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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.FlowLayout;
  28 import java.awt.Font;
  29 import java.awt.GridBagConstraints;
  30 import java.awt.GridBagLayout;
  31 import java.awt.GridLayout;
  32 import java.awt.Insets;
  33 import java.awt.Rectangle;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.FocusEvent;
  37 import java.awt.event.KeyEvent;
  38 import java.awt.event.KeyListener;
  39 import java.awt.event.MouseAdapter;
  40 import java.awt.event.MouseEvent;
  41 import java.util.Arrays;
  42 import java.util.List;
  43
  44 import javax.swing.AbstractCellEditor;
  45 import javax.swing.BorderFactory;
  46 import javax.swing.ButtonGroup;
  47 import javax.swing.DefaultListCellRenderer;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFileChooser;
  52 import javax.swing.JLabel;
  53 import javax.swing.JPanel;
  54 import javax.swing.JPasswordField;
  55 import javax.swing.JRadioButton;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSpinner;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.JTable;
  60 import javax.swing.JTextArea;
  61 import javax.swing.JTextField;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.SpinnerModel;
  64 import javax.swing.SpinnerNumberModel;
  65 import javax.swing.SwingConstants;
  66 import javax.swing.border.Border;
  67 import javax.swing.border.EmptyBorder;
  68 import javax.swing.border.EtchedBorder;
  69 import javax.swing.border.TitledBorder;
  70 import javax.swing.event.ChangeEvent;
  71 import javax.swing.event.ChangeListener;
  72 import javax.swing.table.TableCellEditor;
  73 import javax.swing.table.TableCellRenderer;
  74
  75 import jalview.bin.Cache;
  76 import jalview.fts.core.FTSDataColumnPreferences;
  77 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  78 import jalview.fts.service.pdb.PDBFTSRestClient;
  79 import jalview.gui.Desktop;
  80 import jalview.gui.JalviewBooleanRadioButtons;
  81 import jalview.gui.JvOptionPane;
  82 import jalview.gui.JvSwingUtils;
  83 import jalview.gui.StructureViewer.ViewerType;
  84 import jalview.io.BackupFilenameParts;
  85 import jalview.io.BackupFiles;
  86 import jalview.io.BackupFilesPresetEntry;
  87 import jalview.io.IntKeyStringValueEntry;
  88 import jalview.util.MessageManager;
  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 httpLabel = new JLabel();
 231
 232   protected JLabel httpsLabel = new JLabel();
 233
 234   protected JLabel portLabel = new JLabel();
 235
 236   protected JLabel serverLabel = new JLabel();
 237
 238   protected JLabel portLabel2 = new JLabel();
 239
 240   protected JLabel serverLabel2 = new JLabel();
 241
 242   protected JLabel proxyAuthUsernameLabel = new JLabel();
 243
 244   protected JLabel proxyAuthPasswordLabel = new JLabel();
 245
 246   protected JTextField proxyServerHttpTB = new JTextField();
 247
 248   protected JTextField proxyPortHttpTB = new JTextField();
 249
 250   protected JTextField proxyServerHttpsTB = new JTextField();
 251
 252   protected JTextField proxyPortHttpsTB = new JTextField();
 253
 254   protected JCheckBox proxyAuth = new JCheckBox();
 255
 256   protected JTextField proxyAuthUsernameTB = new JTextField();
 257
 258   protected JTextField proxyAuthPasswordTB = new JPasswordField();
 259
 260   protected JTextField defaultBrowser = new JTextField();
 261
 262   protected ButtonGroup proxyType = new ButtonGroup();
 263
 264   protected JRadioButton noProxy = new JRadioButton();
 265
 266   protected JRadioButton systemProxy = new JRadioButton();
 267
 268   protected JRadioButton customProxy = new JRadioButton();
 269
 270   protected JCheckBox usagestats = new JCheckBox();
 271
 272   protected JCheckBox questionnaire = new JCheckBox();
 273
 274   protected JCheckBox versioncheck = new JCheckBox();
 275
 276   /*
 277    * Output tab components
 278    */
 279   protected JComboBox<Object> epsRendering = new JComboBox<>();
 280
 281   protected JLabel userIdWidthlabel = new JLabel();
 282
 283   protected JCheckBox autoIdWidth = new JCheckBox();
 284
 285   protected JTextField userIdWidth = new JTextField();
 286
 287   protected JCheckBox blcjv = new JCheckBox();
 288
 289   protected JCheckBox pileupjv = new JCheckBox();
 290
 291   protected JCheckBox clustaljv = new JCheckBox();
 292
 293   protected JCheckBox msfjv = new JCheckBox();
 294
 295   protected JCheckBox fastajv = new JCheckBox();
 296
 297   protected JCheckBox pfamjv = new JCheckBox();
 298
 299   protected JCheckBox pirjv = new JCheckBox();
 300
 301   protected JCheckBox modellerOutput = new JCheckBox();
 302
 303   protected JCheckBox embbedBioJSON = new JCheckBox();
 304
 305   /*
 306    * Editing tab components
 307    */
 308   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 309
 310   protected JCheckBox padGaps = new JCheckBox();
 311
 312   protected JCheckBox sortByTree = new JCheckBox();
 313
 314   /*
 315    * Web Services tab
 316    */
 317   protected JPanel wsTab = new JPanel();
 318
 319   /*
 320    * Backups tab components
 321    * a lot of these are member variables instead of local variables only so that they
 322    * can be enabled/disabled easily in one go
 323    */
 324
 325   protected JCheckBox enableBackupFiles = new JCheckBox();
 326
 327   protected JPanel presetsPanel = new JPanel();
 328
 329   protected JLabel presetsComboLabel = new JLabel();
 330
 331   protected JCheckBox customiseCheckbox = new JCheckBox();
 332
 333   protected JButton revertButton = new JButton();
 334
 335   protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 336
 337   private int backupfilesPresetsComboLastSelected = 0;
 338
 339   protected JPanel suffixPanel = new JPanel();
 340
 341   protected JPanel keepfilesPanel = new JPanel();
 342
 343   protected JPanel exampleFilesPanel = new JPanel();
 344
 345   protected JTextField suffixTemplate = new JTextField(null, 8);
 346
 347   protected JLabel suffixTemplateLabel = new JLabel();
 348
 349   protected JLabel suffixDigitsLabel = new JLabel();
 350
 351   protected JSpinner suffixDigitsSpinner = new JSpinner();
 352
 353   protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
 354
 355   protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
 356
 357   public JSpinner backupfilesRollMaxSpinner = new JSpinner();
 358
 359   protected JLabel oldBackupFilesLabel = new JLabel();
 360
 361   protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
 362
 363   protected JTextArea backupfilesExampleLabel = new JTextArea();
 364
 365   /**
 366    * Creates a new GPreferences object.
 367    */
 368   public GPreferences()
 369   {
 370     try
 371     {
 372       jbInit();
 373     } catch (Exception ex)
 374     {
 375       ex.printStackTrace();
 376     }
 377   }
 378
 379   /**
 380    * Construct the panel and its tabbed sub-panels.
 381    *
 382    * @throws Exception
 383    */
 384   private void jbInit() throws Exception
 385   {
 386     final JTabbedPane tabbedPane = new JTabbedPane();
 387     this.setLayout(new BorderLayout());
 388     JPanel okCancelPanel = initOkCancelPanel();
 389     this.add(tabbedPane, BorderLayout.CENTER);
 390     this.add(okCancelPanel, BorderLayout.SOUTH);
 391
 392     tabbedPane.add(initVisualTab(),
 393             MessageManager.getString("label.visual"));
 394
 395     tabbedPane.add(initColoursTab(),
 396             MessageManager.getString("label.colours"));
 397
 398     tabbedPane.add(initOverviewTab(),
 399             MessageManager.getString("label.overview"));
 400
 401     tabbedPane.add(initStructureTab(),
 402             MessageManager.getString("label.structure"));
 403
 404     tabbedPane.add(initConnectionsTab(),
 405             MessageManager.getString("label.connections"));
 406
 407     tabbedPane.add(initBackupsTab(),
 408             MessageManager.getString("label.backups"));
 409
 410     tabbedPane.add(initLinksTab(),
 411             MessageManager.getString("label.urllinks"));
 412
 413     tabbedPane.add(initOutputTab(),
 414             MessageManager.getString("label.output"));
 415
 416     tabbedPane.add(initEditingTab(),
 417             MessageManager.getString("label.editing"));
 418
 419     /*
 420      * See WsPreferences for the real work of configuring this tab.
 421      */
 422     wsTab.setLayout(new BorderLayout());
 423     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 424
 425     /*
 426      * Handler to validate a tab before leaving it - currently only for
 427      * Structure.
 428      */
 429     tabbedPane.addChangeListener(new ChangeListener()
 430     {
 431       private Component lastTab;
 432
 433       @Override
 434       public void stateChanged(ChangeEvent e)
 435       {
 436         if (lastTab == structureTab
 437                 && tabbedPane.getSelectedComponent() != structureTab)
 438         {
 439           if (!validateStructure())
 440           {
 441             tabbedPane.setSelectedComponent(structureTab);
 442             return;
 443           }
 444         }
 445         lastTab = tabbedPane.getSelectedComponent();
 446       }
 447
 448     });
 449   }
 450
 451   /**
 452    * Initialises the Editing tabbed panel.
 453    *
 454    * @return
 455    */
 456   private JPanel initEditingTab()
 457   {
 458     JPanel editingTab = new JPanel();
 459     editingTab.setLayout(null);
 460     autoCalculateConsCheck.setFont(LABEL_FONT);
 461     autoCalculateConsCheck.setText(
 462             MessageManager.getString("label.autocalculate_consensus"));
 463     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 464     padGaps.setFont(LABEL_FONT);
 465     padGaps.setText(
 466             MessageManager.getString("label.pad_gaps_when_editing"));
 467     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 468     sortByTree.setFont(LABEL_FONT);
 469     sortByTree
 470             .setText(MessageManager.getString("label.sort_with_new_tree"));
 471     sortByTree.setToolTipText(MessageManager.getString(
 472             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 473     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 474     editingTab.add(autoCalculateConsCheck);
 475     editingTab.add(padGaps);
 476     editingTab.add(sortByTree);
 477     return editingTab;
 478   }
 479
 480   /**
 481    * Initialises the Output tabbed panel.
 482    *
 483    * @return
 484    */
 485   private JPanel initOutputTab()
 486   {
 487     JPanel outputTab = new JPanel();
 488     outputTab.setLayout(null);
 489     JLabel epsLabel = new JLabel();
 490     epsLabel.setFont(LABEL_FONT);
 491     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 492     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 493     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 494     epsRendering.setFont(LABEL_FONT);
 495     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 496     JLabel jLabel1 = new JLabel();
 497     jLabel1.setFont(LABEL_FONT);
 498     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 499     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 500     jLabel1.setFont(LABEL_FONT);
 501     fastajv.setFont(LABEL_FONT);
 502     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 503     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 504     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 505     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 506     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 507     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 508     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 509     msfjv.setFont(LABEL_FONT);
 510     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 511     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 512     JPanel jPanel11 = new JPanel();
 513     jPanel11.setFont(LABEL_FONT);
 514     TitledBorder titledBorder2 = new TitledBorder(
 515             MessageManager.getString("label.file_output"));
 516     jPanel11.setBorder(titledBorder2);
 517     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 518     GridLayout gridLayout3 = new GridLayout();
 519     jPanel11.setLayout(gridLayout3);
 520     gridLayout3.setRows(8);
 521     blcjv.setFont(LABEL_FONT);
 522     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 523     clustaljv.setFont(LABEL_FONT);
 524     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 525     pfamjv.setFont(LABEL_FONT);
 526     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 527     pileupjv.setFont(LABEL_FONT);
 528     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 529     pirjv.setFont(LABEL_FONT);
 530     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 531     autoIdWidth.setFont(LABEL_FONT);
 532     autoIdWidth.setText(
 533             MessageManager.getString("label.automatically_set_id_width"));
 534     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 535             .getString("label.adjusts_width_generated_eps_png")));
 536     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 537     autoIdWidth.addActionListener(new ActionListener()
 538     {
 539
 540       @Override
 541       public void actionPerformed(ActionEvent e)
 542       {
 543         autoIdWidth_actionPerformed();
 544       }
 545     });
 546     userIdWidthlabel.setFont(LABEL_FONT);
 547     userIdWidthlabel.setText(
 548             MessageManager.getString("label.figure_id_column_width"));
 549     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 550             .getString("label.manually_specify_width_left_column")));
 551     userIdWidthlabel.setToolTipText(
 552             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 553                     "label.manually_specify_width_left_column")));
 554     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 555     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 556     userIdWidth.setText("");
 557     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 558     userIdWidth.addActionListener(new ActionListener()
 559     {
 560
 561       @Override
 562       public void actionPerformed(ActionEvent e)
 563       {
 564         userIdWidth_actionPerformed();
 565       }
 566     });
 567     modellerOutput.setFont(LABEL_FONT);
 568     modellerOutput
 569             .setText(MessageManager.getString("label.use_modeller_output"));
 570     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 571     embbedBioJSON.setFont(LABEL_FONT);
 572     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 573     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 574
 575     jPanel11.add(jLabel1);
 576     jPanel11.add(blcjv);
 577     jPanel11.add(clustaljv);
 578     jPanel11.add(fastajv);
 579     jPanel11.add(msfjv);
 580     jPanel11.add(pfamjv);
 581     jPanel11.add(pileupjv);
 582     jPanel11.add(pirjv);
 583     outputTab.add(autoIdWidth);
 584     outputTab.add(userIdWidth);
 585     outputTab.add(userIdWidthlabel);
 586     outputTab.add(modellerOutput);
 587     outputTab.add(embbedBioJSON);
 588     outputTab.add(epsLabel);
 589     outputTab.add(epsRendering);
 590     outputTab.add(jPanel11);
 591     return outputTab;
 592   }
 593
 594   /**
 595    * Initialises the Connections tabbed panel.
 596    *
 597    * @return
 598    */
 599   private JPanel initConnectionsTab()
 600   {
 601     JPanel connectTab = new JPanel();
 602     connectTab.setLayout(new GridBagLayout());
 603
 604     // Label for browser text box
 605     JLabel browserLabel = new JLabel();
 606     browserLabel.setFont(LABEL_FONT);
 607     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 608     browserLabel.setText(
 609             MessageManager.getString("label.default_browser_unix"));
 610     defaultBrowser.setFont(LABEL_FONT);
 611     defaultBrowser.setText("");
 612     final String tooltip = JvSwingUtils.wrapTooltip(true,
 613             MessageManager.getString("label.double_click_to_browse"));
 614     defaultBrowser.setToolTipText(tooltip);
 615     defaultBrowser.addMouseListener(new MouseAdapter()
 616     {
 617       @Override
 618       public void mouseClicked(MouseEvent e)
 619       {
 620         if (e.getClickCount() > 1)
 621         {
 622           defaultBrowser_mouseClicked(e);
 623         }
 624       }
 625     });
 626
 627     JPanel proxyPanel = initConnTabProxyPanel();
 628     initConnTabCheckboxes();
 629
 630     // Add default Browser text box
 631     connectTab.add(browserLabel,
 632             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 633                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 634                     new Insets(10, 0, 5, 5), 5, 1));
 635     defaultBrowser.setFont(LABEL_FONT);
 636     defaultBrowser.setText("");
 637
 638     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 639             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 640             new Insets(10, 0, 5, 10), 30, 1));
 641
 642     // Add proxy server panel
 643     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 644             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 645             new Insets(10, 0, 5, 12), 4, 10));
 646
 647     // Add usage stats, version check and questionnaire checkboxes
 648     connectTab.add(usagestats,
 649             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 650                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 651                     new Insets(0, 2, 5, 5), 70, 1));
 652     connectTab.add(questionnaire,
 653             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 654                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 655                     new Insets(0, 2, 5, 10), 70, 1));
 656     connectTab.add(versioncheck,
 657             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 658                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 659                     new Insets(0, 2, 5, 5), 70, 1));
 660
 661     versioncheck.setVisible(false);
 662
 663     // Add padding so the panel doesn't look ridiculous
 664     JPanel spacePanel = new JPanel();
 665     connectTab.add(spacePanel,
 666             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 667                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 668                     new Insets(0, 0, 0, 5), 70, 1));
 669
 670     return connectTab;
 671   }
 672
 673   /**
 674    * Initialises the Links tabbed panel.
 675    *
 676    * @return
 677    */
 678   private JPanel initLinksTab()
 679   {
 680     JPanel linkTab = new JPanel();
 681     linkTab.setLayout(new GridBagLayout());
 682
 683     // Set up table for Url links
 684     linkUrlTable.getTableHeader().setReorderingAllowed(false);
 685     linkUrlTable.setFillsViewportHeight(true);
 686     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 687     linkUrlTable.setAutoCreateRowSorter(true);
 688     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 689
 690     // adjust row height so radio buttons actually fit
 691     // don't do this in the renderer, it causes the awt thread to activate
 692     // constantly
 693     JRadioButton temp = new JRadioButton();
 694     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 695
 696     // Table in scrollpane so that the table is given a scrollbar
 697     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 698     linkScrollPane.setBorder(null);
 699
 700     // Panel for links functionality
 701     JPanel linkPanel = new JPanel(new GridBagLayout());
 702     linkPanel.setBorder(new TitledBorder(
 703             MessageManager.getString("label.url_linkfrom_sequence_id")));
 704
 705     // Put the Url links panel together
 706
 707     // Buttons go at top right, resizing only resizes the blank space vertically
 708     JPanel buttonPanel = initLinkTabUrlButtons();
 709     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 710     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 711     linkConstraints1.gridx = 0;
 712     linkConstraints1.gridy = 0;
 713     linkConstraints1.weightx = 1.0;
 714     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 715     linkTab.add(buttonPanel, linkConstraints1);
 716
 717     // Links table goes at top left, resizing resizes the table
 718     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 719     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 720     linkConstraints2.gridx = 0;
 721     linkConstraints2.gridy = 1;
 722     linkConstraints2.weightx = 1.0;
 723     linkConstraints2.weighty = 1.0;
 724     linkConstraints2.fill = GridBagConstraints.BOTH;
 725     linkTab.add(linkScrollPane, linkConstraints2);
 726
 727     // Filter box and buttons goes at bottom left, resizing resizes the text box
 728     JPanel filterPanel = initLinkTabFilterPanel();
 729     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 730     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 731     linkConstraints3.gridx = 0;
 732     linkConstraints3.gridy = 2;
 733     linkConstraints3.weightx = 1.0;
 734     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 735     linkTab.add(filterPanel, linkConstraints3);
 736
 737     return linkTab;
 738   }
 739
 740   private JPanel initLinkTabFilterPanel()
 741   {
 742     // Filter textbox and reset button
 743     JLabel filterLabel = new JLabel(
 744             MessageManager.getString("label.filter"));
 745     filterLabel.setFont(LABEL_FONT);
 746     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 747     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 748
 749     filterTB.setFont(LABEL_FONT);
 750     filterTB.setText("");
 751
 752     doReset.setText(MessageManager.getString("action.showall"));
 753     userOnly.setText(MessageManager.getString("action.customfilter"));
 754
 755     // Panel for filter functionality
 756     JPanel filterPanel = new JPanel(new GridBagLayout());
 757     filterPanel.setBorder(new TitledBorder("Filter"));
 758     GridBagConstraints gbc = new GridBagConstraints();
 759     gbc.gridx = 0;
 760     gbc.gridy = 0;
 761     gbc.fill = GridBagConstraints.NONE;
 762     gbc.anchor = GridBagConstraints.WEST;
 763
 764     filterPanel.add(filterLabel, gbc);
 765
 766     GridBagConstraints gbc1 = new GridBagConstraints();
 767     gbc1.gridx = 1;
 768     gbc1.gridwidth = 2;
 769     gbc1.fill = GridBagConstraints.HORIZONTAL;
 770     gbc1.anchor = GridBagConstraints.WEST;
 771     gbc1.weightx = 1.0;
 772     filterPanel.add(filterTB, gbc1);
 773
 774     GridBagConstraints gbc2 = new GridBagConstraints();
 775     gbc2.gridx = 3;
 776     gbc2.fill = GridBagConstraints.NONE;
 777     gbc2.anchor = GridBagConstraints.WEST;
 778     filterPanel.add(doReset, gbc2);
 779
 780     GridBagConstraints gbc3 = new GridBagConstraints();
 781     gbc3.gridx = 4;
 782     gbc3.fill = GridBagConstraints.NONE;
 783     gbc3.anchor = GridBagConstraints.WEST;
 784     filterPanel.add(userOnly, gbc3);
 785
 786     return filterPanel;
 787   }
 788
 789   private JPanel initLinkTabUrlButtons()
 790   {
 791     // Buttons for new / edit / delete Url links
 792     JButton newLink = new JButton();
 793     newLink.setText(MessageManager.getString("action.new"));
 794
 795     editLink.setText(MessageManager.getString("action.edit"));
 796
 797     deleteLink.setText(MessageManager.getString("action.delete"));
 798
 799     // no current selection, so initially disable delete/edit buttons
 800     editLink.setEnabled(false);
 801     deleteLink.setEnabled(false);
 802
 803     newLink.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       @Override
 806       public void actionPerformed(ActionEvent e)
 807       {
 808         newLink_actionPerformed(e);
 809       }
 810     });
 811
 812     editLink.setText(MessageManager.getString("action.edit"));
 813     editLink.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       @Override
 816       public void actionPerformed(ActionEvent e)
 817       {
 818         editLink_actionPerformed(e);
 819       }
 820     });
 821
 822     deleteLink.setText(MessageManager.getString("action.delete"));
 823     deleteLink.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       @Override
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         deleteLink_actionPerformed(e);
 829       }
 830     });
 831
 832     JPanel buttonPanel = new JPanel(new GridBagLayout());
 833     buttonPanel.setBorder(new TitledBorder("Edit links"));
 834     GridBagConstraints gbc = new GridBagConstraints();
 835     gbc.gridx = 0;
 836     gbc.gridy = 0;
 837     gbc.fill = GridBagConstraints.NONE;
 838     buttonPanel.add(newLink, gbc);
 839
 840     GridBagConstraints gbc1 = new GridBagConstraints();
 841     gbc1.gridx = 1;
 842     gbc1.gridy = 0;
 843     gbc1.fill = GridBagConstraints.NONE;
 844     buttonPanel.add(editLink, gbc1);
 845
 846     GridBagConstraints gbc2 = new GridBagConstraints();
 847     gbc2.gridx = 2;
 848     gbc2.gridy = 0;
 849     gbc2.fill = GridBagConstraints.NONE;
 850     buttonPanel.add(deleteLink, gbc2);
 851
 852     GridBagConstraints gbc3 = new GridBagConstraints();
 853     gbc3.gridx = 3;
 854     gbc3.gridy = 0;
 855     gbc3.fill = GridBagConstraints.HORIZONTAL;
 856     gbc3.weightx = 1.0;
 857     JPanel spacePanel = new JPanel();
 858     spacePanel.setBorder(null);
 859     buttonPanel.add(spacePanel, gbc3);
 860
 861     return buttonPanel;
 862   }
 863
 864   /**
 865    * Initialises the proxy server panel in the Connections tab
 866    *
 867    * @return the proxy server panel
 868    */
 869   private JPanel initConnTabProxyPanel()
 870   {
 871     // Label for server text box
 872     serverLabel.setText(MessageManager.getString("label.host") + ": ");
 873     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 874     serverLabel.setFont(LABEL_FONT);
 875     serverLabel2.setText(MessageManager.getString("label.host") + ": ");
 876     serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
 877     serverLabel2.setFont(LABEL_FONT);
 878
 879     // Proxy server and port text boxes
 880     proxyServerHttpTB.setFont(LABEL_FONT);
 881     proxyServerHttpTB.setColumns(40);
 882     proxyPortHttpTB.setFont(LABEL_FONT);
 883     proxyPortHttpTB.setColumns(4);
 884     proxyServerHttpsTB.setFont(LABEL_FONT);
 885     proxyServerHttpsTB.setColumns(40);
 886     proxyPortHttpsTB.setFont(LABEL_FONT);
 887     proxyPortHttpsTB.setColumns(4);
 888     proxyAuthUsernameTB.setFont(LABEL_FONT);
 889     proxyAuthUsernameTB.setColumns(30);
 890     proxyAuthPasswordTB.setFont(LABEL_FONT);
 891     proxyAuthPasswordTB.setColumns(30);
 892
 893     // Label for Port text box
 894     portLabel.setFont(LABEL_FONT);
 895     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 896     portLabel.setText(MessageManager.getString("label.port") + ": ");
 897     portLabel2.setFont(LABEL_FONT);
 898     portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
 899     portLabel2.setText(MessageManager.getString("label.port") + ": ");
 900
 901     httpLabel.setText("HTTP");
 902     httpLabel.setFont(LABEL_FONT_BOLD);
 903     httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
 904     httpsLabel.setText("HTTPS");
 905     httpsLabel.setFont(LABEL_FONT_BOLD);
 906     httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
 907
 908     proxyAuthUsernameLabel
 909             .setText(MessageManager.getString("label.username") + ": ");
 910     proxyAuthUsernameLabel.setFont(LABEL_FONT);
 911     proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 912     proxyAuthPasswordLabel
 913             .setText(MessageManager.getString("label.password") + ": ");
 914     proxyAuthPasswordLabel.setFont(LABEL_FONT);
 915     proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 916
 917     // Proxy type radio buttons
 918     noProxy.setFont(LABEL_FONT);
 919     noProxy.setHorizontalAlignment(SwingConstants.LEFT);
 920     noProxy.setText(MessageManager.getString("label.no_proxy"));
 921     systemProxy.setFont(LABEL_FONT);
 922     systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
 923     systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
 924             displayHostPort(Cache.startupProxyProperties[0],
 925                     Cache.startupProxyProperties[1]),
 926             displayHostPort(Cache.startupProxyProperties[2],
 927                     Cache.startupProxyProperties[3])));
 928     customProxy.setFont(LABEL_FONT);
 929     customProxy.setHorizontalAlignment(SwingConstants.LEFT);
 930     customProxy.setText(
 931             MessageManager.getString("label.use_proxy_server") + ":");
 932     ActionListener al = new ActionListener()
 933     {
 934       @Override
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         proxyType_actionPerformed();
 938       }
 939     };
 940     noProxy.addActionListener(al);
 941     systemProxy.addActionListener(al);
 942     customProxy.addActionListener(al);
 943     proxyType.add(noProxy);
 944     proxyType.add(systemProxy);
 945     proxyType.add(customProxy);
 946
 947     proxyAuth.setFont(LABEL_FONT);
 948     proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
 949     proxyAuth.setText(MessageManager.getString("label.auth_required"));
 950     proxyAuth.addActionListener(new ActionListener()
 951     {
 952       @Override
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         proxyAuth_actionPerformed();
 956       }
 957     });
 958
 959     setCustomProxyEnabled();
 960     setProxyAuthEnabled();
 961
 962     // Make proxy server panel
 963     JPanel proxyPanel = new JPanel();
 964     TitledBorder titledBorder1 = new TitledBorder(
 965             MessageManager.getString("label.proxy_servers"));
 966     proxyPanel.setBorder(titledBorder1);
 967     GridBagConstraints gbc = new GridBagConstraints();
 968     proxyPanel.setLayout(new GridBagLayout());
 969
 970     gbc.gridx = 0;
 971     gbc.gridy = 0;
 972     gbc.weightx = 1.0;
 973     gbc.gridheight = 1;
 974     gbc.anchor = GridBagConstraints.WEST;
 975     gbc.fill = GridBagConstraints.BOTH;
 976
 977     gbc.gridwidth = 5;
 978     proxyPanel.add(noProxy, gbc);
 979
 980     gbc.gridy++;
 981     proxyPanel.add(systemProxy, gbc);
 982
 983     gbc.gridy++;
 984     proxyPanel.add(customProxy, gbc);
 985
 986     gbc.gridwidth = 1;
 987     gbc.gridy++;
 988     gbc.gridx = 0;
 989     gbc.weightx = 0.1;
 990     proxyPanel.add(httpLabel, gbc);
 991
 992     gbc.gridx++;
 993     gbc.anchor = GridBagConstraints.EAST;
 994     gbc.weightx = 0.15;
 995     proxyPanel.add(serverLabel, gbc);
 996
 997     gbc.gridx++;
 998     gbc.anchor = GridBagConstraints.WEST;
 999     gbc.weightx = 0.5;
1000     proxyPanel.add(proxyServerHttpTB, gbc);
1001
1002     gbc.gridx++;
1003     gbc.anchor = GridBagConstraints.EAST;
1004     gbc.weightx = 0.15;
1005     proxyPanel.add(portLabel, gbc);
1006
1007     gbc.gridx++;
1008     gbc.anchor = GridBagConstraints.WEST;
1009     gbc.weightx = 0.1;
1010     proxyPanel.add(proxyPortHttpTB, gbc);
1011
1012     gbc.gridy++;
1013     gbc.gridx = 0;
1014     gbc.anchor = GridBagConstraints.WEST;
1015     gbc.weightx = 0.1;
1016     proxyPanel.add(httpsLabel, gbc);
1017
1018     gbc.gridx++;
1019     gbc.anchor = GridBagConstraints.EAST;
1020     gbc.weightx = 0.15;
1021     proxyPanel.add(serverLabel2, gbc);
1022
1023     gbc.gridx++;
1024     gbc.anchor = GridBagConstraints.WEST;
1025     gbc.weightx = 0.5;
1026     proxyPanel.add(proxyServerHttpsTB, gbc);
1027
1028     gbc.gridx++;
1029     gbc.anchor = GridBagConstraints.EAST;
1030     gbc.weightx = 0.15;
1031     proxyPanel.add(portLabel2, gbc);
1032
1033     gbc.gridx++;
1034     gbc.anchor = GridBagConstraints.WEST;
1035     gbc.weightx = 0.1;
1036     proxyPanel.add(proxyPortHttpsTB, gbc);
1037
1038     gbc.gridy++;
1039     gbc.gridx = 0;
1040     gbc.gridwidth = 5;
1041     gbc.anchor = GridBagConstraints.WEST;
1042     gbc.weightx = 0.1;
1043     proxyPanel.add(proxyAuth, gbc);
1044
1045     gbc.gridy++;
1046     gbc.gridx = 0;
1047     gbc.gridwidth = 1;
1048     gbc.anchor = GridBagConstraints.EAST;
1049     proxyPanel.add(proxyAuthUsernameLabel, gbc);
1050
1051     gbc.gridx++;
1052     gbc.gridwidth = 4;
1053     gbc.anchor = GridBagConstraints.WEST;
1054     proxyPanel.add(proxyAuthUsernameTB, gbc);
1055
1056     gbc.gridy++;
1057     gbc.gridx = 0;
1058     gbc.gridwidth = 1;
1059     gbc.anchor = GridBagConstraints.EAST;
1060     proxyPanel.add(proxyAuthPasswordLabel, gbc);
1061
1062     gbc.gridx++;
1063     gbc.gridwidth = 4;
1064     gbc.anchor = GridBagConstraints.WEST;
1065     proxyPanel.add(proxyAuthPasswordTB, gbc);
1066
1067     return proxyPanel;
1068   }
1069
1070   private String displayHostPort(String host, String port)
1071   {
1072     boolean hostBlank = (host == null || host.isEmpty());
1073     boolean portBlank = (port == null || port.isEmpty());
1074     if (hostBlank && portBlank)
1075     {
1076       return MessageManager.getString("label.none");
1077     }
1078
1079     StringBuilder sb = new StringBuilder();
1080     sb.append(hostBlank ? "" : host);
1081     if (!portBlank)
1082     {
1083       sb.append(":");
1084       sb.append(port);
1085     }
1086     return sb.toString();
1087   }
1088
1089   /**
1090    * Initialises the checkboxes in the Connections tab
1091    */
1092   private void initConnTabCheckboxes()
1093   {
1094     // Usage stats checkbox label
1095     usagestats.setText(
1096             MessageManager.getString("label.send_usage_statistics"));
1097     usagestats.setFont(LABEL_FONT);
1098     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1099     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1100
1101     // Questionnaire checkbox label
1102     questionnaire.setText(
1103             MessageManager.getString("label.check_for_questionnaires"));
1104     questionnaire.setFont(LABEL_FONT);
1105     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1106     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1107
1108     // Check for latest version checkbox label
1109     versioncheck.setText(
1110             MessageManager.getString("label.check_for_latest_version"));
1111     versioncheck.setFont(LABEL_FONT);
1112     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1113     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1114   }
1115
1116   /**
1117    * Initialises the parent panel which contains the tabbed sections.
1118    *
1119    * @return
1120    */
1121   private JPanel initOkCancelPanel()
1122   {
1123     JButton ok = new JButton();
1124     ok.setText(MessageManager.getString("action.ok"));
1125     ok.addActionListener(new ActionListener()
1126     {
1127       @Override
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         ok_actionPerformed(e);
1131       }
1132     });
1133     JButton cancel = new JButton();
1134     cancel.setText(MessageManager.getString("action.cancel"));
1135     cancel.addActionListener(new ActionListener()
1136     {
1137       @Override
1138       public void actionPerformed(ActionEvent e)
1139       {
1140         cancel_actionPerformed(e);
1141       }
1142     });
1143     JPanel okCancelPanel = new JPanel();
1144     okCancelPanel.add(ok);
1145     okCancelPanel.add(cancel);
1146     return okCancelPanel;
1147   }
1148
1149   /**
1150    * Initialises the Colours tabbed panel.
1151    *
1152    * @return
1153    */
1154   private JPanel initColoursTab()
1155   {
1156     JPanel coloursTab = new JPanel();
1157     coloursTab.setBorder(new TitledBorder(
1158             MessageManager.getString("action.open_new_alignment")));
1159     coloursTab.setLayout(new FlowLayout());
1160     JLabel mincolourLabel = new JLabel();
1161     mincolourLabel.setFont(LABEL_FONT);
1162     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1163     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1164     minColour.setFont(LABEL_FONT);
1165     minColour.setBorder(BorderFactory.createEtchedBorder());
1166     minColour.setPreferredSize(new Dimension(40, 20));
1167     minColour.addMouseListener(new MouseAdapter()
1168     {
1169       @Override
1170       public void mousePressed(MouseEvent e)
1171       {
1172         minColour_actionPerformed(minColour);
1173       }
1174     });
1175     JLabel maxcolourLabel = new JLabel();
1176     maxcolourLabel.setFont(LABEL_FONT);
1177     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1178     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1179     maxColour.setFont(LABEL_FONT);
1180     maxColour.setBorder(BorderFactory.createEtchedBorder());
1181     maxColour.setPreferredSize(new Dimension(40, 20));
1182     maxColour.addMouseListener(new MouseAdapter()
1183     {
1184       @Override
1185       public void mousePressed(MouseEvent e)
1186       {
1187         maxColour_actionPerformed(maxColour);
1188       }
1189     });
1190
1191     protColour.setFont(LABEL_FONT);
1192     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1193     JLabel protColourLabel = new JLabel();
1194     protColourLabel.setFont(LABEL_FONT);
1195     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1196     protColourLabel.setText(
1197             MessageManager.getString("label.prot_alignment_colour") + " ");
1198     JvSwingUtils.addtoLayout(coloursTab,
1199             MessageManager
1200                     .getString("label.default_colour_scheme_for_alignment"),
1201             protColourLabel, protColour);
1202
1203     nucColour.setFont(LABEL_FONT);
1204     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1205     JLabel nucColourLabel = new JLabel();
1206     nucColourLabel.setFont(LABEL_FONT);
1207     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1208     nucColourLabel.setText(
1209             MessageManager.getString("label.nuc_alignment_colour") + " ");
1210     JvSwingUtils.addtoLayout(coloursTab,
1211             MessageManager
1212                     .getString("label.default_colour_scheme_for_alignment"),
1213             nucColourLabel, nucColour);
1214
1215     JPanel annotationShding = new JPanel();
1216     annotationShding.setBorder(new TitledBorder(
1217             MessageManager.getString("label.annotation_shading_default")));
1218     annotationShding.setLayout(new GridLayout(1, 2));
1219     JvSwingUtils.addtoLayout(annotationShding,
1220             MessageManager.getString(
1221                     "label.default_minimum_colour_annotation_shading"),
1222             mincolourLabel, minColour);
1223     JvSwingUtils.addtoLayout(annotationShding,
1224             MessageManager.getString(
1225                     "label.default_maximum_colour_annotation_shading"),
1226             maxcolourLabel, maxColour);
1227     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1228     return coloursTab;
1229   }
1230
1231   /**
1232    * Initialises the Overview tabbed panel.
1233    *
1234    * @return
1235    */
1236   private JPanel initOverviewTab()
1237   {
1238     JPanel overviewPanel = new JPanel();
1239     overviewPanel.setBorder(new TitledBorder(
1240             MessageManager.getString("label.overview_settings")));
1241
1242     gapColour.setFont(LABEL_FONT);
1243     // fixing the border colours stops apparent colour bleed from the panel
1244     gapColour.setBorder(
1245             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1246     gapColour.setPreferredSize(new Dimension(40, 20));
1247     gapColour.addMouseListener(new MouseAdapter()
1248     {
1249       @Override
1250       public void mousePressed(MouseEvent e)
1251       {
1252         gapColour_actionPerformed(gapColour);
1253       }
1254     });
1255
1256     hiddenColour.setFont(LABEL_FONT);
1257     // fixing the border colours stops apparent colour bleed from the panel
1258     hiddenColour.setBorder(
1259             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1260     hiddenColour.setPreferredSize(new Dimension(40, 20));
1261     hiddenColour.addMouseListener(new MouseAdapter()
1262     {
1263       @Override
1264       public void mousePressed(MouseEvent e)
1265       {
1266         hiddenColour_actionPerformed(hiddenColour);
1267       }
1268     });
1269
1270     useLegacyGap = new JCheckBox(
1271             MessageManager.getString("label.ov_legacy_gap"));
1272     useLegacyGap.setFont(LABEL_FONT);
1273     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1274     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1275     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1276     gapLabel.setFont(LABEL_FONT);
1277     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1278     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1279     showHiddenAtStart = new JCheckBox(
1280             MessageManager.getString("label.ov_show_hide_default"));
1281     showHiddenAtStart.setFont(LABEL_FONT);
1282     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1283     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1284     JLabel hiddenLabel = new JLabel(
1285             MessageManager.getString("label.hidden_colour"));
1286     hiddenLabel.setFont(LABEL_FONT);
1287     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1288     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1289
1290     useLegacyGap.addActionListener(new ActionListener()
1291     {
1292       @Override
1293       public void actionPerformed(ActionEvent e)
1294       {
1295         useLegacyGaps_actionPerformed(e);
1296       }
1297     });
1298
1299     overviewPanel.setLayout(new GridBagLayout());
1300     GridBagConstraints c1 = new GridBagConstraints();
1301
1302     c1.fill = GridBagConstraints.HORIZONTAL;
1303     c1.gridx = 0;
1304     c1.gridy = 0;
1305     c1.weightx = 1;
1306     c1.ipady = 20;
1307     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1308     overviewPanel.add(useLegacyGap, c1);
1309
1310     GridBagConstraints c2 = new GridBagConstraints();
1311     c2.fill = GridBagConstraints.HORIZONTAL;
1312     c2.gridx = 1;
1313     c2.gridy = 0;
1314     c2.insets = new Insets(0, 15, 0, 10);
1315     overviewPanel.add(gapLabel, c2);
1316
1317     GridBagConstraints c3 = new GridBagConstraints();
1318     c3.fill = GridBagConstraints.HORIZONTAL;
1319     c3.gridx = 2;
1320     c3.gridy = 0;
1321     c3.insets = new Insets(0, 0, 0, 15);
1322     overviewPanel.add(gapColour, c3);
1323
1324     GridBagConstraints c4 = new GridBagConstraints();
1325     c4.fill = GridBagConstraints.HORIZONTAL;
1326     c4.gridx = 0;
1327     c4.gridy = 1;
1328     c4.weightx = 1;
1329     overviewPanel.add(showHiddenAtStart, c4);
1330
1331     GridBagConstraints c5 = new GridBagConstraints();
1332     c5.fill = GridBagConstraints.HORIZONTAL;
1333     c5.gridx = 1;
1334     c5.gridy = 1;
1335     c5.insets = new Insets(0, 15, 0, 10);
1336     overviewPanel.add(hiddenLabel, c5);
1337
1338     GridBagConstraints c6 = new GridBagConstraints();
1339     c6.fill = GridBagConstraints.HORIZONTAL;
1340     c6.gridx = 2;
1341     c6.gridy = 1;
1342     c6.insets = new Insets(0, 0, 0, 15);
1343     overviewPanel.add(hiddenColour, c6);
1344
1345     JButton resetButton = new JButton(
1346             MessageManager.getString("label.reset_to_defaults"));
1347
1348     resetButton.addActionListener(new ActionListener()
1349     {
1350       @Override
1351       public void actionPerformed(ActionEvent e)
1352       {
1353         resetOvDefaults_actionPerformed(e);
1354       }
1355     });
1356
1357     GridBagConstraints c7 = new GridBagConstraints();
1358     c7.fill = GridBagConstraints.NONE;
1359     c7.gridx = 0;
1360     c7.gridy = 2;
1361     c7.insets = new Insets(10, 0, 0, 0);
1362     c7.anchor = GridBagConstraints.WEST;
1363     overviewPanel.add(resetButton, c7);
1364
1365     // Add padding so the panel doesn't look ridiculous
1366     JPanel spacePanel = new JPanel();
1367     overviewPanel.add(spacePanel,
1368             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1369                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1370                     new Insets(0, 0, 0, 5), 0, 0));
1371
1372     return overviewPanel;
1373   }
1374
1375   /**
1376    * Initialises the Structure tabbed panel.
1377    *
1378    * @return
1379    */
1380   private JPanel initStructureTab()
1381   {
1382     structureTab = new JPanel();
1383
1384     structureTab.setBorder(new TitledBorder(
1385             MessageManager.getString("label.structure_options")));
1386     structureTab.setLayout(null);
1387     final int width = 400;
1388     final int height = 22;
1389     final int lineSpacing = 25;
1390     int ypos = 15;
1391
1392     structFromPdb.setFont(LABEL_FONT);
1393     structFromPdb
1394             .setText(MessageManager.getString("label.struct_from_pdb"));
1395     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1396     structFromPdb.addActionListener(new ActionListener()
1397     {
1398       @Override
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         boolean selected = structFromPdb.isSelected();
1402         // enable other options only when the first is checked
1403         useRnaView.setEnabled(selected);
1404         addSecondaryStructure.setEnabled(selected);
1405         addTempFactor.setEnabled(selected);
1406       }
1407     });
1408     structureTab.add(structFromPdb);
1409
1410     // indent checkboxes that are conditional on the first one
1411     ypos += lineSpacing;
1412     useRnaView.setFont(LABEL_FONT);
1413     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1414     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1415     structureTab.add(useRnaView);
1416
1417     ypos += lineSpacing;
1418     addSecondaryStructure.setFont(LABEL_FONT);
1419     addSecondaryStructure
1420             .setText(MessageManager.getString("label.autoadd_secstr"));
1421     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1422     structureTab.add(addSecondaryStructure);
1423
1424     ypos += lineSpacing;
1425     addTempFactor.setFont(LABEL_FONT);
1426     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1427     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1428     structureTab.add(addTempFactor);
1429
1430     ypos += lineSpacing;
1431     JLabel viewerLabel = new JLabel();
1432     viewerLabel.setFont(LABEL_FONT);
1433     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1434     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1435     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1436     structureTab.add(viewerLabel);
1437
1438     structViewer.setFont(LABEL_FONT);
1439     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1440     structViewer.addItem(ViewerType.JMOL.name());
1441     structViewer.addItem(ViewerType.CHIMERA.name());
1442     structViewer.addActionListener(new ActionListener()
1443     {
1444       @Override
1445       public void actionPerformed(ActionEvent e)
1446       {
1447         structureViewer_actionPerformed(
1448                 (String) structViewer.getSelectedItem());
1449       }
1450     });
1451     structureTab.add(structViewer);
1452
1453     ypos += lineSpacing;
1454     JLabel pathLabel = new JLabel();
1455     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1456     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1457     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1458     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1459     structureTab.add(pathLabel);
1460
1461     chimeraPath.setFont(LABEL_FONT);
1462     chimeraPath.setText("");
1463     final String tooltip = JvSwingUtils.wrapTooltip(true,
1464             MessageManager.getString("label.chimera_path_tip"));
1465     chimeraPath.setToolTipText(tooltip);
1466     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1467     chimeraPath.addMouseListener(new MouseAdapter()
1468     {
1469       @Override
1470       public void mouseClicked(MouseEvent e)
1471       {
1472         if (e.getClickCount() == 2)
1473         {
1474           String chosen = openFileChooser();
1475           if (chosen != null)
1476           {
1477             chimeraPath.setText(chosen);
1478           }
1479         }
1480       }
1481     });
1482     structureTab.add(chimeraPath);
1483
1484     ypos += lineSpacing;
1485     nwMapping.setFont(LABEL_FONT);
1486     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1487     siftsMapping.setFont(LABEL_FONT);
1488     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1489     mappingMethod.add(nwMapping);
1490     mappingMethod.add(siftsMapping);
1491     JPanel mappingPanel = new JPanel();
1492     mappingPanel.setFont(LABEL_FONT);
1493     TitledBorder mmTitledBorder = new TitledBorder(
1494             MessageManager.getString("label.mapping_method"));
1495     mmTitledBorder.setTitleFont(LABEL_FONT);
1496     mappingPanel.setBorder(mmTitledBorder);
1497     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1498     // GridLayout mappingLayout = new GridLayout();
1499     mappingPanel.setLayout(new GridLayout());
1500     mappingPanel.add(nwMapping);
1501     mappingPanel.add(siftsMapping);
1502     structureTab.add(mappingPanel);
1503
1504     ypos += lineSpacing;
1505     ypos += lineSpacing;
1506     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1507             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1508     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1509     structureTab.add(docFieldPref);
1510
1511     return structureTab;
1512   }
1513
1514   /**
1515    * Action on choosing a structure viewer from combobox options.
1516    *
1517    * @param selectedItem
1518    */
1519   protected void structureViewer_actionPerformed(String selectedItem)
1520   {
1521   }
1522
1523   /**
1524    * Show a dialog for the user to choose a file. Returns the chosen path, or
1525    * null on Cancel.
1526    *
1527    * @return
1528    */
1529   protected String openFileChooser()
1530   {
1531     String choice = null;
1532     JFileChooser chooser = new JFileChooser();
1533
1534     // chooser.setFileView(new JalviewFileView());
1535     chooser.setDialogTitle(
1536             MessageManager.getString("label.open_local_file"));
1537     chooser.setToolTipText(MessageManager.getString("action.open"));
1538
1539     int value = chooser.showOpenDialog(this);
1540
1541     if (value == JFileChooser.APPROVE_OPTION)
1542     {
1543       choice = chooser.getSelectedFile().getPath();
1544     }
1545     return choice;
1546   }
1547
1548   /**
1549    * Validate the structure tab preferences; if invalid, set focus on this tab.
1550    *
1551    * @param e
1552    */
1553   protected boolean validateStructure(FocusEvent e)
1554   {
1555     if (!validateStructure())
1556     {
1557       e.getComponent().requestFocusInWindow();
1558       return false;
1559     }
1560     return true;
1561   }
1562
1563   protected boolean validateStructure()
1564   {
1565     return false;
1566   }
1567
1568   /**
1569    * Initialises the Visual tabbed panel.
1570    *
1571    * @return
1572    */
1573   private JPanel initVisualTab()
1574   {
1575     JPanel visualTab = new JPanel();
1576     visualTab.setBorder(new TitledBorder(
1577             MessageManager.getString("action.open_new_alignment")));
1578     visualTab.setLayout(null);
1579     fullScreen.setFont(LABEL_FONT);
1580     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1581     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1582     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1583     quality.setEnabled(false);
1584     quality.setFont(LABEL_FONT);
1585     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1586     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1587     quality.setSelected(true);
1588     quality.setText(MessageManager.getString("label.quality"));
1589     conservation.setEnabled(false);
1590     conservation.setFont(LABEL_FONT);
1591     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1592     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1593     conservation.setSelected(true);
1594     conservation.setText(MessageManager.getString("label.conservation"));
1595     identity.setEnabled(false);
1596     identity.setFont(LABEL_FONT);
1597     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1598     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1599     identity.setSelected(true);
1600     identity.setText(MessageManager.getString("label.consensus"));
1601     showOccupancy.setFont(LABEL_FONT);
1602     showOccupancy.setEnabled(false);
1603     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1604     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1605     showOccupancy.setSelected(true);
1606     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1607
1608     JLabel showGroupbits = new JLabel();
1609     showGroupbits.setFont(LABEL_FONT);
1610     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1611     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1612     showGroupbits
1613             .setText(MessageManager.getString("action.show_group") + ":");
1614     JLabel showConsensbits = new JLabel();
1615     showConsensbits.setFont(LABEL_FONT);
1616     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1617     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1618     showConsensbits
1619             .setText(MessageManager.getString("label.consensus") + ":");
1620     showConsensHistogram.setEnabled(false);
1621     showConsensHistogram.setFont(LABEL_FONT);
1622     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1623     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1624     showConsensHistogram.setSelected(true);
1625     showConsensHistogram
1626             .setText(MessageManager.getString("label.histogram"));
1627     showConsensLogo.setEnabled(false);
1628     showConsensLogo.setFont(LABEL_FONT);
1629     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1630     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1631     showConsensLogo.setSelected(true);
1632     showConsensLogo.setText(MessageManager.getString("label.logo"));
1633     showGroupConsensus.setEnabled(false);
1634     showGroupConsensus.setFont(LABEL_FONT);
1635     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1636     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1637     showGroupConsensus.setSelected(true);
1638     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1639     showGroupConservation.setEnabled(false);
1640     showGroupConservation.setFont(LABEL_FONT);
1641     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1642     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1643     showGroupConservation.setSelected(true);
1644     showGroupConservation
1645             .setText(MessageManager.getString("label.conservation"));
1646     showNpTooltip.setEnabled(true);
1647     showNpTooltip.setFont(LABEL_FONT);
1648     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1649     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1650     showNpTooltip.setSelected(true);
1651     showNpTooltip.setText(
1652             MessageManager.getString("label.non_positional_features"));
1653     showDbRefTooltip.setEnabled(true);
1654     showDbRefTooltip.setFont(LABEL_FONT);
1655     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1656     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1657     showDbRefTooltip.setSelected(true);
1658     showDbRefTooltip
1659             .setText(MessageManager.getString("label.database_references"));
1660     annotations.setFont(LABEL_FONT);
1661     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1662     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1663     annotations.setSelected(true);
1664     annotations.setText(MessageManager.getString("label.show_annotations"));
1665     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1666     annotations.addActionListener(new ActionListener()
1667     {
1668       @Override
1669       public void actionPerformed(ActionEvent e)
1670       {
1671         annotations_actionPerformed(e);
1672       }
1673     });
1674     identity.addActionListener(new ActionListener()
1675     {
1676       @Override
1677       public void actionPerformed(ActionEvent e)
1678       {
1679         annotations_actionPerformed(e);
1680       }
1681     });
1682     showGroupConsensus.addActionListener(new ActionListener()
1683     {
1684       @Override
1685       public void actionPerformed(ActionEvent e)
1686       {
1687         annotations_actionPerformed(e);
1688       }
1689     });
1690     showUnconserved.setFont(LABEL_FONT);
1691     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1692     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1693     showUnconserved.setSelected(true);
1694     showUnconserved
1695             .setText(MessageManager.getString("action.show_unconserved"));
1696     showUnconserved.addActionListener(new ActionListener()
1697     {
1698       @Override
1699       public void actionPerformed(ActionEvent e)
1700       {
1701         showunconserved_actionPerformed(e);
1702       }
1703     });
1704
1705     // TODO these are not yet added to / action from Preferences
1706     // JCheckBox shareSelections = new JCheckBox();
1707     // shareSelections.setFont(verdana11);
1708     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1709     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1710     // shareSelections.setSelected(true);
1711     // shareSelections.setText(MessageManager
1712     // .getString("label.share_selection_across_views"));
1713     // JCheckBox followHighlight = new JCheckBox();
1714     // followHighlight.setFont(verdana11);
1715     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1716     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1717     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1718     // followHighlight.setSelected(true);
1719     // followHighlight.setText(MessageManager
1720     // .getString("label.scroll_highlighted_regions"));
1721
1722     seqLimit.setFont(LABEL_FONT);
1723     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1724     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1725     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1726     smoothFont.setFont(LABEL_FONT);
1727     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1728     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1729     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1730     scaleProteinToCdna.setFont(LABEL_FONT);
1731     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1732     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1733     scaleProteinToCdna.setText(
1734             MessageManager.getString("label.scale_protein_to_cdna"));
1735     scaleProteinToCdna.setToolTipText(
1736             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1737     JLabel gapLabel = new JLabel();
1738     gapLabel.setFont(LABEL_FONT);
1739     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1740     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1741     JLabel fontLabel = new JLabel();
1742     fontLabel.setFont(LABEL_FONT);
1743     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1744     fontLabel.setText(MessageManager.getString("label.font"));
1745     fontSizeCB.setFont(LABEL_FONT);
1746     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1747     fontStyleCB.setFont(LABEL_FONT);
1748     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1749     fontNameCB.setFont(LABEL_FONT);
1750     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1751     gapSymbolCB.setFont(LABEL_FONT);
1752     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1753     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1754     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1755     gapSymbolCB.setRenderer(dlcr);
1756
1757     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1758     startupCheckbox.setFont(LABEL_FONT);
1759     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1760     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1761     startupCheckbox.setSelected(true);
1762     startupFileTextfield.setFont(LABEL_FONT);
1763     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1764     final String tooltip = JvSwingUtils.wrapTooltip(true,
1765             MessageManager.getString("label.double_click_to_browse"));
1766     startupFileTextfield.setToolTipText(tooltip);
1767     startupFileTextfield.addMouseListener(new MouseAdapter()
1768     {
1769       @Override
1770       public void mouseClicked(MouseEvent e)
1771       {
1772         if (e.getClickCount() > 1)
1773         {
1774           startupFileTextfield_mouseClicked();
1775         }
1776       }
1777     });
1778
1779     sortby.setFont(LABEL_FONT);
1780     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1781     JLabel sortLabel = new JLabel();
1782     sortLabel.setFont(LABEL_FONT);
1783     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1784     sortLabel.setText(MessageManager.getString("label.sort_by"));
1785     sortAnnBy.setFont(LABEL_FONT);
1786     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1787     JLabel sortAnnLabel = new JLabel();
1788     sortAnnLabel.setFont(LABEL_FONT);
1789     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1790     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1791     sortAutocalc.setFont(LABEL_FONT);
1792     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1793
1794     JPanel annsettingsPanel = new JPanel();
1795     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1796     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1797     annsettingsPanel.setBorder(new EtchedBorder());
1798     visualTab.add(annsettingsPanel);
1799     Border jb = new EmptyBorder(1, 1, 4, 5);
1800     annotations.setBorder(jb);
1801     showOccupancy.setBorder(jb);
1802     quality.setBorder(jb);
1803     conservation.setBorder(jb);
1804     identity.setBorder(jb);
1805     showConsensbits.setBorder(jb);
1806     showGroupbits.setBorder(jb);
1807     showGroupConsensus.setBorder(jb);
1808     showGroupConservation.setBorder(jb);
1809     showConsensHistogram.setBorder(jb);
1810     showConsensLogo.setBorder(jb);
1811
1812     JPanel autoAnnotSettings = new JPanel();
1813     annsettingsPanel.add(autoAnnotSettings);
1814     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1815     autoAnnotSettings.add(annotations);
1816     autoAnnotSettings.add(quality);
1817     // second row of autoannotation box
1818     autoAnnotSettings = new JPanel();
1819     annsettingsPanel.add(autoAnnotSettings);
1820
1821     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1822     autoAnnotSettings.add(conservation);
1823     autoAnnotSettings.add(identity);
1824     autoAnnotSettings.add(showOccupancy);
1825     autoAnnotSettings.add(showGroupbits);
1826     autoAnnotSettings.add(showGroupConservation);
1827     autoAnnotSettings.add(showGroupConsensus);
1828     autoAnnotSettings.add(showConsensbits);
1829     autoAnnotSettings.add(showConsensHistogram);
1830     autoAnnotSettings.add(showConsensLogo);
1831
1832     JPanel tooltipSettings = new JPanel();
1833     tooltipSettings.setBorder(new TitledBorder(
1834             MessageManager.getString("label.sequence_id_tooltip")));
1835     tooltipSettings.setBounds(173, 140, 220, 62);
1836     tooltipSettings.setLayout(new GridLayout(2, 1));
1837     tooltipSettings.add(showDbRefTooltip);
1838     tooltipSettings.add(showNpTooltip);
1839     visualTab.add(tooltipSettings);
1840
1841     wrap.setFont(LABEL_FONT);
1842     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1843     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1844     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1845     rightAlign.setFont(LABEL_FONT);
1846     rightAlign.setForeground(Color.black);
1847     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1848     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1849     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1850     idItalics.setFont(LABEL_FONT_ITALIC);
1851     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1852     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1853     idItalics.setText(
1854             MessageManager.getString("label.sequence_name_italics"));
1855     openoverv.setFont(LABEL_FONT);
1856     openoverv.setActionCommand(
1857             MessageManager.getString("label.open_overview"));
1858     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1859     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1860     openoverv.setText(MessageManager.getString("label.open_overview"));
1861     JPanel jPanel2 = new JPanel();
1862     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1863     jPanel2.setLayout(new GridLayout(14, 1));
1864     jPanel2.add(fullScreen);
1865     jPanel2.add(openoverv);
1866     jPanel2.add(seqLimit);
1867     jPanel2.add(rightAlign);
1868     jPanel2.add(fontLabel);
1869     jPanel2.add(showUnconserved);
1870     jPanel2.add(idItalics);
1871     jPanel2.add(smoothFont);
1872     jPanel2.add(scaleProteinToCdna);
1873     jPanel2.add(gapLabel);
1874     jPanel2.add(wrap);
1875     jPanel2.add(sortLabel);
1876     jPanel2.add(sortAnnLabel);
1877     jPanel2.add(startupCheckbox);
1878     visualTab.add(jPanel2);
1879     visualTab.add(startupFileTextfield);
1880     visualTab.add(sortby);
1881     visualTab.add(sortAnnBy);
1882     visualTab.add(sortAutocalc);
1883     visualTab.add(gapSymbolCB);
1884     visualTab.add(fontNameCB);
1885     visualTab.add(fontSizeCB);
1886     visualTab.add(fontStyleCB);
1887     return visualTab;
1888   }
1889
1890   /**
1891    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
1892    */
1893
1894   protected void loadLastSavedBackupsOptions()
1895   {
1896     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
1897             .getSavedBackupEntry();
1898     enableBackupFiles
1899             .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
1900
1901     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
1902             .createBackupFilesPresetEntry(Cache
1903                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
1904     if (backupfilesCustomEntry == null)
1905     {
1906       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1907               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
1908     }
1909     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1910             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
1911             backupfilesCustomEntry);
1912
1913     setComboIntStringKey(backupfilesPresetsCombo,
1914             Cache.getDefault(BackupFiles.NS + "_PRESET",
1915                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
1916
1917     backupsSetOptions(savedPreset);
1918
1919     backupsOptionsSetEnabled();
1920     updateBackupFilesExampleLabel();
1921   }
1922
1923   private boolean warnAboutSuffixReverseChange()
1924   {
1925     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
1926             .getSavedBackupEntry();
1927     boolean savedSuffixReverse = bfpe.reverse;
1928     int savedSuffixDigits = bfpe.digits;
1929     String savedSuffixTemplate = bfpe.suffix;
1930
1931     boolean nowSuffixReverse = suffixReverse.isSelected();
1932     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
1933     String nowSuffixTemplate = suffixTemplate.getText();
1934     return nowSuffixReverse != savedSuffixReverse
1935             && nowSuffixDigits == savedSuffixDigits
1936             && nowSuffixTemplate != null
1937             && nowSuffixTemplate.equals(savedSuffixTemplate);
1938   }
1939
1940   /**
1941    * Initialises the Backups tabbed panel.
1942    *
1943    * @return
1944    */
1945   private JPanel initBackupsTab()
1946   {
1947     JPanel backupsTab = new JPanel();
1948     backupsTab.setBorder(new TitledBorder(
1949             MessageManager.getString("label.backup_files")));
1950     backupsTab.setLayout(new GridBagLayout());
1951
1952     GridBagConstraints gbc = new GridBagConstraints();
1953     gbc.weightx = 0.0;
1954     gbc.weighty = 0.0;
1955     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1956     gbc.fill = GridBagConstraints.NONE;
1957
1958     initBackupsTabPresetsPanel();
1959     initBackupsTabSuffixPanel();
1960     initBackupsTabKeepFilesPanel();
1961     initBackupsTabFilenameExamplesPanel();
1962
1963     enableBackupFiles.setFont(LABEL_FONT_BOLD);
1964     enableBackupFiles
1965             .setText(MessageManager.getString("label.enable_backupfiles"));
1966     enableBackupFiles.addActionListener(new ActionListener()
1967     {
1968       @Override
1969       public void actionPerformed(ActionEvent e)
1970       {
1971         // enable other options only when the first is checked
1972         backupsOptionsSetEnabled();
1973       }
1974     });
1975
1976     // enable checkbox 1 col
1977     gbc.gridwidth = 1;
1978     gbc.gridheight = 1;
1979     gbc.gridx = 0;
1980     gbc.gridy = 0; // row 0
1981     backupsTab.add(enableBackupFiles, gbc);
1982
1983     // summary of scheme box (over two rows)
1984     gbc.gridx = 1;
1985     gbc.weightx = 0.0;
1986     gbc.gridheight = 2;
1987     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
1988     gbc.fill = GridBagConstraints.BOTH;
1989     backupsTab.add(exampleFilesPanel, gbc);
1990     gbc.gridheight = 1;
1991     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1992     gbc.fill = GridBagConstraints.NONE;
1993
1994     // fill empty space on right
1995     gbc.gridx++;
1996     gbc.weightx = 1.0;
1997     backupsTab.add(new JPanel(), gbc);
1998
1999     // schemes box
2000     gbc.weightx = 0.0;
2001     gbc.gridx = 0;
2002     gbc.gridy++; // row 1
2003     backupsTab.add(presetsPanel, gbc);
2004
2005     // now using whole row
2006     gbc.gridwidth = 2;
2007     gbc.gridheight = 1;
2008     // keep files box
2009     gbc.gridx = 0;
2010     gbc.gridy++; // row 2
2011     backupsTab.add(keepfilesPanel, gbc);
2012
2013     // filename strategy box
2014     gbc.gridy++; // row 3
2015     backupsTab.add(suffixPanel, gbc);
2016
2017     // fill empty space
2018     gbc.gridy++; // row 4
2019     gbc.weighty = 1.0;
2020     backupsTab.add(new JPanel(), gbc);
2021
2022     backupsOptionsSetEnabled();
2023     return backupsTab;
2024   }
2025
2026   private JPanel initBackupsTabPresetsPanel()
2027   {
2028
2029     String title = MessageManager.getString("label.schemes");
2030
2031     presetsPanel.setLayout(new GridBagLayout());
2032
2033     GridBagConstraints gbc = new GridBagConstraints();
2034     gbc.weightx = 0.0;
2035     gbc.weighty = 0.0;
2036     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2037     gbc.fill = GridBagConstraints.NONE;
2038     gbc.gridwidth = 1;
2039     gbc.gridheight = 1;
2040
2041     // "Scheme: "
2042     gbc.gridx = 0;
2043     gbc.gridy = 0;
2044
2045     presetsComboLabel = new JLabel(title + ":");
2046     presetsPanel.add(presetsComboLabel, gbc);
2047
2048     List<Object> entries = Arrays.asList(
2049             (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2050     List<String> tooltips = Arrays.asList(
2051             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2052     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2053             tooltips);
2054     /*
2055     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2056     {
2057       backupfilesPresetsCombo
2058               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2059     }
2060     */
2061
2062     backupfilesPresetsCombo.addActionListener(new ActionListener()
2063     {
2064       @Override
2065       public void actionPerformed(ActionEvent e)
2066       {
2067         int key = getComboIntStringKey(backupfilesPresetsCombo);
2068         if (!customiseCheckbox.isSelected())
2069         {
2070           backupfilesPresetsComboLastSelected = key;
2071         }
2072         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2073         {
2074           if (customiseCheckbox.isSelected())
2075           {
2076             // got here by clicking on customiseCheckbox so don't change the
2077             // values
2078             backupfilesCustomOptionsSetEnabled();
2079           }
2080           else
2081           {
2082             backupsTabUpdatePresets();
2083             backupfilesCustomOptionsSetEnabled();
2084           }
2085         }
2086         else
2087         {
2088           customiseCheckbox.setSelected(false);
2089           backupsTabUpdatePresets();
2090           backupfilesCustomOptionsSetEnabled();
2091         }
2092       }
2093     });
2094
2095     // dropdown list of preset schemes
2096     gbc.gridx = 1;
2097     presetsPanel.add(backupfilesPresetsCombo, gbc);
2098
2099     revertButton.setText(MessageManager.getString("label.cancel_changes"));
2100     revertButton.setToolTipText(
2101             MessageManager.getString("label.cancel_changes_description"));
2102     revertButton.addActionListener(new ActionListener()
2103     {
2104       @Override
2105       public void actionPerformed(ActionEvent e)
2106       {
2107         backupsSetOptions(
2108                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2109                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2110         backupfilesCustomOptionsSetEnabled();
2111       }
2112
2113     });
2114     revertButton.setFont(LABEL_FONT);
2115
2116     customiseCheckbox.setFont(LABEL_FONT);
2117     customiseCheckbox.setText(MessageManager.getString("label.customise"));
2118     customiseCheckbox.addActionListener(new ActionListener()
2119     {
2120       @Override
2121       public void actionPerformed(ActionEvent e)
2122       {
2123         int currently = getComboIntStringKey(backupfilesPresetsCombo);
2124         if (customiseCheckbox.isSelected())
2125         {
2126           backupfilesPresetsComboLastSelected = currently;
2127           setComboIntStringKey(backupfilesPresetsCombo,
2128                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2129         }
2130         else
2131         {
2132           setComboIntStringKey(backupfilesPresetsCombo,
2133                   backupfilesPresetsComboLastSelected);
2134
2135         }
2136         backupfilesCustomOptionsSetEnabled();
2137       }
2138     });
2139     customiseCheckbox.setToolTipText(
2140             MessageManager.getString("label.customise_description"));
2141
2142     // customise checkbox
2143     gbc.gridx = 0;
2144     gbc.gridy++;
2145     presetsPanel.add(customiseCheckbox, gbc);
2146
2147     // "Cancel changes" button (aligned with combo box above)
2148     gbc.gridx = 1;
2149     presetsPanel.add(revertButton, gbc);
2150
2151     return presetsPanel;
2152   }
2153
2154   private JPanel initBackupsTabFilenameExamplesPanel()
2155   {
2156     String title = MessageManager.getString("label.scheme_examples");
2157     TitledBorder tb = new TitledBorder(title);
2158     exampleFilesPanel.setBorder(tb);
2159     exampleFilesPanel.setLayout(new GridBagLayout());
2160
2161     backupfilesExampleLabel.setEditable(false);
2162     backupfilesExampleLabel
2163             .setBackground(exampleFilesPanel.getBackground());
2164
2165     updateBackupFilesExampleLabel();
2166
2167     GridBagConstraints gbc = new GridBagConstraints();
2168     gbc.weightx = 1.0;
2169     gbc.weighty = 1.0;
2170     gbc.fill = GridBagConstraints.NONE;
2171     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2172
2173     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2174     return exampleFilesPanel;
2175   }
2176
2177   private void backupsTabUpdatePresets()
2178   {
2179     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2180             .getSelectedItem();
2181     int key = entry.k;
2182     String value = entry.v;
2183
2184     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2185             .containsKey(key))
2186     {
2187       backupsSetOptions(
2188               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2189                       .get(key));
2190     }
2191     else
2192     {
2193       Cache.log.error(
2194               "Preset '" + value + "' [key:" + key + "] not implemented");
2195     }
2196
2197     // Custom options will now be enabled when the customiseCheckbox is checked
2198     // (performed above)
2199     // backupfilesCustomOptionsSetEnabled();
2200     updateBackupFilesExampleLabel();
2201   }
2202
2203   protected int getComboIntStringKey(
2204           JComboBox<Object> backupfilesPresetsCombo2)
2205   {
2206     IntKeyStringValueEntry e;
2207     try
2208     {
2209       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2210               .getSelectedItem();
2211     } catch (Exception ex)
2212     {
2213       Cache.log.error(
2214               "Problem casting Combo entry to IntKeyStringValueEntry.");
2215       e = null;
2216     }
2217     return e != null ? e.k : 0;
2218   }
2219
2220   protected void setComboIntStringKey(
2221           JComboBox<Object> backupfilesPresetsCombo2, int key)
2222   {
2223     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2224     {
2225       IntKeyStringValueEntry e;
2226       try
2227       {
2228         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2229       } catch (Exception ex)
2230       {
2231         Cache.log.error(
2232                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2233         continue;
2234       }
2235       if (e.k == key)
2236       {
2237         backupfilesPresetsCombo2.setSelectedIndex(i);
2238         break;
2239       }
2240     }
2241     // backupsTabUpdatePresets();
2242   }
2243
2244   private JPanel initBackupsTabSuffixPanel()
2245   {
2246     suffixPanel.setBorder(new TitledBorder(
2247             MessageManager.getString("label.backup_filename_strategy")));
2248     suffixPanel.setLayout(new GridBagLayout());
2249
2250     suffixTemplateLabel
2251             .setText(MessageManager.getString("label.append_to_filename"));
2252     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2253     suffixTemplateLabel.setFont(LABEL_FONT);
2254
2255     final String tooltip = JvSwingUtils.wrapTooltip(true,
2256             MessageManager.getString("label.append_to_filename_tooltip"));
2257     suffixTemplate.setToolTipText(tooltip);
2258     suffixTemplate.addActionListener(new ActionListener()
2259     {
2260       @Override
2261       public void actionPerformed(ActionEvent e)
2262       {
2263         updateBackupFilesExampleLabel();
2264         backupfilesCustomOptionsSetEnabled();
2265         backupfilesRevertButtonSetEnabled(true);
2266       }
2267
2268     });
2269     suffixTemplate.addKeyListener(new KeyListener()
2270     {
2271       @Override
2272       public void keyReleased(KeyEvent e)
2273       {
2274         updateBackupFilesExampleLabel();
2275         backupfilesCustomOptionsSetEnabled();
2276         backupfilesRevertButtonSetEnabled(true);
2277       }
2278
2279       @Override
2280       public void keyPressed(KeyEvent e)
2281       {
2282       }
2283
2284       // disable use of ':' or '/' or '\'
2285       @Override
2286       public void keyTyped(KeyEvent e)
2287       {
2288         char c = e.getKeyChar();
2289         if (c == ':' || c == '/' || c == '\\')
2290         {
2291           // don't process ':' or '/' or '\'
2292           e.consume();
2293         }
2294       }
2295
2296     });
2297
2298     // digits spinner
2299     suffixDigitsLabel
2300             .setText(MessageManager.getString("label.index_digits"));
2301     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2302     suffixDigitsLabel.setFont(LABEL_FONT);
2303     ChangeListener c = new ChangeListener()
2304     {
2305       @Override
2306       public void stateChanged(ChangeEvent e)
2307       {
2308         backupfilesRevertButtonSetEnabled(true);
2309         updateBackupFilesExampleLabel();
2310       }
2311
2312     };
2313     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2314             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2315
2316     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2317             MessageManager.getString("label.increment_index"));
2318     suffixReverse.addActionListener(new ActionListener()
2319     {
2320       @Override
2321       public void actionPerformed(ActionEvent e)
2322       {
2323         boolean okay = true;
2324         if (warnAboutSuffixReverseChange())
2325         {
2326           // Warning popup
2327           okay = confirmSuffixReverseChange();
2328         }
2329         if (okay)
2330         {
2331           backupfilesRevertButtonSetEnabled(true);
2332           updateBackupFilesExampleLabel();
2333         }
2334         else
2335         {
2336           boolean savedSuffixReverse = BackupFilesPresetEntry
2337                   .getSavedBackupEntry().reverse;
2338           suffixReverse.setSelected(savedSuffixReverse);
2339         }
2340       }
2341     });
2342
2343     GridBagConstraints sgbc = new GridBagConstraints();
2344
2345     // first row (template text box)
2346     sgbc.anchor = GridBagConstraints.WEST;
2347     sgbc.gridx = 0;
2348     sgbc.gridy = 0;
2349     sgbc.gridwidth = 1;
2350     sgbc.gridheight = 1;
2351     sgbc.weightx = 1.0;
2352     sgbc.weighty = 0.0;
2353     sgbc.fill = GridBagConstraints.NONE;
2354     suffixPanel.add(suffixTemplateLabel, sgbc);
2355
2356     sgbc.gridx = 1;
2357     sgbc.fill = GridBagConstraints.HORIZONTAL;
2358     suffixPanel.add(suffixTemplate, sgbc);
2359
2360     // second row (number of digits spinner)
2361     sgbc.gridy = 1;
2362
2363     sgbc.gridx = 0;
2364     sgbc.fill = GridBagConstraints.NONE;
2365     suffixPanel.add(suffixDigitsLabel, sgbc);
2366
2367     sgbc.gridx = 1;
2368     sgbc.fill = GridBagConstraints.HORIZONTAL;
2369     suffixPanel.add(suffixDigitsSpinner, sgbc);
2370
2371     // third row (forward order radio selection)
2372     sgbc.gridx = 0;
2373     sgbc.gridy = 2;
2374     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2375     sgbc.fill = GridBagConstraints.HORIZONTAL;
2376     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2377
2378     // fourth row (reverse order radio selection)
2379     sgbc.gridy = 3;
2380     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2381     return suffixPanel;
2382   }
2383
2384   private boolean confirmSuffixReverseChange()
2385   {
2386     boolean ret = false;
2387     String warningMessage = MessageManager
2388             .getString("label.warning_confirm_change_reverse");
2389     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2390             warningMessage,
2391             MessageManager.getString("label.change_increment_decrement"),
2392             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2393
2394     ret = (confirm == JvOptionPane.YES_OPTION);
2395     return ret;
2396   }
2397
2398   private JPanel initBackupsTabKeepFilesPanel()
2399   {
2400     keepfilesPanel.setBorder(
2401             new TitledBorder(MessageManager.getString("label.keep_files")));
2402     keepfilesPanel.setLayout(new GridBagLayout());
2403
2404     backupfilesKeepAll.setLabels(
2405             MessageManager.getString("label.keep_all_backup_files"),
2406             MessageManager.getString(
2407                     "label.keep_only_this_number_of_backup_files"));
2408     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2409     {
2410       @Override
2411       public void actionPerformed(ActionEvent e)
2412       {
2413         backupfilesRevertButtonSetEnabled(true);
2414         updateBackupFilesExampleLabel();
2415       }
2416     });
2417     backupfilesKeepAll.addActionListener(new ActionListener()
2418     {
2419       @Override
2420       public void actionPerformed(ActionEvent e)
2421       {
2422         backupfilesRevertButtonSetEnabled(true);
2423         keepRollMaxOptionsEnabled();
2424         updateBackupFilesExampleLabel();
2425       }
2426     });
2427
2428     ChangeListener c = new ChangeListener()
2429     {
2430       @Override
2431       public void stateChanged(ChangeEvent e)
2432       {
2433         backupfilesRevertButtonSetEnabled(true);
2434         updateBackupFilesExampleLabel();
2435       }
2436
2437     };
2438     setIntegerSpinner(backupfilesRollMaxSpinner,
2439             BackupFilesPresetEntry.ROLLMAXMIN,
2440             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2441
2442     backupfilesConfirmDelete.setLabels(
2443             MessageManager.getString("label.always_ask"),
2444             MessageManager.getString("label.auto_delete"));
2445     backupfilesConfirmDelete.addActionListener(new ActionListener()
2446     {
2447       @Override
2448       public void actionPerformed(ActionEvent e)
2449       {
2450         backupfilesRevertButtonSetEnabled(true);
2451       }
2452     });
2453     // update the enabled section
2454     keepRollMaxOptionsEnabled();
2455
2456     GridBagConstraints kgbc = new GridBagConstraints();
2457
2458     // first row (template text box)
2459     kgbc.anchor = GridBagConstraints.WEST;
2460     kgbc.gridx = 0;
2461     kgbc.gridy = 0;
2462     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2463     kgbc.gridheight = 1;
2464     kgbc.weightx = 1.0;
2465     kgbc.weighty = 0.0;
2466     kgbc.fill = GridBagConstraints.HORIZONTAL;
2467     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2468
2469     // second row
2470     kgbc.gridy = 1;
2471
2472     kgbc.gridx = 0;
2473     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2474     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2475
2476     kgbc.gridx = 1;
2477     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2478     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2479
2480     // third row (indented)
2481     kgbc.gridy = 2;
2482     kgbc.insets = new Insets(0, 20, 0, 0);
2483
2484     kgbc.gridx = 0;
2485     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2486     kgbc.fill = GridBagConstraints.HORIZONTAL;
2487     kgbc.weightx = 1.0;
2488
2489     JPanel jp = new JPanel();
2490     jp.setLayout(new FlowLayout());
2491     oldBackupFilesLabel.setText(
2492             MessageManager.getString("label.autodelete_old_backup_files"));
2493     oldBackupFilesLabel.setFont(LABEL_FONT);
2494     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2495     jp.add(oldBackupFilesLabel);
2496     jp.add(backupfilesConfirmDelete.getTrueButton());
2497     jp.add(backupfilesConfirmDelete.getFalseButton());
2498     keepfilesPanel.add(jp, kgbc);
2499
2500     return keepfilesPanel;
2501   }
2502
2503   protected void updateBackupFilesExampleLabel()
2504   {
2505     int exampleindex = 12;
2506     String base = MessageManager.getString("label.filename") + ".fa";
2507     if (base == null || base.length() == 0)
2508     {
2509       base = "file_name.fa";
2510     }
2511
2512     boolean reverse = suffixReverse.isSelected();
2513     boolean keepAll = backupfilesKeepAll.isSelected();
2514     int rollMax = 4;
2515     String suffix = suffixTemplate.getText();
2516     int digits = 3;
2517
2518     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2519     if (suffix == null || suffix.length() == 0)
2520     {
2521       backupfilesExampleLabel
2522               .setText(MessageManager.getString("label.no_backup_files"));
2523       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2524       return;
2525     }
2526
2527     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2528     rollMax = rollMax < 1 ? 1 : rollMax;
2529
2530     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2531     {
2532       rollMax = 1;
2533     }
2534
2535     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2536     digits = digits < 1 ? 1 : digits;
2537
2538     int lowersurround = 2;
2539     int uppersurround = 0;
2540     StringBuilder exampleSB = new StringBuilder();
2541     boolean firstLine = true;
2542     int lineNumber = 0;
2543     if (reverse)
2544     {
2545
2546       int min = 1;
2547       int max = keepAll ? exampleindex : rollMax;
2548       for (int index = min; index <= max; index++)
2549       {
2550         if (index == min + lowersurround && index < max - uppersurround - 1)
2551         {
2552           exampleSB.append("\n...");
2553           lineNumber++;
2554         }
2555         else if (index > min + lowersurround && index < max - uppersurround)
2556         {
2557           // nothing
2558         }
2559         else
2560         {
2561           if (firstLine)
2562           {
2563             firstLine = false;
2564           }
2565           else
2566           {
2567             exampleSB.append("\n");
2568             lineNumber++;
2569           }
2570           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2571                   base, suffix, digits));
2572           if (min == max)
2573           {
2574             // no extra text needed
2575           }
2576           else if (index == min)
2577           {
2578             String newest = MessageManager.getString("label.braced_newest");
2579             if (newest != null && newest.length() > 0)
2580             {
2581               exampleSB.append(" " + newest);
2582             }
2583           }
2584           else if (index == max)
2585           {
2586             String oldest = MessageManager.getString("label.braced_oldest");
2587             if (oldest != null && oldest.length() > 0)
2588             {
2589               exampleSB.append(" " + oldest);
2590             }
2591           }
2592         }
2593       }
2594     }
2595     else
2596     {
2597
2598       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2599               : exampleindex - rollMax + 1;
2600       int max = exampleindex;
2601
2602       for (int index = min; index <= max; index++)
2603       {
2604
2605         if (index == min + lowersurround && index < max - uppersurround - 1)
2606         {
2607           exampleSB.append("\n...");
2608           lineNumber++;
2609         }
2610         else if (index > min + lowersurround && index < max - uppersurround)
2611         {
2612           // nothing
2613         }
2614         else
2615         {
2616           if (firstLine)
2617           {
2618             firstLine = false;
2619           }
2620           else
2621           {
2622             exampleSB.append("\n");
2623             lineNumber++;
2624           }
2625           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2626                   base, suffix, digits));
2627           if (min == max)
2628           {
2629             // no extra text needed
2630           }
2631           else if (index == min)
2632           {
2633             String oldest = MessageManager.getString("label.braced_oldest");
2634             if (oldest != null && oldest.length() > 0)
2635             {
2636               exampleSB.append(" " + oldest);
2637             }
2638           }
2639           else if (index == max)
2640           {
2641             String newest = MessageManager.getString("label.braced_newest");
2642             if (newest != null && newest.length() > 0)
2643             {
2644               exampleSB.append(" " + newest);
2645             }
2646           }
2647         }
2648       }
2649
2650     }
2651
2652     // add some extra empty lines to pad out the example files box. ugh, please
2653     // tell
2654     // me how to do this better
2655     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2656     if (remainingLines > 0)
2657     {
2658       for (int i = 0; i < remainingLines; i++)
2659       {
2660         exampleSB.append("\n ");
2661         lineNumber++;
2662       }
2663     }
2664
2665     backupfilesExampleLabel.setText(exampleSB.toString());
2666   }
2667
2668   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2669           boolean useExistingVal, ChangeListener c)
2670   {
2671     int i = def;
2672     if (useExistingVal)
2673     {
2674       try
2675       {
2676         i = ((Integer) s.getValue()).intValue();
2677       } catch (Exception e)
2678       {
2679         Cache.log.error(
2680                 "Exception casting the initial value of s.getValue()");
2681       }
2682     }
2683
2684     setIntegerSpinner(s, min, max, i, c);
2685   }
2686
2687   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2688           ChangeListener c)
2689   {
2690     // integer spinner for number of digits
2691     if (def > max)
2692     {
2693       max = def;
2694     }
2695     if (def < min)
2696     {
2697       def = min;
2698     }
2699     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2700     s.setModel(sModel);
2701
2702     s.addChangeListener(c);
2703
2704   }
2705
2706   protected static int getSpinnerInt(JSpinner s, int def)
2707   {
2708     int i = def;
2709     try
2710     {
2711       s.commitEdit();
2712       i = (Integer) s.getValue();
2713     } catch (Exception e)
2714     {
2715       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2716     }
2717     return i;
2718   }
2719
2720   private void keepRollMaxOptionsEnabled()
2721   {
2722     boolean enabled = backupfilesKeepAll.isEnabled()
2723             && !backupfilesKeepAll.isSelected();
2724     oldBackupFilesLabel.setEnabled(enabled);
2725     backupfilesRollMaxSpinner.setEnabled(enabled);
2726     backupfilesConfirmDelete.setEnabled(enabled);
2727   }
2728
2729   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2730   {
2731     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2732             && customiseCheckbox.isSelected() && suffixTemplate.getText()
2733                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2734     keepfilesPanel.setEnabled(enabled);
2735     backupfilesKeepAll.setEnabled(enabled);
2736     oldBackupFilesLabel.setEnabled(enabled);
2737     keepRollMaxOptionsEnabled();
2738   }
2739
2740   private void backupfilesSuffixTemplateDigitsSetEnabled()
2741   {
2742     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2743             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2744     suffixDigitsLabel.setEnabled(enabled);
2745     suffixDigitsSpinner.setEnabled(enabled);
2746     suffixReverse.setEnabled(enabled);
2747   }
2748
2749   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2750   {
2751     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2752             && customiseCheckbox.isSelected();
2753     suffixPanel.setEnabled(enabled);
2754     suffixTemplateLabel.setEnabled(enabled);
2755     suffixTemplate.setEnabled(enabled);
2756     backupfilesSuffixTemplateDigitsSetEnabled();
2757   }
2758
2759   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2760   {
2761     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2762             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2763     revertButton.setEnabled(enabled);
2764   }
2765
2766   private boolean backupfilesCustomChanged()
2767   {
2768     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2769             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2770     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2771     return !custom.equals(current);
2772   }
2773
2774   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2775   {
2776     String suffix = suffixTemplate.getText();
2777     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2778     boolean reverse = suffixReverse.isSelected();
2779     boolean keepAll = backupfilesKeepAll.isSelected();
2780     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
2781     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
2782
2783     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
2784             reverse, keepAll, rollMax, confirmDelete);
2785
2786     return bfpe;
2787   }
2788
2789   protected void backupfilesCustomOptionsSetEnabled()
2790   {
2791     boolean enabled = customiseCheckbox.isSelected();
2792
2793     backupfilesRevertButtonSetEnabled(enabled);
2794     backupfilesSuffixTemplateSetEnabled(enabled);
2795     backupfilesKeepAllSetEnabled(enabled);
2796   }
2797
2798   private void backupfilesSummarySetEnabled()
2799   {
2800     boolean enabled = enableBackupFiles.isSelected();
2801     backupfilesExampleLabel.setEnabled(enabled);
2802     exampleFilesPanel.setEnabled(enabled);
2803   }
2804
2805   private void backupfilesPresetsSetEnabled()
2806   {
2807     boolean enabled = enableBackupFiles.isSelected();
2808     presetsPanel.setEnabled(enabled);
2809     presetsComboLabel.setEnabled(enabled);
2810     backupfilesPresetsCombo.setEnabled(enabled);
2811     customiseCheckbox.setEnabled(enabled);
2812     revertButton.setEnabled(enabled);
2813   }
2814
2815   protected void backupsOptionsSetEnabled()
2816   {
2817     backupfilesPresetsSetEnabled();
2818     backupfilesSummarySetEnabled();
2819     backupfilesCustomOptionsSetEnabled();
2820   }
2821
2822   protected void backupsSetOptions(String suffix, int digits,
2823           boolean reverse, boolean keepAll, int rollMax,
2824           boolean confirmDelete)
2825   {
2826     suffixTemplate.setText(suffix);
2827     suffixDigitsSpinner.setValue(digits);
2828     suffixReverse.setSelected(reverse);
2829     backupfilesKeepAll.setSelected(keepAll);
2830     backupfilesRollMaxSpinner.setValue(rollMax);
2831     backupfilesConfirmDelete.setSelected(confirmDelete);
2832   }
2833
2834   protected void backupsSetOptions(BackupFilesPresetEntry p)
2835   {
2836     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
2837             p.confirmDelete);
2838   }
2839
2840   protected void autoIdWidth_actionPerformed()
2841   {
2842     // TODO Auto-generated method stub
2843
2844   }
2845
2846   protected void userIdWidth_actionPerformed()
2847   {
2848     // TODO Auto-generated method stub
2849
2850   }
2851
2852   protected void maxColour_actionPerformed(JPanel panel)
2853   {
2854   }
2855
2856   protected void minColour_actionPerformed(JPanel panel)
2857   {
2858   }
2859
2860   protected void gapColour_actionPerformed(JPanel panel)
2861   {
2862   }
2863
2864   protected void hiddenColour_actionPerformed(JPanel panel)
2865   {
2866   }
2867
2868   protected void showunconserved_actionPerformed(ActionEvent e)
2869   {
2870     // TODO Auto-generated method stub
2871
2872   }
2873
2874   protected void useLegacyGaps_actionPerformed(ActionEvent e)
2875   {
2876   }
2877
2878   protected void resetOvDefaults_actionPerformed(ActionEvent e)
2879   {
2880   }
2881
2882   /**
2883    * DOCUMENT ME!
2884    *
2885    * @param e
2886    *          DOCUMENT ME!
2887    */
2888   public void ok_actionPerformed(ActionEvent e)
2889   {
2890   }
2891
2892   /**
2893    * DOCUMENT ME!
2894    *
2895    * @param e
2896    *          DOCUMENT ME!
2897    */
2898   public void cancel_actionPerformed(ActionEvent e)
2899   {
2900   }
2901
2902   /**
2903    * DOCUMENT ME!
2904    *
2905    * @param e
2906    *          DOCUMENT ME!
2907    */
2908   public void annotations_actionPerformed(ActionEvent e)
2909   {
2910   }
2911
2912   /**
2913    * DOCUMENT ME!
2914    */
2915   public void startupFileTextfield_mouseClicked()
2916   {
2917   }
2918
2919   public void newLink_actionPerformed(ActionEvent e)
2920   {
2921
2922   }
2923
2924   public void editLink_actionPerformed(ActionEvent e)
2925   {
2926
2927   }
2928
2929   public void deleteLink_actionPerformed(ActionEvent e)
2930   {
2931
2932   }
2933
2934   public void defaultBrowser_mouseClicked(MouseEvent e)
2935   {
2936
2937   }
2938
2939   public void linkURLList_keyTyped(KeyEvent e)
2940   {
2941
2942   }
2943
2944   public void setProxyAuthEnabled()
2945   {
2946     boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
2947     proxyAuthUsernameLabel.setEnabled(enabled);
2948     proxyAuthPasswordLabel.setEnabled(enabled);
2949     proxyAuthUsernameTB.setEnabled(enabled);
2950     proxyAuthPasswordTB.setEnabled(enabled);
2951   }
2952
2953   public void setCustomProxyEnabled()
2954   {
2955     boolean enabled = customProxy.isSelected();
2956     portLabel.setEnabled(enabled);
2957     serverLabel.setEnabled(enabled);
2958     portLabel2.setEnabled(enabled);
2959     serverLabel2.setEnabled(enabled);
2960     httpLabel.setEnabled(enabled);
2961     httpsLabel.setEnabled(enabled);
2962     proxyServerHttpTB.setEnabled(enabled);
2963     proxyPortHttpTB.setEnabled(enabled);
2964     proxyServerHttpsTB.setEnabled(enabled);
2965     proxyPortHttpsTB.setEnabled(enabled);
2966     proxyAuth.setEnabled(enabled);
2967     setProxyAuthEnabled();
2968   }
2969
2970   public void proxyType_actionPerformed()
2971   {
2972     setCustomProxyEnabled();
2973   }
2974
2975   public void proxyAuth_actionPerformed()
2976   {
2977     setProxyAuthEnabled();
2978   }
2979
2980   /**
2981    * Customer renderer for JTable: supports column of radio buttons
2982    */
2983   public class RadioButtonRenderer extends JRadioButton
2984           implements TableCellRenderer
2985   {
2986     public RadioButtonRenderer()
2987     {
2988       setHorizontalAlignment(CENTER);
2989       setToolTipText(MessageManager.getString("label.urltooltip"));
2990     }
2991
2992     @Override
2993     public Component getTableCellRendererComponent(JTable table,
2994             Object value, boolean isSelected, boolean hasFocus, int row,
2995             int column)
2996     {
2997       setSelected((boolean) value);
2998
2999       // set colours to match rest of table
3000       if (isSelected)
3001       {
3002         setBackground(table.getSelectionBackground());
3003         setForeground(table.getSelectionForeground());
3004       }
3005       else
3006       {
3007         setBackground(table.getBackground());
3008         setForeground(table.getForeground());
3009       }
3010       return this;
3011     }
3012   }
3013
3014   /**
3015    * Customer cell editor for JTable: supports column of radio buttons in
3016    * conjunction with renderer
3017    */
3018   public class RadioButtonEditor extends AbstractCellEditor
3019           implements TableCellEditor
3020   {
3021     private JRadioButton button = new JRadioButton();
3022
3023     public RadioButtonEditor()
3024     {
3025       button.setHorizontalAlignment(SwingConstants.CENTER);
3026       this.button.addActionListener(new ActionListener()
3027       {
3028         @Override
3029         public void actionPerformed(ActionEvent e)
3030         {
3031           fireEditingStopped();
3032         }
3033       });
3034     }
3035
3036     @Override
3037     public Component getTableCellEditorComponent(JTable table, Object value,
3038             boolean isSelected, int row, int column)
3039     {
3040       button.setSelected((boolean) value);
3041       return button;
3042     }
3043
3044     @Override
3045     public Object getCellEditorValue()
3046     {
3047       return button.isSelected();
3048     }
3049
3050   }
3051 }