328     showGroupConservation.setBorder(jb);
1329     showConsensHistogram.setBorder(jb);
1330     showConsensLogo.setBorder(jb);
1331
1332     JPanel autoAnnotSettings = new JPanel();
1333     autoAnnotSettings.setLayout(new GridLayout(3, 3));
1334     annsettingsPanel.add(autoAnnotSettings);
1335     autoAnnotSettings.add(quality);
1336     autoAnnotSettings.add(conservation);
1337     autoAnnotSettings.add(identity);
1338     autoAnnotSettings.add(showGroupbits);
1339     autoAnnotSettings.add(showGroupConservation);
1340     autoAnnotSettings.add(showGroupConsensus);
1341     autoAnnotSettings.add(showConsensbits);
1342     autoAnnotSettings.add(showConsensHistogram);
1343     autoAnnotSettings.add(showConsensLogo);
1344
1345     JPanel tooltipSettings = new JPanel();
1346     tooltipSettings.setBorder(new TitledBorder(MessageManager
1347             .getString("label.sequence_id_tooltip")));
1348     tooltipSettings.setBounds(173, 140, 220, 62);
1349     tooltipSettings.setLayout(new GridLayout(2, 1));
1350     tooltipSettings.add(showDbRefTooltip);
1351     tooltipSettings.add(showNpTooltip);
1352     visualTab.add(tooltipSettings);
1353
1354     wrap.setFont(LABEL_FONT);
1355     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1356     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1357     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1358     rightAlign.setFont(LABEL_FONT);
1359     rightAlign.setForeground(Color.black);
1360     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1361     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1362     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1363     idItalics.setFont(LABEL_FONT_ITALIC);
1364     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1365     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1366     idItalics.setText(MessageManager
1367             .getString("label.sequence_name_italics"));
1368     openoverv.setFont(LABEL_FONT);
1369     openoverv.setActionCommand(MessageManager
1370             .getString("label.open_overview"));
1371     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1372     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1373     openoverv.setText(MessageManager.getString("label.open_overview"));
1374     JPanel jPanel2 = new JPanel();
1375     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1376     jPanel2.setLayout(new GridLayout(14, 1));
1377     jPanel2.add(fullScreen);
1378     jPanel2.add(openoverv);
1379     jPanel2.add(seqLimit);
1380     jPanel2.add(rightAlign);
1381     jPanel2.add(fontLabel);
1382     jPanel2.add(showUnconserved);
1383     jPanel2.add(idItalics);
1384     jPanel2.add(smoothFont);
1385     jPanel2.add(scaleProteinToCdna);
1386     jPanel2.add(gapLabel);
1387     jPanel2.add(wrap);
1388     jPanel2.add(sortLabel);
1389     jPanel2.add(sortAnnLabel);
1390     jPanel2.add(startupCheckbox);
1391     visualTab.add(jPanel2);
1392     visualTab.add(annotations);
1393     visualTab.add(startupFileTextfield);
1394     visualTab.add(sortby);
1395     visualTab.add(sortAnnBy);
1396     visualTab.add(sortAutocalc);
1397     visualTab.add(gapSymbolCB);
1398     visualTab.add(fontNameCB);
1399     visualTab.add(fontSizeCB);
1400     visualTab.add(fontStyleCB);
1401     return visualTab;
1402   }
1403
1404   protected void autoIdWidth_actionPerformed()
1405   {
1406     // TODO Auto-generated method stub
1407
1408   }
1409
1410   protected void userIdWidth_actionPerformed()
1411   {
1412     // TODO Auto-generated method stub
1413
1414   }
1415
1416   protected void maxColour_actionPerformed(JPanel panel)
1417   {
1418   }
1419
1420   protected void minColour_actionPerformed(JPanel panel)
1421   {
1422   }
1423
1424   protected void showunconserved_actionPerformed(ActionEvent e)
1425   {
1426     // TODO Auto-generated method stub
1427
1428   }
1429
1430   /**
1431    * DOCUMENT ME!
1432    *
1433    * @param e
1434    *          DOCUMENT ME!
1435    */
1436   public void ok_actionPerformed(ActionEvent e)
1437   {
1438   }
1439
1440   /**
1441    * DOCUMENT ME!
1442    *
1443    * @param e
1444    *          DOCUMENT ME!
1445    */
1446   public void cancel_actionPerformed(ActionEvent e)
1447   {
1448   }
1449
1450   /**
1451    * DOCUMENT ME!
1452    *
1453    * @param e
1454    *          DOCUMENT ME!
1455    */
1456   public void annotations_actionPerformed(ActionEvent e)
1457   {
1458   }
1459
1460   /**
1461    * DOCUMENT ME!
1462    */
1463   public void startupFileTextfield_mouseClicked()
1464   {
1465   }
1466
1467   public void newLink_actionPerformed(ActionEvent e)
1468   {
1469
1470   }
1471
1472   public void editLink_actionPerformed(ActionEvent e)
1473   {
1474
1475   }
1476
1477   public void deleteLink_actionPerformed(ActionEvent e)
1478   {
1479
1480   }
1481
1482   public void defaultBrowser_mouseClicked(MouseEvent e)
1483   {
1484
1485   }
1486
1487   public void linkURLList_keyTyped(KeyEvent e)
1488   {
1489
1490   }
1491
1492   public void useProxy_actionPerformed()
1493   {
1494     boolean enabled = useProxy.isSelected();
1495     portLabel.setEnabled(enabled);
1496     serverLabel.setEnabled(enabled);
1497     proxyServerTB.setEnabled(enabled);
1498     proxyPortTB.setEnabled(enabled);
1499   }
1500
1501   public class RadioButtonRenderer extends JRadioButton implements
1502           TableCellRenderer
1503   {
1504     public RadioButtonRenderer()
1505     {
1506       setHorizontalAlignment(CENTER);
1507     }
1508
1509     @Override
1510     public Component getTableCellRendererComponent(JTable table,
1511             Object value, boolean isSelected, boolean hasFocus, int row,
1512             int column)
1513     {
1514       setSelected((boolean) value);
1515
1516       // set colours to match rest of table
1517       if (isSelected)
1518       {
1519         setBackground(table.getSelectionBackground());
1520         setForeground(table.getSelectionForeground());
1521       }
1522       else
1523       {
1524         setBackground(table.getBackground());
1525         setForeground(table.getForeground());
1526       }
1527
1528       // adjust row height so radio buttons actually fit
1529       table.setRowHeight(row, getMinimumSize().height);
1530
1531       return this;
1532     }
1533   }
1534
1535   public class RadioButtonEditor extends AbstractCellEditor implements
1536           TableCellEditor
1537   {
1538     private JRadioButton button = new JRadioButton();
1539
1540     public RadioButtonEditor()
1541     {
1542       this.button.setHorizontalAlignment(SwingConstants.CENTER);
1543       this.button.addActionListener(new ActionListener()
1544       {
1545         @Override
1546         public void actionPerformed(ActionEvent e)
1547         {
1548           fireEditingStopped();
1549         }
1550       });
1551     }
1552
1553     @Override
1554     public Component getTableCellEditorComponent(JTable table,
1555             Object value, boolean isSelected, int row, int column)
1556     {
1557       button.setSelected((boolean) value);
1558       return button;
1559     }
1560
1561     @Override
1562     public Object getCellEditorValue()
1563     {
1564       return button.isSelected();
1565     }
1566
1567   }
1568 }