src/jalview/jbgui/GPreferences.java

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