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     versioncheck.setVisible(false);
 671
 672     // Add padding so the panel doesn't look ridiculous
 673     JPanel spacePanel = new JPanel();
 674     connectTab.add(spacePanel,
 675             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 676                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 677                     new Insets(0, 0, 0, 5), 70, 1));
 678
 679     return connectTab;
 680   }
 681
 682   /**
 683    * Initialises the Links tabbed panel.
 684    *
 685    * @return
 686    */
 687   private JPanel initLinksTab()
 688   {
 689     JPanel linkTab = new JPanel();
 690     linkTab.setLayout(new GridBagLayout());
 691
 692     // Set up table for Url links
 693     linkUrlTable.getTableHeader().setReorderingAllowed(false);
 694     linkUrlTable.setFillsViewportHeight(true);
 695     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 696     linkUrlTable.setAutoCreateRowSorter(true);
 697     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 698
 699     // adjust row height so radio buttons actually fit
 700     // don't do this in the renderer, it causes the awt thread to activate
 701     // constantly
 702     JRadioButton temp = new JRadioButton();
 703     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 704
 705     // Table in scrollpane so that the table is given a scrollbar
 706     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 707     linkScrollPane.setBorder(null);
 708
 709     // Panel for links functionality
 710     JPanel linkPanel = new JPanel(new GridBagLayout());
 711     linkPanel.setBorder(new TitledBorder(
 712             MessageManager.getString("label.url_linkfrom_sequence_id")));
 713
 714     // Put the Url links panel together
 715
 716     // Buttons go at top right, resizing only resizes the blank space vertically
 717     JPanel buttonPanel = initLinkTabUrlButtons();
 718     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 719     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 720     linkConstraints1.gridx = 0;
 721     linkConstraints1.gridy = 0;
 722     linkConstraints1.weightx = 1.0;
 723     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 724     linkTab.add(buttonPanel, linkConstraints1);
 725
 726     // Links table goes at top left, resizing resizes the table
 727     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 728     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 729     linkConstraints2.gridx = 0;
 730     linkConstraints2.gridy = 1;
 731     linkConstraints2.weightx = 1.0;
 732     linkConstraints2.weighty = 1.0;
 733     linkConstraints2.fill = GridBagConstraints.BOTH;
 734     linkTab.add(linkScrollPane, linkConstraints2);
 735
 736     // Filter box and buttons goes at bottom left, resizing resizes the text box
 737     JPanel filterPanel = initLinkTabFilterPanel();
 738     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 739     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 740     linkConstraints3.gridx = 0;
 741     linkConstraints3.gridy = 2;
 742     linkConstraints3.weightx = 1.0;
 743     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 744     linkTab.add(filterPanel, linkConstraints3);
 745
 746     return linkTab;
 747   }
 748
 749   private JPanel initLinkTabFilterPanel()
 750   {
 751     // Filter textbox and reset button
 752     JLabel filterLabel = new JLabel(
 753             MessageManager.getString("label.filter"));
 754     filterLabel.setFont(LABEL_FONT);
 755     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 756     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 757
 758     filterTB.setFont(LABEL_FONT);
 759     filterTB.setText("");
 760
 761     doReset.setText(MessageManager.getString("action.showall"));
 762     userOnly.setText(MessageManager.getString("action.customfilter"));
 763
 764     // Panel for filter functionality
 765     JPanel filterPanel = new JPanel(new GridBagLayout());
 766     filterPanel.setBorder(new TitledBorder("Filter"));
 767     GridBagConstraints gbc = new GridBagConstraints();
 768     gbc.gridx = 0;
 769     gbc.gridy = 0;
 770     gbc.fill = GridBagConstraints.NONE;
 771     gbc.anchor = GridBagConstraints.WEST;
 772
 773     filterPanel.add(filterLabel, gbc);
 774
 775     GridBagConstraints gbc1 = new GridBagConstraints();
 776     gbc1.gridx = 1;
 777     gbc1.gridwidth = 2;
 778     gbc1.fill = GridBagConstraints.HORIZONTAL;
 779     gbc1.anchor = GridBagConstraints.WEST;
 780     gbc1.weightx = 1.0;
 781     filterPanel.add(filterTB, gbc1);
 782
 783     GridBagConstraints gbc2 = new GridBagConstraints();
 784     gbc2.gridx = 3;
 785     gbc2.fill = GridBagConstraints.NONE;
 786     gbc2.anchor = GridBagConstraints.WEST;
 787     filterPanel.add(doReset, gbc2);
 788
 789     GridBagConstraints gbc3 = new GridBagConstraints();
 790     gbc3.gridx = 4;
 791     gbc3.fill = GridBagConstraints.NONE;
 792     gbc3.anchor = GridBagConstraints.WEST;
 793     filterPanel.add(userOnly, gbc3);
 794
 795     return filterPanel;
 796   }
 797
 798   private JPanel initLinkTabUrlButtons()
 799   {
 800     // Buttons for new / edit / delete Url links
 801     JButton newLink = new JButton();
 802     newLink.setText(MessageManager.getString("action.new"));
 803
 804     editLink.setText(MessageManager.getString("action.edit"));
 805
 806     deleteLink.setText(MessageManager.getString("action.delete"));
 807
 808     // no current selection, so initially disable delete/edit buttons
 809     editLink.setEnabled(false);
 810     deleteLink.setEnabled(false);
 811
 812     newLink.addActionListener(new java.awt.event.ActionListener()
 813     {
 814       @Override
 815       public void actionPerformed(ActionEvent e)
 816       {
 817         newLink_actionPerformed(e);
 818       }
 819     });
 820
 821     editLink.setText(MessageManager.getString("action.edit"));
 822     editLink.addActionListener(new java.awt.event.ActionListener()
 823     {
 824       @Override
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         editLink_actionPerformed(e);
 828       }
 829     });
 830
 831     deleteLink.setText(MessageManager.getString("action.delete"));
 832     deleteLink.addActionListener(new java.awt.event.ActionListener()
 833     {
 834       @Override
 835       public void actionPerformed(ActionEvent e)
 836       {
 837         deleteLink_actionPerformed(e);
 838       }
 839     });
 840
 841     JPanel buttonPanel = new JPanel(new GridBagLayout());
 842     buttonPanel.setBorder(new TitledBorder("Edit links"));
 843     GridBagConstraints gbc = new GridBagConstraints();
 844     gbc.gridx = 0;
 845     gbc.gridy = 0;
 846     gbc.fill = GridBagConstraints.NONE;
 847     buttonPanel.add(newLink, gbc);
 848
 849     GridBagConstraints gbc1 = new GridBagConstraints();
 850     gbc1.gridx = 1;
 851     gbc1.gridy = 0;
 852     gbc1.fill = GridBagConstraints.NONE;
 853     buttonPanel.add(editLink, gbc1);
 854
 855     GridBagConstraints gbc2 = new GridBagConstraints();
 856     gbc2.gridx = 2;
 857     gbc2.gridy = 0;
 858     gbc2.fill = GridBagConstraints.NONE;
 859     buttonPanel.add(deleteLink, gbc2);
 860
 861     GridBagConstraints gbc3 = new GridBagConstraints();
 862     gbc3.gridx = 3;
 863     gbc3.gridy = 0;
 864     gbc3.fill = GridBagConstraints.HORIZONTAL;
 865     gbc3.weightx = 1.0;
 866     JPanel spacePanel = new JPanel();
 867     spacePanel.setBorder(null);
 868     buttonPanel.add(spacePanel, gbc3);
 869
 870     return buttonPanel;
 871   }
 872
 873   /**
 874    * Initialises the proxy server panel in the Connections tab
 875    *
 876    * @return the proxy server panel
 877    */
 878   private JPanel initConnTabProxyPanel()
 879   {
 880     // Label for server text box
 881     serverLabel.setText(MessageManager.getString("label.address"));
 882     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 883     serverLabel.setFont(LABEL_FONT);
 884
 885     // Proxy server and port text boxes
 886     proxyServerTB.setFont(LABEL_FONT);
 887     proxyPortTB.setFont(LABEL_FONT);
 888
 889     // Label for Port text box
 890     portLabel.setFont(LABEL_FONT);
 891     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 892     portLabel.setText(MessageManager.getString("label.port"));
 893
 894     // Use proxy server checkbox
 895     useProxy.setFont(LABEL_FONT);
 896     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 897     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 898     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 899     useProxy.addActionListener(new ActionListener()
 900     {
 901       @Override
 902       public void actionPerformed(ActionEvent e)
 903       {
 904         useProxy_actionPerformed();
 905       }
 906     });
 907
 908     // Make proxy server panel
 909     JPanel proxyPanel = new JPanel();
 910     TitledBorder titledBorder1 = new TitledBorder(
 911             MessageManager.getString("label.proxy_server"));
 912     proxyPanel.setBorder(titledBorder1);
 913     proxyPanel.setLayout(new GridBagLayout());
 914     proxyPanel.add(serverLabel,
 915             new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
 916                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 917                     new Insets(0, 2, 2, 0), 5, 0));
 918     proxyPanel.add(portLabel,
 919             new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 920                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 921                     new Insets(0, 0, 2, 0), 11, 0));
 922     proxyPanel.add(useProxy,
 923             new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 924                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 925                     new Insets(0, 2, 5, 185), 2, -4));
 926     proxyPanel.add(proxyPortTB,
 927             new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
 928                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 929                     new Insets(0, 2, 2, 2), 54, 1));
 930     proxyPanel.add(proxyServerTB,
 931             new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
 932                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 933                     new Insets(0, 2, 2, 0), 263, 1));
 934
 935     return proxyPanel;
 936   }
 937
 938   /**
 939    * Initialises the checkboxes in the Connections tab
 940    */
 941   private void initConnTabCheckboxes()
 942   {
 943     // Usage stats checkbox label
 944     usagestats.setText(
 945             MessageManager.getString("label.send_usage_statistics"));
 946     usagestats.setFont(LABEL_FONT);
 947     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 948     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 949
 950     // Questionnaire checkbox label
 951     questionnaire.setText(
 952             MessageManager.getString("label.check_for_questionnaires"));
 953     questionnaire.setFont(LABEL_FONT);
 954     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 955     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 956
 957     // Check for latest version checkbox label
 958     versioncheck.setText(
 959             MessageManager.getString("label.check_for_latest_version"));
 960     versioncheck.setFont(LABEL_FONT);
 961     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 962     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 963   }
 964
 965   /**
 966    * Initialises the parent panel which contains the tabbed sections.
 967    *
 968    * @return
 969    */
 970   private JPanel initOkCancelPanel()
 971   {
 972     JButton ok = new JButton();
 973     ok.setText(MessageManager.getString("action.ok"));
 974     ok.addActionListener(new ActionListener()
 975     {
 976       @Override
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         ok_actionPerformed(e);
 980       }
 981     });
 982     JButton cancel = new JButton();
 983     cancel.setText(MessageManager.getString("action.cancel"));
 984     cancel.addActionListener(new ActionListener()
 985     {
 986       @Override
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         cancel_actionPerformed(e);
 990       }
 991     });
 992     JPanel okCancelPanel = new JPanel();
 993     okCancelPanel.add(ok);
 994     okCancelPanel.add(cancel);
 995     return okCancelPanel;
 996   }
 997
 998   /**
 999    * Initialises the Colours tabbed panel.
1000    *
1001    * @return
1002    */
1003   private JPanel initColoursTab()
1004   {
1005     JPanel coloursTab = new JPanel();
1006     coloursTab.setBorder(new TitledBorder(
1007             MessageManager.getString("action.open_new_alignment")));
1008     coloursTab.setLayout(new FlowLayout());
1009     JLabel mincolourLabel = new JLabel();
1010     mincolourLabel.setFont(LABEL_FONT);
1011     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1012     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1013     minColour.setFont(LABEL_FONT);
1014     minColour.setBorder(BorderFactory.createEtchedBorder());
1015     minColour.setPreferredSize(new Dimension(40, 20));
1016     minColour.addMouseListener(new MouseAdapter()
1017     {
1018       @Override
1019       public void mousePressed(MouseEvent e)
1020       {
1021         minColour_actionPerformed(minColour);
1022       }
1023     });
1024     JLabel maxcolourLabel = new JLabel();
1025     maxcolourLabel.setFont(LABEL_FONT);
1026     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1027     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1028     maxColour.setFont(LABEL_FONT);
1029     maxColour.setBorder(BorderFactory.createEtchedBorder());
1030     maxColour.setPreferredSize(new Dimension(40, 20));
1031     maxColour.addMouseListener(new MouseAdapter()
1032     {
1033       @Override
1034       public void mousePressed(MouseEvent e)
1035       {
1036         maxColour_actionPerformed(maxColour);
1037       }
1038     });
1039
1040     protColour.setFont(LABEL_FONT);
1041     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1042     JLabel protColourLabel = new JLabel();
1043     protColourLabel.setFont(LABEL_FONT);
1044     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1045     protColourLabel.setText(
1046             MessageManager.getString("label.prot_alignment_colour") + " ");
1047     JvSwingUtils.addtoLayout(coloursTab,
1048             MessageManager
1049                     .getString("label.default_colour_scheme_for_alignment"),
1050             protColourLabel, protColour);
1051
1052     nucColour.setFont(LABEL_FONT);
1053     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1054     JLabel nucColourLabel = new JLabel();
1055     nucColourLabel.setFont(LABEL_FONT);
1056     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1057     nucColourLabel.setText(
1058             MessageManager.getString("label.nuc_alignment_colour") + " ");
1059     JvSwingUtils.addtoLayout(coloursTab,
1060             MessageManager
1061                     .getString("label.default_colour_scheme_for_alignment"),
1062             nucColourLabel, nucColour);
1063
1064     JPanel annotationShding = new JPanel();
1065     annotationShding.setBorder(new TitledBorder(
1066             MessageManager.getString("label.annotation_shading_default")));
1067     annotationShding.setLayout(new GridLayout(1, 2));
1068     JvSwingUtils.addtoLayout(annotationShding,
1069             MessageManager.getString(
1070                     "label.default_minimum_colour_annotation_shading"),
1071             mincolourLabel, minColour);
1072     JvSwingUtils.addtoLayout(annotationShding,
1073             MessageManager.getString(
1074                     "label.default_maximum_colour_annotation_shading"),
1075             maxcolourLabel, maxColour);
1076     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1077     return coloursTab;
1078   }
1079
1080   /**
1081    * Initialises the Overview tabbed panel.
1082    *
1083    * @return
1084    */
1085   private JPanel initOverviewTab()
1086   {
1087     JPanel overviewPanel = new JPanel();
1088     overviewPanel.setBorder(new TitledBorder(
1089             MessageManager.getString("label.overview_settings")));
1090
1091     gapColour.setFont(LABEL_FONT);
1092     // fixing the border colours stops apparent colour bleed from the panel
1093     gapColour.setBorder(
1094             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1095     gapColour.setPreferredSize(new Dimension(40, 20));
1096     gapColour.addMouseListener(new MouseAdapter()
1097     {
1098       @Override
1099       public void mousePressed(MouseEvent e)
1100       {
1101         gapColour_actionPerformed(gapColour);
1102       }
1103     });
1104
1105     hiddenColour.setFont(LABEL_FONT);
1106     // fixing the border colours stops apparent colour bleed from the panel
1107     hiddenColour.setBorder(
1108             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1109     hiddenColour.setPreferredSize(new Dimension(40, 20));
1110     hiddenColour.addMouseListener(new MouseAdapter()
1111     {
1112       @Override
1113       public void mousePressed(MouseEvent e)
1114       {
1115         hiddenColour_actionPerformed(hiddenColour);
1116       }
1117     });
1118
1119     useLegacyGap = new JCheckBox(
1120             MessageManager.getString("label.ov_legacy_gap"));
1121     useLegacyGap.setFont(LABEL_FONT);
1122     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1123     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1124     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1125     gapLabel.setFont(LABEL_FONT);
1126     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1127     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1128     showHiddenAtStart = new JCheckBox(
1129             MessageManager.getString("label.ov_show_hide_default"));
1130     showHiddenAtStart.setFont(LABEL_FONT);
1131     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1132     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1133     JLabel hiddenLabel = new JLabel(
1134             MessageManager.getString("label.hidden_colour"));
1135     hiddenLabel.setFont(LABEL_FONT);
1136     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1137     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1138
1139     useLegacyGap.addActionListener(new ActionListener()
1140     {
1141       @Override
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         useLegacyGaps_actionPerformed(e);
1145       }
1146     });
1147
1148     overviewPanel.setLayout(new GridBagLayout());
1149     GridBagConstraints c1 = new GridBagConstraints();
1150
1151     c1.fill = GridBagConstraints.HORIZONTAL;
1152     c1.gridx = 0;
1153     c1.gridy = 0;
1154     c1.weightx = 1;
1155     c1.ipady = 20;
1156     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1157     overviewPanel.add(useLegacyGap, c1);
1158
1159     GridBagConstraints c2 = new GridBagConstraints();
1160     c2.fill = GridBagConstraints.HORIZONTAL;
1161     c2.gridx = 1;
1162     c2.gridy = 0;
1163     c2.insets = new Insets(0, 15, 0, 10);
1164     overviewPanel.add(gapLabel, c2);
1165
1166     GridBagConstraints c3 = new GridBagConstraints();
1167     c3.fill = GridBagConstraints.HORIZONTAL;
1168     c3.gridx = 2;
1169     c3.gridy = 0;
1170     c3.insets = new Insets(0, 0, 0, 15);
1171     overviewPanel.add(gapColour, c3);
1172
1173     GridBagConstraints c4 = new GridBagConstraints();
1174     c4.fill = GridBagConstraints.HORIZONTAL;
1175     c4.gridx = 0;
1176     c4.gridy = 1;
1177     c4.weightx = 1;
1178     overviewPanel.add(showHiddenAtStart, c4);
1179
1180     GridBagConstraints c5 = new GridBagConstraints();
1181     c5.fill = GridBagConstraints.HORIZONTAL;
1182     c5.gridx = 1;
1183     c5.gridy = 1;
1184     c5.insets = new Insets(0, 15, 0, 10);
1185     overviewPanel.add(hiddenLabel, c5);
1186
1187     GridBagConstraints c6 = new GridBagConstraints();
1188     c6.fill = GridBagConstraints.HORIZONTAL;
1189     c6.gridx = 2;
1190     c6.gridy = 1;
1191     c6.insets = new Insets(0, 0, 0, 15);
1192     overviewPanel.add(hiddenColour, c6);
1193
1194     JButton resetButton = new JButton(
1195             MessageManager.getString("label.reset_to_defaults"));
1196
1197     resetButton.addActionListener(new ActionListener()
1198     {
1199       @Override
1200       public void actionPerformed(ActionEvent e)
1201       {
1202         resetOvDefaults_actionPerformed(e);
1203       }
1204     });
1205
1206     GridBagConstraints c7 = new GridBagConstraints();
1207     c7.fill = GridBagConstraints.NONE;
1208     c7.gridx = 0;
1209     c7.gridy = 2;
1210     c7.insets = new Insets(10, 0, 0, 0);
1211     c7.anchor = GridBagConstraints.WEST;
1212     overviewPanel.add(resetButton, c7);
1213
1214     // Add padding so the panel doesn't look ridiculous
1215     JPanel spacePanel = new JPanel();
1216     overviewPanel.add(spacePanel,
1217             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1218                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1219                     new Insets(0, 0, 0, 5), 0, 0));
1220
1221     return overviewPanel;
1222   }
1223
1224   /**
1225    * Initialises the Structure tabbed panel.
1226    *
1227    * @return
1228    */
1229   private JPanel initStructureTab()
1230   {
1231     structureTab = new JPanel();
1232
1233     structureTab.setBorder(new TitledBorder(
1234             MessageManager.getString("label.structure_options")));
1235     structureTab.setLayout(null);
1236     final int width = 400;
1237     final int height = 22;
1238     final int lineSpacing = 25;
1239     int ypos = 15;
1240
1241     structFromPdb.setFont(LABEL_FONT);
1242     structFromPdb
1243             .setText(MessageManager.getString("label.struct_from_pdb"));
1244     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1245     structFromPdb.addActionListener(new ActionListener()
1246     {
1247       @Override
1248       public void actionPerformed(ActionEvent e)
1249       {
1250         boolean selected = structFromPdb.isSelected();
1251         // enable other options only when the first is checked
1252         useRnaView.setEnabled(selected);
1253         addSecondaryStructure.setEnabled(selected);
1254         addTempFactor.setEnabled(selected);
1255       }
1256     });
1257     structureTab.add(structFromPdb);
1258
1259     // indent checkboxes that are conditional on the first one
1260     ypos += lineSpacing;
1261     useRnaView.setFont(LABEL_FONT);
1262     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1263     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1264     structureTab.add(useRnaView);
1265
1266     ypos += lineSpacing;
1267     addSecondaryStructure.setFont(LABEL_FONT);
1268     addSecondaryStructure
1269             .setText(MessageManager.getString("label.autoadd_secstr"));
1270     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1271     structureTab.add(addSecondaryStructure);
1272
1273     ypos += lineSpacing;
1274     addTempFactor.setFont(LABEL_FONT);
1275     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1276     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1277     structureTab.add(addTempFactor);
1278
1279     ypos += lineSpacing;
1280     JLabel viewerLabel = new JLabel();
1281     viewerLabel.setFont(LABEL_FONT);
1282     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1283     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1284     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1285     structureTab.add(viewerLabel);
1286
1287     structViewer.setFont(LABEL_FONT);
1288     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1289     structViewer.addItem(ViewerType.JMOL.name());
1290     structViewer.addItem(ViewerType.CHIMERA.name());
1291     structViewer.addActionListener(new ActionListener()
1292     {
1293       @Override
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         structureViewer_actionPerformed(
1297                 (String) structViewer.getSelectedItem());
1298       }
1299     });
1300     structureTab.add(structViewer);
1301
1302     ypos += lineSpacing;
1303     JLabel pathLabel = new JLabel();
1304     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1305     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1306     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1307     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1308     structureTab.add(pathLabel);
1309
1310     chimeraPath.setFont(LABEL_FONT);
1311     chimeraPath.setText("");
1312     final String tooltip = JvSwingUtils.wrapTooltip(true,
1313             MessageManager.getString("label.chimera_path_tip"));
1314     chimeraPath.setToolTipText(tooltip);
1315     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1316     chimeraPath.addMouseListener(new MouseAdapter()
1317     {
1318       @Override
1319       public void mouseClicked(MouseEvent e)
1320       {
1321         if (e.getClickCount() == 2)
1322         {
1323           String chosen = openFileChooser();
1324           if (chosen != null)
1325           {
1326             chimeraPath.setText(chosen);
1327           }
1328         }
1329       }
1330     });
1331     structureTab.add(chimeraPath);
1332
1333     ypos += lineSpacing;
1334     nwMapping.setFont(LABEL_FONT);
1335     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1336     siftsMapping.setFont(LABEL_FONT);
1337     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1338     mappingMethod.add(nwMapping);
1339     mappingMethod.add(siftsMapping);
1340     JPanel mappingPanel = new JPanel();
1341     mappingPanel.setFont(LABEL_FONT);
1342     TitledBorder mmTitledBorder = new TitledBorder(
1343             MessageManager.getString("label.mapping_method"));
1344     mmTitledBorder.setTitleFont(LABEL_FONT);
1345     mappingPanel.setBorder(mmTitledBorder);
1346     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1347     // GridLayout mappingLayout = new GridLayout();
1348     mappingPanel.setLayout(new GridLayout());
1349     mappingPanel.add(nwMapping);
1350     mappingPanel.add(siftsMapping);
1351     structureTab.add(mappingPanel);
1352
1353     ypos += lineSpacing;
1354     ypos += lineSpacing;
1355     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1356             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1357     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1358     structureTab.add(docFieldPref);
1359
1360     /*
1361      * hide Chimera options in JalviewJS
1362      */
1363     if (Platform.isJS())
1364     {
1365       pathLabel.setVisible(false);
1366       chimeraPath.setVisible(false);
1367       viewerLabel.setVisible(false);
1368       structViewer.setVisible(false);
1369     }
1370
1371     return structureTab;
1372   }
1373
1374   /**
1375    * Action on choosing a structure viewer from combobox options.
1376    *
1377    * @param selectedItem
1378    */
1379   protected void structureViewer_actionPerformed(String selectedItem)
1380   {
1381   }
1382
1383   /**
1384    * Show a dialog for the user to choose a file. Returns the chosen path, or
1385    * null on Cancel.
1386    *
1387    * @return
1388    */
1389   protected String openFileChooser()
1390   {
1391     String choice = null;
1392     JFileChooser chooser = new JFileChooser();
1393
1394     // chooser.setFileView(new JalviewFileView());
1395     chooser.setDialogTitle(
1396             MessageManager.getString("label.open_local_file"));
1397     chooser.setToolTipText(MessageManager.getString("action.open"));
1398
1399     int value = chooser.showOpenDialog(this);
1400
1401     if (value == JFileChooser.APPROVE_OPTION)
1402     {
1403       choice = chooser.getSelectedFile().getPath();
1404     }
1405     return choice;
1406   }
1407
1408   /**
1409    * Validate the structure tab preferences; if invalid, set focus on this tab.
1410    *
1411    * @param e
1412    */
1413   protected boolean validateStructure(FocusEvent e)
1414   {
1415     if (!validateStructure())
1416     {
1417       e.getComponent().requestFocusInWindow();
1418       return false;
1419     }
1420     return true;
1421   }
1422
1423   protected boolean validateStructure()
1424   {
1425     return false;
1426   }
1427
1428   /**
1429    * Initialises the Visual tabbed panel.
1430    *
1431    * @return
1432    */
1433   private JPanel initVisualTab()
1434   {
1435     JPanel visualTab = new JPanel();
1436     visualTab.setBorder(new TitledBorder(
1437             MessageManager.getString("action.open_new_alignment")));
1438     visualTab.setLayout(null);
1439     fullScreen.setFont(LABEL_FONT);
1440     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1441     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1442     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1443     quality.setEnabled(false);
1444     quality.setFont(LABEL_FONT);
1445     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1446     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1447     quality.setSelected(true);
1448     quality.setText(MessageManager.getString("label.quality"));
1449     conservation.setEnabled(false);
1450     conservation.setFont(LABEL_FONT);
1451     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1452     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1453     conservation.setSelected(true);
1454     conservation.setText(MessageManager.getString("label.conservation"));
1455     identity.setEnabled(false);
1456     identity.setFont(LABEL_FONT);
1457     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1458     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1459     identity.setSelected(true);
1460     identity.setText(MessageManager.getString("label.consensus"));
1461     showOccupancy.setFont(LABEL_FONT);
1462     showOccupancy.setEnabled(false);
1463     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1464     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1465     showOccupancy.setSelected(true);
1466     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1467
1468     JLabel showGroupbits = new JLabel();
1469     showGroupbits.setFont(LABEL_FONT);
1470     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1471     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1472     showGroupbits
1473             .setText(MessageManager.getString("action.show_group") + ":");
1474     JLabel showConsensbits = new JLabel();
1475     showConsensbits.setFont(LABEL_FONT);
1476     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1477     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1478     showConsensbits
1479             .setText(MessageManager.getString("label.consensus") + ":");
1480     showConsensHistogram.setEnabled(false);
1481     showConsensHistogram.setFont(LABEL_FONT);
1482     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1483     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1484     showConsensHistogram.setSelected(true);
1485     showConsensHistogram
1486             .setText(MessageManager.getString("label.histogram"));
1487     showConsensLogo.setEnabled(false);
1488     showConsensLogo.setFont(LABEL_FONT);
1489     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1490     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1491     showConsensLogo.setSelected(true);
1492     showConsensLogo.setText(MessageManager.getString("label.logo"));
1493     showGroupConsensus.setEnabled(false);
1494     showGroupConsensus.setFont(LABEL_FONT);
1495     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1496     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1497     showGroupConsensus.setSelected(true);
1498     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1499     showGroupConservation.setEnabled(false);
1500     showGroupConservation.setFont(LABEL_FONT);
1501     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1502     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1503     showGroupConservation.setSelected(true);
1504     showGroupConservation
1505             .setText(MessageManager.getString("label.conservation"));
1506     showNpTooltip.setEnabled(true);
1507     showNpTooltip.setFont(LABEL_FONT);
1508     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1509     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1510     showNpTooltip.setSelected(true);
1511     showNpTooltip.setText(
1512             MessageManager.getString("label.non_positional_features"));
1513     showDbRefTooltip.setEnabled(true);
1514     showDbRefTooltip.setFont(LABEL_FONT);
1515     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1516     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1517     showDbRefTooltip.setSelected(true);
1518     showDbRefTooltip
1519             .setText(MessageManager.getString("label.database_references"));
1520     annotations.setFont(LABEL_FONT);
1521     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1522     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1523     annotations.setSelected(true);
1524     annotations.setText(MessageManager.getString("label.show_annotations"));
1525     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1526     annotations.addActionListener(new ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         annotations_actionPerformed(e);
1532       }
1533     });
1534     identity.addActionListener(new ActionListener()
1535     {
1536       @Override
1537       public void actionPerformed(ActionEvent e)
1538       {
1539         annotations_actionPerformed(e);
1540       }
1541     });
1542     showGroupConsensus.addActionListener(new ActionListener()
1543     {
1544       @Override
1545       public void actionPerformed(ActionEvent e)
1546       {
1547         annotations_actionPerformed(e);
1548       }
1549     });
1550     showUnconserved.setFont(LABEL_FONT);
1551     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1552     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1553     showUnconserved.setSelected(true);
1554     showUnconserved
1555             .setText(MessageManager.getString("action.show_unconserved"));
1556     showUnconserved.addActionListener(new ActionListener()
1557     {
1558       @Override
1559       public void actionPerformed(ActionEvent e)
1560       {
1561         showunconserved_actionPerformed(e);
1562       }
1563     });
1564
1565     // TODO these are not yet added to / action from Preferences
1566     // JCheckBox shareSelections = new JCheckBox();
1567     // shareSelections.setFont(verdana11);
1568     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1569     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1570     // shareSelections.setSelected(true);
1571     // shareSelections.setText(MessageManager
1572     // .getString("label.share_selection_across_views"));
1573     // JCheckBox followHighlight = new JCheckBox();
1574     // followHighlight.setFont(verdana11);
1575     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1576     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1577     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1578     // followHighlight.setSelected(true);
1579     // followHighlight.setText(MessageManager
1580     // .getString("label.scroll_highlighted_regions"));
1581
1582     seqLimit.setFont(LABEL_FONT);
1583     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1584     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1585     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1586     smoothFont.setFont(LABEL_FONT);
1587     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1588     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1589     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1590     scaleProteinToCdna.setFont(LABEL_FONT);
1591     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1592     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1593     scaleProteinToCdna.setText(
1594             MessageManager.getString("label.scale_protein_to_cdna"));
1595     scaleProteinToCdna.setToolTipText(
1596             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1597     JLabel gapLabel = new JLabel();
1598     gapLabel.setFont(LABEL_FONT);
1599     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1600     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1601     JLabel fontLabel = new JLabel();
1602     fontLabel.setFont(LABEL_FONT);
1603     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1604     fontLabel.setText(MessageManager.getString("label.font"));
1605     fontSizeCB.setFont(LABEL_FONT);
1606     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1607     fontStyleCB.setFont(LABEL_FONT);
1608     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1609     fontNameCB.setFont(LABEL_FONT);
1610     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1611     gapSymbolCB.setFont(LABEL_FONT);
1612     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1613     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1614     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1615     gapSymbolCB.setRenderer(dlcr);
1616
1617     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1618     startupCheckbox.setFont(LABEL_FONT);
1619     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1620     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1621     startupCheckbox.setSelected(true);
1622     startupFileTextfield.setFont(LABEL_FONT);
1623     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1624     final String tooltip = JvSwingUtils.wrapTooltip(true,
1625             MessageManager.getString("label.double_click_to_browse"));
1626     startupFileTextfield.setToolTipText(tooltip);
1627     startupFileTextfield.addMouseListener(new MouseAdapter()
1628     {
1629       @Override
1630       public void mouseClicked(MouseEvent e)
1631       {
1632         if (e.getClickCount() > 1)
1633         {
1634           startupFileTextfield_mouseClicked();
1635         }
1636       }
1637     });
1638
1639     sortby.setFont(LABEL_FONT);
1640     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1641     JLabel sortLabel = new JLabel();
1642     sortLabel.setFont(LABEL_FONT);
1643     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1644     sortLabel.setText(MessageManager.getString("label.sort_by"));
1645     sortAnnBy.setFont(LABEL_FONT);
1646     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1647     JLabel sortAnnLabel = new JLabel();
1648     sortAnnLabel.setFont(LABEL_FONT);
1649     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1650     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1651     sortAutocalc.setFont(LABEL_FONT);
1652     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1653
1654     JPanel annsettingsPanel = new JPanel();
1655     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1656     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1657     annsettingsPanel.setBorder(new EtchedBorder());
1658     visualTab.add(annsettingsPanel);
1659     Border jb = new EmptyBorder(1, 1, 4, 5);
1660     annotations.setBorder(jb);
1661     showOccupancy.setBorder(jb);
1662     quality.setBorder(jb);
1663     conservation.setBorder(jb);
1664     identity.setBorder(jb);
1665     showConsensbits.setBorder(jb);
1666     showGroupbits.setBorder(jb);
1667     showGroupConsensus.setBorder(jb);
1668     showGroupConservation.setBorder(jb);
1669     showConsensHistogram.setBorder(jb);
1670     showConsensLogo.setBorder(jb);
1671
1672     JPanel autoAnnotSettings = new JPanel();
1673     annsettingsPanel.add(autoAnnotSettings);
1674     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1675     autoAnnotSettings.add(annotations);
1676     autoAnnotSettings.add(quality);
1677     // second row of autoannotation box
1678     autoAnnotSettings = new JPanel();
1679     annsettingsPanel.add(autoAnnotSettings);
1680
1681     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1682     autoAnnotSettings.add(conservation);
1683     autoAnnotSettings.add(identity);
1684     autoAnnotSettings.add(showOccupancy);
1685     autoAnnotSettings.add(showGroupbits);
1686     autoAnnotSettings.add(showGroupConservation);
1687     autoAnnotSettings.add(showGroupConsensus);
1688     autoAnnotSettings.add(showConsensbits);
1689     autoAnnotSettings.add(showConsensHistogram);
1690     autoAnnotSettings.add(showConsensLogo);
1691
1692     JPanel tooltipSettings = new JPanel();
1693     tooltipSettings.setBorder(new TitledBorder(
1694             MessageManager.getString("label.sequence_id_tooltip")));
1695     tooltipSettings.setBounds(173, 140, 220, 62);
1696     tooltipSettings.setLayout(new GridLayout(2, 1));
1697     tooltipSettings.add(showDbRefTooltip);
1698     tooltipSettings.add(showNpTooltip);
1699     visualTab.add(tooltipSettings);
1700
1701     wrap.setFont(LABEL_FONT);
1702     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1703     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1704     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1705     rightAlign.setFont(LABEL_FONT);
1706     rightAlign.setForeground(Color.black);
1707     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1708     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1709     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1710     idItalics.setFont(LABEL_FONT_ITALIC);
1711     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1712     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1713     idItalics.setText(
1714             MessageManager.getString("label.sequence_name_italics"));
1715     openoverv.setFont(LABEL_FONT);
1716     openoverv.setActionCommand(
1717             MessageManager.getString("label.open_overview"));
1718     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1719     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1720     openoverv.setText(MessageManager.getString("label.open_overview"));
1721     JPanel jPanel2 = new JPanel();
1722     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1723     jPanel2.setLayout(new GridLayout(14, 1));
1724     jPanel2.add(fullScreen);
1725     jPanel2.add(openoverv);
1726     jPanel2.add(seqLimit);
1727     jPanel2.add(rightAlign);
1728     jPanel2.add(fontLabel);
1729     jPanel2.add(showUnconserved);
1730     jPanel2.add(idItalics);
1731     jPanel2.add(smoothFont);
1732     jPanel2.add(scaleProteinToCdna);
1733     jPanel2.add(gapLabel);
1734     jPanel2.add(wrap);
1735     jPanel2.add(sortLabel);
1736     jPanel2.add(sortAnnLabel);
1737     jPanel2.add(startupCheckbox);
1738     visualTab.add(jPanel2);
1739     visualTab.add(startupFileTextfield);
1740     visualTab.add(sortby);
1741     visualTab.add(sortAnnBy);
1742     visualTab.add(sortAutocalc);
1743     visualTab.add(gapSymbolCB);
1744     visualTab.add(fontNameCB);
1745     visualTab.add(fontSizeCB);
1746     visualTab.add(fontStyleCB);
1747
1748     if (Platform.isJS())
1749     {
1750       startupCheckbox.setVisible(false);
1751       startupFileTextfield.setVisible(false);
1752     }
1753
1754     return visualTab;
1755   }
1756
1757   /**
1758    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
1759    */
1760
1761   protected void loadLastSavedBackupsOptions()
1762   {
1763     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
1764             .getSavedBackupEntry();
1765     enableBackupFiles
1766             .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
1767
1768     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
1769             .createBackupFilesPresetEntry(Cache
1770                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
1771     if (backupfilesCustomEntry == null)
1772     {
1773       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1774               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
1775     }
1776     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1777             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
1778             backupfilesCustomEntry);
1779
1780     setComboIntStringKey(backupfilesPresetsCombo,
1781             Cache.getDefault(BackupFiles.NS + "_PRESET",
1782                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
1783
1784     backupsSetOptions(savedPreset);
1785
1786     backupsOptionsSetEnabled();
1787     updateBackupFilesExampleLabel();
1788   }
1789
1790   private boolean warnAboutSuffixReverseChange()
1791   {
1792     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
1793             .getSavedBackupEntry();
1794     boolean savedSuffixReverse = bfpe.reverse;
1795     int savedSuffixDigits = bfpe.digits;
1796     String savedSuffixTemplate = bfpe.suffix;
1797
1798     boolean nowSuffixReverse = suffixReverse.isSelected();
1799     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
1800     String nowSuffixTemplate = suffixTemplate.getText();
1801     return nowSuffixReverse != savedSuffixReverse
1802             && nowSuffixDigits == savedSuffixDigits
1803             && nowSuffixTemplate != null
1804             && nowSuffixTemplate.equals(savedSuffixTemplate);
1805   }
1806
1807   /**
1808    * Initialises the Backups tabbed panel.
1809    *
1810    * @return
1811    */
1812   private JPanel initBackupsTab()
1813   {
1814     JPanel backupsTab = new JPanel();
1815     backupsTab.setBorder(new TitledBorder(
1816             MessageManager.getString("label.backup_files")));
1817     backupsTab.setLayout(new GridBagLayout());
1818
1819     GridBagConstraints gbc = new GridBagConstraints();
1820     gbc.weightx = 0.0;
1821     gbc.weighty = 0.0;
1822     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1823     gbc.fill = GridBagConstraints.NONE;
1824
1825     initBackupsTabPresetsPanel();
1826     initBackupsTabSuffixPanel();
1827     initBackupsTabKeepFilesPanel();
1828     initBackupsTabFilenameExamplesPanel();
1829
1830     enableBackupFiles.setFont(LABEL_FONT_BOLD);
1831     enableBackupFiles
1832             .setText(MessageManager.getString("label.enable_backupfiles"));
1833     enableBackupFiles.addActionListener(new ActionListener()
1834     {
1835       @Override
1836       public void actionPerformed(ActionEvent e)
1837       {
1838         // enable other options only when the first is checked
1839         backupsOptionsSetEnabled();
1840       }
1841     });
1842
1843
1844     // enable checkbox 1 col
1845     gbc.gridwidth = 1;
1846     gbc.gridheight = 1;
1847     gbc.gridx = 0;
1848     gbc.gridy = 0; // row 0
1849     backupsTab.add(enableBackupFiles, gbc);
1850
1851     // summary of scheme box (over two rows)
1852     gbc.gridx = 1;
1853     gbc.weightx = 0.0;
1854     gbc.gridheight = 2;
1855     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
1856     gbc.fill = GridBagConstraints.BOTH;
1857     backupsTab.add(exampleFilesPanel, gbc);
1858     gbc.gridheight = 1;
1859     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1860     gbc.fill = GridBagConstraints.NONE;
1861
1862     // fill empty space on right
1863     gbc.gridx++;
1864     gbc.weightx = 1.0;
1865     backupsTab.add(new JPanel(), gbc);
1866
1867     // schemes box
1868     gbc.weightx = 0.0;
1869     gbc.gridx = 0;
1870     gbc.gridy++; // row 1
1871     backupsTab.add(presetsPanel, gbc);
1872
1873     // now using whole row
1874     gbc.gridwidth = 2;
1875     gbc.gridheight = 1;
1876     // keep files box
1877     gbc.gridx = 0;
1878     gbc.gridy++; // row 2
1879     backupsTab.add(keepfilesPanel, gbc);
1880
1881     // filename strategy box
1882     gbc.gridy++; // row 3
1883     backupsTab.add(suffixPanel, gbc);
1884
1885     // fill empty space
1886     gbc.gridy++; // row 4
1887     gbc.weighty = 1.0;
1888     backupsTab.add(new JPanel(), gbc);
1889
1890     backupsOptionsSetEnabled();
1891     return backupsTab;
1892   }
1893
1894   private JPanel initBackupsTabPresetsPanel()
1895   {
1896
1897     String title = MessageManager.getString("label.schemes");
1898
1899     presetsPanel.setLayout(new GridBagLayout());
1900
1901     GridBagConstraints gbc = new GridBagConstraints();
1902     gbc.weightx = 0.0;
1903     gbc.weighty = 0.0;
1904     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
1905     gbc.fill = GridBagConstraints.NONE;
1906     gbc.gridwidth = 1;
1907     gbc.gridheight = 1;
1908
1909     // "Scheme: "
1910     gbc.gridx = 0;
1911     gbc.gridy = 0;
1912
1913     presetsComboLabel = new JLabel(title + ":");
1914     presetsPanel.add(presetsComboLabel, gbc);
1915
1916     List<Object> entries = Arrays
1917             .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
1918     List<String> tooltips = Arrays.asList(
1919             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
1920     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
1921             tooltips);
1922     /*
1923     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
1924     {
1925       backupfilesPresetsCombo
1926               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
1927     }
1928     */
1929
1930     backupfilesPresetsCombo.addActionListener(new ActionListener()
1931     {
1932       @Override
1933       public void actionPerformed(ActionEvent e)
1934       {
1935         int key = getComboIntStringKey(backupfilesPresetsCombo);
1936         if (!customiseCheckbox.isSelected())
1937         {
1938           backupfilesPresetsComboLastSelected = key;
1939         }
1940         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1941         {
1942           if (customiseCheckbox.isSelected())
1943           {
1944             // got here by clicking on customiseCheckbox so don't change the values
1945             backupfilesCustomOptionsSetEnabled();
1946           }
1947           else
1948           {
1949             backupsTabUpdatePresets();
1950             backupfilesCustomOptionsSetEnabled();
1951           }
1952         }
1953         else
1954         {
1955           customiseCheckbox.setSelected(false);
1956           backupsTabUpdatePresets();
1957           backupfilesCustomOptionsSetEnabled();
1958         }
1959       }
1960     });
1961
1962     // dropdown list of preset schemes
1963     gbc.gridx = 1;
1964     presetsPanel.add(backupfilesPresetsCombo, gbc);
1965
1966     revertButton.setText(MessageManager.getString("label.cancel_changes"));
1967     revertButton.setToolTipText(
1968             MessageManager.getString("label.cancel_changes_description"));
1969     revertButton.addActionListener(new ActionListener()
1970     {
1971       @Override
1972       public void actionPerformed(ActionEvent e)
1973       {
1974         backupsSetOptions(
1975                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
1976                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
1977         backupfilesCustomOptionsSetEnabled();
1978       }
1979
1980     });
1981     revertButton.setFont(LABEL_FONT);
1982
1983     customiseCheckbox.setFont(LABEL_FONT);
1984     customiseCheckbox.setText(MessageManager.getString("label.customise"));
1985     customiseCheckbox.addActionListener(new ActionListener()
1986     {
1987       @Override
1988       public void actionPerformed(ActionEvent e)
1989       {
1990         int currently = getComboIntStringKey(backupfilesPresetsCombo);
1991         if (customiseCheckbox.isSelected())
1992         {
1993           backupfilesPresetsComboLastSelected = currently;
1994           setComboIntStringKey(backupfilesPresetsCombo,
1995                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
1996         }
1997         else
1998         {
1999           setComboIntStringKey(backupfilesPresetsCombo,
2000                   backupfilesPresetsComboLastSelected);
2001
2002         }
2003         backupfilesCustomOptionsSetEnabled();
2004       }
2005     });
2006     customiseCheckbox.setToolTipText(
2007             MessageManager.getString("label.customise_description"));
2008
2009     // customise checkbox
2010     gbc.gridx = 0;
2011     gbc.gridy++;
2012     presetsPanel.add(customiseCheckbox, gbc);
2013
2014     // "Cancel changes" button (aligned with combo box above)
2015     gbc.gridx = 1;
2016     presetsPanel.add(revertButton, gbc);
2017
2018     return presetsPanel;
2019   }
2020
2021   private JPanel initBackupsTabFilenameExamplesPanel()
2022   {
2023     String title = MessageManager
2024             .getString("label.scheme_examples");
2025     TitledBorder tb = new TitledBorder(title);
2026     exampleFilesPanel.setBorder(tb);
2027     exampleFilesPanel.setLayout(new GridBagLayout());
2028
2029
2030     backupfilesExampleLabel.setEditable(false);
2031     backupfilesExampleLabel
2032             .setBackground(exampleFilesPanel.getBackground());
2033
2034     updateBackupFilesExampleLabel();
2035
2036     GridBagConstraints gbc = new GridBagConstraints();
2037     gbc.weightx = 1.0;
2038     gbc.weighty = 1.0;
2039     gbc.fill = GridBagConstraints.NONE;
2040     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2041
2042     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2043     return exampleFilesPanel;
2044   }
2045
2046   private void backupsTabUpdatePresets()
2047   {
2048     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2049             .getSelectedItem();
2050     int key = entry.k;
2051     String value = entry.v;
2052
2053     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2054             .containsKey(key))
2055     {
2056       backupsSetOptions(
2057               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2058                       .get(key));
2059     }
2060     else
2061     {
2062       Cache.log.error(
2063               "Preset '" + value + "' [key:" + key + "] not implemented");
2064     }
2065
2066     // Custom options will now be enabled when the customiseCheckbox is checked
2067     // (performed above)
2068     // backupfilesCustomOptionsSetEnabled();
2069     updateBackupFilesExampleLabel();
2070   }
2071
2072   protected int getComboIntStringKey(
2073           JComboBox<Object> backupfilesPresetsCombo2)
2074   {
2075     IntKeyStringValueEntry e;
2076     try
2077     {
2078       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2079               .getSelectedItem();
2080     } catch (Exception ex)
2081     {
2082       Cache.log.error(
2083               "Problem casting Combo entry to IntKeyStringValueEntry.");
2084       e = null;
2085     }
2086     return e != null ? e.k : 0;
2087   }
2088
2089   protected void setComboIntStringKey(
2090           JComboBox<Object> backupfilesPresetsCombo2,
2091           int key)
2092   {
2093     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2094     {
2095       IntKeyStringValueEntry e;
2096       try
2097       {
2098         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2099       } catch (Exception ex)
2100       {
2101         Cache.log.error(
2102                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2103         continue;
2104       }
2105       if (e.k == key)
2106       {
2107         backupfilesPresetsCombo2.setSelectedIndex(i);
2108         break;
2109       }
2110     }
2111     // backupsTabUpdatePresets();
2112   }
2113
2114   private JPanel initBackupsTabSuffixPanel()
2115   {
2116     suffixPanel.setBorder(new TitledBorder(
2117             MessageManager.getString("label.backup_filename_strategy")));
2118     suffixPanel.setLayout(new GridBagLayout());
2119
2120     suffixTemplateLabel
2121             .setText(MessageManager.getString("label.append_to_filename"));
2122     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2123     suffixTemplateLabel.setFont(LABEL_FONT);
2124
2125     final String tooltip = JvSwingUtils.wrapTooltip(true,
2126             MessageManager.getString("label.append_to_filename_tooltip"));
2127     suffixTemplate.setToolTipText(tooltip);
2128     suffixTemplate.addActionListener(new ActionListener()
2129     {
2130       @Override
2131       public void actionPerformed(ActionEvent e)
2132       {
2133         updateBackupFilesExampleLabel();
2134         backupfilesCustomOptionsSetEnabled();
2135         backupfilesRevertButtonSetEnabled(true);
2136       }
2137
2138     });
2139     suffixTemplate.addKeyListener(new KeyListener()
2140     {
2141       @Override
2142       public void keyReleased(KeyEvent e)
2143       {
2144         updateBackupFilesExampleLabel();
2145         backupfilesCustomOptionsSetEnabled();
2146         backupfilesRevertButtonSetEnabled(true);
2147       }
2148
2149       @Override
2150       public void keyPressed(KeyEvent e)
2151       {
2152       }
2153
2154       // disable use of ':' or '/' or '\'
2155       @Override
2156       public void keyTyped(KeyEvent e)
2157       {
2158         char c = e.getKeyChar();
2159         if (c == ':' || c == '/' || c == '\\')
2160         {
2161           // don't process ':' or '/' or '\'
2162           e.consume();
2163         }
2164       }
2165
2166     });
2167
2168     // digits spinner
2169     suffixDigitsLabel
2170             .setText(MessageManager.getString("label.index_digits"));
2171     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2172     suffixDigitsLabel.setFont(LABEL_FONT);
2173     ChangeListener c = new ChangeListener()
2174     {
2175       @Override
2176       public void stateChanged(ChangeEvent e)
2177       {
2178         backupfilesRevertButtonSetEnabled(true);
2179         updateBackupFilesExampleLabel();
2180       }
2181
2182     };
2183     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2184             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2185
2186     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2187             MessageManager.getString("label.increment_index"));
2188     suffixReverse.addActionListener(new ActionListener()
2189     {
2190       @Override
2191       public void actionPerformed(ActionEvent e)
2192       {
2193         boolean okay = true;
2194         if (warnAboutSuffixReverseChange())
2195         {
2196           // Warning popup
2197           okay = confirmSuffixReverseChange();
2198         }
2199         if (okay)
2200         {
2201           backupfilesRevertButtonSetEnabled(true);
2202           updateBackupFilesExampleLabel();
2203         }
2204         else
2205         {
2206           boolean savedSuffixReverse = BackupFilesPresetEntry
2207                   .getSavedBackupEntry().reverse;
2208           suffixReverse.setSelected(savedSuffixReverse);
2209         }
2210       }
2211     });
2212
2213     GridBagConstraints sgbc = new GridBagConstraints();
2214
2215     // first row (template text box)
2216     sgbc.anchor = GridBagConstraints.WEST;
2217     sgbc.gridx = 0;
2218     sgbc.gridy = 0;
2219     sgbc.gridwidth = 1;
2220     sgbc.gridheight = 1;
2221     sgbc.weightx = 1.0;
2222     sgbc.weighty = 0.0;
2223     sgbc.fill = GridBagConstraints.NONE;
2224     suffixPanel.add(suffixTemplateLabel, sgbc);
2225
2226     sgbc.gridx = 1;
2227     sgbc.fill = GridBagConstraints.HORIZONTAL;
2228     suffixPanel.add(suffixTemplate, sgbc);
2229
2230     // second row (number of digits spinner)
2231     sgbc.gridy = 1;
2232
2233     sgbc.gridx = 0;
2234     sgbc.fill = GridBagConstraints.NONE;
2235     suffixPanel.add(suffixDigitsLabel, sgbc);
2236
2237     sgbc.gridx = 1;
2238     sgbc.fill = GridBagConstraints.HORIZONTAL;
2239     suffixPanel.add(suffixDigitsSpinner, sgbc);
2240
2241     // third row (forward order radio selection)
2242     sgbc.gridx = 0;
2243     sgbc.gridy = 2;
2244     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2245     sgbc.fill = GridBagConstraints.HORIZONTAL;
2246     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2247
2248     // fourth row (reverse order radio selection)
2249     sgbc.gridy = 3;
2250     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2251     return suffixPanel;
2252   }
2253
2254   private boolean confirmSuffixReverseChange()
2255   {
2256     boolean ret = false;
2257     String warningMessage = MessageManager
2258             .getString("label.warning_confirm_change_reverse");
2259     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2260             warningMessage,
2261             MessageManager.getString("label.change_increment_decrement"),
2262             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2263
2264     ret = (confirm == JvOptionPane.YES_OPTION);
2265     return ret;
2266   }
2267
2268   private JPanel initBackupsTabKeepFilesPanel()
2269   {
2270     keepfilesPanel.setBorder(
2271             new TitledBorder(MessageManager.getString("label.keep_files")));
2272     keepfilesPanel.setLayout(new GridBagLayout());
2273
2274     backupfilesKeepAll.setLabels(
2275             MessageManager.getString("label.keep_all_backup_files"),
2276             MessageManager.getString(
2277                     "label.keep_only_this_number_of_backup_files"));
2278     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2279     {
2280       @Override
2281       public void actionPerformed(ActionEvent e)
2282       {
2283         backupfilesRevertButtonSetEnabled(true);
2284         updateBackupFilesExampleLabel();
2285       }
2286     });
2287     backupfilesKeepAll.addActionListener(new ActionListener()
2288     {
2289       @Override
2290       public void actionPerformed(ActionEvent e)
2291       {
2292         backupfilesRevertButtonSetEnabled(true);
2293         keepRollMaxOptionsEnabled();
2294         updateBackupFilesExampleLabel();
2295       }
2296     });
2297
2298     ChangeListener c = new ChangeListener()
2299     {
2300       @Override
2301       public void stateChanged(ChangeEvent e)
2302       {
2303         backupfilesRevertButtonSetEnabled(true);
2304         updateBackupFilesExampleLabel();
2305       }
2306
2307     };
2308     setIntegerSpinner(backupfilesRollMaxSpinner,
2309             BackupFilesPresetEntry.ROLLMAXMIN,
2310             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2311
2312     backupfilesConfirmDelete.setLabels(
2313             MessageManager.getString("label.always_ask"),
2314             MessageManager.getString("label.auto_delete"));
2315     backupfilesConfirmDelete.addActionListener(new ActionListener()
2316     {
2317       @Override
2318       public void actionPerformed(ActionEvent e)
2319       {
2320         backupfilesRevertButtonSetEnabled(true);
2321       }
2322     });
2323     // update the enabled section
2324     keepRollMaxOptionsEnabled();
2325
2326     GridBagConstraints kgbc = new GridBagConstraints();
2327
2328     // first row (template text box)
2329     kgbc.anchor = GridBagConstraints.WEST;
2330     kgbc.gridx = 0;
2331     kgbc.gridy = 0;
2332     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2333     kgbc.gridheight = 1;
2334     kgbc.weightx = 1.0;
2335     kgbc.weighty = 0.0;
2336     kgbc.fill = GridBagConstraints.HORIZONTAL;
2337     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2338
2339     // second row
2340     kgbc.gridy = 1;
2341
2342     kgbc.gridx = 0;
2343     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2344     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2345
2346     kgbc.gridx = 1;
2347     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2348     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2349
2350     // third row (indented)
2351     kgbc.gridy = 2;
2352     kgbc.insets = new Insets(0, 20, 0, 0);
2353
2354     kgbc.gridx = 0;
2355     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2356     kgbc.fill = GridBagConstraints.HORIZONTAL;
2357     kgbc.weightx = 1.0;
2358
2359     JPanel jp = new JPanel();
2360     jp.setLayout(new FlowLayout());
2361     oldBackupFilesLabel
2362             .setText(MessageManager
2363                     .getString("label.autodelete_old_backup_files"));
2364     oldBackupFilesLabel.setFont(LABEL_FONT);
2365     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2366     jp.add(oldBackupFilesLabel);
2367     jp.add(backupfilesConfirmDelete.getTrueButton());
2368     jp.add(backupfilesConfirmDelete.getFalseButton());
2369     keepfilesPanel.add(jp, kgbc);
2370
2371     return keepfilesPanel;
2372   }
2373
2374   protected void updateBackupFilesExampleLabel()
2375   {
2376     int exampleindex = 12;
2377     String base = MessageManager.getString("label.filename") + ".fa";
2378     if (base == null || base.length() == 0)
2379     {
2380       base = "file_name.fa";
2381     }
2382
2383     boolean reverse = suffixReverse.isSelected();
2384     boolean keepAll = backupfilesKeepAll.isSelected();
2385     int rollMax = 4;
2386     String suffix = suffixTemplate.getText();
2387     int digits = 3;
2388
2389     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2390     if (suffix == null || suffix.length() == 0)
2391     {
2392       backupfilesExampleLabel
2393               .setText(MessageManager.getString("label.no_backup_files"));
2394       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2395       return;
2396     }
2397
2398     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2399     rollMax = rollMax < 1 ? 1 : rollMax;
2400
2401     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2402     {
2403       rollMax = 1;
2404     }
2405
2406     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2407     digits = digits < 1 ? 1 : digits;
2408
2409     int lowersurround = 2;
2410     int uppersurround = 0;
2411     StringBuilder exampleSB = new StringBuilder();
2412     boolean firstLine = true;
2413     int lineNumber = 0;
2414     if (reverse)
2415     {
2416
2417       int min = 1;
2418       int max = keepAll ? exampleindex : rollMax;
2419       for (int index = min; index <= max; index++)
2420       {
2421         if (index == min + lowersurround && index < max - uppersurround - 1)
2422         {
2423           exampleSB.append("\n...");
2424           lineNumber++;
2425         }
2426         else if (index > min + lowersurround && index < max - uppersurround)
2427         {
2428           // nothing
2429         }
2430         else
2431         {
2432           if (firstLine)
2433           {
2434             firstLine = false;
2435           }
2436           else
2437           {
2438             exampleSB.append("\n");
2439             lineNumber++;
2440           }
2441           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2442                   base, suffix, digits));
2443           if (min == max)
2444           {
2445             // no extra text needed
2446           }
2447           else if (index == min)
2448           {
2449             String newest = MessageManager.getString("label.braced_newest");
2450             if (newest != null && newest.length() > 0)
2451             {
2452               exampleSB.append(" " + newest);
2453             }
2454           }
2455           else if (index == max)
2456           {
2457             String oldest = MessageManager.getString("label.braced_oldest");
2458             if (oldest != null && oldest.length() > 0)
2459             {
2460               exampleSB.append(" " + oldest);
2461             }
2462           }
2463         }
2464       }
2465     }
2466     else
2467     {
2468
2469       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2470               : exampleindex - rollMax + 1;
2471       int max = exampleindex;
2472
2473       for (int index = min; index <= max; index++)
2474       {
2475
2476         if (index == min + lowersurround && index < max - uppersurround - 1)
2477         {
2478           exampleSB.append("\n...");
2479           lineNumber++;
2480         }
2481         else if (index > min + lowersurround && index < max - uppersurround)
2482         {
2483           // nothing
2484         }
2485         else
2486         {
2487           if (firstLine)
2488           {
2489             firstLine = false;
2490           }
2491           else
2492           {
2493             exampleSB.append("\n");
2494             lineNumber++;
2495           }
2496           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2497                   base, suffix, digits));
2498           if (min == max)
2499           {
2500             // no extra text needed
2501           }
2502           else if (index == min)
2503           {
2504             String oldest = MessageManager.getString("label.braced_oldest");
2505             if (oldest != null && oldest.length() > 0)
2506             {
2507               exampleSB.append(" " + oldest);
2508             }
2509           }
2510           else if (index == max)
2511           {
2512             String newest = MessageManager.getString("label.braced_newest");
2513             if (newest != null && newest.length() > 0)
2514             {
2515               exampleSB.append(" " + newest);
2516             }
2517           }
2518         }
2519       }
2520
2521     }
2522
2523     // add some extra empty lines to pad out the example files box. ugh, please tell
2524     // me how to do this better
2525     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2526     if (remainingLines > 0)
2527     {
2528       for (int i = 0; i < remainingLines; i++)
2529       {
2530         exampleSB.append("\n ");
2531         lineNumber++;
2532       }
2533     }
2534
2535     backupfilesExampleLabel.setText(exampleSB.toString());
2536   }
2537
2538   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2539           boolean useExistingVal, ChangeListener c)
2540   {
2541     int i = def;
2542     if (useExistingVal)
2543     {
2544       try
2545       {
2546         i = ((Integer) s.getValue()).intValue();
2547       } catch (Exception e)
2548       {
2549         Cache.log.error(
2550                 "Exception casting the initial value of s.getValue()");
2551       }
2552     }
2553
2554     setIntegerSpinner(s, min, max, i, c);
2555   }
2556
2557   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2558           ChangeListener c)
2559   {
2560     // integer spinner for number of digits
2561     if (def > max)
2562     {
2563       max = def;
2564     }
2565     if (def < min)
2566     {
2567       def = min;
2568     }
2569     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2570     s.setModel(sModel);
2571
2572     s.addChangeListener(c);
2573
2574   }
2575
2576   protected static int getSpinnerInt(JSpinner s, int def)
2577   {
2578     int i = def;
2579     try
2580     {
2581       s.commitEdit();
2582       i = (Integer) s.getValue();
2583     } catch (Exception e)
2584     {
2585       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2586     }
2587     return i;
2588   }
2589
2590   private void keepRollMaxOptionsEnabled()
2591   {
2592     boolean enabled = backupfilesKeepAll.isEnabled()
2593             && !backupfilesKeepAll.isSelected();
2594     oldBackupFilesLabel.setEnabled(enabled);
2595     backupfilesRollMaxSpinner.setEnabled(enabled);
2596     backupfilesConfirmDelete.setEnabled(enabled);
2597   }
2598
2599   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2600   {
2601     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2602             && customiseCheckbox.isSelected()
2603             && suffixTemplate.getText()
2604                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2605     keepfilesPanel.setEnabled(enabled);
2606     backupfilesKeepAll.setEnabled(enabled);
2607     oldBackupFilesLabel.setEnabled(enabled);
2608     keepRollMaxOptionsEnabled();
2609   }
2610
2611   private void backupfilesSuffixTemplateDigitsSetEnabled()
2612   {
2613     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2614             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2615     suffixDigitsLabel.setEnabled(enabled);
2616     suffixDigitsSpinner.setEnabled(enabled);
2617     suffixReverse.setEnabled(enabled);
2618   }
2619
2620   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2621   {
2622     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2623             && customiseCheckbox.isSelected();
2624     suffixPanel.setEnabled(enabled);
2625     suffixTemplateLabel.setEnabled(enabled);
2626     suffixTemplate.setEnabled(enabled);
2627     backupfilesSuffixTemplateDigitsSetEnabled();
2628   }
2629
2630   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2631   {
2632     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2633             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2634     revertButton.setEnabled(enabled);
2635   }
2636
2637   private boolean backupfilesCustomChanged()
2638   {
2639     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2640             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2641     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2642     return !custom.equals(current);
2643   }
2644
2645   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2646   {
2647     String suffix = suffixTemplate.getText();
2648     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2649     boolean reverse = suffixReverse.isSelected();
2650     boolean keepAll = backupfilesKeepAll.isSelected();
2651     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
2652     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
2653
2654     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
2655             reverse, keepAll, rollMax, confirmDelete);
2656
2657     return bfpe;
2658   }
2659
2660   protected void backupfilesCustomOptionsSetEnabled()
2661   {
2662     boolean enabled = customiseCheckbox.isSelected();
2663
2664     backupfilesRevertButtonSetEnabled(enabled);
2665     backupfilesSuffixTemplateSetEnabled(enabled);
2666     backupfilesKeepAllSetEnabled(enabled);
2667   }
2668
2669   private void backupfilesSummarySetEnabled()
2670   {
2671     boolean enabled = enableBackupFiles.isSelected();
2672     backupfilesExampleLabel.setEnabled(enabled);
2673     exampleFilesPanel.setEnabled(enabled);
2674   }
2675
2676   private void backupfilesPresetsSetEnabled()
2677   {
2678     boolean enabled = enableBackupFiles.isSelected();
2679     presetsPanel.setEnabled(enabled);
2680     presetsComboLabel.setEnabled(enabled);
2681     backupfilesPresetsCombo.setEnabled(enabled);
2682     customiseCheckbox.setEnabled(enabled);
2683     revertButton.setEnabled(enabled);
2684   }
2685
2686   protected void backupsOptionsSetEnabled()
2687   {
2688     backupfilesPresetsSetEnabled();
2689     backupfilesSummarySetEnabled();
2690     backupfilesCustomOptionsSetEnabled();
2691   }
2692
2693   protected void backupsSetOptions(String suffix, int digits,
2694           boolean reverse, boolean keepAll, int rollMax,
2695           boolean confirmDelete)
2696   {
2697     suffixTemplate.setText(suffix);
2698     suffixDigitsSpinner.setValue(digits);
2699     suffixReverse.setSelected(reverse);
2700     backupfilesKeepAll.setSelected(keepAll);
2701     backupfilesRollMaxSpinner.setValue(rollMax);
2702     backupfilesConfirmDelete.setSelected(confirmDelete);
2703   }
2704
2705   protected void backupsSetOptions(BackupFilesPresetEntry p)
2706   {
2707     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
2708             p.confirmDelete);
2709   }
2710
2711   protected void autoIdWidth_actionPerformed()
2712   {
2713     // TODO Auto-generated method stub
2714
2715   }
2716
2717   protected void userIdWidth_actionPerformed()
2718   {
2719     // TODO Auto-generated method stub
2720
2721   }
2722
2723   protected void maxColour_actionPerformed(JPanel panel)
2724   {
2725   }
2726
2727   protected void minColour_actionPerformed(JPanel panel)
2728   {
2729   }
2730
2731   protected void gapColour_actionPerformed(JPanel panel)
2732   {
2733   }
2734
2735   protected void hiddenColour_actionPerformed(JPanel panel)
2736   {
2737   }
2738
2739   protected void showunconserved_actionPerformed(ActionEvent e)
2740   {
2741     // TODO Auto-generated method stub
2742
2743   }
2744
2745   protected void useLegacyGaps_actionPerformed(ActionEvent e)
2746   {
2747   }
2748
2749   protected void resetOvDefaults_actionPerformed(ActionEvent e)
2750   {
2751   }
2752
2753   /**
2754    * DOCUMENT ME!
2755    *
2756    * @param e
2757    *          DOCUMENT ME!
2758    */
2759   public void ok_actionPerformed(ActionEvent e)
2760   {
2761   }
2762
2763   /**
2764    * DOCUMENT ME!
2765    *
2766    * @param e
2767    *          DOCUMENT ME!
2768    */
2769   public void cancel_actionPerformed(ActionEvent e)
2770   {
2771   }
2772
2773   /**
2774    * DOCUMENT ME!
2775    *
2776    * @param e
2777    *          DOCUMENT ME!
2778    */
2779   public void annotations_actionPerformed(ActionEvent e)
2780   {
2781   }
2782
2783   /**
2784    * DOCUMENT ME!
2785    */
2786   public void startupFileTextfield_mouseClicked()
2787   {
2788   }
2789
2790   public void newLink_actionPerformed(ActionEvent e)
2791   {
2792
2793   }
2794
2795   public void editLink_actionPerformed(ActionEvent e)
2796   {
2797
2798   }
2799
2800   public void deleteLink_actionPerformed(ActionEvent e)
2801   {
2802
2803   }
2804
2805   public void defaultBrowser_mouseClicked(MouseEvent e)
2806   {
2807
2808   }
2809
2810   public void linkURLList_keyTyped(KeyEvent e)
2811   {
2812
2813   }
2814
2815   public void useProxy_actionPerformed()
2816   {
2817     boolean enabled = useProxy.isSelected();
2818     portLabel.setEnabled(enabled);
2819     serverLabel.setEnabled(enabled);
2820     proxyServerTB.setEnabled(enabled);
2821     proxyPortTB.setEnabled(enabled);
2822   }
2823
2824   /**
2825    * Customer renderer for JTable: supports column of radio buttons
2826    */
2827   public class RadioButtonRenderer extends JRadioButton
2828           implements TableCellRenderer
2829   {
2830     public RadioButtonRenderer()
2831     {
2832       setHorizontalAlignment(CENTER);
2833       setToolTipText(MessageManager.getString("label.urltooltip"));
2834     }
2835
2836     @Override
2837     public Component getTableCellRendererComponent(JTable table,
2838             Object value, boolean isSelected, boolean hasFocus, int row,
2839             int column)
2840     {
2841       setSelected((boolean) value);
2842
2843       // set colours to match rest of table
2844       if (isSelected)
2845       {
2846         setBackground(table.getSelectionBackground());
2847         setForeground(table.getSelectionForeground());
2848       }
2849       else
2850       {
2851         setBackground(table.getBackground());
2852         setForeground(table.getForeground());
2853       }
2854       return this;
2855     }
2856   }
2857
2858   /**
2859    * Customer cell editor for JTable: supports column of radio buttons in
2860    * conjunction with renderer
2861    */
2862   public class RadioButtonEditor extends AbstractCellEditor
2863           implements TableCellEditor
2864   {
2865     private JRadioButton button = new JRadioButton();
2866
2867     public RadioButtonEditor()
2868     {
2869       button.setHorizontalAlignment(SwingConstants.CENTER);
2870       this.button.addActionListener(new ActionListener()
2871       {
2872         @Override
2873         public void actionPerformed(ActionEvent e)
2874         {
2875           fireEditingStopped();
2876         }
2877       });
2878     }
2879
2880     @Override
2881     public Component getTableCellEditorComponent(JTable table, Object value,
2882             boolean isSelected, int row, int column)
2883     {
2884       button.setSelected((boolean) value);
2885       return button;
2886     }
2887
2888     @Override
2889     public Object getCellEditorValue()
2890     {
2891       return button.isSelected();
2892     }
2893
2894   }
2895 }
2896