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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.ext.pymol.PymolManager;
  57 import jalview.gui.Help.HelpId;
  58 import jalview.gui.StructureViewer.ViewerType;
  59 import jalview.io.BackupFiles;
  60 import jalview.io.BackupFilesPresetEntry;
  61 import jalview.io.FileFormatI;
  62 import jalview.io.JalviewFileChooser;
  63 import jalview.io.JalviewFileView;
  64 import jalview.jbgui.GPreferences;
  65 import jalview.jbgui.GSequenceLink;
  66 import jalview.schemes.ColourSchemeI;
  67 import jalview.schemes.ColourSchemes;
  68 import jalview.schemes.ResidueColourScheme;
  69 import jalview.urls.UrlLinkTableModel;
  70 import jalview.urls.api.UrlProviderFactoryI;
  71 import jalview.urls.api.UrlProviderI;
  72 import jalview.urls.desktop.DesktopUrlProviderFactory;
  73 import jalview.util.MessageManager;
  74 import jalview.util.Platform;
  75 import jalview.util.UrlConstants;
  76 import jalview.ws.sifts.SiftsSettings;
  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 CHIMERAX_PATH = "CHIMERAX_PATH";
 109
 110   public static final String PYMOL_PATH = "PYMOL_PATH";
 111
 112   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 113
 114   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 115
 116   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 117
 118   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 119
 120   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 121
 122   public static final String GAP_COLOUR = "GAP_COLOUR";
 123
 124   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 125
 126   private static final int MIN_FONT_SIZE = 1;
 127
 128   private static final int MAX_FONT_SIZE = 30;
 129
 130   /**
 131    * Holds name and link separated with | character. Sequence ID must be
 132    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 133    */
 134   public static UrlProviderI sequenceUrlLinks;
 135
 136   public static UrlLinkTableModel dataModel;
 137
 138   /**
 139    * Holds name and link separated with | character. Sequence IDS and Sequences
 140    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 141    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 142    * for first and second token specified after a pipe character at end |,|.
 143    * (TODO: proper escape for using | to separate ids or sequences
 144    */
 145
 146   public static List<String> groupURLLinks;
 147   static
 148   {
 149     // get links selected to be in the menu (SEQUENCE_LINKS)
 150     // and links entered by the user but not selected (STORED_LINKS)
 151     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 152     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 153     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 154             UrlConstants.DEFAULT_LABEL);
 155
 156     // if both links lists are empty, add the DEFAULT_URL link
 157     // otherwise we assume the default link is in one of the lists
 158     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 159     {
 160       inMenuString = UrlConstants.DEFAULT_STRING;
 161     }
 162     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 163             inMenuString, notInMenuString);
 164     sequenceUrlLinks = factory.createUrlProvider();
 165     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 166
 167     /**
 168      * TODO: reformulate groupURL encoding so two or more can be stored in the
 169      * .properties file as '|' separated strings
 170      */
 171
 172     groupURLLinks = new ArrayList<>();
 173   }
 174
 175   JInternalFrame frame;
 176
 177   private WsPreferences wsPrefs;
 178
 179   private OptionsParam promptEachTimeOpt = new OptionsParam(
 180           MessageManager.getString("label.prompt_each_time"),
 181           "Prompt each time");
 182
 183   private OptionsParam lineArtOpt = new OptionsParam(
 184           MessageManager.getString("label.lineart"), "Lineart");
 185
 186   private OptionsParam textOpt = new OptionsParam(
 187           MessageManager.getString("action.text"), "Text");
 188
 189   /**
 190    * Creates a new Preferences object.
 191    */
 192   public Preferences()
 193   {
 194     super();
 195     frame = new JInternalFrame();
 196     frame.setContentPane(this);
 197     if (!Platform.isJS())
 198     /**
 199      * Java only
 200      *
 201      * @j2sIgnore
 202      */
 203     {
 204       wsPrefs = new WsPreferences();
 205       wsTab.add(wsPrefs, BorderLayout.CENTER);
 206     }
 207     int width = 500, height = 450;
 208     if (Platform.isAMacAndNotJS())
 209     {
 210       width = 570;
 211       height = 480;
 212     }
 213
 214     Desktop.addInternalFrame(frame,
 215             MessageManager.getString("label.preferences"), width, height);
 216     frame.setMinimumSize(new Dimension(width, height));
 217
 218     /*
 219      * Set Visual tab defaults
 220      */
 221     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 222     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 223     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 224     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 225
 226     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 227     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 228     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 229     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 230     showUnconserved
 231             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 232     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 233     showGroupConsensus
 234             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 235     showGroupConservation.setSelected(
 236             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 237     showConsensHistogram.setSelected(
 238             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 239     showConsensLogo
 240             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 241     showNpTooltip
 242             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 243     showDbRefTooltip
 244             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 245
 246     String[] fonts = java.awt.GraphicsEnvironment
 247             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 248     for (int i = 0; i < fonts.length; i++)
 249     {
 250       fontNameCB.addItem(fonts[i]);
 251     }
 252
 253     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 254     {
 255       fontSizeCB.addItem(i + "");
 256     }
 257
 258     fontStyleCB.addItem("plain");
 259     fontStyleCB.addItem("bold");
 260     fontStyleCB.addItem("italic");
 261
 262     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 263     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 264     fontStyleCB.setSelectedItem(
 265             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 266
 267     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 268     scaleProteinToCdna
 269             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 270
 271     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 272
 273     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 274
 275     gapSymbolCB.addItem("-");
 276     gapSymbolCB.addItem(".");
 277
 278     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 279
 280     sortby.addItem("No sort");
 281     sortby.addItem("Id");
 282     sortby.addItem("Pairwise Identity");
 283     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 284
 285     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 286     sortAnnBy
 287             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 288     sortAnnBy
 289             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 290     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 291             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 292                     SequenceAnnotationOrder.NONE.name()));
 293     sortAnnBy.setSelectedItem(savedSort.toString());
 294
 295     sortAutocalc.addItem("Autocalculated first");
 296     sortAutocalc.addItem("Autocalculated last");
 297     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 298     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 299             : sortAutocalc.getItemAt(1));
 300     startupCheckbox
 301             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 302     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 303             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 304                     + "/examples/exampleFile_2_3.jar"));
 305
 306     /*
 307      * Set Colours tab defaults
 308      */
 309     protColour.addItem(ResidueColourScheme.NONE);
 310     nucColour.addItem(ResidueColourScheme.NONE);
 311     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 312     {
 313       String name = cs.getSchemeName();
 314       protColour.addItem(name);
 315       nucColour.addItem(name);
 316     }
 317     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 318             ResidueColourScheme.NONE);
 319     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 320     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 321     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 322     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 323     minColour.setBackground(
 324             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 325     maxColour.setBackground(
 326             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 327
 328     /*
 329      * Set overview panel defaults
 330      */
 331     gapColour.setBackground(
 332             Cache.getDefaultColour(GAP_COLOUR,
 333                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 334     hiddenColour.setBackground(
 335             Cache.getDefaultColour(HIDDEN_COLOUR,
 336                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 337     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 338     gapLabel.setEnabled(!useLegacyGap.isSelected());
 339     gapColour.setEnabled(!useLegacyGap.isSelected());
 340     showHiddenAtStart
 341             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 342
 343     /*
 344      * Set Structure tab defaults
 345      */
 346     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 347     structFromPdb.setSelected(structSelected);
 348     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 349     useRnaView.setEnabled(structSelected);
 350     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 351     addSecondaryStructure.setEnabled(structSelected);
 352     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 353     addTempFactor.setEnabled(structSelected);
 354
 355     /*
 356      * set choice of structure viewer, and path if saved as a preference;
 357      * default to Jmol (first choice) if an unexpected value is found
 358      */
 359     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 360     structViewer.setSelectedItem(viewerType);
 361     String viewerPath = "";
 362     ViewerType type = null;
 363     try
 364     {
 365       type = ViewerType.valueOf(viewerType);
 366       switch (type)
 367       {
 368       case JMOL:
 369         break;
 370       case CHIMERA:
 371         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 372         break;
 373       case CHIMERAX:
 374         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 375         break;
 376       case PYMOL:
 377         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 378         break;
 379       }
 380     } catch (IllegalArgumentException e)
 381     {
 382       Cache.log.error("Unknown structure viewer type: " + viewerType
 383               + ", defaulting to Jmol");
 384       type = ViewerType.JMOL;
 385     }
 386     structureViewerPath.setText(viewerPath);
 387
 388     structureViewerPath.addActionListener(new ActionListener()
 389     {
 390       @Override
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         if (validateViewerPath())
 394         {
 395           Cache.setProperty(structViewer.getSelectedItem()
 396                   .equals(ViewerType.CHIMERAX.name())
 397                   ? CHIMERAX_PATH
 398                   : CHIMERA_PATH, structureViewerPath.getText());
 399         }
 400       }
 401     });
 402
 403     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 404     {
 405       siftsMapping.setSelected(true);
 406     }
 407     else
 408     {
 409       nwMapping.setSelected(true);
 410     }
 411
 412     SiftsSettings
 413             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 414
 415     /*
 416      * Set Connections tab defaults
 417      */
 418
 419     // set up sorting
 420     linkUrlTable.setModel(dataModel);
 421     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 422             linkUrlTable.getModel());
 423     linkUrlTable.setRowSorter(sorter);
 424     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 425
 426     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 427     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 428             SortOrder.DESCENDING));
 429     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 430             SortOrder.DESCENDING));
 431     sortKeys.add(
 432             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 433
 434     sorter.setSortKeys(sortKeys);
 435     // BH 2018 setSortKeys will do the sort
 436     // sorter.sort();
 437
 438     // set up filtering
 439     ActionListener onReset;
 440     onReset = new ActionListener()
 441     {
 442       @Override
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         filterTB.setText("");
 446         sorter.setRowFilter(RowFilter.regexFilter(""));
 447       }
 448
 449     };
 450     doReset.addActionListener(onReset);
 451
 452     // filter to display only custom urls
 453     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 454     {
 455       @Override
 456       public boolean include(
 457               Entry<? extends TableModel, ? extends Object> entry)
 458       {
 459         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 460       }
 461     };
 462
 463     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 464             linkUrlTable.getModel());
 465     customSorter.setRowFilter(customUrlFilter);
 466
 467     ActionListener onCustomOnly;
 468     onCustomOnly = new ActionListener()
 469     {
 470       @Override
 471       public void actionPerformed(ActionEvent e)
 472       {
 473         filterTB.setText("");
 474         sorter.setRowFilter(customUrlFilter);
 475       }
 476     };
 477     userOnly.addActionListener(onCustomOnly);
 478
 479     filterTB.getDocument().addDocumentListener(new DocumentListener()
 480     {
 481       String caseInsensitiveFlag = "(?i)";
 482
 483       @Override
 484       public void changedUpdate(DocumentEvent e)
 485       {
 486         sorter.setRowFilter(RowFilter
 487                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 488       }
 489
 490       @Override
 491       public void removeUpdate(DocumentEvent e)
 492       {
 493         sorter.setRowFilter(RowFilter
 494                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 495       }
 496
 497       @Override
 498       public void insertUpdate(DocumentEvent e)
 499       {
 500         sorter.setRowFilter(RowFilter
 501                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 502       }
 503     });
 504
 505     // set up list selection functionality
 506     linkUrlTable.getSelectionModel()
 507             .addListSelectionListener(new UrlListSelectionHandler());
 508
 509     // set up radio buttons
 510     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 511             .getPrimaryColumn();
 512     String onClickName = linkUrlTable.getColumnName(onClickCol);
 513     linkUrlTable.getColumn(onClickName)
 514             .setCellRenderer(new RadioButtonRenderer());
 515     linkUrlTable.getColumn(onClickName)
 516             .setCellEditor(new RadioButtonEditor());
 517
 518     // get boolean columns and resize those to min possible
 519     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 520     {
 521       if (linkUrlTable.getModel().getColumnClass(column)
 522               .equals(Boolean.class))
 523       {
 524         TableColumn tableColumn = linkUrlTable.getColumnModel()
 525                 .getColumn(column);
 526         int preferredWidth = tableColumn.getMinWidth();
 527
 528         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 529                 column);
 530         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 531         int cwidth = c.getPreferredSize().width
 532                 + linkUrlTable.getIntercellSpacing().width;
 533         preferredWidth = Math.max(preferredWidth, cwidth);
 534
 535         tableColumn.setPreferredWidth(preferredWidth);
 536       }
 537     }
 538
 539     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 540     switch (proxyTypeString)
 541     {
 542     case "none":
 543       proxyType.setSelected(noProxy.getModel(), true);
 544       break;
 545     case "false":
 546       proxyType.setSelected(systemProxy.getModel(), true);
 547       break;
 548     case "true":
 549       proxyType.setSelected(customProxy.getModel(), true);
 550       break;
 551     default:
 552       String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 553               + proxyTypeString;
 554       Cache.log.warn(message);
 555     }
 556     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 557     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 558     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 559     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 560
 561     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 562
 563     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 564     // note antisense here: default is true
 565     questionnaire
 566             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 567     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 568
 569     /*
 570      * Set Output tab defaults
 571      */
 572     setupOutputCombo(epsRendering, "EPS_RENDERING");
 573     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 574     setupOutputCombo(svgRendering, "SVG_RENDERING");
 575     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 576     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 577     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 578     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 579     userIdWidth.setText(wi == null ? "" : wi.toString());
 580     // TODO: refactor to use common enum via FormatAdapter and allow extension
 581     // for new flat file formats
 582     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 583     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 584     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 585     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 586     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 587     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 588     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 589     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 590     embbedBioJSON
 591             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 592
 593     /*
 594      * Set Editing tab defaults
 595      */
 596     autoCalculateConsCheck
 597             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 598     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 599     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 600
 601     annotations_actionPerformed(null); // update the display of the annotation
 602                                        // settings
 603
 604
 605     /*
 606      * Set Backups tab defaults
 607      */
 608     loadLastSavedBackupsOptions();
 609   }
 610
 611   /**
 612    * A helper method that sets the items and initial selection in a character
 613    * rendering option list (Prompt each time/Lineart/Text)
 614    *
 615    * @param comboBox
 616    * @param propertyKey
 617    */
 618   protected void setupOutputCombo(JComboBox<Object> comboBox,
 619           String propertyKey)
 620   {
 621     comboBox.addItem(promptEachTimeOpt);
 622     comboBox.addItem(lineArtOpt);
 623     comboBox.addItem(textOpt);
 624
 625     /*
 626      * JalviewJS doesn't support Lineart so force it to Text
 627      */
 628     String defaultOption = Platform.isJS() ? "Text"
 629             : Cache.getDefault(propertyKey, "Prompt each time");
 630     if (defaultOption.equalsIgnoreCase("Text"))
 631     {
 632       comboBox.setSelectedItem(textOpt);
 633     }
 634     else if (defaultOption.equalsIgnoreCase("Lineart"))
 635     {
 636       comboBox.setSelectedItem(lineArtOpt);
 637     }
 638     else
 639     {
 640       comboBox.setSelectedItem(promptEachTimeOpt);
 641     }
 642   }
 643
 644   /**
 645    * Save user selections on the Preferences tabs to the Cache and write out to
 646    * file.
 647    *
 648    * @param e
 649    */
 650   @Override
 651   public void ok_actionPerformed(ActionEvent e)
 652   {
 653     if (!validateSettings())
 654     {
 655       return;
 656     }
 657
 658     /*
 659      * Save Visual settings
 660      */
 661     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 662             Boolean.toString(seqLimit.isSelected()));
 663     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 664             Boolean.toString(rightAlign.isSelected()));
 665     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 666             Boolean.toString(fullScreen.isSelected()));
 667     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 668             Boolean.toString(openoverv.isSelected()));
 669     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 670             Boolean.toString(annotations.isSelected()));
 671     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 672             Boolean.toString(conservation.isSelected()));
 673     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 674             Boolean.toString(quality.isSelected()));
 675     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 676             Boolean.toString(identity.isSelected()));
 677
 678     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 679             gapSymbolCB.getSelectedItem().toString());
 680
 681     Cache.applicationProperties.setProperty("FONT_NAME",
 682             fontNameCB.getSelectedItem().toString());
 683     Cache.applicationProperties.setProperty("FONT_STYLE",
 684             fontStyleCB.getSelectedItem().toString());
 685     Cache.applicationProperties.setProperty("FONT_SIZE",
 686             fontSizeCB.getSelectedItem().toString());
 687
 688     Cache.applicationProperties.setProperty("ID_ITALICS",
 689             Boolean.toString(idItalics.isSelected()));
 690     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 691             Boolean.toString(showUnconserved.isSelected()));
 692     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 693             Boolean.toString(showOccupancy.isSelected()));
 694     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 695             Boolean.toString(showGroupConsensus.isSelected()));
 696     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 697             Boolean.toString(showGroupConservation.isSelected()));
 698     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 699             Boolean.toString(showConsensHistogram.isSelected()));
 700     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 701             Boolean.toString(showConsensLogo.isSelected()));
 702     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 703             Boolean.toString(smoothFont.isSelected()));
 704     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 705             Boolean.toString(scaleProteinToCdna.isSelected()));
 706     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 707             Boolean.toString(showNpTooltip.isSelected()));
 708     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 709             Boolean.toString(showDbRefTooltip.isSelected()));
 710
 711     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 712             Boolean.toString(wrap.isSelected()));
 713
 714     Cache.applicationProperties.setProperty("STARTUP_FILE",
 715             startupFileTextfield.getText());
 716     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 717             Boolean.toString(startupCheckbox.isSelected()));
 718
 719     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 720             sortby.getSelectedItem().toString());
 721
 722     // convert description of sort order to enum name for save
 723     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 724             .forDescription(sortAnnBy.getSelectedItem().toString());
 725     if (annSortOrder != null)
 726     {
 727       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 728               annSortOrder.name());
 729     }
 730
 731     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 732     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 733             Boolean.valueOf(showAutocalcFirst).toString());
 734
 735     /*
 736      * Save Colours settings
 737      */
 738     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 739             protColour.getSelectedItem().toString());
 740     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 741             nucColour.getSelectedItem().toString());
 742     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 743             minColour.getBackground());
 744     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 745             maxColour.getBackground());
 746
 747     /*
 748      * Save Overview settings
 749      */
 750     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 751     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 752     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 753             Boolean.toString(useLegacyGap.isSelected()));
 754     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 755             Boolean.toString(showHiddenAtStart.isSelected()));
 756
 757     /*
 758      * Save Structure settings
 759      */
 760     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 761             Boolean.toString(addTempFactor.isSelected()));
 762     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 763             Boolean.toString(addSecondaryStructure.isSelected()));
 764     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 765             Boolean.toString(useRnaView.isSelected()));
 766     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 767             Boolean.toString(structFromPdb.isSelected()));
 768     String viewer = structViewer.getSelectedItem().toString();
 769     String viewerPath = structureViewerPath.getText();
 770     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 771             viewer);
 772     if (viewer.equals(ViewerType.CHIMERA.name()))
 773     {
 774       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 775     }
 776     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 777     {
 778       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 779     }
 780     else if (viewer.equals(ViewerType.PYMOL.name()))
 781     {
 782       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 783     }
 784     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 785             Boolean.toString(siftsMapping.isSelected()));
 786     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 787
 788     /*
 789      * Save Output settings
 790      */
 791     Cache.applicationProperties.setProperty("EPS_RENDERING",
 792             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 793     Cache.applicationProperties.setProperty("HTML_RENDERING",
 794             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 795     Cache.applicationProperties.setProperty("SVG_RENDERING",
 796             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 797
 798     /*
 799      * Save Connections settings
 800      */
 801     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 802
 803     jalview.util.BrowserLauncher.resetBrowser();
 804
 805     // save user-defined and selected links
 806     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 807     if (menuLinks.isEmpty())
 808     {
 809       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 810     }
 811     else
 812     {
 813       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 814               menuLinks.toString());
 815     }
 816
 817     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 818     if (nonMenuLinks.isEmpty())
 819     {
 820       Cache.applicationProperties.remove("STORED_LINKS");
 821     }
 822     else
 823     {
 824       Cache.applicationProperties.setProperty("STORED_LINKS",
 825               nonMenuLinks.toString());
 826     }
 827
 828     Cache.applicationProperties.setProperty("DEFAULT_URL",
 829             sequenceUrlLinks.getPrimaryUrlId());
 830
 831     Cache.applicationProperties.setProperty("USE_PROXY",
 832             customProxy.isSelected() ? "true"
 833                     : noProxy.isSelected() ? "none" : "false");
 834
 835     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 836
 837     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 838
 839     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 840
 841     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 842
 843     if (noProxy.isSelected())
 844     {
 845       Cache.log.warn("Setting no proxy settings");
 846       Cache.setProxyProperties(null, null, null, null);
 847     }
 848     else if (customProxy.isSelected())
 849     {
 850       Cache.log.warn("Setting custom proxy settings");
 851       Cache.setProxyProperties(proxyServerHttpTB.getText(),
 852               proxyPortHttpTB.getText(), proxyServerHttpsTB.getText(),
 853               proxyPortHttpsTB.getText());
 854     }
 855     else // systemProxy should be selected and is sensible default
 856     {
 857       Cache.log.warn("Setting system proxy settings");
 858       Cache.resetProxyProperties();
 859     }
 860
 861     Cache.setProperty("VERSION_CHECK",
 862             Boolean.toString(versioncheck.isSelected()));
 863     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 864     {
 865       // default is false - we only set this if the user has actively agreed
 866       Cache.setProperty("USAGESTATS",
 867               Boolean.toString(usagestats.isSelected()));
 868     }
 869     if (!questionnaire.isSelected())
 870     {
 871       Cache.setProperty("NOQUESTIONNAIRES", "true");
 872     }
 873     else
 874     {
 875       // special - made easy to edit a property file to disable questionnaires
 876       // by just adding the given line
 877       Cache.removeProperty("NOQUESTIONNAIRES");
 878     }
 879
 880     /*
 881      * Save Output settings
 882      */
 883     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 884             Boolean.toString(blcjv.isSelected()));
 885     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 886             Boolean.toString(clustaljv.isSelected()));
 887     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 888             Boolean.toString(fastajv.isSelected()));
 889     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 890             Boolean.toString(msfjv.isSelected()));
 891     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 892             Boolean.toString(pfamjv.isSelected()));
 893     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 894             Boolean.toString(pileupjv.isSelected()));
 895     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 896             Boolean.toString(pirjv.isSelected()));
 897     Cache.applicationProperties.setProperty("PIR_MODELLER",
 898             Boolean.toString(modellerOutput.isSelected()));
 899     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 900             Boolean.toString(embbedBioJSON.isSelected()));
 901     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 902
 903     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 904             Boolean.toString(autoIdWidth.isSelected()));
 905     userIdWidth_actionPerformed();
 906     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 907             userIdWidth.getText());
 908
 909     /*
 910      * Save Editing settings
 911      */
 912     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 913             Boolean.toString(autoCalculateConsCheck.isSelected()));
 914     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 915             Boolean.toString(sortByTree.isSelected()));
 916     Cache.applicationProperties.setProperty("PAD_GAPS",
 917             Boolean.toString(padGaps.isSelected()));
 918
 919     if (!Platform.isJS())
 920     {
 921       wsPrefs.updateAndRefreshWsMenuConfig(false);
 922     }
 923
 924     /*
 925      * Save Backups settings
 926      */
 927     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 928             Boolean.toString(enableBackupFiles.isSelected()));
 929     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 930     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 931
 932     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 933     {
 934       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 935       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 936               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 937       Cache.applicationProperties
 938               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 939                       customBFPE.toString());
 940     }
 941
 942     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 943             .get(preset);
 944     Cache.applicationProperties.setProperty(
 945             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 946
 947     Cache.saveProperties();
 948     Desktop.instance.doConfigureStructurePrefs();
 949     try
 950     {
 951       frame.setClosed(true);
 952     } catch (Exception ex)
 953     {
 954     }
 955   }
 956
 957   /**
 958    * Do any necessary validation before saving settings. Return focus to the
 959    * first tab which fails validation.
 960    *
 961    * @return
 962    */
 963   private boolean validateSettings()
 964   {
 965     if (!validateStructure())
 966     {
 967       structureTab.requestFocusInWindow();
 968       return false;
 969     }
 970     return true;
 971   }
 972
 973   @Override
 974   protected boolean validateStructure()
 975   {
 976     return validateViewerPath();
 977
 978   }
 979
 980   /**
 981    * DOCUMENT ME!
 982    */
 983   @Override
 984   public void startupFileTextfield_mouseClicked()
 985   {
 986     // TODO: JAL-3048 not needed for Jalview-JS
 987     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 988     JalviewFileChooser chooser = JalviewFileChooser
 989             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 990     chooser.setFileView(new JalviewFileView());
 991     chooser.setDialogTitle(
 992             MessageManager.getString("label.select_startup_file"));
 993
 994     int value = chooser.showOpenDialog(this);
 995
 996     if (value == JalviewFileChooser.APPROVE_OPTION)
 997     {
 998       FileFormatI format = chooser.getSelectedFormat();
 999       if (format != null)
1000       {
1001         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1002                 format.getName());
1003       }
1004       startupFileTextfield
1005               .setText(chooser.getSelectedFile().getAbsolutePath());
1006     }
1007   }
1008
1009   /**
1010    * DOCUMENT ME!
1011    *
1012    * @param e
1013    *          DOCUMENT ME!
1014    */
1015   @Override
1016   public void cancel_actionPerformed(ActionEvent e)
1017   {
1018     try
1019     {
1020       if (!Platform.isJS())
1021       {
1022         wsPrefs.updateWsMenuConfig(true);
1023         wsPrefs.refreshWs_actionPerformed(e);
1024       }
1025       frame.setClosed(true);
1026     } catch (Exception ex)
1027     {
1028     }
1029   }
1030
1031   /**
1032    * DOCUMENT ME!
1033    *
1034    * @param e
1035    *          DOCUMENT ME!
1036    */
1037   @Override
1038   public void annotations_actionPerformed(ActionEvent e)
1039   {
1040     conservation.setEnabled(annotations.isSelected());
1041     quality.setEnabled(annotations.isSelected());
1042     identity.setEnabled(annotations.isSelected());
1043     showOccupancy.setEnabled(annotations.isSelected());
1044     showGroupConsensus.setEnabled(annotations.isSelected());
1045     showGroupConservation.setEnabled(annotations.isSelected());
1046     showConsensHistogram.setEnabled(annotations.isSelected()
1047             && (identity.isSelected() || showGroupConsensus.isSelected()));
1048     showConsensLogo.setEnabled(annotations.isSelected()
1049             && (identity.isSelected() || showGroupConsensus.isSelected()));
1050   }
1051
1052   @Override
1053   public void newLink_actionPerformed(ActionEvent e)
1054   {
1055     GSequenceLink link = new GSequenceLink();
1056     boolean valid = false;
1057     while (!valid)
1058     {
1059       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1060               MessageManager.getString("label.new_sequence_url_link"),
1061               JvOptionPane.OK_CANCEL_OPTION, -1,
1062               null) == JvOptionPane.OK_OPTION)
1063       {
1064         if (link.checkValid())
1065         {
1066           if (((UrlLinkTableModel) linkUrlTable.getModel())
1067                   .isUniqueName(link.getName()))
1068           {
1069             ((UrlLinkTableModel) linkUrlTable.getModel())
1070                     .insertRow(link.getName(), link.getURL());
1071             valid = true;
1072           }
1073           else
1074           {
1075             link.notifyDuplicate();
1076             continue;
1077           }
1078         }
1079       }
1080       else
1081       {
1082         break;
1083       }
1084     }
1085   }
1086
1087   @Override
1088   public void editLink_actionPerformed(ActionEvent e)
1089   {
1090     GSequenceLink link = new GSequenceLink();
1091
1092     int index = linkUrlTable.getSelectedRow();
1093     if (index == -1)
1094     {
1095       // button no longer enabled if row is not selected
1096       Cache.log.debug("Edit with no row selected in linkUrlTable");
1097       return;
1098     }
1099
1100     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1101             .getNameColumn();
1102     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1103             .getUrlColumn();
1104     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1105     link.setName(oldName);
1106     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1107
1108     boolean valid = false;
1109     while (!valid)
1110     {
1111       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1112               MessageManager.getString("label.edit_sequence_url_link"),
1113               JvOptionPane.OK_CANCEL_OPTION, -1,
1114               null) == JvOptionPane.OK_OPTION)
1115       {
1116         if (link.checkValid())
1117         {
1118           if ((oldName.equals(link.getName()))
1119                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1120                           .isUniqueName(link.getName())))
1121           {
1122             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1123             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1124             valid = true;
1125           }
1126           else
1127           {
1128             link.notifyDuplicate();
1129             continue;
1130           }
1131         }
1132       }
1133       else
1134       {
1135         break;
1136       }
1137     }
1138   }
1139
1140   @Override
1141   public void deleteLink_actionPerformed(ActionEvent e)
1142   {
1143     int index = linkUrlTable.getSelectedRow();
1144     int modelIndex = -1;
1145     if (index == -1)
1146     {
1147       // button no longer enabled if row is not selected
1148       Cache.log.debug("Delete with no row selected in linkUrlTable");
1149       return;
1150     }
1151     else
1152     {
1153       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1154     }
1155
1156     // make sure we use the model index to delete, and not the table index
1157     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1158   }
1159
1160   @Override
1161   public void defaultBrowser_mouseClicked(MouseEvent e)
1162   {
1163     // TODO: JAL-3048 not needed for j2s
1164     if (!Platform.isJS()) // BH 2019
1165     /**
1166      * Java only
1167      *
1168      * @j2sIgnore
1169      */
1170     {
1171       JFileChooser chooser = new JFileChooser(".");
1172       chooser.setDialogTitle(
1173               MessageManager.getString("label.select_default_browser"));
1174
1175       int value = chooser.showOpenDialog(this);
1176
1177       if (value == JFileChooser.APPROVE_OPTION)
1178       {
1179         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1180       }
1181     }
1182   }
1183
1184   /*
1185    * (non-Javadoc)
1186    *
1187    * @see
1188    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1189    * .ActionEvent)
1190    */
1191   @Override
1192   protected void showunconserved_actionPerformed(ActionEvent e)
1193   {
1194     // TODO Auto-generated method stub
1195     super.showunconserved_actionPerformed(e);
1196   }
1197
1198   public static List<String> getGroupURLLinks()
1199   {
1200     return groupURLLinks;
1201   }
1202
1203   @Override
1204   public void minColour_actionPerformed(JPanel panel)
1205   {
1206     JalviewColourChooser.showColourChooser(this,
1207             MessageManager.getString("label.select_colour_minimum_value"),
1208             panel);
1209   }
1210
1211   @Override
1212   public void maxColour_actionPerformed(JPanel panel)
1213   {
1214     JalviewColourChooser.showColourChooser(this,
1215             MessageManager.getString("label.select_colour_maximum_value"),
1216             panel);
1217   }
1218
1219   @Override
1220   public void gapColour_actionPerformed(JPanel gap)
1221   {
1222     if (!useLegacyGap.isSelected())
1223     {
1224       JalviewColourChooser.showColourChooser(this,
1225               MessageManager.getString("label.select_gap_colour"),
1226               gap);
1227     }
1228   }
1229
1230   @Override
1231   public void hiddenColour_actionPerformed(JPanel hidden)
1232   {
1233     JalviewColourChooser.showColourChooser(this,
1234             MessageManager.getString("label.select_hidden_colour"),
1235             hidden);
1236   }
1237
1238   @Override
1239   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1240   {
1241     boolean enabled = useLegacyGap.isSelected();
1242     if (enabled)
1243     {
1244       gapColour.setBackground(
1245               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1246     }
1247     else
1248     {
1249       gapColour.setBackground(
1250               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1251     }
1252     gapColour.setEnabled(!enabled);
1253     gapLabel.setEnabled(!enabled);
1254   }
1255
1256   @Override
1257   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1258   {
1259     useLegacyGap.setSelected(false);
1260     useLegacyGaps_actionPerformed(null);
1261     showHiddenAtStart.setSelected(false);
1262     hiddenColour.setBackground(
1263             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1264   }
1265
1266   @Override
1267   protected void userIdWidth_actionPerformed()
1268   {
1269     try
1270     {
1271       String val = userIdWidth.getText().trim();
1272       if (val.length() > 0)
1273       {
1274         Integer iw = Integer.parseInt(val);
1275         if (iw.intValue() < 12)
1276         {
1277           throw new NumberFormatException();
1278         }
1279         userIdWidth.setText(iw.toString());
1280       }
1281     } catch (NumberFormatException x)
1282     {
1283       userIdWidth.setText("");
1284       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1285               MessageManager
1286                       .getString("warn.user_defined_width_requirements"),
1287               MessageManager.getString("label.invalid_id_column_width"),
1288               JvOptionPane.WARNING_MESSAGE);
1289     }
1290   }
1291
1292   @Override
1293   protected void autoIdWidth_actionPerformed()
1294   {
1295     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1296     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1297   }
1298
1299   /**
1300    * Returns true if structure viewer path is to a valid executable, else shows
1301    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1302    * (built in to Jalview) or when Jalview is left to try default paths.
1303    */
1304   private boolean validateViewerPath()
1305   {
1306     if (structureViewerPath.getText().trim().length() > 0)
1307     {
1308       File f = new File(structureViewerPath.getText());
1309       if (!f.canExecute())
1310       {
1311         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1312                 MessageManager.getString("label.invalid_viewer_path"),
1313                 MessageManager.getString("label.invalid_viewer_path"),
1314                 JvOptionPane.ERROR_MESSAGE);
1315         return false;
1316       }
1317     }
1318     return true;
1319   }
1320
1321   /**
1322    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1323    * default or user-specified path, if not show a warning/help dialog
1324    */
1325   @Override
1326   protected void structureViewer_actionPerformed(String selectedItem)
1327   {
1328     if (selectedItem.equals(ViewerType.JMOL.name()))
1329     {
1330       structureViewerPath.setEnabled(false);
1331       structureViewerPathLabel.setEnabled(false);
1332       return;
1333     }
1334     boolean found = false;
1335     structureViewerPath.setEnabled(true);
1336     structureViewerPathLabel.setEnabled(true);
1337     structureViewerPathLabel.setText(MessageManager
1338             .formatMessage("label.viewer_path", selectedItem));
1339
1340     /*
1341      * Try user-specified and standard paths for structure viewer executable
1342      */
1343     String viewerPath = "";
1344     List<String> paths = null;
1345     try
1346     {
1347       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1348       switch (viewerType)
1349       {
1350       case JMOL:
1351         // dealt with above
1352         break;
1353       case CHIMERA:
1354         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1355         paths = StructureManager.getChimeraPaths(false);
1356         break;
1357       case CHIMERAX:
1358         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1359         paths = StructureManager.getChimeraPaths(true);
1360         break;
1361       case PYMOL:
1362         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1363         paths = PymolManager.getPymolPaths();
1364         break;
1365       }
1366     } catch (IllegalArgumentException e)
1367     {
1368       // only valid entries should be in the drop-down
1369     }
1370     structureViewerPath.setText(viewerPath);
1371
1372     paths.add(0, structureViewerPath.getText());
1373     for (String path : paths)
1374     {
1375       if (new File(path.trim()).canExecute())
1376       {
1377         found = true;
1378         break;
1379       }
1380     }
1381
1382     if (!found)
1383     {
1384       String[] options = { "OK", "Help" };
1385       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1386               JvSwingUtils.wrapTooltip(true,
1387                       MessageManager.getString("label.viewer_missing")),
1388               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1389               null, options, options[0]);
1390       if (showHelp == JvOptionPane.NO_OPTION)
1391       {
1392         try
1393         {
1394           Help.showHelpWindow(HelpId.StructureViewer);
1395         } catch (HelpSetException e)
1396         {
1397           e.printStackTrace();
1398         }
1399       }
1400     }
1401   }
1402
1403   public class OptionsParam
1404   {
1405     private String name;
1406
1407     private String code;
1408
1409     public OptionsParam(String name, String code)
1410     {
1411       this.name = name;
1412       this.code = code;
1413     }
1414
1415     public String getName()
1416     {
1417       return name;
1418     }
1419
1420     public void setName(String name)
1421     {
1422       this.name = name;
1423     }
1424
1425     public String getCode()
1426     {
1427       return code;
1428     }
1429
1430     public void setCode(String code)
1431     {
1432       this.code = code;
1433     }
1434
1435     @Override
1436     public String toString()
1437     {
1438       return name;
1439     }
1440
1441     @Override
1442     public boolean equals(Object that)
1443     {
1444       if (!(that instanceof OptionsParam))
1445       {
1446         return false;
1447       }
1448       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1449     }
1450
1451     @Override
1452     public int hashCode()
1453     {
1454       return name.hashCode() + code.hashCode();
1455     }
1456   }
1457
1458   private class UrlListSelectionHandler implements ListSelectionListener
1459   {
1460
1461     @Override
1462     public void valueChanged(ListSelectionEvent e)
1463     {
1464       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1465
1466       int index = lsm.getMinSelectionIndex();
1467       if (index == -1)
1468       {
1469         // no selection, so disable delete/edit buttons
1470         editLink.setEnabled(false);
1471         deleteLink.setEnabled(false);
1472         return;
1473       }
1474       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1475
1476       // enable/disable edit and delete link buttons
1477       if (((UrlLinkTableModel) linkUrlTable.getModel())
1478               .isRowDeletable(modelIndex))
1479       {
1480         deleteLink.setEnabled(true);
1481       }
1482       else
1483       {
1484         deleteLink.setEnabled(false);
1485       }
1486
1487       if (((UrlLinkTableModel) linkUrlTable.getModel())
1488               .isRowEditable(modelIndex))
1489       {
1490         editLink.setEnabled(true);
1491       }
1492       else
1493       {
1494         editLink.setEnabled(false);
1495       }
1496     }
1497   }
1498 }