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