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