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