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
  85           .getLabelFont(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<>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<>();
 103
 104   protected JCheckBox showOccupancy = new JCheckBox();
 105
 106   protected JCheckBox showUnconserved = new JCheckBox();
 107
 108   protected JCheckBox idItalics = new JCheckBox();
 109
 110   protected JCheckBox smoothFont = new JCheckBox();
 111
 112   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 113
 114   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 115
 116   protected JCheckBox wrap = new JCheckBox();
 117
 118   protected JComboBox<String> sortby = new JComboBox<>();
 119
 120   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 121
 122   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 123
 124   protected JCheckBox startupCheckbox = new JCheckBox();
 125
 126   protected JTextField startupFileTextfield = new JTextField();
 127
 128   // below are in the 'second column'
 129   protected JCheckBox annotations = new JCheckBox();
 130
 131   protected JCheckBox quality = new JCheckBox();
 132
 133   protected JCheckBox conservation = new JCheckBox();
 134
 135   protected JCheckBox identity = new JCheckBox();
 136
 137   protected JCheckBox showGroupConsensus = new JCheckBox();
 138
 139   protected JCheckBox showGroupConservation = new JCheckBox();
 140
 141   protected JCheckBox showConsensHistogram = new JCheckBox();
 142
 143   protected JCheckBox showConsensLogo = new JCheckBox();
 144
 145   protected JCheckBox showDbRefTooltip = new JCheckBox();
 146
 147   protected JCheckBox showNpTooltip = new JCheckBox();
 148
 149   /*
 150    * Structure tab and components
 151    */
 152   protected JPanel structureTab;
 153
 154   protected JCheckBox structFromPdb = new JCheckBox();
 155
 156   protected JCheckBox useRnaView = new JCheckBox();
 157
 158   protected JCheckBox addSecondaryStructure = new JCheckBox();
 159
 160   protected JCheckBox addTempFactor = new JCheckBox();
 161
 162   protected JComboBox<String> structViewer = new JComboBox<>();
 163
 164   protected JTextField chimeraPath = new JTextField();
 165
 166   protected ButtonGroup mappingMethod = new ButtonGroup();
 167
 168   protected JRadioButton siftsMapping = new JRadioButton();
 169
 170   protected JRadioButton nwMapping = new JRadioButton();
 171
 172   /*
 173    * Colours tab components
 174    */
 175   protected JPanel minColour = new JPanel();
 176
 177   protected JPanel maxColour = new JPanel();
 178
 179   protected JComboBox<String> protColour = new JComboBox<>();
 180
 181   protected JComboBox<String> nucColour = new JComboBox<>();
 182
 183   /*
 184    * Overview tab components
 185    */
 186   protected JPanel overviewTab;
 187
 188   protected JPanel gapColour = new JPanel();
 189
 190   protected JPanel hiddenColour = new JPanel();
 191
 192   protected JCheckBox useLegacyGap;
 193
 194   protected JCheckBox showHiddenAtStart;
 195
 196   protected JLabel gapLabel;
 197
 198   /*
 199    * Connections tab components
 200    */
 201   protected JTable linkUrlTable = new JTable();
 202
 203   protected JButton editLink = new JButton();
 204
 205   protected JButton deleteLink = new JButton();
 206
 207   protected JTextField filterTB = new JTextField();
 208
 209   protected JButton doReset = new JButton();
 210
 211   protected JButton userOnly = new JButton();
 212
 213   protected JLabel portLabel = new JLabel();
 214
 215   protected JLabel serverLabel = new JLabel();
 216
 217   protected JTextField proxyServerTB = new JTextField();
 218
 219   protected JTextField proxyPortTB = new JTextField();
 220
 221   protected JTextField defaultBrowser = new JTextField();
 222
 223   protected JCheckBox useProxy = new JCheckBox();
 224
 225   protected JCheckBox usagestats = new JCheckBox();
 226
 227   protected JCheckBox questionnaire = new JCheckBox();
 228
 229   protected JCheckBox versioncheck = new JCheckBox();
 230
 231   /*
 232    * Output tab components
 233    */
 234   protected JComboBox<Object> epsRendering = new JComboBox<>();
 235
 236   protected JLabel userIdWidthlabel = new JLabel();
 237
 238   protected JCheckBox autoIdWidth = new JCheckBox();
 239
 240   protected JTextField userIdWidth = new JTextField();
 241
 242   protected JCheckBox blcjv = new JCheckBox();
 243
 244   protected JCheckBox pileupjv = new JCheckBox();
 245
 246   protected JCheckBox clustaljv = new JCheckBox();
 247
 248   protected JCheckBox msfjv = new JCheckBox();
 249
 250   protected JCheckBox fastajv = new JCheckBox();
 251
 252   protected JCheckBox pfamjv = new JCheckBox();
 253
 254   protected JCheckBox pirjv = new JCheckBox();
 255
 256   protected JCheckBox modellerOutput = new JCheckBox();
 257
 258   protected JCheckBox embbedBioJSON = new JCheckBox();
 259
 260   /*
 261    * Editing tab components
 262    */
 263   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 264
 265   protected JCheckBox padGaps = new JCheckBox();
 266
 267   protected JCheckBox sortByTree = new JCheckBox();
 268
 269   /*
 270    * DAS Settings tab
 271    */
 272   protected JPanel dasTab = new JPanel();
 273
 274   /*
 275    * Web Services tab
 276    */
 277   protected JPanel wsTab = new JPanel();
 278
 279   /**
 280    * Creates a new GPreferences object.
 281    */
 282   public GPreferences()
 283   {
 284     try
 285     {
 286       jbInit();
 287     } catch (Exception ex)
 288     {
 289       ex.printStackTrace();
 290     }
 291   }
 292
 293   /**
 294    * Construct the panel and its tabbed sub-panels.
 295    *
 296    * @throws Exception
 297    */
 298   private void jbInit() throws Exception
 299   {
 300     final JTabbedPane tabbedPane = new JTabbedPane();
 301     this.setLayout(new BorderLayout());
 302     JPanel okCancelPanel = initOkCancelPanel();
 303     this.add(tabbedPane, BorderLayout.CENTER);
 304     this.add(okCancelPanel, BorderLayout.SOUTH);
 305
 306     tabbedPane.add(initVisualTab(),
 307             MessageManager.getString("label.visual"));
 308
 309     tabbedPane.add(initColoursTab(),
 310             MessageManager.getString("label.colours"));
 311
 312     tabbedPane.add(initOverviewTab(),
 313             MessageManager.getString("label.overview"));
 314
 315     tabbedPane.add(initStructureTab(),
 316             MessageManager.getString("label.structure"));
 317
 318     tabbedPane.add(initConnectionsTab(),
 319             MessageManager.getString("label.connections"));
 320
 321     tabbedPane.add(initLinksTab(),
 322             MessageManager.getString("label.urllinks"));
 323
 324     tabbedPane.add(initOutputTab(),
 325             MessageManager.getString("label.output"));
 326
 327     tabbedPane.add(initEditingTab(),
 328             MessageManager.getString("label.editing"));
 329
 330     /*
 331      * See DasSourceBrowser for the real work of configuring this tab.
 332      */
 333     dasTab.setLayout(new BorderLayout());
 334     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 335
 336     /*
 337      * See WsPreferences for the real work of configuring this tab.
 338      */
 339     wsTab.setLayout(new BorderLayout());
 340     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 341
 342     /*
 343      * Handler to validate a tab before leaving it - currently only for
 344      * Structure.
 345      */
 346     tabbedPane.addChangeListener(new ChangeListener()
 347     {
 348       private Component lastTab;
 349
 350       @Override
 351       public void stateChanged(ChangeEvent e)
 352       {
 353         if (lastTab == structureTab
 354                 && tabbedPane.getSelectedComponent() != structureTab)
 355         {
 356           if (!validateStructure())
 357           {
 358             tabbedPane.setSelectedComponent(structureTab);
 359             return;
 360           }
 361         }
 362         lastTab = tabbedPane.getSelectedComponent();
 363       }
 364
 365     });
 366   }
 367
 368   /**
 369    * Initialises the Editing tabbed panel.
 370    *
 371    * @return
 372    */
 373   private JPanel initEditingTab()
 374   {
 375     JPanel editingTab = new JPanel();
 376     editingTab.setLayout(null);
 377     autoCalculateConsCheck.setFont(LABEL_FONT);
 378     autoCalculateConsCheck.setText(
 379             MessageManager.getString("label.autocalculate_consensus"));
 380     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 381     padGaps.setFont(LABEL_FONT);
 382     padGaps.setText(
 383             MessageManager.getString("label.pad_gaps_when_editing"));
 384     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 385     sortByTree.setFont(LABEL_FONT);
 386     sortByTree
 387             .setText(MessageManager.getString("label.sort_with_new_tree"));
 388     sortByTree.setToolTipText(MessageManager.getString(
 389             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 390     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 391     editingTab.add(autoCalculateConsCheck);
 392     editingTab.add(padGaps);
 393     editingTab.add(sortByTree);
 394     return editingTab;
 395   }
 396
 397   /**
 398    * Initialises the Output tabbed panel.
 399    *
 400    * @return
 401    */
 402   private JPanel initOutputTab()
 403   {
 404     JPanel outputTab = new JPanel();
 405     outputTab.setLayout(null);
 406     JLabel epsLabel = new JLabel();
 407     epsLabel.setFont(LABEL_FONT);
 408     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 409     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 410     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 411     epsRendering.setFont(LABEL_FONT);
 412     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 413     JLabel jLabel1 = new JLabel();
 414     jLabel1.setFont(LABEL_FONT);
 415     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 416     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 417     jLabel1.setFont(LABEL_FONT);
 418     fastajv.setFont(LABEL_FONT);
 419     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 420     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 421     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 422     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 423     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 424     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 425     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 426     msfjv.setFont(LABEL_FONT);
 427     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 428     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 429     JPanel jPanel11 = new JPanel();
 430     jPanel11.setFont(LABEL_FONT);
 431     TitledBorder titledBorder2 = new TitledBorder(
 432             MessageManager.getString("label.file_output"));
 433     jPanel11.setBorder(titledBorder2);
 434     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 435     GridLayout gridLayout3 = new GridLayout();
 436     jPanel11.setLayout(gridLayout3);
 437     gridLayout3.setRows(8);
 438     blcjv.setFont(LABEL_FONT);
 439     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 440     clustaljv.setFont(LABEL_FONT);
 441     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 442     pfamjv.setFont(LABEL_FONT);
 443     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 444     pileupjv.setFont(LABEL_FONT);
 445     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 446     pirjv.setFont(LABEL_FONT);
 447     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 448     autoIdWidth.setFont(LABEL_FONT);
 449     autoIdWidth.setText(
 450             MessageManager.getString("label.automatically_set_id_width"));
 451     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 452             .getString("label.adjusts_width_generated_eps_png")));
 453     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 454     autoIdWidth.addActionListener(new ActionListener()
 455     {
 456
 457       @Override
 458       public void actionPerformed(ActionEvent e)
 459       {
 460         autoIdWidth_actionPerformed();
 461       }
 462     });
 463     userIdWidthlabel.setFont(LABEL_FONT);
 464     userIdWidthlabel.setText(
 465             MessageManager.getString("label.figure_id_column_width"));
 466     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 467             .getString("label.manually_specify_width_left_column")));
 468     userIdWidthlabel.setToolTipText(
 469             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 470                     "label.manually_specify_width_left_column")));
 471     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 472     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 473     userIdWidth.setText("");
 474     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 475     userIdWidth.addActionListener(new ActionListener()
 476     {
 477
 478       @Override
 479       public void actionPerformed(ActionEvent e)
 480       {
 481         userIdWidth_actionPerformed();
 482       }
 483     });
 484     modellerOutput.setFont(LABEL_FONT);
 485     modellerOutput
 486             .setText(MessageManager.getString("label.use_modeller_output"));
 487     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 488     embbedBioJSON.setFont(LABEL_FONT);
 489     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 490     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 491
 492     jPanel11.add(jLabel1);
 493     jPanel11.add(blcjv);
 494     jPanel11.add(clustaljv);
 495     jPanel11.add(fastajv);
 496     jPanel11.add(msfjv);
 497     jPanel11.add(pfamjv);
 498     jPanel11.add(pileupjv);
 499     jPanel11.add(pirjv);
 500     outputTab.add(autoIdWidth);
 501     outputTab.add(userIdWidth);
 502     outputTab.add(userIdWidthlabel);
 503     outputTab.add(modellerOutput);
 504     outputTab.add(embbedBioJSON);
 505     outputTab.add(epsLabel);
 506     outputTab.add(epsRendering);
 507     outputTab.add(jPanel11);
 508     return outputTab;
 509   }
 510
 511   /**
 512    * Initialises the Connections tabbed panel.
 513    *
 514    * @return
 515    */
 516   private JPanel initConnectionsTab()
 517   {
 518     JPanel connectTab = new JPanel();
 519     connectTab.setLayout(new GridBagLayout());
 520
 521     // Label for browser text box
 522     JLabel browserLabel = new JLabel();
 523     browserLabel.setFont(LABEL_FONT);
 524     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 525     browserLabel.setText(
 526             MessageManager.getString("label.default_browser_unix"));
 527     defaultBrowser.setFont(LABEL_FONT);
 528     defaultBrowser.setText("");
 529
 530     defaultBrowser.addMouseListener(new MouseAdapter()
 531     {
 532       @Override
 533       public void mouseClicked(MouseEvent e)
 534       {
 535         if (e.getClickCount() > 1)
 536         {
 537           defaultBrowser_mouseClicked(e);
 538         }
 539       }
 540     });
 541
 542     JPanel proxyPanel = initConnTabProxyPanel();
 543     initConnTabCheckboxes();
 544
 545     // Add default Browser text box
 546     connectTab.add(browserLabel,
 547             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 548                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 549                     new Insets(10, 0, 5, 5), 5, 1));
 550     defaultBrowser.setFont(LABEL_FONT);
 551     defaultBrowser.setText("");
 552
 553     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 554             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 555             new Insets(10, 0, 5, 10), 30, 1));
 556
 557     // Add proxy server panel
 558     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 559             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 560             new Insets(10, 0, 5, 12), 4, 10));
 561
 562     // Add usage stats, version check and questionnaire checkboxes
 563     connectTab.add(usagestats,
 564             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 565                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 566                     new Insets(0, 2, 5, 5), 70, 1));
 567     connectTab.add(questionnaire,
 568             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 569                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 570                     new Insets(0, 2, 5, 10), 70, 1));
 571     connectTab.add(versioncheck,
 572             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 573                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 574                     new Insets(0, 2, 5, 5), 70, 1));
 575
 576     // Add padding so the panel doesn't look ridiculous
 577     JPanel spacePanel = new JPanel();
 578     connectTab.add(spacePanel,
 579             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 580                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 581                     new Insets(0, 0, 0, 5), 70, 1));
 582
 583     return connectTab;
 584   }
 585
 586   /**
 587    * Initialises the Links tabbed panel.
 588    *
 589    * @return
 590    */
 591   private JPanel initLinksTab()
 592   {
 593     JPanel linkTab = new JPanel();
 594     linkTab.setLayout(new GridBagLayout());
 595
 596     // Set up table for Url links
 597     linkUrlTable.setFillsViewportHeight(true);
 598     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 599     linkUrlTable.setAutoCreateRowSorter(true);
 600     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 601
 602     // adjust row height so radio buttons actually fit
 603     // don't do this in the renderer, it causes the awt thread to activate
 604     // constantly
 605     JRadioButton temp = new JRadioButton();
 606     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 607
 608     // Table in scrollpane so that the table is given a scrollbar
 609     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 610     linkScrollPane.setBorder(null);
 611
 612     // Panel for links functionality
 613     JPanel linkPanel = new JPanel(new GridBagLayout());
 614     linkPanel.setBorder(new TitledBorder(
 615             MessageManager.getString("label.url_linkfrom_sequence_id")));
 616
 617     // Put the Url links panel together
 618
 619     // Buttons go at top right, resizing only resizes the blank space vertically
 620     JPanel buttonPanel = initLinkTabUrlButtons();
 621     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 622     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 623     linkConstraints1.gridx = 0;
 624     linkConstraints1.gridy = 0;
 625     linkConstraints1.weightx = 1.0;
 626     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 627     linkTab.add(buttonPanel, linkConstraints1);
 628
 629     // Links table goes at top left, resizing resizes the table
 630     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 631     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 632     linkConstraints2.gridx = 0;
 633     linkConstraints2.gridy = 1;
 634     linkConstraints2.weightx = 1.0;
 635     linkConstraints2.weighty = 1.0;
 636     linkConstraints2.fill = GridBagConstraints.BOTH;
 637     linkTab.add(linkScrollPane, linkConstraints2);
 638
 639     // Filter box and buttons goes at bottom left, resizing resizes the text box
 640     JPanel filterPanel = initLinkTabFilterPanel();
 641     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 642     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 643     linkConstraints3.gridx = 0;
 644     linkConstraints3.gridy = 2;
 645     linkConstraints3.weightx = 1.0;
 646     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 647     linkTab.add(filterPanel, linkConstraints3);
 648
 649     return linkTab;
 650   }
 651
 652   private JPanel initLinkTabFilterPanel()
 653   {
 654     // Filter textbox and reset button
 655     JLabel filterLabel = new JLabel(
 656             MessageManager.getString("label.filter"));
 657     filterLabel.setFont(LABEL_FONT);
 658     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 659     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 660
 661     filterTB.setFont(LABEL_FONT);
 662     filterTB.setText("");
 663
 664     doReset.setText(MessageManager.getString("action.showall"));
 665     userOnly.setText(MessageManager.getString("action.customfilter"));
 666
 667     // Panel for filter functionality
 668     JPanel filterPanel = new JPanel(new GridBagLayout());
 669     filterPanel.setBorder(new TitledBorder("Filter"));
 670     GridBagConstraints gbc = new GridBagConstraints();
 671     gbc.gridx = 0;
 672     gbc.gridy = 0;
 673     gbc.fill = GridBagConstraints.NONE;
 674     gbc.anchor = GridBagConstraints.WEST;
 675
 676     filterPanel.add(filterLabel, gbc);
 677
 678     GridBagConstraints gbc1 = new GridBagConstraints();
 679     gbc1.gridx = 1;
 680     gbc1.gridwidth = 2;
 681     gbc1.fill = GridBagConstraints.HORIZONTAL;
 682     gbc1.anchor = GridBagConstraints.WEST;
 683     gbc1.weightx = 1.0;
 684     filterPanel.add(filterTB, gbc1);
 685
 686     GridBagConstraints gbc2 = new GridBagConstraints();
 687     gbc2.gridx = 3;
 688     gbc2.fill = GridBagConstraints.NONE;
 689     gbc2.anchor = GridBagConstraints.WEST;
 690     filterPanel.add(doReset, gbc2);
 691
 692     GridBagConstraints gbc3 = new GridBagConstraints();
 693     gbc3.gridx = 4;
 694     gbc3.fill = GridBagConstraints.NONE;
 695     gbc3.anchor = GridBagConstraints.WEST;
 696     filterPanel.add(userOnly, gbc3);
 697
 698     return filterPanel;
 699   }
 700
 701   private JPanel initLinkTabUrlButtons()
 702   {
 703     // Buttons for new / edit / delete Url links
 704     JButton newLink = new JButton();
 705     newLink.setText(MessageManager.getString("action.new"));
 706
 707     editLink.setText(MessageManager.getString("action.edit"));
 708
 709     deleteLink.setText(MessageManager.getString("action.delete"));
 710
 711     // no current selection, so initially disable delete/edit buttons
 712     editLink.setEnabled(false);
 713     deleteLink.setEnabled(false);
 714
 715     newLink.addActionListener(new java.awt.event.ActionListener()
 716     {
 717       @Override
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         newLink_actionPerformed(e);
 721       }
 722     });
 723
 724     editLink.setText(MessageManager.getString("action.edit"));
 725     editLink.addActionListener(new java.awt.event.ActionListener()
 726     {
 727       @Override
 728       public void actionPerformed(ActionEvent e)
 729       {
 730         editLink_actionPerformed(e);
 731       }
 732     });
 733
 734     deleteLink.setText(MessageManager.getString("action.delete"));
 735     deleteLink.addActionListener(new java.awt.event.ActionListener()
 736     {
 737       @Override
 738       public void actionPerformed(ActionEvent e)
 739       {
 740         deleteLink_actionPerformed(e);
 741       }
 742     });
 743
 744     JPanel buttonPanel = new JPanel(new GridBagLayout());
 745     buttonPanel.setBorder(new TitledBorder("Edit links"));
 746     GridBagConstraints gbc = new GridBagConstraints();
 747     gbc.gridx = 0;
 748     gbc.gridy = 0;
 749     gbc.fill = GridBagConstraints.NONE;
 750     buttonPanel.add(newLink, gbc);
 751
 752     GridBagConstraints gbc1 = new GridBagConstraints();
 753     gbc1.gridx = 1;
 754     gbc1.gridy = 0;
 755     gbc1.fill = GridBagConstraints.NONE;
 756     buttonPanel.add(editLink, gbc1);
 757
 758     GridBagConstraints gbc2 = new GridBagConstraints();
 759     gbc2.gridx = 2;
 760     gbc2.gridy = 0;
 761     gbc2.fill = GridBagConstraints.NONE;
 762     buttonPanel.add(deleteLink, gbc2);
 763
 764     GridBagConstraints gbc3 = new GridBagConstraints();
 765     gbc3.gridx = 3;
 766     gbc3.gridy = 0;
 767     gbc3.fill = GridBagConstraints.HORIZONTAL;
 768     gbc3.weightx = 1.0;
 769     JPanel spacePanel = new JPanel();
 770     spacePanel.setBorder(null);
 771     buttonPanel.add(spacePanel, gbc3);
 772
 773     return buttonPanel;
 774   }
 775
 776   /**
 777    * Initialises the proxy server panel in the Connections tab
 778    *
 779    * @return the proxy server panel
 780    */
 781   private JPanel initConnTabProxyPanel()
 782   {
 783     // Label for server text box
 784     serverLabel.setText(MessageManager.getString("label.address"));
 785     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 786     serverLabel.setFont(LABEL_FONT);
 787
 788     // Proxy server and port text boxes
 789     proxyServerTB.setFont(LABEL_FONT);
 790     proxyPortTB.setFont(LABEL_FONT);
 791
 792     // Label for Port text box
 793     portLabel.setFont(LABEL_FONT);
 794     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 795     portLabel.setText(MessageManager.getString("label.port"));
 796
 797     // Use proxy server checkbox
 798     useProxy.setFont(LABEL_FONT);
 799     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 800     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 801     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 802     useProxy.addActionListener(new ActionListener()
 803     {
 804       @Override
 805       public void actionPerformed(ActionEvent e)
 806       {
 807         useProxy_actionPerformed();
 808       }
 809     });
 810
 811     // Make proxy server panel
 812     JPanel proxyPanel = new JPanel();
 813     TitledBorder titledBorder1 = new TitledBorder(
 814             MessageManager.getString("label.proxy_server"));
 815     proxyPanel.setBorder(titledBorder1);
 816     proxyPanel.setLayout(new GridBagLayout());
 817     proxyPanel.add(serverLabel,
 818             new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 819                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 820                     new Insets(0, 2, 2, 0), 5, 0));
 821     proxyPanel.add(portLabel,
 822             new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 823                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 824                     new Insets(0, 0, 2, 0), 11, 0));
 825     proxyPanel.add(useProxy,
 826             new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 827                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 828                     new Insets(0, 2, 5, 185), 2, -4));
 829     proxyPanel.add(proxyPortTB,
 830             new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 831                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 832                     new Insets(0, 2, 2, 2), 54, 1));
 833     proxyPanel.add(proxyServerTB,
 834             new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 835                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 836                     new Insets(0, 2, 2, 0), 263, 1));
 837
 838     return proxyPanel;
 839   }
 840
 841   /**
 842    * Initialises the checkboxes in the Connections tab
 843    */
 844   private void initConnTabCheckboxes()
 845   {
 846     // Usage stats checkbox label
 847     usagestats.setText(
 848             MessageManager.getString("label.send_usage_statistics"));
 849     usagestats.setFont(LABEL_FONT);
 850     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 851     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 852
 853     // Questionnaire checkbox label
 854     questionnaire.setText(
 855             MessageManager.getString("label.check_for_questionnaires"));
 856     questionnaire.setFont(LABEL_FONT);
 857     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 858     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 859
 860     // Check for latest version checkbox label
 861     versioncheck.setText(
 862             MessageManager.getString("label.check_for_latest_version"));
 863     versioncheck.setFont(LABEL_FONT);
 864     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 865     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 866   }
 867
 868   /**
 869    * Initialises the parent panel which contains the tabbed sections.
 870    *
 871    * @return
 872    */
 873   private JPanel initOkCancelPanel()
 874   {
 875     JButton ok = new JButton();
 876     ok.setText(MessageManager.getString("action.ok"));
 877     ok.addActionListener(new ActionListener()
 878     {
 879       @Override
 880       public void actionPerformed(ActionEvent e)
 881       {
 882         ok_actionPerformed(e);
 883       }
 884     });
 885     JButton cancel = new JButton();
 886     cancel.setText(MessageManager.getString("action.cancel"));
 887     cancel.addActionListener(new ActionListener()
 888     {
 889       @Override
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         cancel_actionPerformed(e);
 893       }
 894     });
 895     JPanel okCancelPanel = new JPanel();
 896     okCancelPanel.add(ok);
 897     okCancelPanel.add(cancel);
 898     return okCancelPanel;
 899   }
 900
 901   /**
 902    * Initialises the Colours tabbed panel.
 903    *
 904    * @return
 905    */
 906   private JPanel initColoursTab()
 907   {
 908     JPanel coloursTab = new JPanel();
 909     coloursTab.setBorder(new TitledBorder(
 910             MessageManager.getString("action.open_new_alignment")));
 911     coloursTab.setLayout(new FlowLayout());
 912     JLabel mincolourLabel = new JLabel();
 913     mincolourLabel.setFont(LABEL_FONT);
 914     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 915     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 916     minColour.setFont(LABEL_FONT);
 917     minColour.setBorder(BorderFactory.createEtchedBorder());
 918     minColour.setPreferredSize(new Dimension(40, 20));
 919     minColour.addMouseListener(new MouseAdapter()
 920     {
 921       @Override
 922       public void mousePressed(MouseEvent e)
 923       {
 924         minColour_actionPerformed(minColour);
 925       }
 926     });
 927     JLabel maxcolourLabel = new JLabel();
 928     maxcolourLabel.setFont(LABEL_FONT);
 929     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 930     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 931     maxColour.setFont(LABEL_FONT);
 932     maxColour.setBorder(BorderFactory.createEtchedBorder());
 933     maxColour.setPreferredSize(new Dimension(40, 20));
 934     maxColour.addMouseListener(new MouseAdapter()
 935     {
 936       @Override
 937       public void mousePressed(MouseEvent e)
 938       {
 939         maxColour_actionPerformed(maxColour);
 940       }
 941     });
 942
 943     protColour.setFont(LABEL_FONT);
 944     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 945     JLabel protColourLabel = new JLabel();
 946     protColourLabel.setFont(LABEL_FONT);
 947     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 948     protColourLabel.setText(
 949             MessageManager.getString("label.prot_alignment_colour") + " ");
 950     JvSwingUtils.addtoLayout(coloursTab,
 951             MessageManager
 952                     .getString("label.default_colour_scheme_for_alignment"),
 953             protColourLabel, protColour);
 954
 955     nucColour.setFont(LABEL_FONT);
 956     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 957     JLabel nucColourLabel = new JLabel();
 958     nucColourLabel.setFont(LABEL_FONT);
 959     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 960     nucColourLabel.setText(
 961             MessageManager.getString("label.nuc_alignment_colour") + " ");
 962     JvSwingUtils.addtoLayout(coloursTab,
 963             MessageManager
 964                     .getString("label.default_colour_scheme_for_alignment"),
 965             nucColourLabel, nucColour);
 966
 967     JPanel annotationShding = new JPanel();
 968     annotationShding.setBorder(new TitledBorder(
 969             MessageManager.getString("label.annotation_shading_default")));
 970     annotationShding.setLayout(new GridLayout(1, 2));
 971     JvSwingUtils.addtoLayout(annotationShding,
 972             MessageManager.getString(
 973                     "label.default_minimum_colour_annotation_shading"),
 974             mincolourLabel, minColour);
 975     JvSwingUtils.addtoLayout(annotationShding,
 976             MessageManager.getString(
 977                     "label.default_maximum_colour_annotation_shading"),
 978             maxcolourLabel, maxColour);
 979     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 980     return coloursTab;
 981   }
 982
 983   /**
 984    * Initialises the Overview tabbed panel.
 985    *
 986    * @return
 987    */
 988   private JPanel initOverviewTab()
 989   {
 990     JPanel overviewPanel = new JPanel();
 991     overviewPanel.setBorder(new TitledBorder(
 992             MessageManager.getString("label.overview_settings")));
 993
 994     gapColour.setFont(LABEL_FONT);
 995     // fixing the border colours stops apparent colour bleed from the panel
 996     gapColour.setBorder(
 997             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
 998     gapColour.setPreferredSize(new Dimension(40, 20));
 999     gapColour.addMouseListener(new MouseAdapter()
1000     {
1001       @Override
1002       public void mousePressed(MouseEvent e)
1003       {
1004         gapColour_actionPerformed(gapColour);
1005       }
1006     });
1007
1008     hiddenColour.setFont(LABEL_FONT);
1009     // fixing the border colours stops apparent colour bleed from the panel
1010     hiddenColour.setBorder(
1011             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1012     hiddenColour.setPreferredSize(new Dimension(40, 20));
1013     hiddenColour.addMouseListener(new MouseAdapter()
1014     {
1015       @Override
1016       public void mousePressed(MouseEvent e)
1017       {
1018         hiddenColour_actionPerformed(hiddenColour);
1019       }
1020     });
1021
1022     useLegacyGap = new JCheckBox(
1023             MessageManager.getString("label.ov_legacy_gap"));
1024     useLegacyGap.setFont(LABEL_FONT);
1025     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1026     gapLabel = new JLabel(
1027             MessageManager.getString("label.gap_colour"));
1028     gapLabel.setFont(LABEL_FONT);
1029     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1030     showHiddenAtStart = new JCheckBox(
1031             MessageManager.getString("label.ov_show_hide_default"));
1032     showHiddenAtStart.setFont(LABEL_FONT);
1033     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1034     JLabel hiddenLabel = new JLabel(
1035             MessageManager.getString("label.hidden_colour"));
1036     hiddenLabel.setFont(LABEL_FONT);
1037     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1038
1039     useLegacyGap.addActionListener(new ActionListener()
1040     {
1041       @Override
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         useLegacyGaps_actionPerformed(e);
1045       }
1046     });
1047
1048     overviewPanel.setLayout(new GridBagLayout());
1049     GridBagConstraints c1 = new GridBagConstraints();
1050
1051     c1.fill = GridBagConstraints.HORIZONTAL;
1052     c1.gridx = 0;
1053     c1.gridy = 0;
1054     c1.weightx = 1;
1055     c1.ipady = 20;
1056     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1057     overviewPanel.add(useLegacyGap, c1);
1058
1059     GridBagConstraints c2 = new GridBagConstraints();
1060     c2.fill = GridBagConstraints.HORIZONTAL;
1061     c2.gridx = 1;
1062     c2.gridy = 0;
1063     c2.insets = new Insets(0, 15, 0, 10);
1064     overviewPanel.add(gapLabel, c2);
1065
1066     GridBagConstraints c3 = new GridBagConstraints();
1067     c3.fill = GridBagConstraints.HORIZONTAL;
1068     c3.gridx = 2;
1069     c3.gridy = 0;
1070     c3.insets = new Insets(0, 0, 0, 15);
1071     overviewPanel.add(gapColour, c3);
1072
1073     GridBagConstraints c4 = new GridBagConstraints();
1074     c4.fill = GridBagConstraints.HORIZONTAL;
1075     c4.gridx = 0;
1076     c4.gridy = 1;
1077     c4.weightx = 1;
1078     overviewPanel.add(showHiddenAtStart, c4);
1079
1080     GridBagConstraints c5 = new GridBagConstraints();
1081     c5.fill = GridBagConstraints.HORIZONTAL;
1082     c5.gridx = 1;
1083     c5.gridy = 1;
1084     c5.insets = new Insets(0, 15, 0, 10);
1085     overviewPanel.add(hiddenLabel, c5);
1086
1087     GridBagConstraints c6 = new GridBagConstraints();
1088     c6.fill = GridBagConstraints.HORIZONTAL;
1089     c6.gridx = 2;
1090     c6.gridy = 1;
1091     c6.insets = new Insets(0, 0, 0, 15);
1092     overviewPanel.add(hiddenColour, c6);
1093
1094     // Add padding so the panel doesn't look ridiculous
1095     JPanel spacePanel = new JPanel();
1096     overviewPanel.add(spacePanel,
1097             new GridBagConstraints(0, 2, 1, 1, 1.0, 1.0,
1098                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1099                     new Insets(0, 0, 0, 5), 0, 0));
1100
1101     return overviewPanel;
1102   }
1103
1104   /**
1105    * Initialises the Structure tabbed panel.
1106    *
1107    * @return
1108    */
1109   private JPanel initStructureTab()
1110   {
1111     structureTab = new JPanel();
1112
1113     structureTab.setBorder(new TitledBorder(
1114             MessageManager.getString("label.structure_options")));
1115     structureTab.setLayout(null);
1116     final int width = 400;
1117     final int height = 22;
1118     final int lineSpacing = 25;
1119     int ypos = 15;
1120
1121     structFromPdb.setFont(LABEL_FONT);
1122     structFromPdb
1123             .setText(MessageManager.getString("label.struct_from_pdb"));
1124     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1125     structFromPdb.addActionListener(new ActionListener()
1126     {
1127       @Override
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         boolean selected = structFromPdb.isSelected();
1131         // enable other options only when the first is checked
1132         useRnaView.setEnabled(selected);
1133         addSecondaryStructure.setEnabled(selected);
1134         addTempFactor.setEnabled(selected);
1135       }
1136     });
1137     structureTab.add(structFromPdb);
1138
1139     // indent checkboxes that are conditional on the first one
1140     ypos += lineSpacing;
1141     useRnaView.setFont(LABEL_FONT);
1142     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1143     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1144     structureTab.add(useRnaView);
1145
1146     ypos += lineSpacing;
1147     addSecondaryStructure.setFont(LABEL_FONT);
1148     addSecondaryStructure
1149             .setText(MessageManager.getString("label.autoadd_secstr"));
1150     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1151     structureTab.add(addSecondaryStructure);
1152
1153     ypos += lineSpacing;
1154     addTempFactor.setFont(LABEL_FONT);
1155     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1156     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1157     structureTab.add(addTempFactor);
1158
1159     ypos += lineSpacing;
1160     JLabel viewerLabel = new JLabel();
1161     viewerLabel.setFont(LABEL_FONT);
1162     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1163     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1164     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1165     structureTab.add(viewerLabel);
1166
1167     structViewer.setFont(LABEL_FONT);
1168     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1169     structViewer.addItem(ViewerType.JMOL.name());
1170     structViewer.addItem(ViewerType.CHIMERA.name());
1171     structViewer.addActionListener(new ActionListener()
1172     {
1173       @Override
1174       public void actionPerformed(ActionEvent e)
1175       {
1176         structureViewer_actionPerformed(
1177                 (String) structViewer.getSelectedItem());
1178       }
1179     });
1180     structureTab.add(structViewer);
1181
1182     ypos += lineSpacing;
1183     JLabel pathLabel = new JLabel();
1184     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1185     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1186     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1187     final String tooltip = JvSwingUtils.wrapTooltip(true,
1188             MessageManager.getString("label.chimera_path_tip"));
1189     pathLabel.setToolTipText(tooltip);
1190     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1191     structureTab.add(pathLabel);
1192
1193     chimeraPath.setFont(LABEL_FONT);
1194     chimeraPath.setText("");
1195     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1196     chimeraPath.addMouseListener(new MouseAdapter()
1197     {
1198       @Override
1199       public void mouseClicked(MouseEvent e)
1200       {
1201         if (e.getClickCount() == 2)
1202         {
1203           String chosen = openFileChooser();
1204           if (chosen != null)
1205           {
1206             chimeraPath.setText(chosen);
1207           }
1208         }
1209       }
1210     });
1211     structureTab.add(chimeraPath);
1212
1213     ypos += lineSpacing;
1214     nwMapping.setFont(LABEL_FONT);
1215     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1216     siftsMapping.setFont(LABEL_FONT);
1217     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1218     mappingMethod.add(nwMapping);
1219     mappingMethod.add(siftsMapping);
1220     JPanel mappingPanel = new JPanel();
1221     mappingPanel.setFont(LABEL_FONT);
1222     TitledBorder mmTitledBorder = new TitledBorder(
1223             MessageManager.getString("label.mapping_method"));
1224     mmTitledBorder.setTitleFont(LABEL_FONT);
1225     mappingPanel.setBorder(mmTitledBorder);
1226     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1227     // GridLayout mappingLayout = new GridLayout();
1228     mappingPanel.setLayout(new GridLayout());
1229     mappingPanel.add(nwMapping);
1230     mappingPanel.add(siftsMapping);
1231     structureTab.add(mappingPanel);
1232
1233     ypos += lineSpacing;
1234     ypos += lineSpacing;
1235     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1236             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1237     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1238     structureTab.add(docFieldPref);
1239
1240     return structureTab;
1241   }
1242
1243   /**
1244    * Action on choosing a structure viewer from combobox options.
1245    *
1246    * @param selectedItem
1247    */
1248   protected void structureViewer_actionPerformed(String selectedItem)
1249   {
1250   }
1251
1252   /**
1253    * Show a dialog for the user to choose a file. Returns the chosen path, or
1254    * null on Cancel.
1255    *
1256    * @return
1257    */
1258   protected String openFileChooser()
1259   {
1260     String choice = null;
1261     JFileChooser chooser = new JFileChooser();
1262
1263     // chooser.setFileView(new JalviewFileView());
1264     chooser.setDialogTitle(
1265             MessageManager.getString("label.open_local_file"));
1266     chooser.setToolTipText(MessageManager.getString("action.open"));
1267
1268     int value = chooser.showOpenDialog(this);
1269
1270     if (value == JFileChooser.APPROVE_OPTION)
1271     {
1272       choice = chooser.getSelectedFile().getPath();
1273     }
1274     return choice;
1275   }
1276
1277   /**
1278    * Validate the structure tab preferences; if invalid, set focus on this tab.
1279    *
1280    * @param e
1281    */
1282   protected boolean validateStructure(FocusEvent e)
1283   {
1284     if (!validateStructure())
1285     {
1286       e.getComponent().requestFocusInWindow();
1287       return false;
1288     }
1289     return true;
1290   }
1291
1292   protected boolean validateStructure()
1293   {
1294     return false;
1295   }
1296
1297   /**
1298    * Initialises the Visual tabbed panel.
1299    *
1300    * @return
1301    */
1302   private JPanel initVisualTab()
1303   {
1304     JPanel visualTab = new JPanel();
1305     visualTab.setBorder(new TitledBorder(
1306             MessageManager.getString("action.open_new_alignment")));
1307     visualTab.setLayout(null);
1308     fullScreen.setFont(LABEL_FONT);
1309     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1310     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1311     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1312     quality.setEnabled(false);
1313     quality.setFont(LABEL_FONT);
1314     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1315     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1316     quality.setSelected(true);
1317     quality.setText(MessageManager.getString("label.quality"));
1318     conservation.setEnabled(false);
1319     conservation.setFont(LABEL_FONT);
1320     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1321     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1322     conservation.setSelected(true);
1323     conservation.setText(MessageManager.getString("label.conservation"));
1324     identity.setEnabled(false);
1325     identity.setFont(LABEL_FONT);
1326     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1327     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1328     identity.setSelected(true);
1329     identity.setText(MessageManager.getString("label.consensus"));
1330     showOccupancy.setFont(LABEL_FONT);
1331     showOccupancy.setEnabled(false);
1332     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1333     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1334     showOccupancy.setSelected(true);
1335     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1336
1337     JLabel showGroupbits = new JLabel();
1338     showGroupbits.setFont(LABEL_FONT);
1339     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1340     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1341     showGroupbits
1342             .setText(MessageManager.getString("action.show_group") + ":");
1343     JLabel showConsensbits = new JLabel();
1344     showConsensbits.setFont(LABEL_FONT);
1345     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1346     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1347     showConsensbits
1348             .setText(MessageManager.getString("label.consensus") + ":");
1349     showConsensHistogram.setEnabled(false);
1350     showConsensHistogram.setFont(LABEL_FONT);
1351     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1352     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1353     showConsensHistogram.setSelected(true);
1354     showConsensHistogram
1355             .setText(MessageManager.getString("label.histogram"));
1356     showConsensLogo.setEnabled(false);
1357     showConsensLogo.setFont(LABEL_FONT);
1358     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1359     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1360     showConsensLogo.setSelected(true);
1361     showConsensLogo.setText(MessageManager.getString("label.logo"));
1362     showGroupConsensus.setEnabled(false);
1363     showGroupConsensus.setFont(LABEL_FONT);
1364     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1365     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1366     showGroupConsensus.setSelected(true);
1367     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1368     showGroupConservation.setEnabled(false);
1369     showGroupConservation.setFont(LABEL_FONT);
1370     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1371     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1372     showGroupConservation.setSelected(true);
1373     showGroupConservation
1374             .setText(MessageManager.getString("label.conservation"));
1375     showNpTooltip.setEnabled(true);
1376     showNpTooltip.setFont(LABEL_FONT);
1377     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1378     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1379     showNpTooltip.setSelected(true);
1380     showNpTooltip.setText(
1381             MessageManager.getString("label.non_positional_features"));
1382     showDbRefTooltip.setEnabled(true);
1383     showDbRefTooltip.setFont(LABEL_FONT);
1384     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1385     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1386     showDbRefTooltip.setSelected(true);
1387     showDbRefTooltip
1388             .setText(MessageManager.getString("label.database_references"));
1389     annotations.setFont(LABEL_FONT);
1390     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1391     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1392     annotations.setSelected(true);
1393     annotations.setText(MessageManager.getString("label.show_annotations"));
1394     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1395     annotations.addActionListener(new ActionListener()
1396     {
1397       @Override
1398       public void actionPerformed(ActionEvent e)
1399       {
1400         annotations_actionPerformed(e);
1401       }
1402     });
1403     identity.addActionListener(new ActionListener()
1404     {
1405       @Override
1406       public void actionPerformed(ActionEvent e)
1407       {
1408         annotations_actionPerformed(e);
1409       }
1410     });
1411     showGroupConsensus.addActionListener(new ActionListener()
1412     {
1413       @Override
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         annotations_actionPerformed(e);
1417       }
1418     });
1419     showUnconserved.setFont(LABEL_FONT);
1420     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1421     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1422     showUnconserved.setSelected(true);
1423     showUnconserved
1424             .setText(MessageManager.getString("action.show_unconserved"));
1425     showUnconserved.addActionListener(new ActionListener()
1426     {
1427       @Override
1428       public void actionPerformed(ActionEvent e)
1429       {
1430         showunconserved_actionPerformed(e);
1431       }
1432     });
1433
1434     // TODO these are not yet added to / action from Preferences
1435     // JCheckBox shareSelections = new JCheckBox();
1436     // shareSelections.setFont(verdana11);
1437     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1438     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1439     // shareSelections.setSelected(true);
1440     // shareSelections.setText(MessageManager
1441     // .getString("label.share_selection_across_views"));
1442     // JCheckBox followHighlight = new JCheckBox();
1443     // followHighlight.setFont(verdana11);
1444     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1445     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1446     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1447     // followHighlight.setSelected(true);
1448     // followHighlight.setText(MessageManager
1449     // .getString("label.scroll_highlighted_regions"));
1450
1451     seqLimit.setFont(LABEL_FONT);
1452     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1453     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1454     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1455     smoothFont.setFont(LABEL_FONT);
1456     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1457     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1458     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1459     scaleProteinToCdna.setFont(LABEL_FONT);
1460     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1461     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1462     scaleProteinToCdna.setText(
1463             MessageManager.getString("label.scale_protein_to_cdna"));
1464     scaleProteinToCdna.setToolTipText(
1465             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1466     JLabel gapLabel = new JLabel();
1467     gapLabel.setFont(LABEL_FONT);
1468     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1469     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1470     JLabel fontLabel = new JLabel();
1471     fontLabel.setFont(LABEL_FONT);
1472     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1473     fontLabel.setText(MessageManager.getString("label.font"));
1474     fontSizeCB.setFont(LABEL_FONT);
1475     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1476     fontStyleCB.setFont(LABEL_FONT);
1477     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1478     fontNameCB.setFont(LABEL_FONT);
1479     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1480     gapSymbolCB.setFont(LABEL_FONT);
1481     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1482     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1483     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1484     gapSymbolCB.setRenderer(dlcr);
1485
1486     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1487     startupCheckbox.setFont(LABEL_FONT);
1488     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1489     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1490     startupCheckbox.setSelected(true);
1491     startupFileTextfield.setFont(LABEL_FONT);
1492     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1493     startupFileTextfield.addMouseListener(new MouseAdapter()
1494     {
1495       @Override
1496       public void mouseClicked(MouseEvent e)
1497       {
1498         if (e.getClickCount() > 1)
1499         {
1500           startupFileTextfield_mouseClicked();
1501         }
1502       }
1503     });
1504
1505     sortby.setFont(LABEL_FONT);
1506     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1507     JLabel sortLabel = new JLabel();
1508     sortLabel.setFont(LABEL_FONT);
1509     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1510     sortLabel.setText(MessageManager.getString("label.sort_by"));
1511     sortAnnBy.setFont(LABEL_FONT);
1512     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1513     JLabel sortAnnLabel = new JLabel();
1514     sortAnnLabel.setFont(LABEL_FONT);
1515     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1516     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1517     sortAutocalc.setFont(LABEL_FONT);
1518     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1519
1520     JPanel annsettingsPanel = new JPanel();
1521     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1522     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1523     annsettingsPanel.setBorder(new EtchedBorder());
1524     visualTab.add(annsettingsPanel);
1525     Border jb = new EmptyBorder(1, 1, 4, 5);
1526     annotations.setBorder(jb);
1527     showOccupancy.setBorder(jb);
1528     quality.setBorder(jb);
1529     conservation.setBorder(jb);
1530     identity.setBorder(jb);
1531     showConsensbits.setBorder(jb);
1532     showGroupbits.setBorder(jb);
1533     showGroupConsensus.setBorder(jb);
1534     showGroupConservation.setBorder(jb);
1535     showConsensHistogram.setBorder(jb);
1536     showConsensLogo.setBorder(jb);
1537
1538     JPanel autoAnnotSettings = new JPanel();
1539     annsettingsPanel.add(autoAnnotSettings);
1540     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1541     autoAnnotSettings.add(annotations);
1542     autoAnnotSettings.add(quality);
1543     // second row of autoannotation box
1544     autoAnnotSettings = new JPanel();
1545     annsettingsPanel.add(autoAnnotSettings);
1546
1547     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1548     autoAnnotSettings.add(conservation);
1549     autoAnnotSettings.add(identity);
1550     autoAnnotSettings.add(showOccupancy);
1551     autoAnnotSettings.add(showGroupbits);
1552     autoAnnotSettings.add(showGroupConservation);
1553     autoAnnotSettings.add(showGroupConsensus);
1554     autoAnnotSettings.add(showConsensbits);
1555     autoAnnotSettings.add(showConsensHistogram);
1556     autoAnnotSettings.add(showConsensLogo);
1557
1558     JPanel tooltipSettings = new JPanel();
1559     tooltipSettings.setBorder(new TitledBorder(
1560             MessageManager.getString("label.sequence_id_tooltip")));
1561     tooltipSettings.setBounds(173, 140, 220, 62);
1562     tooltipSettings.setLayout(new GridLayout(2, 1));
1563     tooltipSettings.add(showDbRefTooltip);
1564     tooltipSettings.add(showNpTooltip);
1565     visualTab.add(tooltipSettings);
1566
1567     wrap.setFont(LABEL_FONT);
1568     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1569     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1570     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1571     rightAlign.setFont(LABEL_FONT);
1572     rightAlign.setForeground(Color.black);
1573     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1574     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1575     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1576     idItalics.setFont(LABEL_FONT_ITALIC);
1577     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1578     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1579     idItalics.setText(
1580             MessageManager.getString("label.sequence_name_italics"));
1581     openoverv.setFont(LABEL_FONT);
1582     openoverv.setActionCommand(
1583             MessageManager.getString("label.open_overview"));
1584     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1585     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1586     openoverv.setText(MessageManager.getString("label.open_overview"));
1587     JPanel jPanel2 = new JPanel();
1588     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1589     jPanel2.setLayout(new GridLayout(14, 1));
1590     jPanel2.add(fullScreen);
1591     jPanel2.add(openoverv);
1592     jPanel2.add(seqLimit);
1593     jPanel2.add(rightAlign);
1594     jPanel2.add(fontLabel);
1595     jPanel2.add(showUnconserved);
1596     jPanel2.add(idItalics);
1597     jPanel2.add(smoothFont);
1598     jPanel2.add(scaleProteinToCdna);
1599     jPanel2.add(gapLabel);
1600     jPanel2.add(wrap);
1601     jPanel2.add(sortLabel);
1602     jPanel2.add(sortAnnLabel);
1603     jPanel2.add(startupCheckbox);
1604     visualTab.add(jPanel2);
1605     visualTab.add(startupFileTextfield);
1606     visualTab.add(sortby);
1607     visualTab.add(sortAnnBy);
1608     visualTab.add(sortAutocalc);
1609     visualTab.add(gapSymbolCB);
1610     visualTab.add(fontNameCB);
1611     visualTab.add(fontSizeCB);
1612     visualTab.add(fontStyleCB);
1613     return visualTab;
1614   }
1615
1616   protected void autoIdWidth_actionPerformed()
1617   {
1618     // TODO Auto-generated method stub
1619
1620   }
1621
1622   protected void userIdWidth_actionPerformed()
1623   {
1624     // TODO Auto-generated method stub
1625
1626   }
1627
1628   protected void maxColour_actionPerformed(JPanel panel)
1629   {
1630   }
1631
1632   protected void minColour_actionPerformed(JPanel panel)
1633   {
1634   }
1635
1636   protected void gapColour_actionPerformed(JPanel panel)
1637   {
1638   }
1639
1640   protected void hiddenColour_actionPerformed(JPanel panel)
1641   {
1642   }
1643
1644   protected void showunconserved_actionPerformed(ActionEvent e)
1645   {
1646     // TODO Auto-generated method stub
1647
1648   }
1649
1650   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1651   {
1652     boolean enabled = useLegacyGap.isSelected();
1653     if (enabled)
1654     {
1655       gapColour.setBackground(Color.WHITE);
1656     }
1657     gapColour.setEnabled(!enabled);
1658     gapLabel.setEnabled(!enabled);
1659   }
1660
1661   /**
1662    * DOCUMENT ME!
1663    *
1664    * @param e
1665    *          DOCUMENT ME!
1666    */
1667   public void ok_actionPerformed(ActionEvent e)
1668   {
1669   }
1670
1671   /**
1672    * DOCUMENT ME!
1673    *
1674    * @param e
1675    *          DOCUMENT ME!
1676    */
1677   public void cancel_actionPerformed(ActionEvent e)
1678   {
1679   }
1680
1681   /**
1682    * DOCUMENT ME!
1683    *
1684    * @param e
1685    *          DOCUMENT ME!
1686    */
1687   public void annotations_actionPerformed(ActionEvent e)
1688   {
1689   }
1690
1691   /**
1692    * DOCUMENT ME!
1693    */
1694   public void startupFileTextfield_mouseClicked()
1695   {
1696   }
1697
1698   public void newLink_actionPerformed(ActionEvent e)
1699   {
1700
1701   }
1702
1703   public void editLink_actionPerformed(ActionEvent e)
1704   {
1705
1706   }
1707
1708   public void deleteLink_actionPerformed(ActionEvent e)
1709   {
1710
1711   }
1712
1713   public void defaultBrowser_mouseClicked(MouseEvent e)
1714   {
1715
1716   }
1717
1718   public void linkURLList_keyTyped(KeyEvent e)
1719   {
1720
1721   }
1722
1723   public void useProxy_actionPerformed()
1724   {
1725     boolean enabled = useProxy.isSelected();
1726     portLabel.setEnabled(enabled);
1727     serverLabel.setEnabled(enabled);
1728     proxyServerTB.setEnabled(enabled);
1729     proxyPortTB.setEnabled(enabled);
1730   }
1731
1732   /**
1733    * Customer renderer for JTable: supports column of radio buttons
1734    */
1735   public class RadioButtonRenderer extends JRadioButton
1736           implements TableCellRenderer
1737   {
1738     public RadioButtonRenderer()
1739     {
1740       setHorizontalAlignment(CENTER);
1741       setToolTipText(MessageManager.getString("label.urltooltip"));
1742     }
1743
1744     @Override
1745     public Component getTableCellRendererComponent(JTable table,
1746             Object value, boolean isSelected, boolean hasFocus, int row,
1747             int column)
1748     {
1749       setSelected((boolean) value);
1750
1751       // set colours to match rest of table
1752       if (isSelected)
1753       {
1754         setBackground(table.getSelectionBackground());
1755         setForeground(table.getSelectionForeground());
1756       }
1757       else
1758       {
1759         setBackground(table.getBackground());
1760         setForeground(table.getForeground());
1761       }
1762       return this;
1763     }
1764   }
1765
1766   /**
1767    * Customer cell editor for JTable: supports column of radio buttons in
1768    * conjunction with renderer
1769    */
1770   public class RadioButtonEditor extends AbstractCellEditor
1771           implements TableCellEditor
1772   {
1773     private JRadioButton button = new JRadioButton();
1774
1775     public RadioButtonEditor()
1776     {
1777       button.setHorizontalAlignment(SwingConstants.CENTER);
1778       this.button.addActionListener(new ActionListener()
1779       {
1780         @Override
1781         public void actionPerformed(ActionEvent e)
1782         {
1783           fireEditingStopped();
1784         }
1785       });
1786     }
1787
1788     @Override
1789     public Component getTableCellEditorComponent(JTable table, Object value,
1790             boolean isSelected, int row, int column)
1791     {
1792       button.setSelected((boolean) value);
1793       return button;
1794     }
1795
1796     @Override
1797     public Object getCellEditorValue()
1798     {
1799       return button.isSelected();
1800     }
1801
1802   }
1803 }