src/jalview/gui/Preferences.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.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  28 import jalview.io.BackupFilesPresetEntry;
  29 import jalview.io.FileFormatI;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32 import jalview.jbgui.GPreferences;
  33 import jalview.jbgui.GSequenceLink;
  34 import jalview.schemes.ColourSchemeI;
  35 import jalview.schemes.ColourSchemes;
  36 import jalview.schemes.ResidueColourScheme;
  37 import jalview.urls.UrlLinkTableModel;
  38 import jalview.urls.api.UrlProviderFactoryI;
  39 import jalview.urls.api.UrlProviderI;
  40 import jalview.urls.desktop.DesktopUrlProviderFactory;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JComboBox;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 109
 110   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 111
 112   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 113
 114   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 115
 116   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 117
 118   public static final String GAP_COLOUR = "GAP_COLOUR";
 119
 120   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 121
 122   private static final int MIN_FONT_SIZE = 1;
 123
 124   private static final int MAX_FONT_SIZE = 30;
 125
 126   /**
 127    * Holds name and link separated with | character. Sequence ID must be
 128    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 129    */
 130   public static UrlProviderI sequenceUrlLinks;
 131
 132   public static UrlLinkTableModel dataModel;
 133
 134   /**
 135    * Holds name and link separated with | character. Sequence IDS and Sequences
 136    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 137    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 138    * for first and second token specified after a pipe character at end |,|.
 139    * (TODO: proper escape for using | to separate ids or sequences
 140    */
 141
 142   public static List<String> groupURLLinks;
 143   static
 144   {
 145     // get links selected to be in the menu (SEQUENCE_LINKS)
 146     // and links entered by the user but not selected (STORED_LINKS)
 147     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 148     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 149     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 150             UrlConstants.DEFAULT_LABEL);
 151
 152     // if both links lists are empty, add the DEFAULT_URL link
 153     // otherwise we assume the default link is in one of the lists
 154     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 155     {
 156       inMenuString = UrlConstants.DEFAULT_STRING;
 157     }
 158     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 159             inMenuString, notInMenuString);
 160     sequenceUrlLinks = factory.createUrlProvider();
 161     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 162
 163     /**
 164      * TODO: reformulate groupURL encoding so two or more can be stored in the
 165      * .properties file as '|' separated strings
 166      */
 167
 168     groupURLLinks = new ArrayList<>();
 169   }
 170
 171   JInternalFrame frame;
 172
 173   private WsPreferences wsPrefs;
 174
 175   private OptionsParam promptEachTimeOpt = new OptionsParam(
 176           MessageManager.getString("label.prompt_each_time"),
 177           "Prompt each time");
 178
 179   private OptionsParam lineArtOpt = new OptionsParam(
 180           MessageManager.getString("label.lineart"), "Lineart");
 181
 182   private OptionsParam textOpt = new OptionsParam(
 183           MessageManager.getString("action.text"), "Text");
 184
 185   /**
 186    * Creates a new Preferences object.
 187    */
 188   public Preferences()
 189   {
 190     super();
 191     frame = new JInternalFrame();
 192     frame.setContentPane(this);
 193     if (!Platform.isJS())
 194     /**
 195      * Java only
 196      *
 197      * @j2sIgnore
 198      */
 199     {
 200       wsPrefs = new WsPreferences();
 201       wsTab.add(wsPrefs, BorderLayout.CENTER);
 202     }
 203     int width = 500, height = 450;
 204     if (Platform.isAMacAndNotJS())
 205     {
 206       width = 570;
 207       height = 480;
 208     }
 209
 210     Desktop.addInternalFrame(frame,
 211             MessageManager.getString("label.preferences"), width, height);
 212     frame.setMinimumSize(new Dimension(width, height));
 213
 214     /*
 215      * Set Visual tab defaults
 216      */
 217     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 218     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 219     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 220     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 221
 222     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 223     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 224     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 225     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 226     showUnconserved
 227             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 228     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 229     showGroupConsensus
 230             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 231     showGroupConservation.setSelected(
 232             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 233     showConsensHistogram.setSelected(
 234             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 235     showConsensLogo
 236             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 237     showNpTooltip
 238             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 239     showDbRefTooltip
 240             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 241
 242     String[] fonts = java.awt.GraphicsEnvironment
 243             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 244     for (int i = 0; i < fonts.length; i++)
 245     {
 246       fontNameCB.addItem(fonts[i]);
 247     }
 248
 249     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 250     {
 251       fontSizeCB.addItem(i + "");
 252     }
 253
 254     fontStyleCB.addItem("plain");
 255     fontStyleCB.addItem("bold");
 256     fontStyleCB.addItem("italic");
 257
 258     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 259     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 260     fontStyleCB.setSelectedItem(
 261             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 262
 263     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 264     scaleProteinToCdna
 265             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 266
 267     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 268
 269     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 270
 271     gapSymbolCB.addItem("-");
 272     gapSymbolCB.addItem(".");
 273
 274     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 275
 276     sortby.addItem("No sort");
 277     sortby.addItem("Id");
 278     sortby.addItem("Pairwise Identity");
 279     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 280
 281     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 282     sortAnnBy
 283             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 284     sortAnnBy
 285             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 286     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 287             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 288                     SequenceAnnotationOrder.NONE.name()));
 289     sortAnnBy.setSelectedItem(savedSort.toString());
 290
 291     sortAutocalc.addItem("Autocalculated first");
 292     sortAutocalc.addItem("Autocalculated last");
 293     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 294     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 295             : sortAutocalc.getItemAt(1));
 296     startupCheckbox
 297             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 298     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 299             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 300                     + "/examples/exampleFile_2_3.jar"));
 301
 302     /*
 303      * Set Colours tab defaults
 304      */
 305     protColour.addItem(ResidueColourScheme.NONE);
 306     nucColour.addItem(ResidueColourScheme.NONE);
 307     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 308     {
 309       String name = cs.getSchemeName();
 310       protColour.addItem(name);
 311       nucColour.addItem(name);
 312     }
 313     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 314             ResidueColourScheme.NONE);
 315     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 316     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 317     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 318     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 319     minColour.setBackground(
 320             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 321     maxColour.setBackground(
 322             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 323
 324     /*
 325      * Set overview panel defaults
 326      */
 327     gapColour.setBackground(
 328             Cache.getDefaultColour(GAP_COLOUR,
 329                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 330     hiddenColour.setBackground(
 331             Cache.getDefaultColour(HIDDEN_COLOUR,
 332                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 333     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 334     gapLabel.setEnabled(!useLegacyGap.isSelected());
 335     gapColour.setEnabled(!useLegacyGap.isSelected());
 336     showHiddenAtStart
 337             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 338
 339     /*
 340      * Set Structure tab defaults.
 341      */
 342     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 343     structFromPdb.setSelected(structSelected);
 344     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 345     useRnaView.setEnabled(structSelected);
 346     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 347     addSecondaryStructure.setEnabled(structSelected);
 348     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 349     addTempFactor.setEnabled(structSelected);
 350     structViewer.setSelectedItem(
 351             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 352     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 353     chimeraPath.addActionListener(new ActionListener()
 354     {
 355       @Override
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         validateChimeraPath();
 359       }
 360     });
 361
 362     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 363     {
 364       siftsMapping.setSelected(true);
 365     }
 366     else
 367     {
 368       nwMapping.setSelected(true);
 369     }
 370
 371     SiftsSettings
 372             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 373
 374     /*
 375      * Set Connections tab defaults
 376      */
 377
 378     // set up sorting
 379     linkUrlTable.setModel(dataModel);
 380     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 381             linkUrlTable.getModel());
 382     linkUrlTable.setRowSorter(sorter);
 383     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 384
 385     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 386     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 387             SortOrder.DESCENDING));
 388     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 389             SortOrder.DESCENDING));
 390     sortKeys.add(
 391             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 392
 393     sorter.setSortKeys(sortKeys);
 394     // BH 2018 setSortKeys will do the sort
 395     // sorter.sort();
 396
 397     // set up filtering
 398     ActionListener onReset;
 399     onReset = new ActionListener()
 400     {
 401       @Override
 402       public void actionPerformed(ActionEvent e)
 403       {
 404         filterTB.setText("");
 405         sorter.setRowFilter(RowFilter.regexFilter(""));
 406       }
 407
 408     };
 409     doReset.addActionListener(onReset);
 410
 411     // filter to display only custom urls
 412     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 413     {
 414       @Override
 415       public boolean include(
 416               Entry<? extends TableModel, ? extends Object> entry)
 417       {
 418         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 419       }
 420     };
 421
 422     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 423             linkUrlTable.getModel());
 424     customSorter.setRowFilter(customUrlFilter);
 425
 426     ActionListener onCustomOnly;
 427     onCustomOnly = new ActionListener()
 428     {
 429       @Override
 430       public void actionPerformed(ActionEvent e)
 431       {
 432         filterTB.setText("");
 433         sorter.setRowFilter(customUrlFilter);
 434       }
 435     };
 436     userOnly.addActionListener(onCustomOnly);
 437
 438     filterTB.getDocument().addDocumentListener(new DocumentListener()
 439     {
 440       String caseInsensitiveFlag = "(?i)";
 441
 442       @Override
 443       public void changedUpdate(DocumentEvent e)
 444       {
 445         sorter.setRowFilter(RowFilter
 446                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 447       }
 448
 449       @Override
 450       public void removeUpdate(DocumentEvent e)
 451       {
 452         sorter.setRowFilter(RowFilter
 453                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 454       }
 455
 456       @Override
 457       public void insertUpdate(DocumentEvent e)
 458       {
 459         sorter.setRowFilter(RowFilter
 460                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 461       }
 462     });
 463
 464     // set up list selection functionality
 465     linkUrlTable.getSelectionModel()
 466             .addListSelectionListener(new UrlListSelectionHandler());
 467
 468     // set up radio buttons
 469     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 470             .getPrimaryColumn();
 471     String onClickName = linkUrlTable.getColumnName(onClickCol);
 472     linkUrlTable.getColumn(onClickName)
 473             .setCellRenderer(new RadioButtonRenderer());
 474     linkUrlTable.getColumn(onClickName)
 475             .setCellEditor(new RadioButtonEditor());
 476
 477     // get boolean columns and resize those to min possible
 478     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 479     {
 480       if (linkUrlTable.getModel().getColumnClass(column)
 481               .equals(Boolean.class))
 482       {
 483         TableColumn tableColumn = linkUrlTable.getColumnModel()
 484                 .getColumn(column);
 485         int preferredWidth = tableColumn.getMinWidth();
 486
 487         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 488                 column);
 489         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 490         int cwidth = c.getPreferredSize().width
 491                 + linkUrlTable.getIntercellSpacing().width;
 492         preferredWidth = Math.max(preferredWidth, cwidth);
 493
 494         tableColumn.setPreferredWidth(preferredWidth);
 495       }
 496     }
 497
 498     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 499     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 500     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 501     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 502
 503     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 504
 505     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 506     // note antisense here: default is true
 507     questionnaire
 508             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 509     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 510
 511     /*
 512      * Set Output tab defaults
 513      */
 514     setupOutputCombo(epsRendering, "EPS_RENDERING");
 515     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 516     setupOutputCombo(svgRendering, "SVG_RENDERING");
 517     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 518     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 519     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 520     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 521     userIdWidth.setText(wi == null ? "" : wi.toString());
 522     // TODO: refactor to use common enum via FormatAdapter and allow extension
 523     // for new flat file formats
 524     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 525     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 526     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 527     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 528     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 529     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 530     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 531     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 532     embbedBioJSON
 533             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 534
 535     /*
 536      * Set Editing tab defaults
 537      */
 538     autoCalculateConsCheck
 539             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 540     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 541     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 542
 543     annotations_actionPerformed(null); // update the display of the annotation
 544                                        // settings
 545
 546
 547     /*
 548      * Set Backups tab defaults
 549      */
 550     loadLastSavedBackupsOptions();
 551   }
 552
 553   /**
 554    * A helper method that sets the items and initial selection in a character
 555    * rendering option list (Prompt each time/Lineart/Text)
 556    *
 557    * @param comboBox
 558    * @param propertyKey
 559    */
 560   protected void setupOutputCombo(JComboBox<Object> comboBox,
 561           String propertyKey)
 562   {
 563     comboBox.addItem(promptEachTimeOpt);
 564     comboBox.addItem(lineArtOpt);
 565     comboBox.addItem(textOpt);
 566
 567     /*
 568      * JalviewJS doesn't support Lineart so force it to Text
 569      */
 570     String defaultOption = Platform.isJS() ? "Text"
 571             : Cache.getDefault(propertyKey, "Prompt each time");
 572     if (defaultOption.equalsIgnoreCase("Text"))
 573     {
 574       comboBox.setSelectedItem(textOpt);
 575     }
 576     else if (defaultOption.equalsIgnoreCase("Lineart"))
 577     {
 578       comboBox.setSelectedItem(lineArtOpt);
 579     }
 580     else
 581     {
 582       comboBox.setSelectedItem(promptEachTimeOpt);
 583     }
 584   }
 585
 586   /**
 587    * Save user selections on the Preferences tabs to the Cache and write out to
 588    * file.
 589    *
 590    * @param e
 591    */
 592   @Override
 593   public void ok_actionPerformed(ActionEvent e)
 594   {
 595     if (!validateSettings())
 596     {
 597       return;
 598     }
 599
 600     /*
 601      * Save Visual settings
 602      */
 603     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 604             Boolean.toString(seqLimit.isSelected()));
 605     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 606             Boolean.toString(rightAlign.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 608             Boolean.toString(fullScreen.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 610             Boolean.toString(openoverv.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 612             Boolean.toString(annotations.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 614             Boolean.toString(conservation.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 616             Boolean.toString(quality.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 618             Boolean.toString(identity.isSelected()));
 619
 620     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 621             gapSymbolCB.getSelectedItem().toString());
 622
 623     Cache.applicationProperties.setProperty("FONT_NAME",
 624             fontNameCB.getSelectedItem().toString());
 625     Cache.applicationProperties.setProperty("FONT_STYLE",
 626             fontStyleCB.getSelectedItem().toString());
 627     Cache.applicationProperties.setProperty("FONT_SIZE",
 628             fontSizeCB.getSelectedItem().toString());
 629
 630     Cache.applicationProperties.setProperty("ID_ITALICS",
 631             Boolean.toString(idItalics.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 633             Boolean.toString(showUnconserved.isSelected()));
 634     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 635             Boolean.toString(showOccupancy.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 637             Boolean.toString(showGroupConsensus.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 639             Boolean.toString(showGroupConservation.isSelected()));
 640     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 641             Boolean.toString(showConsensHistogram.isSelected()));
 642     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 643             Boolean.toString(showConsensLogo.isSelected()));
 644     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 645             Boolean.toString(smoothFont.isSelected()));
 646     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 647             Boolean.toString(scaleProteinToCdna.isSelected()));
 648     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 649             Boolean.toString(showNpTooltip.isSelected()));
 650     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 651             Boolean.toString(showDbRefTooltip.isSelected()));
 652
 653     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 654             Boolean.toString(wrap.isSelected()));
 655
 656     Cache.applicationProperties.setProperty("STARTUP_FILE",
 657             startupFileTextfield.getText());
 658     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 659             Boolean.toString(startupCheckbox.isSelected()));
 660
 661     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 662             sortby.getSelectedItem().toString());
 663
 664     // convert description of sort order to enum name for save
 665     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 666             .forDescription(sortAnnBy.getSelectedItem().toString());
 667     if (annSortOrder != null)
 668     {
 669       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 670               annSortOrder.name());
 671     }
 672
 673     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 674     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 675             Boolean.valueOf(showAutocalcFirst).toString());
 676
 677     /*
 678      * Save Colours settings
 679      */
 680     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 681             protColour.getSelectedItem().toString());
 682     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 683             nucColour.getSelectedItem().toString());
 684     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 685             minColour.getBackground());
 686     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 687             maxColour.getBackground());
 688
 689     /*
 690      * Save Overview settings
 691      */
 692     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 693     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 694     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 695             Boolean.toString(useLegacyGap.isSelected()));
 696     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 697             Boolean.toString(showHiddenAtStart.isSelected()));
 698
 699     /*
 700      * Save Structure settings
 701      */
 702     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 703             Boolean.toString(addTempFactor.isSelected()));
 704     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 705             Boolean.toString(addSecondaryStructure.isSelected()));
 706     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 707             Boolean.toString(useRnaView.isSelected()));
 708     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 709             Boolean.toString(structFromPdb.isSelected()));
 710     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 711             structViewer.getSelectedItem().toString());
 712     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 713     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 714             Boolean.toString(siftsMapping.isSelected()));
 715     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 716
 717     /*
 718      * Save Output settings
 719      */
 720     Cache.applicationProperties.setProperty("EPS_RENDERING",
 721             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 722     Cache.applicationProperties.setProperty("HTML_RENDERING",
 723             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 724     Cache.applicationProperties.setProperty("SVG_RENDERING",
 725             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 726
 727     /*
 728      * Save Connections settings
 729      */
 730     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 731
 732     jalview.util.BrowserLauncher.resetBrowser();
 733
 734     // save user-defined and selected links
 735     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 736     if (menuLinks.isEmpty())
 737     {
 738       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 739     }
 740     else
 741     {
 742       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 743               menuLinks.toString());
 744     }
 745
 746     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 747     if (nonMenuLinks.isEmpty())
 748     {
 749       Cache.applicationProperties.remove("STORED_LINKS");
 750     }
 751     else
 752     {
 753       Cache.applicationProperties.setProperty("STORED_LINKS",
 754               nonMenuLinks.toString());
 755     }
 756
 757     Cache.applicationProperties.setProperty("DEFAULT_URL",
 758             sequenceUrlLinks.getPrimaryUrlId());
 759
 760     Cache.applicationProperties.setProperty("USE_PROXY",
 761             Boolean.toString(useProxy.isSelected()));
 762
 763     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 764
 765     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 766
 767     if (useProxy.isSelected())
 768     {
 769       System.setProperty("http.proxyHost", proxyServerTB.getText());
 770       System.setProperty("http.proxyPort", proxyPortTB.getText());
 771     }
 772     else
 773     {
 774       System.setProperty("http.proxyHost", "");
 775       System.setProperty("http.proxyPort", "");
 776     }
 777     Cache.setProperty("VERSION_CHECK",
 778             Boolean.toString(versioncheck.isSelected()));
 779     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 780     {
 781       // default is false - we only set this if the user has actively agreed
 782       Cache.setProperty("USAGESTATS",
 783               Boolean.toString(usagestats.isSelected()));
 784     }
 785     if (!questionnaire.isSelected())
 786     {
 787       Cache.setProperty("NOQUESTIONNAIRES", "true");
 788     }
 789     else
 790     {
 791       // special - made easy to edit a property file to disable questionnaires
 792       // by just adding the given line
 793       Cache.removeProperty("NOQUESTIONNAIRES");
 794     }
 795
 796     /*
 797      * Save Output settings
 798      */
 799     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 800             Boolean.toString(blcjv.isSelected()));
 801     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 802             Boolean.toString(clustaljv.isSelected()));
 803     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 804             Boolean.toString(fastajv.isSelected()));
 805     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 806             Boolean.toString(msfjv.isSelected()));
 807     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 808             Boolean.toString(pfamjv.isSelected()));
 809     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 810             Boolean.toString(pileupjv.isSelected()));
 811     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 812             Boolean.toString(pirjv.isSelected()));
 813     Cache.applicationProperties.setProperty("PIR_MODELLER",
 814             Boolean.toString(modellerOutput.isSelected()));
 815     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 816             Boolean.toString(embbedBioJSON.isSelected()));
 817     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 818
 819     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 820             Boolean.toString(autoIdWidth.isSelected()));
 821     userIdWidth_actionPerformed();
 822     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 823             userIdWidth.getText());
 824
 825     /*
 826      * Save Editing settings
 827      */
 828     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 829             Boolean.toString(autoCalculateConsCheck.isSelected()));
 830     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 831             Boolean.toString(sortByTree.isSelected()));
 832     Cache.applicationProperties.setProperty("PAD_GAPS",
 833             Boolean.toString(padGaps.isSelected()));
 834
 835     if (!Platform.isJS())
 836     {
 837       wsPrefs.updateAndRefreshWsMenuConfig(false);
 838     }
 839
 840     /*
 841      * Save Backups settings
 842      */
 843     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 844             Boolean.toString(enableBackupFiles.isSelected()));
 845     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 846     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 847
 848     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 849     {
 850       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 851       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 852               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 853       Cache.applicationProperties
 854               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 855                       customBFPE.toString());
 856     }
 857
 858     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 859             .get(preset);
 860     Cache.applicationProperties.setProperty(
 861             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 862
 863     Cache.saveProperties();
 864     Desktop.instance.doConfigureStructurePrefs();
 865     try
 866     {
 867       frame.setClosed(true);
 868     } catch (Exception ex)
 869     {
 870     }
 871   }
 872
 873   /**
 874    * Do any necessary validation before saving settings. Return focus to the
 875    * first tab which fails validation.
 876    *
 877    * @return
 878    */
 879   private boolean validateSettings()
 880   {
 881     if (!validateStructure())
 882     {
 883       structureTab.requestFocusInWindow();
 884       return false;
 885     }
 886     return true;
 887   }
 888
 889   @Override
 890   protected boolean validateStructure()
 891   {
 892     return validateChimeraPath();
 893
 894   }
 895
 896   /**
 897    * DOCUMENT ME!
 898    */
 899   @Override
 900   public void startupFileTextfield_mouseClicked()
 901   {
 902     // TODO: JAL-3048 not needed for Jalview-JS
 903     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 904     JalviewFileChooser chooser = JalviewFileChooser
 905             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 906     chooser.setFileView(new JalviewFileView());
 907     chooser.setDialogTitle(
 908             MessageManager.getString("label.select_startup_file"));
 909
 910     int value = chooser.showOpenDialog(this);
 911
 912     if (value == JalviewFileChooser.APPROVE_OPTION)
 913     {
 914       FileFormatI format = chooser.getSelectedFormat();
 915       if (format != null)
 916       {
 917         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 918                 format.getName());
 919       }
 920       startupFileTextfield
 921               .setText(chooser.getSelectedFile().getAbsolutePath());
 922     }
 923   }
 924
 925   /**
 926    * DOCUMENT ME!
 927    *
 928    * @param e
 929    *          DOCUMENT ME!
 930    */
 931   @Override
 932   public void cancel_actionPerformed(ActionEvent e)
 933   {
 934     try
 935     {
 936       if (!Platform.isJS())
 937       {
 938         wsPrefs.updateWsMenuConfig(true);
 939         wsPrefs.refreshWs_actionPerformed(e);
 940       }
 941       frame.setClosed(true);
 942     } catch (Exception ex)
 943     {
 944     }
 945   }
 946
 947   /**
 948    * DOCUMENT ME!
 949    *
 950    * @param e
 951    *          DOCUMENT ME!
 952    */
 953   @Override
 954   public void annotations_actionPerformed(ActionEvent e)
 955   {
 956     conservation.setEnabled(annotations.isSelected());
 957     quality.setEnabled(annotations.isSelected());
 958     identity.setEnabled(annotations.isSelected());
 959     showOccupancy.setEnabled(annotations.isSelected());
 960     showGroupConsensus.setEnabled(annotations.isSelected());
 961     showGroupConservation.setEnabled(annotations.isSelected());
 962     showConsensHistogram.setEnabled(annotations.isSelected()
 963             && (identity.isSelected() || showGroupConsensus.isSelected()));
 964     showConsensLogo.setEnabled(annotations.isSelected()
 965             && (identity.isSelected() || showGroupConsensus.isSelected()));
 966   }
 967
 968   @Override
 969   public void newLink_actionPerformed(ActionEvent e)
 970   {
 971     GSequenceLink link = new GSequenceLink();
 972     boolean valid = false;
 973     while (!valid)
 974     {
 975       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 976               MessageManager.getString("label.new_sequence_url_link"),
 977               JvOptionPane.OK_CANCEL_OPTION, -1,
 978               null) == JvOptionPane.OK_OPTION)
 979       {
 980         if (link.checkValid())
 981         {
 982           if (((UrlLinkTableModel) linkUrlTable.getModel())
 983                   .isUniqueName(link.getName()))
 984           {
 985             ((UrlLinkTableModel) linkUrlTable.getModel())
 986                     .insertRow(link.getName(), link.getURL());
 987             valid = true;
 988           }
 989           else
 990           {
 991             link.notifyDuplicate();
 992             continue;
 993           }
 994         }
 995       }
 996       else
 997       {
 998         break;
 999       }
1000     }
1001   }
1002
1003   @Override
1004   public void editLink_actionPerformed(ActionEvent e)
1005   {
1006     GSequenceLink link = new GSequenceLink();
1007
1008     int index = linkUrlTable.getSelectedRow();
1009     if (index == -1)
1010     {
1011       // button no longer enabled if row is not selected
1012       Cache.log.debug("Edit with no row selected in linkUrlTable");
1013       return;
1014     }
1015
1016     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1017             .getNameColumn();
1018     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1019             .getUrlColumn();
1020     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1021     link.setName(oldName);
1022     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1023
1024     boolean valid = false;
1025     while (!valid)
1026     {
1027       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1028               MessageManager.getString("label.edit_sequence_url_link"),
1029               JvOptionPane.OK_CANCEL_OPTION, -1,
1030               null) == JvOptionPane.OK_OPTION)
1031       {
1032         if (link.checkValid())
1033         {
1034           if ((oldName.equals(link.getName()))
1035                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1036                           .isUniqueName(link.getName())))
1037           {
1038             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1039             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1040             valid = true;
1041           }
1042           else
1043           {
1044             link.notifyDuplicate();
1045             continue;
1046           }
1047         }
1048       }
1049       else
1050       {
1051         break;
1052       }
1053     }
1054   }
1055
1056   @Override
1057   public void deleteLink_actionPerformed(ActionEvent e)
1058   {
1059     int index = linkUrlTable.getSelectedRow();
1060     int modelIndex = -1;
1061     if (index == -1)
1062     {
1063       // button no longer enabled if row is not selected
1064       Cache.log.debug("Delete with no row selected in linkUrlTable");
1065       return;
1066     }
1067     else
1068     {
1069       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1070     }
1071
1072     // make sure we use the model index to delete, and not the table index
1073     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1074   }
1075
1076   @Override
1077   public void defaultBrowser_mouseClicked(MouseEvent e)
1078   {
1079     // TODO: JAL-3048 not needed for j2s
1080     if (!Platform.isJS()) // BH 2019
1081     /**
1082      * Java only
1083      *
1084      * @j2sIgnore
1085      */
1086     {
1087       JFileChooser chooser = new JFileChooser(".");
1088       chooser.setDialogTitle(
1089               MessageManager.getString("label.select_default_browser"));
1090
1091       int value = chooser.showOpenDialog(this);
1092
1093       if (value == JFileChooser.APPROVE_OPTION)
1094       {
1095         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1096       }
1097     }
1098   }
1099
1100   /*
1101    * (non-Javadoc)
1102    *
1103    * @see
1104    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1105    * .ActionEvent)
1106    */
1107   @Override
1108   protected void showunconserved_actionPerformed(ActionEvent e)
1109   {
1110     // TODO Auto-generated method stub
1111     super.showunconserved_actionPerformed(e);
1112   }
1113
1114   public static List<String> getGroupURLLinks()
1115   {
1116     return groupURLLinks;
1117   }
1118
1119   @Override
1120   public void minColour_actionPerformed(JPanel panel)
1121   {
1122     JalviewColourChooser.showColourChooser(this,
1123             MessageManager.getString("label.select_colour_minimum_value"),
1124             panel);
1125   }
1126
1127   @Override
1128   public void maxColour_actionPerformed(JPanel panel)
1129   {
1130     JalviewColourChooser.showColourChooser(this,
1131             MessageManager.getString("label.select_colour_maximum_value"),
1132             panel);
1133   }
1134
1135   @Override
1136   public void gapColour_actionPerformed(JPanel gap)
1137   {
1138     if (!useLegacyGap.isSelected())
1139     {
1140       JalviewColourChooser.showColourChooser(this,
1141               MessageManager.getString("label.select_gap_colour"),
1142               gap);
1143     }
1144   }
1145
1146   @Override
1147   public void hiddenColour_actionPerformed(JPanel hidden)
1148   {
1149     JalviewColourChooser.showColourChooser(this,
1150             MessageManager.getString("label.select_hidden_colour"),
1151             hidden);
1152   }
1153
1154   @Override
1155   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1156   {
1157     boolean enabled = useLegacyGap.isSelected();
1158     if (enabled)
1159     {
1160       gapColour.setBackground(
1161               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1162     }
1163     else
1164     {
1165       gapColour.setBackground(
1166               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1167     }
1168     gapColour.setEnabled(!enabled);
1169     gapLabel.setEnabled(!enabled);
1170   }
1171
1172   @Override
1173   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1174   {
1175     useLegacyGap.setSelected(false);
1176     useLegacyGaps_actionPerformed(null);
1177     showHiddenAtStart.setSelected(false);
1178     hiddenColour.setBackground(
1179             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1180   }
1181
1182   @Override
1183   protected void userIdWidth_actionPerformed()
1184   {
1185     try
1186     {
1187       String val = userIdWidth.getText().trim();
1188       if (val.length() > 0)
1189       {
1190         Integer iw = Integer.parseInt(val);
1191         if (iw.intValue() < 12)
1192         {
1193           throw new NumberFormatException();
1194         }
1195         userIdWidth.setText(iw.toString());
1196       }
1197     } catch (NumberFormatException x)
1198     {
1199       userIdWidth.setText("");
1200       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1201               MessageManager
1202                       .getString("warn.user_defined_width_requirements"),
1203               MessageManager.getString("label.invalid_id_column_width"),
1204               JvOptionPane.WARNING_MESSAGE);
1205     }
1206   }
1207
1208   @Override
1209   protected void autoIdWidth_actionPerformed()
1210   {
1211     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1212     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1213   }
1214
1215   /**
1216    * Returns true if chimera path is to a valid executable, else show an error
1217    * dialog.
1218    */
1219   private boolean validateChimeraPath()
1220   {
1221     if (chimeraPath.getText().trim().length() > 0)
1222     {
1223       File f = new File(chimeraPath.getText());
1224       if (!f.canExecute())
1225       {
1226         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1227                 MessageManager.getString("label.invalid_chimera_path"),
1228                 MessageManager.getString("label.invalid_name"),
1229                 JvOptionPane.ERROR_MESSAGE);
1230         return false;
1231       }
1232     }
1233     return true;
1234   }
1235
1236   /**
1237    * If Chimera is selected, check it can be found on default or user-specified
1238    * path, if not show a warning/help dialog.
1239    */
1240   @Override
1241   protected void structureViewer_actionPerformed(String selectedItem)
1242   {
1243     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1244     {
1245       return;
1246     }
1247     boolean found = false;
1248
1249     /*
1250      * Try user-specified and standard paths for Chimera executable.
1251      */
1252     List<String> paths = StructureManager.getChimeraPaths();
1253     paths.add(0, chimeraPath.getText());
1254     for (String path : paths)
1255     {
1256       if (new File(path.trim()).canExecute())
1257       {
1258         found = true;
1259         break;
1260       }
1261     }
1262     if (!found)
1263     {
1264       String[] options = { "OK", "Help" };
1265       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1266               JvSwingUtils.wrapTooltip(true,
1267                       MessageManager.getString("label.chimera_missing")),
1268               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1269               null, options, options[0]);
1270       if (showHelp == JvOptionPane.NO_OPTION)
1271       {
1272         try
1273         {
1274           Help.showHelpWindow(HelpId.StructureViewer);
1275         } catch (HelpSetException e)
1276         {
1277           e.printStackTrace();
1278         }
1279       }
1280     }
1281   }
1282
1283   public class OptionsParam
1284   {
1285     private String name;
1286
1287     private String code;
1288
1289     public OptionsParam(String name, String code)
1290     {
1291       this.name = name;
1292       this.code = code;
1293     }
1294
1295     public String getName()
1296     {
1297       return name;
1298     }
1299
1300     public void setName(String name)
1301     {
1302       this.name = name;
1303     }
1304
1305     public String getCode()
1306     {
1307       return code;
1308     }
1309
1310     public void setCode(String code)
1311     {
1312       this.code = code;
1313     }
1314
1315     @Override
1316     public String toString()
1317     {
1318       return name;
1319     }
1320
1321     @Override
1322     public boolean equals(Object that)
1323     {
1324       if (!(that instanceof OptionsParam))
1325       {
1326         return false;
1327       }
1328       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1329     }
1330
1331     @Override
1332     public int hashCode()
1333     {
1334       return name.hashCode() + code.hashCode();
1335     }
1336   }
1337
1338   private class UrlListSelectionHandler implements ListSelectionListener
1339   {
1340
1341     @Override
1342     public void valueChanged(ListSelectionEvent e)
1343     {
1344       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1345
1346       int index = lsm.getMinSelectionIndex();
1347       if (index == -1)
1348       {
1349         // no selection, so disable delete/edit buttons
1350         editLink.setEnabled(false);
1351         deleteLink.setEnabled(false);
1352         return;
1353       }
1354       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1355
1356       // enable/disable edit and delete link buttons
1357       if (((UrlLinkTableModel) linkUrlTable.getModel())
1358               .isRowDeletable(modelIndex))
1359       {
1360         deleteLink.setEnabled(true);
1361       }
1362       else
1363       {
1364         deleteLink.setEnabled(false);
1365       }
1366
1367       if (((UrlLinkTableModel) linkUrlTable.getModel())
1368               .isRowEditable(modelIndex))
1369       {
1370         editLink.setEnabled(true);
1371       }
1372       else
1373       {
1374         editLink.setEnabled(false);
1375       }
1376     }
1377   }
1378 }