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
 994     // check for any change to enable applyProxyButton
 995     DocumentListener d = new DocumentListener()
 996     {
 997       @Override
 998       public void changedUpdate(DocumentEvent e)
 999       {
1000         applyProxyButtonEnabled(true);
1001       }
1002
1003       @Override
1004       public void insertUpdate(DocumentEvent e)
1005       {
1006         applyProxyButtonEnabled(true);
1007       }
1008
1009       @Override
1010       public void removeUpdate(DocumentEvent e)
1011       {
1012         applyProxyButtonEnabled(true);
1013       }
1014     };
1015     proxyServerHttpTB.getDocument().addDocumentListener(d);
1016     proxyPortHttpTB.getDocument().addDocumentListener(d);
1017     proxyServerHttpsTB.getDocument().addDocumentListener(d);
1018     proxyPortHttpsTB.getDocument().addDocumentListener(d);
1019     proxyAuthUsernameTB.getDocument().addDocumentListener(d);
1020     proxyAuthPasswordPB.setFont(LABEL_FONT);
1021     proxyAuthPasswordPB.setColumns(30);
1022     proxyAuthPasswordPB.getDocument()
1023             .addDocumentListener(new DocumentListener()
1024             {
1025               @Override
1026               public void changedUpdate(DocumentEvent e)
1027               {
1028                 proxyAuthPasswordCheckHighlight(true);
1029                 applyProxyButtonEnabled(true);
1030               }
1031
1032               @Override
1033               public void insertUpdate(DocumentEvent e)
1034               {
1035                 proxyAuthPasswordCheckHighlight(true);
1036                 applyProxyButtonEnabled(true);
1037               }
1038
1039               @Override
1040               public void removeUpdate(DocumentEvent e)
1041               {
1042                 proxyAuthPasswordCheckHighlight(true);
1043                 applyProxyButtonEnabled(true);
1044               }
1045
1046             });
1047
1048     // Label for Port text box
1049     portLabel.setFont(LABEL_FONT);
1050     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1051     portLabel.setText(MessageManager.getString("label.port") + ": ");
1052     portLabel2.setFont(LABEL_FONT);
1053     portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1054     portLabel2.setText(MessageManager.getString("label.port") + ": ");
1055
1056     httpLabel.setText("HTTP");
1057     httpLabel.setFont(LABEL_FONT_BOLD);
1058     httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1059     httpsLabel.setText("HTTPS");
1060     httpsLabel.setFont(LABEL_FONT_BOLD);
1061     httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1062
1063     proxyAuthUsernameLabel
1064             .setText(MessageManager.getString("label.username") + ": ");
1065     proxyAuthUsernameLabel.setFont(LABEL_FONT);
1066     proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1067     proxyAuthPasswordLabel
1068             .setText(MessageManager.getString("label.password") + ": ");
1069     proxyAuthPasswordLabel.setFont(LABEL_FONT);
1070     proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1071     passwordNotStoredLabel.setText(
1072             "(" + MessageManager.getString("label.not_stored") + ")");
1073     passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1074     passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1075
1076     // Proxy type radio buttons
1077     noProxy.setFont(LABEL_FONT);
1078     noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1079     noProxy.setText(MessageManager.getString("label.no_proxy"));
1080     systemProxy.setFont(LABEL_FONT);
1081     systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1082     systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1083             displayUserHostPort(Cache.startupProxyProperties[4],
1084                     Cache.startupProxyProperties[0],
1085                     Cache.startupProxyProperties[1]),
1086             displayUserHostPort(Cache.startupProxyProperties[6],
1087                     Cache.startupProxyProperties[2],
1088                     Cache.startupProxyProperties[3])));
1089     customProxy.setFont(LABEL_FONT);
1090     customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1091     customProxy.setText(
1092             MessageManager.getString("label.use_proxy_server") + ":");
1093     ActionListener al = new ActionListener()
1094     {
1095       @Override
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         proxyType_actionPerformed();
1099       }
1100     };
1101     noProxy.addActionListener(al);
1102     systemProxy.addActionListener(al);
1103     customProxy.addActionListener(al);
1104     proxyType.add(noProxy);
1105     proxyType.add(systemProxy);
1106     proxyType.add(customProxy);
1107
1108     proxyAuth.setFont(LABEL_FONT);
1109     proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1110     proxyAuth.setText(MessageManager.getString("label.auth_required"));
1111     proxyAuth.addActionListener(new ActionListener()
1112     {
1113       @Override
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         proxyAuth_actionPerformed();
1117       }
1118     });
1119
1120     setCustomProxyEnabled();
1121
1122     // Make proxy server panel
1123     JPanel proxyPanel = new JPanel();
1124     TitledBorder titledBorder1 = new TitledBorder(
1125             MessageManager.getString("label.proxy_servers"));
1126     proxyPanel.setBorder(titledBorder1);
1127     proxyPanel.setLayout(new GridBagLayout());
1128     GridBagConstraints gbc = new GridBagConstraints();
1129     gbc.fill = GridBagConstraints.HORIZONTAL;
1130     gbc.weightx = 1.0;
1131
1132     GridBagConstraints c = new GridBagConstraints();
1133     // Proxy type radio buttons (3)
1134     JPanel ptPanel = new JPanel();
1135     ptPanel.setLayout(new GridBagLayout());
1136     c.weightx = 1.0;
1137     c.gridy = 0;
1138     c.gridx = 0;
1139     c.gridwidth = 1;
1140     c.fill = GridBagConstraints.HORIZONTAL;
1141     ptPanel.add(noProxy, c);
1142     c.gridy++;
1143     ptPanel.add(systemProxy, c);
1144     c.gridy++;
1145     ptPanel.add(customProxy, c);
1146
1147     gbc.gridy = 0;
1148     proxyPanel.add(ptPanel, gbc);
1149
1150     // host and port text boxes
1151     JPanel hpPanel = new JPanel();
1152     hpPanel.setLayout(new GridBagLayout());
1153     // HTTP host port row
1154     c.gridy = 0;
1155     c.gridx = 0;
1156
1157     c.weightx = 0.1;
1158     c.anchor = GridBagConstraints.LINE_START;
1159     hpPanel.add(httpLabel, c);
1160
1161     c.gridx++;
1162     c.weightx = 0.1;
1163     c.anchor = GridBagConstraints.LINE_END;
1164     hpPanel.add(serverLabel, c);
1165
1166     c.gridx++;
1167     c.weightx = 1.0;
1168     c.anchor = GridBagConstraints.LINE_START;
1169     hpPanel.add(proxyServerHttpTB, c);
1170
1171     c.gridx++;
1172     c.weightx = 0.1;
1173     c.anchor = GridBagConstraints.LINE_END;
1174     hpPanel.add(portLabel, c);
1175
1176     c.gridx++;
1177     c.weightx = 0.2;
1178     c.anchor = GridBagConstraints.LINE_START;
1179     hpPanel.add(proxyPortHttpTB, c);
1180
1181     // HTTPS host port row
1182     c.gridy++;
1183     c.gridx = 0;
1184     c.gridwidth = 1;
1185
1186     c.anchor = GridBagConstraints.LINE_START;
1187     hpPanel.add(httpsLabel, c);
1188
1189     c.gridx++;
1190     c.anchor = GridBagConstraints.LINE_END;
1191     hpPanel.add(serverLabel2, c);
1192
1193     c.gridx++;
1194     c.anchor = GridBagConstraints.LINE_START;
1195     hpPanel.add(proxyServerHttpsTB, c);
1196
1197     c.gridx++;
1198     c.anchor = GridBagConstraints.LINE_END;
1199     hpPanel.add(portLabel2, c);
1200
1201     c.gridx++;
1202     c.anchor = GridBagConstraints.LINE_START;
1203     hpPanel.add(proxyPortHttpsTB, c);
1204
1205     gbc.gridy++;
1206     proxyPanel.add(hpPanel, gbc);
1207
1208     if (!Platform.isJS())
1209     /**
1210      * java.net.Authenticator is not implemented in SwingJS. Not displaying the
1211      * Authentication options in Preferences.
1212      *
1213      * @j2sIgnore
1214      *
1215      */
1216     {
1217       // Require authentication checkbox
1218       gbc.gridy++;
1219       proxyPanel.add(proxyAuth, gbc);
1220
1221       // username and password
1222       JPanel upPanel = new JPanel();
1223       upPanel.setLayout(new GridBagLayout());
1224       // username row
1225       c.gridy = 0;
1226       c.gridx = 0;
1227       c.gridwidth = 1;
1228       c.weightx = 0.4;
1229       c.anchor = GridBagConstraints.LINE_END;
1230       upPanel.add(proxyAuthUsernameLabel, c);
1231
1232       c.gridx++;
1233       c.weightx = 1.0;
1234       c.anchor = GridBagConstraints.LINE_START;
1235       upPanel.add(proxyAuthUsernameTB, c);
1236
1237       // password row
1238       c.gridy++;
1239       c.gridx = 0;
1240       c.weightx = 0.4;
1241       c.anchor = GridBagConstraints.LINE_END;
1242       upPanel.add(proxyAuthPasswordLabel, c);
1243
1244       c.gridx++;
1245       c.weightx = 1.0;
1246       c.anchor = GridBagConstraints.LINE_START;
1247       upPanel.add(proxyAuthPasswordPB, c);
1248
1249       c.gridx++;
1250       c.weightx = 0.4;
1251       c.anchor = GridBagConstraints.LINE_START;
1252       upPanel.add(passwordNotStoredLabel, c);
1253
1254       gbc.gridy++;
1255       proxyPanel.add(upPanel, gbc);
1256
1257     } // end j2sIgnore
1258
1259     applyProxyButton.setText(MessageManager.getString("action.apply"));
1260     applyProxyButton.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         saveProxySettings();
1266         applyProxyButton.setEnabled(false);
1267       }
1268     });
1269     gbc.gridy++;
1270     gbc.fill = GridBagConstraints.NONE;
1271     gbc.anchor = GridBagConstraints.LINE_END;
1272     proxyPanel.add(applyProxyButton, gbc);
1273
1274     return proxyPanel;
1275   }
1276
1277   public void proxyAuthPasswordCheckHighlight(boolean enabled)
1278   {
1279     proxyAuthPasswordCheckHighlight(enabled, false);
1280   }
1281
1282   public void proxyAuthPasswordCheckHighlight(boolean enabled,
1283           boolean grabFocus)
1284   {
1285     if (enabled && proxyType.isSelected(customProxy.getModel())
1286             && proxyAuth.isSelected()
1287             && !proxyAuthUsernameTB.getText().isEmpty()
1288             && proxyAuthPasswordPB.getDocument().getLength() == 0)
1289     {
1290       if (grabFocus)
1291         proxyAuthPasswordPB.grabFocus();
1292       proxyAuthPasswordPB.setBackground(Color.PINK);
1293     }
1294     else
1295     {
1296       proxyAuthPasswordPB.setBackground(Color.WHITE);
1297     }
1298   }
1299
1300   public void applyProxyButtonEnabled(boolean enabled)
1301   {
1302     applyProxyButton.setEnabled(enabled);
1303   }
1304
1305   public void saveProxySettings()
1306   {
1307     // overridden in Preferences
1308   }
1309
1310   private String displayUserHostPort(String user, String host, String port)
1311   {
1312     boolean hostBlank = (host == null || host.isEmpty());
1313     boolean portBlank = (port == null || port.isEmpty());
1314     if (hostBlank && portBlank)
1315     {
1316       return MessageManager.getString("label.none");
1317     }
1318
1319     StringBuilder sb = new StringBuilder();
1320     if (user != null)
1321     {
1322       sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1323               : user);
1324       sb.append("@");
1325     }
1326     sb.append(hostBlank ? "" : host);
1327     if (!portBlank)
1328     {
1329       sb.append(":");
1330       sb.append(port);
1331     }
1332     return sb.toString();
1333   }
1334
1335   /**
1336    * Initialises the checkboxes in the Connections tab
1337    */
1338   private void initConnTabCheckboxes()
1339   {
1340     // Usage stats checkbox label
1341     usagestats.setText(
1342             MessageManager.getString("label.send_usage_statistics"));
1343     usagestats.setFont(LABEL_FONT);
1344     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1345     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1346
1347     // Questionnaire checkbox label
1348     questionnaire.setText(
1349             MessageManager.getString("label.check_for_questionnaires"));
1350     questionnaire.setFont(LABEL_FONT);
1351     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1352     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1353
1354     // Check for latest version checkbox label
1355     versioncheck.setText(
1356             MessageManager.getString("label.check_for_latest_version"));
1357     versioncheck.setFont(LABEL_FONT);
1358     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1359     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1360   }
1361
1362   /**
1363    * Initialises the parent panel which contains the tabbed sections.
1364    *
1365    * @return
1366    */
1367   private JPanel initOkCancelPanel()
1368   {
1369     JButton ok = new JButton();
1370     ok.setText(MessageManager.getString("action.ok"));
1371     ok.addActionListener(new ActionListener()
1372     {
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         ok_actionPerformed(e);
1377       }
1378     });
1379     JButton cancel = new JButton();
1380     cancel.setText(MessageManager.getString("action.cancel"));
1381     cancel.addActionListener(new ActionListener()
1382     {
1383       @Override
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         cancel_actionPerformed(e);
1387       }
1388     });
1389     JPanel okCancelPanel = new JPanel();
1390     okCancelPanel.add(ok);
1391     okCancelPanel.add(cancel);
1392     return okCancelPanel;
1393   }
1394
1395   /**
1396    * Initialises the Colours tabbed panel.
1397    *
1398    * @return
1399    */
1400   private JPanel initColoursTab()
1401   {
1402     JPanel coloursTab = new JPanel();
1403     coloursTab.setBorder(new TitledBorder(
1404             MessageManager.getString("action.open_new_alignment")));
1405     coloursTab.setLayout(new FlowLayout());
1406     JLabel mincolourLabel = new JLabel();
1407     mincolourLabel.setFont(LABEL_FONT);
1408     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1409     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1410     minColour.setFont(LABEL_FONT);
1411     minColour.setBorder(BorderFactory.createEtchedBorder());
1412     minColour.setPreferredSize(new Dimension(40, 20));
1413     minColour.addMouseListener(new MouseAdapter()
1414     {
1415       @Override
1416       public void mousePressed(MouseEvent e)
1417       {
1418         minColour_actionPerformed(minColour);
1419       }
1420     });
1421     JLabel maxcolourLabel = new JLabel();
1422     maxcolourLabel.setFont(LABEL_FONT);
1423     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1424     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1425     maxColour.setFont(LABEL_FONT);
1426     maxColour.setBorder(BorderFactory.createEtchedBorder());
1427     maxColour.setPreferredSize(new Dimension(40, 20));
1428     maxColour.addMouseListener(new MouseAdapter()
1429     {
1430       @Override
1431       public void mousePressed(MouseEvent e)
1432       {
1433         maxColour_actionPerformed(maxColour);
1434       }
1435     });
1436
1437     protColour.setFont(LABEL_FONT);
1438     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1439     JLabel protColourLabel = new JLabel();
1440     protColourLabel.setFont(LABEL_FONT);
1441     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1442     protColourLabel.setText(
1443             MessageManager.getString("label.prot_alignment_colour") + " ");
1444     JvSwingUtils.addtoLayout(coloursTab,
1445             MessageManager
1446                     .getString("label.default_colour_scheme_for_alignment"),
1447             protColourLabel, protColour);
1448
1449     nucColour.setFont(LABEL_FONT);
1450     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1451     JLabel nucColourLabel = new JLabel();
1452     nucColourLabel.setFont(LABEL_FONT);
1453     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1454     nucColourLabel.setText(
1455             MessageManager.getString("label.nuc_alignment_colour") + " ");
1456     JvSwingUtils.addtoLayout(coloursTab,
1457             MessageManager
1458                     .getString("label.default_colour_scheme_for_alignment"),
1459             nucColourLabel, nucColour);
1460
1461     JPanel annotationShding = new JPanel();
1462     annotationShding.setBorder(new TitledBorder(
1463             MessageManager.getString("label.annotation_shading_default")));
1464     annotationShding.setLayout(new GridLayout(1, 2));
1465     JvSwingUtils.addtoLayout(annotationShding,
1466             MessageManager.getString(
1467                     "label.default_minimum_colour_annotation_shading"),
1468             mincolourLabel, minColour);
1469     JvSwingUtils.addtoLayout(annotationShding,
1470             MessageManager.getString(
1471                     "label.default_maximum_colour_annotation_shading"),
1472             maxcolourLabel, maxColour);
1473     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1474     return coloursTab;
1475   }
1476
1477   /**
1478    * Initialises the Overview tabbed panel.
1479    *
1480    * @return
1481    */
1482   private JPanel initOverviewTab()
1483   {
1484     JPanel overviewPanel = new JPanel();
1485     overviewPanel.setBorder(new TitledBorder(
1486             MessageManager.getString("label.overview_settings")));
1487
1488     gapColour.setFont(LABEL_FONT);
1489     // fixing the border colours stops apparent colour bleed from the panel
1490     gapColour.setBorder(
1491             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1492     gapColour.setPreferredSize(new Dimension(40, 20));
1493     gapColour.addMouseListener(new MouseAdapter()
1494     {
1495       @Override
1496       public void mousePressed(MouseEvent e)
1497       {
1498         gapColour_actionPerformed(gapColour);
1499       }
1500     });
1501
1502     hiddenColour.setFont(LABEL_FONT);
1503     // fixing the border colours stops apparent colour bleed from the panel
1504     hiddenColour.setBorder(
1505             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1506     hiddenColour.setPreferredSize(new Dimension(40, 20));
1507     hiddenColour.addMouseListener(new MouseAdapter()
1508     {
1509       @Override
1510       public void mousePressed(MouseEvent e)
1511       {
1512         hiddenColour_actionPerformed(hiddenColour);
1513       }
1514     });
1515
1516     useLegacyGap = new JCheckBox(
1517             MessageManager.getString("label.ov_legacy_gap"));
1518     useLegacyGap.setFont(LABEL_FONT);
1519     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1520     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1521     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1522     gapLabel.setFont(LABEL_FONT);
1523     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1524     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1525     showHiddenAtStart = new JCheckBox(
1526             MessageManager.getString("label.ov_show_hide_default"));
1527     showHiddenAtStart.setFont(LABEL_FONT);
1528     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1529     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1530     JLabel hiddenLabel = new JLabel(
1531             MessageManager.getString("label.hidden_colour"));
1532     hiddenLabel.setFont(LABEL_FONT);
1533     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1534     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1535
1536     useLegacyGap.addActionListener(new ActionListener()
1537     {
1538       @Override
1539       public void actionPerformed(ActionEvent e)
1540       {
1541         useLegacyGaps_actionPerformed(e);
1542       }
1543     });
1544
1545     overviewPanel.setLayout(new GridBagLayout());
1546     GridBagConstraints c1 = new GridBagConstraints();
1547
1548     c1.fill = GridBagConstraints.HORIZONTAL;
1549     c1.gridx = 0;
1550     c1.gridy = 0;
1551     c1.weightx = 1;
1552     c1.ipady = 20;
1553     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1554     overviewPanel.add(useLegacyGap, c1);
1555
1556     GridBagConstraints c2 = new GridBagConstraints();
1557     c2.fill = GridBagConstraints.HORIZONTAL;
1558     c2.gridx = 1;
1559     c2.gridy = 0;
1560     c2.insets = new Insets(0, 15, 0, 10);
1561     overviewPanel.add(gapLabel, c2);
1562
1563     GridBagConstraints c3 = new GridBagConstraints();
1564     c3.fill = GridBagConstraints.HORIZONTAL;
1565     c3.gridx = 2;
1566     c3.gridy = 0;
1567     c3.insets = new Insets(0, 0, 0, 15);
1568     overviewPanel.add(gapColour, c3);
1569
1570     GridBagConstraints c4 = new GridBagConstraints();
1571     c4.fill = GridBagConstraints.HORIZONTAL;
1572     c4.gridx = 0;
1573     c4.gridy = 1;
1574     c4.weightx = 1;
1575     overviewPanel.add(showHiddenAtStart, c4);
1576
1577     GridBagConstraints c5 = new GridBagConstraints();
1578     c5.fill = GridBagConstraints.HORIZONTAL;
1579     c5.gridx = 1;
1580     c5.gridy = 1;
1581     c5.insets = new Insets(0, 15, 0, 10);
1582     overviewPanel.add(hiddenLabel, c5);
1583
1584     GridBagConstraints c6 = new GridBagConstraints();
1585     c6.fill = GridBagConstraints.HORIZONTAL;
1586     c6.gridx = 2;
1587     c6.gridy = 1;
1588     c6.insets = new Insets(0, 0, 0, 15);
1589     overviewPanel.add(hiddenColour, c6);
1590
1591     JButton resetButton = new JButton(
1592             MessageManager.getString("label.reset_to_defaults"));
1593
1594     resetButton.addActionListener(new ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         resetOvDefaults_actionPerformed(e);
1600       }
1601     });
1602
1603     GridBagConstraints c7 = new GridBagConstraints();
1604     c7.fill = GridBagConstraints.NONE;
1605     c7.gridx = 0;
1606     c7.gridy = 2;
1607     c7.insets = new Insets(10, 0, 0, 0);
1608     c7.anchor = GridBagConstraints.WEST;
1609     overviewPanel.add(resetButton, c7);
1610
1611     // Add padding so the panel doesn't look ridiculous
1612     JPanel spacePanel = new JPanel();
1613     overviewPanel.add(spacePanel,
1614             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1615                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1616                     new Insets(0, 0, 0, 5), 0, 0));
1617
1618     return overviewPanel;
1619   }
1620
1621   /**
1622    * Initialises the Structure tabbed panel.
1623    *
1624    * @return
1625    */
1626   private JPanel initStructureTab()
1627   {
1628     structureTab = new JPanel();
1629
1630     structureTab.setBorder(new TitledBorder(
1631             MessageManager.getString("label.structure_options")));
1632     structureTab.setLayout(null);
1633     final int width = 420;
1634     final int height = 22;
1635     final int lineSpacing = 25;
1636     int ypos = 15;
1637
1638     structFromPdb.setFont(LABEL_FONT);
1639     structFromPdb
1640             .setText(MessageManager.getString("label.struct_from_pdb"));
1641     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1642     structFromPdb.addActionListener(new ActionListener()
1643     {
1644       @Override
1645       public void actionPerformed(ActionEvent e)
1646       {
1647         boolean selected = structFromPdb.isSelected();
1648         // enable other options only when the first is checked
1649         useRnaView.setEnabled(selected);
1650         addSecondaryStructure.setEnabled(selected);
1651         addTempFactor.setEnabled(selected);
1652       }
1653     });
1654     structureTab.add(structFromPdb);
1655
1656     // indent checkboxes that are conditional on the first one
1657     ypos += lineSpacing;
1658     useRnaView.setFont(LABEL_FONT);
1659     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1660     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1661     structureTab.add(useRnaView);
1662
1663     ypos += lineSpacing;
1664     addSecondaryStructure.setFont(LABEL_FONT);
1665     addSecondaryStructure
1666             .setText(MessageManager.getString("label.autoadd_secstr"));
1667     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1668     structureTab.add(addSecondaryStructure);
1669
1670     ypos += lineSpacing;
1671     addTempFactor.setFont(LABEL_FONT);
1672     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1673     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1674     structureTab.add(addTempFactor);
1675
1676     ypos += lineSpacing;
1677     JLabel viewerLabel = new JLabel();
1678     viewerLabel.setFont(LABEL_FONT);
1679     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1680     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1681     viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1682     structureTab.add(viewerLabel);
1683
1684     /*
1685      * add all external viewers as options here - check
1686      * when selected whether the program is installed
1687      */
1688     structViewer.setFont(LABEL_FONT);
1689     structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1690     structViewer.addItem(ViewerType.JMOL.name());
1691     structViewer.addItem(ViewerType.CHIMERA.name());
1692     structViewer.addItem(ViewerType.CHIMERAX.name());
1693     structViewer.addItem(ViewerType.PYMOL.name());
1694     structViewer.addActionListener(new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent e)
1698       {
1699         structureViewer_actionPerformed(
1700                 (String) structViewer.getSelectedItem());
1701       }
1702     });
1703     structureTab.add(structViewer);
1704
1705     ypos += lineSpacing;
1706     structureViewerPathLabel = new JLabel();
1707     structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
1708                                                  // 11));
1709     structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1710     structureViewerPathLabel.setText(MessageManager
1711             .formatMessage("label.viewer_path", "Chimera(X)"));
1712     structureViewerPathLabel
1713             .setBounds(new Rectangle(10, ypos, 170, height));
1714     structureViewerPathLabel.setEnabled(false);
1715     structureTab.add(structureViewerPathLabel);
1716
1717     structureViewerPath.setFont(LABEL_FONT);
1718     structureViewerPath.setText("");
1719     structureViewerPath.setEnabled(false);
1720     final String tooltip = JvSwingUtils.wrapTooltip(true,
1721             MessageManager.getString("label.viewer_path_tip"));
1722     structureViewerPath.setToolTipText(tooltip);
1723     structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1724     structureViewerPath.addMouseListener(new MouseAdapter()
1725     {
1726       @Override
1727       public void mouseClicked(MouseEvent e)
1728       {
1729         if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1730         {
1731           String chosen = openFileChooser();
1732           if (chosen != null)
1733           {
1734             structureViewerPath.setText(chosen);
1735           }
1736         }
1737       }
1738     });
1739     structureTab.add(structureViewerPath);
1740
1741     ypos += lineSpacing;
1742     nwMapping.setFont(LABEL_FONT);
1743     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1744     siftsMapping.setFont(LABEL_FONT);
1745     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1746     mappingMethod.add(nwMapping);
1747     mappingMethod.add(siftsMapping);
1748     JPanel mappingPanel = new JPanel();
1749     mappingPanel.setFont(LABEL_FONT);
1750     TitledBorder mmTitledBorder = new TitledBorder(
1751             MessageManager.getString("label.mapping_method"));
1752     mmTitledBorder.setTitleFont(LABEL_FONT);
1753     mappingPanel.setBorder(mmTitledBorder);
1754     mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1755     // GridLayout mappingLayout = new GridLayout();
1756     mappingPanel.setLayout(new GridLayout());
1757     mappingPanel.add(nwMapping);
1758     mappingPanel.add(siftsMapping);
1759     structureTab.add(mappingPanel);
1760
1761     ypos += lineSpacing;
1762     ypos += lineSpacing;
1763     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1764             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1765     docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1766     structureTab.add(docFieldPref);
1767
1768     /*
1769      * hide Chimera options in JalviewJS
1770      */
1771     if (Platform.isJS())
1772     {
1773       structureViewerPathLabel.setVisible(false);
1774       structureViewerPath.setVisible(false);
1775       viewerLabel.setVisible(false);
1776       structViewer.setVisible(false);
1777     }
1778
1779     return structureTab;
1780   }
1781
1782   /**
1783    * Action on choosing a structure viewer from combobox options.
1784    *
1785    * @param selectedItem
1786    */
1787   protected void structureViewer_actionPerformed(String selectedItem)
1788   {
1789   }
1790
1791   /**
1792    * Show a dialog for the user to choose a file. Returns the chosen path, or
1793    * null on Cancel.
1794    *
1795    * @return
1796    */
1797   protected String openFileChooser()
1798   {
1799     String choice = null;
1800     JFileChooser chooser = new JFileChooser();
1801
1802     // Enable appBundleIsTraversable in macOS FileChooser to allow selecting
1803     // hidden executables within .app dirs
1804     if (Platform.isMac())
1805     {
1806       chooser.putClientProperty("JFileChooser.appBundleIsTraversable",
1807               true);
1808     }
1809
1810     // chooser.setFileView(new JalviewFileView());
1811     chooser.setDialogTitle(
1812             MessageManager.getString("label.open_local_file"));
1813     chooser.setToolTipText(MessageManager.getString("action.open"));
1814
1815     int value = chooser.showOpenDialog(this);
1816
1817     if (value == JFileChooser.APPROVE_OPTION)
1818     {
1819       choice = chooser.getSelectedFile().getPath();
1820     }
1821     return choice;
1822   }
1823
1824   /**
1825    * Validate the structure tab preferences; if invalid, set focus on this tab.
1826    *
1827    * @param e
1828    */
1829   protected boolean validateStructure(FocusEvent e)
1830   {
1831     if (!validateStructure())
1832     {
1833       e.getComponent().requestFocusInWindow();
1834       return false;
1835     }
1836     return true;
1837   }
1838
1839   protected boolean validateStructure()
1840   {
1841     return false;
1842   }
1843
1844   /**
1845    * Initialises the Visual tabbed panel.
1846    *
1847    * @return
1848    */
1849   private JPanel initVisualTab()
1850   {
1851     JPanel visualTab = new JPanel();
1852     visualTab.setBorder(new TitledBorder(
1853             MessageManager.getString("action.open_new_alignment")));
1854     visualTab.setLayout(null);
1855     fullScreen.setFont(LABEL_FONT);
1856     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1857     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1858     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1859     quality.setEnabled(false);
1860     quality.setFont(LABEL_FONT);
1861     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1862     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1863     quality.setSelected(true);
1864     quality.setText(MessageManager.getString("label.quality"));
1865     conservation.setEnabled(false);
1866     conservation.setFont(LABEL_FONT);
1867     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1868     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1869     conservation.setSelected(true);
1870     conservation.setText(MessageManager.getString("label.conservation"));
1871     identity.setEnabled(false);
1872     identity.setFont(LABEL_FONT);
1873     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1874     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1875     identity.setSelected(true);
1876     identity.setText(MessageManager.getString("label.consensus"));
1877     showOccupancy.setFont(LABEL_FONT);
1878     showOccupancy.setEnabled(false);
1879     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1880     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1881     showOccupancy.setSelected(true);
1882     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1883
1884     JLabel showGroupbits = new JLabel();
1885     showGroupbits.setFont(LABEL_FONT);
1886     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1887     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1888     showGroupbits
1889             .setText(MessageManager.getString("action.show_group") + ":");
1890     JLabel showConsensbits = new JLabel();
1891     showConsensbits.setFont(LABEL_FONT);
1892     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1893     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1894     showConsensbits
1895             .setText(MessageManager.getString("label.consensus") + ":");
1896     showConsensHistogram.setEnabled(false);
1897     showConsensHistogram.setFont(LABEL_FONT);
1898     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1899     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1900     showConsensHistogram.setSelected(true);
1901     showConsensHistogram
1902             .setText(MessageManager.getString("label.histogram"));
1903     showConsensLogo.setEnabled(false);
1904     showConsensLogo.setFont(LABEL_FONT);
1905     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1906     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1907     showConsensLogo.setSelected(true);
1908     showConsensLogo.setText(MessageManager.getString("label.logo"));
1909     showGroupConsensus.setEnabled(false);
1910     showGroupConsensus.setFont(LABEL_FONT);
1911     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1912     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1913     showGroupConsensus.setSelected(true);
1914     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1915     showGroupConservation.setEnabled(false);
1916     showGroupConservation.setFont(LABEL_FONT);
1917     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1918     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1919     showGroupConservation.setSelected(true);
1920     showGroupConservation
1921             .setText(MessageManager.getString("label.conservation"));
1922     showNpTooltip.setEnabled(true);
1923     showNpTooltip.setFont(LABEL_FONT);
1924     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1925     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1926     showNpTooltip.setSelected(true);
1927     showNpTooltip.setText(
1928             MessageManager.getString("label.non_positional_features"));
1929     showDbRefTooltip.setEnabled(true);
1930     showDbRefTooltip.setFont(LABEL_FONT);
1931     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1932     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1933     showDbRefTooltip.setSelected(true);
1934     showDbRefTooltip
1935             .setText(MessageManager.getString("label.database_references"));
1936     annotations.setFont(LABEL_FONT);
1937     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1938     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1939     annotations.setSelected(true);
1940     annotations.setText(MessageManager.getString("label.show_annotations"));
1941     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1942     annotations.addActionListener(new ActionListener()
1943     {
1944       @Override
1945       public void actionPerformed(ActionEvent e)
1946       {
1947         annotations_actionPerformed(e);
1948       }
1949     });
1950     identity.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         annotations_actionPerformed(e);
1956       }
1957     });
1958     showGroupConsensus.addActionListener(new ActionListener()
1959     {
1960       @Override
1961       public void actionPerformed(ActionEvent e)
1962       {
1963         annotations_actionPerformed(e);
1964       }
1965     });
1966     showUnconserved.setFont(LABEL_FONT);
1967     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1968     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1969     showUnconserved.setSelected(true);
1970     showUnconserved
1971             .setText(MessageManager.getString("action.show_unconserved"));
1972     showUnconserved.addActionListener(new ActionListener()
1973     {
1974       @Override
1975       public void actionPerformed(ActionEvent e)
1976       {
1977         showunconserved_actionPerformed(e);
1978       }
1979     });
1980
1981     // TODO these are not yet added to / action from Preferences
1982     // JCheckBox shareSelections = new JCheckBox();
1983     // shareSelections.setFont(verdana11);
1984     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1985     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1986     // shareSelections.setSelected(true);
1987     // shareSelections.setText(MessageManager
1988     // .getString("label.share_selection_across_views"));
1989     // JCheckBox followHighlight = new JCheckBox();
1990     // followHighlight.setFont(verdana11);
1991     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1992     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1993     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1994     // followHighlight.setSelected(true);
1995     // followHighlight.setText(MessageManager
1996     // .getString("label.scroll_highlighted_regions"));
1997
1998     seqLimit.setFont(LABEL_FONT);
1999     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
2000     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
2001     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
2002     smoothFont.setFont(LABEL_FONT);
2003     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
2004     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
2005     smoothFont.setText(MessageManager.getString("label.smooth_font"));
2006     scaleProteinToCdna.setFont(LABEL_FONT);
2007     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
2008     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
2009     scaleProteinToCdna.setText(
2010             MessageManager.getString("label.scale_protein_to_cdna"));
2011     scaleProteinToCdna.setToolTipText(
2012             MessageManager.getString("label.scale_protein_to_cdna_tip"));
2013     JLabel gapLabel = new JLabel();
2014     gapLabel.setFont(LABEL_FONT);
2015     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2016     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
2017     JLabel fontLabel = new JLabel();
2018     fontLabel.setFont(LABEL_FONT);
2019     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2020     fontLabel.setText(MessageManager.getString("label.font"));
2021     fontSizeCB.setFont(LABEL_FONT);
2022     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
2023     fontStyleCB.setFont(LABEL_FONT);
2024     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
2025     fontNameCB.setFont(LABEL_FONT);
2026     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
2027     gapSymbolCB.setFont(LABEL_FONT);
2028     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
2029     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
2030     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
2031     gapSymbolCB.setRenderer(dlcr);
2032
2033     startupCheckbox.setText(MessageManager.getString("action.open_file"));
2034     startupCheckbox.setFont(LABEL_FONT);
2035     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
2036     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
2037     startupCheckbox.setSelected(true);
2038     startupFileTextfield.setFont(LABEL_FONT);
2039     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
2040     final String tooltip = JvSwingUtils.wrapTooltip(true,
2041             MessageManager.getString("label.double_click_to_browse"));
2042     startupFileTextfield.setToolTipText(tooltip);
2043     startupFileTextfield.addMouseListener(new MouseAdapter()
2044     {
2045       @Override
2046       public void mouseClicked(MouseEvent e)
2047       {
2048         if (e.getClickCount() > 1)
2049         {
2050           startupFileTextfield_mouseClicked();
2051         }
2052       }
2053     });
2054
2055     sortby.setFont(LABEL_FONT);
2056     sortby.setBounds(new Rectangle(172, 260, 155, 21));
2057     JLabel sortLabel = new JLabel();
2058     sortLabel.setFont(LABEL_FONT);
2059     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2060     sortLabel.setText(MessageManager.getString("label.sort_by"));
2061     sortAnnBy.setFont(LABEL_FONT);
2062     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
2063     JLabel sortAnnLabel = new JLabel();
2064     sortAnnLabel.setFont(LABEL_FONT);
2065     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2066     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
2067     sortAutocalc.setFont(LABEL_FONT);
2068     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2069
2070     JPanel annsettingsPanel = new JPanel();
2071     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2072     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2073     annsettingsPanel.setBorder(new EtchedBorder());
2074     visualTab.add(annsettingsPanel);
2075     Border jb = new EmptyBorder(1, 1, 4, 5);
2076     annotations.setBorder(jb);
2077     showOccupancy.setBorder(jb);
2078     quality.setBorder(jb);
2079     conservation.setBorder(jb);
2080     identity.setBorder(jb);
2081     showConsensbits.setBorder(jb);
2082     showGroupbits.setBorder(jb);
2083     showGroupConsensus.setBorder(jb);
2084     showGroupConservation.setBorder(jb);
2085     showConsensHistogram.setBorder(jb);
2086     showConsensLogo.setBorder(jb);
2087
2088     JPanel autoAnnotSettings = new JPanel();
2089     annsettingsPanel.add(autoAnnotSettings);
2090     autoAnnotSettings.setLayout(new GridLayout(0, 2));
2091     autoAnnotSettings.add(annotations);
2092     autoAnnotSettings.add(quality);
2093     // second row of autoannotation box
2094     autoAnnotSettings = new JPanel();
2095     annsettingsPanel.add(autoAnnotSettings);
2096
2097     autoAnnotSettings.setLayout(new GridLayout(0, 3));
2098     autoAnnotSettings.add(conservation);
2099     autoAnnotSettings.add(identity);
2100     autoAnnotSettings.add(showOccupancy);
2101     autoAnnotSettings.add(showGroupbits);
2102     autoAnnotSettings.add(showGroupConservation);
2103     autoAnnotSettings.add(showGroupConsensus);
2104     autoAnnotSettings.add(showConsensbits);
2105     autoAnnotSettings.add(showConsensHistogram);
2106     autoAnnotSettings.add(showConsensLogo);
2107
2108     JPanel tooltipSettings = new JPanel();
2109     tooltipSettings.setBorder(new TitledBorder(
2110             MessageManager.getString("label.sequence_id_tooltip")));
2111     tooltipSettings.setBounds(173, 140, 220, 62);
2112     tooltipSettings.setLayout(new GridLayout(2, 1));
2113     tooltipSettings.add(showDbRefTooltip);
2114     tooltipSettings.add(showNpTooltip);
2115     visualTab.add(tooltipSettings);
2116
2117     wrap.setFont(LABEL_FONT);
2118     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2119     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2120     wrap.setText(MessageManager.getString("label.wrap_alignment"));
2121     rightAlign.setFont(LABEL_FONT);
2122     rightAlign.setForeground(Color.black);
2123     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2124     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2125     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2126     idItalics.setFont(LABEL_FONT_ITALIC);
2127     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2128     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2129     idItalics.setText(
2130             MessageManager.getString("label.sequence_name_italics"));
2131     openoverv.setFont(LABEL_FONT);
2132     openoverv.setActionCommand(
2133             MessageManager.getString("label.open_overview"));
2134     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2135     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2136     openoverv.setText(MessageManager.getString("label.open_overview"));
2137     JPanel jPanel2 = new JPanel();
2138     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2139     jPanel2.setLayout(new GridLayout(14, 1));
2140     jPanel2.add(fullScreen);
2141     jPanel2.add(openoverv);
2142     jPanel2.add(seqLimit);
2143     jPanel2.add(rightAlign);
2144     jPanel2.add(fontLabel);
2145     jPanel2.add(showUnconserved);
2146     jPanel2.add(idItalics);
2147     jPanel2.add(smoothFont);
2148     jPanel2.add(scaleProteinToCdna);
2149     jPanel2.add(gapLabel);
2150     jPanel2.add(wrap);
2151     jPanel2.add(sortLabel);
2152     jPanel2.add(sortAnnLabel);
2153     jPanel2.add(startupCheckbox);
2154     visualTab.add(jPanel2);
2155     visualTab.add(startupFileTextfield);
2156     visualTab.add(sortby);
2157     visualTab.add(sortAnnBy);
2158     visualTab.add(sortAutocalc);
2159     visualTab.add(gapSymbolCB);
2160     visualTab.add(fontNameCB);
2161     visualTab.add(fontSizeCB);
2162     visualTab.add(fontStyleCB);
2163
2164     if (Platform.isJS())
2165     {
2166       startupCheckbox.setVisible(false);
2167       startupFileTextfield.setVisible(false);
2168     }
2169
2170     return visualTab;
2171   }
2172
2173   /**
2174    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2175    */
2176
2177   protected void loadLastSavedBackupsOptions()
2178   {
2179     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2180             .getSavedBackupEntry();
2181     enableBackupFiles.setSelected(
2182             Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2183
2184     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2185             .createBackupFilesPresetEntry(Cache
2186                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2187     if (backupfilesCustomEntry == null)
2188     {
2189       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2190               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2191     }
2192     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2193             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2194             backupfilesCustomEntry);
2195
2196     setComboIntStringKey(backupfilesPresetsCombo,
2197             Cache.getDefault(BackupFiles.NS + "_PRESET",
2198                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2199
2200     backupsSetOptions(savedPreset);
2201
2202     backupsOptionsSetEnabled();
2203     updateBackupFilesExampleLabel();
2204   }
2205
2206   private boolean warnAboutSuffixReverseChange()
2207   {
2208     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2209             .getSavedBackupEntry();
2210     boolean savedSuffixReverse = bfpe.reverse;
2211     int savedSuffixDigits = bfpe.digits;
2212     String savedSuffixTemplate = bfpe.suffix;
2213
2214     boolean nowSuffixReverse = suffixReverse.isSelected();
2215     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2216     String nowSuffixTemplate = suffixTemplate.getText();
2217     return nowSuffixReverse != savedSuffixReverse
2218             && nowSuffixDigits == savedSuffixDigits
2219             && nowSuffixTemplate != null
2220             && nowSuffixTemplate.equals(savedSuffixTemplate);
2221   }
2222
2223   /**
2224    * Initialises the Backups tabbed panel.
2225    *
2226    * @return
2227    */
2228   private JPanel initBackupsTab()
2229   {
2230     JPanel backupsTab = new JPanel();
2231     backupsTab.setBorder(new TitledBorder(
2232             MessageManager.getString("label.backup_files")));
2233     backupsTab.setLayout(new GridBagLayout());
2234
2235     GridBagConstraints gbc = new GridBagConstraints();
2236     gbc.weightx = 0.0;
2237     gbc.weighty = 0.0;
2238     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2239     gbc.fill = GridBagConstraints.NONE;
2240
2241     initBackupsTabPresetsPanel();
2242     initBackupsTabSuffixPanel();
2243     initBackupsTabKeepFilesPanel();
2244     initBackupsTabFilenameExamplesPanel();
2245
2246     enableBackupFiles.setFont(LABEL_FONT_BOLD);
2247     enableBackupFiles
2248             .setText(MessageManager.getString("label.enable_backupfiles"));
2249     enableBackupFiles.addActionListener(new ActionListener()
2250     {
2251       @Override
2252       public void actionPerformed(ActionEvent e)
2253       {
2254         // enable other options only when the first is checked
2255         backupsOptionsSetEnabled();
2256       }
2257     });
2258
2259     // enable checkbox 1 col
2260     gbc.gridwidth = 1;
2261     gbc.gridheight = 1;
2262     gbc.gridx = 0;
2263     gbc.gridy = 0; // row 0
2264     backupsTab.add(enableBackupFiles, gbc);
2265
2266     // summary of scheme box (over two rows)
2267     gbc.gridx = 1;
2268     gbc.weightx = 0.0;
2269     gbc.gridheight = 2;
2270     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2271     gbc.fill = GridBagConstraints.BOTH;
2272     backupsTab.add(exampleFilesPanel, gbc);
2273     gbc.gridheight = 1;
2274     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2275     gbc.fill = GridBagConstraints.NONE;
2276
2277     // fill empty space on right
2278     gbc.gridx++;
2279     gbc.weightx = 1.0;
2280     backupsTab.add(new JPanel(), gbc);
2281
2282     // schemes box
2283     gbc.weightx = 0.0;
2284     gbc.gridx = 0;
2285     gbc.gridy++; // row 1
2286     backupsTab.add(presetsPanel, gbc);
2287
2288     // now using whole row
2289     gbc.gridwidth = 2;
2290     gbc.gridheight = 1;
2291     // keep files box
2292     gbc.gridx = 0;
2293     gbc.gridy++; // row 2
2294     backupsTab.add(keepfilesPanel, gbc);
2295
2296     // filename strategy box
2297     gbc.gridy++; // row 3
2298     backupsTab.add(suffixPanel, gbc);
2299
2300     // fill empty space
2301     gbc.gridy++; // row 4
2302     gbc.weighty = 1.0;
2303     backupsTab.add(new JPanel(), gbc);
2304
2305     backupsOptionsSetEnabled();
2306     return backupsTab;
2307   }
2308
2309   private JPanel initBackupsTabPresetsPanel()
2310   {
2311
2312     String title = MessageManager.getString("label.schemes");
2313
2314     presetsPanel.setLayout(new GridBagLayout());
2315
2316     GridBagConstraints gbc = new GridBagConstraints();
2317     gbc.weightx = 0.0;
2318     gbc.weighty = 0.0;
2319     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2320     gbc.fill = GridBagConstraints.NONE;
2321     gbc.gridwidth = 1;
2322     gbc.gridheight = 1;
2323
2324     // "Scheme: "
2325     gbc.gridx = 0;
2326     gbc.gridy = 0;
2327
2328     presetsComboLabel = new JLabel(title + ":");
2329     presetsPanel.add(presetsComboLabel, gbc);
2330
2331     List<Object> entries = Arrays.asList(
2332             (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2333     List<String> tooltips = Arrays.asList(
2334             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2335     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2336             tooltips);
2337     /*
2338     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2339     {
2340       backupfilesPresetsCombo
2341               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2342     }
2343     */
2344
2345     backupfilesPresetsCombo.addActionListener(new ActionListener()
2346     {
2347       @Override
2348       public void actionPerformed(ActionEvent e)
2349       {
2350         int key = getComboIntStringKey(backupfilesPresetsCombo);
2351         if (!customiseCheckbox.isSelected())
2352         {
2353           backupfilesPresetsComboLastSelected = key;
2354         }
2355         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2356         {
2357           if (customiseCheckbox.isSelected())
2358           {
2359             // got here by clicking on customiseCheckbox so don't change the
2360             // values
2361             backupfilesCustomOptionsSetEnabled();
2362           }
2363           else
2364           {
2365             backupsTabUpdatePresets();
2366             backupfilesCustomOptionsSetEnabled();
2367           }
2368         }
2369         else
2370         {
2371           customiseCheckbox.setSelected(false);
2372           backupsTabUpdatePresets();
2373           backupfilesCustomOptionsSetEnabled();
2374         }
2375       }
2376     });
2377
2378     // dropdown list of preset schemes
2379     gbc.gridx = 1;
2380     presetsPanel.add(backupfilesPresetsCombo, gbc);
2381
2382     revertButton.setText(MessageManager.getString("label.cancel_changes"));
2383     revertButton.setToolTipText(
2384             MessageManager.getString("label.cancel_changes_description"));
2385     revertButton.addActionListener(new ActionListener()
2386     {
2387       @Override
2388       public void actionPerformed(ActionEvent e)
2389       {
2390         backupsSetOptions(
2391                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2392                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2393         backupfilesCustomOptionsSetEnabled();
2394       }
2395
2396     });
2397     revertButton.setFont(LABEL_FONT);
2398
2399     customiseCheckbox.setFont(LABEL_FONT);
2400     customiseCheckbox.setText(MessageManager.getString("label.customise"));
2401     customiseCheckbox.addActionListener(new ActionListener()
2402     {
2403       @Override
2404       public void actionPerformed(ActionEvent e)
2405       {
2406         int currently = getComboIntStringKey(backupfilesPresetsCombo);
2407         if (customiseCheckbox.isSelected())
2408         {
2409           backupfilesPresetsComboLastSelected = currently;
2410           setComboIntStringKey(backupfilesPresetsCombo,
2411                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2412         }
2413         else
2414         {
2415           setComboIntStringKey(backupfilesPresetsCombo,
2416                   backupfilesPresetsComboLastSelected);
2417
2418         }
2419         backupfilesCustomOptionsSetEnabled();
2420       }
2421     });
2422     customiseCheckbox.setToolTipText(
2423             MessageManager.getString("label.customise_description"));
2424
2425     // customise checkbox
2426     gbc.gridx = 0;
2427     gbc.gridy++;
2428     presetsPanel.add(customiseCheckbox, gbc);
2429
2430     // "Cancel changes" button (aligned with combo box above)
2431     gbc.gridx = 1;
2432     presetsPanel.add(revertButton, gbc);
2433
2434     return presetsPanel;
2435   }
2436
2437   private JPanel initBackupsTabFilenameExamplesPanel()
2438   {
2439     String title = MessageManager.getString("label.scheme_examples");
2440     TitledBorder tb = new TitledBorder(title);
2441     exampleFilesPanel.setBorder(tb);
2442     exampleFilesPanel.setLayout(new GridBagLayout());
2443
2444     backupfilesExampleLabel.setEditable(false);
2445     backupfilesExampleLabel
2446             .setBackground(exampleFilesPanel.getBackground());
2447
2448     updateBackupFilesExampleLabel();
2449
2450     GridBagConstraints gbc = new GridBagConstraints();
2451     gbc.weightx = 1.0;
2452     gbc.weighty = 1.0;
2453     gbc.fill = GridBagConstraints.NONE;
2454     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2455
2456     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2457     return exampleFilesPanel;
2458   }
2459
2460   private void backupsTabUpdatePresets()
2461   {
2462     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2463             .getSelectedItem();
2464     int key = entry.k;
2465     String value = entry.v;
2466
2467     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2468             .containsKey(key))
2469     {
2470       backupsSetOptions(
2471               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2472                       .get(key));
2473     }
2474     else
2475     {
2476       Cache.log.error(
2477               "Preset '" + value + "' [key:" + key + "] not implemented");
2478     }
2479
2480     // Custom options will now be enabled when the customiseCheckbox is checked
2481     // (performed above)
2482     // backupfilesCustomOptionsSetEnabled();
2483     updateBackupFilesExampleLabel();
2484   }
2485
2486   protected int getComboIntStringKey(
2487           JComboBox<Object> backupfilesPresetsCombo2)
2488   {
2489     IntKeyStringValueEntry e;
2490     try
2491     {
2492       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2493               .getSelectedItem();
2494     } catch (Exception ex)
2495     {
2496       Cache.log.error(
2497               "Problem casting Combo entry to IntKeyStringValueEntry.");
2498       e = null;
2499     }
2500     return e != null ? e.k : 0;
2501   }
2502
2503   protected void setComboIntStringKey(
2504           JComboBox<Object> backupfilesPresetsCombo2, int key)
2505   {
2506     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2507     {
2508       IntKeyStringValueEntry e;
2509       try
2510       {
2511         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2512       } catch (Exception ex)
2513       {
2514         Cache.log.error(
2515                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2516         continue;
2517       }
2518       if (e.k == key)
2519       {
2520         backupfilesPresetsCombo2.setSelectedIndex(i);
2521         break;
2522       }
2523     }
2524     // backupsTabUpdatePresets();
2525   }
2526
2527   private JPanel initBackupsTabSuffixPanel()
2528   {
2529     suffixPanel.setBorder(new TitledBorder(
2530             MessageManager.getString("label.backup_filename_strategy")));
2531     suffixPanel.setLayout(new GridBagLayout());
2532
2533     suffixTemplateLabel
2534             .setText(MessageManager.getString("label.append_to_filename"));
2535     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2536     suffixTemplateLabel.setFont(LABEL_FONT);
2537
2538     final String tooltip = JvSwingUtils.wrapTooltip(true,
2539             MessageManager.getString("label.append_to_filename_tooltip"));
2540     suffixTemplate.setToolTipText(tooltip);
2541     suffixTemplate.addActionListener(new ActionListener()
2542     {
2543       @Override
2544       public void actionPerformed(ActionEvent e)
2545       {
2546         updateBackupFilesExampleLabel();
2547         backupfilesCustomOptionsSetEnabled();
2548         backupfilesRevertButtonSetEnabled(true);
2549       }
2550
2551     });
2552     suffixTemplate.addKeyListener(new KeyListener()
2553     {
2554       @Override
2555       public void keyReleased(KeyEvent e)
2556       {
2557         updateBackupFilesExampleLabel();
2558         backupfilesCustomOptionsSetEnabled();
2559         backupfilesRevertButtonSetEnabled(true);
2560       }
2561
2562       @Override
2563       public void keyPressed(KeyEvent e)
2564       {
2565       }
2566
2567       // disable use of ':' or '/' or '\'
2568       @Override
2569       public void keyTyped(KeyEvent e)
2570       {
2571         char c = e.getKeyChar();
2572         if (c == ':' || c == '/' || c == '\\')
2573         {
2574           // don't process ':' or '/' or '\'
2575           e.consume();
2576         }
2577       }
2578
2579     });
2580
2581     // digits spinner
2582     suffixDigitsLabel
2583             .setText(MessageManager.getString("label.index_digits"));
2584     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2585     suffixDigitsLabel.setFont(LABEL_FONT);
2586     ChangeListener c = new ChangeListener()
2587     {
2588       @Override
2589       public void stateChanged(ChangeEvent e)
2590       {
2591         backupfilesRevertButtonSetEnabled(true);
2592         updateBackupFilesExampleLabel();
2593       }
2594
2595     };
2596     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2597             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2598
2599     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2600             MessageManager.getString("label.increment_index"));
2601     suffixReverse.addActionListener(new ActionListener()
2602     {
2603       @Override
2604       public void actionPerformed(ActionEvent e)
2605       {
2606         boolean okay = true;
2607         if (warnAboutSuffixReverseChange())
2608         {
2609           // Warning popup
2610           okay = confirmSuffixReverseChange();
2611         }
2612         if (okay)
2613         {
2614           backupfilesRevertButtonSetEnabled(true);
2615           updateBackupFilesExampleLabel();
2616         }
2617         else
2618         {
2619           boolean savedSuffixReverse = BackupFilesPresetEntry
2620                   .getSavedBackupEntry().reverse;
2621           suffixReverse.setSelected(savedSuffixReverse);
2622         }
2623       }
2624     });
2625
2626     GridBagConstraints sgbc = new GridBagConstraints();
2627
2628     // first row (template text box)
2629     sgbc.anchor = GridBagConstraints.WEST;
2630     sgbc.gridx = 0;
2631     sgbc.gridy = 0;
2632     sgbc.gridwidth = 1;
2633     sgbc.gridheight = 1;
2634     sgbc.weightx = 1.0;
2635     sgbc.weighty = 0.0;
2636     sgbc.fill = GridBagConstraints.NONE;
2637     suffixPanel.add(suffixTemplateLabel, sgbc);
2638
2639     sgbc.gridx = 1;
2640     sgbc.fill = GridBagConstraints.HORIZONTAL;
2641     suffixPanel.add(suffixTemplate, sgbc);
2642
2643     // second row (number of digits spinner)
2644     sgbc.gridy = 1;
2645
2646     sgbc.gridx = 0;
2647     sgbc.fill = GridBagConstraints.NONE;
2648     suffixPanel.add(suffixDigitsLabel, sgbc);
2649
2650     sgbc.gridx = 1;
2651     sgbc.fill = GridBagConstraints.HORIZONTAL;
2652     suffixPanel.add(suffixDigitsSpinner, sgbc);
2653
2654     // third row (forward order radio selection)
2655     sgbc.gridx = 0;
2656     sgbc.gridy = 2;
2657     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2658     sgbc.fill = GridBagConstraints.HORIZONTAL;
2659     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2660
2661     // fourth row (reverse order radio selection)
2662     sgbc.gridy = 3;
2663     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2664     return suffixPanel;
2665   }
2666
2667   private boolean confirmSuffixReverseChange()
2668   {
2669     boolean ret = false;
2670     String warningMessage = MessageManager
2671             .getString("label.warning_confirm_change_reverse");
2672     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2673             warningMessage,
2674             MessageManager.getString("label.change_increment_decrement"),
2675             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2676
2677     ret = (confirm == JvOptionPane.YES_OPTION);
2678     return ret;
2679   }
2680
2681   private JPanel initBackupsTabKeepFilesPanel()
2682   {
2683     keepfilesPanel.setBorder(
2684             new TitledBorder(MessageManager.getString("label.keep_files")));
2685     keepfilesPanel.setLayout(new GridBagLayout());
2686
2687     backupfilesKeepAll.setLabels(
2688             MessageManager.getString("label.keep_all_backup_files"),
2689             MessageManager.getString(
2690                     "label.keep_only_this_number_of_backup_files"));
2691     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2692     {
2693       @Override
2694       public void actionPerformed(ActionEvent e)
2695       {
2696         backupfilesRevertButtonSetEnabled(true);
2697         updateBackupFilesExampleLabel();
2698       }
2699     });
2700     backupfilesKeepAll.addActionListener(new ActionListener()
2701     {
2702       @Override
2703       public void actionPerformed(ActionEvent e)
2704       {
2705         backupfilesRevertButtonSetEnabled(true);
2706         keepRollMaxOptionsEnabled();
2707         updateBackupFilesExampleLabel();
2708       }
2709     });
2710
2711     ChangeListener c = new ChangeListener()
2712     {
2713       @Override
2714       public void stateChanged(ChangeEvent e)
2715       {
2716         backupfilesRevertButtonSetEnabled(true);
2717         updateBackupFilesExampleLabel();
2718       }
2719
2720     };
2721     setIntegerSpinner(backupfilesRollMaxSpinner,
2722             BackupFilesPresetEntry.ROLLMAXMIN,
2723             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2724
2725     backupfilesConfirmDelete.setLabels(
2726             MessageManager.getString("label.always_ask"),
2727             MessageManager.getString("label.auto_delete"));
2728     backupfilesConfirmDelete.addActionListener(new ActionListener()
2729     {
2730       @Override
2731       public void actionPerformed(ActionEvent e)
2732       {
2733         backupfilesRevertButtonSetEnabled(true);
2734       }
2735     });
2736     // update the enabled section
2737     keepRollMaxOptionsEnabled();
2738
2739     GridBagConstraints kgbc = new GridBagConstraints();
2740
2741     // first row (template text box)
2742     kgbc.anchor = GridBagConstraints.WEST;
2743     kgbc.gridx = 0;
2744     kgbc.gridy = 0;
2745     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2746     kgbc.gridheight = 1;
2747     kgbc.weightx = 1.0;
2748     kgbc.weighty = 0.0;
2749     kgbc.fill = GridBagConstraints.HORIZONTAL;
2750     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2751
2752     // second row
2753     kgbc.gridy = 1;
2754
2755     kgbc.gridx = 0;
2756     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2757     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2758
2759     kgbc.gridx = 1;
2760     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2761     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2762
2763     // third row (indented)
2764     kgbc.gridy = 2;
2765     kgbc.insets = new Insets(0, 20, 0, 0);
2766
2767     kgbc.gridx = 0;
2768     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2769     kgbc.fill = GridBagConstraints.HORIZONTAL;
2770     kgbc.weightx = 1.0;
2771
2772     JPanel jp = new JPanel();
2773     jp.setLayout(new FlowLayout());
2774     oldBackupFilesLabel.setText(
2775             MessageManager.getString("label.autodelete_old_backup_files"));
2776     oldBackupFilesLabel.setFont(LABEL_FONT);
2777     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2778     jp.add(oldBackupFilesLabel);
2779     jp.add(backupfilesConfirmDelete.getTrueButton());
2780     jp.add(backupfilesConfirmDelete.getFalseButton());
2781     keepfilesPanel.add(jp, kgbc);
2782
2783     return keepfilesPanel;
2784   }
2785
2786   protected void updateBackupFilesExampleLabel()
2787   {
2788     int exampleindex = 12;
2789     String base = MessageManager.getString("label.filename") + ".fa";
2790     if (base == null || base.length() == 0)
2791     {
2792       base = "file_name.fa";
2793     }
2794
2795     boolean reverse = suffixReverse.isSelected();
2796     boolean keepAll = backupfilesKeepAll.isSelected();
2797     int rollMax = 4;
2798     String suffix = suffixTemplate.getText();
2799     int digits = 3;
2800
2801     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2802     if (suffix == null || suffix.length() == 0)
2803     {
2804       backupfilesExampleLabel
2805               .setText(MessageManager.getString("label.no_backup_files"));
2806       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2807       return;
2808     }
2809
2810     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2811     rollMax = rollMax < 1 ? 1 : rollMax;
2812
2813     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2814     {
2815       rollMax = 1;
2816     }
2817
2818     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2819     digits = digits < 1 ? 1 : digits;
2820
2821     int lowersurround = 2;
2822     int uppersurround = 0;
2823     StringBuilder exampleSB = new StringBuilder();
2824     boolean firstLine = true;
2825     int lineNumber = 0;
2826     if (reverse)
2827     {
2828
2829       int min = 1;
2830       int max = keepAll ? exampleindex : rollMax;
2831       for (int index = min; index <= max; index++)
2832       {
2833         if (index == min + lowersurround && index < max - uppersurround - 1)
2834         {
2835           exampleSB.append("\n...");
2836           lineNumber++;
2837         }
2838         else if (index > min + lowersurround && index < max - uppersurround)
2839         {
2840           // nothing
2841         }
2842         else
2843         {
2844           if (firstLine)
2845           {
2846             firstLine = false;
2847           }
2848           else
2849           {
2850             exampleSB.append("\n");
2851             lineNumber++;
2852           }
2853           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2854                   base, suffix, digits));
2855           if (min == max)
2856           {
2857             // no extra text needed
2858           }
2859           else if (index == min)
2860           {
2861             String newest = MessageManager.getString("label.braced_newest");
2862             if (newest != null && newest.length() > 0)
2863             {
2864               exampleSB.append(" " + newest);
2865             }
2866           }
2867           else if (index == max)
2868           {
2869             String oldest = MessageManager.getString("label.braced_oldest");
2870             if (oldest != null && oldest.length() > 0)
2871             {
2872               exampleSB.append(" " + oldest);
2873             }
2874           }
2875         }
2876       }
2877     }
2878     else
2879     {
2880
2881       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2882               : exampleindex - rollMax + 1;
2883       int max = exampleindex;
2884
2885       for (int index = min; index <= max; index++)
2886       {
2887
2888         if (index == min + lowersurround && index < max - uppersurround - 1)
2889         {
2890           exampleSB.append("\n...");
2891           lineNumber++;
2892         }
2893         else if (index > min + lowersurround && index < max - uppersurround)
2894         {
2895           // nothing
2896         }
2897         else
2898         {
2899           if (firstLine)
2900           {
2901             firstLine = false;
2902           }
2903           else
2904           {
2905             exampleSB.append("\n");
2906             lineNumber++;
2907           }
2908           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2909                   base, suffix, digits));
2910           if (min == max)
2911           {
2912             // no extra text needed
2913           }
2914           else if (index == min)
2915           {
2916             String oldest = MessageManager.getString("label.braced_oldest");
2917             if (oldest != null && oldest.length() > 0)
2918             {
2919               exampleSB.append(" " + oldest);
2920             }
2921           }
2922           else if (index == max)
2923           {
2924             String newest = MessageManager.getString("label.braced_newest");
2925             if (newest != null && newest.length() > 0)
2926             {
2927               exampleSB.append(" " + newest);
2928             }
2929           }
2930         }
2931       }
2932
2933     }
2934
2935     // add some extra empty lines to pad out the example files box. ugh, please
2936     // tell
2937     // me how to do this better
2938     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2939     if (remainingLines > 0)
2940     {
2941       for (int i = 0; i < remainingLines; i++)
2942       {
2943         exampleSB.append("\n ");
2944         lineNumber++;
2945       }
2946     }
2947
2948     backupfilesExampleLabel.setText(exampleSB.toString());
2949   }
2950
2951   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2952           boolean useExistingVal, ChangeListener c)
2953   {
2954     int i = def;
2955     if (useExistingVal)
2956     {
2957       try
2958       {
2959         i = ((Integer) s.getValue()).intValue();
2960       } catch (Exception e)
2961       {
2962         Cache.log.error(
2963                 "Exception casting the initial value of s.getValue()");
2964       }
2965     }
2966
2967     setIntegerSpinner(s, min, max, i, c);
2968   }
2969
2970   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2971           ChangeListener c)
2972   {
2973     // integer spinner for number of digits
2974     if (def > max)
2975     {
2976       max = def;
2977     }
2978     if (def < min)
2979     {
2980       def = min;
2981     }
2982     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2983     s.setModel(sModel);
2984
2985     s.addChangeListener(c);
2986
2987   }
2988
2989   protected static int getSpinnerInt(JSpinner s, int def)
2990   {
2991     int i = def;
2992     try
2993     {
2994       s.commitEdit();
2995       i = (Integer) s.getValue();
2996     } catch (Exception e)
2997     {
2998       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2999     }
3000     return i;
3001   }
3002
3003   private void keepRollMaxOptionsEnabled()
3004   {
3005     boolean enabled = backupfilesKeepAll.isEnabled()
3006             && !backupfilesKeepAll.isSelected();
3007     oldBackupFilesLabel.setEnabled(enabled);
3008     backupfilesRollMaxSpinner.setEnabled(enabled);
3009     backupfilesConfirmDelete.setEnabled(enabled);
3010   }
3011
3012   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
3013   {
3014     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3015             && customiseCheckbox.isSelected() && suffixTemplate.getText()
3016                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3017     keepfilesPanel.setEnabled(enabled);
3018     backupfilesKeepAll.setEnabled(enabled);
3019     oldBackupFilesLabel.setEnabled(enabled);
3020     keepRollMaxOptionsEnabled();
3021   }
3022
3023   private void backupfilesSuffixTemplateDigitsSetEnabled()
3024   {
3025     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
3026             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3027     suffixDigitsLabel.setEnabled(enabled);
3028     suffixDigitsSpinner.setEnabled(enabled);
3029     suffixReverse.setEnabled(enabled);
3030   }
3031
3032   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
3033   {
3034     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3035             && customiseCheckbox.isSelected();
3036     suffixPanel.setEnabled(enabled);
3037     suffixTemplateLabel.setEnabled(enabled);
3038     suffixTemplate.setEnabled(enabled);
3039     backupfilesSuffixTemplateDigitsSetEnabled();
3040   }
3041
3042   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
3043   {
3044     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3045             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
3046     revertButton.setEnabled(enabled);
3047   }
3048
3049   private boolean backupfilesCustomChanged()
3050   {
3051     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
3052             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
3053     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
3054     return !custom.equals(current);
3055   }
3056
3057   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
3058   {
3059     String suffix = suffixTemplate.getText();
3060     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
3061     boolean reverse = suffixReverse.isSelected();
3062     boolean keepAll = backupfilesKeepAll.isSelected();
3063     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3064     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3065
3066     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3067             reverse, keepAll, rollMax, confirmDelete);
3068
3069     return bfpe;
3070   }
3071
3072   protected void backupfilesCustomOptionsSetEnabled()
3073   {
3074     boolean enabled = customiseCheckbox.isSelected();
3075
3076     backupfilesRevertButtonSetEnabled(enabled);
3077     backupfilesSuffixTemplateSetEnabled(enabled);
3078     backupfilesKeepAllSetEnabled(enabled);
3079   }
3080
3081   private void backupfilesSummarySetEnabled()
3082   {
3083     boolean enabled = enableBackupFiles.isSelected();
3084     backupfilesExampleLabel.setEnabled(enabled);
3085     exampleFilesPanel.setEnabled(enabled);
3086   }
3087
3088   private void backupfilesPresetsSetEnabled()
3089   {
3090     boolean enabled = enableBackupFiles.isSelected();
3091     presetsPanel.setEnabled(enabled);
3092     presetsComboLabel.setEnabled(enabled);
3093     backupfilesPresetsCombo.setEnabled(enabled);
3094     customiseCheckbox.setEnabled(enabled);
3095     revertButton.setEnabled(enabled);
3096   }
3097
3098   protected void backupsOptionsSetEnabled()
3099   {
3100     backupfilesPresetsSetEnabled();
3101     backupfilesSummarySetEnabled();
3102     backupfilesCustomOptionsSetEnabled();
3103   }
3104
3105   protected void backupsSetOptions(String suffix, int digits,
3106           boolean reverse, boolean keepAll, int rollMax,
3107           boolean confirmDelete)
3108   {
3109     suffixTemplate.setText(suffix);
3110     suffixDigitsSpinner.setValue(digits);
3111     suffixReverse.setSelected(reverse);
3112     backupfilesKeepAll.setSelected(keepAll);
3113     backupfilesRollMaxSpinner.setValue(rollMax);
3114     backupfilesConfirmDelete.setSelected(confirmDelete);
3115   }
3116
3117   protected void backupsSetOptions(BackupFilesPresetEntry p)
3118   {
3119     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3120             p.confirmDelete);
3121   }
3122
3123   protected void autoIdWidth_actionPerformed()
3124   {
3125     // TODO Auto-generated method stub
3126
3127   }
3128
3129   protected void userIdWidth_actionPerformed()
3130   {
3131     // TODO Auto-generated method stub
3132
3133   }
3134
3135   protected void maxColour_actionPerformed(JPanel panel)
3136   {
3137   }
3138
3139   protected void minColour_actionPerformed(JPanel panel)
3140   {
3141   }
3142
3143   protected void gapColour_actionPerformed(JPanel panel)
3144   {
3145   }
3146
3147   protected void hiddenColour_actionPerformed(JPanel panel)
3148   {
3149   }
3150
3151   protected void showunconserved_actionPerformed(ActionEvent e)
3152   {
3153     // TODO Auto-generated method stub
3154
3155   }
3156
3157   protected void useLegacyGaps_actionPerformed(ActionEvent e)
3158   {
3159   }
3160
3161   protected void resetOvDefaults_actionPerformed(ActionEvent e)
3162   {
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   public void ok_actionPerformed(ActionEvent e)
3172   {
3173   }
3174
3175   /**
3176    * DOCUMENT ME!
3177    *
3178    * @param e
3179    *          DOCUMENT ME!
3180    */
3181   public void cancel_actionPerformed(ActionEvent e)
3182   {
3183   }
3184
3185   /**
3186    * DOCUMENT ME!
3187    *
3188    * @param e
3189    *          DOCUMENT ME!
3190    */
3191   public void annotations_actionPerformed(ActionEvent e)
3192   {
3193   }
3194
3195   /**
3196    * DOCUMENT ME!
3197    */
3198   public void startupFileTextfield_mouseClicked()
3199   {
3200   }
3201
3202   public void newLink_actionPerformed(ActionEvent e)
3203   {
3204
3205   }
3206
3207   public void editLink_actionPerformed(ActionEvent e)
3208   {
3209
3210   }
3211
3212   public void deleteLink_actionPerformed(ActionEvent e)
3213   {
3214
3215   }
3216
3217   public void defaultBrowser_mouseClicked(MouseEvent e)
3218   {
3219
3220   }
3221
3222   public void linkURLList_keyTyped(KeyEvent e)
3223   {
3224
3225   }
3226
3227   public void setProxyAuthEnabled()
3228   {
3229     boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3230     proxyAuthUsernameLabel.setEnabled(enabled);
3231     proxyAuthPasswordLabel.setEnabled(enabled);
3232     passwordNotStoredLabel.setEnabled(enabled);
3233     proxyAuthUsernameTB.setEnabled(enabled);
3234     proxyAuthPasswordPB.setEnabled(enabled);
3235   }
3236
3237   public void setCustomProxyEnabled()
3238   {
3239     boolean enabled = customProxy.isSelected();
3240     portLabel.setEnabled(enabled);
3241     serverLabel.setEnabled(enabled);
3242     portLabel2.setEnabled(enabled);
3243     serverLabel2.setEnabled(enabled);
3244     httpLabel.setEnabled(enabled);
3245     httpsLabel.setEnabled(enabled);
3246     proxyServerHttpTB.setEnabled(enabled);
3247     proxyPortHttpTB.setEnabled(enabled);
3248     proxyServerHttpsTB.setEnabled(enabled);
3249     proxyPortHttpsTB.setEnabled(enabled);
3250     proxyAuth.setEnabled(enabled);
3251     setProxyAuthEnabled();
3252   }
3253
3254   public void proxyType_actionPerformed()
3255   {
3256     setCustomProxyEnabled();
3257     proxyAuthPasswordCheckHighlight(true);
3258     applyProxyButtonEnabled(true);
3259   }
3260
3261   public void proxyAuth_actionPerformed()
3262   {
3263     setProxyAuthEnabled();
3264     proxyAuthPasswordCheckHighlight(true);
3265     applyProxyButtonEnabled(true);
3266   }
3267
3268   /**
3269    * Customer renderer for JTable: supports column of radio buttons
3270    */
3271   public class RadioButtonRenderer extends JRadioButton
3272           implements TableCellRenderer
3273   {
3274     public RadioButtonRenderer()
3275     {
3276       setHorizontalAlignment(CENTER);
3277       setToolTipText(MessageManager.getString("label.urltooltip"));
3278     }
3279
3280     @Override
3281     public Component getTableCellRendererComponent(JTable table,
3282             Object value, boolean isSelected, boolean hasFocus, int row,
3283             int column)
3284     {
3285       setSelected((boolean) value);
3286
3287       // set colours to match rest of table
3288       if (isSelected)
3289       {
3290         setBackground(table.getSelectionBackground());
3291         setForeground(table.getSelectionForeground());
3292       }
3293       else
3294       {
3295         setBackground(table.getBackground());
3296         setForeground(table.getForeground());
3297       }
3298       return this;
3299     }
3300   }
3301
3302   /**
3303    * Customer cell editor for JTable: supports column of radio buttons in
3304    * conjunction with renderer
3305    */
3306   public class RadioButtonEditor extends AbstractCellEditor
3307           implements TableCellEditor
3308   {
3309     private JRadioButton button = new JRadioButton();
3310
3311     public RadioButtonEditor()
3312     {
3313       button.setHorizontalAlignment(SwingConstants.CENTER);
3314       this.button.addActionListener(new ActionListener()
3315       {
3316         @Override
3317         public void actionPerformed(ActionEvent e)
3318         {
3319           fireEditingStopped();
3320         }
3321       });
3322     }
3323
3324     @Override
3325     public Component getTableCellEditorComponent(JTable table, Object value,
3326             boolean isSelected, int row, int column)
3327     {
3328       button.setSelected((boolean) value);
3329       return button;
3330     }
3331
3332     @Override
3333     public Object getCellEditorValue()
3334     {
3335       return button.isSelected();
3336     }
3337
3338   }
3339 }