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