src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.fts.core.FTSDataColumnPreferences;
  25 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  26 import jalview.fts.service.pdb.PDBFTSRestClient;
  27 import jalview.gui.Desktop;
  28 import jalview.gui.JalviewBooleanRadioButtons;
  29 import jalview.gui.JvOptionPane;
  30 import jalview.gui.JvSwingUtils;
  31 import jalview.gui.StructureViewer.ViewerType;
  32 import jalview.io.BackupFilenameParts;
  33 import jalview.io.BackupFiles;
  34 import jalview.io.BackupFilesPresetEntry;
  35 import jalview.io.IntKeyStringValueEntry;
  36 import jalview.util.MessageManager;
  37 import jalview.util.Platform;
  38
  39 import java.awt.BorderLayout;
  40 import java.awt.Color;
  41 import java.awt.Component;
  42 import java.awt.Dimension;
  43 import java.awt.FlowLayout;
  44 import java.awt.Font;
  45 import java.awt.GridBagConstraints;
  46 import java.awt.GridBagLayout;
  47 import java.awt.GridLayout;
  48 import java.awt.Insets;
  49 import java.awt.Rectangle;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.KeyEvent;
  53 import java.awt.event.KeyListener;
  54 import java.awt.event.MouseAdapter;
  55 import java.awt.event.MouseEvent;
  56 import java.util.Arrays;
  57 import java.util.List;
  58
  59 import javax.swing.AbstractButton;
  60 import javax.swing.AbstractCellEditor;
  61 import javax.swing.BorderFactory;
  62 import javax.swing.BoxLayout;
  63 import javax.swing.ButtonGroup;
  64 import javax.swing.DefaultListCellRenderer;
  65 import javax.swing.JButton;
  66 import javax.swing.JCheckBox;
  67 import javax.swing.JComboBox;
  68 import javax.swing.JComponent;
  69 import javax.swing.JFileChooser;
  70 import javax.swing.JLabel;
  71 import javax.swing.JPanel;
  72 import javax.swing.JRadioButton;
  73 import javax.swing.JScrollPane;
  74 import javax.swing.JSpinner;
  75 import javax.swing.JTabbedPane;
  76 import javax.swing.JTable;
  77 import javax.swing.JTextArea;
  78 import javax.swing.JTextField;
  79 import javax.swing.ListSelectionModel;
  80 import javax.swing.SpinnerModel;
  81 import javax.swing.SpinnerNumberModel;
  82 import javax.swing.SwingConstants;
  83 import javax.swing.border.Border;
  84 import javax.swing.border.EmptyBorder;
  85 import javax.swing.border.EtchedBorder;
  86 import javax.swing.border.TitledBorder;
  87 import javax.swing.event.ChangeEvent;
  88 import javax.swing.event.ChangeListener;
  89 import javax.swing.table.TableCellEditor;
  90 import javax.swing.table.TableCellRenderer;
  91
  92 import net.miginfocom.swing.MigLayout;
  93
  94 /**
  95  * Base class for the Preferences panel.
  96  *
  97  * @author $author$
  98  * @version $Revision$
  99  */
 100 public class GPreferences extends JPanel
 101 {
 102   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
 103
 104   private static final Font LABEL_FONT_ITALIC = JvSwingUtils
 105           .getLabelFont(false, true);
 106
 107   private static final Font LABEL_FONT_BOLD = JvSwingUtils
 108           .getLabelFont(true, false);
 109
 110   /*
 111    * Visual tab components
 112    */
 113   protected JCheckBox fullScreen = new JCheckBox();
 114
 115   protected JCheckBox openoverv = new JCheckBox();
 116
 117   protected JCheckBox seqLimit = new JCheckBox();
 118
 119   protected JCheckBox rightAlign = new JCheckBox();
 120
 121   protected JComboBox<String> fontSizeCB = new JComboBox<>();
 122
 123   protected JComboBox<String> fontStyleCB = new JComboBox<>();
 124
 125   protected JComboBox<String> fontNameCB = new JComboBox<>();
 126
 127   protected JCheckBox showOccupancy = new JCheckBox();
 128
 129   protected JCheckBox showUnconserved = new JCheckBox();
 130
 131   protected JCheckBox idItalics = new JCheckBox();
 132
 133   protected JCheckBox smoothFont = new JCheckBox();
 134
 135   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 136
 137   protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 138
 139   protected JCheckBox wrap = new JCheckBox();
 140
 141   protected JComboBox<String> sortby = new JComboBox<>();
 142
 143   protected JComboBox<String> sortAnnBy = new JComboBox<>();
 144
 145   protected JComboBox<String> sortAutocalc = new JComboBox<>();
 146
 147   protected JCheckBox startupCheckbox = new JCheckBox();
 148
 149   protected JTextField startupFileTextfield = new JTextField();
 150
 151   // below are in the 'second column'
 152   protected JCheckBox annotations = new JCheckBox();
 153
 154   protected JCheckBox quality = new JCheckBox();
 155
 156   protected JCheckBox conservation = new JCheckBox();
 157
 158   protected JCheckBox identity = new JCheckBox();
 159
 160   protected JCheckBox showGroupConsensus = new JCheckBox();
 161
 162   protected JCheckBox showGroupConservation = new JCheckBox();
 163
 164   protected JCheckBox showConsensHistogram = new JCheckBox();
 165
 166   protected JCheckBox showConsensLogo = new JCheckBox();
 167
 168   protected JCheckBox showInformationHistogram = new JCheckBox();
 169
 170   protected JCheckBox showHMMLogo = new JCheckBox();
 171
 172   protected JCheckBox showDbRefTooltip = new JCheckBox();
 173
 174   protected JCheckBox showNpTooltip = new JCheckBox();
 175
 176
 177   /*
 178    * Structure tab and components
 179    */
 180   protected JPanel structureTab;
 181
 182   protected JCheckBox structFromPdb = new JCheckBox();
 183
 184   protected JCheckBox useRnaView = new JCheckBox();
 185
 186   protected JCheckBox addSecondaryStructure = new JCheckBox();
 187
 188   protected JCheckBox addTempFactor = new JCheckBox();
 189
 190   protected JComboBox<String> structViewer = new JComboBox<>();
 191
 192   protected JTextField chimeraPath = new JTextField();
 193
 194   protected ButtonGroup mappingMethod = new ButtonGroup();
 195
 196   protected JRadioButton siftsMapping = new JRadioButton();
 197
 198   protected JRadioButton nwMapping = new JRadioButton();
 199
 200   /*
 201    * Colours tab components
 202    */
 203   protected JPanel minColour = new JPanel();
 204
 205   protected JPanel maxColour = new JPanel();
 206
 207   protected JComboBox<String> protColour = new JComboBox<>();
 208
 209   protected JComboBox<String> nucColour = new JComboBox<>();
 210
 211   /*
 212    * Overview tab components
 213    */
 214   protected JPanel gapColour = new JPanel();
 215
 216   protected JPanel hiddenColour = new JPanel();
 217
 218   protected JCheckBox useLegacyGap;
 219
 220   protected JCheckBox showHiddenAtStart;
 221
 222   protected JLabel gapLabel;
 223
 224   /*
 225    * Connections tab components
 226    */
 227   protected JTable linkUrlTable = new JTable();
 228
 229   protected JButton editLink = new JButton();
 230
 231   protected JButton deleteLink = new JButton();
 232
 233   protected JTextField filterTB = new JTextField();
 234
 235   protected JButton doReset = new JButton();
 236
 237   protected JButton userOnly = new JButton();
 238
 239   protected JLabel portLabel = new JLabel();
 240
 241   protected JLabel serverLabel = new JLabel();
 242
 243   protected JTextField proxyServerTB = new JTextField();
 244
 245   protected JTextField proxyPortTB = new JTextField();
 246
 247   protected JTextField defaultBrowser = new JTextField();
 248
 249   protected JCheckBox useProxy = new JCheckBox();
 250
 251   protected JCheckBox usagestats = new JCheckBox();
 252
 253   protected JCheckBox questionnaire = new JCheckBox();
 254
 255   protected JCheckBox versioncheck = new JCheckBox();
 256
 257   /*
 258    * Output tab components
 259    */
 260   protected JComboBox<Object> epsRendering = new JComboBox<>();
 261
 262   protected JComboBox<Object> htmlRendering = new JComboBox<>();
 263
 264   protected JComboBox<Object> svgRendering = new JComboBox<>();
 265
 266   protected JLabel userIdWidthlabel = new JLabel();
 267
 268   protected JCheckBox autoIdWidth = new JCheckBox();
 269
 270   protected JTextField userIdWidth = new JTextField();
 271
 272   protected JCheckBox blcjv = new JCheckBox();
 273
 274   protected JCheckBox pileupjv = new JCheckBox();
 275
 276   protected JCheckBox clustaljv = new JCheckBox();
 277
 278   protected JCheckBox msfjv = new JCheckBox();
 279
 280   protected JCheckBox fastajv = new JCheckBox();
 281
 282   protected JCheckBox pfamjv = new JCheckBox();
 283
 284   protected JCheckBox pirjv = new JCheckBox();
 285
 286   protected JCheckBox modellerOutput = new JCheckBox();
 287
 288   protected JCheckBox embbedBioJSON = new JCheckBox();
 289
 290   /*
 291    * Editing tab components
 292    */
 293   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 294
 295   protected JCheckBox padGaps = new JCheckBox();
 296
 297   protected JCheckBox sortByTree = new JCheckBox();
 298
 299   /*
 300    * hmmer tab and components
 301    */
 302   protected JPanel hmmerTab;
 303
 304   protected JCheckBox hmmrTrimTermini;
 305
 306   protected AbstractButton hmmerBackgroundUniprot;
 307
 308   protected AbstractButton hmmerBackgroundAlignment;
 309
 310   protected JTextField hmmerSequenceCount;
 311
 312   protected JTextField hmmerPath;
 313
 314   protected JTextField cygwinPath;
 315
 316   /*
 317    * Web Services tab
 318    */
 319   protected JPanel wsTab = new JPanel();
 320
 321   /*
 322    * Backups tab components
 323    * a lot of these are member variables instead of local variables only so that they
 324    * can be enabled/disabled easily in one go
 325    */
 326
 327   protected JCheckBox enableBackupFiles = new JCheckBox();
 328
 329   protected JPanel presetsPanel = new JPanel();
 330
 331   protected JLabel presetsComboLabel = new JLabel();
 332
 333   protected JCheckBox customiseCheckbox = new JCheckBox();
 334
 335   protected JButton revertButton = new JButton();
 336
 337   protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 338
 339   private int backupfilesPresetsComboLastSelected = 0;
 340
 341   protected JPanel suffixPanel = new JPanel();
 342
 343   protected JPanel keepfilesPanel = new JPanel();
 344
 345   protected JPanel exampleFilesPanel = new JPanel();
 346
 347   protected JTextField suffixTemplate = new JTextField(null, 8);
 348
 349   protected JLabel suffixTemplateLabel = new JLabel();
 350
 351   protected JLabel suffixDigitsLabel = new JLabel();
 352
 353   protected JSpinner suffixDigitsSpinner = new JSpinner();
 354
 355   protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
 356
 357   protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
 358
 359   public JSpinner backupfilesRollMaxSpinner = new JSpinner();
 360
 361   protected JLabel oldBackupFilesLabel = new JLabel();
 362
 363   protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
 364
 365   protected JTextArea backupfilesExampleLabel = new JTextArea();
 366
 367   /**
 368    * Creates a new GPreferences object.
 369    */
 370   public GPreferences()
 371   {
 372     try
 373     {
 374       jbInit();
 375     } catch (Exception ex)
 376     {
 377       ex.printStackTrace();
 378     }
 379   }
 380
 381   /**
 382    * Construct the panel and its tabbed sub-panels.
 383    *
 384    * @throws Exception
 385    */
 386   private void jbInit() throws Exception
 387   {
 388     final JTabbedPane tabbedPane = new JTabbedPane();
 389     this.setLayout(new BorderLayout());
 390     JPanel okCancelPanel = initOkCancelPanel();
 391     this.add(tabbedPane, BorderLayout.CENTER);
 392     this.add(okCancelPanel, BorderLayout.SOUTH);
 393
 394     tabbedPane.add(initVisualTab(),
 395             MessageManager.getString("label.visual"));
 396
 397     tabbedPane.add(initColoursTab(),
 398             MessageManager.getString("label.colours"));
 399
 400     tabbedPane.add(initOverviewTab(),
 401             MessageManager.getString("label.overview"));
 402
 403     tabbedPane.add(initStructureTab(),
 404             MessageManager.getString("label.structure"));
 405
 406     tabbedPane.add(initConnectionsTab(),
 407             MessageManager.getString("label.connections"));
 408
 409         if (!Platform.isJS())
 410         {
 411           tabbedPane.add(initBackupsTab(),
 412                         MessageManager.getString("label.backups"));
 413         }
 414
 415     tabbedPane.add(initLinksTab(),
 416             MessageManager.getString("label.urllinks"));
 417
 418     tabbedPane.add(initOutputTab(),
 419             MessageManager.getString("label.output"));
 420
 421     tabbedPane.add(initEditingTab(),
 422             MessageManager.getString("label.editing"));
 423
 424     tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
 425
 426     /*
 427      * See WsPreferences for the real work of configuring this tab.
 428      */
 429     if (!Platform.isJS())
 430     {
 431       wsTab.setLayout(new BorderLayout());
 432       tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 433     }
 434
 435     /*
 436      * Handler to validate a tab before leaving it - currently only for
 437      * Structure
 438      */
 439     tabbedPane.addChangeListener(new ChangeListener()
 440     {
 441       private Component lastTab;
 442
 443       @Override
 444       public void stateChanged(ChangeEvent e)
 445       {
 446         if (lastTab == structureTab
 447                 && tabbedPane.getSelectedComponent() != structureTab)
 448         {
 449           if (!validateStructure())
 450           {
 451             tabbedPane.setSelectedComponent(structureTab);
 452             return;
 453           }
 454         }
 455         lastTab = tabbedPane.getSelectedComponent();
 456       }
 457
 458     });
 459   }
 460
 461   /**
 462    * Initialises the Editing tabbed panel.
 463    *
 464    * @return
 465    */
 466   private JPanel initEditingTab()
 467   {
 468     JPanel editingTab = new JPanel();
 469     editingTab.setLayout(null);
 470     autoCalculateConsCheck.setFont(LABEL_FONT);
 471     autoCalculateConsCheck.setText(
 472             MessageManager.getString("label.autocalculate_consensus"));
 473     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 474     padGaps.setFont(LABEL_FONT);
 475     padGaps.setText(
 476             MessageManager.getString("label.pad_gaps_when_editing"));
 477     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 478     sortByTree.setFont(LABEL_FONT);
 479     sortByTree
 480             .setText(MessageManager.getString("label.sort_with_new_tree"));
 481     sortByTree.setToolTipText(MessageManager.getString(
 482             "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 483     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 484     editingTab.add(autoCalculateConsCheck);
 485     editingTab.add(padGaps);
 486     editingTab.add(sortByTree);
 487     return editingTab;
 488   }
 489
 490   /**
 491    * Initialises the hmmer tabbed panel
 492    *
 493    * @return
 494    */
 495   private JPanel initHMMERTab()
 496   {
 497     hmmerTab = new JPanel();
 498     hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
 499     hmmerTab.setLayout(new MigLayout("flowy"));
 500
 501     /*
 502      * path to hmmer binaries folder
 503      */
 504     JPanel installationPanel = new JPanel(new MigLayout("flowy"));
 505     // new FlowLayout(FlowLayout.LEFT));
 506     JvSwingUtils.createTitledBorder(installationPanel,
 507             MessageManager.getString("label.installation"), true);
 508     hmmerTab.add(installationPanel);
 509     JLabel hmmerLocation = new JLabel(
 510             MessageManager.getString("label.hmmer_location"));
 511     hmmerLocation.setFont(LABEL_FONT);
 512     final int pathFieldLength = 40;
 513     hmmerPath = new JTextField(pathFieldLength);
 514     hmmerPath.addMouseListener(new MouseAdapter()
 515     {
 516       @Override
 517       public void mouseClicked(MouseEvent e)
 518       {
 519         if (e.getClickCount() == 2)
 520         {
 521           String chosen = openFileChooser(true);
 522           if (chosen != null)
 523           {
 524             hmmerPath.setText(chosen);
 525             validateHmmerPath();
 526           }
 527         }
 528       }
 529     });
 530     installationPanel.add(hmmerLocation);
 531     installationPanel.add(hmmerPath);
 532
 533     /*
 534      * path to Cygwin binaries folder (for Windows)
 535      */
 536     if (Platform.isWindowsAndNotJS())
 537     {
 538       JLabel cygwinLocation = new JLabel(
 539               MessageManager.getString("label.cygwin_location"));
 540       cygwinLocation.setFont(LABEL_FONT);
 541       cygwinPath = new JTextField(pathFieldLength);
 542       cygwinPath.addMouseListener(new MouseAdapter()
 543       {
 544         @Override
 545         public void mouseClicked(MouseEvent e)
 546         {
 547           if (e.getClickCount() == 2)
 548           {
 549             String chosen = openFileChooser(true);
 550             if (chosen != null)
 551             {
 552               cygwinPath.setText(chosen);
 553               validateCygwinPath();
 554             }
 555           }
 556         }
 557       });
 558       installationPanel.add(cygwinLocation);
 559       installationPanel.add(cygwinPath);
 560     }
 561
 562     /*
 563      * preferences for hmmalign
 564      */
 565     JPanel alignOptionsPanel = new JPanel(new MigLayout());
 566     // new FlowLayout(FlowLayout.LEFT));
 567     JvSwingUtils.createTitledBorder(alignOptionsPanel,
 568             MessageManager.getString("label.hmmalign_options"), true);
 569     hmmerTab.add(alignOptionsPanel);
 570     hmmrTrimTermini = new JCheckBox();
 571     hmmrTrimTermini.setFont(LABEL_FONT);
 572     hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
 573     alignOptionsPanel.add(hmmrTrimTermini);
 574
 575     /*
 576      * preferences for hmmsearch
 577      */
 578     JPanel searchOptions = new JPanel(new MigLayout());
 579     // FlowLayout(FlowLayout.LEFT));
 580     JvSwingUtils.createTitledBorder(searchOptions,
 581             MessageManager.getString("label.hmmsearch_options"), true);
 582     hmmerTab.add(searchOptions);
 583     JLabel sequencesToKeep = new JLabel(
 584             MessageManager.getString("label.no_of_sequences"));
 585     sequencesToKeep.setFont(LABEL_FONT);
 586     searchOptions.add(sequencesToKeep);
 587     hmmerSequenceCount = new JTextField(5);
 588     searchOptions.add(hmmerSequenceCount);
 589
 590     /*
 591      * preferences for Information Content annotation
 592      */
 593     // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
 594     JPanel annotationOptions = new JPanel(new MigLayout("left"));
 595     JvSwingUtils.createTitledBorder(annotationOptions,
 596             MessageManager.getString("label.information_annotation"), true);
 597     // dummy.add(annotationOptions);
 598     hmmerTab.add(annotationOptions);
 599     ButtonGroup backgroundOptions = new ButtonGroup();
 600     hmmerBackgroundUniprot = new JRadioButton(
 601             MessageManager.getString("label.freq_uniprot"));
 602     hmmerBackgroundUniprot.setFont(LABEL_FONT);
 603     hmmerBackgroundAlignment = new JRadioButton(
 604             MessageManager.getString("label.freq_alignment"));
 605     hmmerBackgroundAlignment.setFont(LABEL_FONT);
 606     backgroundOptions.add(hmmerBackgroundUniprot);
 607     backgroundOptions.add(hmmerBackgroundAlignment);
 608     backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
 609     // disable buttons for now as annotation only uses Uniprot background
 610     hmmerBackgroundAlignment.setEnabled(false);
 611     hmmerBackgroundUniprot.setEnabled(false);
 612     annotationOptions.add(hmmerBackgroundUniprot, "wrap");
 613     annotationOptions.add(hmmerBackgroundAlignment);
 614
 615     return hmmerTab;
 616   }
 617
 618   /**
 619    * Initialises the Output tabbed panel.
 620    *
 621    * @return
 622    */
 623   private JPanel initOutputTab()
 624   {
 625     JPanel outputTab = new JPanel();
 626     outputTab.setLayout(null);
 627
 628     JLabel epsLabel = new JLabel(
 629             MessageManager.formatMessage("label.rendering_style", "EPS"));
 630     epsLabel.setFont(LABEL_FONT);
 631     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 632     epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
 633     epsRendering.setFont(LABEL_FONT);
 634     epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
 635     JLabel htmlLabel = new JLabel(
 636             MessageManager.formatMessage("label.rendering_style", "HTML"));
 637     htmlLabel.setFont(LABEL_FONT);
 638     htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 639     htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
 640     htmlRendering.setFont(LABEL_FONT);
 641     htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
 642     JLabel svgLabel = new JLabel(
 643             MessageManager.formatMessage("label.rendering_style", "SVG"));
 644     svgLabel.setFont(LABEL_FONT);
 645     svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 646     svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
 647     svgRendering.setFont(LABEL_FONT);
 648     svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
 649
 650     JLabel jLabel1 = new JLabel();
 651     jLabel1.setFont(LABEL_FONT);
 652     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 653     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 654     jLabel1.setFont(LABEL_FONT);
 655
 656     fastajv.setFont(LABEL_FONT);
 657     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 658     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 659     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 660     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 661     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 662     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 663     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 664     msfjv.setFont(LABEL_FONT);
 665     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 666     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 667     JPanel jPanel11 = new JPanel();
 668     jPanel11.setFont(LABEL_FONT);
 669     TitledBorder titledBorder2 = new TitledBorder(
 670             MessageManager.getString("label.file_output"));
 671     jPanel11.setBorder(titledBorder2);
 672     jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
 673     GridLayout gridLayout3 = new GridLayout();
 674     jPanel11.setLayout(gridLayout3);
 675     gridLayout3.setRows(8);
 676     blcjv.setFont(LABEL_FONT);
 677     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 678     clustaljv.setFont(LABEL_FONT);
 679     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 680     pfamjv.setFont(LABEL_FONT);
 681     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 682     pileupjv.setFont(LABEL_FONT);
 683     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 684     pirjv.setFont(LABEL_FONT);
 685     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 686     autoIdWidth.setFont(LABEL_FONT);
 687     autoIdWidth.setText(
 688             MessageManager.getString("label.automatically_set_id_width"));
 689     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 690             .getString("label.adjusts_width_generated_eps_png")));
 691     autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
 692     autoIdWidth.addActionListener(new ActionListener()
 693     {
 694
 695       @Override
 696       public void actionPerformed(ActionEvent e)
 697       {
 698         autoIdWidth_actionPerformed();
 699       }
 700     });
 701     userIdWidthlabel.setFont(LABEL_FONT);
 702     userIdWidthlabel.setText(
 703             MessageManager.getString("label.figure_id_column_width"));
 704     userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 705             .getString("label.manually_specify_width_left_column")));
 706     userIdWidthlabel.setToolTipText(
 707             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
 708                     "label.manually_specify_width_left_column")));
 709     userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
 710     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 711     userIdWidth.setText("");
 712     userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
 713     userIdWidth.addActionListener(new ActionListener()
 714     {
 715
 716       @Override
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         userIdWidth_actionPerformed();
 720       }
 721     });
 722     modellerOutput.setFont(LABEL_FONT);
 723     modellerOutput
 724             .setText(MessageManager.getString("label.use_modeller_output"));
 725     modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
 726     embbedBioJSON.setFont(LABEL_FONT);
 727     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 728     embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 729
 730     jPanel11.add(jLabel1);
 731     jPanel11.add(blcjv);
 732     jPanel11.add(clustaljv);
 733     jPanel11.add(fastajv);
 734     jPanel11.add(msfjv);
 735     jPanel11.add(pfamjv);
 736     jPanel11.add(pileupjv);
 737     jPanel11.add(pirjv);
 738     outputTab.add(autoIdWidth);
 739     outputTab.add(userIdWidth);
 740     outputTab.add(userIdWidthlabel);
 741     outputTab.add(modellerOutput);
 742     if (!Platform.isJS())
 743     {
 744       /*
 745        * JalviewJS doesn't support Lineart option or SVG output
 746        */
 747       outputTab.add(embbedBioJSON);
 748       outputTab.add(epsLabel);
 749       outputTab.add(epsRendering);
 750       outputTab.add(htmlLabel);
 751       outputTab.add(htmlRendering);
 752       outputTab.add(svgLabel);
 753       outputTab.add(svgRendering);
 754     }
 755     outputTab.add(jPanel11);
 756     return outputTab;
 757   }
 758
 759   /**
 760    * Initialises the Connections tabbed panel.
 761    *
 762    * @return
 763    */
 764   private JPanel initConnectionsTab()
 765   {
 766     JPanel connectTab = new JPanel();
 767     connectTab.setLayout(new GridBagLayout());
 768
 769     // Label for browser text box
 770     JLabel browserLabel = new JLabel();
 771     browserLabel.setFont(LABEL_FONT);
 772     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 773     browserLabel.setText(
 774             MessageManager.getString("label.default_browser_unix"));
 775     defaultBrowser.setFont(LABEL_FONT);
 776     defaultBrowser.setText("");
 777     final String tooltip = JvSwingUtils.wrapTooltip(true,
 778             MessageManager.getString("label.double_click_to_browse"));
 779     defaultBrowser.setToolTipText(tooltip);
 780     defaultBrowser.addMouseListener(new MouseAdapter()
 781     {
 782       @Override
 783       public void mouseClicked(MouseEvent e)
 784       {
 785         if (e.getClickCount() > 1)
 786         {
 787           defaultBrowser_mouseClicked(e);
 788         }
 789       }
 790     });
 791
 792     JPanel proxyPanel = initConnTabProxyPanel();
 793     initConnTabCheckboxes();
 794
 795     // Add default Browser text box
 796     connectTab.add(browserLabel,
 797             new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
 798                     GridBagConstraints.WEST, GridBagConstraints.NONE,
 799                     new Insets(10, 0, 5, 5), 5, 1));
 800     defaultBrowser.setFont(LABEL_FONT);
 801     defaultBrowser.setText("");
 802
 803     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 804             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 805             new Insets(10, 0, 5, 10), 30, 1));
 806
 807     // Add proxy server panel
 808     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 809             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 810             new Insets(10, 0, 5, 12), 4, 10));
 811
 812     // Add usage stats, version check and questionnaire checkboxes
 813     connectTab.add(usagestats,
 814             new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 815                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 816                     new Insets(0, 2, 5, 5), 70, 1));
 817     connectTab.add(questionnaire,
 818             new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
 819                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 820                     new Insets(0, 2, 5, 10), 70, 1));
 821     connectTab.add(versioncheck,
 822             new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
 823                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 824                     new Insets(0, 2, 5, 5), 70, 1));
 825
 826     versioncheck.setVisible(false);
 827
 828     // Add padding so the panel doesn't look ridiculous
 829     JPanel spacePanel = new JPanel();
 830     connectTab.add(spacePanel,
 831             new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 832                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
 833                     new Insets(0, 0, 0, 5), 70, 1));
 834
 835     return connectTab;
 836   }
 837
 838   /**
 839    * Initialises the Links tabbed panel.
 840    *
 841    * @return
 842    */
 843   private JPanel initLinksTab()
 844   {
 845     JPanel linkTab = new JPanel();
 846     linkTab.setLayout(new GridBagLayout());
 847
 848     // Set up table for Url links
 849     linkUrlTable.getTableHeader().setReorderingAllowed(false);
 850     linkUrlTable.setFillsViewportHeight(true);
 851     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 852     linkUrlTable.setAutoCreateRowSorter(true);
 853     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 854
 855     // adjust row height so radio buttons actually fit
 856     // don't do this in the renderer, it causes the awt thread to activate
 857     // constantly
 858     JRadioButton temp = new JRadioButton();
 859     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 860
 861     // Table in scrollpane so that the table is given a scrollbar
 862     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 863     linkScrollPane.setBorder(null);
 864
 865     // Panel for links functionality
 866     JPanel linkPanel = new JPanel(new GridBagLayout());
 867     linkPanel.setBorder(new TitledBorder(
 868             MessageManager.getString("label.url_linkfrom_sequence_id")));
 869
 870     // Put the Url links panel together
 871
 872     // Buttons go at top right, resizing only resizes the blank space vertically
 873     JPanel buttonPanel = initLinkTabUrlButtons();
 874     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 875     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 876     linkConstraints1.gridx = 0;
 877     linkConstraints1.gridy = 0;
 878     linkConstraints1.weightx = 1.0;
 879     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 880     linkTab.add(buttonPanel, linkConstraints1);
 881
 882     // Links table goes at top left, resizing resizes the table
 883     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 884     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 885     linkConstraints2.gridx = 0;
 886     linkConstraints2.gridy = 1;
 887     linkConstraints2.weightx = 1.0;
 888     linkConstraints2.weighty = 1.0;
 889     linkConstraints2.fill = GridBagConstraints.BOTH;
 890     linkTab.add(linkScrollPane, linkConstraints2);
 891
 892     // Filter box and buttons goes at bottom left, resizing resizes the text box
 893     JPanel filterPanel = initLinkTabFilterPanel();
 894     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 895     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 896     linkConstraints3.gridx = 0;
 897     linkConstraints3.gridy = 2;
 898     linkConstraints3.weightx = 1.0;
 899     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 900     linkTab.add(filterPanel, linkConstraints3);
 901
 902     return linkTab;
 903   }
 904
 905   private JPanel initLinkTabFilterPanel()
 906   {
 907     // Filter textbox and reset button
 908     JLabel filterLabel = new JLabel(
 909             MessageManager.getString("label.filter"));
 910     filterLabel.setFont(LABEL_FONT);
 911     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 912     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 913
 914     filterTB.setFont(LABEL_FONT);
 915     filterTB.setText("");
 916
 917     doReset.setText(MessageManager.getString("action.showall"));
 918     userOnly.setText(MessageManager.getString("action.customfilter"));
 919
 920     // Panel for filter functionality
 921     JPanel filterPanel = new JPanel(new GridBagLayout());
 922     filterPanel.setBorder(new TitledBorder("Filter"));
 923     GridBagConstraints gbc = new GridBagConstraints();
 924     gbc.gridx = 0;
 925     gbc.gridy = 0;
 926     gbc.fill = GridBagConstraints.NONE;
 927     gbc.anchor = GridBagConstraints.WEST;
 928
 929     filterPanel.add(filterLabel, gbc);
 930
 931     GridBagConstraints gbc1 = new GridBagConstraints();
 932     gbc1.gridx = 1;
 933     gbc1.gridwidth = 2;
 934     gbc1.fill = GridBagConstraints.HORIZONTAL;
 935     gbc1.anchor = GridBagConstraints.WEST;
 936     gbc1.weightx = 1.0;
 937     filterPanel.add(filterTB, gbc1);
 938
 939     GridBagConstraints gbc2 = new GridBagConstraints();
 940     gbc2.gridx = 3;
 941     gbc2.fill = GridBagConstraints.NONE;
 942     gbc2.anchor = GridBagConstraints.WEST;
 943     filterPanel.add(doReset, gbc2);
 944
 945     GridBagConstraints gbc3 = new GridBagConstraints();
 946     gbc3.gridx = 4;
 947     gbc3.fill = GridBagConstraints.NONE;
 948     gbc3.anchor = GridBagConstraints.WEST;
 949     filterPanel.add(userOnly, gbc3);
 950
 951     return filterPanel;
 952   }
 953
 954   private JPanel initLinkTabUrlButtons()
 955   {
 956     // Buttons for new / edit / delete Url links
 957     JButton newLink = new JButton();
 958     newLink.setText(MessageManager.getString("action.new"));
 959
 960     editLink.setText(MessageManager.getString("action.edit"));
 961
 962     deleteLink.setText(MessageManager.getString("action.delete"));
 963
 964     // no current selection, so initially disable delete/edit buttons
 965     editLink.setEnabled(false);
 966     deleteLink.setEnabled(false);
 967
 968     newLink.addActionListener(new java.awt.event.ActionListener()
 969     {
 970       @Override
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         newLink_actionPerformed(e);
 974       }
 975     });
 976
 977     editLink.setText(MessageManager.getString("action.edit"));
 978     editLink.addActionListener(new java.awt.event.ActionListener()
 979     {
 980       @Override
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         editLink_actionPerformed(e);
 984       }
 985     });
 986
 987     deleteLink.setText(MessageManager.getString("action.delete"));
 988     deleteLink.addActionListener(new java.awt.event.ActionListener()
 989     {
 990       @Override
 991       public void actionPerformed(ActionEvent e)
 992       {
 993         deleteLink_actionPerformed(e);
 994       }
 995     });
 996
 997     JPanel buttonPanel = new JPanel(new GridBagLayout());
 998     buttonPanel.setBorder(new TitledBorder("Edit links"));
 999     GridBagConstraints gbc = new GridBagConstraints();
1000     gbc.gridx = 0;
1001     gbc.gridy = 0;
1002     gbc.fill = GridBagConstraints.NONE;
1003     buttonPanel.add(newLink, gbc);
1004
1005     GridBagConstraints gbc1 = new GridBagConstraints();
1006     gbc1.gridx = 1;
1007     gbc1.gridy = 0;
1008     gbc1.fill = GridBagConstraints.NONE;
1009     buttonPanel.add(editLink, gbc1);
1010
1011     GridBagConstraints gbc2 = new GridBagConstraints();
1012     gbc2.gridx = 2;
1013     gbc2.gridy = 0;
1014     gbc2.fill = GridBagConstraints.NONE;
1015     buttonPanel.add(deleteLink, gbc2);
1016
1017     GridBagConstraints gbc3 = new GridBagConstraints();
1018     gbc3.gridx = 3;
1019     gbc3.gridy = 0;
1020     gbc3.fill = GridBagConstraints.HORIZONTAL;
1021     gbc3.weightx = 1.0;
1022     JPanel spacePanel = new JPanel();
1023     spacePanel.setBorder(null);
1024     buttonPanel.add(spacePanel, gbc3);
1025
1026     return buttonPanel;
1027   }
1028
1029   /**
1030    * Initialises the proxy server panel in the Connections tab
1031    *
1032    * @return the proxy server panel
1033    */
1034   private JPanel initConnTabProxyPanel()
1035   {
1036     // Label for server text box
1037     serverLabel.setText(MessageManager.getString("label.address"));
1038     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1039     serverLabel.setFont(LABEL_FONT);
1040
1041     // Proxy server and port text boxes
1042     proxyServerTB.setFont(LABEL_FONT);
1043     proxyPortTB.setFont(LABEL_FONT);
1044
1045     // Label for Port text box
1046     portLabel.setFont(LABEL_FONT);
1047     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1048     portLabel.setText(MessageManager.getString("label.port"));
1049
1050     // Use proxy server checkbox
1051     useProxy.setFont(LABEL_FONT);
1052     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
1053     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
1054     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
1055     useProxy.addActionListener(new ActionListener()
1056     {
1057       @Override
1058       public void actionPerformed(ActionEvent e)
1059       {
1060         useProxy_actionPerformed();
1061       }
1062     });
1063
1064     // Make proxy server panel
1065     JPanel proxyPanel = new JPanel();
1066     TitledBorder titledBorder1 = new TitledBorder(
1067             MessageManager.getString("label.proxy_server"));
1068     proxyPanel.setBorder(titledBorder1);
1069     proxyPanel.setLayout(new GridBagLayout());
1070     proxyPanel.add(serverLabel,
1071             new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
1072                     GridBagConstraints.WEST, GridBagConstraints.NONE,
1073                     new Insets(0, 2, 2, 0), 5, 0));
1074     proxyPanel.add(portLabel,
1075             new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
1076                     GridBagConstraints.WEST, GridBagConstraints.NONE,
1077                     new Insets(0, 0, 2, 0), 11, 0));
1078     proxyPanel.add(useProxy,
1079             new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
1080                     GridBagConstraints.WEST, GridBagConstraints.NONE,
1081                     new Insets(0, 2, 5, 185), 2, -4));
1082     proxyPanel.add(proxyPortTB,
1083             new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
1084                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
1085                     new Insets(0, 2, 2, 2), 54, 1));
1086     proxyPanel.add(proxyServerTB,
1087             new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
1088                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
1089                     new Insets(0, 2, 2, 0), 263, 1));
1090
1091     return proxyPanel;
1092   }
1093
1094   /**
1095    * Initialises the checkboxes in the Connections tab
1096    */
1097   private void initConnTabCheckboxes()
1098   {
1099     // Usage stats checkbox label
1100     usagestats.setText(
1101             MessageManager.getString("label.send_usage_statistics"));
1102     usagestats.setFont(LABEL_FONT);
1103     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1104     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1105
1106     // Questionnaire checkbox label
1107     questionnaire.setText(
1108             MessageManager.getString("label.check_for_questionnaires"));
1109     questionnaire.setFont(LABEL_FONT);
1110     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1111     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1112
1113     // Check for latest version checkbox label
1114     versioncheck.setText(
1115             MessageManager.getString("label.check_for_latest_version"));
1116     versioncheck.setFont(LABEL_FONT);
1117     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1118     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1119   }
1120
1121   /**
1122    * Initialises the parent panel which contains the tabbed sections.
1123    *
1124    * @return
1125    */
1126   private JPanel initOkCancelPanel()
1127   {
1128     JButton ok = new JButton();
1129     ok.setText(MessageManager.getString("action.ok"));
1130     ok.addActionListener(new ActionListener()
1131     {
1132       @Override
1133       public void actionPerformed(ActionEvent e)
1134       {
1135         ok_actionPerformed(e);
1136       }
1137     });
1138     JButton cancel = new JButton();
1139     cancel.setText(MessageManager.getString("action.cancel"));
1140     cancel.addActionListener(new ActionListener()
1141     {
1142       @Override
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         cancel_actionPerformed(e);
1146       }
1147     });
1148     JPanel okCancelPanel = new JPanel();
1149     okCancelPanel.add(ok);
1150     okCancelPanel.add(cancel);
1151     return okCancelPanel;
1152   }
1153
1154   /**
1155    * Initialises the Colours tabbed panel.
1156    *
1157    * @return
1158    */
1159   private JPanel initColoursTab()
1160   {
1161     JPanel coloursTab = new JPanel();
1162     coloursTab.setBorder(new TitledBorder(
1163             MessageManager.getString("action.open_new_alignment")));
1164     coloursTab.setLayout(new FlowLayout());
1165     JLabel mincolourLabel = new JLabel();
1166     mincolourLabel.setFont(LABEL_FONT);
1167     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1168     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1169     minColour.setFont(LABEL_FONT);
1170     minColour.setBorder(BorderFactory.createEtchedBorder());
1171     minColour.setPreferredSize(new Dimension(40, 20));
1172     minColour.addMouseListener(new MouseAdapter()
1173     {
1174       @Override
1175       public void mousePressed(MouseEvent e)
1176       {
1177         minColour_actionPerformed(minColour);
1178       }
1179     });
1180     JLabel maxcolourLabel = new JLabel();
1181     maxcolourLabel.setFont(LABEL_FONT);
1182     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1183     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1184     maxColour.setFont(LABEL_FONT);
1185     maxColour.setBorder(BorderFactory.createEtchedBorder());
1186     maxColour.setPreferredSize(new Dimension(40, 20));
1187     maxColour.addMouseListener(new MouseAdapter()
1188     {
1189       @Override
1190       public void mousePressed(MouseEvent e)
1191       {
1192         maxColour_actionPerformed(maxColour);
1193       }
1194     });
1195
1196     protColour.setFont(LABEL_FONT);
1197     protColour.setBounds(new Rectangle(172, 225, 155, 21));
1198     JLabel protColourLabel = new JLabel();
1199     protColourLabel.setFont(LABEL_FONT);
1200     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1201     protColourLabel.setText(
1202             MessageManager.getString("label.prot_alignment_colour") + " ");
1203     GPreferences.addtoLayout(coloursTab,
1204             MessageManager
1205                     .getString("label.default_colour_scheme_for_alignment"),
1206             protColourLabel, protColour);
1207
1208     nucColour.setFont(LABEL_FONT);
1209     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1210     JLabel nucColourLabel = new JLabel();
1211     nucColourLabel.setFont(LABEL_FONT);
1212     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1213     nucColourLabel.setText(
1214             MessageManager.getString("label.nuc_alignment_colour") + " ");
1215     GPreferences.addtoLayout(coloursTab,
1216             MessageManager
1217                     .getString("label.default_colour_scheme_for_alignment"),
1218             nucColourLabel, nucColour);
1219
1220     JPanel annotationShding = new JPanel();
1221     annotationShding.setBorder(new TitledBorder(
1222             MessageManager.getString("label.annotation_shading_default")));
1223     annotationShding.setLayout(new GridLayout(1, 2));
1224     GPreferences.addtoLayout(annotationShding,
1225             MessageManager.getString(
1226                     "label.default_minimum_colour_annotation_shading"),
1227             mincolourLabel, minColour);
1228     GPreferences.addtoLayout(annotationShding,
1229             MessageManager.getString(
1230                     "label.default_maximum_colour_annotation_shading"),
1231             maxcolourLabel, maxColour);
1232     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1233     return coloursTab;
1234   }
1235
1236   /**
1237    * Initialises the Overview tabbed panel.
1238    *
1239    * @return
1240    */
1241   private JPanel initOverviewTab()
1242   {
1243     JPanel overviewPanel = new JPanel();
1244     overviewPanel.setBorder(new TitledBorder(
1245             MessageManager.getString("label.overview_settings")));
1246
1247     gapColour.setFont(LABEL_FONT);
1248     // fixing the border colours stops apparent colour bleed from the panel
1249     gapColour.setBorder(
1250             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1251     gapColour.setPreferredSize(new Dimension(40, 20));
1252     gapColour.addMouseListener(new MouseAdapter()
1253     {
1254       @Override
1255       public void mousePressed(MouseEvent e)
1256       {
1257         gapColour_actionPerformed(gapColour);
1258       }
1259     });
1260
1261     hiddenColour.setFont(LABEL_FONT);
1262     // fixing the border colours stops apparent colour bleed from the panel
1263     hiddenColour.setBorder(
1264             BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1265     hiddenColour.setPreferredSize(new Dimension(40, 20));
1266     hiddenColour.addMouseListener(new MouseAdapter()
1267     {
1268       @Override
1269       public void mousePressed(MouseEvent e)
1270       {
1271         hiddenColour_actionPerformed(hiddenColour);
1272       }
1273     });
1274
1275     useLegacyGap = new JCheckBox(
1276             MessageManager.getString("label.ov_legacy_gap"));
1277     useLegacyGap.setFont(LABEL_FONT);
1278     useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1279     useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1280     gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1281     gapLabel.setFont(LABEL_FONT);
1282     gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1283     gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1284     showHiddenAtStart = new JCheckBox(
1285             MessageManager.getString("label.ov_show_hide_default"));
1286     showHiddenAtStart.setFont(LABEL_FONT);
1287     showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1288     showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1289     JLabel hiddenLabel = new JLabel(
1290             MessageManager.getString("label.hidden_colour"));
1291     hiddenLabel.setFont(LABEL_FONT);
1292     hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1293     hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1294
1295     useLegacyGap.addActionListener(new ActionListener()
1296     {
1297       @Override
1298       public void actionPerformed(ActionEvent e)
1299       {
1300         useLegacyGaps_actionPerformed(e);
1301       }
1302     });
1303
1304     overviewPanel.setLayout(new GridBagLayout());
1305     GridBagConstraints c1 = new GridBagConstraints();
1306
1307     c1.fill = GridBagConstraints.HORIZONTAL;
1308     c1.gridx = 0;
1309     c1.gridy = 0;
1310     c1.weightx = 1;
1311     c1.ipady = 20;
1312     c1.anchor = GridBagConstraints.FIRST_LINE_START;
1313     overviewPanel.add(useLegacyGap, c1);
1314
1315     GridBagConstraints c2 = new GridBagConstraints();
1316     c2.fill = GridBagConstraints.HORIZONTAL;
1317     c2.gridx = 1;
1318     c2.gridy = 0;
1319     c2.insets = new Insets(0, 15, 0, 10);
1320     overviewPanel.add(gapLabel, c2);
1321
1322     GridBagConstraints c3 = new GridBagConstraints();
1323     c3.fill = GridBagConstraints.HORIZONTAL;
1324     c3.gridx = 2;
1325     c3.gridy = 0;
1326     c3.insets = new Insets(0, 0, 0, 15);
1327     overviewPanel.add(gapColour, c3);
1328
1329     GridBagConstraints c4 = new GridBagConstraints();
1330     c4.fill = GridBagConstraints.HORIZONTAL;
1331     c4.gridx = 0;
1332     c4.gridy = 1;
1333     c4.weightx = 1;
1334     overviewPanel.add(showHiddenAtStart, c4);
1335
1336     GridBagConstraints c5 = new GridBagConstraints();
1337     c5.fill = GridBagConstraints.HORIZONTAL;
1338     c5.gridx = 1;
1339     c5.gridy = 1;
1340     c5.insets = new Insets(0, 15, 0, 10);
1341     overviewPanel.add(hiddenLabel, c5);
1342
1343     GridBagConstraints c6 = new GridBagConstraints();
1344     c6.fill = GridBagConstraints.HORIZONTAL;
1345     c6.gridx = 2;
1346     c6.gridy = 1;
1347     c6.insets = new Insets(0, 0, 0, 15);
1348     overviewPanel.add(hiddenColour, c6);
1349
1350     JButton resetButton = new JButton(
1351             MessageManager.getString("label.reset_to_defaults"));
1352
1353     resetButton.addActionListener(new ActionListener()
1354     {
1355       @Override
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         resetOvDefaults_actionPerformed(e);
1359       }
1360     });
1361
1362     GridBagConstraints c7 = new GridBagConstraints();
1363     c7.fill = GridBagConstraints.NONE;
1364     c7.gridx = 0;
1365     c7.gridy = 2;
1366     c7.insets = new Insets(10, 0, 0, 0);
1367     c7.anchor = GridBagConstraints.WEST;
1368     overviewPanel.add(resetButton, c7);
1369
1370     // Add padding so the panel doesn't look ridiculous
1371     JPanel spacePanel = new JPanel();
1372     overviewPanel.add(spacePanel,
1373             new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1374                     GridBagConstraints.WEST, GridBagConstraints.BOTH,
1375                     new Insets(0, 0, 0, 5), 0, 0));
1376
1377     return overviewPanel;
1378   }
1379
1380   /**
1381    * Initialises the Structure tabbed panel.
1382    *
1383    * @return
1384    */
1385   private JPanel initStructureTab()
1386   {
1387     structureTab = new JPanel();
1388
1389     structureTab.setBorder(new TitledBorder(
1390             MessageManager.getString("label.structure_options")));
1391     structureTab.setLayout(null);
1392     final int width = 400;
1393     final int height = 22;
1394     final int lineSpacing = 25;
1395     int ypos = 15;
1396
1397     structFromPdb.setFont(LABEL_FONT);
1398     structFromPdb
1399             .setText(MessageManager.getString("label.struct_from_pdb"));
1400     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1401     structFromPdb.addActionListener(new ActionListener()
1402     {
1403       @Override
1404       public void actionPerformed(ActionEvent e)
1405       {
1406         boolean selected = structFromPdb.isSelected();
1407         // enable other options only when the first is checked
1408         useRnaView.setEnabled(selected);
1409         addSecondaryStructure.setEnabled(selected);
1410         addTempFactor.setEnabled(selected);
1411       }
1412     });
1413     structureTab.add(structFromPdb);
1414
1415     // indent checkboxes that are conditional on the first one
1416     ypos += lineSpacing;
1417     useRnaView.setFont(LABEL_FONT);
1418     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1419     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1420     structureTab.add(useRnaView);
1421
1422     ypos += lineSpacing;
1423     addSecondaryStructure.setFont(LABEL_FONT);
1424     addSecondaryStructure
1425             .setText(MessageManager.getString("label.autoadd_secstr"));
1426     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1427     structureTab.add(addSecondaryStructure);
1428
1429     ypos += lineSpacing;
1430     addTempFactor.setFont(LABEL_FONT);
1431     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1432     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1433     structureTab.add(addTempFactor);
1434
1435     ypos += lineSpacing;
1436     JLabel viewerLabel = new JLabel();
1437     viewerLabel.setFont(LABEL_FONT);
1438     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1439     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1440     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1441     structureTab.add(viewerLabel);
1442
1443     structViewer.setFont(LABEL_FONT);
1444     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1445     structViewer.addItem(ViewerType.JMOL.name());
1446     structViewer.addItem(ViewerType.CHIMERA.name());
1447     structViewer.addActionListener(new ActionListener()
1448     {
1449       @Override
1450       public void actionPerformed(ActionEvent e)
1451       {
1452         structureViewer_actionPerformed(
1453                 (String) structViewer.getSelectedItem());
1454       }
1455     });
1456     structureTab.add(structViewer);
1457
1458     ypos += lineSpacing;
1459     JLabel pathLabel = new JLabel();
1460     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1461     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1462     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1463     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1464     structureTab.add(pathLabel);
1465
1466     chimeraPath.setFont(LABEL_FONT);
1467     chimeraPath.setText("");
1468     final String tooltip = JvSwingUtils.wrapTooltip(true,
1469             MessageManager.getString("label.chimera_path_tip"));
1470     chimeraPath.setToolTipText(tooltip);
1471     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1472     chimeraPath.addMouseListener(new MouseAdapter()
1473     {
1474       @Override
1475       public void mouseClicked(MouseEvent e)
1476       {
1477         if (e.getClickCount() == 2)
1478         {
1479           String chosen = openFileChooser(false);
1480           if (chosen != null)
1481           {
1482             chimeraPath.setText(chosen);
1483           }
1484         }
1485       }
1486     });
1487     structureTab.add(chimeraPath);
1488
1489     ypos += lineSpacing;
1490     nwMapping.setFont(LABEL_FONT);
1491     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1492     siftsMapping.setFont(LABEL_FONT);
1493     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1494     mappingMethod.add(nwMapping);
1495     mappingMethod.add(siftsMapping);
1496     JPanel mappingPanel = new JPanel();
1497     mappingPanel.setFont(LABEL_FONT);
1498     TitledBorder mmTitledBorder = new TitledBorder(
1499             MessageManager.getString("label.mapping_method"));
1500     mmTitledBorder.setTitleFont(LABEL_FONT);
1501     mappingPanel.setBorder(mmTitledBorder);
1502     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1503     // GridLayout mappingLayout = new GridLayout();
1504     mappingPanel.setLayout(new GridLayout());
1505     mappingPanel.add(nwMapping);
1506     mappingPanel.add(siftsMapping);
1507     structureTab.add(mappingPanel);
1508
1509     ypos += lineSpacing;
1510     ypos += lineSpacing;
1511     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1512             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1513     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1514     structureTab.add(docFieldPref);
1515
1516     /*
1517      * hide Chimera options in JalviewJS
1518      */
1519     if (Platform.isJS())
1520     {
1521       pathLabel.setVisible(false);
1522       chimeraPath.setVisible(false);
1523       viewerLabel.setVisible(false);
1524       structViewer.setVisible(false);
1525     }
1526
1527     return structureTab;
1528   }
1529
1530   /**
1531    * Action on choosing a structure viewer from combobox options.
1532    *
1533    * @param selectedItem
1534    */
1535   protected void structureViewer_actionPerformed(String selectedItem)
1536   {
1537   }
1538
1539   /**
1540    * Show a dialog for the user to choose a file. Returns the chosen path, or
1541    * null on Cancel.
1542    *
1543    * @return
1544    */
1545   protected String openFileChooser(boolean forFolder)
1546   {
1547     String choice = null;
1548     JFileChooser chooser = new JFileChooser();
1549     if (forFolder)
1550     {
1551       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1552     }
1553
1554     // chooser.setFileView(new JalviewFileView());
1555     chooser.setDialogTitle(
1556             MessageManager.getString("label.open_local_file"));
1557     chooser.setToolTipText(MessageManager.getString("action.open"));
1558
1559     int value = chooser.showOpenDialog(this);
1560
1561     if (value == JFileChooser.APPROVE_OPTION)
1562     {
1563       choice = chooser.getSelectedFile().getPath();
1564     }
1565     return choice;
1566   }
1567
1568   protected boolean validateStructure()
1569   {
1570     return false;
1571   }
1572
1573   /**
1574    * Initialises the Visual tabbed panel.
1575    *
1576    * @return
1577    */
1578   private JPanel initVisualTab()
1579   {
1580     JPanel visualTab = new JPanel();
1581     visualTab.setBorder(new TitledBorder(
1582             MessageManager.getString("action.open_new_alignment")));
1583     visualTab.setLayout(null);
1584     fullScreen.setFont(LABEL_FONT);
1585     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1586     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1587     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1588     quality.setEnabled(false);
1589     quality.setFont(LABEL_FONT);
1590     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1591     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1592     quality.setSelected(true);
1593     quality.setText(MessageManager.getString("label.quality"));
1594     conservation.setEnabled(false);
1595     conservation.setFont(LABEL_FONT);
1596     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1597     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1598     conservation.setSelected(true);
1599     conservation.setText(MessageManager.getString("label.conservation"));
1600     identity.setEnabled(false);
1601     identity.setFont(LABEL_FONT);
1602     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1603     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1604     identity.setSelected(true);
1605     identity.setText(MessageManager.getString("label.consensus"));
1606     showOccupancy.setFont(LABEL_FONT);
1607     showOccupancy.setEnabled(false);
1608     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1609     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1610     showOccupancy.setSelected(true);
1611     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1612
1613     JLabel showGroupbits = new JLabel();
1614     showGroupbits.setFont(LABEL_FONT);
1615     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1616     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1617     showGroupbits
1618             .setText(MessageManager.getString("action.show_group") + ":");
1619     JLabel showConsensbits = new JLabel();
1620     showConsensbits.setFont(LABEL_FONT);
1621     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1622     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1623     showConsensbits
1624             .setText(MessageManager.getString("label.consensus") + ":");
1625     showConsensHistogram.setEnabled(false);
1626     showConsensHistogram.setFont(LABEL_FONT);
1627     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1628     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1629     showConsensHistogram.setSelected(true);
1630     showConsensHistogram
1631             .setText(MessageManager.getString("label.histogram"));
1632     showConsensLogo.setEnabled(false);
1633     showConsensLogo.setFont(LABEL_FONT);
1634     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1635     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1636     showConsensLogo.setSelected(true);
1637     showConsensLogo.setText(MessageManager.getString("label.logo"));
1638     showGroupConsensus.setEnabled(false);
1639     showGroupConsensus.setFont(LABEL_FONT);
1640     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1641     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1642     showGroupConsensus.setSelected(true);
1643     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1644     showGroupConservation.setEnabled(false);
1645     showGroupConservation.setFont(LABEL_FONT);
1646     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1647     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1648     showGroupConservation.setSelected(true);
1649     showGroupConservation
1650             .setText(MessageManager.getString("label.conservation"));
1651     showNpTooltip.setEnabled(true);
1652     showNpTooltip.setFont(LABEL_FONT);
1653     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1654     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1655     showNpTooltip.setSelected(true);
1656     showNpTooltip.setText(
1657             MessageManager.getString("label.non_positional_features"));
1658     showDbRefTooltip.setEnabled(true);
1659     showDbRefTooltip.setFont(LABEL_FONT);
1660     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1661     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1662     showDbRefTooltip.setSelected(true);
1663     showDbRefTooltip
1664             .setText(MessageManager.getString("label.database_references"));
1665     annotations.setFont(LABEL_FONT);
1666     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1667     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1668     annotations.setSelected(true);
1669     annotations.setText(MessageManager.getString("label.show_annotations"));
1670     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1671     annotations.addActionListener(new ActionListener()
1672     {
1673       @Override
1674       public void actionPerformed(ActionEvent e)
1675       {
1676         annotations_actionPerformed(e);
1677       }
1678     });
1679     identity.addActionListener(new ActionListener()
1680     {
1681       @Override
1682       public void actionPerformed(ActionEvent e)
1683       {
1684         annotations_actionPerformed(e);
1685       }
1686     });
1687     showGroupConsensus.addActionListener(new ActionListener()
1688     {
1689       @Override
1690       public void actionPerformed(ActionEvent e)
1691       {
1692         annotations_actionPerformed(e);
1693       }
1694     });
1695     showUnconserved.setFont(LABEL_FONT);
1696     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1697     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1698     showUnconserved.setSelected(true);
1699     showUnconserved
1700             .setText(MessageManager.getString("action.show_unconserved"));
1701     showUnconserved.addActionListener(new ActionListener()
1702     {
1703       @Override
1704       public void actionPerformed(ActionEvent e)
1705       {
1706         showunconserved_actionPerformed(e);
1707       }
1708     });
1709
1710     // TODO these are not yet added to / action from Preferences
1711     // JCheckBox shareSelections = new JCheckBox();
1712     // shareSelections.setFont(verdana11);
1713     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1714     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1715     // shareSelections.setSelected(true);
1716     // shareSelections.setText(MessageManager
1717     // .getString("label.share_selection_across_views"));
1718     // JCheckBox followHighlight = new JCheckBox();
1719     // followHighlight.setFont(verdana11);
1720     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1721     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1722     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1723     // followHighlight.setSelected(true);
1724     // followHighlight.setText(MessageManager
1725     // .getString("label.scroll_highlighted_regions"));
1726
1727     seqLimit.setFont(LABEL_FONT);
1728     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1729     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1730     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1731     smoothFont.setFont(LABEL_FONT);
1732     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1733     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1734     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1735     scaleProteinToCdna.setFont(LABEL_FONT);
1736     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1737     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1738     scaleProteinToCdna.setText(
1739             MessageManager.getString("label.scale_protein_to_cdna"));
1740     scaleProteinToCdna.setToolTipText(
1741             MessageManager.getString("label.scale_protein_to_cdna_tip"));
1742     JLabel gapLabel = new JLabel();
1743     gapLabel.setFont(LABEL_FONT);
1744     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1745     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1746     JLabel fontLabel = new JLabel();
1747     fontLabel.setFont(LABEL_FONT);
1748     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1749     fontLabel.setText(MessageManager.getString("label.font"));
1750     fontSizeCB.setFont(LABEL_FONT);
1751     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1752     fontStyleCB.setFont(LABEL_FONT);
1753     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1754     fontNameCB.setFont(LABEL_FONT);
1755     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1756     gapSymbolCB.setFont(LABEL_FONT);
1757     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1758     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1759     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1760     gapSymbolCB.setRenderer(dlcr);
1761
1762     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1763     startupCheckbox.setFont(LABEL_FONT);
1764     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1765     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1766     startupCheckbox.setSelected(true);
1767     startupFileTextfield.setFont(LABEL_FONT);
1768     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1769     final String tooltip = JvSwingUtils.wrapTooltip(true,
1770             MessageManager.getString("label.double_click_to_browse"));
1771     startupFileTextfield.setToolTipText(tooltip);
1772     startupFileTextfield.addMouseListener(new MouseAdapter()
1773     {
1774       @Override
1775       public void mouseClicked(MouseEvent e)
1776       {
1777         if (e.getClickCount() > 1)
1778         {
1779           startupFileTextfield_mouseClicked();
1780         }
1781       }
1782     });
1783
1784     sortby.setFont(LABEL_FONT);
1785     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1786     JLabel sortLabel = new JLabel();
1787     sortLabel.setFont(LABEL_FONT);
1788     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1789     sortLabel.setText(MessageManager.getString("label.sort_by"));
1790     sortAnnBy.setFont(LABEL_FONT);
1791     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1792     JLabel sortAnnLabel = new JLabel();
1793     sortAnnLabel.setFont(LABEL_FONT);
1794     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1795     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1796     sortAutocalc.setFont(LABEL_FONT);
1797     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1798
1799     JPanel annsettingsPanel = new JPanel();
1800     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1801     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1802     annsettingsPanel.setBorder(new EtchedBorder());
1803     visualTab.add(annsettingsPanel);
1804     Border jb = new EmptyBorder(1, 1, 4, 5);
1805     annotations.setBorder(jb);
1806     showOccupancy.setBorder(jb);
1807     quality.setBorder(jb);
1808     conservation.setBorder(jb);
1809     identity.setBorder(jb);
1810     showConsensbits.setBorder(jb);
1811     showGroupbits.setBorder(jb);
1812     showGroupConsensus.setBorder(jb);
1813     showGroupConservation.setBorder(jb);
1814     showConsensHistogram.setBorder(jb);
1815     showConsensLogo.setBorder(jb);
1816
1817     JPanel autoAnnotSettings = new JPanel();
1818     annsettingsPanel.add(autoAnnotSettings);
1819     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1820     autoAnnotSettings.add(annotations);
1821     autoAnnotSettings.add(quality);
1822     // second row of autoannotation box
1823     autoAnnotSettings = new JPanel();
1824     annsettingsPanel.add(autoAnnotSettings);
1825
1826     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1827     autoAnnotSettings.add(conservation);
1828     autoAnnotSettings.add(identity);
1829     autoAnnotSettings.add(showOccupancy);
1830     autoAnnotSettings.add(showGroupbits);
1831     autoAnnotSettings.add(showGroupConservation);
1832     autoAnnotSettings.add(showGroupConsensus);
1833     autoAnnotSettings.add(showConsensbits);
1834     autoAnnotSettings.add(showConsensHistogram);
1835     autoAnnotSettings.add(showConsensLogo);
1836
1837     JPanel tooltipSettings = new JPanel();
1838     tooltipSettings.setBorder(new TitledBorder(
1839             MessageManager.getString("label.sequence_id_tooltip")));
1840     tooltipSettings.setBounds(173, 140, 220, 62);
1841     tooltipSettings.setLayout(new GridLayout(2, 1));
1842     tooltipSettings.add(showDbRefTooltip);
1843     tooltipSettings.add(showNpTooltip);
1844     visualTab.add(tooltipSettings);
1845
1846     wrap.setFont(LABEL_FONT);
1847     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1848     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1849     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1850     rightAlign.setFont(LABEL_FONT);
1851     rightAlign.setForeground(Color.black);
1852     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1853     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1854     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1855     idItalics.setFont(LABEL_FONT_ITALIC);
1856     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1857     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1858     idItalics.setText(
1859             MessageManager.getString("label.sequence_name_italics"));
1860     openoverv.setFont(LABEL_FONT);
1861     openoverv.setActionCommand(
1862             MessageManager.getString("label.open_overview"));
1863     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1864     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1865     openoverv.setText(MessageManager.getString("label.open_overview"));
1866     JPanel jPanel2 = new JPanel();
1867     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1868     jPanel2.setLayout(new GridLayout(14, 1));
1869     jPanel2.add(fullScreen);
1870     jPanel2.add(openoverv);
1871     jPanel2.add(seqLimit);
1872     jPanel2.add(rightAlign);
1873     jPanel2.add(fontLabel);
1874     jPanel2.add(showUnconserved);
1875     jPanel2.add(idItalics);
1876     jPanel2.add(smoothFont);
1877     jPanel2.add(scaleProteinToCdna);
1878     jPanel2.add(gapLabel);
1879     jPanel2.add(wrap);
1880     jPanel2.add(sortLabel);
1881     jPanel2.add(sortAnnLabel);
1882     jPanel2.add(startupCheckbox);
1883     visualTab.add(jPanel2);
1884     visualTab.add(startupFileTextfield);
1885     visualTab.add(sortby);
1886     visualTab.add(sortAnnBy);
1887     visualTab.add(sortAutocalc);
1888     visualTab.add(gapSymbolCB);
1889     visualTab.add(fontNameCB);
1890     visualTab.add(fontSizeCB);
1891     visualTab.add(fontStyleCB);
1892
1893     if (Platform.isJS())
1894     {
1895       startupCheckbox.setVisible(false);
1896       startupFileTextfield.setVisible(false);
1897     }
1898
1899     return visualTab;
1900   }
1901
1902   /**
1903    * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
1904    */
1905
1906   protected void loadLastSavedBackupsOptions()
1907   {
1908     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
1909             .getSavedBackupEntry();
1910     enableBackupFiles
1911             .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
1912
1913     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
1914             .createBackupFilesPresetEntry(Cache
1915                     .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
1916     if (backupfilesCustomEntry == null)
1917     {
1918       backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1919               .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
1920     }
1921     BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1922             BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
1923             backupfilesCustomEntry);
1924
1925     setComboIntStringKey(backupfilesPresetsCombo,
1926             Cache.getDefault(BackupFiles.NS + "_PRESET",
1927                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
1928
1929     backupsSetOptions(savedPreset);
1930
1931     backupsOptionsSetEnabled();
1932     updateBackupFilesExampleLabel();
1933   }
1934
1935   private boolean warnAboutSuffixReverseChange()
1936   {
1937     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
1938             .getSavedBackupEntry();
1939     boolean savedSuffixReverse = bfpe.reverse;
1940     int savedSuffixDigits = bfpe.digits;
1941     String savedSuffixTemplate = bfpe.suffix;
1942
1943     boolean nowSuffixReverse = suffixReverse.isSelected();
1944     int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
1945     String nowSuffixTemplate = suffixTemplate.getText();
1946     return nowSuffixReverse != savedSuffixReverse
1947             && nowSuffixDigits == savedSuffixDigits
1948             && nowSuffixTemplate != null
1949             && nowSuffixTemplate.equals(savedSuffixTemplate);
1950   }
1951
1952   /**
1953    * Initialises the Backups tabbed panel.
1954    *
1955    * @return
1956    */
1957   private JPanel initBackupsTab()
1958   {
1959     JPanel backupsTab = new JPanel();
1960     backupsTab.setBorder(new TitledBorder(
1961             MessageManager.getString("label.backup_files")));
1962     backupsTab.setLayout(new GridBagLayout());
1963
1964     GridBagConstraints gbc = new GridBagConstraints();
1965     gbc.weightx = 0.0;
1966     gbc.weighty = 0.0;
1967     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
1968     gbc.fill = GridBagConstraints.NONE;
1969
1970     initBackupsTabPresetsPanel();
1971     initBackupsTabSuffixPanel();
1972     initBackupsTabKeepFilesPanel();
1973     initBackupsTabFilenameExamplesPanel();
1974
1975     enableBackupFiles.setFont(LABEL_FONT_BOLD);
1976     enableBackupFiles
1977             .setText(MessageManager.getString("label.enable_backupfiles"));
1978     enableBackupFiles.addActionListener(new ActionListener()
1979     {
1980       @Override
1981       public void actionPerformed(ActionEvent e)
1982       {
1983         // enable other options only when the first is checked
1984         backupsOptionsSetEnabled();
1985       }
1986     });
1987
1988
1989     // enable checkbox 1 col
1990     gbc.gridwidth = 1;
1991     gbc.gridheight = 1;
1992     gbc.gridx = 0;
1993     gbc.gridy = 0; // row 0
1994     backupsTab.add(enableBackupFiles, gbc);
1995
1996     // summary of scheme box (over two rows)
1997     gbc.gridx = 1;
1998     gbc.weightx = 0.0;
1999     gbc.gridheight = 2;
2000     gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2001     gbc.fill = GridBagConstraints.BOTH;
2002     backupsTab.add(exampleFilesPanel, gbc);
2003     gbc.gridheight = 1;
2004     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2005     gbc.fill = GridBagConstraints.NONE;
2006
2007     // fill empty space on right
2008     gbc.gridx++;
2009     gbc.weightx = 1.0;
2010     backupsTab.add(new JPanel(), gbc);
2011
2012     // schemes box
2013     gbc.weightx = 0.0;
2014     gbc.gridx = 0;
2015     gbc.gridy++; // row 1
2016     backupsTab.add(presetsPanel, gbc);
2017
2018     // now using whole row
2019     gbc.gridwidth = 2;
2020     gbc.gridheight = 1;
2021     // keep files box
2022     gbc.gridx = 0;
2023     gbc.gridy++; // row 2
2024     backupsTab.add(keepfilesPanel, gbc);
2025
2026     // filename strategy box
2027     gbc.gridy++; // row 3
2028     backupsTab.add(suffixPanel, gbc);
2029
2030     // fill empty space
2031     gbc.gridy++; // row 4
2032     gbc.weighty = 1.0;
2033     backupsTab.add(new JPanel(), gbc);
2034
2035     backupsOptionsSetEnabled();
2036     return backupsTab;
2037   }
2038
2039   private JPanel initBackupsTabPresetsPanel()
2040   {
2041
2042     String title = MessageManager.getString("label.schemes");
2043
2044     presetsPanel.setLayout(new GridBagLayout());
2045
2046     GridBagConstraints gbc = new GridBagConstraints();
2047     gbc.weightx = 0.0;
2048     gbc.weighty = 0.0;
2049     gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2050     gbc.fill = GridBagConstraints.NONE;
2051     gbc.gridwidth = 1;
2052     gbc.gridheight = 1;
2053
2054     // "Scheme: "
2055     gbc.gridx = 0;
2056     gbc.gridy = 0;
2057
2058     presetsComboLabel = new JLabel(title + ":");
2059     presetsPanel.add(presetsComboLabel, gbc);
2060
2061     List<Object> entries = Arrays
2062             .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2063     List<String> tooltips = Arrays.asList(
2064             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2065     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2066             tooltips);
2067     /*
2068     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2069     {
2070       backupfilesPresetsCombo
2071               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2072     }
2073     */
2074
2075     backupfilesPresetsCombo.addActionListener(new ActionListener()
2076     {
2077       @Override
2078       public void actionPerformed(ActionEvent e)
2079       {
2080         int key = getComboIntStringKey(backupfilesPresetsCombo);
2081         if (!customiseCheckbox.isSelected())
2082         {
2083           backupfilesPresetsComboLastSelected = key;
2084         }
2085         if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2086         {
2087           if (customiseCheckbox.isSelected())
2088           {
2089             // got here by clicking on customiseCheckbox so don't change the values
2090             backupfilesCustomOptionsSetEnabled();
2091           }
2092           else
2093           {
2094             backupsTabUpdatePresets();
2095             backupfilesCustomOptionsSetEnabled();
2096           }
2097         }
2098         else
2099         {
2100           customiseCheckbox.setSelected(false);
2101           backupsTabUpdatePresets();
2102           backupfilesCustomOptionsSetEnabled();
2103         }
2104       }
2105     });
2106
2107     // dropdown list of preset schemes
2108     gbc.gridx = 1;
2109     presetsPanel.add(backupfilesPresetsCombo, gbc);
2110
2111     revertButton.setText(MessageManager.getString("label.cancel_changes"));
2112     revertButton.setToolTipText(
2113             MessageManager.getString("label.cancel_changes_description"));
2114     revertButton.addActionListener(new ActionListener()
2115     {
2116       @Override
2117       public void actionPerformed(ActionEvent e)
2118       {
2119         backupsSetOptions(
2120                 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2121                         BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2122         backupfilesCustomOptionsSetEnabled();
2123       }
2124
2125     });
2126     revertButton.setFont(LABEL_FONT);
2127
2128     customiseCheckbox.setFont(LABEL_FONT);
2129     customiseCheckbox.setText(MessageManager.getString("label.customise"));
2130     customiseCheckbox.addActionListener(new ActionListener()
2131     {
2132       @Override
2133       public void actionPerformed(ActionEvent e)
2134       {
2135         int currently = getComboIntStringKey(backupfilesPresetsCombo);
2136         if (customiseCheckbox.isSelected())
2137         {
2138           backupfilesPresetsComboLastSelected = currently;
2139           setComboIntStringKey(backupfilesPresetsCombo,
2140                   BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2141         }
2142         else
2143         {
2144           setComboIntStringKey(backupfilesPresetsCombo,
2145                   backupfilesPresetsComboLastSelected);
2146
2147         }
2148         backupfilesCustomOptionsSetEnabled();
2149       }
2150     });
2151     customiseCheckbox.setToolTipText(
2152             MessageManager.getString("label.customise_description"));
2153
2154     // customise checkbox
2155     gbc.gridx = 0;
2156     gbc.gridy++;
2157     presetsPanel.add(customiseCheckbox, gbc);
2158
2159     // "Cancel changes" button (aligned with combo box above)
2160     gbc.gridx = 1;
2161     presetsPanel.add(revertButton, gbc);
2162
2163     return presetsPanel;
2164   }
2165
2166   private JPanel initBackupsTabFilenameExamplesPanel()
2167   {
2168     String title = MessageManager
2169             .getString("label.scheme_examples");
2170     TitledBorder tb = new TitledBorder(title);
2171     exampleFilesPanel.setBorder(tb);
2172     exampleFilesPanel.setLayout(new GridBagLayout());
2173
2174
2175     backupfilesExampleLabel.setEditable(false);
2176     backupfilesExampleLabel
2177             .setBackground(exampleFilesPanel.getBackground());
2178
2179     updateBackupFilesExampleLabel();
2180
2181     GridBagConstraints gbc = new GridBagConstraints();
2182     gbc.weightx = 1.0;
2183     gbc.weighty = 1.0;
2184     gbc.fill = GridBagConstraints.NONE;
2185     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2186
2187     exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2188     return exampleFilesPanel;
2189   }
2190
2191   private void backupsTabUpdatePresets()
2192   {
2193     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2194             .getSelectedItem();
2195     int key = entry.k;
2196     String value = entry.v;
2197
2198     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2199             .containsKey(key))
2200     {
2201       backupsSetOptions(
2202               BackupFilesPresetEntry.backupfilesPresetEntriesValues
2203                       .get(key));
2204     }
2205     else
2206     {
2207       Cache.log.error(
2208               "Preset '" + value + "' [key:" + key + "] not implemented");
2209     }
2210
2211     // Custom options will now be enabled when the customiseCheckbox is checked
2212     // (performed above)
2213     // backupfilesCustomOptionsSetEnabled();
2214     updateBackupFilesExampleLabel();
2215   }
2216
2217   protected int getComboIntStringKey(
2218           JComboBox<Object> backupfilesPresetsCombo2)
2219   {
2220     IntKeyStringValueEntry e;
2221     try
2222     {
2223       e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2224               .getSelectedItem();
2225     } catch (Exception ex)
2226     {
2227       Cache.log.error(
2228               "Problem casting Combo entry to IntKeyStringValueEntry.");
2229       e = null;
2230     }
2231     return e != null ? e.k : 0;
2232   }
2233
2234   protected void setComboIntStringKey(
2235           JComboBox<Object> backupfilesPresetsCombo2,
2236           int key)
2237   {
2238     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2239     {
2240       IntKeyStringValueEntry e;
2241       try
2242       {
2243         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2244       } catch (Exception ex)
2245       {
2246         Cache.log.error(
2247                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2248         continue;
2249       }
2250       if (e.k == key)
2251       {
2252         backupfilesPresetsCombo2.setSelectedIndex(i);
2253         break;
2254       }
2255     }
2256     // backupsTabUpdatePresets();
2257   }
2258
2259   private JPanel initBackupsTabSuffixPanel()
2260   {
2261     suffixPanel.setBorder(new TitledBorder(
2262             MessageManager.getString("label.backup_filename_strategy")));
2263     suffixPanel.setLayout(new GridBagLayout());
2264
2265     suffixTemplateLabel
2266             .setText(MessageManager.getString("label.append_to_filename"));
2267     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2268     suffixTemplateLabel.setFont(LABEL_FONT);
2269
2270     final String tooltip = JvSwingUtils.wrapTooltip(true,
2271             MessageManager.getString("label.append_to_filename_tooltip"));
2272     suffixTemplate.setToolTipText(tooltip);
2273     suffixTemplate.addActionListener(new ActionListener()
2274     {
2275       @Override
2276       public void actionPerformed(ActionEvent e)
2277       {
2278         updateBackupFilesExampleLabel();
2279         backupfilesCustomOptionsSetEnabled();
2280         backupfilesRevertButtonSetEnabled(true);
2281       }
2282
2283     });
2284     suffixTemplate.addKeyListener(new KeyListener()
2285     {
2286       @Override
2287       public void keyReleased(KeyEvent e)
2288       {
2289         updateBackupFilesExampleLabel();
2290         backupfilesCustomOptionsSetEnabled();
2291         backupfilesRevertButtonSetEnabled(true);
2292       }
2293
2294       @Override
2295       public void keyPressed(KeyEvent e)
2296       {
2297       }
2298
2299       // disable use of ':' or '/' or '\'
2300       @Override
2301       public void keyTyped(KeyEvent e)
2302       {
2303         char c = e.getKeyChar();
2304         if (c == ':' || c == '/' || c == '\\')
2305         {
2306           // don't process ':' or '/' or '\'
2307           e.consume();
2308         }
2309       }
2310
2311     });
2312
2313     // digits spinner
2314     suffixDigitsLabel
2315             .setText(MessageManager.getString("label.index_digits"));
2316     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2317     suffixDigitsLabel.setFont(LABEL_FONT);
2318     ChangeListener c = new ChangeListener()
2319     {
2320       @Override
2321       public void stateChanged(ChangeEvent e)
2322       {
2323         backupfilesRevertButtonSetEnabled(true);
2324         updateBackupFilesExampleLabel();
2325       }
2326
2327     };
2328     setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2329             BackupFilesPresetEntry.DIGITSMAX, 3, c);
2330
2331     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2332             MessageManager.getString("label.increment_index"));
2333     suffixReverse.addActionListener(new ActionListener()
2334     {
2335       @Override
2336       public void actionPerformed(ActionEvent e)
2337       {
2338         boolean okay = true;
2339         if (warnAboutSuffixReverseChange())
2340         {
2341           // Warning popup
2342           okay = confirmSuffixReverseChange();
2343         }
2344         if (okay)
2345         {
2346           backupfilesRevertButtonSetEnabled(true);
2347           updateBackupFilesExampleLabel();
2348         }
2349         else
2350         {
2351           boolean savedSuffixReverse = BackupFilesPresetEntry
2352                   .getSavedBackupEntry().reverse;
2353           suffixReverse.setSelected(savedSuffixReverse);
2354         }
2355       }
2356     });
2357
2358     GridBagConstraints sgbc = new GridBagConstraints();
2359
2360     // first row (template text box)
2361     sgbc.anchor = GridBagConstraints.WEST;
2362     sgbc.gridx = 0;
2363     sgbc.gridy = 0;
2364     sgbc.gridwidth = 1;
2365     sgbc.gridheight = 1;
2366     sgbc.weightx = 1.0;
2367     sgbc.weighty = 0.0;
2368     sgbc.fill = GridBagConstraints.NONE;
2369     suffixPanel.add(suffixTemplateLabel, sgbc);
2370
2371     sgbc.gridx = 1;
2372     sgbc.fill = GridBagConstraints.HORIZONTAL;
2373     suffixPanel.add(suffixTemplate, sgbc);
2374
2375     // second row (number of digits spinner)
2376     sgbc.gridy = 1;
2377
2378     sgbc.gridx = 0;
2379     sgbc.fill = GridBagConstraints.NONE;
2380     suffixPanel.add(suffixDigitsLabel, sgbc);
2381
2382     sgbc.gridx = 1;
2383     sgbc.fill = GridBagConstraints.HORIZONTAL;
2384     suffixPanel.add(suffixDigitsSpinner, sgbc);
2385
2386     // third row (forward order radio selection)
2387     sgbc.gridx = 0;
2388     sgbc.gridy = 2;
2389     sgbc.gridwidth = GridBagConstraints.REMAINDER;
2390     sgbc.fill = GridBagConstraints.HORIZONTAL;
2391     suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2392
2393     // fourth row (reverse order radio selection)
2394     sgbc.gridy = 3;
2395     suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2396     return suffixPanel;
2397   }
2398
2399   private boolean confirmSuffixReverseChange()
2400   {
2401     boolean ret = false;
2402     String warningMessage = MessageManager
2403             .getString("label.warning_confirm_change_reverse");
2404     int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2405             warningMessage,
2406             MessageManager.getString("label.change_increment_decrement"),
2407             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2408
2409     ret = (confirm == JvOptionPane.YES_OPTION);
2410     return ret;
2411   }
2412
2413   private JPanel initBackupsTabKeepFilesPanel()
2414   {
2415     keepfilesPanel.setBorder(
2416             new TitledBorder(MessageManager.getString("label.keep_files")));
2417     keepfilesPanel.setLayout(new GridBagLayout());
2418
2419     backupfilesKeepAll.setLabels(
2420             MessageManager.getString("label.keep_all_backup_files"),
2421             MessageManager.getString(
2422                     "label.keep_only_this_number_of_backup_files"));
2423     backupfilesKeepAll.addTrueActionListener(new ActionListener()
2424     {
2425       @Override
2426       public void actionPerformed(ActionEvent e)
2427       {
2428         backupfilesRevertButtonSetEnabled(true);
2429         updateBackupFilesExampleLabel();
2430       }
2431     });
2432     backupfilesKeepAll.addActionListener(new ActionListener()
2433     {
2434       @Override
2435       public void actionPerformed(ActionEvent e)
2436       {
2437         backupfilesRevertButtonSetEnabled(true);
2438         keepRollMaxOptionsEnabled();
2439         updateBackupFilesExampleLabel();
2440       }
2441     });
2442
2443     ChangeListener c = new ChangeListener()
2444     {
2445       @Override
2446       public void stateChanged(ChangeEvent e)
2447       {
2448         backupfilesRevertButtonSetEnabled(true);
2449         updateBackupFilesExampleLabel();
2450       }
2451
2452     };
2453     setIntegerSpinner(backupfilesRollMaxSpinner,
2454             BackupFilesPresetEntry.ROLLMAXMIN,
2455             BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2456
2457     backupfilesConfirmDelete.setLabels(
2458             MessageManager.getString("label.always_ask"),
2459             MessageManager.getString("label.auto_delete"));
2460     backupfilesConfirmDelete.addActionListener(new ActionListener()
2461     {
2462       @Override
2463       public void actionPerformed(ActionEvent e)
2464       {
2465         backupfilesRevertButtonSetEnabled(true);
2466       }
2467     });
2468     // update the enabled section
2469     keepRollMaxOptionsEnabled();
2470
2471     GridBagConstraints kgbc = new GridBagConstraints();
2472
2473     // first row (template text box)
2474     kgbc.anchor = GridBagConstraints.WEST;
2475     kgbc.gridx = 0;
2476     kgbc.gridy = 0;
2477     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2478     kgbc.gridheight = 1;
2479     kgbc.weightx = 1.0;
2480     kgbc.weighty = 0.0;
2481     kgbc.fill = GridBagConstraints.HORIZONTAL;
2482     keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2483
2484     // second row
2485     kgbc.gridy = 1;
2486
2487     kgbc.gridx = 0;
2488     kgbc.gridwidth = GridBagConstraints.RELATIVE;
2489     keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2490
2491     kgbc.gridx = 1;
2492     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2493     keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2494
2495     // third row (indented)
2496     kgbc.gridy = 2;
2497     kgbc.insets = new Insets(0, 20, 0, 0);
2498
2499     kgbc.gridx = 0;
2500     kgbc.gridwidth = GridBagConstraints.REMAINDER;
2501     kgbc.fill = GridBagConstraints.HORIZONTAL;
2502     kgbc.weightx = 1.0;
2503
2504     JPanel jp = new JPanel();
2505     jp.setLayout(new FlowLayout());
2506     oldBackupFilesLabel
2507             .setText(MessageManager
2508                     .getString("label.autodelete_old_backup_files"));
2509     oldBackupFilesLabel.setFont(LABEL_FONT);
2510     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2511     jp.add(oldBackupFilesLabel);
2512     jp.add(backupfilesConfirmDelete.getTrueButton());
2513     jp.add(backupfilesConfirmDelete.getFalseButton());
2514     keepfilesPanel.add(jp, kgbc);
2515
2516     return keepfilesPanel;
2517   }
2518
2519   protected void updateBackupFilesExampleLabel()
2520   {
2521     int exampleindex = 12;
2522     String base = MessageManager.getString("label.filename") + ".fa";
2523     if (base == null || base.length() == 0)
2524     {
2525       base = "file_name.fa";
2526     }
2527
2528     boolean reverse = suffixReverse.isSelected();
2529     boolean keepAll = backupfilesKeepAll.isSelected();
2530     int rollMax = 4;
2531     String suffix = suffixTemplate.getText();
2532     int digits = 3;
2533
2534     backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2535     if (suffix == null || suffix.length() == 0)
2536     {
2537       backupfilesExampleLabel
2538               .setText(MessageManager.getString("label.no_backup_files"));
2539       backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2540       return;
2541     }
2542
2543     rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2544     rollMax = rollMax < 1 ? 1 : rollMax;
2545
2546     if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2547     {
2548       rollMax = 1;
2549     }
2550
2551     digits = getSpinnerInt(suffixDigitsSpinner, 3);
2552     digits = digits < 1 ? 1 : digits;
2553
2554     int lowersurround = 2;
2555     int uppersurround = 0;
2556     StringBuilder exampleSB = new StringBuilder();
2557     boolean firstLine = true;
2558     int lineNumber = 0;
2559     if (reverse)
2560     {
2561
2562       int min = 1;
2563       int max = keepAll ? exampleindex : rollMax;
2564       for (int index = min; index <= max; index++)
2565       {
2566         if (index == min + lowersurround && index < max - uppersurround - 1)
2567         {
2568           exampleSB.append("\n...");
2569           lineNumber++;
2570         }
2571         else if (index > min + lowersurround && index < max - uppersurround)
2572         {
2573           // nothing
2574         }
2575         else
2576         {
2577           if (firstLine)
2578           {
2579             firstLine = false;
2580           }
2581           else
2582           {
2583             exampleSB.append("\n");
2584             lineNumber++;
2585           }
2586           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2587                   base, suffix, digits));
2588           if (min == max)
2589           {
2590             // no extra text needed
2591           }
2592           else if (index == min)
2593           {
2594             String newest = MessageManager.getString("label.braced_newest");
2595             if (newest != null && newest.length() > 0)
2596             {
2597               exampleSB.append(" " + newest);
2598             }
2599           }
2600           else if (index == max)
2601           {
2602             String oldest = MessageManager.getString("label.braced_oldest");
2603             if (oldest != null && oldest.length() > 0)
2604             {
2605               exampleSB.append(" " + oldest);
2606             }
2607           }
2608         }
2609       }
2610     }
2611     else
2612     {
2613
2614       int min = (keepAll || exampleindex - rollMax < 0) ? 1
2615               : exampleindex - rollMax + 1;
2616       int max = exampleindex;
2617
2618       for (int index = min; index <= max; index++)
2619       {
2620
2621         if (index == min + lowersurround && index < max - uppersurround - 1)
2622         {
2623           exampleSB.append("\n...");
2624           lineNumber++;
2625         }
2626         else if (index > min + lowersurround && index < max - uppersurround)
2627         {
2628           // nothing
2629         }
2630         else
2631         {
2632           if (firstLine)
2633           {
2634             firstLine = false;
2635           }
2636           else
2637           {
2638             exampleSB.append("\n");
2639             lineNumber++;
2640           }
2641           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2642                   base, suffix, digits));
2643           if (min == max)
2644           {
2645             // no extra text needed
2646           }
2647           else if (index == min)
2648           {
2649             String oldest = MessageManager.getString("label.braced_oldest");
2650             if (oldest != null && oldest.length() > 0)
2651             {
2652               exampleSB.append(" " + oldest);
2653             }
2654           }
2655           else if (index == max)
2656           {
2657             String newest = MessageManager.getString("label.braced_newest");
2658             if (newest != null && newest.length() > 0)
2659             {
2660               exampleSB.append(" " + newest);
2661             }
2662           }
2663         }
2664       }
2665
2666     }
2667
2668     // add some extra empty lines to pad out the example files box. ugh, please tell
2669     // me how to do this better
2670     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2671     if (remainingLines > 0)
2672     {
2673       for (int i = 0; i < remainingLines; i++)
2674       {
2675         exampleSB.append("\n ");
2676         lineNumber++;
2677       }
2678     }
2679
2680     backupfilesExampleLabel.setText(exampleSB.toString());
2681   }
2682
2683   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2684           boolean useExistingVal, ChangeListener c)
2685   {
2686     int i = def;
2687     if (useExistingVal)
2688     {
2689       try
2690       {
2691         i = ((Integer) s.getValue()).intValue();
2692       } catch (Exception e)
2693       {
2694         Cache.log.error(
2695                 "Exception casting the initial value of s.getValue()");
2696       }
2697     }
2698
2699     setIntegerSpinner(s, min, max, i, c);
2700   }
2701
2702   protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2703           ChangeListener c)
2704   {
2705     // integer spinner for number of digits
2706     if (def > max)
2707     {
2708       max = def;
2709     }
2710     if (def < min)
2711     {
2712       def = min;
2713     }
2714     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2715     s.setModel(sModel);
2716
2717     s.addChangeListener(c);
2718
2719   }
2720
2721   protected static int getSpinnerInt(JSpinner s, int def)
2722   {
2723     int i = def;
2724     try
2725     {
2726       s.commitEdit();
2727       i = (Integer) s.getValue();
2728     } catch (Exception e)
2729     {
2730       Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2731     }
2732     return i;
2733   }
2734
2735   private void keepRollMaxOptionsEnabled()
2736   {
2737     boolean enabled = backupfilesKeepAll.isEnabled()
2738             && !backupfilesKeepAll.isSelected();
2739     oldBackupFilesLabel.setEnabled(enabled);
2740     backupfilesRollMaxSpinner.setEnabled(enabled);
2741     backupfilesConfirmDelete.setEnabled(enabled);
2742   }
2743
2744   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2745   {
2746     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2747             && customiseCheckbox.isSelected()
2748             && suffixTemplate.getText()
2749                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2750     keepfilesPanel.setEnabled(enabled);
2751     backupfilesKeepAll.setEnabled(enabled);
2752     oldBackupFilesLabel.setEnabled(enabled);
2753     keepRollMaxOptionsEnabled();
2754   }
2755
2756   private void backupfilesSuffixTemplateDigitsSetEnabled()
2757   {
2758     boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2759             .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2760     suffixDigitsLabel.setEnabled(enabled);
2761     suffixDigitsSpinner.setEnabled(enabled);
2762     suffixReverse.setEnabled(enabled);
2763   }
2764
2765   private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2766   {
2767     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2768             && customiseCheckbox.isSelected();
2769     suffixPanel.setEnabled(enabled);
2770     suffixTemplateLabel.setEnabled(enabled);
2771     suffixTemplate.setEnabled(enabled);
2772     backupfilesSuffixTemplateDigitsSetEnabled();
2773   }
2774
2775   private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2776   {
2777     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2778             && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2779     revertButton.setEnabled(enabled);
2780   }
2781
2782   private boolean backupfilesCustomChanged()
2783   {
2784     BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2785             .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2786     BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2787     return !custom.equals(current);
2788   }
2789
2790   protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
2791   {
2792     String suffix = suffixTemplate.getText();
2793     int digits = getSpinnerInt(suffixDigitsSpinner, 3);
2794     boolean reverse = suffixReverse.isSelected();
2795     boolean keepAll = backupfilesKeepAll.isSelected();
2796     int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
2797     boolean confirmDelete = backupfilesConfirmDelete.isSelected();
2798
2799     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
2800             reverse, keepAll, rollMax, confirmDelete);
2801
2802     return bfpe;
2803   }
2804
2805   protected void backupfilesCustomOptionsSetEnabled()
2806   {
2807     boolean enabled = customiseCheckbox.isSelected();
2808
2809     backupfilesRevertButtonSetEnabled(enabled);
2810     backupfilesSuffixTemplateSetEnabled(enabled);
2811     backupfilesKeepAllSetEnabled(enabled);
2812   }
2813
2814   private void backupfilesSummarySetEnabled()
2815   {
2816     boolean enabled = enableBackupFiles.isSelected();
2817     backupfilesExampleLabel.setEnabled(enabled);
2818     exampleFilesPanel.setEnabled(enabled);
2819   }
2820
2821   private void backupfilesPresetsSetEnabled()
2822   {
2823     boolean enabled = enableBackupFiles.isSelected();
2824     presetsPanel.setEnabled(enabled);
2825     presetsComboLabel.setEnabled(enabled);
2826     backupfilesPresetsCombo.setEnabled(enabled);
2827     customiseCheckbox.setEnabled(enabled);
2828     revertButton.setEnabled(enabled);
2829   }
2830
2831   protected void backupsOptionsSetEnabled()
2832   {
2833     backupfilesPresetsSetEnabled();
2834     backupfilesSummarySetEnabled();
2835     backupfilesCustomOptionsSetEnabled();
2836   }
2837
2838   protected void backupsSetOptions(String suffix, int digits,
2839           boolean reverse, boolean keepAll, int rollMax,
2840           boolean confirmDelete)
2841   {
2842     suffixTemplate.setText(suffix);
2843     suffixDigitsSpinner.setValue(digits);
2844     suffixReverse.setSelected(reverse);
2845     backupfilesKeepAll.setSelected(keepAll);
2846     backupfilesRollMaxSpinner.setValue(rollMax);
2847     backupfilesConfirmDelete.setSelected(confirmDelete);
2848   }
2849
2850   protected void backupsSetOptions(BackupFilesPresetEntry p)
2851   {
2852     backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
2853             p.confirmDelete);
2854   }
2855
2856   protected void autoIdWidth_actionPerformed()
2857   {
2858     // TODO Auto-generated method stub
2859
2860   }
2861
2862   protected void userIdWidth_actionPerformed()
2863   {
2864     // TODO Auto-generated method stub
2865
2866   }
2867
2868   protected void maxColour_actionPerformed(JPanel panel)
2869   {
2870   }
2871
2872   protected void minColour_actionPerformed(JPanel panel)
2873   {
2874   }
2875
2876   protected void gapColour_actionPerformed(JPanel panel)
2877   {
2878   }
2879
2880   protected void hiddenColour_actionPerformed(JPanel panel)
2881   {
2882   }
2883
2884   protected void showunconserved_actionPerformed(ActionEvent e)
2885   {
2886     // TODO Auto-generated method stub
2887
2888   }
2889
2890   protected void useLegacyGaps_actionPerformed(ActionEvent e)
2891   {
2892   }
2893
2894   protected void resetOvDefaults_actionPerformed(ActionEvent e)
2895   {
2896   }
2897
2898   /**
2899    * DOCUMENT ME!
2900    *
2901    * @param e
2902    *          DOCUMENT ME!
2903    */
2904   public void ok_actionPerformed(ActionEvent e)
2905   {
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   public void cancel_actionPerformed(ActionEvent e)
2915   {
2916   }
2917
2918   /**
2919    * DOCUMENT ME!
2920    *
2921    * @param e
2922    *          DOCUMENT ME!
2923    */
2924   public void annotations_actionPerformed(ActionEvent e)
2925   {
2926   }
2927
2928   /**
2929    * DOCUMENT ME!
2930    */
2931   public void startupFileTextfield_mouseClicked()
2932   {
2933   }
2934
2935   public void newLink_actionPerformed(ActionEvent e)
2936   {
2937
2938   }
2939
2940   public void editLink_actionPerformed(ActionEvent e)
2941   {
2942
2943   }
2944
2945   public void deleteLink_actionPerformed(ActionEvent e)
2946   {
2947
2948   }
2949
2950   public void defaultBrowser_mouseClicked(MouseEvent e)
2951   {
2952
2953   }
2954
2955   public void linkURLList_keyTyped(KeyEvent e)
2956   {
2957
2958   }
2959
2960   public void useProxy_actionPerformed()
2961   {
2962     boolean enabled = useProxy.isSelected();
2963     portLabel.setEnabled(enabled);
2964     serverLabel.setEnabled(enabled);
2965     proxyServerTB.setEnabled(enabled);
2966     proxyPortTB.setEnabled(enabled);
2967   }
2968
2969   /**
2970    * Customer renderer for JTable: supports column of radio buttons
2971    */
2972   public class RadioButtonRenderer extends JRadioButton
2973           implements TableCellRenderer
2974   {
2975     public RadioButtonRenderer()
2976     {
2977       setHorizontalAlignment(CENTER);
2978       setToolTipText(MessageManager.getString("label.urltooltip"));
2979     }
2980
2981     @Override
2982     public Component getTableCellRendererComponent(JTable table,
2983             Object value, boolean isSelected, boolean hasFocus, int row,
2984             int column)
2985     {
2986       setSelected((boolean) value);
2987
2988       // set colours to match rest of table
2989       if (isSelected)
2990       {
2991         setBackground(table.getSelectionBackground());
2992         setForeground(table.getSelectionForeground());
2993       }
2994       else
2995       {
2996         setBackground(table.getBackground());
2997         setForeground(table.getForeground());
2998       }
2999       return this;
3000     }
3001   }
3002
3003   /**
3004    * Customer cell editor for JTable: supports column of radio buttons in
3005    * conjunction with renderer
3006    */
3007   public class RadioButtonEditor extends AbstractCellEditor
3008           implements TableCellEditor
3009   {
3010     private JRadioButton button = new JRadioButton();
3011
3012     public RadioButtonEditor()
3013     {
3014       button.setHorizontalAlignment(SwingConstants.CENTER);
3015       this.button.addActionListener(new ActionListener()
3016       {
3017         @Override
3018         public void actionPerformed(ActionEvent e)
3019         {
3020           fireEditingStopped();
3021         }
3022       });
3023     }
3024
3025     @Override
3026     public Component getTableCellEditorComponent(JTable table, Object value,
3027             boolean isSelected, int row, int column)
3028     {
3029       button.setSelected((boolean) value);
3030       return button;
3031     }
3032
3033     @Override
3034     public Object getCellEditorValue()
3035     {
3036       return button.isSelected();
3037     }
3038
3039   }
3040
3041   protected void validateHmmerPath()
3042   {
3043   }
3044
3045   protected void validateCygwinPath()
3046   {
3047   }
3048
3049   /**
3050    * A helper method to add a panel containing a label and a component to a
3051    * panel
3052    *
3053    * @param panel
3054    * @param tooltip
3055    * @param label
3056    * @param valBox
3057    */
3058   protected static void addtoLayout(JPanel panel, String tooltip,
3059           JComponent label, JComponent valBox)
3060   {
3061     JPanel laypanel = new JPanel(new GridLayout(1, 2));
3062     JPanel labPanel = new JPanel(new BorderLayout());
3063     JPanel valPanel = new JPanel();
3064     labPanel.setBounds(new Rectangle(7, 7, 158, 23));
3065     valPanel.setBounds(new Rectangle(172, 7, 270, 23));
3066     labPanel.add(label, BorderLayout.WEST);
3067     valPanel.add(valBox);
3068     laypanel.add(labPanel);
3069     laypanel.add(valPanel);
3070     valPanel.setToolTipText(tooltip);
3071     labPanel.setToolTipText(tooltip);
3072     valBox.setToolTipText(tooltip);
3073     panel.add(laypanel);
3074     panel.validate();
3075   }
3076 }
3077