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 gapColour = new JPanel();
 187
 188   protected JPanel hiddenColour = new JPanel();
 189
 190   protected JCheckBox useLegacyGap;
 191
 192   protected JCheckBox showHiddenAtStart;
 193
 194   protected JLabel gapLabel;
 195
 196   /*
 197    * Connections tab components
 198    */
 199   protected JTable linkUrlTable = new JTable();
 200
 201   protected JButton editLink = new JButton();
 202
 203   protected JButton deleteLink = new JButton();
 204
 205   protected JTextField filterTB = new JTextField();
 206
 207   protected JButton doReset = new JButton();
 208
 209   protected JButton userOnly = new JButton();
 210
 211   protected JLabel portLabel = new JLabel();
 212
 213   protected JLabel serverLabel = new JLabel();
 214
 215   protected JTextField proxyServerTB = new JTextField();
 216
 217   protected JTextField proxyPortTB = new JTextField();
 218
 219   protected JTextField defaultBrowser = new JTextField();
 220
 221   protected JCheckBox useProxy = new JCheckBox();
 222
 223   protected JCheckBox usagestats = new JCheckBox();
 224
 225   protected JCheckBox questionnaire = new JCheckBox();
 226
 227   protected JCheckBox versioncheck = new JCheckBox();
 228
 229   /*
 230    * Output tab components
 231    */
 232   protected JComboBox<Object> epsRendering = new JComboBox<>();
 233
 234   protected JComboBox<Object> htmlRendering = new JComboBox<>();
 235
 236   protected JComboBox<Object> svgRendering = new JComboBox<>();
 237
 238   protected JLabel userIdWidthlabel = new JLabel();
 239
 240   protected JCheckBox autoIdWidth = new JCheckBox();
 241
 242   protected JTextField userIdWidth = new JTextField();
 243
 244   protected JCheckBox blcjv = new JCheckBox();
 245
 246   protected JCheckBox pileupjv = new JCheckBox();
 247
 248   protected JCheckBox clustaljv = new JCheckBox();
 249
 250   protected JCheckBox msfjv = new JCheckBox();
 251
 252   protected JCheckBox fastajv = new JCheckBox();
 253
 254   protected JCheckBox pfamjv = new JCheckBox();
 255
 256   protected JCheckBox pirjv = new JCheckBox();
 257
 258   protected JCheckBox modellerOutput = new JCheckBox();
 259
 260   protected JCheckBox embbedBioJSON = new JCheckBox();
 261
 262   /*
 263    * Editing tab components
 264    */
 265   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 266
 267   protected JCheckBox padGaps = new JCheckBox();
 268
 269   protected JCheckBox sortByTree = new JCheckBox();
 270
 271
 272   /*
 273    * Web Services tab
 274    */
 275   protected JPanel wsTab = new JPanel();
 276
 277   /**
 278    * Creates a new GPreferences object.
 279    */
 280   public GPreferences()
 281   {
 282     try
 283     {
 284       jbInit();
 285     } catch (Exception ex)
 286     {
 287       ex.printStackTrace();
 288     }
 289   }
 290
 291   /**
 292    * Construct the panel and its tabbed sub-panels.
 293    *
 294    * @throws Exception
 295    */
 296   private void jbInit() throws Exception
 297   {
 298     final JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
 299     this.setLayout(new BorderLayout());
 300     JPanel okCancelPanel = initOkCancelPanel();
 301     this.add(tabbedPane, BorderLayout.CENTER);
 302     this.add(okCancelPanel, BorderLayout.SOUTH);
 303
 304     tabbedPane.add(initVisualTab(),
 305             MessageManager.getString("label.visual"));
 306
 307     tabbedPane.add(initColoursTab(),
 308             MessageManager.getString("label.colours"));
 309
 310     tabbedPane.add(initOverviewTab(),
 311             MessageManager.getString("label.overview"));
 312
 313     tabbedPane.add(initStructureTab(),
 314             MessageManager.getString("label.structure"));
 315
 316     tabbedPane.add(initConnectionsTab(),
 317             MessageManager.getString("label.connections"));
 318
 319     tabbedPane.add(initLinksTab(),
 320             MessageManager.getString("label.urllinks"));
 321
 322     tabbedPane.add(initOutputTab(),
 323             MessageManager.getString("label.output"));
 324
 325     tabbedPane.add(initEditingTab(),
 326             MessageManager.getString("label.editing"));
 327
 328     /*
 329      * See WsPreferences for the real work of configuring this tab.
 330      */
 331     wsTab.setLayout(new BorderLayout());
 332     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 333
 334     /*
 335      * Handler to validate a tab before leaving it - currently only for
 336      * Structure.
 337      */
 338     tabbedPane.addChangeListener(new ChangeListener()
 339     {
 340       private Component lastTab;
 341
 342       @Override
 343       public void stateChanged(ChangeEvent e)
 344       {
 345         if (lastTab == structureTab
 346                 && tabbedPane.getSelectedComponent() != structureTab)
 347         {
 348           if (!validateStructure())
 349           {
 350             tabbedPane.setSelectedComponent(structureTab);
 351             return;
 352           }
 353         }
 354         lastTab = tabbedPane.getSelectedComponent();
 355       }
 356
 357     });
 358   }
 359
 360   /**
 361    * Initialises the Editing tabbed panel.
 362    *
 363    * @return
 364    */
 365   private JPanel initEditingTab()
 366   {
 367     JPanel editingTab = new JPanel();
 368     editingTab.setLayout(null);
 369     autoCalculateConsCheck.setFont(LABEL_FONT);
 370     autoCalculateConsCheck.setText(
 371             MessageManager.getString("label.autocalculate_consensus"));
 372     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 373     padGaps.setFont(LABEL_FONT);
 374     padGaps.setText(
 375             MessageManager.getString("label.pad_gaps_when_editing"));
 376     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 377     sortByTree.setFont(LABEL_FONT);
 378     sortByTree
 379             .setText(MessageManager.getString("label.sort_with_new_tree"));
 380     sortByTree.setToolTipText(MessageManager.getString(
 381             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 382     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 383     editingTab.add(autoCalculateConsCheck);
 384     editingTab.add(padGaps);
 385     editingTab.add(sortByTree);
 386     return editingTab;
 387   }
 388
 389   /**
 390    * Initialises the Output tab
 391    *
 392    * @return
 393    */
 394   private JPanel initOutputTab()
 395   {
 396     JPanel outputTab = new JPanel();
 397     outputTab.setLayout(null);
 398
 399     JLabel epsLabel = new JLabel(
 400             MessageManager.formatMessage("label.rendering_style", "EPS"));
 401     epsLabel.setFont(LABEL_FONT);
 402     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 403     epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
 404     epsRendering.setFont(LABEL_FONT);
 405     epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
 406     JLabel htmlLabel = new JLabel(
 407             MessageManager.formatMessage("label.rendering_style", "HTML"));
 408     htmlLabel.setFont(LABEL_FONT);
 409     htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 410     htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
 411     htmlRendering.setFont(LABEL_FONT);
 412     htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
 413     JLabel svgLabel = new JLabel(
 414             MessageManager.formatMessage("label.rendering_style", "SVG"));
 415     svgLabel.setFont(LABEL_FONT);
 416     svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 417     svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
 418     svgRendering.setFont(LABEL_FONT);
 419     svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
 420
 421     JLabel jLabel1 = new JLabel();
 422     jLabel1.setFont(LABEL_FONT);
 423     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 424     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 425     jLabel1.setFont(LABEL_FONT);
 426
 427     fastajv.setFont(LABEL_FONT);
 428     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 429     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 430     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 431     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 432     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 433     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 434     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 435     msfjv.setFont(LABEL_FONT);
 436     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 437     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 438     JPanel jPanel11 = new JPanel();
 439     jPanel11.setFont(LABEL_FONT);
 440     TitledBorder titledBorder2 = new TitledBorder(
 441             MessageManager.getString("label.file_output"));
 442     jPanel11.setBorder(titledBorder2);
 443     jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
 444     GridLayout gridLayout3 = new GridLayout();
 445     jPanel11.setLayout(gridLayout3);
 446     gridLayout3.setRows(8);
 447     blcjv.setFont(LABEL_FONT);
 448     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 449     clustaljv.setFont(LABEL_FONT);
 450     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 451     pfamjv.setFont(LABEL_FONT);
 452     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 453     pileupjv.setFont(LABEL_FONT);
 454     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 455     pirjv.setFont(LABEL_FONT);
 456     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 457     autoIdWidth.setFont(LABEL_FONT);
 458     autoIdWidth.setText(
 459             MessageManager.getString("label.automatically_set_id_width"));
 460     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 461             .getString("label.adjusts_width_generated_eps_png")));
 462     autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
 463     autoIdWidth.addActionListener(new ActionListener()
 464     {
 465
 466       @Override
 467       public void actionPerformed(ActionEvent e)
 468       {
 469         autoIdWidth_actionPerformed();
 470       }
 471     });
 472     userIdWidthlabel.setFont(LABEL_FONT);
 473     userIdWidthlabel.setText(
 474             MessageManager.getString("label.figure_id_column_width"));
 475     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 476             .getString("label.manually_specify_width_left_column")));
 477     userIdWidthlabel.setToolTipText(
 478             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 479                     "label.manually_specify_width_left_column")));
 480     userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
 481     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 482     userIdWidth.setText("");
 483     userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
 484     userIdWidth.addActionListener(new ActionListener()
 485     {
 486
 487       @Override
 488       public void actionPerformed(ActionEvent e)
 489       {
 490         userIdWidth_actionPerformed();
 491       }
 492     });
 493     modellerOutput.setFont(LABEL_FONT);
 494     modellerOutput
 495             .setText(MessageManager.getString("label.use_modeller_output"));
 496     modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
 497     embbedBioJSON.setFont(LABEL_FONT);
 498     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 499     embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 500
 501     jPanel11.add(jLabel1);
 502     jPanel11.add(blcjv);
 503     jPanel11.add(clustaljv);
 504     jPanel11.add(fastajv);
 505     jPanel11.add(msfjv);
 506     jPanel11.add(pfamjv);
 507     jPanel11.add(pileupjv);
 508     jPanel11.add(pirjv);
 509     outputTab.add(autoIdWidth);
 510     outputTab.add(userIdWidth);
 511     outputTab.add(userIdWidthlabel);
 512     outputTab.add(modellerOutput);
 513     outputTab.add(embbedBioJSON);
 514     outputTab.add(epsLabel);
 515     outputTab.add(epsRendering);
 516     outputTab.add(htmlLabel);
 517     outputTab.add(htmlRendering);
 518     outputTab.add(svgLabel);
 519     outputTab.add(svgRendering);
 520     outputTab.add(jPanel11);
 521     return outputTab;
 522   }
 523
 524   /**
 525    * Initialises the Connections tabbed panel.
 526    *
 527    * @return
 528    */
 529   private JPanel initConnectionsTab()
 530   {
 531     JPanel connectTab = new JPanel();
 532     connectTab.setLayout(new GridBagLayout());
 533
 534     // Label for browser text box
 535     JLabel browserLabel = new JLabel();
 536     browserLabel.setFont(LABEL_FONT);
 537     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 538     browserLabel.setText(
 539             MessageManager.getString("label.default_browser_unix"));
 540     defaultBrowser.setFont(LABEL_FONT);
 541     defaultBrowser.setText("");
 542     final String tooltip = JvSwingUtils.wrapTooltip(true,
 543             MessageManager.getString("label.double_click_to_browse"));
 544     defaultBrowser.setToolTipText(tooltip);
 545     defaultBrowser.addMouseListener(new MouseAdapter()
 546     {
 547       @Override
 548       public void mouseClicked(MouseEvent e)
 549       {
 550         if (e.getClickCount() > 1)
 551         {
 552           defaultBrowser_mouseClicked(e);
 553         }
 554       }
 555     });
 556
 557     JPanel proxyPanel = initConnTabProxyPanel();
 558     initConnTabCheckboxes();
 559
 560     // Add default Browser text box
 561     connectTab.add(browserLabel,
 562             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 563                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 564                     new Insets(10, 0, 5, 5), 5, 1));
 565     defaultBrowser.setFont(LABEL_FONT);
 566     defaultBrowser.setText("");
 567
 568     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 569             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 570             new Insets(10, 0, 5, 10), 30, 1));
 571
 572     // Add proxy server panel
 573     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 574             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 575             new Insets(10, 0, 5, 12), 4, 10));
 576
 577     // Add usage stats, version check and questionnaire checkboxes
 578     connectTab.add(usagestats,
 579             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 580                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 581                     new Insets(0, 2, 5, 5), 70, 1));
 582     connectTab.add(questionnaire,
 583             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 584                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 585                     new Insets(0, 2, 5, 10), 70, 1));
 586     connectTab.add(versioncheck,
 587             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 588                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 589                     new Insets(0, 2, 5, 5), 70, 1));
 590
 591     // Add padding so the panel doesn't look ridiculous
 592     JPanel spacePanel = new JPanel();
 593     connectTab.add(spacePanel,
 594             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 595                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 596                     new Insets(0, 0, 0, 5), 70, 1));
 597
 598     return connectTab;
 599   }
 600
 601   /**
 602    * Initialises the Links tabbed panel.
 603    *
 604    * @return
 605    */
 606   private JPanel initLinksTab()
 607   {
 608     JPanel linkTab = new JPanel();
 609     linkTab.setLayout(new GridBagLayout());
 610
 611     // Set up table for Url links
 612     linkUrlTable.setFillsViewportHeight(true);
 613     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 614     linkUrlTable.setAutoCreateRowSorter(true);
 615     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 616
 617     // adjust row height so radio buttons actually fit
 618     // don't do this in the renderer, it causes the awt thread to activate
 619     // constantly
 620     JRadioButton temp = new JRadioButton();
 621     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 622
 623     // Table in scrollpane so that the table is given a scrollbar
 624     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 625     linkScrollPane.setBorder(null);
 626
 627     // Panel for links functionality
 628     JPanel linkPanel = new JPanel(new GridBagLayout());
 629     linkPanel.setBorder(new TitledBorder(
 630             MessageManager.getString("label.url_linkfrom_sequence_id")));
 631
 632     // Put the Url links panel together
 633
 634     // Buttons go at top right, resizing only resizes the blank space vertically
 635     JPanel buttonPanel = initLinkTabUrlButtons();
 636     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 637     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 638     linkConstraints1.gridx = 0;
 639     linkConstraints1.gridy = 0;
 640     linkConstraints1.weightx = 1.0;
 641     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 642     linkTab.add(buttonPanel, linkConstraints1);
 643
 644     // Links table goes at top left, resizing resizes the table
 645     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 646     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 647     linkConstraints2.gridx = 0;
 648     linkConstraints2.gridy = 1;
 649     linkConstraints2.weightx = 1.0;
 650     linkConstraints2.weighty = 1.0;
 651     linkConstraints2.fill = GridBagConstraints.BOTH;
 652     linkTab.add(linkScrollPane, linkConstraints2);
 653
 654     // Filter box and buttons goes at bottom left, resizing resizes the text box
 655     JPanel filterPanel = initLinkTabFilterPanel();
 656     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 657     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 658     linkConstraints3.gridx = 0;
 659     linkConstraints3.gridy = 2;
 660     linkConstraints3.weightx = 1.0;
 661     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 662     linkTab.add(filterPanel, linkConstraints3);
 663
 664     return linkTab;
 665   }
 666
 667   private JPanel initLinkTabFilterPanel()
 668   {
 669     // Filter textbox and reset button
 670     JLabel filterLabel = new JLabel(
 671             MessageManager.getString("label.filter"));
 672     filterLabel.setFont(LABEL_FONT);
 673     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 674     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 675
 676     filterTB.setFont(LABEL_FONT);
 677     filterTB.setText("");
 678
 679     doReset.setText(MessageManager.getString("action.showall"));
 680     userOnly.setText(MessageManager.getString("action.customfilter"));
 681
 682     // Panel for filter functionality
 683     JPanel filterPanel = new JPanel(new GridBagLayout());
 684     filterPanel.setBorder(new TitledBorder("Filter"));
 685     GridBagConstraints gbc = new GridBagConstraints();
 686     gbc.gridx = 0;
 687     gbc.gridy = 0;
 688     gbc.fill = GridBagConstraints.NONE;
 689     gbc.anchor = GridBagConstraints.WEST;
 690
 691     filterPanel.add(filterLabel, gbc);
 692
 693     GridBagConstraints gbc1 = new GridBagConstraints();
 694     gbc1.gridx = 1;
 695     gbc1.gridwidth = 2;
 696     gbc1.fill = GridBagConstraints.HORIZONTAL;
 697     gbc1.anchor = GridBagConstraints.WEST;
 698     gbc1.weightx = 1.0;
 699     filterPanel.add(filterTB, gbc1);
 700
 701     GridBagConstraints gbc2 = new GridBagConstraints();
 702     gbc2.gridx = 3;
 703     gbc2.fill = GridBagConstraints.NONE;
 704     gbc2.anchor = GridBagConstraints.WEST;
 705     filterPanel.add(doReset, gbc2);
 706
 707     GridBagConstraints gbc3 = new GridBagConstraints();
 708     gbc3.gridx = 4;
 709     gbc3.fill = GridBagConstraints.NONE;
 710     gbc3.anchor = GridBagConstraints.WEST;
 711     filterPanel.add(userOnly, gbc3);
 712
 713     return filterPanel;
 714   }
 715
 716   private JPanel initLinkTabUrlButtons()
 717   {
 718     // Buttons for new / edit / delete Url links
 719     JButton newLink = new JButton();
 720     newLink.setText(MessageManager.getString("action.new"));
 721
 722     editLink.setText(MessageManager.getString("action.edit"));
 723
 724     deleteLink.setText(MessageManager.getString("action.delete"));
 725
 726     // no current selection, so initially disable delete/edit buttons
 727     editLink.setEnabled(false);
 728     deleteLink.setEnabled(false);
 729
 730     newLink.addActionListener(new java.awt.event.ActionListener()
 731     {
 732       @Override
 733       public void actionPerformed(ActionEvent e)
 734       {
 735         newLink_actionPerformed(e);
 736       }
 737     });
 738
 739     editLink.setText(MessageManager.getString("action.edit"));
 740     editLink.addActionListener(new java.awt.event.ActionListener()
 741     {
 742       @Override
 743       public void actionPerformed(ActionEvent e)
 744       {
 745         editLink_actionPerformed(e);
 746       }
 747     });
 748
 749     deleteLink.setText(MessageManager.getString("action.delete"));
 750     deleteLink.addActionListener(new java.awt.event.ActionListener()
 751     {
 752       @Override
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         deleteLink_actionPerformed(e);
 756       }
 757     });
 758
 759     JPanel buttonPanel = new JPanel(new GridBagLayout());
 760     buttonPanel.setBorder(new TitledBorder("Edit links"));
 761     GridBagConstraints gbc = new GridBagConstraints();
 762     gbc.gridx = 0;
 763     gbc.gridy = 0;
 764     gbc.fill = GridBagConstraints.NONE;
 765     buttonPanel.add(newLink, gbc);
 766
 767     GridBagConstraints gbc1 = new GridBagConstraints();
 768     gbc1.gridx = 1;
 769     gbc1.gridy = 0;
 770     gbc1.fill = GridBagConstraints.NONE;
 771     buttonPanel.add(editLink, gbc1);
 772
 773     GridBagConstraints gbc2 = new GridBagConstraints();
 774     gbc2.gridx = 2;
 775     gbc2.gridy = 0;
 776     gbc2.fill = GridBagConstraints.NONE;
 777     buttonPanel.add(deleteLink, gbc2);
 778
 779     GridBagConstraints gbc3 = new GridBagConstraints();
 780     gbc3.gridx = 3;
 781     gbc3.gridy = 0;
 782     gbc3.fill = GridBagConstraints.HORIZONTAL;
 783     gbc3.weightx = 1.0;
 784     JPanel spacePanel = new JPanel();
 785     spacePanel.setBorder(null);
 786     buttonPanel.add(spacePanel, gbc3);
 787
 788     return buttonPanel;
 789   }
 790
 791   /**
 792    * Initialises the proxy server panel in the Connections tab
 793    *
 794    * @return the proxy server panel
 795    */
 796   private JPanel initConnTabProxyPanel()
 797   {
 798     // Label for server text box
 799     serverLabel.setText(MessageManager.getString("label.address"));
 800     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 801     serverLabel.setFont(LABEL_FONT);
 802
 803     // Proxy server and port text boxes
 804     proxyServerTB.setFont(LABEL_FONT);
 805     proxyPortTB.setFont(LABEL_FONT);
 806
 807     // Label for Port text box
 808     portLabel.setFont(LABEL_FONT);
 809     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 810     portLabel.setText(MessageManager.getString("label.port"));
 811
 812     // Use proxy server checkbox
 813     useProxy.setFont(LABEL_FONT);
 814     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 815     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 816     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 817     useProxy.addActionListener(new ActionListener()
 818     {
 819       @Override
 820       public void actionPerformed(ActionEvent e)
 821       {
 822         useProxy_actionPerformed();
 823       }
 824     });
 825
 826     // Make proxy server panel
 827     JPanel proxyPanel = new JPanel();
 828     TitledBorder titledBorder1 = new TitledBorder(
 829             MessageManager.getString("label.proxy_server"));
 830     proxyPanel.setBorder(titledBorder1);
 831     proxyPanel.setLayout(new GridBagLayout());
 832     proxyPanel.add(serverLabel,
 833             new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 834                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 835                     new Insets(0, 2, 2, 0), 5, 0));
 836     proxyPanel.add(portLabel,
 837             new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 838                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 839                     new Insets(0, 0, 2, 0), 11, 0));
 840     proxyPanel.add(useProxy,
 841             new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 842                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 843                     new Insets(0, 2, 5, 185), 2, -4));
 844     proxyPanel.add(proxyPortTB,
 845             new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 846                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 847                     new Insets(0, 2, 2, 2), 54, 1));
 848     proxyPanel.add(proxyServerTB,
 849             new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 850                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 851                     new Insets(0, 2, 2, 0), 263, 1));
 852
 853     return proxyPanel;
 854   }
 855
 856   /**
 857    * Initialises the checkboxes in the Connections tab
 858    */
 859   private void initConnTabCheckboxes()
 860   {
 861     // Usage stats checkbox label
 862     usagestats.setText(
 863             MessageManager.getString("label.send_usage_statistics"));
 864     usagestats.setFont(LABEL_FONT);
 865     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 866     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 867
 868     // Questionnaire checkbox label
 869     questionnaire.setText(
 870             MessageManager.getString("label.check_for_questionnaires"));
 871     questionnaire.setFont(LABEL_FONT);
 872     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 873     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 874
 875     // Check for latest version checkbox label
 876     versioncheck.setText(
 877             MessageManager.getString("label.check_for_latest_version"));
 878     versioncheck.setFont(LABEL_FONT);
 879     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 880     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 881   }
 882
 883   /**
 884    * Initialises the parent panel which contains the tabbed sections.
 885    *
 886    * @return
 887    */
 888   private JPanel initOkCancelPanel()
 889   {
 890     JButton ok = new JButton();
 891     ok.setText(MessageManager.getString("action.ok"));
 892     ok.addActionListener(new ActionListener()
 893     {
 894       @Override
 895       public void actionPerformed(ActionEvent e)
 896       {
 897         ok_actionPerformed(e);
 898       }
 899     });
 900     JButton cancel = new JButton();
 901     cancel.setText(MessageManager.getString("action.cancel"));
 902     cancel.addActionListener(new ActionListener()
 903     {
 904       @Override
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         cancel_actionPerformed(e);
 908       }
 909     });
 910     JPanel okCancelPanel = new JPanel();
 911     okCancelPanel.add(ok);
 912     okCancelPanel.add(cancel);
 913     return okCancelPanel;
 914   }
 915
 916   /**
 917    * Initialises the Colours tabbed panel.
 918    *
 919    * @return
 920    */
 921   private JPanel initColoursTab()
 922   {
 923     JPanel coloursTab = new JPanel();
 924     coloursTab.setBorder(new TitledBorder(
 925             MessageManager.getString("action.open_new_alignment")));
 926     coloursTab.setLayout(new FlowLayout());
 927     JLabel mincolourLabel = new JLabel();
 928     mincolourLabel.setFont(LABEL_FONT);
 929     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 930     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 931     minColour.setFont(LABEL_FONT);
 932     minColour.setBorder(BorderFactory.createEtchedBorder());
 933     minColour.setPreferredSize(new Dimension(40, 20));
 934     minColour.addMouseListener(new MouseAdapter()
 935     {
 936       @Override
 937       public void mousePressed(MouseEvent e)
 938       {
 939         minColour_actionPerformed(minColour);
 940       }
 941     });
 942     JLabel maxcolourLabel = new JLabel();
 943     maxcolourLabel.setFont(LABEL_FONT);
 944     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 945     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 946     maxColour.setFont(LABEL_FONT);
 947     maxColour.setBorder(BorderFactory.createEtchedBorder());
 948     maxColour.setPreferredSize(new Dimension(40, 20));
 949     maxColour.addMouseListener(new MouseAdapter()
 950     {
 951       @Override
 952       public void mousePressed(MouseEvent e)
 953       {
 954         maxColour_actionPerformed(maxColour);
 955       }
 956     });
 957
 958     protColour.setFont(LABEL_FONT);
 959     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 960     JLabel protColourLabel = new JLabel();
 961     protColourLabel.setFont(LABEL_FONT);
 962     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 963     protColourLabel.setText(
 964             MessageManager.getString("label.prot_alignment_colour") + " ");
 965     JvSwingUtils.addtoLayout(coloursTab,
 966             MessageManager
 967                     .getString("label.default_colour_scheme_for_alignment"),
 968             protColourLabel, protColour);
 969
 970     nucColour.setFont(LABEL_FONT);
 971     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 972     JLabel nucColourLabel = new JLabel();
 973     nucColourLabel.setFont(LABEL_FONT);
 974     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 975     nucColourLabel.setText(
 976             MessageManager.getString("label.nuc_alignment_colour") + " ");
 977     JvSwingUtils.addtoLayout(coloursTab,
 978             MessageManager
 979                     .getString("label.default_colour_scheme_for_alignment"),
 980             nucColourLabel, nucColour);
 981
 982     JPanel annotationShding = new JPanel();
 983     annotationShding.setBorder(new TitledBorder(
 984             MessageManager.getString("label.annotation_shading_default")));
 985     annotationShding.setLayout(new GridLayout(1, 2));
 986     JvSwingUtils.addtoLayout(annotationShding,
 987             MessageManager.getString(
 988                     "label.default_minimum_colour_annotation_shading"),
 989             mincolourLabel, minColour);
 990     JvSwingUtils.addtoLayout(annotationShding,
 991             MessageManager.getString(
 992                     "label.default_maximum_colour_annotation_shading"),
 993             maxcolourLabel, maxColour);
 994     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 995     return coloursTab;
 996   }
 997
 998   /**
 999    * Initialises the Overview tabbed panel.
1000    *
1001    * @return
1002    */
1003   private JPanel initOverviewTab()
1004   {
1005     JPanel overviewPanel = new JPanel();
1006     overviewPanel.setBorder(new TitledBorder(
1007             MessageManager.getString("label.overview_settings")));
1008
1009     gapColour.setFont(LABEL_FONT);
1010     // fixing the border colours stops apparent colour bleed from the panel
1011     gapColour.setBorder(
1012             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1013     gapColour.setPreferredSize(new Dimension(40, 20));
1014     gapColour.addMouseListener(new MouseAdapter()
1015     {
1016       @Override
1017       public void mousePressed(MouseEvent e)
1018       {
1019         gapColour_actionPerformed(gapColour);
1020       }
1021     });
1022
1023     hiddenColour.setFont(LABEL_FONT);
1024     // fixing the border colours stops apparent colour bleed from the panel
1025     hiddenColour.setBorder(
1026             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1027     hiddenColour.setPreferredSize(new Dimension(40, 20));
1028     hiddenColour.addMouseListener(new MouseAdapter()
1029     {
1030       @Override
1031       public void mousePressed(MouseEvent e)
1032       {
1033         hiddenColour_actionPerformed(hiddenColour);
1034       }
1035     });
1036
1037     useLegacyGap = new JCheckBox(
1038             MessageManager.getString("label.ov_legacy_gap"));
1039     useLegacyGap.setFont(LABEL_FONT);
1040     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1041     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1042     gapLabel = new JLabel(
1043             MessageManager.getString("label.gap_colour"));
1044     gapLabel.setFont(LABEL_FONT);
1045     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1046     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1047     showHiddenAtStart = new JCheckBox(
1048             MessageManager.getString("label.ov_show_hide_default"));
1049     showHiddenAtStart.setFont(LABEL_FONT);
1050     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1051     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1052     JLabel hiddenLabel = new JLabel(
1053             MessageManager.getString("label.hidden_colour"));
1054     hiddenLabel.setFont(LABEL_FONT);
1055     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1056     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1057
1058     useLegacyGap.addActionListener(new ActionListener()
1059     {
1060       @Override
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         useLegacyGaps_actionPerformed(e);
1064       }
1065     });
1066
1067     overviewPanel.setLayout(new GridBagLayout());
1068     GridBagConstraints c1 = new GridBagConstraints();
1069
1070     c1.fill = GridBagConstraints.HORIZONTAL;
1071     c1.gridx = 0;
1072     c1.gridy = 0;
1073     c1.weightx = 1;
1074     c1.ipady = 20;
1075     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1076     overviewPanel.add(useLegacyGap, c1);
1077
1078     GridBagConstraints c2 = new GridBagConstraints();
1079     c2.fill = GridBagConstraints.HORIZONTAL;
1080     c2.gridx = 1;
1081     c2.gridy = 0;
1082     c2.insets = new Insets(0, 15, 0, 10);
1083     overviewPanel.add(gapLabel, c2);
1084
1085     GridBagConstraints c3 = new GridBagConstraints();
1086     c3.fill = GridBagConstraints.HORIZONTAL;
1087     c3.gridx = 2;
1088     c3.gridy = 0;
1089     c3.insets = new Insets(0, 0, 0, 15);
1090     overviewPanel.add(gapColour, c3);
1091
1092     GridBagConstraints c4 = new GridBagConstraints();
1093     c4.fill = GridBagConstraints.HORIZONTAL;
1094     c4.gridx = 0;
1095     c4.gridy = 1;
1096     c4.weightx = 1;
1097     overviewPanel.add(showHiddenAtStart, c4);
1098
1099     GridBagConstraints c5 = new GridBagConstraints();
1100     c5.fill = GridBagConstraints.HORIZONTAL;
1101     c5.gridx = 1;
1102     c5.gridy = 1;
1103     c5.insets = new Insets(0, 15, 0, 10);
1104     overviewPanel.add(hiddenLabel, c5);
1105
1106     GridBagConstraints c6 = new GridBagConstraints();
1107     c6.fill = GridBagConstraints.HORIZONTAL;
1108     c6.gridx = 2;
1109     c6.gridy = 1;
1110     c6.insets = new Insets(0, 0, 0, 15);
1111     overviewPanel.add(hiddenColour, c6);
1112
1113     JButton resetButton = new JButton(
1114             MessageManager.getString("label.reset_to_defaults"));
1115
1116     resetButton.addActionListener(new ActionListener()
1117     {
1118       @Override
1119       public void actionPerformed(ActionEvent e)
1120       {
1121         resetOvDefaults_actionPerformed(e);
1122       }
1123     });
1124
1125     GridBagConstraints c7 = new GridBagConstraints();
1126     c7.fill = GridBagConstraints.NONE;
1127     c7.gridx = 0;
1128     c7.gridy = 2;
1129     c7.insets = new Insets(10, 0, 0, 0);
1130     c7.anchor = GridBagConstraints.WEST;
1131     overviewPanel.add(resetButton, c7);
1132
1133     // Add padding so the panel doesn't look ridiculous
1134     JPanel spacePanel = new JPanel();
1135     overviewPanel.add(spacePanel,
1136             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1137                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1138                     new Insets(0, 0, 0, 5), 0, 0));
1139
1140     return overviewPanel;
1141   }
1142
1143   /**
1144    * Initialises the Structure tabbed panel.
1145    *
1146    * @return
1147    */
1148   private JPanel initStructureTab()
1149   {
1150     structureTab = new JPanel();
1151
1152     structureTab.setBorder(new TitledBorder(
1153             MessageManager.getString("label.structure_options")));
1154     structureTab.setLayout(null);
1155     final int width = 400;
1156     final int height = 22;
1157     final int lineSpacing = 25;
1158     int ypos = 15;
1159
1160     structFromPdb.setFont(LABEL_FONT);
1161     structFromPdb
1162             .setText(MessageManager.getString("label.struct_from_pdb"));
1163     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1164     structFromPdb.addActionListener(new ActionListener()
1165     {
1166       @Override
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         boolean selected = structFromPdb.isSelected();
1170         // enable other options only when the first is checked
1171         useRnaView.setEnabled(selected);
1172         addSecondaryStructure.setEnabled(selected);
1173         addTempFactor.setEnabled(selected);
1174       }
1175     });
1176     structureTab.add(structFromPdb);
1177
1178     // indent checkboxes that are conditional on the first one
1179     ypos += lineSpacing;
1180     useRnaView.setFont(LABEL_FONT);
1181     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1182     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1183     structureTab.add(useRnaView);
1184
1185     ypos += lineSpacing;
1186     addSecondaryStructure.setFont(LABEL_FONT);
1187     addSecondaryStructure
1188             .setText(MessageManager.getString("label.autoadd_secstr"));
1189     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1190     structureTab.add(addSecondaryStructure);
1191
1192     ypos += lineSpacing;
1193     addTempFactor.setFont(LABEL_FONT);
1194     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1195     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1196     structureTab.add(addTempFactor);
1197
1198     ypos += lineSpacing;
1199     JLabel viewerLabel = new JLabel();
1200     viewerLabel.setFont(LABEL_FONT);
1201     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1202     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1203     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1204     structureTab.add(viewerLabel);
1205
1206     structViewer.setFont(LABEL_FONT);
1207     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1208     structViewer.addItem(ViewerType.JMOL.name());
1209     structViewer.addItem(ViewerType.CHIMERA.name());
1210     structViewer.addActionListener(new ActionListener()
1211     {
1212       @Override
1213       public void actionPerformed(ActionEvent e)
1214       {
1215         structureViewer_actionPerformed(
1216                 (String) structViewer.getSelectedItem());
1217       }
1218     });
1219     structureTab.add(structViewer);
1220
1221     ypos += lineSpacing;
1222     JLabel pathLabel = new JLabel();
1223     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1224     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1225     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1226     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1227     structureTab.add(pathLabel);
1228
1229     chimeraPath.setFont(LABEL_FONT);
1230     chimeraPath.setText("");
1231     final String tooltip = JvSwingUtils.wrapTooltip(true,
1232             MessageManager.getString("label.chimera_path_tip"));
1233     chimeraPath.setToolTipText(tooltip);
1234     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1235     chimeraPath.addMouseListener(new MouseAdapter()
1236     {
1237       @Override
1238       public void mouseClicked(MouseEvent e)
1239       {
1240         if (e.getClickCount() == 2)
1241         {
1242           String chosen = openFileChooser();
1243           if (chosen != null)
1244           {
1245             chimeraPath.setText(chosen);
1246           }
1247         }
1248       }
1249     });
1250     structureTab.add(chimeraPath);
1251
1252     ypos += lineSpacing;
1253     nwMapping.setFont(LABEL_FONT);
1254     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1255     siftsMapping.setFont(LABEL_FONT);
1256     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1257     mappingMethod.add(nwMapping);
1258     mappingMethod.add(siftsMapping);
1259     JPanel mappingPanel = new JPanel();
1260     mappingPanel.setFont(LABEL_FONT);
1261     TitledBorder mmTitledBorder = new TitledBorder(
1262             MessageManager.getString("label.mapping_method"));
1263     mmTitledBorder.setTitleFont(LABEL_FONT);
1264     mappingPanel.setBorder(mmTitledBorder);
1265     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1266     // GridLayout mappingLayout = new GridLayout();
1267     mappingPanel.setLayout(new GridLayout());
1268     mappingPanel.add(nwMapping);
1269     mappingPanel.add(siftsMapping);
1270     structureTab.add(mappingPanel);
1271
1272     ypos += lineSpacing;
1273     ypos += lineSpacing;
1274     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1275             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1276     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1277     structureTab.add(docFieldPref);
1278
1279     return structureTab;
1280   }
1281
1282   /**
1283    * Action on choosing a structure viewer from combobox options.
1284    *
1285    * @param selectedItem
1286    */
1287   protected void structureViewer_actionPerformed(String selectedItem)
1288   {
1289   }
1290
1291   /**
1292    * Show a dialog for the user to choose a file. Returns the chosen path, or
1293    * null on Cancel.
1294    *
1295    * @return
1296    */
1297   protected String openFileChooser()
1298   {
1299     String choice = null;
1300     JFileChooser chooser = new JFileChooser();
1301
1302     // chooser.setFileView(new JalviewFileView());
1303     chooser.setDialogTitle(
1304             MessageManager.getString("label.open_local_file"));
1305     chooser.setToolTipText(MessageManager.getString("action.open"));
1306
1307     int value = chooser.showOpenDialog(this);
1308
1309     if (value == JFileChooser.APPROVE_OPTION)
1310     {
1311       choice = chooser.getSelectedFile().getPath();
1312     }
1313     return choice;
1314   }
1315
1316   /**
1317    * Validate the structure tab preferences; if invalid, set focus on this tab.
1318    *
1319    * @param e
1320    */
1321   protected boolean validateStructure(FocusEvent e)
1322   {
1323     if (!validateStructure())
1324     {
1325       e.getComponent().requestFocusInWindow();
1326       return false;
1327     }
1328     return true;
1329   }
1330
1331   protected boolean validateStructure()
1332   {
1333     return false;
1334   }
1335
1336   /**
1337    * Initialises the Visual tabbed panel.
1338    *
1339    * @return
1340    */
1341   private JPanel initVisualTab()
1342   {
1343     JPanel visualTab = new JPanel();
1344     visualTab.setBorder(new TitledBorder(
1345             MessageManager.getString("action.open_new_alignment")));
1346     visualTab.setLayout(null);
1347     fullScreen.setFont(LABEL_FONT);
1348     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1349     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1350     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1351     quality.setEnabled(false);
1352     quality.setFont(LABEL_FONT);
1353     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1354     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1355     quality.setSelected(true);
1356     quality.setText(MessageManager.getString("label.quality"));
1357     conservation.setEnabled(false);
1358     conservation.setFont(LABEL_FONT);
1359     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1360     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1361     conservation.setSelected(true);
1362     conservation.setText(MessageManager.getString("label.conservation"));
1363     identity.setEnabled(false);
1364     identity.setFont(LABEL_FONT);
1365     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1366     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1367     identity.setSelected(true);
1368     identity.setText(MessageManager.getString("label.consensus"));
1369     showOccupancy.setFont(LABEL_FONT);
1370     showOccupancy.setEnabled(false);
1371     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1372     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1373     showOccupancy.setSelected(true);
1374     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1375
1376     JLabel showGroupbits = new JLabel();
1377     showGroupbits.setFont(LABEL_FONT);
1378     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1379     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1380     showGroupbits
1381             .setText(MessageManager.getString("action.show_group") + ":");
1382     JLabel showConsensbits = new JLabel();
1383     showConsensbits.setFont(LABEL_FONT);
1384     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1385     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1386     showConsensbits
1387             .setText(MessageManager.getString("label.consensus") + ":");
1388     showConsensHistogram.setEnabled(false);
1389     showConsensHistogram.setFont(LABEL_FONT);
1390     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1391     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1392     showConsensHistogram.setSelected(true);
1393     showConsensHistogram
1394             .setText(MessageManager.getString("label.histogram"));
1395     showConsensLogo.setEnabled(false);
1396     showConsensLogo.setFont(LABEL_FONT);
1397     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1398     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1399     showConsensLogo.setSelected(true);
1400     showConsensLogo.setText(MessageManager.getString("label.logo"));
1401     showGroupConsensus.setEnabled(false);
1402     showGroupConsensus.setFont(LABEL_FONT);
1403     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1404     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1405     showGroupConsensus.setSelected(true);
1406     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1407     showGroupConservation.setEnabled(false);
1408     showGroupConservation.setFont(LABEL_FONT);
1409     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1410     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1411     showGroupConservation.setSelected(true);
1412     showGroupConservation
1413             .setText(MessageManager.getString("label.conservation"));
1414     showNpTooltip.setEnabled(true);
1415     showNpTooltip.setFont(LABEL_FONT);
1416     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1417     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1418     showNpTooltip.setSelected(true);
1419     showNpTooltip.setText(
1420             MessageManager.getString("label.non_positional_features"));
1421     showDbRefTooltip.setEnabled(true);
1422     showDbRefTooltip.setFont(LABEL_FONT);
1423     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1424     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1425     showDbRefTooltip.setSelected(true);
1426     showDbRefTooltip
1427             .setText(MessageManager.getString("label.database_references"));
1428     annotations.setFont(LABEL_FONT);
1429     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1430     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1431     annotations.setSelected(true);
1432     annotations.setText(MessageManager.getString("label.show_annotations"));
1433     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1434     annotations.addActionListener(new ActionListener()
1435     {
1436       @Override
1437       public void actionPerformed(ActionEvent e)
1438       {
1439         annotations_actionPerformed(e);
1440       }
1441     });
1442     identity.addActionListener(new ActionListener()
1443     {
1444       @Override
1445       public void actionPerformed(ActionEvent e)
1446       {
1447         annotations_actionPerformed(e);
1448       }
1449     });
1450     showGroupConsensus.addActionListener(new ActionListener()
1451     {
1452       @Override
1453       public void actionPerformed(ActionEvent e)
1454       {
1455         annotations_actionPerformed(e);
1456       }
1457     });
1458     showUnconserved.setFont(LABEL_FONT);
1459     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1460     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1461     showUnconserved.setSelected(true);
1462     showUnconserved
1463             .setText(MessageManager.getString("action.show_unconserved"));
1464     showUnconserved.addActionListener(new ActionListener()
1465     {
1466       @Override
1467       public void actionPerformed(ActionEvent e)
1468       {
1469         showunconserved_actionPerformed(e);
1470       }
1471     });
1472
1473     // TODO these are not yet added to / action from Preferences
1474     // JCheckBox shareSelections = new JCheckBox();
1475     // shareSelections.setFont(verdana11);
1476     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1477     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1478     // shareSelections.setSelected(true);
1479     // shareSelections.setText(MessageManager
1480     // .getString("label.share_selection_across_views"));
1481     // JCheckBox followHighlight = new JCheckBox();
1482     // followHighlight.setFont(verdana11);
1483     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1484     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1485     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1486     // followHighlight.setSelected(true);
1487     // followHighlight.setText(MessageManager
1488     // .getString("label.scroll_highlighted_regions"));
1489
1490     seqLimit.setFont(LABEL_FONT);
1491     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1492     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1493     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1494     smoothFont.setFont(LABEL_FONT);
1495     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1496     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1497     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1498     scaleProteinToCdna.setFont(LABEL_FONT);
1499     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1500     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1501     scaleProteinToCdna.setText(
1502             MessageManager.getString("label.scale_protein_to_cdna"));
1503     scaleProteinToCdna.setToolTipText(
1504             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1505     JLabel gapLabel = new JLabel();
1506     gapLabel.setFont(LABEL_FONT);
1507     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1508     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1509     JLabel fontLabel = new JLabel();
1510     fontLabel.setFont(LABEL_FONT);
1511     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1512     fontLabel.setText(MessageManager.getString("label.font"));
1513     fontSizeCB.setFont(LABEL_FONT);
1514     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1515     fontStyleCB.setFont(LABEL_FONT);
1516     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1517     fontNameCB.setFont(LABEL_FONT);
1518     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1519     gapSymbolCB.setFont(LABEL_FONT);
1520     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1521     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1522     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1523     gapSymbolCB.setRenderer(dlcr);
1524
1525     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1526     startupCheckbox.setFont(LABEL_FONT);
1527     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1528     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1529     startupCheckbox.setSelected(true);
1530     startupFileTextfield.setFont(LABEL_FONT);
1531     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1532     final String tooltip = JvSwingUtils.wrapTooltip(true,
1533             MessageManager.getString("label.double_click_to_browse"));
1534     startupFileTextfield.setToolTipText(tooltip);
1535     startupFileTextfield.addMouseListener(new MouseAdapter()
1536     {
1537       @Override
1538       public void mouseClicked(MouseEvent e)
1539       {
1540         if (e.getClickCount() > 1)
1541         {
1542           startupFileTextfield_mouseClicked();
1543         }
1544       }
1545     });
1546
1547     sortby.setFont(LABEL_FONT);
1548     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1549     JLabel sortLabel = new JLabel();
1550     sortLabel.setFont(LABEL_FONT);
1551     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1552     sortLabel.setText(MessageManager.getString("label.sort_by"));
1553     sortAnnBy.setFont(LABEL_FONT);
1554     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1555     JLabel sortAnnLabel = new JLabel();
1556     sortAnnLabel.setFont(LABEL_FONT);
1557     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1558     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1559     sortAutocalc.setFont(LABEL_FONT);
1560     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1561
1562     JPanel annsettingsPanel = new JPanel();
1563     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1564     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1565     annsettingsPanel.setBorder(new EtchedBorder());
1566     visualTab.add(annsettingsPanel);
1567     Border jb = new EmptyBorder(1, 1, 4, 5);
1568     annotations.setBorder(jb);
1569     showOccupancy.setBorder(jb);
1570     quality.setBorder(jb);
1571     conservation.setBorder(jb);
1572     identity.setBorder(jb);
1573     showConsensbits.setBorder(jb);
1574     showGroupbits.setBorder(jb);
1575     showGroupConsensus.setBorder(jb);
1576     showGroupConservation.setBorder(jb);
1577     showConsensHistogram.setBorder(jb);
1578     showConsensLogo.setBorder(jb);
1579
1580     JPanel autoAnnotSettings = new JPanel();
1581     annsettingsPanel.add(autoAnnotSettings);
1582     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1583     autoAnnotSettings.add(annotations);
1584     autoAnnotSettings.add(quality);
1585     // second row of autoannotation box
1586     autoAnnotSettings = new JPanel();
1587     annsettingsPanel.add(autoAnnotSettings);
1588
1589     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1590     autoAnnotSettings.add(conservation);
1591     autoAnnotSettings.add(identity);
1592     autoAnnotSettings.add(showOccupancy);
1593     autoAnnotSettings.add(showGroupbits);
1594     autoAnnotSettings.add(showGroupConservation);
1595     autoAnnotSettings.add(showGroupConsensus);
1596     autoAnnotSettings.add(showConsensbits);
1597     autoAnnotSettings.add(showConsensHistogram);
1598     autoAnnotSettings.add(showConsensLogo);
1599
1600     JPanel tooltipSettings = new JPanel();
1601     tooltipSettings.setBorder(new TitledBorder(
1602             MessageManager.getString("label.sequence_id_tooltip")));
1603     tooltipSettings.setBounds(173, 140, 220, 62);
1604     tooltipSettings.setLayout(new GridLayout(2, 1));
1605     tooltipSettings.add(showDbRefTooltip);
1606     tooltipSettings.add(showNpTooltip);
1607     visualTab.add(tooltipSettings);
1608
1609     wrap.setFont(LABEL_FONT);
1610     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1611     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1612     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1613     rightAlign.setFont(LABEL_FONT);
1614     rightAlign.setForeground(Color.black);
1615     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1616     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1617     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1618     idItalics.setFont(LABEL_FONT_ITALIC);
1619     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1620     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1621     idItalics.setText(
1622             MessageManager.getString("label.sequence_name_italics"));
1623     openoverv.setFont(LABEL_FONT);
1624     openoverv.setActionCommand(
1625             MessageManager.getString("label.open_overview"));
1626     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1627     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1628     openoverv.setText(MessageManager.getString("label.open_overview"));
1629     JPanel jPanel2 = new JPanel();
1630     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1631     jPanel2.setLayout(new GridLayout(14, 1));
1632     jPanel2.add(fullScreen);
1633     jPanel2.add(openoverv);
1634     jPanel2.add(seqLimit);
1635     jPanel2.add(rightAlign);
1636     jPanel2.add(fontLabel);
1637     jPanel2.add(showUnconserved);
1638     jPanel2.add(idItalics);
1639     jPanel2.add(smoothFont);
1640     jPanel2.add(scaleProteinToCdna);
1641     jPanel2.add(gapLabel);
1642     jPanel2.add(wrap);
1643     jPanel2.add(sortLabel);
1644     jPanel2.add(sortAnnLabel);
1645     jPanel2.add(startupCheckbox);
1646     visualTab.add(jPanel2);
1647     visualTab.add(startupFileTextfield);
1648     visualTab.add(sortby);
1649     visualTab.add(sortAnnBy);
1650     visualTab.add(sortAutocalc);
1651     visualTab.add(gapSymbolCB);
1652     visualTab.add(fontNameCB);
1653     visualTab.add(fontSizeCB);
1654     visualTab.add(fontStyleCB);
1655     return visualTab;
1656   }
1657
1658   protected void autoIdWidth_actionPerformed()
1659   {
1660     // TODO Auto-generated method stub
1661
1662   }
1663
1664   protected void userIdWidth_actionPerformed()
1665   {
1666     // TODO Auto-generated method stub
1667
1668   }
1669
1670   protected void maxColour_actionPerformed(JPanel panel)
1671   {
1672   }
1673
1674   protected void minColour_actionPerformed(JPanel panel)
1675   {
1676   }
1677
1678   protected void gapColour_actionPerformed(JPanel panel)
1679   {
1680   }
1681
1682   protected void hiddenColour_actionPerformed(JPanel panel)
1683   {
1684   }
1685
1686   protected void showunconserved_actionPerformed(ActionEvent e)
1687   {
1688     // TODO Auto-generated method stub
1689
1690   }
1691
1692   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1693   {
1694   }
1695
1696   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1697   {
1698   }
1699
1700   /**
1701    * DOCUMENT ME!
1702    *
1703    * @param e
1704    *          DOCUMENT ME!
1705    */
1706   public void ok_actionPerformed(ActionEvent e)
1707   {
1708   }
1709
1710   /**
1711    * DOCUMENT ME!
1712    *
1713    * @param e
1714    *          DOCUMENT ME!
1715    */
1716   public void cancel_actionPerformed(ActionEvent e)
1717   {
1718   }
1719
1720   /**
1721    * DOCUMENT ME!
1722    *
1723    * @param e
1724    *          DOCUMENT ME!
1725    */
1726   public void annotations_actionPerformed(ActionEvent e)
1727   {
1728   }
1729
1730   /**
1731    * DOCUMENT ME!
1732    */
1733   public void startupFileTextfield_mouseClicked()
1734   {
1735   }
1736
1737   public void newLink_actionPerformed(ActionEvent e)
1738   {
1739
1740   }
1741
1742   public void editLink_actionPerformed(ActionEvent e)
1743   {
1744
1745   }
1746
1747   public void deleteLink_actionPerformed(ActionEvent e)
1748   {
1749
1750   }
1751
1752   public void defaultBrowser_mouseClicked(MouseEvent e)
1753   {
1754
1755   }
1756
1757   public void linkURLList_keyTyped(KeyEvent e)
1758   {
1759
1760   }
1761
1762   public void useProxy_actionPerformed()
1763   {
1764     boolean enabled = useProxy.isSelected();
1765     portLabel.setEnabled(enabled);
1766     serverLabel.setEnabled(enabled);
1767     proxyServerTB.setEnabled(enabled);
1768     proxyPortTB.setEnabled(enabled);
1769   }
1770
1771   /**
1772    * Customer renderer for JTable: supports column of radio buttons
1773    */
1774   public class RadioButtonRenderer extends JRadioButton
1775           implements TableCellRenderer
1776   {
1777     public RadioButtonRenderer()
1778     {
1779       setHorizontalAlignment(CENTER);
1780       setToolTipText(MessageManager.getString("label.urltooltip"));
1781     }
1782
1783     @Override
1784     public Component getTableCellRendererComponent(JTable table,
1785             Object value, boolean isSelected, boolean hasFocus, int row,
1786             int column)
1787     {
1788       setSelected((boolean) value);
1789
1790       // set colours to match rest of table
1791       if (isSelected)
1792       {
1793         setBackground(table.getSelectionBackground());
1794         setForeground(table.getSelectionForeground());
1795       }
1796       else
1797       {
1798         setBackground(table.getBackground());
1799         setForeground(table.getForeground());
1800       }
1801       return this;
1802     }
1803   }
1804
1805   /**
1806    * Customer cell editor for JTable: supports column of radio buttons in
1807    * conjunction with renderer
1808    */
1809   public class RadioButtonEditor extends AbstractCellEditor
1810           implements TableCellEditor
1811   {
1812     private JRadioButton button = new JRadioButton();
1813
1814     public RadioButtonEditor()
1815     {
1816       button.setHorizontalAlignment(SwingConstants.CENTER);
1817       this.button.addActionListener(new ActionListener()
1818       {
1819         @Override
1820         public void actionPerformed(ActionEvent e)
1821         {
1822           fireEditingStopped();
1823         }
1824       });
1825     }
1826
1827     @Override
1828     public Component getTableCellEditorComponent(JTable table, Object value,
1829             boolean isSelected, int row, int column)
1830     {
1831       button.setSelected((boolean) value);
1832       return button;
1833     }
1834
1835     @Override
1836     public Object getCellEditorValue()
1837     {
1838       return button.isSelected();
1839     }
1840
1841   }
1842 }