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 /*
  85  * for merge with Jalview-JS
  86  public class Preferences extends GPreferences implements ApplicationSingletonI
  87  */
  88 public class Preferences extends GPreferences
  89 {
  90   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  91
  92   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  93
  94   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  95
  96   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  97
  98   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  99
 100   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 101
 102   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 103
 104   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 105
 106   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 107
 108   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 109
 110   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 111
 112   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 113
 114   public static final String PYMOL_PATH = "PYMOL_PATH";
 115
 116   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 117
 118   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 119
 120   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 121
 122   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 123
 124   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 125
 126   public static final String GAP_COLOUR = "GAP_COLOUR";
 127
 128   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 129
 130   private static final int MIN_FONT_SIZE = 1;
 131
 132   private static final int MAX_FONT_SIZE = 30;
 133
 134   private String previousProxyType;
 135
 136   private static Preferences INSTANCE = null; // add "final"
 137
 138   /**
 139    * Holds name and link separated with | character. Sequence ID must be
 140    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 141    */
 142   public static UrlProviderI sequenceUrlLinks;
 143
 144   public static UrlLinkTableModel dataModel;
 145
 146   /**
 147    * Holds name and link separated with | character. Sequence IDS and Sequences
 148    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 149    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 150    * for first and second token specified after a pipe character at end |,|.
 151    * (TODO: proper escape for using | to separate ids or sequences
 152    */
 153
 154   public static List<String> groupURLLinks;
 155   static
 156   {
 157     // get links selected to be in the menu (SEQUENCE_LINKS)
 158     // and links entered by the user but not selected (STORED_LINKS)
 159     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 160     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 161     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 162             UrlConstants.DEFAULT_LABEL);
 163
 164     // if both links lists are empty, add the DEFAULT_URL link
 165     // otherwise we assume the default link is in one of the lists
 166     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 167     {
 168       inMenuString = UrlConstants.DEFAULT_STRING;
 169     }
 170     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 171             inMenuString, notInMenuString);
 172     sequenceUrlLinks = factory.createUrlProvider();
 173     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 174
 175     /**
 176      * TODO: reformulate groupURL encoding so two or more can be stored in the
 177      * .properties file as '|' separated strings
 178      */
 179
 180     groupURLLinks = new ArrayList<>();
 181   }
 182
 183   JInternalFrame frame;
 184
 185   private WsPreferences wsPrefs;
 186
 187   private OptionsParam promptEachTimeOpt = new OptionsParam(
 188           MessageManager.getString("label.prompt_each_time"),
 189           "Prompt each time");
 190
 191   private OptionsParam lineArtOpt = new OptionsParam(
 192           MessageManager.getString("label.lineart"), "Lineart");
 193
 194   private OptionsParam textOpt = new OptionsParam(
 195           MessageManager.getString("action.text"), "Text");
 196
 197   // get singleton Preferences instance
 198   public static Preferences getInstance()
 199   {
 200     if (INSTANCE == null || INSTANCE.frame == null
 201             || INSTANCE.frame.isClosed())
 202     {
 203       INSTANCE = new Preferences();
 204     }
 205     return INSTANCE;
 206
 207     /*
 208      * Replace code with the following for Jalvew-JS
 209     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 210     if (INSTANCE == null || INSTANCE.frame == null
 211             || INSTANCE.frame.isClosed())
 212     {
 213       ApplicationSingletonProvider.remove(Preferences.class);
 214       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 215     }
 216     return INSTANCE;
 217     */
 218   }
 219
 220   public static void openPreferences()
 221   {
 222     openPreferences(0, null);
 223   }
 224
 225   public static void openPreferences(int selectTab, String message)
 226   {
 227     Preferences p = getInstance();
 228     p.selectTab(selectTab);
 229     p.setMessage(message);
 230     p.frame.show();
 231     p.frame.moveToFront();
 232     p.frame.grabFocus();
 233   }
 234
 235   /**
 236    * Creates a new Preferences object.
 237    */
 238   private Preferences()
 239   {
 240     super();
 241     frame = new JInternalFrame();
 242     frame.setContentPane(this);
 243     if (!Platform.isJS())
 244     /**
 245      * Java only
 246      *
 247      * @j2sIgnore
 248      */
 249     {
 250       wsPrefs = new WsPreferences();
 251       wsTab.add(wsPrefs, BorderLayout.CENTER);
 252     }
 253     int width = 500, height = 450;
 254     if (Platform.isAMacAndNotJS())
 255     {
 256       width = 570;
 257       height = 480;
 258     }
 259
 260     Desktop.addInternalFrame(frame,
 261             MessageManager.getString("label.preferences"), width, height);
 262     frame.setMinimumSize(new Dimension(width, height));
 263
 264     /*
 265      * Set Visual tab defaults
 266      */
 267     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 268     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 269     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 270     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 271
 272     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 273     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 274     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 275     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 276     showUnconserved
 277             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 278     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 279     showGroupConsensus
 280             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 281     showGroupConservation.setSelected(
 282             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 283     showConsensHistogram.setSelected(
 284             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 285     showConsensLogo
 286             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 287     showNpTooltip
 288             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 289     showDbRefTooltip
 290             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 291
 292     String[] fonts = java.awt.GraphicsEnvironment
 293             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 294     for (int i = 0; i < fonts.length; i++)
 295     {
 296       fontNameCB.addItem(fonts[i]);
 297     }
 298
 299     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 300     {
 301       fontSizeCB.addItem(i + "");
 302     }
 303
 304     fontStyleCB.addItem("plain");
 305     fontStyleCB.addItem("bold");
 306     fontStyleCB.addItem("italic");
 307
 308     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 309     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 310     fontStyleCB.setSelectedItem(
 311             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 312
 313     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 314     scaleProteinToCdna
 315             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 316
 317     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 318
 319     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 320
 321     gapSymbolCB.addItem("-");
 322     gapSymbolCB.addItem(".");
 323
 324     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 325
 326     sortby.addItem("No sort");
 327     sortby.addItem("Id");
 328     sortby.addItem("Pairwise Identity");
 329     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 330
 331     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 332     sortAnnBy
 333             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 334     sortAnnBy
 335             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 336     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 337             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 338                     SequenceAnnotationOrder.NONE.name()));
 339     sortAnnBy.setSelectedItem(savedSort.toString());
 340
 341     sortAutocalc.addItem("Autocalculated first");
 342     sortAutocalc.addItem("Autocalculated last");
 343     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 344     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 345             : sortAutocalc.getItemAt(1));
 346     startupCheckbox
 347             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 348     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 349             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 350                     + "/examples/exampleFile_2_3.jar"));
 351
 352     /*
 353      * Set Colours tab defaults
 354      */
 355     protColour.addItem(ResidueColourScheme.NONE);
 356     nucColour.addItem(ResidueColourScheme.NONE);
 357     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 358     {
 359       String name = cs.getSchemeName();
 360       protColour.addItem(name);
 361       nucColour.addItem(name);
 362     }
 363     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 364             ResidueColourScheme.NONE);
 365     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 366     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 367     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 368     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 369     minColour.setBackground(
 370             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 371     maxColour.setBackground(
 372             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 373
 374     /*
 375      * Set overview panel defaults
 376      */
 377     gapColour.setBackground(
 378             Cache.getDefaultColour(GAP_COLOUR,
 379                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 380     hiddenColour.setBackground(
 381             Cache.getDefaultColour(HIDDEN_COLOUR,
 382                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 383     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 384     gapLabel.setEnabled(!useLegacyGap.isSelected());
 385     gapColour.setEnabled(!useLegacyGap.isSelected());
 386     showHiddenAtStart
 387             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 388
 389     /*
 390      * Set Structure tab defaults
 391      */
 392     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 393     structFromPdb.setSelected(structSelected);
 394     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 395     useRnaView.setEnabled(structSelected);
 396     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 397     addSecondaryStructure.setEnabled(structSelected);
 398     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 399     addTempFactor.setEnabled(structSelected);
 400
 401     /*
 402      * set choice of structure viewer, and path if saved as a preference;
 403      * default to Jmol (first choice) if an unexpected value is found
 404      */
 405     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 406     structViewer.setSelectedItem(viewerType);
 407     String viewerPath = "";
 408     ViewerType type = null;
 409     try
 410     {
 411       type = ViewerType.valueOf(viewerType);
 412       switch (type)
 413       {
 414       case JMOL:
 415         break;
 416       case CHIMERA:
 417         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 418         break;
 419       case CHIMERAX:
 420         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 421         break;
 422       case PYMOL:
 423         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 424         break;
 425       }
 426     } catch (IllegalArgumentException e)
 427     {
 428       Cache.log.error("Unknown structure viewer type: " + viewerType
 429               + ", defaulting to Jmol");
 430       type = ViewerType.JMOL;
 431     }
 432     structureViewerPath.setText(viewerPath);
 433
 434     structureViewerPath.addActionListener(new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         if (validateViewerPath())
 440         {
 441           Cache.setProperty(structViewer.getSelectedItem()
 442                   .equals(ViewerType.CHIMERAX.name())
 443                   ? CHIMERAX_PATH
 444                   : CHIMERA_PATH, structureViewerPath.getText());
 445         }
 446       }
 447     });
 448
 449     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 450     {
 451       siftsMapping.setSelected(true);
 452     }
 453     else
 454     {
 455       nwMapping.setSelected(true);
 456     }
 457
 458     SiftsSettings
 459             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 460
 461     /*
 462      * Set Connections tab defaults
 463      */
 464
 465     // set up sorting
 466     linkUrlTable.setModel(dataModel);
 467     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 468             linkUrlTable.getModel());
 469     linkUrlTable.setRowSorter(sorter);
 470     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 471
 472     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 473     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 474             SortOrder.DESCENDING));
 475     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 476             SortOrder.DESCENDING));
 477     sortKeys.add(
 478             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 479
 480     sorter.setSortKeys(sortKeys);
 481     // BH 2018 setSortKeys will do the sort
 482     // sorter.sort();
 483
 484     // set up filtering
 485     ActionListener onReset;
 486     onReset = new ActionListener()
 487     {
 488       @Override
 489       public void actionPerformed(ActionEvent e)
 490       {
 491         filterTB.setText("");
 492         sorter.setRowFilter(RowFilter.regexFilter(""));
 493       }
 494
 495     };
 496     doReset.addActionListener(onReset);
 497
 498     // filter to display only custom urls
 499     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 500     {
 501       @Override
 502       public boolean include(
 503               Entry<? extends TableModel, ? extends Object> entry)
 504       {
 505         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 506       }
 507     };
 508
 509     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 510             linkUrlTable.getModel());
 511     customSorter.setRowFilter(customUrlFilter);
 512
 513     ActionListener onCustomOnly;
 514     onCustomOnly = new ActionListener()
 515     {
 516       @Override
 517       public void actionPerformed(ActionEvent e)
 518       {
 519         filterTB.setText("");
 520         sorter.setRowFilter(customUrlFilter);
 521       }
 522     };
 523     userOnly.addActionListener(onCustomOnly);
 524
 525     filterTB.getDocument().addDocumentListener(new DocumentListener()
 526     {
 527       String caseInsensitiveFlag = "(?i)";
 528
 529       @Override
 530       public void changedUpdate(DocumentEvent e)
 531       {
 532         sorter.setRowFilter(RowFilter
 533                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 534       }
 535
 536       @Override
 537       public void removeUpdate(DocumentEvent e)
 538       {
 539         sorter.setRowFilter(RowFilter
 540                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 541       }
 542
 543       @Override
 544       public void insertUpdate(DocumentEvent e)
 545       {
 546         sorter.setRowFilter(RowFilter
 547                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 548       }
 549     });
 550
 551     // set up list selection functionality
 552     linkUrlTable.getSelectionModel()
 553             .addListSelectionListener(new UrlListSelectionHandler());
 554
 555     // set up radio buttons
 556     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 557             .getPrimaryColumn();
 558     String onClickName = linkUrlTable.getColumnName(onClickCol);
 559     linkUrlTable.getColumn(onClickName)
 560             .setCellRenderer(new RadioButtonRenderer());
 561     linkUrlTable.getColumn(onClickName)
 562             .setCellEditor(new RadioButtonEditor());
 563
 564     // get boolean columns and resize those to min possible
 565     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 566     {
 567       if (linkUrlTable.getModel().getColumnClass(column)
 568               .equals(Boolean.class))
 569       {
 570         TableColumn tableColumn = linkUrlTable.getColumnModel()
 571                 .getColumn(column);
 572         int preferredWidth = tableColumn.getMinWidth();
 573
 574         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 575                 column);
 576         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 577         int cwidth = c.getPreferredSize().width
 578                 + linkUrlTable.getIntercellSpacing().width;
 579         preferredWidth = Math.max(preferredWidth, cwidth);
 580
 581         tableColumn.setPreferredWidth(preferredWidth);
 582       }
 583     }
 584
 585     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 586     previousProxyType = proxyTypeString;
 587     switch (proxyTypeString)
 588     {
 589     case Cache.PROXYTYPE_NONE:
 590       proxyType.setSelected(noProxy.getModel(), true);
 591       break;
 592     case Cache.PROXYTYPE_SYSTEM:
 593       proxyType.setSelected(systemProxy.getModel(), true);
 594       break;
 595     case Cache.PROXYTYPE_CUSTOM:
 596       proxyType.setSelected(customProxy.getModel(), true);
 597       break;
 598     default:
 599       Cache.log.warn(
 600               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 601                       + proxyTypeString);
 602     }
 603     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 604     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 605     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 606     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 607     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 608     proxyAuthUsernameTB
 609             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 610     // we are not storing or retrieving proxy password from .jalview_properties
 611     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 612             : new String(Cache.proxyAuthPassword));
 613     setCustomProxyEnabled();
 614     applyProxyButtonEnabled(false);
 615
 616     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 617
 618     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 619     // note antisense here: default is true
 620     questionnaire
 621             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 622     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 623
 624     /*
 625      * Set Output tab defaults
 626      */
 627     setupOutputCombo(epsRendering, "EPS_RENDERING");
 628     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 629     setupOutputCombo(svgRendering, "SVG_RENDERING");
 630     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 631     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 632     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 633     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 634     userIdWidth.setText(wi == null ? "" : wi.toString());
 635     // TODO: refactor to use common enum via FormatAdapter and allow extension
 636     // for new flat file formats
 637     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 638     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 639     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 640     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 641     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 642     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 643     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 644     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 645     embbedBioJSON
 646             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 647
 648     /*
 649      * Set Editing tab defaults
 650      */
 651     autoCalculateConsCheck
 652             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 653     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 654     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 655
 656     annotations_actionPerformed(null); // update the display of the annotation
 657                                        // settings
 658
 659
 660     /*
 661      * Set Backups tab defaults
 662      */
 663     loadLastSavedBackupsOptions();
 664   }
 665
 666   /**
 667    * A helper method that sets the items and initial selection in a character
 668    * rendering option list (Prompt each time/Lineart/Text)
 669    *
 670    * @param comboBox
 671    * @param propertyKey
 672    */
 673   protected void setupOutputCombo(JComboBox<Object> comboBox,
 674           String propertyKey)
 675   {
 676     comboBox.addItem(promptEachTimeOpt);
 677     comboBox.addItem(lineArtOpt);
 678     comboBox.addItem(textOpt);
 679
 680     /*
 681      * JalviewJS doesn't support Lineart so force it to Text
 682      */
 683     String defaultOption = Platform.isJS() ? "Text"
 684             : Cache.getDefault(propertyKey, "Prompt each time");
 685     if (defaultOption.equalsIgnoreCase("Text"))
 686     {
 687       comboBox.setSelectedItem(textOpt);
 688     }
 689     else if (defaultOption.equalsIgnoreCase("Lineart"))
 690     {
 691       comboBox.setSelectedItem(lineArtOpt);
 692     }
 693     else
 694     {
 695       comboBox.setSelectedItem(promptEachTimeOpt);
 696     }
 697   }
 698
 699   /**
 700    * Save user selections on the Preferences tabs to the Cache and write out to
 701    * file.
 702    *
 703    * @param e
 704    */
 705   @Override
 706   public void ok_actionPerformed(ActionEvent e)
 707   {
 708     if (!validateSettings())
 709     {
 710       return;
 711     }
 712
 713     /*
 714      * Set proxy settings first (to be before web services refresh)
 715      */
 716     saveProxySettings();
 717
 718     /*
 719      * Save Visual settings
 720      */
 721     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 722             Boolean.toString(seqLimit.isSelected()));
 723     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 724             Boolean.toString(rightAlign.isSelected()));
 725     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 726             Boolean.toString(fullScreen.isSelected()));
 727     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 728             Boolean.toString(openoverv.isSelected()));
 729     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 730             Boolean.toString(annotations.isSelected()));
 731     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 732             Boolean.toString(conservation.isSelected()));
 733     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 734             Boolean.toString(quality.isSelected()));
 735     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 736             Boolean.toString(identity.isSelected()));
 737
 738     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 739             gapSymbolCB.getSelectedItem().toString());
 740
 741     Cache.applicationProperties.setProperty("FONT_NAME",
 742             fontNameCB.getSelectedItem().toString());
 743     Cache.applicationProperties.setProperty("FONT_STYLE",
 744             fontStyleCB.getSelectedItem().toString());
 745     Cache.applicationProperties.setProperty("FONT_SIZE",
 746             fontSizeCB.getSelectedItem().toString());
 747
 748     Cache.applicationProperties.setProperty("ID_ITALICS",
 749             Boolean.toString(idItalics.isSelected()));
 750     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 751             Boolean.toString(showUnconserved.isSelected()));
 752     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 753             Boolean.toString(showOccupancy.isSelected()));
 754     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 755             Boolean.toString(showGroupConsensus.isSelected()));
 756     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 757             Boolean.toString(showGroupConservation.isSelected()));
 758     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 759             Boolean.toString(showConsensHistogram.isSelected()));
 760     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 761             Boolean.toString(showConsensLogo.isSelected()));
 762     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 763             Boolean.toString(smoothFont.isSelected()));
 764     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 765             Boolean.toString(scaleProteinToCdna.isSelected()));
 766     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 767             Boolean.toString(showNpTooltip.isSelected()));
 768     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 769             Boolean.toString(showDbRefTooltip.isSelected()));
 770
 771     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 772             Boolean.toString(wrap.isSelected()));
 773
 774     Cache.applicationProperties.setProperty("STARTUP_FILE",
 775             startupFileTextfield.getText());
 776     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 777             Boolean.toString(startupCheckbox.isSelected()));
 778
 779     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 780             sortby.getSelectedItem().toString());
 781
 782     // convert description of sort order to enum name for save
 783     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 784             .forDescription(sortAnnBy.getSelectedItem().toString());
 785     if (annSortOrder != null)
 786     {
 787       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 788               annSortOrder.name());
 789     }
 790
 791     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 792     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 793             Boolean.valueOf(showAutocalcFirst).toString());
 794
 795     /*
 796      * Save Colours settings
 797      */
 798     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 799             protColour.getSelectedItem().toString());
 800     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 801             nucColour.getSelectedItem().toString());
 802     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 803             minColour.getBackground());
 804     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 805             maxColour.getBackground());
 806
 807     /*
 808      * Save Overview settings
 809      */
 810     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 811     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 812     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 813             Boolean.toString(useLegacyGap.isSelected()));
 814     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 815             Boolean.toString(showHiddenAtStart.isSelected()));
 816
 817     /*
 818      * Save Structure settings
 819      */
 820     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 821             Boolean.toString(addTempFactor.isSelected()));
 822     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 823             Boolean.toString(addSecondaryStructure.isSelected()));
 824     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 825             Boolean.toString(useRnaView.isSelected()));
 826     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 827             Boolean.toString(structFromPdb.isSelected()));
 828     String viewer = structViewer.getSelectedItem().toString();
 829     String viewerPath = structureViewerPath.getText();
 830     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 831             viewer);
 832     if (viewer.equals(ViewerType.CHIMERA.name()))
 833     {
 834       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 835     }
 836     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 837     {
 838       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 839     }
 840     else if (viewer.equals(ViewerType.PYMOL.name()))
 841     {
 842       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 843     }
 844     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 845             Boolean.toString(siftsMapping.isSelected()));
 846     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 847
 848     /*
 849      * Save Output settings
 850      */
 851     Cache.applicationProperties.setProperty("EPS_RENDERING",
 852             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 853     Cache.applicationProperties.setProperty("HTML_RENDERING",
 854             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 855     Cache.applicationProperties.setProperty("SVG_RENDERING",
 856             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 857
 858     /*
 859      * Save Connections settings
 860      */
 861     // Proxy settings set first (to catch web services)
 862
 863     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 864
 865     jalview.util.BrowserLauncher.resetBrowser();
 866
 867     // save user-defined and selected links
 868     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 869     if (menuLinks.isEmpty())
 870     {
 871       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 872     }
 873     else
 874     {
 875       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 876               menuLinks.toString());
 877     }
 878
 879     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 880     if (nonMenuLinks.isEmpty())
 881     {
 882       Cache.applicationProperties.remove("STORED_LINKS");
 883     }
 884     else
 885     {
 886       Cache.applicationProperties.setProperty("STORED_LINKS",
 887               nonMenuLinks.toString());
 888     }
 889
 890     Cache.applicationProperties.setProperty("DEFAULT_URL",
 891             sequenceUrlLinks.getPrimaryUrlId());
 892
 893     Cache.setProperty("VERSION_CHECK",
 894             Boolean.toString(versioncheck.isSelected()));
 895     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 896     {
 897       // default is false - we only set this if the user has actively agreed
 898       Cache.setProperty("USAGESTATS",
 899               Boolean.toString(usagestats.isSelected()));
 900     }
 901     if (!questionnaire.isSelected())
 902     {
 903       Cache.setProperty("NOQUESTIONNAIRES", "true");
 904     }
 905     else
 906     {
 907       // special - made easy to edit a property file to disable questionnaires
 908       // by just adding the given line
 909       Cache.removeProperty("NOQUESTIONNAIRES");
 910     }
 911
 912     /*
 913      * Save Output settings
 914      */
 915     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 916             Boolean.toString(blcjv.isSelected()));
 917     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 918             Boolean.toString(clustaljv.isSelected()));
 919     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 920             Boolean.toString(fastajv.isSelected()));
 921     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 922             Boolean.toString(msfjv.isSelected()));
 923     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 924             Boolean.toString(pfamjv.isSelected()));
 925     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 926             Boolean.toString(pileupjv.isSelected()));
 927     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 928             Boolean.toString(pirjv.isSelected()));
 929     Cache.applicationProperties.setProperty("PIR_MODELLER",
 930             Boolean.toString(modellerOutput.isSelected()));
 931     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 932             Boolean.toString(embbedBioJSON.isSelected()));
 933     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 934
 935     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 936             Boolean.toString(autoIdWidth.isSelected()));
 937     userIdWidth_actionPerformed();
 938     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 939             userIdWidth.getText());
 940
 941     /*
 942      * Save Editing settings
 943      */
 944     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 945             Boolean.toString(autoCalculateConsCheck.isSelected()));
 946     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 947             Boolean.toString(sortByTree.isSelected()));
 948     Cache.applicationProperties.setProperty("PAD_GAPS",
 949             Boolean.toString(padGaps.isSelected()));
 950
 951     if (!Platform.isJS())
 952     {
 953       wsPrefs.updateAndRefreshWsMenuConfig(false);
 954     }
 955
 956     /*
 957      * Save Backups settings
 958      */
 959     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 960             Boolean.toString(enableBackupFiles.isSelected()));
 961     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 962     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 963
 964     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 965     {
 966       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 967       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 968               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 969       Cache.applicationProperties
 970               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 971                       customBFPE.toString());
 972     }
 973
 974     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 975             .get(preset);
 976     Cache.applicationProperties.setProperty(
 977             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 978
 979     Cache.saveProperties();
 980     Desktop.instance.doConfigureStructurePrefs();
 981     try
 982     {
 983       frame.setClosed(true);
 984     } catch (Exception ex)
 985     {
 986     }
 987   }
 988
 989   public void saveProxySettings()
 990   {
 991     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 992             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 993                     : Cache.PROXYTYPE_SYSTEM;
 994     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
 995     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 996     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 997     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 998     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 999     Cache.setOrRemove("PROXY_AUTH",
1000             Boolean.toString(proxyAuth.isSelected()));
1001     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1002     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1003     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1004     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1005             || !newProxyType.equals(previousProxyType))
1006     {
1007       // force a re-lookup of ws if proxytype is custom or has changed
1008       wsPrefs.update++;
1009     }
1010     previousProxyType = newProxyType;
1011   }
1012
1013   /**
1014    * Do any necessary validation before saving settings. Return focus to the
1015    * first tab which fails validation.
1016    *
1017    * @return
1018    */
1019   private boolean validateSettings()
1020   {
1021     if (!validateStructure())
1022     {
1023       structureTab.requestFocusInWindow();
1024       return false;
1025     }
1026     return true;
1027   }
1028
1029   @Override
1030   protected boolean validateStructure()
1031   {
1032     return validateViewerPath();
1033
1034   }
1035
1036   /**
1037    * DOCUMENT ME!
1038    */
1039   @Override
1040   public void startupFileTextfield_mouseClicked()
1041   {
1042     // TODO: JAL-3048 not needed for Jalview-JS
1043     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1044     JalviewFileChooser chooser = JalviewFileChooser
1045             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1046     chooser.setFileView(new JalviewFileView());
1047     chooser.setDialogTitle(
1048             MessageManager.getString("label.select_startup_file"));
1049
1050     int value = chooser.showOpenDialog(this);
1051
1052     if (value == JalviewFileChooser.APPROVE_OPTION)
1053     {
1054       FileFormatI format = chooser.getSelectedFormat();
1055       if (format != null)
1056       {
1057         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1058                 format.getName());
1059       }
1060       startupFileTextfield
1061               .setText(chooser.getSelectedFile().getAbsolutePath());
1062     }
1063   }
1064
1065   /**
1066    * DOCUMENT ME!
1067    *
1068    * @param e
1069    *          DOCUMENT ME!
1070    */
1071   @Override
1072   public void cancel_actionPerformed(ActionEvent e)
1073   {
1074     try
1075     {
1076       if (!Platform.isJS())
1077       {
1078         wsPrefs.updateWsMenuConfig(true);
1079         wsPrefs.refreshWs_actionPerformed(e);
1080       }
1081       frame.setClosed(true);
1082     } catch (Exception ex)
1083     {
1084     }
1085   }
1086
1087   /**
1088    * DOCUMENT ME!
1089    *
1090    * @param e
1091    *          DOCUMENT ME!
1092    */
1093   @Override
1094   public void annotations_actionPerformed(ActionEvent e)
1095   {
1096     conservation.setEnabled(annotations.isSelected());
1097     quality.setEnabled(annotations.isSelected());
1098     identity.setEnabled(annotations.isSelected());
1099     showOccupancy.setEnabled(annotations.isSelected());
1100     showGroupConsensus.setEnabled(annotations.isSelected());
1101     showGroupConservation.setEnabled(annotations.isSelected());
1102     showConsensHistogram.setEnabled(annotations.isSelected()
1103             && (identity.isSelected() || showGroupConsensus.isSelected()));
1104     showConsensLogo.setEnabled(annotations.isSelected()
1105             && (identity.isSelected() || showGroupConsensus.isSelected()));
1106   }
1107
1108   @Override
1109   public void newLink_actionPerformed(ActionEvent e)
1110   {
1111     GSequenceLink link = new GSequenceLink();
1112     boolean valid = false;
1113     while (!valid)
1114     {
1115       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1116               MessageManager.getString("label.new_sequence_url_link"),
1117               JvOptionPane.OK_CANCEL_OPTION, -1,
1118               null) == JvOptionPane.OK_OPTION)
1119       {
1120         if (link.checkValid())
1121         {
1122           if (((UrlLinkTableModel) linkUrlTable.getModel())
1123                   .isUniqueName(link.getName()))
1124           {
1125             ((UrlLinkTableModel) linkUrlTable.getModel())
1126                     .insertRow(link.getName(), link.getURL());
1127             valid = true;
1128           }
1129           else
1130           {
1131             link.notifyDuplicate();
1132             continue;
1133           }
1134         }
1135       }
1136       else
1137       {
1138         break;
1139       }
1140     }
1141   }
1142
1143   @Override
1144   public void editLink_actionPerformed(ActionEvent e)
1145   {
1146     GSequenceLink link = new GSequenceLink();
1147
1148     int index = linkUrlTable.getSelectedRow();
1149     if (index == -1)
1150     {
1151       // button no longer enabled if row is not selected
1152       Cache.log.debug("Edit with no row selected in linkUrlTable");
1153       return;
1154     }
1155
1156     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1157             .getNameColumn();
1158     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1159             .getUrlColumn();
1160     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1161     link.setName(oldName);
1162     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1163
1164     boolean valid = false;
1165     while (!valid)
1166     {
1167       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1168               MessageManager.getString("label.edit_sequence_url_link"),
1169               JvOptionPane.OK_CANCEL_OPTION, -1,
1170               null) == JvOptionPane.OK_OPTION)
1171       {
1172         if (link.checkValid())
1173         {
1174           if ((oldName.equals(link.getName()))
1175                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1176                           .isUniqueName(link.getName())))
1177           {
1178             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1179             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1180             valid = true;
1181           }
1182           else
1183           {
1184             link.notifyDuplicate();
1185             continue;
1186           }
1187         }
1188       }
1189       else
1190       {
1191         break;
1192       }
1193     }
1194   }
1195
1196   @Override
1197   public void deleteLink_actionPerformed(ActionEvent e)
1198   {
1199     int index = linkUrlTable.getSelectedRow();
1200     int modelIndex = -1;
1201     if (index == -1)
1202     {
1203       // button no longer enabled if row is not selected
1204       Cache.log.debug("Delete with no row selected in linkUrlTable");
1205       return;
1206     }
1207     else
1208     {
1209       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1210     }
1211
1212     // make sure we use the model index to delete, and not the table index
1213     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1214   }
1215
1216   @Override
1217   public void defaultBrowser_mouseClicked(MouseEvent e)
1218   {
1219     // TODO: JAL-3048 not needed for j2s
1220     if (!Platform.isJS()) // BH 2019
1221     /**
1222      * Java only
1223      *
1224      * @j2sIgnore
1225      */
1226     {
1227       JFileChooser chooser = new JFileChooser(".");
1228       chooser.setDialogTitle(
1229               MessageManager.getString("label.select_default_browser"));
1230
1231       int value = chooser.showOpenDialog(this);
1232
1233       if (value == JFileChooser.APPROVE_OPTION)
1234       {
1235         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1236       }
1237     }
1238   }
1239
1240   /*
1241    * (non-Javadoc)
1242    *
1243    * @see
1244    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1245    * .ActionEvent)
1246    */
1247   @Override
1248   protected void showunconserved_actionPerformed(ActionEvent e)
1249   {
1250     // TODO Auto-generated method stub
1251     super.showunconserved_actionPerformed(e);
1252   }
1253
1254   public static List<String> getGroupURLLinks()
1255   {
1256     return groupURLLinks;
1257   }
1258
1259   @Override
1260   public void minColour_actionPerformed(JPanel panel)
1261   {
1262     JalviewColourChooser.showColourChooser(this,
1263             MessageManager.getString("label.select_colour_minimum_value"),
1264             panel);
1265   }
1266
1267   @Override
1268   public void maxColour_actionPerformed(JPanel panel)
1269   {
1270     JalviewColourChooser.showColourChooser(this,
1271             MessageManager.getString("label.select_colour_maximum_value"),
1272             panel);
1273   }
1274
1275   @Override
1276   public void gapColour_actionPerformed(JPanel gap)
1277   {
1278     if (!useLegacyGap.isSelected())
1279     {
1280       JalviewColourChooser.showColourChooser(this,
1281               MessageManager.getString("label.select_gap_colour"),
1282               gap);
1283     }
1284   }
1285
1286   @Override
1287   public void hiddenColour_actionPerformed(JPanel hidden)
1288   {
1289     JalviewColourChooser.showColourChooser(this,
1290             MessageManager.getString("label.select_hidden_colour"),
1291             hidden);
1292   }
1293
1294   @Override
1295   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1296   {
1297     boolean enabled = useLegacyGap.isSelected();
1298     if (enabled)
1299     {
1300       gapColour.setBackground(
1301               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1302     }
1303     else
1304     {
1305       gapColour.setBackground(
1306               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1307     }
1308     gapColour.setEnabled(!enabled);
1309     gapLabel.setEnabled(!enabled);
1310   }
1311
1312   @Override
1313   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1314   {
1315     useLegacyGap.setSelected(false);
1316     useLegacyGaps_actionPerformed(null);
1317     showHiddenAtStart.setSelected(false);
1318     hiddenColour.setBackground(
1319             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1320   }
1321
1322   @Override
1323   protected void userIdWidth_actionPerformed()
1324   {
1325     try
1326     {
1327       String val = userIdWidth.getText().trim();
1328       if (val.length() > 0)
1329       {
1330         Integer iw = Integer.parseInt(val);
1331         if (iw.intValue() < 12)
1332         {
1333           throw new NumberFormatException();
1334         }
1335         userIdWidth.setText(iw.toString());
1336       }
1337     } catch (NumberFormatException x)
1338     {
1339       userIdWidth.setText("");
1340       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1341               MessageManager
1342                       .getString("warn.user_defined_width_requirements"),
1343               MessageManager.getString("label.invalid_id_column_width"),
1344               JvOptionPane.WARNING_MESSAGE);
1345     }
1346   }
1347
1348   @Override
1349   protected void autoIdWidth_actionPerformed()
1350   {
1351     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1352     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1353   }
1354
1355   /**
1356    * Returns true if structure viewer path is to a valid executable, else shows
1357    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1358    * (built in to Jalview) or when Jalview is left to try default paths.
1359    */
1360   private boolean validateViewerPath()
1361   {
1362     if (structureViewerPath.getText().trim().length() > 0)
1363     {
1364       File f = new File(structureViewerPath.getText());
1365       if (!f.canExecute())
1366       {
1367         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1368                 MessageManager.getString("label.invalid_viewer_path"),
1369                 MessageManager.getString("label.invalid_viewer_path"),
1370                 JvOptionPane.ERROR_MESSAGE);
1371         return false;
1372       }
1373     }
1374     return true;
1375   }
1376
1377   /**
1378    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1379    * default or user-specified path, if not show a warning/help dialog
1380    */
1381   @Override
1382   protected void structureViewer_actionPerformed(String selectedItem)
1383   {
1384     if (selectedItem.equals(ViewerType.JMOL.name()))
1385     {
1386       structureViewerPath.setEnabled(false);
1387       structureViewerPathLabel.setEnabled(false);
1388       return;
1389     }
1390     boolean found = false;
1391     structureViewerPath.setEnabled(true);
1392     structureViewerPathLabel.setEnabled(true);
1393     structureViewerPathLabel.setText(MessageManager
1394             .formatMessage("label.viewer_path", selectedItem));
1395
1396     /*
1397      * Try user-specified and standard paths for structure viewer executable
1398      */
1399     String viewerPath = "";
1400     List<String> paths = null;
1401     try
1402     {
1403       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1404       switch (viewerType)
1405       {
1406       case JMOL:
1407         // dealt with above
1408         break;
1409       case CHIMERA:
1410         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1411         paths = StructureManager.getChimeraPaths(false);
1412         break;
1413       case CHIMERAX:
1414         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1415         paths = StructureManager.getChimeraPaths(true);
1416         break;
1417       case PYMOL:
1418         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1419         paths = PymolManager.getPymolPaths();
1420         break;
1421       }
1422     } catch (IllegalArgumentException e)
1423     {
1424       // only valid entries should be in the drop-down
1425     }
1426     structureViewerPath.setText(viewerPath);
1427
1428     paths.add(0, structureViewerPath.getText());
1429     for (String path : paths)
1430     {
1431       if (new File(path.trim()).canExecute())
1432       {
1433         found = true;
1434         break;
1435       }
1436     }
1437
1438     if (!found)
1439     {
1440       String[] options = { "OK", "Help" };
1441       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1442               JvSwingUtils.wrapTooltip(true,
1443                       MessageManager.getString("label.viewer_missing")),
1444               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1445               null, options, options[0]);
1446       if (showHelp == JvOptionPane.NO_OPTION)
1447       {
1448         try
1449         {
1450           Help.showHelpWindow(HelpId.StructureViewer);
1451         } catch (HelpSetException e)
1452         {
1453           e.printStackTrace();
1454         }
1455       }
1456     }
1457   }
1458
1459   public class OptionsParam
1460   {
1461     private String name;
1462
1463     private String code;
1464
1465     public OptionsParam(String name, String code)
1466     {
1467       this.name = name;
1468       this.code = code;
1469     }
1470
1471     public String getName()
1472     {
1473       return name;
1474     }
1475
1476     public void setName(String name)
1477     {
1478       this.name = name;
1479     }
1480
1481     public String getCode()
1482     {
1483       return code;
1484     }
1485
1486     public void setCode(String code)
1487     {
1488       this.code = code;
1489     }
1490
1491     @Override
1492     public String toString()
1493     {
1494       return name;
1495     }
1496
1497     @Override
1498     public boolean equals(Object that)
1499     {
1500       if (!(that instanceof OptionsParam))
1501       {
1502         return false;
1503       }
1504       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1505     }
1506
1507     @Override
1508     public int hashCode()
1509     {
1510       return name.hashCode() + code.hashCode();
1511     }
1512   }
1513
1514   private class UrlListSelectionHandler implements ListSelectionListener
1515   {
1516
1517     @Override
1518     public void valueChanged(ListSelectionEvent e)
1519     {
1520       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1521
1522       int index = lsm.getMinSelectionIndex();
1523       if (index == -1)
1524       {
1525         // no selection, so disable delete/edit buttons
1526         editLink.setEnabled(false);
1527         deleteLink.setEnabled(false);
1528         return;
1529       }
1530       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1531
1532       // enable/disable edit and delete link buttons
1533       if (((UrlLinkTableModel) linkUrlTable.getModel())
1534               .isRowDeletable(modelIndex))
1535       {
1536         deleteLink.setEnabled(true);
1537       }
1538       else
1539       {
1540         deleteLink.setEnabled(false);
1541       }
1542
1543       if (((UrlLinkTableModel) linkUrlTable.getModel())
1544               .isRowEditable(modelIndex))
1545       {
1546         editLink.setEnabled(true);
1547       }
1548       else
1549       {
1550         editLink.setEnabled(false);
1551       }
1552     }
1553   }
1554 }