src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.FlowLayout;
  28 import java.awt.Font;
  29 import java.awt.GridBagConstraints;
  30 import java.awt.GridBagLayout;
  31 import java.awt.GridLayout;
  32 import java.awt.Insets;
  33 import java.awt.Rectangle;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.FocusEvent;
  37 import java.awt.event.KeyEvent;
  38 import java.awt.event.KeyListener;
  39 import java.awt.event.MouseAdapter;
  40 import java.awt.event.MouseEvent;
  41 import java.util.Arrays;
  42 import java.util.List;
  43
  44 import javax.swing.AbstractCellEditor;
  45 import javax.swing.BorderFactory;
  46 import javax.swing.ButtonGroup;
  47 import javax.swing.DefaultListCellRenderer;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JLabel;
  53 import javax.swing.JPanel;
  54 import javax.swing.JPasswordField;
  55 import javax.swing.JRadioButton;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSpinner;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.JTable;
  60 import javax.swing.JTextArea;
  61 import javax.swing.JTextField;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.SpinnerModel;
  64 import javax.swing.SpinnerNumberModel;
  65 import javax.swing.SwingConstants;
  66 import javax.swing.border.Border;
  67 import javax.swing.border.EmptyBorder;
  68 import javax.swing.border.EtchedBorder;
  69 import javax.swing.border.TitledBorder;
  70 import javax.swing.event.ChangeEvent;
  71 import javax.swing.event.ChangeListener;
  72 import javax.swing.event.DocumentEvent;
  73 import javax.swing.event.DocumentListener;
  74 import javax.swing.table.TableCellEditor;
  75 import javax.swing.table.TableCellRenderer;
  76
  77 import jalview.bin.Cache;
  78 import jalview.fts.core.FTSDataColumnPreferences;
  79 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  80 import jalview.fts.service.pdb.PDBFTSRestClient;
  81 import jalview.gui.Desktop;
  82 import jalview.gui.JalviewBooleanRadioButtons;
  83 import jalview.gui.JvOptionPane;
  84 import jalview.gui.JvSwingUtils;
  85 import jalview.gui.StructureViewer.ViewerType;
  86 import jalview.io.BackupFilenameParts;
  87 import jalview.io.BackupFiles;
  88 import jalview.io.BackupFilesPresetEntry;
  89 import jalview.io.IntKeyStringValueEntry;
  90 import jalview.util.MessageManager;
  91 import jalview.util.Platform;
  92
  93 /**
  94  * Base class for the Preferences panel.
  95  *
  96  * @author $author$
  97  * @version $Revision$
  98  */
  99 public class GPreferences extends JPanel
 100 {
 101   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
 102
 103   private static final Font LABEL_FONT_ITALIC = JvSwingUtils
 104           .getLabelFont(false, true);
 105
 106   private static final Font LABEL_FONT_BOLD = JvSwingUtils
 107           .getLabelFont(true, false);
 108
 109   /*
 110    * Visual tab components
 111    */
 112   protected JCheckBox fullScreen = new JCheckBox();
 113
 114   protected JCheckBox openoverv = new JCheckBox();
 115
 116   protected JCheckBox seqLimit = new JCheckBox();
 117
 118   protected JCheckBox rightAlign = new JCheckBox();
 119
 120   protected JComboBox<String> fontSizeCB = new JComboBox<>();
 121
 122   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 123
 124   protected JComboBox<String> fontNameCB = new JComboBox<>();
 125
 126   protected JCheckBox showOccupancy = new JCheckBox();
 127
 128   protected JCheckBox showUnconserved = new JCheckBox();
 129
 130   protected JCheckBox idItalics = new JCheckBox();
 131
 132   protected JCheckBox smoothFont = new JCheckBox();
 133
 134   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 135
 136   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 137
 138   protected JCheckBox wrap = new JCheckBox();
 139
 140   protected JComboBox<String> sortby = new JComboBox<>();
 141
 142   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 143
 144   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 145
 146   protected JCheckBox startupCheckbox = new JCheckBox();
 147
 148   protected JTextField startupFileTextfield = new JTextField();
 149
 150   // below are in the 'second column'
 151   protected JCheckBox annotations = new JCheckBox();
 152
 153   protected JCheckBox quality = new JCheckBox();
 154
 155   protected JCheckBox conservation = new JCheckBox();
 156
 157   protected JCheckBox identity = new JCheckBox();
 158
 159   protected JCheckBox showGroupConsensus = new JCheckBox();
 160
 161   protected JCheckBox showGroupConservation = new JCheckBox();
 162
 163   protected JCheckBox showConsensHistogram = new JCheckBox();
 164
 165   protected JCheckBox showConsensLogo = new JCheckBox();
 166
 167   protected JCheckBox showDbRefTooltip = new JCheckBox();
 168
 169   protected JCheckBox showNpTooltip = new JCheckBox();
 170
 171   /*
 172    * Structure tab and components
 173    */
 174   protected JPanel structureTab;
 175
 176   protected JCheckBox structFromPdb = new JCheckBox();
 177
 178   protected JCheckBox useRnaView = new JCheckBox();
 179
 180   protected JCheckBox addSecondaryStructure = new JCheckBox();
 181
 182   protected JCheckBox addTempFactor = new JCheckBox();
 183
 184   protected JComboBox<String> structViewer = new JComboBox<>();
 185
 186   protected JLabel structureViewerPathLabel;
 187
 188   protected JTextField structureViewerPath = new JTextField();
 189
 190   protected ButtonGroup mappingMethod = new ButtonGroup();
 191
 192   protected JRadioButton siftsMapping = new JRadioButton();
 193
 194   protected JRadioButton nwMapping = new JRadioButton();
 195
 196   /*
 197    * Colours tab components
 198    */
 199   protected JPanel minColour = new JPanel();
 200
 201   protected JPanel maxColour = new JPanel();
 202
 203   protected JComboBox<String> protColour = new JComboBox<>();
 204
 205   protected JComboBox<String> nucColour = new JComboBox<>();
 206
 207   /*
 208    * Overview tab components
 209    */
 210   protected JPanel gapColour = new JPanel();
 211
 212   protected JPanel hiddenColour = new JPanel();
 213
 214   protected JCheckBox useLegacyGap;
 215
 216   protected JCheckBox showHiddenAtStart;
 217
 218   protected JLabel gapLabel;
 219
 220   /*
 221    * Connections tab components
 222    */
 223   protected JPanel connectTab;
 224
 225   protected JTable linkUrlTable = new JTable();
 226
 227   protected JButton editLink = new JButton();
 228
 229   protected JButton deleteLink = new JButton();
 230
 231   protected JTextField filterTB = new JTextField();
 232
 233   protected JButton doReset = new JButton();
 234
 235   protected JButton userOnly = new JButton();
 236
 237   protected JLabel httpLabel = new JLabel();
 238
 239   protected JLabel httpsLabel = new JLabel();
 240
 241   protected JLabel portLabel = new JLabel();
 242
 243   protected JLabel serverLabel = new JLabel();
 244
 245   protected JLabel portLabel2 = new JLabel();
 246
 247   protected JLabel serverLabel2 = new JLabel();
 248
 249   protected JLabel proxyAuthUsernameLabel = new JLabel();
 250
 251   protected JLabel proxyAuthPasswordLabel = new JLabel();
 252
 253   protected JLabel passwordNotStoredLabel = new JLabel();
 254
 255   protected JTextField proxyServerHttpTB = new JTextField();
 256
 257   protected JTextField proxyPortHttpTB = new JTextField();
 258
 259   protected JTextField proxyServerHttpsTB = new JTextField();
 260
 261   protected JTextField proxyPortHttpsTB = new JTextField();
 262
 263   protected JCheckBox proxyAuth = new JCheckBox();
 264
 265   protected JTextField proxyAuthUsernameTB = new JTextField();
 266
 267   protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
 268
 269   protected JTextField defaultBrowser = new JTextField();
 270
 271   protected ButtonGroup proxyType = new ButtonGroup();
 272
 273   protected JRadioButton noProxy = new JRadioButton();
 274
 275   protected JRadioButton systemProxy = new JRadioButton();
 276
 277   protected JRadioButton customProxy = new JRadioButton();
 278
 279   protected JButton applyProxyButton = new JButton();
 280
 281   protected JCheckBox usagestats = new JCheckBox();
 282
 283   protected JCheckBox questionnaire = new JCheckBox();
 284
 285   protected JCheckBox versioncheck = new JCheckBox();
 286
 287   /*
 288    * Output tab components
 289    */
 290   protected JComboBox<Object> epsRendering = new JComboBox<>();
 291
 292   protected JComboBox<Object> htmlRendering = new JComboBox<>();
 293
 294   protected JComboBox<Object> svgRendering = new JComboBox<>();
 295
 296   protected JLabel userIdWidthlabel = new JLabel();
 297
 298   protected JCheckBox autoIdWidth = new JCheckBox();
 299
 300   protected JTextField userIdWidth = new JTextField();
 301
 302   protected JCheckBox blcjv = new JCheckBox();
 303
 304   protected JCheckBox pileupjv = new JCheckBox();
 305
 306   protected JCheckBox clustaljv = new JCheckBox();
 307
 308   protected JCheckBox msfjv = new JCheckBox();
 309
 310   protected JCheckBox fastajv = new JCheckBox();
 311
 312   protected JCheckBox pfamjv = new JCheckBox();
 313
 314   protected JCheckBox pirjv = new JCheckBox();
 315
 316   protected JCheckBox modellerOutput = new JCheckBox();
 317
 318   protected JCheckBox embbedBioJSON = new JCheckBox();
 319
 320   /*
 321    * Editing tab components
 322    */
 323   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 324
 325   protected JCheckBox padGaps = new JCheckBox();
 326
 327   protected JCheckBox sortByTree = new JCheckBox();
 328
 329   /*
 330    * Web Services tab
 331    */
 332   protected JPanel wsTab = new JPanel();
 333
 334   /*
 335    * Backups tab components
 336    * a lot of these are member variables instead of local variables only so that they
 337    * can be enabled/disabled easily in one go
 338    */
 339
 340   protected JCheckBox enableBackupFiles = new JCheckBox();
 341
 342   protected JPanel presetsPanel = new JPanel();
 343
 344   protected JLabel presetsComboLabel = new JLabel();
 345
 346   protected JCheckBox customiseCheckbox = new JCheckBox();
 347
 348   protected JButton revertButton = new JButton();
 349
 350   protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 351
 352   private int backupfilesPresetsComboLastSelected = 0;
 353
 354   protected JPanel suffixPanel = new JPanel();
 355
 356   protected JPanel keepfilesPanel = new JPanel();
 357
 358   protected JPanel exampleFilesPanel = new JPanel();
 359
 360   protected JTextField suffixTemplate = new JTextField(null, 8);
 361
 362   protected JLabel suffixTemplateLabel = new JLabel();
 363
 364   protected JLabel suffixDigitsLabel = new JLabel();
 365
 366   protected JSpinner suffixDigitsSpinner = new JSpinner();
 367
 368   protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
 369
 370   protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
 371
 372   public JSpinner backupfilesRollMaxSpinner = new JSpinner();
 373
 374   protected JLabel oldBackupFilesLabel = new JLabel();
 375
 376   protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
 377
 378   protected JTextArea backupfilesExampleLabel = new JTextArea();
 379
 380   private final JTabbedPane tabbedPane = new JTabbedPane();
 381
 382   private JLabel messageLabel = new JLabel("", JLabel.CENTER);
 383
 384   /**
 385    * Creates a new GPreferences object.
 386    */
 387   public GPreferences()
 388   {
 389     try
 390     {
 391       jbInit();
 392     } catch (Exception ex)
 393     {
 394       ex.printStackTrace();
 395     }
 396   }
 397
 398   /**
 399    * Construct the panel and its tabbed sub-panels.
 400    *
 401    * @throws Exception
 402    */
 403   private void jbInit() throws Exception
 404   {
 405     // final JTabbedPane tabbedPane = new JTabbedPane();
 406     this.setLayout(new BorderLayout());
 407
 408     // message label at top
 409     this.add(messageLabel, BorderLayout.NORTH);
 410
 411     JPanel okCancelPanel = initOkCancelPanel();
 412     this.add(tabbedPane, BorderLayout.CENTER);
 413     this.add(okCancelPanel, BorderLayout.SOUTH);
 414
 415     tabbedPane.add(initVisualTab(),
 416             MessageManager.getString("label.visual"));
 417
 418     tabbedPane.add(initColoursTab(),
 419             MessageManager.getString("label.colours"));
 420
 421     tabbedPane.add(initOverviewTab(),
 422             MessageManager.getString("label.overview"));
 423
 424     tabbedPane.add(initStructureTab(),
 425             MessageManager.getString("label.structure"));
 426
 427     tabbedPane.add(initConnectionsTab(),
 428             MessageManager.getString("label.connections"));
 429
 430     if (!Platform.isJS())
 431     {
 432       tabbedPane.add(initBackupsTab(),
 433               MessageManager.getString("label.backups"));
 434     }
 435
 436     tabbedPane.add(initLinksTab(),
 437             MessageManager.getString("label.urllinks"));
 438
 439     tabbedPane.add(initOutputTab(),
 440             MessageManager.getString("label.output"));
 441
 442     tabbedPane.add(initEditingTab(),
 443             MessageManager.getString("label.editing"));
 444
 445     /*
 446      * See WsPreferences for the real work of configuring this tab.
 447      */
 448     if (!Platform.isJS())
 449     {
 450       wsTab.setLayout(new BorderLayout());
 451       tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 452     }
 453
 454     /*
 455      * Handler to validate a tab before leaving it - currently only for
 456      * Structure.
 457      * Adding a clearMessage() so messages are cleared when changing tabs.
 458      */
 459     tabbedPane.addChangeListener(new ChangeListener()
 460     {
 461       private Component lastTab;
 462
 463       @Override
 464       public void stateChanged(ChangeEvent e)
 465       {
 466         if (lastTab == structureTab
 467                 && tabbedPane.getSelectedComponent() != structureTab)
 468         {
 469           if (!validateStructure())
 470           {
 471             tabbedPane.setSelectedComponent(structureTab);
 472             return;
 473           }
 474         }
 475         lastTab = tabbedPane.getSelectedComponent();
 476
 477         clearMessage();
 478       }
 479
 480     });
 481   }
 482
 483   public void setMessage(String message)
 484   {
 485     if (message != null)
 486     {
 487       messageLabel.setText(message);
 488       messageLabel.setFont(LABEL_FONT_BOLD);
 489       messageLabel.setForeground(Color.RED.darker());
 490       messageLabel.revalidate();
 491       messageLabel.repaint();
 492     }
 493     // note message not cleared if message is null. call clearMessage()
 494     // directly.
 495     this.revalidate();
 496     this.repaint();
 497   }
 498
 499   public void clearMessage()
 500   {
 501     // only repaint if message exists
 502     if (messageLabel.getText() != null
 503             && messageLabel.getText().length() > 0)
 504     {
 505       messageLabel.setText("");
 506       messageLabel.revalidate();
 507       messageLabel.repaint();
 508       this.revalidate();
 509       this.repaint();
 510     }
 511   }
 512
 513   public final static int CONNECTIONS_TAB = 5;
 514
 515   public void selectTab(int selectTab)
 516   {
 517     // select a given tab - currently only for Connections
 518     switch (selectTab)
 519     {
 520     case CONNECTIONS_TAB:
 521       tabbedPane.setSelectedComponent(connectTab);
 522       break;
 523     default:
 524     }
 525   }
 526
 527   /**
 528    * Initialises the Editing tabbed panel.
 529    *
 530    * @return
 531    */
 532   private JPanel initEditingTab()
 533   {
 534     JPanel editingTab = new JPanel();
 535     editingTab.setLayout(null);
 536     autoCalculateConsCheck.setFont(LABEL_FONT);
 537     autoCalculateConsCheck.setText(
 538             MessageManager.getString("label.autocalculate_consensus"));
 539     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 540     padGaps.setFont(LABEL_FONT);
 541     padGaps.setText(
 542             MessageManager.getString("label.pad_gaps_when_editing"));
 543     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 544     sortByTree.setFont(LABEL_FONT);
 545     sortByTree
 546             .setText(MessageManager.getString("label.sort_with_new_tree"));
 547     sortByTree.setToolTipText(MessageManager.getString(
 548             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 549     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 550     editingTab.add(autoCalculateConsCheck);
 551     editingTab.add(padGaps);
 552     editingTab.add(sortByTree);
 553     return editingTab;
 554   }
 555
 556   /**
 557    * Initialises the Output tab
 558    *
 559    * @return
 560    */
 561   private JPanel initOutputTab()
 562   {
 563     JPanel outputTab = new JPanel();
 564     outputTab.setLayout(null);
 565
 566     JLabel epsLabel = new JLabel(
 567             MessageManager.formatMessage("label.rendering_style", "EPS"));
 568     epsLabel.setFont(LABEL_FONT);
 569     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 570     epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
 571     epsRendering.setFont(LABEL_FONT);
 572     epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
 573     JLabel htmlLabel = new JLabel(
 574             MessageManager.formatMessage("label.rendering_style", "HTML"));
 575     htmlLabel.setFont(LABEL_FONT);
 576     htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 577     htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
 578     htmlRendering.setFont(LABEL_FONT);
 579     htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
 580     JLabel svgLabel = new JLabel(
 581             MessageManager.formatMessage("label.rendering_style", "SVG"));
 582     svgLabel.setFont(LABEL_FONT);
 583     svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 584     svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
 585     svgRendering.setFont(LABEL_FONT);
 586     svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
 587
 588     JLabel jLabel1 = new JLabel();
 589     jLabel1.setFont(LABEL_FONT);
 590     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 591     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 592     jLabel1.setFont(LABEL_FONT);
 593
 594     fastajv.setFont(LABEL_FONT);
 595     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 596     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 597     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 598     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 599     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 600     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 601     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 602     msfjv.setFont(LABEL_FONT);
 603     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 604     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 605     JPanel jPanel11 = new JPanel();
 606     jPanel11.setFont(LABEL_FONT);
 607     TitledBorder titledBorder2 = new TitledBorder(
 608             MessageManager.getString("label.file_output"));
 609     jPanel11.setBorder(titledBorder2);
 610     jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
 611     GridLayout gridLayout3 = new GridLayout();
 612     jPanel11.setLayout(gridLayout3);
 613     gridLayout3.setRows(8);
 614     blcjv.setFont(LABEL_FONT);
 615     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 616     clustaljv.setFont(LABEL_FONT);
 617     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 618     pfamjv.setFont(LABEL_FONT);
 619     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 620     pileupjv.setFont(LABEL_FONT);
 621     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 622     pirjv.setFont(LABEL_FONT);
 623     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 624     autoIdWidth.setFont(LABEL_FONT);
 625     autoIdWidth.setText(
 626             MessageManager.getString("label.automatically_set_id_width"));
 627     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 628             .getString("label.adjusts_width_generated_eps_png")));
 629     autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
 630     autoIdWidth.addActionListener(new ActionListener()
 631     {
 632
 633       @Override
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         autoIdWidth_actionPerformed();
 637       }
 638     });
 639     userIdWidthlabel.setFont(LABEL_FONT);
 640     userIdWidthlabel.setText(
 641             MessageManager.getString("label.figure_id_column_width"));
 642     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 643             .getString("label.manually_specify_width_left_column")));
 644     userIdWidthlabel.setToolTipText(
 645             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 646                     "label.manually_specify_width_left_column")));
 647     userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
 648     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 649     userIdWidth.setText("");
 650     userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
 651     userIdWidth.addActionListener(new ActionListener()
 652     {
 653
 654       @Override
 655       public void actionPerformed(ActionEvent e)
 656       {
 657         userIdWidth_actionPerformed();
 658       }
 659     });
 660     modellerOutput.setFont(LABEL_FONT);
 661     modellerOutput
 662             .setText(MessageManager.getString("label.use_modeller_output"));
 663     modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
 664     embbedBioJSON.setFont(LABEL_FONT);
 665     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 666     embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 667
 668     jPanel11.add(jLabel1);
 669     jPanel11.add(blcjv);
 670     jPanel11.add(clustaljv);
 671     jPanel11.add(fastajv);
 672     jPanel11.add(msfjv);
 673     jPanel11.add(pfamjv);
 674     jPanel11.add(pileupjv);
 675     jPanel11.add(pirjv);
 676     outputTab.add(autoIdWidth);
 677     outputTab.add(userIdWidth);
 678     outputTab.add(userIdWidthlabel);
 679     outputTab.add(modellerOutput);
 680     if (!Platform.isJS())
 681     {
 682       /*
 683        * JalviewJS doesn't support Lineart option or SVG output
 684        */
 685       outputTab.add(embbedBioJSON);
 686       outputTab.add(epsLabel);
 687       outputTab.add(epsRendering);
 688       outputTab.add(htmlLabel);
 689       outputTab.add(htmlRendering);
 690       outputTab.add(svgLabel);
 691       outputTab.add(svgRendering);
 692     }
 693     outputTab.add(jPanel11);
 694     return outputTab;
 695   }
 696
 697   /**
 698    * Initialises the Connections tabbed panel.
 699    *
 700    * @return
 701    */
 702   private JPanel initConnectionsTab()
 703   {
 704     connectTab = new JPanel();
 705     connectTab.setLayout(new GridBagLayout());
 706
 707     // Label for browser text box
 708     JLabel browserLabel = new JLabel();
 709     browserLabel.setFont(LABEL_FONT);
 710     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 711     browserLabel.setText(
 712             MessageManager.getString("label.default_browser_unix"));
 713     defaultBrowser.setFont(LABEL_FONT);
 714     defaultBrowser.setText("");
 715     final String tooltip = JvSwingUtils.wrapTooltip(true,
 716             MessageManager.getString("label.double_click_to_browse"));
 717     defaultBrowser.setToolTipText(tooltip);
 718     defaultBrowser.addMouseListener(new MouseAdapter()
 719     {
 720       @Override
 721       public void mouseClicked(MouseEvent e)
 722       {
 723         if (e.getClickCount() > 1)
 724         {
 725           defaultBrowser_mouseClicked(e);
 726         }
 727       }
 728     });
 729
 730     JPanel proxyPanel = initConnTabProxyPanel();
 731     initConnTabCheckboxes();
 732
 733     // Add default Browser text box
 734     connectTab.add(browserLabel,
 735             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 736                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 737                     new Insets(10, 0, 5, 5), 5, 1));
 738     defaultBrowser.setFont(LABEL_FONT);
 739     defaultBrowser.setText("");
 740
 741     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 742             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 743             new Insets(10, 0, 5, 10), 30, 1));
 744
 745     // Add proxy server panel
 746     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 747             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 748             new Insets(10, 0, 5, 12), 4, 10));
 749
 750     // Add usage stats, version check and questionnaire checkboxes
 751     connectTab.add(usagestats,
 752             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 753                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 754                     new Insets(0, 2, 5, 5), 70, 1));
 755     connectTab.add(questionnaire,
 756             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 757                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 758                     new Insets(0, 2, 5, 10), 70, 1));
 759     connectTab.add(versioncheck,
 760             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 761                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 762                     new Insets(0, 2, 5, 5), 70, 1));
 763
 764     versioncheck.setVisible(false);
 765
 766     // Add padding so the panel doesn't look ridiculous
 767     JPanel spacePanel = new JPanel();
 768     connectTab.add(spacePanel,
 769             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 770                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 771                     new Insets(0, 0, 0, 5), 70, 1));
 772
 773     return connectTab;
 774   }
 775
 776   /**
 777    * Initialises the Links tabbed panel.
 778    *
 779    * @return
 780    */
 781   private JPanel initLinksTab()
 782   {
 783     JPanel linkTab = new JPanel();
 784     linkTab.setLayout(new GridBagLayout());
 785
 786     // Set up table for Url links
 787     linkUrlTable.getTableHeader().setReorderingAllowed(false);
 788     linkUrlTable.setFillsViewportHeight(true);
 789     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 790     linkUrlTable.setAutoCreateRowSorter(true);
 791     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 792
 793     // adjust row height so radio buttons actually fit
 794     // don't do this in the renderer, it causes the awt thread to activate
 795     // constantly
 796     JRadioButton temp = new JRadioButton();
 797     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 798
 799     // Table in scrollpane so that the table is given a scrollbar
 800     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 801     linkScrollPane.setBorder(null);
 802
 803     // Panel for links functionality
 804     JPanel linkPanel = new JPanel(new GridBagLayout());
 805     linkPanel.setBorder(new TitledBorder(
 806             MessageManager.getString("label.url_linkfrom_sequence_id")));
 807
 808     // Put the Url links panel together
 809
 810     // Buttons go at top right, resizing only resizes the blank space vertically
 811     JPanel buttonPanel = initLinkTabUrlButtons();
 812     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 813     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 814     linkConstraints1.gridx = 0;
 815     linkConstraints1.gridy = 0;
 816     linkConstraints1.weightx = 1.0;
 817     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 818     linkTab.add(buttonPanel, linkConstraints1);
 819
 820     // Links table goes at top left, resizing resizes the table
 821     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 822     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 823     linkConstraints2.gridx = 0;
 824     linkConstraints2.gridy = 1;
 825     linkConstraints2.weightx = 1.0;
 826     linkConstraints2.weighty = 1.0;
 827     linkConstraints2.fill = GridBagConstraints.BOTH;
 828     linkTab.add(linkScrollPane, linkConstraints2);
 829
 830     // Filter box and buttons goes at bottom left, resizing resizes the text box
 831     JPanel filterPanel = initLinkTabFilterPanel();
 832     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 833     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 834     linkConstraints3.gridx = 0;
 835     linkConstraints3.gridy = 2;
 836     linkConstraints3.weightx = 1.0;
 837     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 838     linkTab.add(filterPanel, linkConstraints3);
 839
 840     return linkTab;
 841   }
 842
 843   private JPanel initLinkTabFilterPanel()
 844   {
 845     // Filter textbox and reset button
 846     JLabel filterLabel = new JLabel(
 847             MessageManager.getString("label.filter"));
 848     filterLabel.setFont(LABEL_FONT);
 849     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 850     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 851
 852     filterTB.setFont(LABEL_FONT);
 853     filterTB.setText("");
 854
 855     doReset.setText(MessageManager.getString("action.showall"));
 856     userOnly.setText(MessageManager.getString("action.customfilter"));
 857
 858     // Panel for filter functionality
 859     JPanel filterPanel = new JPanel(new GridBagLayout());
 860     filterPanel.setBorder(new TitledBorder("Filter"));
 861     GridBagConstraints gbc = new GridBagConstraints();
 862     gbc.gridx = 0;
 863     gbc.gridy = 0;
 864     gbc.fill = GridBagConstraints.NONE;
 865     gbc.anchor = GridBagConstraints.WEST;
 866
 867     filterPanel.add(filterLabel, gbc);
 868
 869     GridBagConstraints gbc1 = new GridBagConstraints();
 870     gbc1.gridx = 1;
 871     gbc1.gridwidth = 2;
 872     gbc1.fill = GridBagConstraints.HORIZONTAL;
 873     gbc1.anchor = GridBagConstraints.WEST;
 874     gbc1.weightx = 1.0;
 875     filterPanel.add(filterTB, gbc1);
 876
 877     GridBagConstraints gbc2 = new GridBagConstraints();
 878     gbc2.gridx = 3;
 879     gbc2.fill = GridBagConstraints.NONE;
 880     gbc2.anchor = GridBagConstraints.WEST;
 881     filterPanel.add(doReset, gbc2);
 882
 883     GridBagConstraints gbc3 = new GridBagConstraints();
 884     gbc3.gridx = 4;
 885     gbc3.fill = GridBagConstraints.NONE;
 886     gbc3.anchor = GridBagConstraints.WEST;
 887     filterPanel.add(userOnly, gbc3);
 888
 889     return filterPanel;
 890   }
 891
 892   private JPanel initLinkTabUrlButtons()
 893   {
 894     // Buttons for new / edit / delete Url links
 895     JButton newLink = new JButton();
 896     newLink.setText(MessageManager.getString("action.new"));
 897
 898     editLink.setText(MessageManager.getString("action.edit"));
 899
 900     deleteLink.setText(MessageManager.getString("action.delete"));
 901
 902     // no current selection, so initially disable delete/edit buttons
 903     editLink.setEnabled(false);
 904     deleteLink.setEnabled(false);
 905
 906     newLink.addActionListener(new java.awt.event.ActionListener()
 907     {
 908       @Override
 909       public void actionPerformed(ActionEvent e)
 910       {
 911         newLink_actionPerformed(e);
 912       }
 913     });
 914
 915     editLink.setText(MessageManager.getString("action.edit"));
 916     editLink.addActionListener(new java.awt.event.ActionListener()
 917     {
 918       @Override
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         editLink_actionPerformed(e);
 922       }
 923     });
 924
 925     deleteLink.setText(MessageManager.getString("action.delete"));
 926     deleteLink.addActionListener(new java.awt.event.ActionListener()
 927     {
 928       @Override
 929       public void actionPerformed(ActionEvent e)
 930       {
 931         deleteLink_actionPerformed(e);
 932       }
 933     });
 934
 935     JPanel buttonPanel = new JPanel(new GridBagLayout());
 936     buttonPanel.setBorder(new TitledBorder("Edit links"));
 937     GridBagConstraints gbc = new GridBagConstraints();
 938     gbc.gridx = 0;
 939     gbc.gridy = 0;
 940     gbc.fill = GridBagConstraints.NONE;
 941     buttonPanel.add(newLink, gbc);
 942
 943     GridBagConstraints gbc1 = new GridBagConstraints();
 944     gbc1.gridx = 1;
 945     gbc1.gridy = 0;
 946     gbc1.fill = GridBagConstraints.NONE;
 947     buttonPanel.add(editLink, gbc1);
 948
 949     GridBagConstraints gbc2 = new GridBagConstraints();
 950     gbc2.gridx = 2;
 951     gbc2.gridy = 0;
 952     gbc2.fill = GridBagConstraints.NONE;
 953     buttonPanel.add(deleteLink, gbc2);
 954
 955     GridBagConstraints gbc3 = new GridBagConstraints();
 956     gbc3.gridx = 3;
 957     gbc3.gridy = 0;
 958     gbc3.fill = GridBagConstraints.HORIZONTAL;
 959     gbc3.weightx = 1.0;
 960     JPanel spacePanel = new JPanel();
 961     spacePanel.setBorder(null);
 962     buttonPanel.add(spacePanel, gbc3);
 963
 964     return buttonPanel;
 965   }
 966
 967   /**
 968    * Initialises the proxy server panel in the Connections tab
 969    *
 970    * @return the proxy server panel
 971    */
 972   private JPanel initConnTabProxyPanel()
 973   {
 974     // Label for server text box
 975     serverLabel.setText(MessageManager.getString("label.host") + ": ");
 976     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 977     serverLabel.setFont(LABEL_FONT);
 978     serverLabel2.setText(MessageManager.getString("label.host") + ": ");
 979     serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
 980     serverLabel2.setFont(LABEL_FONT);
 981
 982     // Proxy server and port text boxes
 983     proxyServerHttpTB.setFont(LABEL_FONT);
 984     proxyServerHttpTB.setColumns(40);
 985     proxyPortHttpTB.setFont(LABEL_FONT);
 986     proxyPortHttpTB.setColumns(4);
 987     proxyServerHttpsTB.setFont(LABEL_FONT);
 988     proxyServerHttpsTB.setColumns(40);
 989     proxyPortHttpsTB.setFont(LABEL_FONT);
 990     proxyPortHttpsTB.setColumns(4);
 991     proxyAuthUsernameTB.setFont(LABEL_FONT);
 992     proxyAuthUsernameTB.setColumns(30);
 993
 994     // check for any change to enable applyProxyButton
 995     DocumentListener d = new DocumentListener()
 996     {
 997       @Override
 998       public void changedUpdate(DocumentEvent e)
 999       {
1000         applyProxyButtonEnabled(true);
1001       }
1002
1003       @Override
1004       public void insertUpdate(DocumentEvent e)
1005       {
1006         applyProxyButtonEnabled(true);
1007       }
1008
1009       @Override
1010       public void removeUpdate(DocumentEvent e)
1011       {
1012         applyProxyButtonEnabled(true);
1013       }
1014     };
1015     proxyServerHttpTB.getDocument().addDocumentListener(d);
1016     proxyPortHttpTB.getDocument().addDocumentListener(d);
1017     proxyServerHttpsTB.getDocument().addDocumentListener(d);
1018     proxyPortHttpsTB.getDocument().addDocumentListener(d);
1019     proxyAuthUsernameTB.getDocument().addDocumentListener(d);
1020     proxyAuthPasswordPB.setFont(LABEL_FONT);
1021     proxyAuthPasswordPB.setColumns(30);
1022     proxyAuthPasswordPB.getDocument()
1023             .addDocumentListener(new DocumentListener()
1024             {
1025               @Override
1026               public void changedUpdate(DocumentEvent e)
1027               {
1028                 proxyAuthPasswordCheckHighlight(true);
1029                 applyProxyButtonEnabled(true);
1030               }
1031
1032               @Override
1033               public void insertUpdate(DocumentEvent e)
1034               {
1035                 proxyAuthPasswordCheckHighlight(true);
1036                 applyProxyButtonEnabled(true);
1037               }
1038
1039               @Override
1040               public void removeUpdate(DocumentEvent e)
1041               {
1042                 proxyAuthPasswordCheckHighlight(true);
1043                 applyProxyButtonEnabled(true);
1044               }
1045
1046             });
1047
1048     // Label for Port text box
1049     portLabel.setFont(LABEL_FONT);
1050     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1051     portLabel.setText(MessageManager.getString("label.port") + ": ");
1052     portLabel2.setFont(LABEL_FONT);
1053     portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1054     portLabel2.setText(MessageManager.getString("label.port") + ": ");
1055
1056     httpLabel.setText("HTTP");
1057     httpLabel.setFont(LABEL_FONT_BOLD);
1058     httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1059     httpsLabel.setText("HTTPS");
1060     httpsLabel.setFont(LABEL_FONT_BOLD);
1061     httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1062
1063     proxyAuthUsernameLabel
1064             .setText(MessageManager.getString("label.username") + ": ");
1065     proxyAuthUsernameLabel.setFont(LABEL_FONT);
1066     proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1067     proxyAuthPasswordLabel
1068             .setText(MessageManager.getString("label.password") + ": ");
1069     proxyAuthPasswordLabel.setFont(LABEL_FONT);
1070     proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1071     passwordNotStoredLabel.setText(
1072             "(" + MessageManager.getString("label.not_stored") + ")");
1073     passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1074     passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1075
1076     // Proxy type radio buttons
1077     noProxy.setFont(LABEL_FONT);
1078     noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1079     noProxy.setText(MessageManager.getString("label.no_proxy"));
1080     systemProxy.setFont(LABEL_FONT);
1081     systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1082     systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1083             displayUserHostPort(Cache.startupProxyProperties[4],
1084                     Cache.startupProxyProperties[0],
1085                     Cache.startupProxyProperties[1]),
1086             displayUserHostPort(Cache.startupProxyProperties[6],
1087                     Cache.startupProxyProperties[2],
1088                     Cache.startupProxyProperties[3])));
1089     customProxy.setFont(LABEL_FONT);
1090     customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1091     customProxy.setText(
1092             MessageManager.getString("label.use_proxy_server") + ":");
1093     ActionListener al = new ActionListener()
1094     {
1095       @Override
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         proxyType_actionPerformed();
1099       }
1100     };
1101     noProxy.addActionListener(al);
1102     systemProxy.addActionListener(al);
1103     customProxy.addActionListener(al);
1104     proxyType.add(noProxy);
1105     proxyType.add(systemProxy);
1106     proxyType.add(customProxy);
1107
1108     proxyAuth.setFont(LABEL_FONT);
1109     proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1110     proxyAuth.setText(MessageManager.getString("label.auth_required"));
1111     proxyAuth.addActionListener(new ActionListener()
1112     {
1113       @Override
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         proxyAuth_actionPerformed();
1117       }
1118     });
1119
1120     setCustomProxyEnabled();
1121
1122     // Make proxy server panel
1123     JPanel proxyPanel = new JPanel();
1124     TitledBorder titledBorder1 = new TitledBorder(
1125             MessageManager.getString("label.proxy_servers"));
1126     proxyPanel.setBorder(titledBorder1);
1127     proxyPanel.setLayout(new GridBagLayout());
1128     GridBagConstraints gbc = new GridBagConstraints();
1129     gbc.fill = GridBagConstraints.HORIZONTAL;
1130     gbc.weightx = 1.0;
1131
1132     GridBagConstraints c = new GridBagConstraints();
1133     // Proxy type radio buttons (3)
1134     JPanel ptPanel = new JPanel();
1135     ptPanel.setLayout(new GridBagLayout());
1136     c.weightx = 1.0;
1137     c.gridy = 0;
1138     c.gridx = 0;
1139     c.gridwidth = 1;
1140     c.fill = GridBagConstraints.HORIZONTAL;
1141     ptPanel.add(noProxy, c);
1142     c.gridy++;
1143     ptPanel.add(systemProxy, c);
1144     c.gridy++;
1145     ptPanel.add(customProxy, c);
1146
1147     gbc.gridy = 0;
1148     proxyPanel.add(ptPanel, gbc);
1149
1150     // host and port text boxes
1151     JPanel hpPanel = new JPanel();
1152     hpPanel.setLayout(new GridBagLayout());
1153     // HTTP host port row
1154     c.gridy = 0;
1155     c.gridx = 0;
1156
1157     c.weightx = 0.1;
1158     c.anchor = GridBagConstraints.LINE_START;
1159     hpPanel.add(httpLabel, c);
1160
1161     c.gridx++;
1162     c.weightx = 0.1;
1163     c.anchor = GridBagConstraints.LINE_END;
1164     hpPanel.add(serverLabel, c);
1165
1166     c.gridx++;
1167     c.weightx = 1.0;
1168     c.anchor = GridBagConstraints.LINE_START;
1169     hpPanel.add(proxyServerHttpTB, c);
1170
1171     c.gridx++;
1172     c.weightx = 0.1;
1173     c.anchor = GridBagConstraints.LINE_END;
1174     hpPanel.add(portLabel, c);
1175
1176     c.gridx++;
1177     c.weightx = 0.2;
1178     c.anchor = GridBagConstraints.LINE_START;
1179     hpPanel.add(proxyPortHttpTB, c);
1180
1181     // HTTPS host port row
1182     c.gridy++;
1183     c.gridx = 0;
1184     c.gridwidth = 1;
1185
1186     c.anchor = GridBagConstraints.LINE_START;
1187     hpPanel.add(httpsLabel, c);
1188
1189     c.gridx++;
1190     c.anchor = GridBagConstraints.LINE_END;
1191     hpPanel.add(serverLabel2, c);
1192
1193     c.gridx++;
1194     c.anchor = GridBagConstraints.LINE_START;
1195     hpPanel.add(proxyServerHttpsTB, c);
1196
1197     c.gridx++;
1198     c.anchor = GridBagConstraints.LINE_END;
1199     hpPanel.add(portLabel2, c);
1200
1201     c.gridx++;
1202     c.anchor = GridBagConstraints.LINE_START;
1203     hpPanel.add(proxyPortHttpsTB, c);
1204
1205     gbc.gridy++;
1206     proxyPanel.add(hpPanel, gbc);
1207
1208     if (!Platform.isJS())
1209     /**
1210      * java.net.Authenticator is not implemented in SwingJS. Not displaying the
1211      * Authentication options in Preferences.
1212      *
1213      * @j2sIgnore
1214      *
1215      */
1216     {
1217       // Require authentication checkbox
1218       gbc.gridy++;
1219       proxyPanel.add(proxyAuth, gbc);
1220
1221       // username and password
1222       JPanel upPanel = new JPanel();
1223       upPanel.setLayout(new GridBagLayout());
1224       // username row
1225       c.gridy = 0;
1226       c.gridx = 0;
1227       c.gridwidth = 1;
1228       c.weightx = 0.4;
1229       c.anchor = GridBagConstraints.LINE_END;
1230       upPanel.add(proxyAuthUsernameLabel, c);
1231
1232       c.gridx++;
1233       c.weightx = 1.0;
1234       c.anchor = GridBagConstraints.LINE_START;
1235       upPanel.add(proxyAuthUsernameTB, c);
1236
1237       // password row
1238       c.gridy++;
1239       c.gridx = 0;
1240       c.weightx = 0.4;
1241       c.anchor = GridBagConstraints.LINE_END;
1242       upPanel.add(proxyAuthPasswordLabel, c);
1243
1244       c.gridx++;
1245       c.weightx = 1.0;
1246       c.anchor = GridBagConstraints.LINE_START;
1247       upPanel.add(proxyAuthPasswordPB, c);
1248
1249       c.gridx++;
1250       c.weightx = 0.4;
1251       c.anchor = GridBagConstraints.LINE_START;
1252       upPanel.add(passwordNotStoredLabel, c);
1253
1254       gbc.gridy++;
1255       proxyPanel.add(upPanel, gbc);
1256
1257     } // end j2sIgnore
1258
1259     applyProxyButton.setText(MessageManager.getString("action.apply"));
1260     applyProxyButton.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         saveProxySettings();
1266         applyProxyButton.setEnabled(false);
1267       }
1268     });
1269     gbc.gridy++;
1270     gbc.fill = GridBagConstraints.NONE;
1271     gbc.anchor = GridBagConstraints.LINE_END;
1272     proxyPanel.add(applyProxyButton, gbc);
1273
1274     return proxyPanel;
1275   }
1276
1277   public void proxyAuthPasswordCheckHighlight(boolean enabled)
1278   {
1279     proxyAuthPasswordCheckHighlight(enabled, false);
1280   }
1281
1282   public void proxyAuthPasswordCheckHighlight(boolean enabled,
1283           boolean grabFocus)
1284   {
1285     if (enabled && proxyType.isSelected(customProxy.getModel())
1286             && proxyAuth.isSelected()
1287             && !proxyAuthUsernameTB.getText().isEmpty()
1288             && proxyAuthPasswordPB.getDocument().getLength() == 0)
1289     {
1290       if (grabFocus)
1291         proxyAuthPasswordPB.grabFocus();
1292       proxyAuthPasswordPB.setBackground(Color.PINK);
1293     }
1294     else
1295     {
1296       proxyAuthPasswordPB.setBackground(Color.WHITE);
1297     }
1298   }
1299
1300   public void applyProxyButtonEnabled(boolean enabled)
1301   {
1302     applyProxyButton.setEnabled(enabled);
1303   }
1304
1305   public void saveProxySettings()
1306   {
1307     // overridden in Preferences
1308   }
1309
1310   private String displayUserHostPort(String user, String host, String port)
1311   {
1312     boolean hostBlank = (host == null || host.isEmpty());
1313     boolean portBlank = (port == null || port.isEmpty());
1314     if (hostBlank && portBlank)
1315     {
1316       return MessageManager.getString("label.none");
1317     }
1318
1319     StringBuilder sb = new StringBuilder();
1320     if (user != null)
1321     {
1322       sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1323               : user);
1324       sb.append("@");
1325     }
1326     sb.append(hostBlank ? "" : host);
1327     if (!portBlank)
1328     {
1329       sb.append(":");
1330       sb.append(port);
1331     }
1332     return sb.toString();
1333   }
1334
1335   /**
1336    * Initialises the checkboxes in the Connections tab
1337    */
1338   private void initConnTabCheckboxes()
1339   {
1340     // Usage stats checkbox label
1341     usagestats.setText(
1342             MessageManager.getString("label.send_usage_statistics"));
1343     usagestats.setFont(LABEL_FONT);
1344     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1345     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1346
1347     // Questionnaire checkbox label
1348     questionnaire.setText(
1349             MessageManager.getString("label.check_for_questionnaires"));
1350     questionnaire.setFont(LABEL_FONT);
1351     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1352     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1353
1354     // Check for latest version checkbox label
1355     versioncheck.setText(
1356             MessageManager.getString("label.check_for_latest_version"));
1357     versioncheck.setFont(LABEL_FONT);
1358     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1359     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1360   }
1361
1362   /**
1363    * Initialises the parent panel which contains the tabbed sections.
1364    *
1365    * @return
1366    */
1367   private JPanel initOkCancelPanel()
1368   {
1369     JButton ok = new JButton();
1370     ok.setText(MessageManager.getString("action.ok"));
1371     ok.addActionListener(new ActionListener()
1372     {
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         ok_actionPerformed(e);
1377       }
1378     });
1379     JButton cancel = new JButton();
1380     cancel.setText(MessageManager.getString("action.cancel"));
1381     cancel.addActionListener(new ActionListener()
1382     {
1383       @Override
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         cancel_actionPerformed(e);
1387       }
1388     });
1389     JPanel okCancelPanel = new JPanel();
1390     okCancelPanel.add(ok);
1391     okCancelPanel.add(cancel);
1392     return okCancelPanel;
1393   }
1394
1395   /**
1396    * Initialises the Colours tabbed panel.
1397    *
1398    * @return
1399    */
1400   private JPanel initColoursTab()
1401   {
1402     JPanel coloursTab = new JPanel();
1403     coloursTab.setBorder(new TitledBorder(
1404             MessageManager.getString("action.open_new_alignment")));
1405     coloursTab.setLayout(new FlowLayout());
1406     JLabel mincolourLabel = new JLabel();
1407     mincolourLabel.setFont(LABEL_FONT);
1408     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1409     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1410     minColour.setFont(LABEL_FONT);
1411     minColour.setBorder(BorderFactory.createEtchedBorder());
1412     minColour.setPreferredSize(new Dimension(40, 20));
1413     minColour.addMouseListener(new MouseAdapter()
1414     {
1415       @Override
1416       public void mousePressed(MouseEvent e)
1417       {
1418         minColour_actionPerformed(minColour);
1419       }
1420     });
1421     JLabel maxcolourLabel = new JLabel();
1422     maxcolourLabel.setFont(LABEL_FONT);
1423     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1424     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1425     maxColour.setFont(LABEL_FONT);
1426     maxColour.setBorder(BorderFactory.createEtchedBorder());
1427     maxColour.setPreferredSize(new Dimension(40, 20));
1428     maxColour.addMouseListener(new MouseAdapter()
1429     {
1430       @Override
1431       public void mousePressed(MouseEvent e)
1432       {
1433         maxColour_actionPerformed(maxColour);
1434       }
1435     });
1436
1437     protColour.setFont(LABEL_FONT);
1438     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1439     JLabel protColourLabel = new JLabel();
1440     protColourLabel.setFont(LABEL_FONT);
1441     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1442     protColourLabel.setText(
1443             MessageManager.getString("label.prot_alignment_colour") + " ");
1444     JvSwingUtils.addtoLayout(coloursTab,
1445             MessageManager
1446                     .getString("label.default_colour_scheme_for_alignment"),
1447             protColourLabel, protColour);
1448
1449     nucColour.setFont(LABEL_FONT);
1450     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1451     JLabel nucColourLabel = new JLabel();
1452     nucColourLabel.setFont(LABEL_FONT);
1453     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1454     nucColourLabel.setText(
1455             MessageManager.getString("label.nuc_alignment_colour") + " ");
1456     JvSwingUtils.addtoLayout(coloursTab,
1457             MessageManager
1458                     .getString("label.default_colour_scheme_for_alignment"),
1459             nucColourLabel, nucColour);
1460
1461     JPanel annotationShding = new JPanel();
1462     annotationShding.setBorder(new TitledBorder(
1463             MessageManager.getString("label.annotation_shading_default")));
1464     annotationShding.setLayout(new GridLayout(1, 2));
1465     JvSwingUtils.addtoLayout(annotationShding,
1466             MessageManager.getString(
1467                     "label.default_minimum_colour_annotation_shading"),
1468             mincolourLabel, minColour);
1469     JvSwingUtils.addtoLayout(annotationShding,
1470             MessageManager.getString(
1471                     "label.default_maximum_colour_annotation_shading"),
1472             maxcolourLabel, maxColour);
1473     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1474     return coloursTab;
1475   }
1476
1477   /**
1478    * Initialises the Overview tabbed panel.
1479    *
1480    * @return
1481    */
1482   private JPanel initOverviewTab()
1483   {
1484     JPanel overviewPanel = new JPanel();
1485     overviewPanel.setBorder(new TitledBorder(
1486             MessageManager.getString("label.overview_settings")));
1487
1488     gapColour.setFont(LABEL_FONT);
1489     // fixing the border colours stops apparent colour bleed from the panel
1490     gapColour.setBorder(
1491             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1492     gapColour.setPreferredSize(new Dimension(40, 20));
1493     gapColour.addMouseListener(new MouseAdapter()
1494     {
1495       @Override
1496       public void mousePressed(MouseEvent e)
1497       {
1498         gapColour_actionPerformed(gapColour);
1499       }
1500     });
1501
1502     hiddenColour.setFont(LABEL_FONT);
1503     // fixing the border colours stops apparent colour bleed from the panel
1504     hiddenColour.setBorder(
1505             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1506     hiddenColour.setPreferredSize(new Dimension(40, 20));
1507     hiddenColour.addMouseListener(new MouseAdapter()
1508     {
1509       @Override
1510       public void mousePressed(MouseEvent e)
1511       {
1512         hiddenColour_actionPerformed(hiddenColour);
1513       }
1514     });
1515
1516     useLegacyGap = new JCheckBox(
1517             MessageManager.getString("label.ov_legacy_gap"));
1518     useLegacyGap.setFont(LABEL_FONT);
1519     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1520     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1521     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1522     gapLabel.setFont(LABEL_FONT);
1523     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1524     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1525     showHiddenAtStart = new JCheckBox(
1526             MessageManager.getString("label.ov_show_hide_default"));
1527     showHiddenAtStart.setFont(LABEL_FONT);
1528     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1529     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1530     JLabel hiddenLabel = new JLabel(
1531             MessageManager.getString("label.hidden_colour"));
1532     hiddenLabel.setFont(LABEL_FONT);
1533     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1534     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1535
1536     useLegacyGap.addActionListener(new ActionListener()
1537     {
1538       @Override
1539       public void actionPerformed(ActionEvent e)
1540       {
1541         useLegacyGaps_actionPerformed(e);
1542       }
1543     });
1544
1545     overviewPanel.setLayout(new GridBagLayout());
1546     GridBagConstraints c1 = new GridBagConstraints();
1547
1548     c1.fill = GridBagConstraints.HORIZONTAL;
1549     c1.gridx = 0;
1550     c1.gridy = 0;
1551     c1.weightx = 1;
1552     c1.ipady = 20;
1553     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1554     overviewPanel.add(useLegacyGap, c1);
1555
1556     GridBagConstraints c2 = new GridBagConstraints();
1557     c2.fill = GridBagConstraints.HORIZONTAL;
1558     c2.gridx = 1;
1559     c2.gridy = 0;
1560     c2.insets = new Insets(0, 15, 0, 10);
1561     overviewPanel.add(gapLabel, c2);
1562
1563     GridBagConstraints c3 = new GridBagConstraints();
1564     c3.fill = GridBagConstraints.HORIZONTAL;
1565     c3.gridx = 2;
1566     c3.gridy = 0;
1567     c3.insets = new Insets(0, 0, 0, 15);
1568     overviewPanel.add(gapColour, c3);
1569
1570     GridBagConstraints c4 = new GridBagConstraints();
1571     c4.fill = GridBagConstraints.HORIZONTAL;
1572     c4.gridx = 0;
1573     c4.gridy = 1;
1574     c4.weightx = 1;
1575     overviewPanel.add(showHiddenAtStart, c4);
1576
1577     GridBagConstraints c5 = new GridBagConstraints();
1578     c5.fill = GridBagConstraints.HORIZONTAL;
1579     c5.gridx = 1;
1580     c5.gridy = 1;
1581     c5.insets = new Insets(0, 15, 0, 10);
1582     overviewPanel.add(hiddenLabel, c5);
1583
1584     GridBagConstraints c6 = new GridBagConstraints();
1585     c6.fill = GridBagConstraints.HORIZONTAL;
1586     c6.gridx = 2;
1587     c6.gridy = 1;
1588     c6.insets = new Insets(0, 0, 0, 15);
1589     overviewPanel.add(hiddenColour, c6);
1590
1591     JButton resetButton = new JButton(
1592             MessageManager.getString("label.reset_to_defaults"));
1593
1594     resetButton.addActionListener(new ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         resetOvDefaults_actionPerformed(e);
1600       }
1601     });
1602
1603     GridBagConstraints c7 = new GridBagConstraints();
1604     c7.fill = GridBagConstraints.NONE;
1605     c7.gridx = 0;
1606     c7.gridy = 2;
1607     c7.insets = new Insets(10, 0, 0, 0);
1608     c7.anchor = GridBagConstraints.WEST;
1609     overviewPanel.add(resetButton, c7);
1610
1611     // Add padding so the panel doesn't look ridiculous
1612     JPanel spacePanel = new JPanel();
1613     overviewPanel.add(spacePanel,
1614             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1615                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1616                     new Insets(0, 0, 0, 5), 0, 0));
1617
1618     return overviewPanel;
1619   }
1620
1621   /**
1622    * Initialises the Structure tabbed panel.
1623    *
1624    * @return
1625    */
1626   private JPanel initStructureTab()
1627   {
1628     structureTab = new JPanel();
1629
1630     structureTab.setBorder(new TitledBorder(
1631             MessageManager.getString("label.structure_options")));
1632     structureTab.setLayout(null);
1633     final int width = 420;
1634     final int height = 22;
1635     final int lineSpacing = 25;
1636     int ypos = 15;
1637
1638     structFromPdb.setFont(LABEL_FONT);
1639     structFromPdb
1640             .setText(MessageManager.getString("label.struct_from_pdb"));
1641     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1642     structFromPdb.addActionListener(new ActionListener()
1643     {
1644       @Override
1645       public void actionPerformed(ActionEvent e)
1646       {
1647         boolean selected = structFromPdb.isSelected();
1648         // enable other options only when the first is checked
1649         useRnaView.setEnabled(selected);
1650         addSecondaryStructure.setEnabled(selected);
1651         addTempFactor.setEnabled(selected);
1652       }
1653     });
1654     structureTab.add(structFromPdb);
1655
1656     // indent checkboxes that are conditional on the first one
1657     ypos += lineSpacing;
1658     useRnaView.setFont(LABEL_FONT);
1659     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1660     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1661     structureTab.add(useRnaView);
1662
1663     ypos += lineSpacing;
1664     addSecondaryStructure.setFont(LABEL_FONT);
1665     addSecondaryStructure
1666             .setText(MessageManager.getString("label.autoadd_secstr"));
1667     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1668     structureTab.add(addSecondaryStructure);
1669
1670     ypos += lineSpacing;
1671     addTempFactor.setFont(LABEL_FONT);
1672     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1673     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1674     structureTab.add(addTempFactor);
1675
1676     ypos += lineSpacing;
1677     JLabel viewerLabel = new JLabel();
1678     viewerLabel.setFont(LABEL_FONT);
1679     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1680     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1681     viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1682     structureTab.add(viewerLabel);
1683
1684     /*
1685      * add all external viewers as options here - check
1686      * when selected whether the program is installed
1687      */
1688     structViewer.setFont(LABEL_FONT);
1689     structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1690     structViewer.addItem(ViewerType.JMOL.name());
1691     structViewer.addItem(ViewerType.CHIMERA.name());
1692     structViewer.addItem(ViewerType.CHIMERAX.name());
1693     structViewer.addItem(ViewerType.PYMOL.name());
1694     structViewer.addActionListener(new ActionListener()
1695     {
1696       @Override
1697       public void actionPerformed(ActionEvent e)
1698       {
1699         structureViewer_actionPerformed(
1700                 (String) structViewer.getSelectedItem());
1701       }
1702     });
1703     structureTab.add(structViewer);
1704
1705     ypos += lineSpacing;
1706     structureViewerPathLabel = new JLabel();
1707     structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
1708                                                  // 11));
1709     structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1710     structureViewerPathLabel.setText(MessageManager
1711             .formatMessage("label.viewer_path", "Chimera(X)"));
1712     structureViewerPathLabel
1713             .setBounds(new Rectangle(10, ypos, 170, height));
1714     structureViewerPathLabel.setEnabled(false);
1715     structureTab.add(structureViewerPathLabel);
1716
1717     structureViewerPath.setFont(LABEL_FONT);
1718     structureViewerPath.setText("");
1719     structureViewerPath.setEnabled(false);
1720     final String tooltip = JvSwingUtils.wrapTooltip(true,
1721             MessageManager.getString("label.viewer_path_tip"));
1722     structureViewerPath.setToolTipText(tooltip);
1723     structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1724     structureViewerPath.addMouseListener(new MouseAdapter()
1725     {
1726       @Override
1727       public void mouseClicked(MouseEvent e)
1728       {
1729         if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1730         {
1731           String chosen = openFileChooser();
1732           if (chosen != null)
1733           {
1734             structureViewerPath.setText(chosen);
1735           }
1736         }
1737       }
1738     });
1739     structureTab.add(structureViewerPath);
1740
1741     ypos += lineSpacing;
1742     nwMapping.setFont(LABEL_FONT);
1743     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1744     siftsMapping.setFont(LABEL_FONT);
1745     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1746     mappingMethod.add(nwMapping);
1747     mappingMethod.add(siftsMapping);
1748     JPanel mappingPanel = new JPanel();
1749     mappingPanel.setFont(LABEL_FONT);
1750     TitledBorder mmTitledBorder = new TitledBorder(
1751             MessageManager.getString("label.mapping_method"));
1752     mmTitledBorder.setTitleFont(LABEL_FONT);
1753     mappingPanel.setBorder(mmTitledBorder);
1754     mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1755     // GridLayout mappingLayout = new GridLayout();
1756     mappingPanel.setLayout(new GridLayout());
1757     mappingPanel.add(nwMapping);
1758     mappingPanel.add(siftsMapping);
1759     structureTab.add(mappingPanel);
1760
1761     ypos += lineSpacing;
1762     ypos += lineSpacing;
1763     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1764             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1765     docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1766     structureTab.add(docFieldPref);
1767
1768     /*
1769      * hide Chimera options in JalviewJS
1770      */
1771     if (Platform.isJS())
1772     {
1773       structureViewerPathLabel.setVisible(false);
1774       structureViewerPath.setVisible(false);
1775       viewerLabel.setVisible(false);
1776       structViewer.setVisible(false);
1777     }
1778
1779     return structureTab;
1780   }
1781
1782   /**
1783    * Action on choosing a structure viewer from combobox options.
1784    *
1785    * @param selectedItem
1786    */
1787   protected void structureViewer_actionPerformed(String selectedItem)
1788   {
1789   }
1790
1791   /**
1792    * Show a dialog for the user to choose a file. Returns the chosen path, or
1793    * null on Cancel.
1794    *
1795    * @return
1796    */
1797   protected String openFileChooser()
1798   {
1799     String choice = null;
1800     JFileChooser chooser = new JFileChooser();
1801
1802     // chooser.setFileView(new JalviewFileView());
1803     chooser.setDialogTitle(
1804             MessageManager.getString("label.open_local_file"));
1805     chooser.setToolTipText(MessageManager.getString("action.open"));
1806
1807     int value = chooser.showOpenDialog(this);
1808
1809     if (value == JFileChooser.APPROVE_OPTION)
1810     {
1811       choice = chooser.getSelectedFile().getPath();
1812     }
1813     return choice;
1814   }
1815
1816   /**
1817    * Validate the structure tab preferences; if invalid, set focus on this tab.
1818    *
1819    * @param e
1820    */
1821   protected boolean validateStructure(FocusEvent e)
1822   {
1823     if (!validateStructure())
1824     {
1825       e.getComponent().requestFocusInWindow();
1826       return false;
1827     }
1828     return true;
1829   }
1830
1831   protected boolean validateStructure()
1832   {
1833     return false;
1834   }
1835
1836   /**
1837    * Initialises the Visual tabbed panel.
1838    *
1839    * @return
1840    */
1841   private JPanel initVisualTab()
1842   {
1843     JPanel visualTab = new JPanel();
1844     visualTab.setBorder(new TitledBorder(
1845             MessageManager.getString("action.open_new_alignment")));
1846     visualTab.setLayout(null);
1847     fullScreen.setFont(LABEL_FONT);
1848     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1849     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1850     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1851     quality.setEnabled(false);
1852     quality.setFont(LABEL_FONT);
1853     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1854     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1855     quality.setSelected(true);
1856     quality.setText(MessageManager.getString("label.quality"));
1857     conservation.setEnabled(false);
1858     conservation.setFont(LABEL_FONT);
1859     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1860     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1861     conservation.setSelected(true);
1862     conservation.setText(MessageManager.getString("label.conservation"));
1863     identity.setEnabled(false);
1864     identity.setFont(LABEL_FONT);
1865     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1866     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1867     identity.setSelected(true);
1868     identity.setText(MessageManager.getString("label.consensus"));
1869     showOccupancy.setFont(LABEL_FONT);
1870     showOccupancy.setEnabled(false);
1871     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1872     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1873     showOccupancy.setSelected(true);
1874     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1875
1876     JLabel showGroupbits = new JLabel();
1877     showGroupbits.setFont(LABEL_FONT);
1878     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1879     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1880     showGroupbits
1881             .setText(MessageManager.getString("action.show_group") + ":");
1882     JLabel showConsensbits = new JLabel();
1883     showConsensbits.setFont(LABEL_FONT);
1884     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1885     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1886     showConsensbits
1887             .setText(MessageManager.getString("label.consensus") + ":");
1888     showConsensHistogram.setEnabled(false);
1889     showConsensHistogram.setFont(LABEL_FONT);
1890     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1891     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1892     showConsensHistogram.setSelected(true);
1893     showConsensHistogram
1894             .setText(MessageManager.getString("label.histogram"));
1895     showConsensLogo.setEnabled(false);
1896     showConsensLogo.setFont(LABEL_FONT);
1897     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1898     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1899     showConsensLogo.setSelected(true);
1900     showConsensLogo.setText(MessageManager.getString("label.logo"));
1901     showGroupConsensus.setEnabled(false);
1902     showGroupConsensus.setFont(LABEL_FONT);
1903     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1904     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1905     showGroupConsensus.setSelected(true);
1906     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1907     showGroupConservation.setEnabled(false);
1908     showGroupConservation.setFont(LABEL_FONT);
1909     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1910     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1911     showGroupConservation.setSelected(true);
1912     showGroupConservation
1913             .setText(MessageManager.getString("label.conservation"));
1914     showNpTooltip.setEnabled(true);
1915     showNpTooltip.setFont(LABEL_FONT);
1916     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1917     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1918     showNpTooltip.setSelected(true);
1919     showNpTooltip.setText(
1920             MessageManager.getString("label.non_positional_features"));
1921     showDbRefTooltip.setEnabled(true);
1922     showDbRefTooltip.setFont(LABEL_FONT);
1923     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1924     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1925     showDbRefTooltip.setSelected(true);
1926     showDbRefTooltip
1927             .setText(MessageManager.getString("label.database_references"));
1928     annotations.setFont(LABEL_FONT);
1929     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1930     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1931     annotations.setSelected(true);
1932     annotations.setText(MessageManager.getString("label.show_annotations"));
1933     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1934     annotations.addActionListener(new ActionListener()
1935     {
1936       @Override
1937       public void actionPerformed(ActionEvent e)
1938       {
1939         annotations_actionPerformed(e);
1940       }
1941     });
1942     identity.addActionListener(new ActionListener()
1943     {
1944       @Override
1945       public void actionPerformed(ActionEvent e)
1946       {
1947         annotations_actionPerformed(e);
1948       }
1949     });
1950     showGroupConsensus.addActionListener(new ActionListener()
1951     {
1952       @Override
1953       public void actionPerformed(ActionEvent e)
1954       {
1955         annotations_actionPerformed(e);
1956       }
1957     });
1958     showUnconserved.setFont(LABEL_FONT);
1959     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1960     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1961     showUnconserved.setSelected(true);
1962     showUnconserved
1963             .setText(MessageManager.getString("action.show_unconserved"));
1964     showUnconserved.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         showunconserved_actionPerformed(e);
1970       }
1971     });
1972
1973     // TODO these are not yet added to / action from Preferences
1974     // JCheckBox shareSelections = new JCheckBox();
1975     // shareSelections.setFont(verdana11);
1976     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1977     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1978     // shareSelections.setSelected(true);
1979     // shareSelections.setText(MessageManager
1980     // .getString("label.share_selection_across_views"));
1981     // JCheckBox followHighlight = new JCheckBox();
1982     // followHighlight.setFont(verdana11);
1983     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1984     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1985     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1986     // followHighlight.setSelected(true);
1987     // followHighlight.setText(MessageManager
1988     // .getString("label.scroll_highlighted_regions"));
1989
1990     seqLimit.setFont(LABEL_FONT);
1991     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1992     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1993     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1994     smoothFont.setFont(LABEL_FONT);
1995     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1996     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1997     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1998     scaleProteinToCdna.setFont(LABEL_FONT);
1999     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
2000     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
2001     scaleProteinToCdna.setText(
2002             MessageManager.getString("label.scale_protein_to_cdna"));
2003     scaleProteinToCdna.setToolTipText(
2004             MessageManager.getString("label.scale_protein_to_cdna_tip"));
2005     JLabel gapLabel = new JLabel();
2006     gapLabel.setFont(LABEL_FONT);
2007     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2008     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
2009     JLabel fontLabel = new JLabel();
2010     fontLabel.setFont(LABEL_FONT);
2011     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2012     fontLabel.setText(MessageManager.getString("label.font"));
2013     fontSizeCB.setFont(LABEL_FONT);
2014     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
2015     fontStyleCB.setFont(LABEL_FONT);
2016     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
2017     fontNameCB.setFont(LABEL_FONT);
2018     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
2019     gapSymbolCB.setFont(LABEL_FONT);
2020     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
2021     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
2022     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
2023     gapSymbolCB.setRenderer(dlcr);
2024
2025     startupCheckbox.setText(MessageManager.getString("action.open_file"));
2026     startupCheckbox.setFont(LABEL_FONT);
2027     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
2028     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
2029     startupCheckbox.setSelected(true);
2030     startupFileTextfield.setFont(LABEL_FONT);
2031     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
2032     final String tooltip = JvSwingUtils.wrapTooltip(true,
2033             MessageManager.getString("label.double_click_to_browse"));
2034     startupFileTextfield.setToolTipText(tooltip);
2035     startupFileTextfield.addMouseListener(new MouseAdapter()
2036     {
2037       @Override
2038       public void mouseClicked(MouseEvent e)
2039       {
2040         if (e.getClickCount() > 1)
2041         {
2042           startupFileTextfield_mouseClicked();
2043         }
2044       }
2045     });
2046
2047     sortby.setFont(LABEL_FONT);
2048     sortby.setBounds(new Rectangle(172, 260, 155, 21));
2049     JLabel sortLabel = new JLabel();
2050     sortLabel.setFont(LABEL_FONT);
2051     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2052     sortLabel.setText(MessageManager.getString("label.sort_by"));
2053     sortAnnBy.setFont(LABEL_FONT);
2054     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
2055     JLabel sortAnnLabel = new JLabel();
2056     sortAnnLabel.setFont(LABEL_FONT);
2057     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2058     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
2059     sortAutocalc.setFont(LABEL_FONT);
2060     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2061
2062     JPanel annsettingsPanel = new JPanel();
2063     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2064     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2065     annsettingsPanel.setBorder(new EtchedBorder());
2066     visualTab.add(annsettingsPanel);
2067     Border jb = new EmptyBorder(1, 1, 4, 5);
2068     annotations.setBorder(jb);
2069     showOccupancy.setBorder(jb);
2070     quality.setBorder(jb);
2071     conservation.setBorder(jb);
2072     identity.setBorder(jb);
2073     showConsensbits.setBorder(jb);
2074     showGroupbits.setBorder(jb);
2075     showGroupConsensus.setBorder(jb);
2076     showGroupConservation.setBorder(jb);
2077     showConsensHistogram.setBorder(jb);
2078     showConsensLogo.setBorder(jb);
2079
2080     JPanel autoAnnotSettings = new JPanel();
2081     annsettingsPanel.add(autoAnnotSettings);
2082     autoAnnotSettings.setLayout(new GridLayout(0, 2));
2083     autoAnnotSettings.add(annotations);
2084     autoAnnotSettings.add(quality);
2085     // second row of autoannotation box
2086     autoAnnotSettings = new JPanel();
2087     annsettingsPanel.add(autoAnnotSettings);
2088
2089     autoAnnotSettings.setLayout(new GridLayout(0, 3));
2090     autoAnnotSettings.add(conservation);
2091     autoAnnotSettings.add(identity);
2092     autoAnnotSettings.add(showOccupancy);
2093     autoAnnotSettings.add(showGroupbits);
2094     autoAnnotSettings.add(showGroupConservation);
2095     autoAnnotSettings.add(showGroupConsensus);
2096     autoAnnotSettings.add(showConsensbits);
2097     autoAnnotSettings.add(showConsensHistogram);
2098     autoAnnotSettings.add(showConsensLogo);
2099
2100     JPanel tooltipSettings = new JPanel();
2101     tooltipSettings.setBorder(new TitledBorder(
2102             MessageManager.getString("label.sequence_id_tooltip")));
2103     tooltipSettings.setBounds(173, 140, 220, 62);
2104     tooltipSettings.setLayout(new GridLayout(2, 1));
2105     tooltipSettings.add(showDbRefTooltip);
2106     tooltipSettings.add(showNpTooltip);
2107     visualTab.add(tooltipSettings);
2108
2109     wrap.setFont(LABEL_FONT);
2110     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2111     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2112     wrap.setText(MessageManager.getString("label.wrap_alignment"));
2113     rightAlign.setFont(LABEL_FONT);
2114     rightAlign.setForeground(Color.black);
2115     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2116     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2117     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2118     idItalics.setFont(LABEL_FONT_ITALIC);
2119     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2120     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2121     idItalics.setText(
2122             MessageManager.getString("label.sequence_name_italics"));
2123     openoverv.setFont(LABEL_FONT);
2124     openoverv.setActionCommand(
2125             MessageManager.getString("label.open_overview"));
2126     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2127     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2128     openoverv.setText(MessageManager.getString("label.open_overview"));
2129     JPanel jPanel2 = new JPanel();
2130     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2131     jPanel2.setLayout(new GridLayout(14, 1));
2132     jPanel2.add(fullScreen);
2133     jPanel2.add(openoverv);
2134     jPanel2.add(seqLimit);
2135     jPanel2.add(rightAlign);
2136     jPanel2.add(fontLabel);
2137     jPanel2.add(showUnconserved);
2138     jPanel2.add(idItalics);
2139     jPanel2.add(smoothFont);
2140     jPanel2.add(scaleProteinToCdna);
2141     jPanel2.add(gapLabel);
2142     jPanel2.add(wrap);
2143     jPanel2.add(sortLabel);
2144     jPanel2.add(sortAnnLabel);
2145     jPanel2.add(startupCheckbox);
2146     visualTab.add(jPanel2);
2147     visualTab.add(startupFileTextfield);
2148     visualTab.add(sortby);
2149     visualTab.add(sortAnnBy);
2150     visualTab.add(sortAutocalc);
2151     visualTab.add(gapSymbolCB);
2152     visualTab.add(fontNameCB);
2153     visualTab.add(fontSizeCB);
2154     visualTab.add(fontStyleCB);
2155
2156     if (Platform.isJS())
2157     {
2158       startupCheckbox.setVisible(false);
2159       startupFileTextfield.setVisible(false);
2160     }
2161
2162     return visualTab;
2163   }
2164
2165   /**
2166    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2167    */
2168
2169   protected void loadLastSavedBackupsOptions()
2170   {
2171     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2172             .getSavedBackupEntry();
2173     enableBackupFiles.setSelected(
2174             Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2175
2176     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2177             .createBackupFilesPresetEntry(Cache
2178                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2179     if (backupfilesCustomEntry == null)
2180     {
2181       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2182               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2183     }
2184     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2185             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2186             backupfilesCustomEntry);
2187
2188     setComboIntStringKey(backupfilesPresetsCombo,
2189             Cache.getDefault(BackupFiles.NS + "_PRESET",
2190                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2191
2192     backupsSetOptions(savedPreset);
2193
2194     backupsOptionsSetEnabled();
2195     updateBackupFilesExampleLabel();
2196   }
2197
2198   private boolean warnAboutSuffixReverseChange()
2199   {
2200     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2201             .getSavedBackupEntry();
2202     boolean savedSuffixReverse = bfpe.reverse;
2203     int savedSuffixDigits = bfpe.digits;
2204     String savedSuffixTemplate = bfpe.suffix;
2205
2206     boolean nowSuffixReverse = suffixReverse.isSelected();
2207     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2208     String nowSuffixTemplate = suffixTemplate.getText();
2209     return nowSuffixReverse != savedSuffixReverse
2210             && nowSuffixDigits == savedSuffixDigits
2211             && nowSuffixTemplate != null
2212             && nowSuffixTemplate.equals(savedSuffixTemplate);
2213   }
2214
2215   /**
2216    * Initialises the Backups tabbed panel.
2217    *
2218    * @return
2219    */
2220   private JPanel initBackupsTab()
2221   {
2222     JPanel backupsTab = new JPanel();
2223     backupsTab.setBorder(new TitledBorder(
2224             MessageManager.getString("label.backup_files")));
2225     backupsTab.setLayout(new GridBagLayout());
2226
2227     GridBagConstraints gbc = new GridBagConstraints();
2228     gbc.weightx = 0.0;
2229     gbc.weighty = 0.0;
2230     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2231     gbc.fill = GridBagConstraints.NONE;
2232
2233     initBackupsTabPresetsPanel();
2234     initBackupsTabSuffixPanel();
2235     initBackupsTabKeepFilesPanel();
2236     initBackupsTabFilenameExamplesPanel();
2237
2238     enableBackupFiles.setFont(LABEL_FONT_BOLD);
2239     enableBackupFiles
2240             .setText(MessageManager.getString("label.enable_backupfiles"));
2241     enableBackupFiles.addActionListener(new ActionListener()
2242     {
2243       @Override
2244       public void actionPerformed(ActionEvent e)
2245       {
2246         // enable other options only when the first is checked
2247         backupsOptionsSetEnabled();
2248       }
2249     });
2250
2251     // enable checkbox 1 col
2252     gbc.gridwidth = 1;
2253     gbc.gridheight = 1;
2254     gbc.gridx = 0;
2255     gbc.gridy = 0; // row 0
2256     backupsTab.add(enableBackupFiles, gbc);
2257
2258     // summary of scheme box (over two rows)
2259     gbc.gridx = 1;
2260     gbc.weightx = 0.0;
2261     gbc.gridheight = 2;
2262     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2263     gbc.fill = GridBagConstraints.BOTH;
2264     backupsTab.add(exampleFilesPanel, gbc);
2265     gbc.gridheight = 1;
2266     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2267     gbc.fill = GridBagConstraints.NONE;
2268
2269     // fill empty space on right
2270     gbc.gridx++;
2271     gbc.weightx = 1.0;
2272     backupsTab.add(new JPanel(), gbc);
2273
2274     // schemes box
2275     gbc.weightx = 0.0;
2276     gbc.gridx = 0;
2277     gbc.gridy++; // row 1
2278     backupsTab.add(presetsPanel, gbc);
2279
2280     // now using whole row
2281     gbc.gridwidth = 2;
2282     gbc.gridheight = 1;
2283     // keep files box
2284     gbc.gridx = 0;
2285     gbc.gridy++; // row 2
2286     backupsTab.add(keepfilesPanel, gbc);
2287
2288     // filename strategy box
2289     gbc.gridy++; // row 3
2290     backupsTab.add(suffixPanel, gbc);
2291
2292     // fill empty space
2293     gbc.gridy++; // row 4
2294     gbc.weighty = 1.0;
2295     backupsTab.add(new JPanel(), gbc);
2296
2297     backupsOptionsSetEnabled();
2298     return backupsTab;
2299   }
2300
2301   private JPanel initBackupsTabPresetsPanel()
2302   {
2303
2304     String title = MessageManager.getString("label.schemes");
2305
2306     presetsPanel.setLayout(new GridBagLayout());
2307
2308     GridBagConstraints gbc = new GridBagConstraints();
2309     gbc.weightx = 0.0;
2310     gbc.weighty = 0.0;
2311     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2312     gbc.fill = GridBagConstraints.NONE;
2313     gbc.gridwidth = 1;
2314     gbc.gridheight = 1;
2315
2316     // "Scheme: "
2317     gbc.gridx = 0;
2318     gbc.gridy = 0;
2319
2320     presetsComboLabel = new JLabel(title + ":");
2321     presetsPanel.add(presetsComboLabel, gbc);
2322
2323     List<Object> entries = Arrays.asList(
2324             (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2325     List<String> tooltips = Arrays.asList(
2326             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2327     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2328             tooltips);
2329     /*
2330     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2331     {
2332       backupfilesPresetsCombo
2333               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2334     }
2335     */
2336
2337     backupfilesPresetsCombo.addActionListener(new ActionListener()
2338     {
2339       @Override
2340       public void actionPerformed(ActionEvent e)
2341       {
2342         int key = getComboIntStringKey(backupfilesPresetsCombo);
2343         if (!customiseCheckbox.isSelected())
2344         {
2345           backupfilesPresetsComboLastSelected = key;
2346         }
2347         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2348         {
2349           if (customiseCheckbox.isSelected())
2350           {
2351             // got here by clicking on customiseCheckbox so don't change the
2352             // values
2353             backupfilesCustomOptionsSetEnabled();
2354           }
2355           else
2356           {
2357             backupsTabUpdatePresets();
2358             backupfilesCustomOptionsSetEnabled();
2359           }
2360         }
2361         else
2362         {
2363           customiseCheckbox.setSelected(false);
2364           backupsTabUpdatePresets();
2365           backupfilesCustomOptionsSetEnabled();
2366         }
2367       }
2368     });
2369
2370     // dropdown list of preset schemes
2371     gbc.gridx = 1;
2372     presetsPanel.add(backupfilesPresetsCombo, gbc);
2373
2374     revertButton.setText(MessageManager.getString("label.cancel_changes"));
2375     revertButton.setToolTipText(
2376             MessageManager.getString("label.cancel_changes_description"));
2377     revertButton.addActionListener(new ActionListener()
2378     {
2379       @Override
2380       public void actionPerformed(ActionEvent e)
2381       {
2382         backupsSetOptions(
2383                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2384                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2385         backupfilesCustomOptionsSetEnabled();
2386       }
2387
2388     });
2389     revertButton.setFont(LABEL_FONT);
2390
2391     customiseCheckbox.setFont(LABEL_FONT);
2392     customiseCheckbox.setText(MessageManager.getString("label.customise"));
2393     customiseCheckbox.addActionListener(new ActionListener()
2394     {
2395       @Override
2396       public void actionPerformed(ActionEvent e)
2397       {
2398         int currently = getComboIntStringKey(backupfilesPresetsCombo);
2399         if (customiseCheckbox.isSelected())
2400         {
2401           backupfilesPresetsComboLastSelected = currently;
2402           setComboIntStringKey(backupfilesPresetsCombo,
2403                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2404         }
2405         else
2406         {
2407           setComboIntStringKey(backupfilesPresetsCombo,
2408                   backupfilesPresetsComboLastSelected);
2409
2410         }
2411         backupfilesCustomOptionsSetEnabled();
2412       }
2413     });
2414     customiseCheckbox.setToolTipText(
2415             MessageManager.getString("label.customise_description"));
2416
2417     // customise checkbox
2418     gbc.gridx = 0;
2419     gbc.gridy++;
2420     presetsPanel.add(customiseCheckbox, gbc);
2421
2422     // "Cancel changes" button (aligned with combo box above)
2423     gbc.gridx = 1;
2424     presetsPanel.add(revertButton, gbc);
2425
2426     return presetsPanel;
2427   }
2428
2429   private JPanel initBackupsTabFilenameExamplesPanel()
2430   {
2431     String title = MessageManager.getString("label.scheme_examples");
2432     TitledBorder tb = new TitledBorder(title);
2433     exampleFilesPanel.setBorder(tb);
2434     exampleFilesPanel.setLayout(new GridBagLayout());
2435
2436     backupfilesExampleLabel.setEditable(false);
2437     backupfilesExampleLabel
2438             .setBackground(exampleFilesPanel.getBackground());
2439
2440     updateBackupFilesExampleLabel();
2441
2442     GridBagConstraints gbc = new GridBagConstraints();
2443     gbc.weightx = 1.0;
2444     gbc.weighty = 1.0;
2445     gbc.fill = GridBagConstraints.NONE;
2446     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2447
2448     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2449     return exampleFilesPanel;
2450   }
2451
2452   private void backupsTabUpdatePresets()
2453   {
2454     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2455             .getSelectedItem();
2456     int key = entry.k;
2457     String value = entry.v;
2458
2459     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2460             .containsKey(key))
2461     {
2462       backupsSetOptions(
2463               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2464                       .get(key));
2465     }
2466     else
2467     {
2468       Cache.log.error(
2469               "Preset '" + value + "' [key:" + key + "] not implemented");
2470     }
2471
2472     // Custom options will now be enabled when the customiseCheckbox is checked
2473     // (performed above)
2474     // backupfilesCustomOptionsSetEnabled();
2475     updateBackupFilesExampleLabel();
2476   }
2477
2478   protected int getComboIntStringKey(
2479           JComboBox<Object> backupfilesPresetsCombo2)
2480   {
2481     IntKeyStringValueEntry e;
2482     try
2483     {
2484       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2485               .getSelectedItem();
2486     } catch (Exception ex)
2487     {
2488       Cache.log.error(
2489               "Problem casting Combo entry to IntKeyStringValueEntry.");
2490       e = null;
2491     }
2492     return e != null ? e.k : 0;
2493   }
2494
2495   protected void setComboIntStringKey(
2496           JComboBox<Object> backupfilesPresetsCombo2, int key)
2497   {
2498     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2499     {
2500       IntKeyStringValueEntry e;
2501       try
2502       {
2503         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2504       } catch (Exception ex)
2505       {
2506         Cache.log.error(
2507                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2508         continue;
2509       }
2510       if (e.k == key)
2511       {
2512         backupfilesPresetsCombo2.setSelectedIndex(i);
2513         break;
2514       }
2515     }
2516     // backupsTabUpdatePresets();
2517   }
2518
2519   private JPanel initBackupsTabSuffixPanel()
2520   {
2521     suffixPanel.setBorder(new TitledBorder(
2522             MessageManager.getString("label.backup_filename_strategy")));
2523     suffixPanel.setLayout(new GridBagLayout());
2524
2525     suffixTemplateLabel
2526             .setText(MessageManager.getString("label.append_to_filename"));
2527     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2528     suffixTemplateLabel.setFont(LABEL_FONT);
2529
2530     final String tooltip = JvSwingUtils.wrapTooltip(true,
2531             MessageManager.getString("label.append_to_filename_tooltip"));
2532     suffixTemplate.setToolTipText(tooltip);
2533     suffixTemplate.addActionListener(new ActionListener()
2534     {
2535       @Override
2536       public void actionPerformed(ActionEvent e)
2537       {
2538         updateBackupFilesExampleLabel();
2539         backupfilesCustomOptionsSetEnabled();
2540         backupfilesRevertButtonSetEnabled(true);
2541       }
2542
2543     });
2544     suffixTemplate.addKeyListener(new KeyListener()
2545     {
2546       @Override
2547       public void keyReleased(KeyEvent e)
2548       {
2549         updateBackupFilesExampleLabel();
2550         backupfilesCustomOptionsSetEnabled();
2551         backupfilesRevertButtonSetEnabled(true);
2552       }
2553
2554       @Override
2555       public void keyPressed(KeyEvent e)
2556       {
2557       }
2558
2559       // disable use of ':' or '/' or '\'
2560       @Override
2561       public void keyTyped(KeyEvent e)
2562       {
2563         char c = e.getKeyChar();
2564         if (c == ':' || c == '/' || c == '\\')
2565         {
2566           // don't process ':' or '/' or '\'
2567           e.consume();
2568         }
2569       }
2570
2571     });
2572
2573     // digits spinner
2574     suffixDigitsLabel
2575             .setText(MessageManager.getString("label.index_digits"));
2576     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2577     suffixDigitsLabel.setFont(LABEL_FONT);
2578     ChangeListener c = new ChangeListener()
2579     {
2580       @Override
2581       public void stateChanged(ChangeEvent e)
2582       {
2583         backupfilesRevertButtonSetEnabled(true);
2584         updateBackupFilesExampleLabel();
2585       }
2586
2587     };
2588     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2589             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2590
2591     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2592             MessageManager.getString("label.increment_index"));
2593     suffixReverse.addActionListener(new ActionListener()
2594     {
2595       @Override
2596       public void actionPerformed(ActionEvent e)
2597       {
2598         boolean okay = true;
2599         if (warnAboutSuffixReverseChange())
2600         {
2601           // Warning popup
2602           okay = confirmSuffixReverseChange();
2603         }
2604         if (okay)
2605         {
2606           backupfilesRevertButtonSetEnabled(true);
2607           updateBackupFilesExampleLabel();
2608         }
2609         else
2610         {
2611           boolean savedSuffixReverse = BackupFilesPresetEntry
2612                   .getSavedBackupEntry().reverse;
2613           suffixReverse.setSelected(savedSuffixReverse);
2614         }
2615       }
2616     });
2617
2618     GridBagConstraints sgbc = new GridBagConstraints();
2619
2620     // first row (template text box)
2621     sgbc.anchor = GridBagConstraints.WEST;
2622     sgbc.gridx = 0;
2623     sgbc.gridy = 0;
2624     sgbc.gridwidth = 1;
2625     sgbc.gridheight = 1;
2626     sgbc.weightx = 1.0;
2627     sgbc.weighty = 0.0;
2628     sgbc.fill = GridBagConstraints.NONE;
2629     suffixPanel.add(suffixTemplateLabel, sgbc);
2630
2631     sgbc.gridx = 1;
2632     sgbc.fill = GridBagConstraints.HORIZONTAL;
2633     suffixPanel.add(suffixTemplate, sgbc);
2634
2635     // second row (number of digits spinner)
2636     sgbc.gridy = 1;
2637
2638     sgbc.gridx = 0;
2639     sgbc.fill = GridBagConstraints.NONE;
2640     suffixPanel.add(suffixDigitsLabel, sgbc);
2641
2642     sgbc.gridx = 1;
2643     sgbc.fill = GridBagConstraints.HORIZONTAL;
2644     suffixPanel.add(suffixDigitsSpinner, sgbc);
2645
2646     // third row (forward order radio selection)
2647     sgbc.gridx = 0;
2648     sgbc.gridy = 2;
2649     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2650     sgbc.fill = GridBagConstraints.HORIZONTAL;
2651     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2652
2653     // fourth row (reverse order radio selection)
2654     sgbc.gridy = 3;
2655     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2656     return suffixPanel;
2657   }
2658
2659   private boolean confirmSuffixReverseChange()
2660   {
2661     boolean ret = false;
2662     String warningMessage = MessageManager
2663             .getString("label.warning_confirm_change_reverse");
2664     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2665             warningMessage,
2666             MessageManager.getString("label.change_increment_decrement"),
2667             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2668
2669     ret = (confirm == JvOptionPane.YES_OPTION);
2670     return ret;
2671   }
2672
2673   private JPanel initBackupsTabKeepFilesPanel()
2674   {
2675     keepfilesPanel.setBorder(
2676             new TitledBorder(MessageManager.getString("label.keep_files")));
2677     keepfilesPanel.setLayout(new GridBagLayout());
2678
2679     backupfilesKeepAll.setLabels(
2680             MessageManager.getString("label.keep_all_backup_files"),
2681             MessageManager.getString(
2682                     "label.keep_only_this_number_of_backup_files"));
2683     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2684     {
2685       @Override
2686       public void actionPerformed(ActionEvent e)
2687       {
2688         backupfilesRevertButtonSetEnabled(true);
2689         updateBackupFilesExampleLabel();
2690       }
2691     });
2692     backupfilesKeepAll.addActionListener(new ActionListener()
2693     {
2694       @Override
2695       public void actionPerformed(ActionEvent e)
2696       {
2697         backupfilesRevertButtonSetEnabled(true);
2698         keepRollMaxOptionsEnabled();
2699         updateBackupFilesExampleLabel();
2700       }
2701     });
2702
2703     ChangeListener c = new ChangeListener()
2704     {
2705       @Override
2706       public void stateChanged(ChangeEvent e)
2707       {
2708         backupfilesRevertButtonSetEnabled(true);
2709         updateBackupFilesExampleLabel();
2710       }
2711
2712     };
2713     setIntegerSpinner(backupfilesRollMaxSpinner,
2714             BackupFilesPresetEntry.ROLLMAXMIN,
2715             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2716
2717     backupfilesConfirmDelete.setLabels(
2718             MessageManager.getString("label.always_ask"),
2719             MessageManager.getString("label.auto_delete"));
2720     backupfilesConfirmDelete.addActionListener(new ActionListener()
2721     {
2722       @Override
2723       public void actionPerformed(ActionEvent e)
2724       {
2725         backupfilesRevertButtonSetEnabled(true);
2726       }
2727     });
2728     // update the enabled section
2729     keepRollMaxOptionsEnabled();
2730
2731     GridBagConstraints kgbc = new GridBagConstraints();
2732
2733     // first row (template text box)
2734     kgbc.anchor = GridBagConstraints.WEST;
2735     kgbc.gridx = 0;
2736     kgbc.gridy = 0;
2737     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2738     kgbc.gridheight = 1;
2739     kgbc.weightx = 1.0;
2740     kgbc.weighty = 0.0;
2741     kgbc.fill = GridBagConstraints.HORIZONTAL;
2742     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2743
2744     // second row
2745     kgbc.gridy = 1;
2746
2747     kgbc.gridx = 0;
2748     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2749     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2750
2751     kgbc.gridx = 1;
2752     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2753     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2754
2755     // third row (indented)
2756     kgbc.gridy = 2;
2757     kgbc.insets = new Insets(0, 20, 0, 0);
2758
2759     kgbc.gridx = 0;
2760     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2761     kgbc.fill = GridBagConstraints.HORIZONTAL;
2762     kgbc.weightx = 1.0;
2763
2764     JPanel jp = new JPanel();
2765     jp.setLayout(new FlowLayout());
2766     oldBackupFilesLabel.setText(
2767             MessageManager.getString("label.autodelete_old_backup_files"));
2768     oldBackupFilesLabel.setFont(LABEL_FONT);
2769     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2770     jp.add(oldBackupFilesLabel);
2771     jp.add(backupfilesConfirmDelete.getTrueButton());
2772     jp.add(backupfilesConfirmDelete.getFalseButton());
2773     keepfilesPanel.add(jp, kgbc);
2774
2775     return keepfilesPanel;
2776   }
2777
2778   protected void updateBackupFilesExampleLabel()
2779   {
2780     int exampleindex = 12;
2781     String base = MessageManager.getString("label.filename") + ".fa";
2782     if (base == null || base.length() == 0)
2783     {
2784       base = "file_name.fa";
2785     }
2786
2787     boolean reverse = suffixReverse.isSelected();
2788     boolean keepAll = backupfilesKeepAll.isSelected();
2789     int rollMax = 4;
2790     String suffix = suffixTemplate.getText();
2791     int digits = 3;
2792
2793     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2794     if (suffix == null || suffix.length() == 0)
2795     {
2796       backupfilesExampleLabel
2797               .setText(MessageManager.getString("label.no_backup_files"));
2798       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2799       return;
2800     }
2801
2802     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2803     rollMax = rollMax < 1 ? 1 : rollMax;
2804
2805     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2806     {
2807       rollMax = 1;
2808     }
2809
2810     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2811     digits = digits < 1 ? 1 : digits;
2812
2813     int lowersurround = 2;
2814     int uppersurround = 0;
2815     StringBuilder exampleSB = new StringBuilder();
2816     boolean firstLine = true;
2817     int lineNumber = 0;
2818     if (reverse)
2819     {
2820
2821       int min = 1;
2822       int max = keepAll ? exampleindex : rollMax;
2823       for (int index = min; index <= max; index++)
2824       {
2825         if (index == min + lowersurround && index < max - uppersurround - 1)
2826         {
2827           exampleSB.append("\n...");
2828           lineNumber++;
2829         }
2830         else if (index > min + lowersurround && index < max - uppersurround)
2831         {
2832           // nothing
2833         }
2834         else
2835         {
2836           if (firstLine)
2837           {
2838             firstLine = false;
2839           }
2840           else
2841           {
2842             exampleSB.append("\n");
2843             lineNumber++;
2844           }
2845           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2846                   base, suffix, digits));
2847           if (min == max)
2848           {
2849             // no extra text needed
2850           }
2851           else if (index == min)
2852           {
2853             String newest = MessageManager.getString("label.braced_newest");
2854             if (newest != null && newest.length() > 0)
2855             {
2856               exampleSB.append(" " + newest);
2857             }
2858           }
2859           else if (index == max)
2860           {
2861             String oldest = MessageManager.getString("label.braced_oldest");
2862             if (oldest != null && oldest.length() > 0)
2863             {
2864               exampleSB.append(" " + oldest);
2865             }
2866           }
2867         }
2868       }
2869     }
2870     else
2871     {
2872
2873       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2874               : exampleindex - rollMax + 1;
2875       int max = exampleindex;
2876
2877       for (int index = min; index <= max; index++)
2878       {
2879
2880         if (index == min + lowersurround && index < max - uppersurround - 1)
2881         {
2882           exampleSB.append("\n...");
2883           lineNumber++;
2884         }
2885         else if (index > min + lowersurround && index < max - uppersurround)
2886         {
2887           // nothing
2888         }
2889         else
2890         {
2891           if (firstLine)
2892           {
2893             firstLine = false;
2894           }
2895           else
2896           {
2897             exampleSB.append("\n");
2898             lineNumber++;
2899           }
2900           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2901                   base, suffix, digits));
2902           if (min == max)
2903           {
2904             // no extra text needed
2905           }
2906           else if (index == min)
2907           {
2908             String oldest = MessageManager.getString("label.braced_oldest");
2909             if (oldest != null && oldest.length() > 0)
2910             {
2911               exampleSB.append(" " + oldest);
2912             }
2913           }
2914           else if (index == max)
2915           {
2916             String newest = MessageManager.getString("label.braced_newest");
2917             if (newest != null && newest.length() > 0)
2918             {
2919               exampleSB.append(" " + newest);
2920             }
2921           }
2922         }
2923       }
2924
2925     }
2926
2927     // add some extra empty lines to pad out the example files box. ugh, please
2928     // tell
2929     // me how to do this better
2930     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2931     if (remainingLines > 0)
2932     {
2933       for (int i = 0; i < remainingLines; i++)
2934       {
2935         exampleSB.append("\n ");
2936         lineNumber++;
2937       }
2938     }
2939
2940     backupfilesExampleLabel.setText(exampleSB.toString());
2941   }
2942
2943   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2944           boolean useExistingVal, ChangeListener c)
2945   {
2946     int i = def;
2947     if (useExistingVal)
2948     {
2949       try
2950       {
2951         i = ((Integer) s.getValue()).intValue();
2952       } catch (Exception e)
2953       {
2954         Cache.log.error(
2955                 "Exception casting the initial value of s.getValue()");
2956       }
2957     }
2958
2959     setIntegerSpinner(s, min, max, i, c);
2960   }
2961
2962   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2963           ChangeListener c)
2964   {
2965     // integer spinner for number of digits
2966     if (def > max)
2967     {
2968       max = def;
2969     }
2970     if (def < min)
2971     {
2972       def = min;
2973     }
2974     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2975     s.setModel(sModel);
2976
2977     s.addChangeListener(c);
2978
2979   }
2980
2981   protected static int getSpinnerInt(JSpinner s, int def)
2982   {
2983     int i = def;
2984     try
2985     {
2986       s.commitEdit();
2987       i = (Integer) s.getValue();
2988     } catch (Exception e)
2989     {
2990       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2991     }
2992     return i;
2993   }
2994
2995   private void keepRollMaxOptionsEnabled()
2996   {
2997     boolean enabled = backupfilesKeepAll.isEnabled()
2998             && !backupfilesKeepAll.isSelected();
2999     oldBackupFilesLabel.setEnabled(enabled);
3000     backupfilesRollMaxSpinner.setEnabled(enabled);
3001     backupfilesConfirmDelete.setEnabled(enabled);
3002   }
3003
3004   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
3005   {
3006     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3007             && customiseCheckbox.isSelected() && suffixTemplate.getText()
3008                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3009     keepfilesPanel.setEnabled(enabled);
3010     backupfilesKeepAll.setEnabled(enabled);
3011     oldBackupFilesLabel.setEnabled(enabled);
3012     keepRollMaxOptionsEnabled();
3013   }
3014
3015   private void backupfilesSuffixTemplateDigitsSetEnabled()
3016   {
3017     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
3018             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3019     suffixDigitsLabel.setEnabled(enabled);
3020     suffixDigitsSpinner.setEnabled(enabled);
3021     suffixReverse.setEnabled(enabled);
3022   }
3023
3024   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
3025   {
3026     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3027             && customiseCheckbox.isSelected();
3028     suffixPanel.setEnabled(enabled);
3029     suffixTemplateLabel.setEnabled(enabled);
3030     suffixTemplate.setEnabled(enabled);
3031     backupfilesSuffixTemplateDigitsSetEnabled();
3032   }
3033
3034   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
3035   {
3036     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3037             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
3038     revertButton.setEnabled(enabled);
3039   }
3040
3041   private boolean backupfilesCustomChanged()
3042   {
3043     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
3044             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
3045     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
3046     return !custom.equals(current);
3047   }
3048
3049   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
3050   {
3051     String suffix = suffixTemplate.getText();
3052     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
3053     boolean reverse = suffixReverse.isSelected();
3054     boolean keepAll = backupfilesKeepAll.isSelected();
3055     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3056     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3057
3058     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3059             reverse, keepAll, rollMax, confirmDelete);
3060
3061     return bfpe;
3062   }
3063
3064   protected void backupfilesCustomOptionsSetEnabled()
3065   {
3066     boolean enabled = customiseCheckbox.isSelected();
3067
3068     backupfilesRevertButtonSetEnabled(enabled);
3069     backupfilesSuffixTemplateSetEnabled(enabled);
3070     backupfilesKeepAllSetEnabled(enabled);
3071   }
3072
3073   private void backupfilesSummarySetEnabled()
3074   {
3075     boolean enabled = enableBackupFiles.isSelected();
3076     backupfilesExampleLabel.setEnabled(enabled);
3077     exampleFilesPanel.setEnabled(enabled);
3078   }
3079
3080   private void backupfilesPresetsSetEnabled()
3081   {
3082     boolean enabled = enableBackupFiles.isSelected();
3083     presetsPanel.setEnabled(enabled);
3084     presetsComboLabel.setEnabled(enabled);
3085     backupfilesPresetsCombo.setEnabled(enabled);
3086     customiseCheckbox.setEnabled(enabled);
3087     revertButton.setEnabled(enabled);
3088   }
3089
3090   protected void backupsOptionsSetEnabled()
3091   {
3092     backupfilesPresetsSetEnabled();
3093     backupfilesSummarySetEnabled();
3094     backupfilesCustomOptionsSetEnabled();
3095   }
3096
3097   protected void backupsSetOptions(String suffix, int digits,
3098           boolean reverse, boolean keepAll, int rollMax,
3099           boolean confirmDelete)
3100   {
3101     suffixTemplate.setText(suffix);
3102     suffixDigitsSpinner.setValue(digits);
3103     suffixReverse.setSelected(reverse);
3104     backupfilesKeepAll.setSelected(keepAll);
3105     backupfilesRollMaxSpinner.setValue(rollMax);
3106     backupfilesConfirmDelete.setSelected(confirmDelete);
3107   }
3108
3109   protected void backupsSetOptions(BackupFilesPresetEntry p)
3110   {
3111     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3112             p.confirmDelete);
3113   }
3114
3115   protected void autoIdWidth_actionPerformed()
3116   {
3117     // TODO Auto-generated method stub
3118
3119   }
3120
3121   protected void userIdWidth_actionPerformed()
3122   {
3123     // TODO Auto-generated method stub
3124
3125   }
3126
3127   protected void maxColour_actionPerformed(JPanel panel)
3128   {
3129   }
3130
3131   protected void minColour_actionPerformed(JPanel panel)
3132   {
3133   }
3134
3135   protected void gapColour_actionPerformed(JPanel panel)
3136   {
3137   }
3138
3139   protected void hiddenColour_actionPerformed(JPanel panel)
3140   {
3141   }
3142
3143   protected void showunconserved_actionPerformed(ActionEvent e)
3144   {
3145     // TODO Auto-generated method stub
3146
3147   }
3148
3149   protected void useLegacyGaps_actionPerformed(ActionEvent e)
3150   {
3151   }
3152
3153   protected void resetOvDefaults_actionPerformed(ActionEvent e)
3154   {
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   public void ok_actionPerformed(ActionEvent e)
3164   {
3165   }
3166
3167   /**
3168    * DOCUMENT ME!
3169    *
3170    * @param e
3171    *          DOCUMENT ME!
3172    */
3173   public void cancel_actionPerformed(ActionEvent e)
3174   {
3175   }
3176
3177   /**
3178    * DOCUMENT ME!
3179    *
3180    * @param e
3181    *          DOCUMENT ME!
3182    */
3183   public void annotations_actionPerformed(ActionEvent e)
3184   {
3185   }
3186
3187   /**
3188    * DOCUMENT ME!
3189    */
3190   public void startupFileTextfield_mouseClicked()
3191   {
3192   }
3193
3194   public void newLink_actionPerformed(ActionEvent e)
3195   {
3196
3197   }
3198
3199   public void editLink_actionPerformed(ActionEvent e)
3200   {
3201
3202   }
3203
3204   public void deleteLink_actionPerformed(ActionEvent e)
3205   {
3206
3207   }
3208
3209   public void defaultBrowser_mouseClicked(MouseEvent e)
3210   {
3211
3212   }
3213
3214   public void linkURLList_keyTyped(KeyEvent e)
3215   {
3216
3217   }
3218
3219   public void setProxyAuthEnabled()
3220   {
3221     boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3222     proxyAuthUsernameLabel.setEnabled(enabled);
3223     proxyAuthPasswordLabel.setEnabled(enabled);
3224     passwordNotStoredLabel.setEnabled(enabled);
3225     proxyAuthUsernameTB.setEnabled(enabled);
3226     proxyAuthPasswordPB.setEnabled(enabled);
3227   }
3228
3229   public void setCustomProxyEnabled()
3230   {
3231     boolean enabled = customProxy.isSelected();
3232     portLabel.setEnabled(enabled);
3233     serverLabel.setEnabled(enabled);
3234     portLabel2.setEnabled(enabled);
3235     serverLabel2.setEnabled(enabled);
3236     httpLabel.setEnabled(enabled);
3237     httpsLabel.setEnabled(enabled);
3238     proxyServerHttpTB.setEnabled(enabled);
3239     proxyPortHttpTB.setEnabled(enabled);
3240     proxyServerHttpsTB.setEnabled(enabled);
3241     proxyPortHttpsTB.setEnabled(enabled);
3242     proxyAuth.setEnabled(enabled);
3243     setProxyAuthEnabled();
3244   }
3245
3246   public void proxyType_actionPerformed()
3247   {
3248     setCustomProxyEnabled();
3249     proxyAuthPasswordCheckHighlight(true);
3250     applyProxyButtonEnabled(true);
3251   }
3252
3253   public void proxyAuth_actionPerformed()
3254   {
3255     setProxyAuthEnabled();
3256     proxyAuthPasswordCheckHighlight(true);
3257     applyProxyButtonEnabled(true);
3258   }
3259
3260   /**
3261    * Customer renderer for JTable: supports column of radio buttons
3262    */
3263   public class RadioButtonRenderer extends JRadioButton
3264           implements TableCellRenderer
3265   {
3266     public RadioButtonRenderer()
3267     {
3268       setHorizontalAlignment(CENTER);
3269       setToolTipText(MessageManager.getString("label.urltooltip"));
3270     }
3271
3272     @Override
3273     public Component getTableCellRendererComponent(JTable table,
3274             Object value, boolean isSelected, boolean hasFocus, int row,
3275             int column)
3276     {
3277       setSelected((boolean) value);
3278
3279       // set colours to match rest of table
3280       if (isSelected)
3281       {
3282         setBackground(table.getSelectionBackground());
3283         setForeground(table.getSelectionForeground());
3284       }
3285       else
3286       {
3287         setBackground(table.getBackground());
3288         setForeground(table.getForeground());
3289       }
3290       return this;
3291     }
3292   }
3293
3294   /**
3295    * Customer cell editor for JTable: supports column of radio buttons in
3296    * conjunction with renderer
3297    */
3298   public class RadioButtonEditor extends AbstractCellEditor
3299           implements TableCellEditor
3300   {
3301     private JRadioButton button = new JRadioButton();
3302
3303     public RadioButtonEditor()
3304     {
3305       button.setHorizontalAlignment(SwingConstants.CENTER);
3306       this.button.addActionListener(new ActionListener()
3307       {
3308         @Override
3309         public void actionPerformed(ActionEvent e)
3310         {
3311           fireEditingStopped();
3312         }
3313       });
3314     }
3315
3316     @Override
3317     public Component getTableCellEditorComponent(JTable table, Object value,
3318             boolean isSelected, int row, int column)
3319     {
3320       button.setSelected((boolean) value);
3321       return button;
3322     }
3323
3324     @Override
3325     public Object getCellEditorValue()
3326     {
3327       return button.isSelected();
3328     }
3329
3330   }
3331 }