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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.FlowLayout;
  28 import java.awt.Font;
  29 import java.awt.GridBagConstraints;
  30 import java.awt.GridBagLayout;
  31 import java.awt.GridLayout;
  32 import java.awt.Insets;
  33 import java.awt.Rectangle;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.FocusEvent;
  37 import java.awt.event.KeyEvent;
  38 import java.awt.event.KeyListener;
  39 import java.awt.event.MouseAdapter;
  40 import java.awt.event.MouseEvent;
  41 import java.util.Arrays;
  42 import java.util.List;
  43
  44 import javax.swing.AbstractCellEditor;
  45 import javax.swing.BorderFactory;
  46 import javax.swing.ButtonGroup;
  47 import javax.swing.DefaultListCellRenderer;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JLabel;
  53 import javax.swing.JPanel;
  54 import javax.swing.JPasswordField;
  55 import javax.swing.JRadioButton;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSpinner;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.JTable;
  60 import javax.swing.JTextArea;
  61 import javax.swing.JTextField;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.SpinnerModel;
  64 import javax.swing.SpinnerNumberModel;
  65 import javax.swing.SwingConstants;
  66 import javax.swing.border.Border;
  67 import javax.swing.border.EmptyBorder;
  68 import javax.swing.border.EtchedBorder;
  69 import javax.swing.border.TitledBorder;
  70 import javax.swing.event.ChangeEvent;
  71 import javax.swing.event.ChangeListener;
  72 import javax.swing.event.DocumentEvent;
  73 import javax.swing.event.DocumentListener;
  74 import javax.swing.table.TableCellEditor;
  75 import javax.swing.table.TableCellRenderer;
  76
  77 import jalview.bin.Cache;
  78 import jalview.fts.core.FTSDataColumnPreferences;
  79 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  80 import jalview.fts.service.pdb.PDBFTSRestClient;
  81 import jalview.gui.Desktop;
  82 import jalview.gui.JalviewBooleanRadioButtons;
  83 import jalview.gui.JvOptionPane;
  84 import jalview.gui.JvSwingUtils;
  85 import jalview.gui.StructureViewer.ViewerType;
  86 import jalview.io.BackupFilenameParts;
  87 import jalview.io.BackupFiles;
  88 import jalview.io.BackupFilesPresetEntry;
  89 import jalview.io.IntKeyStringValueEntry;
  90 import jalview.util.MessageManager;
  91 import jalview.util.Platform;
  92
  93 /**
  94  * Base class for the Preferences panel.
  95  *
  96  * @author $author$
  97  * @version $Revision$
  98  */
  99 public class GPreferences extends JPanel
 100 {
 101   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
 102
 103   private static final Font LABEL_FONT_ITALIC = JvSwingUtils
 104           .getLabelFont(false, true);
 105
 106   private static final Font LABEL_FONT_BOLD = JvSwingUtils
 107           .getLabelFont(true, false);
 108
 109   /*
 110    * Visual tab components
 111    */
 112   protected JCheckBox fullScreen = new JCheckBox();
 113
 114   protected JCheckBox openoverv = new JCheckBox();
 115
 116   protected JCheckBox seqLimit = new JCheckBox();
 117
 118   protected JCheckBox rightAlign = new JCheckBox();
 119
 120   protected JComboBox<String> fontSizeCB = new JComboBox<>();
 121
 122   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 123
 124   protected JComboBox<String> fontNameCB = new JComboBox<>();
 125
 126   protected JCheckBox showOccupancy = new JCheckBox();
 127
 128   protected JCheckBox showUnconserved = new JCheckBox();
 129
 130   protected JCheckBox idItalics = new JCheckBox();
 131
 132   protected JCheckBox smoothFont = new JCheckBox();
 133
 134   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 135
 136   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 137
 138   protected JCheckBox wrap = new JCheckBox();
 139
 140   protected JComboBox<String> sortby = new JComboBox<>();
 141
 142   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 143
 144   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 145
 146   protected JCheckBox startupCheckbox = new JCheckBox();
 147
 148   protected JTextField startupFileTextfield = new JTextField();
 149
 150   // below are in the 'second column'
 151   protected JCheckBox annotations = new JCheckBox();
 152
 153   protected JCheckBox quality = new JCheckBox();
 154
 155   protected JCheckBox conservation = new JCheckBox();
 156
 157   protected JCheckBox identity = new JCheckBox();
 158
 159   protected JCheckBox showGroupConsensus = new JCheckBox();
 160
 161   protected JCheckBox showGroupConservation = new JCheckBox();
 162
 163   protected JCheckBox showConsensHistogram = new JCheckBox();
 164
 165   protected JCheckBox showConsensLogo = new JCheckBox();
 166
 167   protected JCheckBox showDbRefTooltip = new JCheckBox();
 168
 169   protected JCheckBox showNpTooltip = new JCheckBox();
 170
 171   /*
 172    * Structure tab and components
 173    */
 174   protected JPanel structureTab;
 175
 176   protected JCheckBox structFromPdb = new JCheckBox();
 177
 178   protected JCheckBox useRnaView = new JCheckBox();
 179
 180   protected JCheckBox addSecondaryStructure = new JCheckBox();
 181
 182   protected JCheckBox addTempFactor = new JCheckBox();
 183
 184   protected JComboBox<String> structViewer = new JComboBox<>();
 185
 186   protected JLabel structureViewerPathLabel;
 187
 188   protected JTextField structureViewerPath = new JTextField();
 189
 190   protected ButtonGroup mappingMethod = new ButtonGroup();
 191
 192   protected JRadioButton siftsMapping = new JRadioButton();
 193
 194   protected JRadioButton nwMapping = new JRadioButton();
 195
 196   /*
 197    * Colours tab components
 198    */
 199   protected JPanel minColour = new JPanel();
 200
 201   protected JPanel maxColour = new JPanel();
 202
 203   protected JComboBox<String> protColour = new JComboBox<>();
 204
 205   protected JComboBox<String> nucColour = new JComboBox<>();
 206
 207   /*
 208    * Overview tab components
 209    */
 210   protected JPanel gapColour = new JPanel();
 211
 212   protected JPanel hiddenColour = new JPanel();
 213
 214   protected JCheckBox useLegacyGap;
 215
 216   protected JCheckBox showHiddenAtStart;
 217
 218   protected JLabel gapLabel;
 219
 220   /*
 221    * Connections tab components
 222    */
 223   protected JPanel connectTab;
 224
 225   protected JTable linkUrlTable = new JTable();
 226
 227   protected JButton editLink = new JButton();
 228
 229   protected JButton deleteLink = new JButton();
 230
 231   protected JTextField filterTB = new JTextField();
 232
 233   protected JButton doReset = new JButton();
 234
 235   protected JButton userOnly = new JButton();
 236
 237   protected JLabel httpLabel = new JLabel();
 238
 239   protected JLabel httpsLabel = new JLabel();
 240
 241   protected JLabel portLabel = new JLabel();
 242
 243   protected JLabel serverLabel = new JLabel();
 244
 245   protected JLabel portLabel2 = new JLabel();
 246
 247   protected JLabel serverLabel2 = new JLabel();
 248
 249   protected JLabel proxyAuthUsernameLabel = new JLabel();
 250
 251   protected JLabel proxyAuthPasswordLabel = new JLabel();
 252
 253   protected JLabel passwordNotStoredLabel = new JLabel();
 254
 255   protected JTextField proxyServerHttpTB = new JTextField();
 256
 257   protected JTextField proxyPortHttpTB = new JTextField();
 258
 259   protected JTextField proxyServerHttpsTB = new JTextField();
 260
 261   protected JTextField proxyPortHttpsTB = new JTextField();
 262
 263   protected JCheckBox proxyAuth = new JCheckBox();
 264
 265   protected JTextField proxyAuthUsernameTB = new JTextField();
 266
 267   protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
 268
 269   protected JTextField defaultBrowser = new JTextField();
 270
 271   protected ButtonGroup proxyType = new ButtonGroup();
 272
 273   protected JRadioButton noProxy = new JRadioButton();
 274
 275   protected JRadioButton systemProxy = new JRadioButton();
 276
 277   protected JRadioButton customProxy = new JRadioButton();
 278
 279   protected JButton applyProxyButton = new JButton();
 280
 281   protected JCheckBox usagestats = new JCheckBox();
 282
 283   protected JCheckBox questionnaire = new JCheckBox();
 284
 285   protected JCheckBox versioncheck = new JCheckBox();
 286
 287   /*
 288    * Output tab components
 289    */
 290   protected JComboBox<Object> epsRendering = new JComboBox<>();
 291
 292   protected JComboBox<Object> htmlRendering = new JComboBox<>();
 293
 294   protected JComboBox<Object> svgRendering = new JComboBox<>();
 295
 296   protected JLabel userIdWidthlabel = new JLabel();
 297
 298   protected JCheckBox autoIdWidth = new JCheckBox();
 299
 300   protected JTextField userIdWidth = new JTextField();
 301
 302   protected JCheckBox blcjv = new JCheckBox();
 303
 304   protected JCheckBox pileupjv = new JCheckBox();
 305
 306   protected JCheckBox clustaljv = new JCheckBox();
 307
 308   protected JCheckBox msfjv = new JCheckBox();
 309
 310   protected JCheckBox fastajv = new JCheckBox();
 311
 312   protected JCheckBox pfamjv = new JCheckBox();
 313
 314   protected JCheckBox pirjv = new JCheckBox();
 315
 316   protected JCheckBox modellerOutput = new JCheckBox();
 317
 318   protected JCheckBox embbedBioJSON = new JCheckBox();
 319
 320   /*
 321    * Editing tab components
 322    */
 323   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 324
 325   protected JCheckBox padGaps = new JCheckBox();
 326
 327   protected JCheckBox sortByTree = new JCheckBox();
 328
 329   /*
 330    * Web Services tab
 331    */
 332   protected JPanel wsTab = new JPanel();
 333
 334   /*
 335    * Backups tab components
 336    * a lot of these are member variables instead of local variables only so that they
 337    * can be enabled/disabled easily in one go
 338    */
 339
 340   protected JCheckBox enableBackupFiles = new JCheckBox();
 341
 342   protected JPanel presetsPanel = new JPanel();
 343
 344   protected JLabel presetsComboLabel = new JLabel();
 345
 346   protected JCheckBox customiseCheckbox = new JCheckBox();
 347
 348   protected JButton revertButton = new JButton();
 349
 350   protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 351
 352   private int backupfilesPresetsComboLastSelected = 0;
 353
 354   protected JPanel suffixPanel = new JPanel();
 355
 356   protected JPanel keepfilesPanel = new JPanel();
 357
 358   protected JPanel exampleFilesPanel = new JPanel();
 359
 360   protected JTextField suffixTemplate = new JTextField(null, 8);
 361
 362   protected JLabel suffixTemplateLabel = new JLabel();
 363
 364   protected JLabel suffixDigitsLabel = new JLabel();
 365
 366   protected JSpinner suffixDigitsSpinner = new JSpinner();
 367
 368   protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
 369
 370   protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
 371
 372   public JSpinner backupfilesRollMaxSpinner = new JSpinner();
 373
 374   protected JLabel oldBackupFilesLabel = new JLabel();
 375
 376   protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
 377
 378   protected JTextArea backupfilesExampleLabel = new JTextArea();
 379
 380   private final JTabbedPane tabbedPane = new JTabbedPane();
 381
 382   private JLabel messageLabel = new JLabel("", JLabel.CENTER);
 383
 384   /**
 385    * Creates a new GPreferences object.
 386    */
 387   public GPreferences()
 388   {
 389     try
 390     {
 391       jbInit();
 392     } catch (Exception ex)
 393     {
 394       ex.printStackTrace();
 395     }
 396   }
 397
 398   /**
 399    * Construct the panel and its tabbed sub-panels.
 400    *
 401    * @throws Exception
 402    */
 403   private void jbInit() throws Exception
 404   {
 405     // final JTabbedPane tabbedPane = new JTabbedPane();
 406     this.setLayout(new BorderLayout());
 407
 408     // message label at top
 409     this.add(messageLabel, BorderLayout.NORTH);
 410
 411     JPanel okCancelPanel = initOkCancelPanel();
 412     this.add(tabbedPane, BorderLayout.CENTER);
 413     this.add(okCancelPanel, BorderLayout.SOUTH);
 414
 415     tabbedPane.add(initVisualTab(),
 416             MessageManager.getString("label.visual"));
 417
 418     tabbedPane.add(initColoursTab(),
 419             MessageManager.getString("label.colours"));
 420
 421     tabbedPane.add(initOverviewTab(),
 422             MessageManager.getString("label.overview"));
 423
 424     tabbedPane.add(initStructureTab(),
 425             MessageManager.getString("label.structure"));
 426
 427     tabbedPane.add(initConnectionsTab(),
 428             MessageManager.getString("label.connections"));
 429
 430         if (!Platform.isJS())
 431         {
 432           tabbedPane.add(initBackupsTab(),
 433                         MessageManager.getString("label.backups"));
 434         }
 435
 436     tabbedPane.add(initLinksTab(),
 437             MessageManager.getString("label.urllinks"));
 438
 439     tabbedPane.add(initOutputTab(),
 440             MessageManager.getString("label.output"));
 441
 442     tabbedPane.add(initEditingTab(),
 443             MessageManager.getString("label.editing"));
 444
 445     /*
 446      * See WsPreferences for the real work of configuring this tab.
 447      */
 448     if (!Platform.isJS())
 449     {
 450       wsTab.setLayout(new BorderLayout());
 451       tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 452     }
 453
 454     /*
 455      * Handler to validate a tab before leaving it - currently only for
 456      * Structure.
 457      * Adding a clearMessage() so messages are cleared when changing tabs.
 458      */
 459     tabbedPane.addChangeListener(new ChangeListener()
 460     {
 461       private Component lastTab;
 462
 463       @Override
 464       public void stateChanged(ChangeEvent e)
 465       {
 466         if (lastTab == structureTab
 467                 && tabbedPane.getSelectedComponent() != structureTab)
 468         {
 469           if (!validateStructure())
 470           {
 471             tabbedPane.setSelectedComponent(structureTab);
 472             return;
 473           }
 474         }
 475         lastTab = tabbedPane.getSelectedComponent();
 476
 477         clearMessage();
 478       }
 479
 480     });
 481   }
 482
 483   public void setMessage(String message)
 484   {
 485     if (message != null)
 486     {
 487       messageLabel.setText(message);
 488       messageLabel.setFont(LABEL_FONT_BOLD);
 489       messageLabel.setForeground(Color.RED.darker());
 490       messageLabel.revalidate();
 491       messageLabel.repaint();
 492     }
 493     // note message not cleared if message is null. call clearMessage()
 494     // directly.
 495     this.revalidate();
 496     this.repaint();
 497   }
 498
 499   public void clearMessage()
 500   {
 501     // only repaint if message exists
 502     if (messageLabel.getText() != null
 503             && messageLabel.getText().length() > 0)
 504     {
 505       messageLabel.setText("");
 506       messageLabel.revalidate();
 507       messageLabel.repaint();
 508       this.revalidate();
 509       this.repaint();
 510     }
 511   }
 512
 513   public final static int CONNECTIONS_TAB = 5;
 514
 515   public void selectTab(int selectTab)
 516   {
 517     // select a given tab - currently only for Connections
 518     switch (selectTab)
 519     {
 520     case CONNECTIONS_TAB:
 521       tabbedPane.setSelectedComponent(connectTab);
 522       break;
 523     default:
 524     }
 525   }
 526
 527   /**
 528    * Initialises the Editing tabbed panel.
 529    *
 530    * @return
 531    */
 532   private JPanel initEditingTab()
 533   {
 534     JPanel editingTab = new JPanel();
 535     editingTab.setLayout(null);
 536     autoCalculateConsCheck.setFont(LABEL_FONT);
 537     autoCalculateConsCheck.setText(
 538             MessageManager.getString("label.autocalculate_consensus"));
 539     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 540     padGaps.setFont(LABEL_FONT);
 541     padGaps.setText(
 542             MessageManager.getString("label.pad_gaps_when_editing"));
 543     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 544     sortByTree.setFont(LABEL_FONT);
 545     sortByTree
 546             .setText(MessageManager.getString("label.sort_with_new_tree"));
 547     sortByTree.setToolTipText(MessageManager.getString(
 548             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 549     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 550     editingTab.add(autoCalculateConsCheck);
 551     editingTab.add(padGaps);
 552     editingTab.add(sortByTree);
 553     return editingTab;
 554   }
 555
 556   /**
 557    * Initialises the Output tab
 558    *
 559    * @return
 560    */
 561   private JPanel initOutputTab()
 562   {
 563     JPanel outputTab = new JPanel();
 564     outputTab.setLayout(null);
 565
 566     JLabel epsLabel = new JLabel(
 567             MessageManager.formatMessage("label.rendering_style", "EPS"));
 568     epsLabel.setFont(LABEL_FONT);
 569     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 570     epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
 571     epsRendering.setFont(LABEL_FONT);
 572     epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
 573     JLabel htmlLabel = new JLabel(
 574             MessageManager.formatMessage("label.rendering_style", "HTML"));
 575     htmlLabel.setFont(LABEL_FONT);
 576     htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 577     htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
 578     htmlRendering.setFont(LABEL_FONT);
 579     htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
 580     JLabel svgLabel = new JLabel(
 581             MessageManager.formatMessage("label.rendering_style", "SVG"));
 582     svgLabel.setFont(LABEL_FONT);
 583     svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 584     svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
 585     svgRendering.setFont(LABEL_FONT);
 586     svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
 587
 588     JLabel jLabel1 = new JLabel();
 589     jLabel1.setFont(LABEL_FONT);
 590     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 591     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 592     jLabel1.setFont(LABEL_FONT);
 593
 594     fastajv.setFont(LABEL_FONT);
 595     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 596     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 597     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 598     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 599     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 600     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 601     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 602     msfjv.setFont(LABEL_FONT);
 603     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 604     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 605     JPanel jPanel11 = new JPanel();
 606     jPanel11.setFont(LABEL_FONT);
 607     TitledBorder titledBorder2 = new TitledBorder(
 608             MessageManager.getString("label.file_output"));
 609     jPanel11.setBorder(titledBorder2);
 610     jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
 611     GridLayout gridLayout3 = new GridLayout();
 612     jPanel11.setLayout(gridLayout3);
 613     gridLayout3.setRows(8);
 614     blcjv.setFont(LABEL_FONT);
 615     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 616     clustaljv.setFont(LABEL_FONT);
 617     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 618     pfamjv.setFont(LABEL_FONT);
 619     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 620     pileupjv.setFont(LABEL_FONT);
 621     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 622     pirjv.setFont(LABEL_FONT);
 623     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 624     autoIdWidth.setFont(LABEL_FONT);
 625     autoIdWidth.setText(
 626             MessageManager.getString("label.automatically_set_id_width"));
 627     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 628             .getString("label.adjusts_width_generated_eps_png")));
 629     autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
 630     autoIdWidth.addActionListener(new ActionListener()
 631     {
 632
 633       @Override
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         autoIdWidth_actionPerformed();
 637       }
 638     });
 639     userIdWidthlabel.setFont(LABEL_FONT);
 640     userIdWidthlabel.setText(
 641             MessageManager.getString("label.figure_id_column_width"));
 642     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 643             .getString("label.manually_specify_width_left_column")));
 644     userIdWidthlabel.setToolTipText(
 645             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 646                     "label.manually_specify_width_left_column")));
 647     userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
 648     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 649     userIdWidth.setText("");
 650     userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
 651     userIdWidth.addActionListener(new ActionListener()
 652     {
 653
 654       @Override
 655       public void actionPerformed(ActionEvent e)
 656       {
 657         userIdWidth_actionPerformed();
 658       }
 659     });
 660     modellerOutput.setFont(LABEL_FONT);
 661     modellerOutput
 662             .setText(MessageManager.getString("label.use_modeller_output"));
 663     modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
 664     embbedBioJSON.setFont(LABEL_FONT);
 665     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 666     embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 667
 668     jPanel11.add(jLabel1);
 669     jPanel11.add(blcjv);
 670     jPanel11.add(clustaljv);
 671     jPanel11.add(fastajv);
 672     jPanel11.add(msfjv);
 673     jPanel11.add(pfamjv);
 674     jPanel11.add(pileupjv);
 675     jPanel11.add(pirjv);
 676     outputTab.add(autoIdWidth);
 677     outputTab.add(userIdWidth);
 678     outputTab.add(userIdWidthlabel);
 679     outputTab.add(modellerOutput);
 680     if (!Platform.isJS())
 681     {
 682       /*
 683        * JalviewJS doesn't support Lineart option or SVG output
 684        */
 685       outputTab.add(embbedBioJSON);
 686       outputTab.add(epsLabel);
 687       outputTab.add(epsRendering);
 688       outputTab.add(htmlLabel);
 689       outputTab.add(htmlRendering);
 690       outputTab.add(svgLabel);
 691       outputTab.add(svgRendering);
 692     }
 693     outputTab.add(jPanel11);
 694     return outputTab;
 695   }
 696
 697   /**
 698    * Initialises the Connections tabbed panel.
 699    *
 700    * @return
 701    */
 702   private JPanel initConnectionsTab()
 703   {
 704     connectTab = new JPanel();
 705     connectTab.setLayout(new GridBagLayout());
 706
 707     // Label for browser text box
 708     JLabel browserLabel = new JLabel();
 709     browserLabel.setFont(LABEL_FONT);
 710     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 711     browserLabel.setText(
 712             MessageManager.getString("label.default_browser_unix"));
 713     defaultBrowser.setFont(LABEL_FONT);
 714     defaultBrowser.setText("");
 715     final String tooltip = JvSwingUtils.wrapTooltip(true,
 716             MessageManager.getString("label.double_click_to_browse"));
 717     defaultBrowser.setToolTipText(tooltip);
 718     defaultBrowser.addMouseListener(new MouseAdapter()
 719     {
 720       @Override
 721       public void mouseClicked(MouseEvent e)
 722       {
 723         if (e.getClickCount() > 1)
 724         {
 725           defaultBrowser_mouseClicked(e);
 726         }
 727       }
 728     });
 729
 730     JPanel proxyPanel = initConnTabProxyPanel();
 731     initConnTabCheckboxes();
 732
 733     // Add default Browser text box
 734     connectTab.add(browserLabel,
 735             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 736                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 737                     new Insets(10, 0, 5, 5), 5, 1));
 738     defaultBrowser.setFont(LABEL_FONT);
 739     defaultBrowser.setText("");
 740
 741     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 742             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 743             new Insets(10, 0, 5, 10), 30, 1));
 744
 745     // Add proxy server panel
 746     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 747             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 748             new Insets(10, 0, 5, 12), 4, 10));
 749
 750     // Add usage stats, version check and questionnaire checkboxes
 751     connectTab.add(usagestats,
 752             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 753                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 754                     new Insets(0, 2, 5, 5), 70, 1));
 755     connectTab.add(questionnaire,
 756             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 757                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 758                     new Insets(0, 2, 5, 10), 70, 1));
 759     connectTab.add(versioncheck,
 760             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 761                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 762                     new Insets(0, 2, 5, 5), 70, 1));
 763
 764     versioncheck.setVisible(false);
 765
 766     // Add padding so the panel doesn't look ridiculous
 767     JPanel spacePanel = new JPanel();
 768     connectTab.add(spacePanel,
 769             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 770                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 771                     new Insets(0, 0, 0, 5), 70, 1));
 772
 773     return connectTab;
 774   }
 775
 776   /**
 777    * Initialises the Links tabbed panel.
 778    *
 779    * @return
 780    */
 781   private JPanel initLinksTab()
 782   {
 783     JPanel linkTab = new JPanel();
 784     linkTab.setLayout(new GridBagLayout());
 785
 786     // Set up table for Url links
 787     linkUrlTable.getTableHeader().setReorderingAllowed(false);
 788     linkUrlTable.setFillsViewportHeight(true);
 789     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 790     linkUrlTable.setAutoCreateRowSorter(true);
 791     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 792
 793     // adjust row height so radio buttons actually fit
 794     // don't do this in the renderer, it causes the awt thread to activate
 795     // constantly
 796     JRadioButton temp = new JRadioButton();
 797     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 798
 799     // Table in scrollpane so that the table is given a scrollbar
 800     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 801     linkScrollPane.setBorder(null);
 802
 803     // Panel for links functionality
 804     JPanel linkPanel = new JPanel(new GridBagLayout());
 805     linkPanel.setBorder(new TitledBorder(
 806             MessageManager.getString("label.url_linkfrom_sequence_id")));
 807
 808     // Put the Url links panel together
 809
 810     // Buttons go at top right, resizing only resizes the blank space vertically
 811     JPanel buttonPanel = initLinkTabUrlButtons();
 812     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 813     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 814     linkConstraints1.gridx = 0;
 815     linkConstraints1.gridy = 0;
 816     linkConstraints1.weightx = 1.0;
 817     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 818     linkTab.add(buttonPanel, linkConstraints1);
 819
 820     // Links table goes at top left, resizing resizes the table
 821     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 822     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 823     linkConstraints2.gridx = 0;
 824     linkConstraints2.gridy = 1;
 825     linkConstraints2.weightx = 1.0;
 826     linkConstraints2.weighty = 1.0;
 827     linkConstraints2.fill = GridBagConstraints.BOTH;
 828     linkTab.add(linkScrollPane, linkConstraints2);
 829
 830     // Filter box and buttons goes at bottom left, resizing resizes the text box
 831     JPanel filterPanel = initLinkTabFilterPanel();
 832     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 833     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 834     linkConstraints3.gridx = 0;
 835     linkConstraints3.gridy = 2;
 836     linkConstraints3.weightx = 1.0;
 837     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 838     linkTab.add(filterPanel, linkConstraints3);
 839
 840     return linkTab;
 841   }
 842
 843   private JPanel initLinkTabFilterPanel()
 844   {
 845     // Filter textbox and reset button
 846     JLabel filterLabel = new JLabel(
 847             MessageManager.getString("label.filter"));
 848     filterLabel.setFont(LABEL_FONT);
 849     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 850     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 851
 852     filterTB.setFont(LABEL_FONT);
 853     filterTB.setText("");
 854
 855     doReset.setText(MessageManager.getString("action.showall"));
 856     userOnly.setText(MessageManager.getString("action.customfilter"));
 857
 858     // Panel for filter functionality
 859     JPanel filterPanel = new JPanel(new GridBagLayout());
 860     filterPanel.setBorder(new TitledBorder("Filter"));
 861     GridBagConstraints gbc = new GridBagConstraints();
 862     gbc.gridx = 0;
 863     gbc.gridy = 0;
 864     gbc.fill = GridBagConstraints.NONE;
 865     gbc.anchor = GridBagConstraints.WEST;
 866
 867     filterPanel.add(filterLabel, gbc);
 868
 869     GridBagConstraints gbc1 = new GridBagConstraints();
 870     gbc1.gridx = 1;
 871     gbc1.gridwidth = 2;
 872     gbc1.fill = GridBagConstraints.HORIZONTAL;
 873     gbc1.anchor = GridBagConstraints.WEST;
 874     gbc1.weightx = 1.0;
 875     filterPanel.add(filterTB, gbc1);
 876
 877     GridBagConstraints gbc2 = new GridBagConstraints();
 878     gbc2.gridx = 3;
 879     gbc2.fill = GridBagConstraints.NONE;
 880     gbc2.anchor = GridBagConstraints.WEST;
 881     filterPanel.add(doReset, gbc2);
 882
 883     GridBagConstraints gbc3 = new GridBagConstraints();
 884     gbc3.gridx = 4;
 885     gbc3.fill = GridBagConstraints.NONE;
 886     gbc3.anchor = GridBagConstraints.WEST;
 887     filterPanel.add(userOnly, gbc3);
 888
 889     return filterPanel;
 890   }
 891
 892   private JPanel initLinkTabUrlButtons()
 893   {
 894     // Buttons for new / edit / delete Url links
 895     JButton newLink = new JButton();
 896     newLink.setText(MessageManager.getString("action.new"));
 897
 898     editLink.setText(MessageManager.getString("action.edit"));
 899
 900     deleteLink.setText(MessageManager.getString("action.delete"));
 901
 902     // no current selection, so initially disable delete/edit buttons
 903     editLink.setEnabled(false);
 904     deleteLink.setEnabled(false);
 905
 906     newLink.addActionListener(new java.awt.event.ActionListener()
 907     {
 908       @Override
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         newLink_actionPerformed(e);
 912       }
 913     });
 914
 915     editLink.setText(MessageManager.getString("action.edit"));
 916     editLink.addActionListener(new java.awt.event.ActionListener()
 917     {
 918       @Override
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         editLink_actionPerformed(e);
 922       }
 923     });
 924
 925     deleteLink.setText(MessageManager.getString("action.delete"));
 926     deleteLink.addActionListener(new java.awt.event.ActionListener()
 927     {
 928       @Override
 929       public void actionPerformed(ActionEvent e)
 930       {
 931         deleteLink_actionPerformed(e);
 932       }
 933     });
 934
 935     JPanel buttonPanel = new JPanel(new GridBagLayout());
 936     buttonPanel.setBorder(new TitledBorder("Edit links"));
 937     GridBagConstraints gbc = new GridBagConstraints();
 938     gbc.gridx = 0;
 939     gbc.gridy = 0;
 940     gbc.fill = GridBagConstraints.NONE;
 941     buttonPanel.add(newLink, gbc);
 942
 943     GridBagConstraints gbc1 = new GridBagConstraints();
 944     gbc1.gridx = 1;
 945     gbc1.gridy = 0;
 946     gbc1.fill = GridBagConstraints.NONE;
 947     buttonPanel.add(editLink, gbc1);
 948
 949     GridBagConstraints gbc2 = new GridBagConstraints();
 950     gbc2.gridx = 2;
 951     gbc2.gridy = 0;
 952     gbc2.fill = GridBagConstraints.NONE;
 953     buttonPanel.add(deleteLink, gbc2);
 954
 955     GridBagConstraints gbc3 = new GridBagConstraints();
 956     gbc3.gridx = 3;
 957     gbc3.gridy = 0;
 958     gbc3.fill = GridBagConstraints.HORIZONTAL;
 959     gbc3.weightx = 1.0;
 960     JPanel spacePanel = new JPanel();
 961     spacePanel.setBorder(null);
 962     buttonPanel.add(spacePanel, gbc3);
 963
 964     return buttonPanel;
 965   }
 966
 967   /**
 968    * Initialises the proxy server panel in the Connections tab
 969    *
 970    * @return the proxy server panel
 971    */
 972   private JPanel initConnTabProxyPanel()
 973   {
 974     // Label for server text box
 975     serverLabel.setText(MessageManager.getString("label.host") + ": ");
 976     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 977     serverLabel.setFont(LABEL_FONT);
 978     serverLabel2.setText(MessageManager.getString("label.host") + ": ");
 979     serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
 980     serverLabel2.setFont(LABEL_FONT);
 981
 982     // Proxy server and port text boxes
 983     proxyServerHttpTB.setFont(LABEL_FONT);
 984     proxyServerHttpTB.setColumns(40);
 985     proxyPortHttpTB.setFont(LABEL_FONT);
 986     proxyPortHttpTB.setColumns(4);
 987     proxyServerHttpsTB.setFont(LABEL_FONT);
 988     proxyServerHttpsTB.setColumns(40);
 989     proxyPortHttpsTB.setFont(LABEL_FONT);
 990     proxyPortHttpsTB.setColumns(4);
 991     proxyAuthUsernameTB.setFont(LABEL_FONT);
 992     proxyAuthUsernameTB.setColumns(30);
 993     proxyAuthPasswordPB.setFont(LABEL_FONT);
 994     proxyAuthPasswordPB.setColumns(30);
 995     proxyAuthPasswordPB.getDocument()
 996             .addDocumentListener(new DocumentListener()
 997             {
 998               @Override
 999               public void changedUpdate(DocumentEvent e)
1000               {
1001                 if (!proxyAuthPasswordPB.getBackground()
1002                         .equals(Color.WHITE))
1003                   proxyAuthPasswordPB.setBackground(Color.WHITE);
1004               }
1005
1006               @Override
1007               public void insertUpdate(DocumentEvent e)
1008               {
1009                 if (!proxyAuthPasswordPB.getBackground()
1010                         .equals(Color.WHITE))
1011                   proxyAuthPasswordPB.setBackground(Color.WHITE);
1012               }
1013
1014               @Override
1015               public void removeUpdate(DocumentEvent e)
1016               {
1017                 if (!proxyAuthPasswordPB.getBackground()
1018                         .equals(Color.WHITE))
1019                   proxyAuthPasswordPB.setBackground(Color.WHITE);
1020               }
1021
1022             });
1023
1024     // Label for Port text box
1025     portLabel.setFont(LABEL_FONT);
1026     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1027     portLabel.setText(MessageManager.getString("label.port") + ": ");
1028     portLabel2.setFont(LABEL_FONT);
1029     portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1030     portLabel2.setText(MessageManager.getString("label.port") + ": ");
1031
1032     httpLabel.setText("HTTP");
1033     httpLabel.setFont(LABEL_FONT_BOLD);
1034     httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1035     httpsLabel.setText("HTTPS");
1036     httpsLabel.setFont(LABEL_FONT_BOLD);
1037     httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1038
1039     proxyAuthUsernameLabel
1040             .setText(MessageManager.getString("label.username") + ": ");
1041     proxyAuthUsernameLabel.setFont(LABEL_FONT);
1042     proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1043     proxyAuthPasswordLabel
1044             .setText(MessageManager.getString("label.password") + ": ");
1045     proxyAuthPasswordLabel.setFont(LABEL_FONT);
1046     proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1047     passwordNotStoredLabel.setText(
1048             "(" + MessageManager.getString("label.not_stored") + ")");
1049     passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1050     passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1051
1052     // Proxy type radio buttons
1053     noProxy.setFont(LABEL_FONT);
1054     noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1055     noProxy.setText(MessageManager.getString("label.no_proxy"));
1056     systemProxy.setFont(LABEL_FONT);
1057     systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1058     systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1059             displayUserHostPort(Cache.startupProxyProperties[4],
1060                     Cache.startupProxyProperties[0],
1061                     Cache.startupProxyProperties[1]),
1062             displayUserHostPort(Cache.startupProxyProperties[6],
1063                     Cache.startupProxyProperties[2],
1064                     Cache.startupProxyProperties[3])));
1065     customProxy.setFont(LABEL_FONT);
1066     customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1067     customProxy.setText(
1068             MessageManager.getString("label.use_proxy_server") + ":");
1069     ActionListener al = new ActionListener()
1070     {
1071       @Override
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         proxyType_actionPerformed();
1075       }
1076     };
1077     noProxy.addActionListener(al);
1078     systemProxy.addActionListener(al);
1079     customProxy.addActionListener(al);
1080     proxyType.add(noProxy);
1081     proxyType.add(systemProxy);
1082     proxyType.add(customProxy);
1083
1084     proxyAuth.setFont(LABEL_FONT);
1085     proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1086     proxyAuth.setText(MessageManager.getString("label.auth_required"));
1087     proxyAuth.addActionListener(new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         proxyAuth_actionPerformed();
1093       }
1094     });
1095
1096     setCustomProxyEnabled();
1097
1098     // Make proxy server panel
1099     JPanel proxyPanel = new JPanel();
1100     TitledBorder titledBorder1 = new TitledBorder(
1101             MessageManager.getString("label.proxy_servers"));
1102     proxyPanel.setBorder(titledBorder1);
1103     proxyPanel.setLayout(new GridBagLayout());
1104     GridBagConstraints gbc = new GridBagConstraints();
1105     gbc.fill = GridBagConstraints.HORIZONTAL;
1106     gbc.weightx = 1.0;
1107
1108     GridBagConstraints c = new GridBagConstraints();
1109     // Proxy type radio buttons (3)
1110     JPanel ptPanel = new JPanel();
1111     ptPanel.setLayout(new GridBagLayout());
1112     c.weightx = 1.0;
1113     c.gridy = 0;
1114     c.gridx = 0;
1115     c.gridwidth = 1;
1116     c.fill = GridBagConstraints.HORIZONTAL;
1117     ptPanel.add(noProxy, c);
1118     c.gridy++;
1119     ptPanel.add(systemProxy, c);
1120     c.gridy++;
1121     ptPanel.add(customProxy, c);
1122
1123     gbc.gridy = 0;
1124     proxyPanel.add(ptPanel, gbc);
1125
1126     // host and port text boxes
1127     JPanel hpPanel = new JPanel();
1128     hpPanel.setLayout(new GridBagLayout());
1129     // HTTP host port row
1130     c.gridy = 0;
1131     c.gridx = 0;
1132
1133     c.weightx = 0.1;
1134     c.anchor = GridBagConstraints.LINE_START;
1135     hpPanel.add(httpLabel, c);
1136
1137     c.gridx++;
1138     c.weightx = 0.1;
1139     c.anchor = GridBagConstraints.LINE_END;
1140     hpPanel.add(serverLabel, c);
1141
1142     c.gridx++;
1143     c.weightx = 1.0;
1144     c.anchor = GridBagConstraints.LINE_START;
1145     hpPanel.add(proxyServerHttpTB, c);
1146
1147     c.gridx++;
1148     c.weightx = 0.1;
1149     c.anchor = GridBagConstraints.LINE_END;
1150     hpPanel.add(portLabel, c);
1151
1152     c.gridx++;
1153     c.weightx = 0.2;
1154     c.anchor = GridBagConstraints.LINE_START;
1155     hpPanel.add(proxyPortHttpTB, c);
1156
1157     // HTTPS host port row
1158     c.gridy++;
1159     c.gridx = 0;
1160     c.gridwidth = 1;
1161
1162     c.anchor = GridBagConstraints.LINE_START;
1163     hpPanel.add(httpsLabel, c);
1164
1165     c.gridx++;
1166     c.anchor = GridBagConstraints.LINE_END;
1167     hpPanel.add(serverLabel2, c);
1168
1169     c.gridx++;
1170     c.anchor = GridBagConstraints.LINE_START;
1171     hpPanel.add(proxyServerHttpsTB, c);
1172
1173     c.gridx++;
1174     c.anchor = GridBagConstraints.LINE_END;
1175     hpPanel.add(portLabel2, c);
1176
1177     c.gridx++;
1178     c.anchor = GridBagConstraints.LINE_START;
1179     hpPanel.add(proxyPortHttpsTB, c);
1180
1181     gbc.gridy++;
1182     proxyPanel.add(hpPanel, gbc);
1183
1184     // Require authentication checkbox
1185     gbc.gridy++;
1186     proxyPanel.add(proxyAuth, gbc);
1187
1188     // username and password
1189     JPanel upPanel = new JPanel();
1190     upPanel.setLayout(new GridBagLayout());
1191     // username row
1192     c.gridy = 0;
1193     c.gridx = 0;
1194     c.gridwidth = 1;
1195     c.weightx = 0.4;
1196     c.anchor = GridBagConstraints.LINE_END;
1197     upPanel.add(proxyAuthUsernameLabel, c);
1198
1199     c.gridx++;
1200     c.weightx = 1.0;
1201     c.anchor = GridBagConstraints.LINE_START;
1202     upPanel.add(proxyAuthUsernameTB, c);
1203
1204     // password row
1205     c.gridy++;
1206     c.gridx = 0;
1207     c.weightx = 0.4;
1208     c.anchor = GridBagConstraints.LINE_END;
1209     upPanel.add(proxyAuthPasswordLabel, c);
1210
1211     c.gridx++;
1212     c.weightx = 1.0;
1213     c.anchor = GridBagConstraints.LINE_START;
1214     upPanel.add(proxyAuthPasswordPB, c);
1215
1216     c.gridx++;
1217     c.weightx = 0.4;
1218     c.anchor = GridBagConstraints.LINE_START;
1219     upPanel.add(passwordNotStoredLabel, c);
1220
1221     gbc.gridy++;
1222     proxyPanel.add(upPanel, gbc);
1223
1224     applyProxyButton.setText(MessageManager.getString("action.apply"));
1225     applyProxyButton.addActionListener(new ActionListener()
1226     {
1227       @Override
1228       public void actionPerformed(ActionEvent e)
1229       {
1230         saveProxySettings();
1231       }
1232     });
1233     gbc.gridy++;
1234     gbc.fill = GridBagConstraints.NONE;
1235     gbc.anchor = GridBagConstraints.LINE_END;
1236     proxyPanel.add(applyProxyButton, gbc);
1237
1238     return proxyPanel;
1239   }
1240
1241   public void proxyAuthPasswordFocus()
1242   {
1243     proxyAuthPasswordPB.grabFocus();
1244     proxyAuthPasswordPB.setBackground(Color.PINK);
1245   }
1246
1247   public void saveProxySettings()
1248   {
1249     // overridden in Preferences
1250   }
1251
1252   private String displayUserHostPort(String user, String host, String port)
1253   {
1254     boolean hostBlank = (host == null || host.isEmpty());
1255     boolean portBlank = (port == null || port.isEmpty());
1256     if (hostBlank && portBlank)
1257     {
1258       return MessageManager.getString("label.none");
1259     }
1260
1261     StringBuilder sb = new StringBuilder();
1262     if (user != null)
1263     {
1264       sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1265               : user);
1266       sb.append("@");
1267     }
1268     sb.append(hostBlank ? "" : host);
1269     if (!portBlank)
1270     {
1271       sb.append(":");
1272       sb.append(port);
1273     }
1274     return sb.toString();
1275   }
1276
1277   /**
1278    * Initialises the checkboxes in the Connections tab
1279    */
1280   private void initConnTabCheckboxes()
1281   {
1282     // Usage stats checkbox label
1283     usagestats.setText(
1284             MessageManager.getString("label.send_usage_statistics"));
1285     usagestats.setFont(LABEL_FONT);
1286     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1287     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1288
1289     // Questionnaire checkbox label
1290     questionnaire.setText(
1291             MessageManager.getString("label.check_for_questionnaires"));
1292     questionnaire.setFont(LABEL_FONT);
1293     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1294     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1295
1296     // Check for latest version checkbox label
1297     versioncheck.setText(
1298             MessageManager.getString("label.check_for_latest_version"));
1299     versioncheck.setFont(LABEL_FONT);
1300     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1301     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1302   }
1303
1304   /**
1305    * Initialises the parent panel which contains the tabbed sections.
1306    *
1307    * @return
1308    */
1309   private JPanel initOkCancelPanel()
1310   {
1311     JButton ok = new JButton();
1312     ok.setText(MessageManager.getString("action.ok"));
1313     ok.addActionListener(new ActionListener()
1314     {
1315       @Override
1316       public void actionPerformed(ActionEvent e)
1317       {
1318         ok_actionPerformed(e);
1319       }
1320     });
1321     JButton cancel = new JButton();
1322     cancel.setText(MessageManager.getString("action.cancel"));
1323     cancel.addActionListener(new ActionListener()
1324     {
1325       @Override
1326       public void actionPerformed(ActionEvent e)
1327       {
1328         cancel_actionPerformed(e);
1329       }
1330     });
1331     JPanel okCancelPanel = new JPanel();
1332     okCancelPanel.add(ok);
1333     okCancelPanel.add(cancel);
1334     return okCancelPanel;
1335   }
1336
1337   /**
1338    * Initialises the Colours tabbed panel.
1339    *
1340    * @return
1341    */
1342   private JPanel initColoursTab()
1343   {
1344     JPanel coloursTab = new JPanel();
1345     coloursTab.setBorder(new TitledBorder(
1346             MessageManager.getString("action.open_new_alignment")));
1347     coloursTab.setLayout(new FlowLayout());
1348     JLabel mincolourLabel = new JLabel();
1349     mincolourLabel.setFont(LABEL_FONT);
1350     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1351     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1352     minColour.setFont(LABEL_FONT);
1353     minColour.setBorder(BorderFactory.createEtchedBorder());
1354     minColour.setPreferredSize(new Dimension(40, 20));
1355     minColour.addMouseListener(new MouseAdapter()
1356     {
1357       @Override
1358       public void mousePressed(MouseEvent e)
1359       {
1360         minColour_actionPerformed(minColour);
1361       }
1362     });
1363     JLabel maxcolourLabel = new JLabel();
1364     maxcolourLabel.setFont(LABEL_FONT);
1365     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1366     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1367     maxColour.setFont(LABEL_FONT);
1368     maxColour.setBorder(BorderFactory.createEtchedBorder());
1369     maxColour.setPreferredSize(new Dimension(40, 20));
1370     maxColour.addMouseListener(new MouseAdapter()
1371     {
1372       @Override
1373       public void mousePressed(MouseEvent e)
1374       {
1375         maxColour_actionPerformed(maxColour);
1376       }
1377     });
1378
1379     protColour.setFont(LABEL_FONT);
1380     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1381     JLabel protColourLabel = new JLabel();
1382     protColourLabel.setFont(LABEL_FONT);
1383     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1384     protColourLabel.setText(
1385             MessageManager.getString("label.prot_alignment_colour") + " ");
1386     JvSwingUtils.addtoLayout(coloursTab,
1387             MessageManager
1388                     .getString("label.default_colour_scheme_for_alignment"),
1389             protColourLabel, protColour);
1390
1391     nucColour.setFont(LABEL_FONT);
1392     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1393     JLabel nucColourLabel = new JLabel();
1394     nucColourLabel.setFont(LABEL_FONT);
1395     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1396     nucColourLabel.setText(
1397             MessageManager.getString("label.nuc_alignment_colour") + " ");
1398     JvSwingUtils.addtoLayout(coloursTab,
1399             MessageManager
1400                     .getString("label.default_colour_scheme_for_alignment"),
1401             nucColourLabel, nucColour);
1402
1403     JPanel annotationShding = new JPanel();
1404     annotationShding.setBorder(new TitledBorder(
1405             MessageManager.getString("label.annotation_shading_default")));
1406     annotationShding.setLayout(new GridLayout(1, 2));
1407     JvSwingUtils.addtoLayout(annotationShding,
1408             MessageManager.getString(
1409                     "label.default_minimum_colour_annotation_shading"),
1410             mincolourLabel, minColour);
1411     JvSwingUtils.addtoLayout(annotationShding,
1412             MessageManager.getString(
1413                     "label.default_maximum_colour_annotation_shading"),
1414             maxcolourLabel, maxColour);
1415     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1416     return coloursTab;
1417   }
1418
1419   /**
1420    * Initialises the Overview tabbed panel.
1421    *
1422    * @return
1423    */
1424   private JPanel initOverviewTab()
1425   {
1426     JPanel overviewPanel = new JPanel();
1427     overviewPanel.setBorder(new TitledBorder(
1428             MessageManager.getString("label.overview_settings")));
1429
1430     gapColour.setFont(LABEL_FONT);
1431     // fixing the border colours stops apparent colour bleed from the panel
1432     gapColour.setBorder(
1433             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1434     gapColour.setPreferredSize(new Dimension(40, 20));
1435     gapColour.addMouseListener(new MouseAdapter()
1436     {
1437       @Override
1438       public void mousePressed(MouseEvent e)
1439       {
1440         gapColour_actionPerformed(gapColour);
1441       }
1442     });
1443
1444     hiddenColour.setFont(LABEL_FONT);
1445     // fixing the border colours stops apparent colour bleed from the panel
1446     hiddenColour.setBorder(
1447             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1448     hiddenColour.setPreferredSize(new Dimension(40, 20));
1449     hiddenColour.addMouseListener(new MouseAdapter()
1450     {
1451       @Override
1452       public void mousePressed(MouseEvent e)
1453       {
1454         hiddenColour_actionPerformed(hiddenColour);
1455       }
1456     });
1457
1458     useLegacyGap = new JCheckBox(
1459             MessageManager.getString("label.ov_legacy_gap"));
1460     useLegacyGap.setFont(LABEL_FONT);
1461     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1462     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1463     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1464     gapLabel.setFont(LABEL_FONT);
1465     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1466     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1467     showHiddenAtStart = new JCheckBox(
1468             MessageManager.getString("label.ov_show_hide_default"));
1469     showHiddenAtStart.setFont(LABEL_FONT);
1470     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1471     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1472     JLabel hiddenLabel = new JLabel(
1473             MessageManager.getString("label.hidden_colour"));
1474     hiddenLabel.setFont(LABEL_FONT);
1475     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1476     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1477
1478     useLegacyGap.addActionListener(new ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         useLegacyGaps_actionPerformed(e);
1484       }
1485     });
1486
1487     overviewPanel.setLayout(new GridBagLayout());
1488     GridBagConstraints c1 = new GridBagConstraints();
1489
1490     c1.fill = GridBagConstraints.HORIZONTAL;
1491     c1.gridx = 0;
1492     c1.gridy = 0;
1493     c1.weightx = 1;
1494     c1.ipady = 20;
1495     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1496     overviewPanel.add(useLegacyGap, c1);
1497
1498     GridBagConstraints c2 = new GridBagConstraints();
1499     c2.fill = GridBagConstraints.HORIZONTAL;
1500     c2.gridx = 1;
1501     c2.gridy = 0;
1502     c2.insets = new Insets(0, 15, 0, 10);
1503     overviewPanel.add(gapLabel, c2);
1504
1505     GridBagConstraints c3 = new GridBagConstraints();
1506     c3.fill = GridBagConstraints.HORIZONTAL;
1507     c3.gridx = 2;
1508     c3.gridy = 0;
1509     c3.insets = new Insets(0, 0, 0, 15);
1510     overviewPanel.add(gapColour, c3);
1511
1512     GridBagConstraints c4 = new GridBagConstraints();
1513     c4.fill = GridBagConstraints.HORIZONTAL;
1514     c4.gridx = 0;
1515     c4.gridy = 1;
1516     c4.weightx = 1;
1517     overviewPanel.add(showHiddenAtStart, c4);
1518
1519     GridBagConstraints c5 = new GridBagConstraints();
1520     c5.fill = GridBagConstraints.HORIZONTAL;
1521     c5.gridx = 1;
1522     c5.gridy = 1;
1523     c5.insets = new Insets(0, 15, 0, 10);
1524     overviewPanel.add(hiddenLabel, c5);
1525
1526     GridBagConstraints c6 = new GridBagConstraints();
1527     c6.fill = GridBagConstraints.HORIZONTAL;
1528     c6.gridx = 2;
1529     c6.gridy = 1;
1530     c6.insets = new Insets(0, 0, 0, 15);
1531     overviewPanel.add(hiddenColour, c6);
1532
1533     JButton resetButton = new JButton(
1534             MessageManager.getString("label.reset_to_defaults"));
1535
1536     resetButton.addActionListener(new ActionListener()
1537     {
1538       @Override
1539       public void actionPerformed(ActionEvent e)
1540       {
1541         resetOvDefaults_actionPerformed(e);
1542       }
1543     });
1544
1545     GridBagConstraints c7 = new GridBagConstraints();
1546     c7.fill = GridBagConstraints.NONE;
1547     c7.gridx = 0;
1548     c7.gridy = 2;
1549     c7.insets = new Insets(10, 0, 0, 0);
1550     c7.anchor = GridBagConstraints.WEST;
1551     overviewPanel.add(resetButton, c7);
1552
1553     // Add padding so the panel doesn't look ridiculous
1554     JPanel spacePanel = new JPanel();
1555     overviewPanel.add(spacePanel,
1556             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1557                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1558                     new Insets(0, 0, 0, 5), 0, 0));
1559
1560     return overviewPanel;
1561   }
1562
1563   /**
1564    * Initialises the Structure tabbed panel.
1565    *
1566    * @return
1567    */
1568   private JPanel initStructureTab()
1569   {
1570     structureTab = new JPanel();
1571
1572     structureTab.setBorder(new TitledBorder(
1573             MessageManager.getString("label.structure_options")));
1574     structureTab.setLayout(null);
1575     final int width = 420;
1576     final int height = 22;
1577     final int lineSpacing = 25;
1578     int ypos = 15;
1579
1580     structFromPdb.setFont(LABEL_FONT);
1581     structFromPdb
1582             .setText(MessageManager.getString("label.struct_from_pdb"));
1583     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1584     structFromPdb.addActionListener(new ActionListener()
1585     {
1586       @Override
1587       public void actionPerformed(ActionEvent e)
1588       {
1589         boolean selected = structFromPdb.isSelected();
1590         // enable other options only when the first is checked
1591         useRnaView.setEnabled(selected);
1592         addSecondaryStructure.setEnabled(selected);
1593         addTempFactor.setEnabled(selected);
1594       }
1595     });
1596     structureTab.add(structFromPdb);
1597
1598     // indent checkboxes that are conditional on the first one
1599     ypos += lineSpacing;
1600     useRnaView.setFont(LABEL_FONT);
1601     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1602     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1603     structureTab.add(useRnaView);
1604
1605     ypos += lineSpacing;
1606     addSecondaryStructure.setFont(LABEL_FONT);
1607     addSecondaryStructure
1608             .setText(MessageManager.getString("label.autoadd_secstr"));
1609     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1610     structureTab.add(addSecondaryStructure);
1611
1612     ypos += lineSpacing;
1613     addTempFactor.setFont(LABEL_FONT);
1614     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1615     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1616     structureTab.add(addTempFactor);
1617
1618     ypos += lineSpacing;
1619     JLabel viewerLabel = new JLabel();
1620     viewerLabel.setFont(LABEL_FONT);
1621     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1622     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1623     viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1624     structureTab.add(viewerLabel);
1625
1626     /*
1627      * add all external viewers as options here - check
1628      * when selected whether the program is installed
1629      */
1630     structViewer.setFont(LABEL_FONT);
1631     structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1632     structViewer.addItem(ViewerType.JMOL.name());
1633     structViewer.addItem(ViewerType.CHIMERA.name());
1634     structViewer.addItem(ViewerType.CHIMERAX.name());
1635     structViewer.addItem(ViewerType.PYMOL.name());
1636     structViewer.addActionListener(new ActionListener()
1637     {
1638       @Override
1639       public void actionPerformed(ActionEvent e)
1640       {
1641         structureViewer_actionPerformed(
1642                 (String) structViewer.getSelectedItem());
1643       }
1644     });
1645     structureTab.add(structViewer);
1646
1647     ypos += lineSpacing;
1648     structureViewerPathLabel = new JLabel();
1649     structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
1650     structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1651     structureViewerPathLabel.setText(MessageManager
1652             .formatMessage("label.viewer_path", "Chimera(X)"));
1653     structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
1654     structureViewerPathLabel.setEnabled(false);
1655     structureTab.add(structureViewerPathLabel);
1656
1657     structureViewerPath.setFont(LABEL_FONT);
1658     structureViewerPath.setText("");
1659     structureViewerPath.setEnabled(false);
1660     final String tooltip = JvSwingUtils.wrapTooltip(true,
1661             MessageManager.getString("label.viewer_path_tip"));
1662     structureViewerPath.setToolTipText(tooltip);
1663     structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1664     structureViewerPath.addMouseListener(new MouseAdapter()
1665     {
1666       @Override
1667       public void mouseClicked(MouseEvent e)
1668       {
1669         if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1670         {
1671           String chosen = openFileChooser();
1672           if (chosen != null)
1673           {
1674             structureViewerPath.setText(chosen);
1675           }
1676         }
1677       }
1678     });
1679     structureTab.add(structureViewerPath);
1680
1681     ypos += lineSpacing;
1682     nwMapping.setFont(LABEL_FONT);
1683     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1684     siftsMapping.setFont(LABEL_FONT);
1685     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1686     mappingMethod.add(nwMapping);
1687     mappingMethod.add(siftsMapping);
1688     JPanel mappingPanel = new JPanel();
1689     mappingPanel.setFont(LABEL_FONT);
1690     TitledBorder mmTitledBorder = new TitledBorder(
1691             MessageManager.getString("label.mapping_method"));
1692     mmTitledBorder.setTitleFont(LABEL_FONT);
1693     mappingPanel.setBorder(mmTitledBorder);
1694     mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1695     // GridLayout mappingLayout = new GridLayout();
1696     mappingPanel.setLayout(new GridLayout());
1697     mappingPanel.add(nwMapping);
1698     mappingPanel.add(siftsMapping);
1699     structureTab.add(mappingPanel);
1700
1701     ypos += lineSpacing;
1702     ypos += lineSpacing;
1703     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1704             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1705     docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1706     structureTab.add(docFieldPref);
1707
1708     /*
1709      * hide Chimera options in JalviewJS
1710      */
1711     if (Platform.isJS())
1712     {
1713       structureViewerPathLabel.setVisible(false);
1714       structureViewerPath.setVisible(false);
1715       viewerLabel.setVisible(false);
1716       structViewer.setVisible(false);
1717     }
1718
1719     return structureTab;
1720   }
1721
1722   /**
1723    * Action on choosing a structure viewer from combobox options.
1724    *
1725    * @param selectedItem
1726    */
1727   protected void structureViewer_actionPerformed(String selectedItem)
1728   {
1729   }
1730
1731   /**
1732    * Show a dialog for the user to choose a file. Returns the chosen path, or
1733    * null on Cancel.
1734    *
1735    * @return
1736    */
1737   protected String openFileChooser()
1738   {
1739     String choice = null;
1740     JFileChooser chooser = new JFileChooser();
1741
1742     // chooser.setFileView(new JalviewFileView());
1743     chooser.setDialogTitle(
1744             MessageManager.getString("label.open_local_file"));
1745     chooser.setToolTipText(MessageManager.getString("action.open"));
1746
1747     int value = chooser.showOpenDialog(this);
1748
1749     if (value == JFileChooser.APPROVE_OPTION)
1750     {
1751       choice = chooser.getSelectedFile().getPath();
1752     }
1753     return choice;
1754   }
1755
1756   /**
1757    * Validate the structure tab preferences; if invalid, set focus on this tab.
1758    *
1759    * @param e
1760    */
1761   protected boolean validateStructure(FocusEvent e)
1762   {
1763     if (!validateStructure())
1764     {
1765       e.getComponent().requestFocusInWindow();
1766       return false;
1767     }
1768     return true;
1769   }
1770
1771   protected boolean validateStructure()
1772   {
1773     return false;
1774   }
1775
1776   /**
1777    * Initialises the Visual tabbed panel.
1778    *
1779    * @return
1780    */
1781   private JPanel initVisualTab()
1782   {
1783     JPanel visualTab = new JPanel();
1784     visualTab.setBorder(new TitledBorder(
1785             MessageManager.getString("action.open_new_alignment")));
1786     visualTab.setLayout(null);
1787     fullScreen.setFont(LABEL_FONT);
1788     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1789     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1790     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1791     quality.setEnabled(false);
1792     quality.setFont(LABEL_FONT);
1793     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1794     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1795     quality.setSelected(true);
1796     quality.setText(MessageManager.getString("label.quality"));
1797     conservation.setEnabled(false);
1798     conservation.setFont(LABEL_FONT);
1799     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1800     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1801     conservation.setSelected(true);
1802     conservation.setText(MessageManager.getString("label.conservation"));
1803     identity.setEnabled(false);
1804     identity.setFont(LABEL_FONT);
1805     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1806     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1807     identity.setSelected(true);
1808     identity.setText(MessageManager.getString("label.consensus"));
1809     showOccupancy.setFont(LABEL_FONT);
1810     showOccupancy.setEnabled(false);
1811     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1812     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1813     showOccupancy.setSelected(true);
1814     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1815
1816     JLabel showGroupbits = new JLabel();
1817     showGroupbits.setFont(LABEL_FONT);
1818     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1819     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1820     showGroupbits
1821             .setText(MessageManager.getString("action.show_group") + ":");
1822     JLabel showConsensbits = new JLabel();
1823     showConsensbits.setFont(LABEL_FONT);
1824     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1825     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1826     showConsensbits
1827             .setText(MessageManager.getString("label.consensus") + ":");
1828     showConsensHistogram.setEnabled(false);
1829     showConsensHistogram.setFont(LABEL_FONT);
1830     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1831     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1832     showConsensHistogram.setSelected(true);
1833     showConsensHistogram
1834             .setText(MessageManager.getString("label.histogram"));
1835     showConsensLogo.setEnabled(false);
1836     showConsensLogo.setFont(LABEL_FONT);
1837     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1838     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1839     showConsensLogo.setSelected(true);
1840     showConsensLogo.setText(MessageManager.getString("label.logo"));
1841     showGroupConsensus.setEnabled(false);
1842     showGroupConsensus.setFont(LABEL_FONT);
1843     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1844     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1845     showGroupConsensus.setSelected(true);
1846     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1847     showGroupConservation.setEnabled(false);
1848     showGroupConservation.setFont(LABEL_FONT);
1849     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1850     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1851     showGroupConservation.setSelected(true);
1852     showGroupConservation
1853             .setText(MessageManager.getString("label.conservation"));
1854     showNpTooltip.setEnabled(true);
1855     showNpTooltip.setFont(LABEL_FONT);
1856     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1857     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1858     showNpTooltip.setSelected(true);
1859     showNpTooltip.setText(
1860             MessageManager.getString("label.non_positional_features"));
1861     showDbRefTooltip.setEnabled(true);
1862     showDbRefTooltip.setFont(LABEL_FONT);
1863     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1864     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1865     showDbRefTooltip.setSelected(true);
1866     showDbRefTooltip
1867             .setText(MessageManager.getString("label.database_references"));
1868     annotations.setFont(LABEL_FONT);
1869     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1870     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1871     annotations.setSelected(true);
1872     annotations.setText(MessageManager.getString("label.show_annotations"));
1873     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1874     annotations.addActionListener(new ActionListener()
1875     {
1876       @Override
1877       public void actionPerformed(ActionEvent e)
1878       {
1879         annotations_actionPerformed(e);
1880       }
1881     });
1882     identity.addActionListener(new ActionListener()
1883     {
1884       @Override
1885       public void actionPerformed(ActionEvent e)
1886       {
1887         annotations_actionPerformed(e);
1888       }
1889     });
1890     showGroupConsensus.addActionListener(new ActionListener()
1891     {
1892       @Override
1893       public void actionPerformed(ActionEvent e)
1894       {
1895         annotations_actionPerformed(e);
1896       }
1897     });
1898     showUnconserved.setFont(LABEL_FONT);
1899     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1900     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1901     showUnconserved.setSelected(true);
1902     showUnconserved
1903             .setText(MessageManager.getString("action.show_unconserved"));
1904     showUnconserved.addActionListener(new ActionListener()
1905     {
1906       @Override
1907       public void actionPerformed(ActionEvent e)
1908       {
1909         showunconserved_actionPerformed(e);
1910       }
1911     });
1912
1913     // TODO these are not yet added to / action from Preferences
1914     // JCheckBox shareSelections = new JCheckBox();
1915     // shareSelections.setFont(verdana11);
1916     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1917     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1918     // shareSelections.setSelected(true);
1919     // shareSelections.setText(MessageManager
1920     // .getString("label.share_selection_across_views"));
1921     // JCheckBox followHighlight = new JCheckBox();
1922     // followHighlight.setFont(verdana11);
1923     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1924     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1925     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1926     // followHighlight.setSelected(true);
1927     // followHighlight.setText(MessageManager
1928     // .getString("label.scroll_highlighted_regions"));
1929
1930     seqLimit.setFont(LABEL_FONT);
1931     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1932     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1933     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1934     smoothFont.setFont(LABEL_FONT);
1935     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1936     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1937     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1938     scaleProteinToCdna.setFont(LABEL_FONT);
1939     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1940     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1941     scaleProteinToCdna.setText(
1942             MessageManager.getString("label.scale_protein_to_cdna"));
1943     scaleProteinToCdna.setToolTipText(
1944             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1945     JLabel gapLabel = new JLabel();
1946     gapLabel.setFont(LABEL_FONT);
1947     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1948     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1949     JLabel fontLabel = new JLabel();
1950     fontLabel.setFont(LABEL_FONT);
1951     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1952     fontLabel.setText(MessageManager.getString("label.font"));
1953     fontSizeCB.setFont(LABEL_FONT);
1954     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1955     fontStyleCB.setFont(LABEL_FONT);
1956     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1957     fontNameCB.setFont(LABEL_FONT);
1958     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1959     gapSymbolCB.setFont(LABEL_FONT);
1960     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1961     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1962     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1963     gapSymbolCB.setRenderer(dlcr);
1964
1965     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1966     startupCheckbox.setFont(LABEL_FONT);
1967     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1968     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1969     startupCheckbox.setSelected(true);
1970     startupFileTextfield.setFont(LABEL_FONT);
1971     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1972     final String tooltip = JvSwingUtils.wrapTooltip(true,
1973             MessageManager.getString("label.double_click_to_browse"));
1974     startupFileTextfield.setToolTipText(tooltip);
1975     startupFileTextfield.addMouseListener(new MouseAdapter()
1976     {
1977       @Override
1978       public void mouseClicked(MouseEvent e)
1979       {
1980         if (e.getClickCount() > 1)
1981         {
1982           startupFileTextfield_mouseClicked();
1983         }
1984       }
1985     });
1986
1987     sortby.setFont(LABEL_FONT);
1988     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1989     JLabel sortLabel = new JLabel();
1990     sortLabel.setFont(LABEL_FONT);
1991     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1992     sortLabel.setText(MessageManager.getString("label.sort_by"));
1993     sortAnnBy.setFont(LABEL_FONT);
1994     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1995     JLabel sortAnnLabel = new JLabel();
1996     sortAnnLabel.setFont(LABEL_FONT);
1997     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1998     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1999     sortAutocalc.setFont(LABEL_FONT);
2000     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2001
2002     JPanel annsettingsPanel = new JPanel();
2003     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2004     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2005     annsettingsPanel.setBorder(new EtchedBorder());
2006     visualTab.add(annsettingsPanel);
2007     Border jb = new EmptyBorder(1, 1, 4, 5);
2008     annotations.setBorder(jb);
2009     showOccupancy.setBorder(jb);
2010     quality.setBorder(jb);
2011     conservation.setBorder(jb);
2012     identity.setBorder(jb);
2013     showConsensbits.setBorder(jb);
2014     showGroupbits.setBorder(jb);
2015     showGroupConsensus.setBorder(jb);
2016     showGroupConservation.setBorder(jb);
2017     showConsensHistogram.setBorder(jb);
2018     showConsensLogo.setBorder(jb);
2019
2020     JPanel autoAnnotSettings = new JPanel();
2021     annsettingsPanel.add(autoAnnotSettings);
2022     autoAnnotSettings.setLayout(new GridLayout(0, 2));
2023     autoAnnotSettings.add(annotations);
2024     autoAnnotSettings.add(quality);
2025     // second row of autoannotation box
2026     autoAnnotSettings = new JPanel();
2027     annsettingsPanel.add(autoAnnotSettings);
2028
2029     autoAnnotSettings.setLayout(new GridLayout(0, 3));
2030     autoAnnotSettings.add(conservation);
2031     autoAnnotSettings.add(identity);
2032     autoAnnotSettings.add(showOccupancy);
2033     autoAnnotSettings.add(showGroupbits);
2034     autoAnnotSettings.add(showGroupConservation);
2035     autoAnnotSettings.add(showGroupConsensus);
2036     autoAnnotSettings.add(showConsensbits);
2037     autoAnnotSettings.add(showConsensHistogram);
2038     autoAnnotSettings.add(showConsensLogo);
2039
2040     JPanel tooltipSettings = new JPanel();
2041     tooltipSettings.setBorder(new TitledBorder(
2042             MessageManager.getString("label.sequence_id_tooltip")));
2043     tooltipSettings.setBounds(173, 140, 220, 62);
2044     tooltipSettings.setLayout(new GridLayout(2, 1));
2045     tooltipSettings.add(showDbRefTooltip);
2046     tooltipSettings.add(showNpTooltip);
2047     visualTab.add(tooltipSettings);
2048
2049     wrap.setFont(LABEL_FONT);
2050     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2051     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2052     wrap.setText(MessageManager.getString("label.wrap_alignment"));
2053     rightAlign.setFont(LABEL_FONT);
2054     rightAlign.setForeground(Color.black);
2055     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2056     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2057     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2058     idItalics.setFont(LABEL_FONT_ITALIC);
2059     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2060     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2061     idItalics.setText(
2062             MessageManager.getString("label.sequence_name_italics"));
2063     openoverv.setFont(LABEL_FONT);
2064     openoverv.setActionCommand(
2065             MessageManager.getString("label.open_overview"));
2066     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2067     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2068     openoverv.setText(MessageManager.getString("label.open_overview"));
2069     JPanel jPanel2 = new JPanel();
2070     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2071     jPanel2.setLayout(new GridLayout(14, 1));
2072     jPanel2.add(fullScreen);
2073     jPanel2.add(openoverv);
2074     jPanel2.add(seqLimit);
2075     jPanel2.add(rightAlign);
2076     jPanel2.add(fontLabel);
2077     jPanel2.add(showUnconserved);
2078     jPanel2.add(idItalics);
2079     jPanel2.add(smoothFont);
2080     jPanel2.add(scaleProteinToCdna);
2081     jPanel2.add(gapLabel);
2082     jPanel2.add(wrap);
2083     jPanel2.add(sortLabel);
2084     jPanel2.add(sortAnnLabel);
2085     jPanel2.add(startupCheckbox);
2086     visualTab.add(jPanel2);
2087     visualTab.add(startupFileTextfield);
2088     visualTab.add(sortby);
2089     visualTab.add(sortAnnBy);
2090     visualTab.add(sortAutocalc);
2091     visualTab.add(gapSymbolCB);
2092     visualTab.add(fontNameCB);
2093     visualTab.add(fontSizeCB);
2094     visualTab.add(fontStyleCB);
2095
2096     if (Platform.isJS())
2097     {
2098       startupCheckbox.setVisible(false);
2099       startupFileTextfield.setVisible(false);
2100     }
2101
2102     return visualTab;
2103   }
2104
2105   /**
2106    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2107    */
2108
2109   protected void loadLastSavedBackupsOptions()
2110   {
2111     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2112             .getSavedBackupEntry();
2113     enableBackupFiles
2114             .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2115
2116     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2117             .createBackupFilesPresetEntry(Cache
2118                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2119     if (backupfilesCustomEntry == null)
2120     {
2121       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2122               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2123     }
2124     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2125             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2126             backupfilesCustomEntry);
2127
2128     setComboIntStringKey(backupfilesPresetsCombo,
2129             Cache.getDefault(BackupFiles.NS + "_PRESET",
2130                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2131
2132     backupsSetOptions(savedPreset);
2133
2134     backupsOptionsSetEnabled();
2135     updateBackupFilesExampleLabel();
2136   }
2137
2138   private boolean warnAboutSuffixReverseChange()
2139   {
2140     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2141             .getSavedBackupEntry();
2142     boolean savedSuffixReverse = bfpe.reverse;
2143     int savedSuffixDigits = bfpe.digits;
2144     String savedSuffixTemplate = bfpe.suffix;
2145
2146     boolean nowSuffixReverse = suffixReverse.isSelected();
2147     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2148     String nowSuffixTemplate = suffixTemplate.getText();
2149     return nowSuffixReverse != savedSuffixReverse
2150             && nowSuffixDigits == savedSuffixDigits
2151             && nowSuffixTemplate != null
2152             && nowSuffixTemplate.equals(savedSuffixTemplate);
2153   }
2154
2155   /**
2156    * Initialises the Backups tabbed panel.
2157    *
2158    * @return
2159    */
2160   private JPanel initBackupsTab()
2161   {
2162     JPanel backupsTab = new JPanel();
2163     backupsTab.setBorder(new TitledBorder(
2164             MessageManager.getString("label.backup_files")));
2165     backupsTab.setLayout(new GridBagLayout());
2166
2167     GridBagConstraints gbc = new GridBagConstraints();
2168     gbc.weightx = 0.0;
2169     gbc.weighty = 0.0;
2170     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2171     gbc.fill = GridBagConstraints.NONE;
2172
2173     initBackupsTabPresetsPanel();
2174     initBackupsTabSuffixPanel();
2175     initBackupsTabKeepFilesPanel();
2176     initBackupsTabFilenameExamplesPanel();
2177
2178     enableBackupFiles.setFont(LABEL_FONT_BOLD);
2179     enableBackupFiles
2180             .setText(MessageManager.getString("label.enable_backupfiles"));
2181     enableBackupFiles.addActionListener(new ActionListener()
2182     {
2183       @Override
2184       public void actionPerformed(ActionEvent e)
2185       {
2186         // enable other options only when the first is checked
2187         backupsOptionsSetEnabled();
2188       }
2189     });
2190
2191
2192     // enable checkbox 1 col
2193     gbc.gridwidth = 1;
2194     gbc.gridheight = 1;
2195     gbc.gridx = 0;
2196     gbc.gridy = 0; // row 0
2197     backupsTab.add(enableBackupFiles, gbc);
2198
2199     // summary of scheme box (over two rows)
2200     gbc.gridx = 1;
2201     gbc.weightx = 0.0;
2202     gbc.gridheight = 2;
2203     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2204     gbc.fill = GridBagConstraints.BOTH;
2205     backupsTab.add(exampleFilesPanel, gbc);
2206     gbc.gridheight = 1;
2207     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2208     gbc.fill = GridBagConstraints.NONE;
2209
2210     // fill empty space on right
2211     gbc.gridx++;
2212     gbc.weightx = 1.0;
2213     backupsTab.add(new JPanel(), gbc);
2214
2215     // schemes box
2216     gbc.weightx = 0.0;
2217     gbc.gridx = 0;
2218     gbc.gridy++; // row 1
2219     backupsTab.add(presetsPanel, gbc);
2220
2221     // now using whole row
2222     gbc.gridwidth = 2;
2223     gbc.gridheight = 1;
2224     // keep files box
2225     gbc.gridx = 0;
2226     gbc.gridy++; // row 2
2227     backupsTab.add(keepfilesPanel, gbc);
2228
2229     // filename strategy box
2230     gbc.gridy++; // row 3
2231     backupsTab.add(suffixPanel, gbc);
2232
2233     // fill empty space
2234     gbc.gridy++; // row 4
2235     gbc.weighty = 1.0;
2236     backupsTab.add(new JPanel(), gbc);
2237
2238     backupsOptionsSetEnabled();
2239     return backupsTab;
2240   }
2241
2242   private JPanel initBackupsTabPresetsPanel()
2243   {
2244
2245     String title = MessageManager.getString("label.schemes");
2246
2247     presetsPanel.setLayout(new GridBagLayout());
2248
2249     GridBagConstraints gbc = new GridBagConstraints();
2250     gbc.weightx = 0.0;
2251     gbc.weighty = 0.0;
2252     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2253     gbc.fill = GridBagConstraints.NONE;
2254     gbc.gridwidth = 1;
2255     gbc.gridheight = 1;
2256
2257     // "Scheme: "
2258     gbc.gridx = 0;
2259     gbc.gridy = 0;
2260
2261     presetsComboLabel = new JLabel(title + ":");
2262     presetsPanel.add(presetsComboLabel, gbc);
2263
2264     List<Object> entries = Arrays
2265             .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2266     List<String> tooltips = Arrays.asList(
2267             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2268     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2269             tooltips);
2270     /*
2271     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2272     {
2273       backupfilesPresetsCombo
2274               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2275     }
2276     */
2277
2278     backupfilesPresetsCombo.addActionListener(new ActionListener()
2279     {
2280       @Override
2281       public void actionPerformed(ActionEvent e)
2282       {
2283         int key = getComboIntStringKey(backupfilesPresetsCombo);
2284         if (!customiseCheckbox.isSelected())
2285         {
2286           backupfilesPresetsComboLastSelected = key;
2287         }
2288         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2289         {
2290           if (customiseCheckbox.isSelected())
2291           {
2292             // got here by clicking on customiseCheckbox so don't change the values
2293             backupfilesCustomOptionsSetEnabled();
2294           }
2295           else
2296           {
2297             backupsTabUpdatePresets();
2298             backupfilesCustomOptionsSetEnabled();
2299           }
2300         }
2301         else
2302         {
2303           customiseCheckbox.setSelected(false);
2304           backupsTabUpdatePresets();
2305           backupfilesCustomOptionsSetEnabled();
2306         }
2307       }
2308     });
2309
2310     // dropdown list of preset schemes
2311     gbc.gridx = 1;
2312     presetsPanel.add(backupfilesPresetsCombo, gbc);
2313
2314     revertButton.setText(MessageManager.getString("label.cancel_changes"));
2315     revertButton.setToolTipText(
2316             MessageManager.getString("label.cancel_changes_description"));
2317     revertButton.addActionListener(new ActionListener()
2318     {
2319       @Override
2320       public void actionPerformed(ActionEvent e)
2321       {
2322         backupsSetOptions(
2323                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2324                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2325         backupfilesCustomOptionsSetEnabled();
2326       }
2327
2328     });
2329     revertButton.setFont(LABEL_FONT);
2330
2331     customiseCheckbox.setFont(LABEL_FONT);
2332     customiseCheckbox.setText(MessageManager.getString("label.customise"));
2333     customiseCheckbox.addActionListener(new ActionListener()
2334     {
2335       @Override
2336       public void actionPerformed(ActionEvent e)
2337       {
2338         int currently = getComboIntStringKey(backupfilesPresetsCombo);
2339         if (customiseCheckbox.isSelected())
2340         {
2341           backupfilesPresetsComboLastSelected = currently;
2342           setComboIntStringKey(backupfilesPresetsCombo,
2343                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2344         }
2345         else
2346         {
2347           setComboIntStringKey(backupfilesPresetsCombo,
2348                   backupfilesPresetsComboLastSelected);
2349
2350         }
2351         backupfilesCustomOptionsSetEnabled();
2352       }
2353     });
2354     customiseCheckbox.setToolTipText(
2355             MessageManager.getString("label.customise_description"));
2356
2357     // customise checkbox
2358     gbc.gridx = 0;
2359     gbc.gridy++;
2360     presetsPanel.add(customiseCheckbox, gbc);
2361
2362     // "Cancel changes" button (aligned with combo box above)
2363     gbc.gridx = 1;
2364     presetsPanel.add(revertButton, gbc);
2365
2366     return presetsPanel;
2367   }
2368
2369   private JPanel initBackupsTabFilenameExamplesPanel()
2370   {
2371     String title = MessageManager
2372             .getString("label.scheme_examples");
2373     TitledBorder tb = new TitledBorder(title);
2374     exampleFilesPanel.setBorder(tb);
2375     exampleFilesPanel.setLayout(new GridBagLayout());
2376
2377
2378     backupfilesExampleLabel.setEditable(false);
2379     backupfilesExampleLabel
2380             .setBackground(exampleFilesPanel.getBackground());
2381
2382     updateBackupFilesExampleLabel();
2383
2384     GridBagConstraints gbc = new GridBagConstraints();
2385     gbc.weightx = 1.0;
2386     gbc.weighty = 1.0;
2387     gbc.fill = GridBagConstraints.NONE;
2388     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2389
2390     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2391     return exampleFilesPanel;
2392   }
2393
2394   private void backupsTabUpdatePresets()
2395   {
2396     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2397             .getSelectedItem();
2398     int key = entry.k;
2399     String value = entry.v;
2400
2401     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2402             .containsKey(key))
2403     {
2404       backupsSetOptions(
2405               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2406                       .get(key));
2407     }
2408     else
2409     {
2410       Cache.log.error(
2411               "Preset '" + value + "' [key:" + key + "] not implemented");
2412     }
2413
2414     // Custom options will now be enabled when the customiseCheckbox is checked
2415     // (performed above)
2416     // backupfilesCustomOptionsSetEnabled();
2417     updateBackupFilesExampleLabel();
2418   }
2419
2420   protected int getComboIntStringKey(
2421           JComboBox<Object> backupfilesPresetsCombo2)
2422   {
2423     IntKeyStringValueEntry e;
2424     try
2425     {
2426       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2427               .getSelectedItem();
2428     } catch (Exception ex)
2429     {
2430       Cache.log.error(
2431               "Problem casting Combo entry to IntKeyStringValueEntry.");
2432       e = null;
2433     }
2434     return e != null ? e.k : 0;
2435   }
2436
2437   protected void setComboIntStringKey(
2438           JComboBox<Object> backupfilesPresetsCombo2,
2439           int key)
2440   {
2441     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2442     {
2443       IntKeyStringValueEntry e;
2444       try
2445       {
2446         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2447       } catch (Exception ex)
2448       {
2449         Cache.log.error(
2450                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2451         continue;
2452       }
2453       if (e.k == key)
2454       {
2455         backupfilesPresetsCombo2.setSelectedIndex(i);
2456         break;
2457       }
2458     }
2459     // backupsTabUpdatePresets();
2460   }
2461
2462   private JPanel initBackupsTabSuffixPanel()
2463   {
2464     suffixPanel.setBorder(new TitledBorder(
2465             MessageManager.getString("label.backup_filename_strategy")));
2466     suffixPanel.setLayout(new GridBagLayout());
2467
2468     suffixTemplateLabel
2469             .setText(MessageManager.getString("label.append_to_filename"));
2470     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2471     suffixTemplateLabel.setFont(LABEL_FONT);
2472
2473     final String tooltip = JvSwingUtils.wrapTooltip(true,
2474             MessageManager.getString("label.append_to_filename_tooltip"));
2475     suffixTemplate.setToolTipText(tooltip);
2476     suffixTemplate.addActionListener(new ActionListener()
2477     {
2478       @Override
2479       public void actionPerformed(ActionEvent e)
2480       {
2481         updateBackupFilesExampleLabel();
2482         backupfilesCustomOptionsSetEnabled();
2483         backupfilesRevertButtonSetEnabled(true);
2484       }
2485
2486     });
2487     suffixTemplate.addKeyListener(new KeyListener()
2488     {
2489       @Override
2490       public void keyReleased(KeyEvent e)
2491       {
2492         updateBackupFilesExampleLabel();
2493         backupfilesCustomOptionsSetEnabled();
2494         backupfilesRevertButtonSetEnabled(true);
2495       }
2496
2497       @Override
2498       public void keyPressed(KeyEvent e)
2499       {
2500       }
2501
2502       // disable use of ':' or '/' or '\'
2503       @Override
2504       public void keyTyped(KeyEvent e)
2505       {
2506         char c = e.getKeyChar();
2507         if (c == ':' || c == '/' || c == '\\')
2508         {
2509           // don't process ':' or '/' or '\'
2510           e.consume();
2511         }
2512       }
2513
2514     });
2515
2516     // digits spinner
2517     suffixDigitsLabel
2518             .setText(MessageManager.getString("label.index_digits"));
2519     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2520     suffixDigitsLabel.setFont(LABEL_FONT);
2521     ChangeListener c = new ChangeListener()
2522     {
2523       @Override
2524       public void stateChanged(ChangeEvent e)
2525       {
2526         backupfilesRevertButtonSetEnabled(true);
2527         updateBackupFilesExampleLabel();
2528       }
2529
2530     };
2531     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2532             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2533
2534     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2535             MessageManager.getString("label.increment_index"));
2536     suffixReverse.addActionListener(new ActionListener()
2537     {
2538       @Override
2539       public void actionPerformed(ActionEvent e)
2540       {
2541         boolean okay = true;
2542         if (warnAboutSuffixReverseChange())
2543         {
2544           // Warning popup
2545           okay = confirmSuffixReverseChange();
2546         }
2547         if (okay)
2548         {
2549           backupfilesRevertButtonSetEnabled(true);
2550           updateBackupFilesExampleLabel();
2551         }
2552         else
2553         {
2554           boolean savedSuffixReverse = BackupFilesPresetEntry
2555                   .getSavedBackupEntry().reverse;
2556           suffixReverse.setSelected(savedSuffixReverse);
2557         }
2558       }
2559     });
2560
2561     GridBagConstraints sgbc = new GridBagConstraints();
2562
2563     // first row (template text box)
2564     sgbc.anchor = GridBagConstraints.WEST;
2565     sgbc.gridx = 0;
2566     sgbc.gridy = 0;
2567     sgbc.gridwidth = 1;
2568     sgbc.gridheight = 1;
2569     sgbc.weightx = 1.0;
2570     sgbc.weighty = 0.0;
2571     sgbc.fill = GridBagConstraints.NONE;
2572     suffixPanel.add(suffixTemplateLabel, sgbc);
2573
2574     sgbc.gridx = 1;
2575     sgbc.fill = GridBagConstraints.HORIZONTAL;
2576     suffixPanel.add(suffixTemplate, sgbc);
2577
2578     // second row (number of digits spinner)
2579     sgbc.gridy = 1;
2580
2581     sgbc.gridx = 0;
2582     sgbc.fill = GridBagConstraints.NONE;
2583     suffixPanel.add(suffixDigitsLabel, sgbc);
2584
2585     sgbc.gridx = 1;
2586     sgbc.fill = GridBagConstraints.HORIZONTAL;
2587     suffixPanel.add(suffixDigitsSpinner, sgbc);
2588
2589     // third row (forward order radio selection)
2590     sgbc.gridx = 0;
2591     sgbc.gridy = 2;
2592     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2593     sgbc.fill = GridBagConstraints.HORIZONTAL;
2594     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2595
2596     // fourth row (reverse order radio selection)
2597     sgbc.gridy = 3;
2598     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2599     return suffixPanel;
2600   }
2601
2602   private boolean confirmSuffixReverseChange()
2603   {
2604     boolean ret = false;
2605     String warningMessage = MessageManager
2606             .getString("label.warning_confirm_change_reverse");
2607     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2608             warningMessage,
2609             MessageManager.getString("label.change_increment_decrement"),
2610             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2611
2612     ret = (confirm == JvOptionPane.YES_OPTION);
2613     return ret;
2614   }
2615
2616   private JPanel initBackupsTabKeepFilesPanel()
2617   {
2618     keepfilesPanel.setBorder(
2619             new TitledBorder(MessageManager.getString("label.keep_files")));
2620     keepfilesPanel.setLayout(new GridBagLayout());
2621
2622     backupfilesKeepAll.setLabels(
2623             MessageManager.getString("label.keep_all_backup_files"),
2624             MessageManager.getString(
2625                     "label.keep_only_this_number_of_backup_files"));
2626     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2627     {
2628       @Override
2629       public void actionPerformed(ActionEvent e)
2630       {
2631         backupfilesRevertButtonSetEnabled(true);
2632         updateBackupFilesExampleLabel();
2633       }
2634     });
2635     backupfilesKeepAll.addActionListener(new ActionListener()
2636     {
2637       @Override
2638       public void actionPerformed(ActionEvent e)
2639       {
2640         backupfilesRevertButtonSetEnabled(true);
2641         keepRollMaxOptionsEnabled();
2642         updateBackupFilesExampleLabel();
2643       }
2644     });
2645
2646     ChangeListener c = new ChangeListener()
2647     {
2648       @Override
2649       public void stateChanged(ChangeEvent e)
2650       {
2651         backupfilesRevertButtonSetEnabled(true);
2652         updateBackupFilesExampleLabel();
2653       }
2654
2655     };
2656     setIntegerSpinner(backupfilesRollMaxSpinner,
2657             BackupFilesPresetEntry.ROLLMAXMIN,
2658             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2659
2660     backupfilesConfirmDelete.setLabels(
2661             MessageManager.getString("label.always_ask"),
2662             MessageManager.getString("label.auto_delete"));
2663     backupfilesConfirmDelete.addActionListener(new ActionListener()
2664     {
2665       @Override
2666       public void actionPerformed(ActionEvent e)
2667       {
2668         backupfilesRevertButtonSetEnabled(true);
2669       }
2670     });
2671     // update the enabled section
2672     keepRollMaxOptionsEnabled();
2673
2674     GridBagConstraints kgbc = new GridBagConstraints();
2675
2676     // first row (template text box)
2677     kgbc.anchor = GridBagConstraints.WEST;
2678     kgbc.gridx = 0;
2679     kgbc.gridy = 0;
2680     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2681     kgbc.gridheight = 1;
2682     kgbc.weightx = 1.0;
2683     kgbc.weighty = 0.0;
2684     kgbc.fill = GridBagConstraints.HORIZONTAL;
2685     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2686
2687     // second row
2688     kgbc.gridy = 1;
2689
2690     kgbc.gridx = 0;
2691     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2692     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2693
2694     kgbc.gridx = 1;
2695     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2696     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2697
2698     // third row (indented)
2699     kgbc.gridy = 2;
2700     kgbc.insets = new Insets(0, 20, 0, 0);
2701
2702     kgbc.gridx = 0;
2703     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2704     kgbc.fill = GridBagConstraints.HORIZONTAL;
2705     kgbc.weightx = 1.0;
2706
2707     JPanel jp = new JPanel();
2708     jp.setLayout(new FlowLayout());
2709     oldBackupFilesLabel
2710             .setText(MessageManager
2711                     .getString("label.autodelete_old_backup_files"));
2712     oldBackupFilesLabel.setFont(LABEL_FONT);
2713     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2714     jp.add(oldBackupFilesLabel);
2715     jp.add(backupfilesConfirmDelete.getTrueButton());
2716     jp.add(backupfilesConfirmDelete.getFalseButton());
2717     keepfilesPanel.add(jp, kgbc);
2718
2719     return keepfilesPanel;
2720   }
2721
2722   protected void updateBackupFilesExampleLabel()
2723   {
2724     int exampleindex = 12;
2725     String base = MessageManager.getString("label.filename") + ".fa";
2726     if (base == null || base.length() == 0)
2727     {
2728       base = "file_name.fa";
2729     }
2730
2731     boolean reverse = suffixReverse.isSelected();
2732     boolean keepAll = backupfilesKeepAll.isSelected();
2733     int rollMax = 4;
2734     String suffix = suffixTemplate.getText();
2735     int digits = 3;
2736
2737     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2738     if (suffix == null || suffix.length() == 0)
2739     {
2740       backupfilesExampleLabel
2741               .setText(MessageManager.getString("label.no_backup_files"));
2742       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2743       return;
2744     }
2745
2746     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2747     rollMax = rollMax < 1 ? 1 : rollMax;
2748
2749     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2750     {
2751       rollMax = 1;
2752     }
2753
2754     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2755     digits = digits < 1 ? 1 : digits;
2756
2757     int lowersurround = 2;
2758     int uppersurround = 0;
2759     StringBuilder exampleSB = new StringBuilder();
2760     boolean firstLine = true;
2761     int lineNumber = 0;
2762     if (reverse)
2763     {
2764
2765       int min = 1;
2766       int max = keepAll ? exampleindex : rollMax;
2767       for (int index = min; index <= max; index++)
2768       {
2769         if (index == min + lowersurround && index < max - uppersurround - 1)
2770         {
2771           exampleSB.append("\n...");
2772           lineNumber++;
2773         }
2774         else if (index > min + lowersurround && index < max - uppersurround)
2775         {
2776           // nothing
2777         }
2778         else
2779         {
2780           if (firstLine)
2781           {
2782             firstLine = false;
2783           }
2784           else
2785           {
2786             exampleSB.append("\n");
2787             lineNumber++;
2788           }
2789           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2790                   base, suffix, digits));
2791           if (min == max)
2792           {
2793             // no extra text needed
2794           }
2795           else if (index == min)
2796           {
2797             String newest = MessageManager.getString("label.braced_newest");
2798             if (newest != null && newest.length() > 0)
2799             {
2800               exampleSB.append(" " + newest);
2801             }
2802           }
2803           else if (index == max)
2804           {
2805             String oldest = MessageManager.getString("label.braced_oldest");
2806             if (oldest != null && oldest.length() > 0)
2807             {
2808               exampleSB.append(" " + oldest);
2809             }
2810           }
2811         }
2812       }
2813     }
2814     else
2815     {
2816
2817       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2818               : exampleindex - rollMax + 1;
2819       int max = exampleindex;
2820
2821       for (int index = min; index <= max; index++)
2822       {
2823
2824         if (index == min + lowersurround && index < max - uppersurround - 1)
2825         {
2826           exampleSB.append("\n...");
2827           lineNumber++;
2828         }
2829         else if (index > min + lowersurround && index < max - uppersurround)
2830         {
2831           // nothing
2832         }
2833         else
2834         {
2835           if (firstLine)
2836           {
2837             firstLine = false;
2838           }
2839           else
2840           {
2841             exampleSB.append("\n");
2842             lineNumber++;
2843           }
2844           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2845                   base, suffix, digits));
2846           if (min == max)
2847           {
2848             // no extra text needed
2849           }
2850           else if (index == min)
2851           {
2852             String oldest = MessageManager.getString("label.braced_oldest");
2853             if (oldest != null && oldest.length() > 0)
2854             {
2855               exampleSB.append(" " + oldest);
2856             }
2857           }
2858           else if (index == max)
2859           {
2860             String newest = MessageManager.getString("label.braced_newest");
2861             if (newest != null && newest.length() > 0)
2862             {
2863               exampleSB.append(" " + newest);
2864             }
2865           }
2866         }
2867       }
2868
2869     }
2870
2871     // add some extra empty lines to pad out the example files box. ugh, please tell
2872     // me how to do this better
2873     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2874     if (remainingLines > 0)
2875     {
2876       for (int i = 0; i < remainingLines; i++)
2877       {
2878         exampleSB.append("\n ");
2879         lineNumber++;
2880       }
2881     }
2882
2883     backupfilesExampleLabel.setText(exampleSB.toString());
2884   }
2885
2886   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2887           boolean useExistingVal, ChangeListener c)
2888   {
2889     int i = def;
2890     if (useExistingVal)
2891     {
2892       try
2893       {
2894         i = ((Integer) s.getValue()).intValue();
2895       } catch (Exception e)
2896       {
2897         Cache.log.error(
2898                 "Exception casting the initial value of s.getValue()");
2899       }
2900     }
2901
2902     setIntegerSpinner(s, min, max, i, c);
2903   }
2904
2905   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2906           ChangeListener c)
2907   {
2908     // integer spinner for number of digits
2909     if (def > max)
2910     {
2911       max = def;
2912     }
2913     if (def < min)
2914     {
2915       def = min;
2916     }
2917     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2918     s.setModel(sModel);
2919
2920     s.addChangeListener(c);
2921
2922   }
2923
2924   protected static int getSpinnerInt(JSpinner s, int def)
2925   {
2926     int i = def;
2927     try
2928     {
2929       s.commitEdit();
2930       i = (Integer) s.getValue();
2931     } catch (Exception e)
2932     {
2933       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2934     }
2935     return i;
2936   }
2937
2938   private void keepRollMaxOptionsEnabled()
2939   {
2940     boolean enabled = backupfilesKeepAll.isEnabled()
2941             && !backupfilesKeepAll.isSelected();
2942     oldBackupFilesLabel.setEnabled(enabled);
2943     backupfilesRollMaxSpinner.setEnabled(enabled);
2944     backupfilesConfirmDelete.setEnabled(enabled);
2945   }
2946
2947   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2948   {
2949     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2950             && customiseCheckbox.isSelected()
2951             && suffixTemplate.getText()
2952                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2953     keepfilesPanel.setEnabled(enabled);
2954     backupfilesKeepAll.setEnabled(enabled);
2955     oldBackupFilesLabel.setEnabled(enabled);
2956     keepRollMaxOptionsEnabled();
2957   }
2958
2959   private void backupfilesSuffixTemplateDigitsSetEnabled()
2960   {
2961     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2962             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2963     suffixDigitsLabel.setEnabled(enabled);
2964     suffixDigitsSpinner.setEnabled(enabled);
2965     suffixReverse.setEnabled(enabled);
2966   }
2967
2968   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2969   {
2970     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2971             && customiseCheckbox.isSelected();
2972     suffixPanel.setEnabled(enabled);
2973     suffixTemplateLabel.setEnabled(enabled);
2974     suffixTemplate.setEnabled(enabled);
2975     backupfilesSuffixTemplateDigitsSetEnabled();
2976   }
2977
2978   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2979   {
2980     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2981             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2982     revertButton.setEnabled(enabled);
2983   }
2984
2985   private boolean backupfilesCustomChanged()
2986   {
2987     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2988             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2989     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2990     return !custom.equals(current);
2991   }
2992
2993   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2994   {
2995     String suffix = suffixTemplate.getText();
2996     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2997     boolean reverse = suffixReverse.isSelected();
2998     boolean keepAll = backupfilesKeepAll.isSelected();
2999     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3000     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3001
3002     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3003             reverse, keepAll, rollMax, confirmDelete);
3004
3005     return bfpe;
3006   }
3007
3008   protected void backupfilesCustomOptionsSetEnabled()
3009   {
3010     boolean enabled = customiseCheckbox.isSelected();
3011
3012     backupfilesRevertButtonSetEnabled(enabled);
3013     backupfilesSuffixTemplateSetEnabled(enabled);
3014     backupfilesKeepAllSetEnabled(enabled);
3015   }
3016
3017   private void backupfilesSummarySetEnabled()
3018   {
3019     boolean enabled = enableBackupFiles.isSelected();
3020     backupfilesExampleLabel.setEnabled(enabled);
3021     exampleFilesPanel.setEnabled(enabled);
3022   }
3023
3024   private void backupfilesPresetsSetEnabled()
3025   {
3026     boolean enabled = enableBackupFiles.isSelected();
3027     presetsPanel.setEnabled(enabled);
3028     presetsComboLabel.setEnabled(enabled);
3029     backupfilesPresetsCombo.setEnabled(enabled);
3030     customiseCheckbox.setEnabled(enabled);
3031     revertButton.setEnabled(enabled);
3032   }
3033
3034   protected void backupsOptionsSetEnabled()
3035   {
3036     backupfilesPresetsSetEnabled();
3037     backupfilesSummarySetEnabled();
3038     backupfilesCustomOptionsSetEnabled();
3039   }
3040
3041   protected void backupsSetOptions(String suffix, int digits,
3042           boolean reverse, boolean keepAll, int rollMax,
3043           boolean confirmDelete)
3044   {
3045     suffixTemplate.setText(suffix);
3046     suffixDigitsSpinner.setValue(digits);
3047     suffixReverse.setSelected(reverse);
3048     backupfilesKeepAll.setSelected(keepAll);
3049     backupfilesRollMaxSpinner.setValue(rollMax);
3050     backupfilesConfirmDelete.setSelected(confirmDelete);
3051   }
3052
3053   protected void backupsSetOptions(BackupFilesPresetEntry p)
3054   {
3055     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3056             p.confirmDelete);
3057   }
3058
3059   protected void autoIdWidth_actionPerformed()
3060   {
3061     // TODO Auto-generated method stub
3062
3063   }
3064
3065   protected void userIdWidth_actionPerformed()
3066   {
3067     // TODO Auto-generated method stub
3068
3069   }
3070
3071   protected void maxColour_actionPerformed(JPanel panel)
3072   {
3073   }
3074
3075   protected void minColour_actionPerformed(JPanel panel)
3076   {
3077   }
3078
3079   protected void gapColour_actionPerformed(JPanel panel)
3080   {
3081   }
3082
3083   protected void hiddenColour_actionPerformed(JPanel panel)
3084   {
3085   }
3086
3087   protected void showunconserved_actionPerformed(ActionEvent e)
3088   {
3089     // TODO Auto-generated method stub
3090
3091   }
3092
3093   protected void useLegacyGaps_actionPerformed(ActionEvent e)
3094   {
3095   }
3096
3097   protected void resetOvDefaults_actionPerformed(ActionEvent e)
3098   {
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   public void ok_actionPerformed(ActionEvent e)
3108   {
3109   }
3110
3111   /**
3112    * DOCUMENT ME!
3113    *
3114    * @param e
3115    *          DOCUMENT ME!
3116    */
3117   public void cancel_actionPerformed(ActionEvent e)
3118   {
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   public void annotations_actionPerformed(ActionEvent e)
3128   {
3129   }
3130
3131   /**
3132    * DOCUMENT ME!
3133    */
3134   public void startupFileTextfield_mouseClicked()
3135   {
3136   }
3137
3138   public void newLink_actionPerformed(ActionEvent e)
3139   {
3140
3141   }
3142
3143   public void editLink_actionPerformed(ActionEvent e)
3144   {
3145
3146   }
3147
3148   public void deleteLink_actionPerformed(ActionEvent e)
3149   {
3150
3151   }
3152
3153   public void defaultBrowser_mouseClicked(MouseEvent e)
3154   {
3155
3156   }
3157
3158   public void linkURLList_keyTyped(KeyEvent e)
3159   {
3160
3161   }
3162
3163   public void setProxyAuthEnabled()
3164   {
3165     boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3166     proxyAuthUsernameLabel.setEnabled(enabled);
3167     proxyAuthPasswordLabel.setEnabled(enabled);
3168     passwordNotStoredLabel.setEnabled(enabled);
3169     proxyAuthUsernameTB.setEnabled(enabled);
3170     proxyAuthPasswordPB.setEnabled(enabled);
3171   }
3172
3173   public void setCustomProxyEnabled()
3174   {
3175     boolean enabled = customProxy.isSelected();
3176     portLabel.setEnabled(enabled);
3177     serverLabel.setEnabled(enabled);
3178     portLabel2.setEnabled(enabled);
3179     serverLabel2.setEnabled(enabled);
3180     httpLabel.setEnabled(enabled);
3181     httpsLabel.setEnabled(enabled);
3182     proxyServerHttpTB.setEnabled(enabled);
3183     proxyPortHttpTB.setEnabled(enabled);
3184     proxyServerHttpsTB.setEnabled(enabled);
3185     proxyPortHttpsTB.setEnabled(enabled);
3186     proxyAuth.setEnabled(enabled);
3187     setProxyAuthEnabled();
3188   }
3189
3190   public void proxyType_actionPerformed()
3191   {
3192     setCustomProxyEnabled();
3193   }
3194
3195   public void proxyAuth_actionPerformed()
3196   {
3197     setProxyAuthEnabled();
3198   }
3199
3200   /**
3201    * Customer renderer for JTable: supports column of radio buttons
3202    */
3203   public class RadioButtonRenderer extends JRadioButton
3204           implements TableCellRenderer
3205   {
3206     public RadioButtonRenderer()
3207     {
3208       setHorizontalAlignment(CENTER);
3209       setToolTipText(MessageManager.getString("label.urltooltip"));
3210     }
3211
3212     @Override
3213     public Component getTableCellRendererComponent(JTable table,
3214             Object value, boolean isSelected, boolean hasFocus, int row,
3215             int column)
3216     {
3217       setSelected((boolean) value);
3218
3219       // set colours to match rest of table
3220       if (isSelected)
3221       {
3222         setBackground(table.getSelectionBackground());
3223         setForeground(table.getSelectionForeground());
3224       }
3225       else
3226       {
3227         setBackground(table.getBackground());
3228         setForeground(table.getForeground());
3229       }
3230       return this;
3231     }
3232   }
3233
3234   /**
3235    * Customer cell editor for JTable: supports column of radio buttons in
3236    * conjunction with renderer
3237    */
3238   public class RadioButtonEditor extends AbstractCellEditor
3239           implements TableCellEditor
3240   {
3241     private JRadioButton button = new JRadioButton();
3242
3243     public RadioButtonEditor()
3244     {
3245       button.setHorizontalAlignment(SwingConstants.CENTER);
3246       this.button.addActionListener(new ActionListener()
3247       {
3248         @Override
3249         public void actionPerformed(ActionEvent e)
3250         {
3251           fireEditingStopped();
3252         }
3253       });
3254     }
3255
3256     @Override
3257     public Component getTableCellEditorComponent(JTable table, Object value,
3258             boolean isSelected, int row, int column)
3259     {
3260       button.setSelected((boolean) value);
3261       return button;
3262     }
3263
3264     @Override
3265     public Object getCellEditorValue()
3266     {
3267       return button.isSelected();
3268     }
3269
3270   }
3271 }
3272