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     if (!Platform.isJS())
 551     {
 552       loadLastSavedBackupsOptions();
 553     }
 554   }
 555
 556   /**
 557    * A helper method that sets the items and initial selection in a character
 558    * rendering option list (Prompt each time/Lineart/Text)
 559    *
 560    * @param comboBox
 561    * @param propertyKey
 562    */
 563   protected void setupOutputCombo(JComboBox<Object> comboBox,
 564           String propertyKey)
 565   {
 566     comboBox.addItem(promptEachTimeOpt);
 567     comboBox.addItem(lineArtOpt);
 568     comboBox.addItem(textOpt);
 569
 570     /*
 571      * JalviewJS doesn't support Lineart so force it to Text
 572      */
 573     String defaultOption = Platform.isJS() ? "Text"
 574             : Cache.getDefault(propertyKey, "Prompt each time");
 575     if (defaultOption.equalsIgnoreCase("Text"))
 576     {
 577       comboBox.setSelectedItem(textOpt);
 578     }
 579     else if (defaultOption.equalsIgnoreCase("Lineart"))
 580     {
 581       comboBox.setSelectedItem(lineArtOpt);
 582     }
 583     else
 584     {
 585       comboBox.setSelectedItem(promptEachTimeOpt);
 586     }
 587   }
 588
 589   /**
 590    * Save user selections on the Preferences tabs to the Cache and write out to
 591    * file.
 592    *
 593    * @param e
 594    */
 595   @Override
 596   public void ok_actionPerformed(ActionEvent e)
 597   {
 598     if (!validateSettings())
 599     {
 600       return;
 601     }
 602
 603     /*
 604      * Save Visual settings
 605      */
 606     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 607             Boolean.toString(seqLimit.isSelected()));
 608     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 609             Boolean.toString(rightAlign.isSelected()));
 610     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 611             Boolean.toString(fullScreen.isSelected()));
 612     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 613             Boolean.toString(openoverv.isSelected()));
 614     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 615             Boolean.toString(annotations.isSelected()));
 616     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 617             Boolean.toString(conservation.isSelected()));
 618     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 619             Boolean.toString(quality.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 621             Boolean.toString(identity.isSelected()));
 622
 623     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 624             gapSymbolCB.getSelectedItem().toString());
 625
 626     Cache.applicationProperties.setProperty("FONT_NAME",
 627             fontNameCB.getSelectedItem().toString());
 628     Cache.applicationProperties.setProperty("FONT_STYLE",
 629             fontStyleCB.getSelectedItem().toString());
 630     Cache.applicationProperties.setProperty("FONT_SIZE",
 631             fontSizeCB.getSelectedItem().toString());
 632
 633     Cache.applicationProperties.setProperty("ID_ITALICS",
 634             Boolean.toString(idItalics.isSelected()));
 635     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 636             Boolean.toString(showUnconserved.isSelected()));
 637     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 638             Boolean.toString(showOccupancy.isSelected()));
 639     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 640             Boolean.toString(showGroupConsensus.isSelected()));
 641     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 642             Boolean.toString(showGroupConservation.isSelected()));
 643     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 644             Boolean.toString(showConsensHistogram.isSelected()));
 645     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 646             Boolean.toString(showConsensLogo.isSelected()));
 647     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 648             Boolean.toString(smoothFont.isSelected()));
 649     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 650             Boolean.toString(scaleProteinToCdna.isSelected()));
 651     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 652             Boolean.toString(showNpTooltip.isSelected()));
 653     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 654             Boolean.toString(showDbRefTooltip.isSelected()));
 655
 656     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 657             Boolean.toString(wrap.isSelected()));
 658
 659     Cache.applicationProperties.setProperty("STARTUP_FILE",
 660             startupFileTextfield.getText());
 661     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 662             Boolean.toString(startupCheckbox.isSelected()));
 663
 664     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 665             sortby.getSelectedItem().toString());
 666
 667     // convert description of sort order to enum name for save
 668     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 669             .forDescription(sortAnnBy.getSelectedItem().toString());
 670     if (annSortOrder != null)
 671     {
 672       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 673               annSortOrder.name());
 674     }
 675
 676     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 677     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 678             Boolean.valueOf(showAutocalcFirst).toString());
 679
 680     /*
 681      * Save Colours settings
 682      */
 683     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 684             protColour.getSelectedItem().toString());
 685     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 686             nucColour.getSelectedItem().toString());
 687     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 688             minColour.getBackground());
 689     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 690             maxColour.getBackground());
 691
 692     /*
 693      * Save Overview settings
 694      */
 695     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 696     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 697     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 698             Boolean.toString(useLegacyGap.isSelected()));
 699     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 700             Boolean.toString(showHiddenAtStart.isSelected()));
 701
 702     /*
 703      * Save Structure settings
 704      */
 705     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 706             Boolean.toString(addTempFactor.isSelected()));
 707     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 708             Boolean.toString(addSecondaryStructure.isSelected()));
 709     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 710             Boolean.toString(useRnaView.isSelected()));
 711     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 712             Boolean.toString(structFromPdb.isSelected()));
 713     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 714             structViewer.getSelectedItem().toString());
 715     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 716     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 717             Boolean.toString(siftsMapping.isSelected()));
 718     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 719
 720     /*
 721      * Save Output settings
 722      */
 723     Cache.applicationProperties.setProperty("EPS_RENDERING",
 724             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 725     Cache.applicationProperties.setProperty("HTML_RENDERING",
 726             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 727     Cache.applicationProperties.setProperty("SVG_RENDERING",
 728             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 729
 730     /*
 731      * Save Connections settings
 732      */
 733     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 734
 735     jalview.util.BrowserLauncher.resetBrowser();
 736
 737     // save user-defined and selected links
 738     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 739     if (menuLinks.isEmpty())
 740     {
 741       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 742     }
 743     else
 744     {
 745       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 746               menuLinks.toString());
 747     }
 748
 749     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 750     if (nonMenuLinks.isEmpty())
 751     {
 752       Cache.applicationProperties.remove("STORED_LINKS");
 753     }
 754     else
 755     {
 756       Cache.applicationProperties.setProperty("STORED_LINKS",
 757               nonMenuLinks.toString());
 758     }
 759
 760     Cache.applicationProperties.setProperty("DEFAULT_URL",
 761             sequenceUrlLinks.getPrimaryUrlId());
 762
 763     Cache.applicationProperties.setProperty("USE_PROXY",
 764             Boolean.toString(useProxy.isSelected()));
 765
 766     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 767
 768     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 769
 770     if (useProxy.isSelected())
 771     {
 772       System.setProperty("http.proxyHost", proxyServerTB.getText());
 773       System.setProperty("http.proxyPort", proxyPortTB.getText());
 774     }
 775     else
 776     {
 777       System.setProperty("http.proxyHost", "");
 778       System.setProperty("http.proxyPort", "");
 779     }
 780     Cache.setProperty("VERSION_CHECK",
 781             Boolean.toString(versioncheck.isSelected()));
 782     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 783     {
 784       // default is false - we only set this if the user has actively agreed
 785       Cache.setProperty("USAGESTATS",
 786               Boolean.toString(usagestats.isSelected()));
 787     }
 788     if (!questionnaire.isSelected())
 789     {
 790       Cache.setProperty("NOQUESTIONNAIRES", "true");
 791     }
 792     else
 793     {
 794       // special - made easy to edit a property file to disable questionnaires
 795       // by just adding the given line
 796       Cache.removeProperty("NOQUESTIONNAIRES");
 797     }
 798
 799     /*
 800      * Save Output settings
 801      */
 802     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 803             Boolean.toString(blcjv.isSelected()));
 804     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 805             Boolean.toString(clustaljv.isSelected()));
 806     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 807             Boolean.toString(fastajv.isSelected()));
 808     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 809             Boolean.toString(msfjv.isSelected()));
 810     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 811             Boolean.toString(pfamjv.isSelected()));
 812     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 813             Boolean.toString(pileupjv.isSelected()));
 814     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 815             Boolean.toString(pirjv.isSelected()));
 816     Cache.applicationProperties.setProperty("PIR_MODELLER",
 817             Boolean.toString(modellerOutput.isSelected()));
 818     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 819             Boolean.toString(embbedBioJSON.isSelected()));
 820     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 821
 822     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 823             Boolean.toString(autoIdWidth.isSelected()));
 824     userIdWidth_actionPerformed();
 825     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 826             userIdWidth.getText());
 827
 828     /*
 829      * Save Editing settings
 830      */
 831     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 832             Boolean.toString(autoCalculateConsCheck.isSelected()));
 833     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 834             Boolean.toString(sortByTree.isSelected()));
 835     Cache.applicationProperties.setProperty("PAD_GAPS",
 836             Boolean.toString(padGaps.isSelected()));
 837
 838     if (!Platform.isJS())
 839     {
 840       wsPrefs.updateAndRefreshWsMenuConfig(false);
 841     }
 842
 843     /*
 844      * Save Backups settings
 845      */
 846     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 847             Boolean.toString(enableBackupFiles.isSelected()));
 848     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 849     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 850
 851     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 852     {
 853       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 854       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 855               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 856       Cache.applicationProperties
 857               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 858                       customBFPE.toString());
 859     }
 860
 861     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 862             .get(preset);
 863     Cache.applicationProperties.setProperty(
 864             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 865
 866     Cache.saveProperties();
 867     Desktop.instance.doConfigureStructurePrefs();
 868     try
 869     {
 870       frame.setClosed(true);
 871     } catch (Exception ex)
 872     {
 873     }
 874   }
 875
 876   /**
 877    * Do any necessary validation before saving settings. Return focus to the
 878    * first tab which fails validation.
 879    *
 880    * @return
 881    */
 882   private boolean validateSettings()
 883   {
 884     if (!validateStructure())
 885     {
 886       structureTab.requestFocusInWindow();
 887       return false;
 888     }
 889     return true;
 890   }
 891
 892   @Override
 893   protected boolean validateStructure()
 894   {
 895     return validateChimeraPath();
 896
 897   }
 898
 899   /**
 900    * DOCUMENT ME!
 901    */
 902   @Override
 903   public void startupFileTextfield_mouseClicked()
 904   {
 905     // TODO: JAL-3048 not needed for Jalview-JS
 906     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 907     JalviewFileChooser chooser = JalviewFileChooser
 908             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 909     chooser.setFileView(new JalviewFileView());
 910     chooser.setDialogTitle(
 911             MessageManager.getString("label.select_startup_file"));
 912
 913     int value = chooser.showOpenDialog(this);
 914
 915     if (value == JalviewFileChooser.APPROVE_OPTION)
 916     {
 917       FileFormatI format = chooser.getSelectedFormat();
 918       if (format != null)
 919       {
 920         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 921                 format.getName());
 922       }
 923       startupFileTextfield
 924               .setText(chooser.getSelectedFile().getAbsolutePath());
 925     }
 926   }
 927
 928   /**
 929    * DOCUMENT ME!
 930    *
 931    * @param e
 932    *          DOCUMENT ME!
 933    */
 934   @Override
 935   public void cancel_actionPerformed(ActionEvent e)
 936   {
 937     try
 938     {
 939       if (!Platform.isJS())
 940       {
 941         wsPrefs.updateWsMenuConfig(true);
 942         wsPrefs.refreshWs_actionPerformed(e);
 943       }
 944       frame.setClosed(true);
 945     } catch (Exception ex)
 946     {
 947     }
 948   }
 949
 950   /**
 951    * DOCUMENT ME!
 952    *
 953    * @param e
 954    *          DOCUMENT ME!
 955    */
 956   @Override
 957   public void annotations_actionPerformed(ActionEvent e)
 958   {
 959     conservation.setEnabled(annotations.isSelected());
 960     quality.setEnabled(annotations.isSelected());
 961     identity.setEnabled(annotations.isSelected());
 962     showOccupancy.setEnabled(annotations.isSelected());
 963     showGroupConsensus.setEnabled(annotations.isSelected());
 964     showGroupConservation.setEnabled(annotations.isSelected());
 965     showConsensHistogram.setEnabled(annotations.isSelected()
 966             && (identity.isSelected() || showGroupConsensus.isSelected()));
 967     showConsensLogo.setEnabled(annotations.isSelected()
 968             && (identity.isSelected() || showGroupConsensus.isSelected()));
 969   }
 970
 971   @Override
 972   public void newLink_actionPerformed(ActionEvent e)
 973   {
 974     GSequenceLink link = new GSequenceLink();
 975     boolean valid = false;
 976     while (!valid)
 977     {
 978       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 979               MessageManager.getString("label.new_sequence_url_link"),
 980               JvOptionPane.OK_CANCEL_OPTION, -1,
 981               null) == JvOptionPane.OK_OPTION)
 982       {
 983         if (link.checkValid())
 984         {
 985           if (((UrlLinkTableModel) linkUrlTable.getModel())
 986                   .isUniqueName(link.getName()))
 987           {
 988             ((UrlLinkTableModel) linkUrlTable.getModel())
 989                     .insertRow(link.getName(), link.getURL());
 990             valid = true;
 991           }
 992           else
 993           {
 994             link.notifyDuplicate();
 995             continue;
 996           }
 997         }
 998       }
 999       else
1000       {
1001         break;
1002       }
1003     }
1004   }
1005
1006   @Override
1007   public void editLink_actionPerformed(ActionEvent e)
1008   {
1009     GSequenceLink link = new GSequenceLink();
1010
1011     int index = linkUrlTable.getSelectedRow();
1012     if (index == -1)
1013     {
1014       // button no longer enabled if row is not selected
1015       Cache.log.debug("Edit with no row selected in linkUrlTable");
1016       return;
1017     }
1018
1019     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1020             .getNameColumn();
1021     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1022             .getUrlColumn();
1023     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1024     link.setName(oldName);
1025     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1026
1027     boolean valid = false;
1028     while (!valid)
1029     {
1030       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1031               MessageManager.getString("label.edit_sequence_url_link"),
1032               JvOptionPane.OK_CANCEL_OPTION, -1,
1033               null) == JvOptionPane.OK_OPTION)
1034       {
1035         if (link.checkValid())
1036         {
1037           if ((oldName.equals(link.getName()))
1038                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1039                           .isUniqueName(link.getName())))
1040           {
1041             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1042             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1043             valid = true;
1044           }
1045           else
1046           {
1047             link.notifyDuplicate();
1048             continue;
1049           }
1050         }
1051       }
1052       else
1053       {
1054         break;
1055       }
1056     }
1057   }
1058
1059   @Override
1060   public void deleteLink_actionPerformed(ActionEvent e)
1061   {
1062     int index = linkUrlTable.getSelectedRow();
1063     int modelIndex = -1;
1064     if (index == -1)
1065     {
1066       // button no longer enabled if row is not selected
1067       Cache.log.debug("Delete with no row selected in linkUrlTable");
1068       return;
1069     }
1070     else
1071     {
1072       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1073     }
1074
1075     // make sure we use the model index to delete, and not the table index
1076     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1077   }
1078
1079   @Override
1080   public void defaultBrowser_mouseClicked(MouseEvent e)
1081   {
1082     // TODO: JAL-3048 not needed for j2s
1083     if (!Platform.isJS()) // BH 2019
1084     /**
1085      * Java only
1086      *
1087      * @j2sIgnore
1088      */
1089     {
1090       JFileChooser chooser = new JFileChooser(".");
1091       chooser.setDialogTitle(
1092               MessageManager.getString("label.select_default_browser"));
1093
1094       int value = chooser.showOpenDialog(this);
1095
1096       if (value == JFileChooser.APPROVE_OPTION)
1097       {
1098         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1099       }
1100     }
1101   }
1102
1103   /*
1104    * (non-Javadoc)
1105    *
1106    * @see
1107    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1108    * .ActionEvent)
1109    */
1110   @Override
1111   protected void showunconserved_actionPerformed(ActionEvent e)
1112   {
1113     // TODO Auto-generated method stub
1114     super.showunconserved_actionPerformed(e);
1115   }
1116
1117   public static List<String> getGroupURLLinks()
1118   {
1119     return groupURLLinks;
1120   }
1121
1122   @Override
1123   public void minColour_actionPerformed(JPanel panel)
1124   {
1125     JalviewColourChooser.showColourChooser(this,
1126             MessageManager.getString("label.select_colour_minimum_value"),
1127             panel);
1128   }
1129
1130   @Override
1131   public void maxColour_actionPerformed(JPanel panel)
1132   {
1133     JalviewColourChooser.showColourChooser(this,
1134             MessageManager.getString("label.select_colour_maximum_value"),
1135             panel);
1136   }
1137
1138   @Override
1139   public void gapColour_actionPerformed(JPanel gap)
1140   {
1141     if (!useLegacyGap.isSelected())
1142     {
1143       JalviewColourChooser.showColourChooser(this,
1144               MessageManager.getString("label.select_gap_colour"),
1145               gap);
1146     }
1147   }
1148
1149   @Override
1150   public void hiddenColour_actionPerformed(JPanel hidden)
1151   {
1152     JalviewColourChooser.showColourChooser(this,
1153             MessageManager.getString("label.select_hidden_colour"),
1154             hidden);
1155   }
1156
1157   @Override
1158   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1159   {
1160     boolean enabled = useLegacyGap.isSelected();
1161     if (enabled)
1162     {
1163       gapColour.setBackground(
1164               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1165     }
1166     else
1167     {
1168       gapColour.setBackground(
1169               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1170     }
1171     gapColour.setEnabled(!enabled);
1172     gapLabel.setEnabled(!enabled);
1173   }
1174
1175   @Override
1176   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1177   {
1178     useLegacyGap.setSelected(false);
1179     useLegacyGaps_actionPerformed(null);
1180     showHiddenAtStart.setSelected(false);
1181     hiddenColour.setBackground(
1182             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1183   }
1184
1185   @Override
1186   protected void userIdWidth_actionPerformed()
1187   {
1188     try
1189     {
1190       String val = userIdWidth.getText().trim();
1191       if (val.length() > 0)
1192       {
1193         Integer iw = Integer.parseInt(val);
1194         if (iw.intValue() < 12)
1195         {
1196           throw new NumberFormatException();
1197         }
1198         userIdWidth.setText(iw.toString());
1199       }
1200     } catch (NumberFormatException x)
1201     {
1202       userIdWidth.setText("");
1203       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1204               MessageManager
1205                       .getString("warn.user_defined_width_requirements"),
1206               MessageManager.getString("label.invalid_id_column_width"),
1207               JvOptionPane.WARNING_MESSAGE);
1208     }
1209   }
1210
1211   @Override
1212   protected void autoIdWidth_actionPerformed()
1213   {
1214     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1215     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1216   }
1217
1218   /**
1219    * Returns true if chimera path is to a valid executable, else show an error
1220    * dialog.
1221    */
1222   private boolean validateChimeraPath()
1223   {
1224     if (chimeraPath.getText().trim().length() > 0)
1225     {
1226       File f = new File(chimeraPath.getText());
1227       if (!f.canExecute())
1228       {
1229         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1230                 MessageManager.getString("label.invalid_chimera_path"),
1231                 MessageManager.getString("label.invalid_name"),
1232                 JvOptionPane.ERROR_MESSAGE);
1233         return false;
1234       }
1235     }
1236     return true;
1237   }
1238
1239   /**
1240    * If Chimera is selected, check it can be found on default or user-specified
1241    * path, if not show a warning/help dialog.
1242    */
1243   @Override
1244   protected void structureViewer_actionPerformed(String selectedItem)
1245   {
1246     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1247     {
1248       return;
1249     }
1250     boolean found = false;
1251
1252     /*
1253      * Try user-specified and standard paths for Chimera executable.
1254      */
1255     List<String> paths = StructureManager.getChimeraPaths();
1256     paths.add(0, chimeraPath.getText());
1257     for (String path : paths)
1258     {
1259       if (new File(path.trim()).canExecute())
1260       {
1261         found = true;
1262         break;
1263       }
1264     }
1265     if (!found)
1266     {
1267       String[] options = { "OK", "Help" };
1268       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1269               JvSwingUtils.wrapTooltip(true,
1270                       MessageManager.getString("label.chimera_missing")),
1271               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1272               null, options, options[0]);
1273       if (showHelp == JvOptionPane.NO_OPTION)
1274       {
1275         try
1276         {
1277           Help.showHelpWindow(HelpId.StructureViewer);
1278         } catch (HelpSetException e)
1279         {
1280           e.printStackTrace();
1281         }
1282       }
1283     }
1284   }
1285
1286   public class OptionsParam
1287   {
1288     private String name;
1289
1290     private String code;
1291
1292     public OptionsParam(String name, String code)
1293     {
1294       this.name = name;
1295       this.code = code;
1296     }
1297
1298     public String getName()
1299     {
1300       return name;
1301     }
1302
1303     public void setName(String name)
1304     {
1305       this.name = name;
1306     }
1307
1308     public String getCode()
1309     {
1310       return code;
1311     }
1312
1313     public void setCode(String code)
1314     {
1315       this.code = code;
1316     }
1317
1318     @Override
1319     public String toString()
1320     {
1321       return name;
1322     }
1323
1324     @Override
1325     public boolean equals(Object that)
1326     {
1327       if (!(that instanceof OptionsParam))
1328       {
1329         return false;
1330       }
1331       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1332     }
1333
1334     @Override
1335     public int hashCode()
1336     {
1337       return name.hashCode() + code.hashCode();
1338     }
1339   }
1340
1341   private class UrlListSelectionHandler implements ListSelectionListener
1342   {
1343
1344     @Override
1345     public void valueChanged(ListSelectionEvent e)
1346     {
1347       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1348
1349       int index = lsm.getMinSelectionIndex();
1350       if (index == -1)
1351       {
1352         // no selection, so disable delete/edit buttons
1353         editLink.setEnabled(false);
1354         deleteLink.setEnabled(false);
1355         return;
1356       }
1357       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1358
1359       // enable/disable edit and delete link buttons
1360       if (((UrlLinkTableModel) linkUrlTable.getModel())
1361               .isRowDeletable(modelIndex))
1362       {
1363         deleteLink.setEnabled(true);
1364       }
1365       else
1366       {
1367         deleteLink.setEnabled(false);
1368       }
1369
1370       if (((UrlLinkTableModel) linkUrlTable.getModel())
1371               .isRowEditable(modelIndex))
1372       {
1373         editLink.setEnabled(true);
1374       }
1375       else
1376       {
1377         editLink.setEnabled(false);
1378       }
1379     }
1380   }
1381 }