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(Cache.getDefaultColour(GAP_COLOUR,
 378             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 379     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 380             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 381     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 382     gapLabel.setEnabled(!useLegacyGap.isSelected());
 383     gapColour.setEnabled(!useLegacyGap.isSelected());
 384     showHiddenAtStart
 385             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 386
 387     /*
 388      * Set Structure tab defaults
 389      */
 390     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 391     structFromPdb.setSelected(structSelected);
 392     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 393     useRnaView.setEnabled(structSelected);
 394     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 395     addSecondaryStructure.setEnabled(structSelected);
 396     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 397     addTempFactor.setEnabled(structSelected);
 398
 399     /*
 400      * set choice of structure viewer, and path if saved as a preference;
 401      * default to Jmol (first choice) if an unexpected value is found
 402      */
 403     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 404             ViewerType.JMOL.name());
 405     structViewer.setSelectedItem(viewerType);
 406     String viewerPath = "";
 407     ViewerType type = null;
 408     try
 409     {
 410       type = ViewerType.valueOf(viewerType);
 411       switch (type)
 412       {
 413       case JMOL:
 414         break;
 415       case CHIMERA:
 416         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 417         break;
 418       case CHIMERAX:
 419         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 420         break;
 421       case PYMOL:
 422         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 423         break;
 424       }
 425     } catch (IllegalArgumentException e)
 426     {
 427       Cache.log.error("Unknown structure viewer type: " + viewerType
 428               + ", defaulting to Jmol");
 429       type = ViewerType.JMOL;
 430     }
 431     structureViewerPath.setText(viewerPath);
 432
 433     structureViewerPath.addActionListener(new ActionListener()
 434     {
 435       @Override
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         if (validateViewerPath())
 439         {
 440           Cache.setProperty(
 441                   structViewer.getSelectedItem().equals(
 442                           ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
 443                                   : CHIMERA_PATH,
 444                   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      * Set Backups tab defaults
 661      */
 662     loadLastSavedBackupsOptions();
 663   }
 664
 665   /**
 666    * A helper method that sets the items and initial selection in a character
 667    * rendering option list (Prompt each time/Lineart/Text)
 668    *
 669    * @param comboBox
 670    * @param propertyKey
 671    */
 672   protected void setupOutputCombo(JComboBox<Object> comboBox,
 673           String propertyKey)
 674   {
 675     comboBox.addItem(promptEachTimeOpt);
 676     comboBox.addItem(lineArtOpt);
 677     comboBox.addItem(textOpt);
 678
 679     /*
 680      * JalviewJS doesn't support Lineart so force it to Text
 681      */
 682     String defaultOption = Platform.isJS() ? "Text"
 683             : Cache.getDefault(propertyKey, "Prompt each time");
 684     if (defaultOption.equalsIgnoreCase("Text"))
 685     {
 686       comboBox.setSelectedItem(textOpt);
 687     }
 688     else if (defaultOption.equalsIgnoreCase("Lineart"))
 689     {
 690       comboBox.setSelectedItem(lineArtOpt);
 691     }
 692     else
 693     {
 694       comboBox.setSelectedItem(promptEachTimeOpt);
 695     }
 696   }
 697
 698   /**
 699    * Save user selections on the Preferences tabs to the Cache and write out to
 700    * file.
 701    *
 702    * @param e
 703    */
 704   @Override
 705   public void ok_actionPerformed(ActionEvent e)
 706   {
 707     if (!validateSettings())
 708     {
 709       return;
 710     }
 711
 712     /*
 713      * Set proxy settings first (to be before web services refresh)
 714      */
 715     saveProxySettings();
 716
 717     /*
 718      * Save Visual settings
 719      */
 720     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 721             Boolean.toString(seqLimit.isSelected()));
 722     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 723             Boolean.toString(rightAlign.isSelected()));
 724     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 725             Boolean.toString(fullScreen.isSelected()));
 726     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 727             Boolean.toString(openoverv.isSelected()));
 728     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 729             Boolean.toString(annotations.isSelected()));
 730     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 731             Boolean.toString(conservation.isSelected()));
 732     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 733             Boolean.toString(quality.isSelected()));
 734     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 735             Boolean.toString(identity.isSelected()));
 736
 737     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 738             gapSymbolCB.getSelectedItem().toString());
 739
 740     Cache.applicationProperties.setProperty("FONT_NAME",
 741             fontNameCB.getSelectedItem().toString());
 742     Cache.applicationProperties.setProperty("FONT_STYLE",
 743             fontStyleCB.getSelectedItem().toString());
 744     Cache.applicationProperties.setProperty("FONT_SIZE",
 745             fontSizeCB.getSelectedItem().toString());
 746
 747     Cache.applicationProperties.setProperty("ID_ITALICS",
 748             Boolean.toString(idItalics.isSelected()));
 749     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 750             Boolean.toString(showUnconserved.isSelected()));
 751     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 752             Boolean.toString(showOccupancy.isSelected()));
 753     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 754             Boolean.toString(showGroupConsensus.isSelected()));
 755     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 756             Boolean.toString(showGroupConservation.isSelected()));
 757     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 758             Boolean.toString(showConsensHistogram.isSelected()));
 759     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 760             Boolean.toString(showConsensLogo.isSelected()));
 761     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 762             Boolean.toString(smoothFont.isSelected()));
 763     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 764             Boolean.toString(scaleProteinToCdna.isSelected()));
 765     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 766             Boolean.toString(showNpTooltip.isSelected()));
 767     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 768             Boolean.toString(showDbRefTooltip.isSelected()));
 769
 770     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 771             Boolean.toString(wrap.isSelected()));
 772
 773     Cache.applicationProperties.setProperty("STARTUP_FILE",
 774             startupFileTextfield.getText());
 775     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 776             Boolean.toString(startupCheckbox.isSelected()));
 777
 778     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 779             sortby.getSelectedItem().toString());
 780
 781     // convert description of sort order to enum name for save
 782     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 783             .forDescription(sortAnnBy.getSelectedItem().toString());
 784     if (annSortOrder != null)
 785     {
 786       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 787               annSortOrder.name());
 788     }
 789
 790     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 791     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 792             Boolean.valueOf(showAutocalcFirst).toString());
 793
 794     /*
 795      * Save Colours settings
 796      */
 797     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 798             protColour.getSelectedItem().toString());
 799     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 800             nucColour.getSelectedItem().toString());
 801     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 802             minColour.getBackground());
 803     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 804             maxColour.getBackground());
 805
 806     /*
 807      * Save Overview settings
 808      */
 809     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 810     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 811     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 812             Boolean.toString(useLegacyGap.isSelected()));
 813     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 814             Boolean.toString(showHiddenAtStart.isSelected()));
 815
 816     /*
 817      * Save Structure settings
 818      */
 819     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 820             Boolean.toString(addTempFactor.isSelected()));
 821     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 822             Boolean.toString(addSecondaryStructure.isSelected()));
 823     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 824             Boolean.toString(useRnaView.isSelected()));
 825     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 826             Boolean.toString(structFromPdb.isSelected()));
 827     String viewer = structViewer.getSelectedItem().toString();
 828     String viewerPath = structureViewerPath.getText();
 829     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 830     if (viewer.equals(ViewerType.CHIMERA.name()))
 831     {
 832       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 833     }
 834     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 835     {
 836       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 837     }
 838     else if (viewer.equals(ViewerType.PYMOL.name()))
 839     {
 840       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 841     }
 842     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 843             Boolean.toString(siftsMapping.isSelected()));
 844     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 845
 846     /*
 847      * Save Output settings
 848      */
 849     Cache.applicationProperties.setProperty("EPS_RENDERING",
 850             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 851     Cache.applicationProperties.setProperty("HTML_RENDERING",
 852             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 853     Cache.applicationProperties.setProperty("SVG_RENDERING",
 854             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 855
 856     /*
 857      * Save Connections settings
 858      */
 859     // Proxy settings set first (to catch web services)
 860
 861     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 862
 863     jalview.util.BrowserLauncher.resetBrowser();
 864
 865     // save user-defined and selected links
 866     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 867     if (menuLinks.isEmpty())
 868     {
 869       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 870     }
 871     else
 872     {
 873       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 874               menuLinks.toString());
 875     }
 876
 877     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 878     if (nonMenuLinks.isEmpty())
 879     {
 880       Cache.applicationProperties.remove("STORED_LINKS");
 881     }
 882     else
 883     {
 884       Cache.applicationProperties.setProperty("STORED_LINKS",
 885               nonMenuLinks.toString());
 886     }
 887
 888     Cache.applicationProperties.setProperty("DEFAULT_URL",
 889             sequenceUrlLinks.getPrimaryUrlId());
 890
 891     Cache.setProperty("VERSION_CHECK",
 892             Boolean.toString(versioncheck.isSelected()));
 893     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 894     {
 895       // default is false - we only set this if the user has actively agreed
 896       Cache.setProperty("USAGESTATS",
 897               Boolean.toString(usagestats.isSelected()));
 898     }
 899     if (!questionnaire.isSelected())
 900     {
 901       Cache.setProperty("NOQUESTIONNAIRES", "true");
 902     }
 903     else
 904     {
 905       // special - made easy to edit a property file to disable questionnaires
 906       // by just adding the given line
 907       Cache.removeProperty("NOQUESTIONNAIRES");
 908     }
 909
 910     /*
 911      * Save Output settings
 912      */
 913     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 914             Boolean.toString(blcjv.isSelected()));
 915     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 916             Boolean.toString(clustaljv.isSelected()));
 917     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 918             Boolean.toString(fastajv.isSelected()));
 919     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 920             Boolean.toString(msfjv.isSelected()));
 921     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 922             Boolean.toString(pfamjv.isSelected()));
 923     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 924             Boolean.toString(pileupjv.isSelected()));
 925     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 926             Boolean.toString(pirjv.isSelected()));
 927     Cache.applicationProperties.setProperty("PIR_MODELLER",
 928             Boolean.toString(modellerOutput.isSelected()));
 929     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 930             Boolean.toString(embbedBioJSON.isSelected()));
 931     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 932
 933     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 934             Boolean.toString(autoIdWidth.isSelected()));
 935     userIdWidth_actionPerformed();
 936     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 937             userIdWidth.getText());
 938
 939     /*
 940      * Save Editing settings
 941      */
 942     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 943             Boolean.toString(autoCalculateConsCheck.isSelected()));
 944     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 945             Boolean.toString(sortByTree.isSelected()));
 946     Cache.applicationProperties.setProperty("PAD_GAPS",
 947             Boolean.toString(padGaps.isSelected()));
 948
 949     if (!Platform.isJS())
 950     {
 951       wsPrefs.updateAndRefreshWsMenuConfig(false);
 952     }
 953
 954     /*
 955      * Save Backups settings
 956      */
 957     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 958             Boolean.toString(enableBackupFiles.isSelected()));
 959     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 960     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 961             Integer.toString(preset));
 962
 963     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 964     {
 965       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 966       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 967               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 968       Cache.applicationProperties.setProperty(
 969               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 970     }
 971
 972     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 973             .get(preset);
 974     Cache.applicationProperties.setProperty(
 975             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 976
 977     Cache.saveProperties();
 978     Desktop.instance.doConfigureStructurePrefs();
 979     try
 980     {
 981       frame.setClosed(true);
 982     } catch (Exception ex)
 983     {
 984     }
 985   }
 986
 987   public void saveProxySettings()
 988   {
 989     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 990             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 991                     : Cache.PROXYTYPE_SYSTEM;
 992     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
 993     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 994     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 995     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 996     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 997     Cache.setOrRemove("PROXY_AUTH",
 998             Boolean.toString(proxyAuth.isSelected()));
 999     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1000     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1001     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1002     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1003             || !newProxyType.equals(previousProxyType))
1004     {
1005       // force a re-lookup of ws if proxytype is custom or has changed
1006       wsPrefs.update++;
1007     }
1008     previousProxyType = newProxyType;
1009   }
1010
1011   /**
1012    * Do any necessary validation before saving settings. Return focus to the
1013    * first tab which fails validation.
1014    *
1015    * @return
1016    */
1017   private boolean validateSettings()
1018   {
1019     if (!validateStructure())
1020     {
1021       structureTab.requestFocusInWindow();
1022       return false;
1023     }
1024     return true;
1025   }
1026
1027   @Override
1028   protected boolean validateStructure()
1029   {
1030     return validateViewerPath();
1031
1032   }
1033
1034   /**
1035    * DOCUMENT ME!
1036    */
1037   @Override
1038   public void startupFileTextfield_mouseClicked()
1039   {
1040     // TODO: JAL-3048 not needed for Jalview-JS
1041     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1042     JalviewFileChooser chooser = JalviewFileChooser
1043             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1044     chooser.setFileView(new JalviewFileView());
1045     chooser.setDialogTitle(
1046             MessageManager.getString("label.select_startup_file"));
1047
1048     int value = chooser.showOpenDialog(this);
1049
1050     if (value == JalviewFileChooser.APPROVE_OPTION)
1051     {
1052       FileFormatI format = chooser.getSelectedFormat();
1053       if (format != null)
1054       {
1055         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1056                 format.getName());
1057       }
1058       startupFileTextfield
1059               .setText(chooser.getSelectedFile().getAbsolutePath());
1060     }
1061   }
1062
1063   /**
1064    * DOCUMENT ME!
1065    *
1066    * @param e
1067    *          DOCUMENT ME!
1068    */
1069   @Override
1070   public void cancel_actionPerformed(ActionEvent e)
1071   {
1072     try
1073     {
1074       if (!Platform.isJS())
1075       {
1076         wsPrefs.updateWsMenuConfig(true);
1077         wsPrefs.refreshWs_actionPerformed(e);
1078       }
1079       frame.setClosed(true);
1080     } catch (Exception ex)
1081     {
1082     }
1083   }
1084
1085   /**
1086    * DOCUMENT ME!
1087    *
1088    * @param e
1089    *          DOCUMENT ME!
1090    */
1091   @Override
1092   public void annotations_actionPerformed(ActionEvent e)
1093   {
1094     conservation.setEnabled(annotations.isSelected());
1095     quality.setEnabled(annotations.isSelected());
1096     identity.setEnabled(annotations.isSelected());
1097     showOccupancy.setEnabled(annotations.isSelected());
1098     showGroupConsensus.setEnabled(annotations.isSelected());
1099     showGroupConservation.setEnabled(annotations.isSelected());
1100     showConsensHistogram.setEnabled(annotations.isSelected()
1101             && (identity.isSelected() || showGroupConsensus.isSelected()));
1102     showConsensLogo.setEnabled(annotations.isSelected()
1103             && (identity.isSelected() || showGroupConsensus.isSelected()));
1104   }
1105
1106   @Override
1107   public void newLink_actionPerformed(ActionEvent e)
1108   {
1109     GSequenceLink link = new GSequenceLink();
1110     boolean valid = false;
1111     while (!valid)
1112     {
1113       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1114               MessageManager.getString("label.new_sequence_url_link"),
1115               JvOptionPane.OK_CANCEL_OPTION, -1,
1116               null) == JvOptionPane.OK_OPTION)
1117       {
1118         if (link.checkValid())
1119         {
1120           if (((UrlLinkTableModel) linkUrlTable.getModel())
1121                   .isUniqueName(link.getName()))
1122           {
1123             ((UrlLinkTableModel) linkUrlTable.getModel())
1124                     .insertRow(link.getName(), link.getURL());
1125             valid = true;
1126           }
1127           else
1128           {
1129             link.notifyDuplicate();
1130             continue;
1131           }
1132         }
1133       }
1134       else
1135       {
1136         break;
1137       }
1138     }
1139   }
1140
1141   @Override
1142   public void editLink_actionPerformed(ActionEvent e)
1143   {
1144     GSequenceLink link = new GSequenceLink();
1145
1146     int index = linkUrlTable.getSelectedRow();
1147     if (index == -1)
1148     {
1149       // button no longer enabled if row is not selected
1150       Cache.log.debug("Edit with no row selected in linkUrlTable");
1151       return;
1152     }
1153
1154     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1155             .getNameColumn();
1156     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1157             .getUrlColumn();
1158     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1159     link.setName(oldName);
1160     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1161
1162     boolean valid = false;
1163     while (!valid)
1164     {
1165       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1166               MessageManager.getString("label.edit_sequence_url_link"),
1167               JvOptionPane.OK_CANCEL_OPTION, -1,
1168               null) == JvOptionPane.OK_OPTION)
1169       {
1170         if (link.checkValid())
1171         {
1172           if ((oldName.equals(link.getName()))
1173                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1174                           .isUniqueName(link.getName())))
1175           {
1176             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1177             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1178             valid = true;
1179           }
1180           else
1181           {
1182             link.notifyDuplicate();
1183             continue;
1184           }
1185         }
1186       }
1187       else
1188       {
1189         break;
1190       }
1191     }
1192   }
1193
1194   @Override
1195   public void deleteLink_actionPerformed(ActionEvent e)
1196   {
1197     int index = linkUrlTable.getSelectedRow();
1198     int modelIndex = -1;
1199     if (index == -1)
1200     {
1201       // button no longer enabled if row is not selected
1202       Cache.log.debug("Delete with no row selected in linkUrlTable");
1203       return;
1204     }
1205     else
1206     {
1207       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1208     }
1209
1210     // make sure we use the model index to delete, and not the table index
1211     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1212   }
1213
1214   @Override
1215   public void defaultBrowser_mouseClicked(MouseEvent e)
1216   {
1217     // TODO: JAL-3048 not needed for j2s
1218     if (!Platform.isJS()) // BH 2019
1219     /**
1220      * Java only
1221      *
1222      * @j2sIgnore
1223      */
1224     {
1225       JFileChooser chooser = new JFileChooser(".");
1226       chooser.setDialogTitle(
1227               MessageManager.getString("label.select_default_browser"));
1228
1229       int value = chooser.showOpenDialog(this);
1230
1231       if (value == JFileChooser.APPROVE_OPTION)
1232       {
1233         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1234       }
1235     }
1236   }
1237
1238   /*
1239    * (non-Javadoc)
1240    *
1241    * @see
1242    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1243    * .ActionEvent)
1244    */
1245   @Override
1246   protected void showunconserved_actionPerformed(ActionEvent e)
1247   {
1248     // TODO Auto-generated method stub
1249     super.showunconserved_actionPerformed(e);
1250   }
1251
1252   public static List<String> getGroupURLLinks()
1253   {
1254     return groupURLLinks;
1255   }
1256
1257   @Override
1258   public void minColour_actionPerformed(JPanel panel)
1259   {
1260     JalviewColourChooser.showColourChooser(this,
1261             MessageManager.getString("label.select_colour_minimum_value"),
1262             panel);
1263   }
1264
1265   @Override
1266   public void maxColour_actionPerformed(JPanel panel)
1267   {
1268     JalviewColourChooser.showColourChooser(this,
1269             MessageManager.getString("label.select_colour_maximum_value"),
1270             panel);
1271   }
1272
1273   @Override
1274   public void gapColour_actionPerformed(JPanel gap)
1275   {
1276     if (!useLegacyGap.isSelected())
1277     {
1278       JalviewColourChooser.showColourChooser(this,
1279               MessageManager.getString("label.select_gap_colour"), gap);
1280     }
1281   }
1282
1283   @Override
1284   public void hiddenColour_actionPerformed(JPanel hidden)
1285   {
1286     JalviewColourChooser.showColourChooser(this,
1287             MessageManager.getString("label.select_hidden_colour"), hidden);
1288   }
1289
1290   @Override
1291   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1292   {
1293     boolean enabled = useLegacyGap.isSelected();
1294     if (enabled)
1295     {
1296       gapColour.setBackground(
1297               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1298     }
1299     else
1300     {
1301       gapColour.setBackground(
1302               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1303     }
1304     gapColour.setEnabled(!enabled);
1305     gapLabel.setEnabled(!enabled);
1306   }
1307
1308   @Override
1309   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1310   {
1311     useLegacyGap.setSelected(false);
1312     useLegacyGaps_actionPerformed(null);
1313     showHiddenAtStart.setSelected(false);
1314     hiddenColour.setBackground(
1315             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1316   }
1317
1318   @Override
1319   protected void userIdWidth_actionPerformed()
1320   {
1321     try
1322     {
1323       String val = userIdWidth.getText().trim();
1324       if (val.length() > 0)
1325       {
1326         Integer iw = Integer.parseInt(val);
1327         if (iw.intValue() < 12)
1328         {
1329           throw new NumberFormatException();
1330         }
1331         userIdWidth.setText(iw.toString());
1332       }
1333     } catch (NumberFormatException x)
1334     {
1335       userIdWidth.setText("");
1336       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1337               MessageManager
1338                       .getString("warn.user_defined_width_requirements"),
1339               MessageManager.getString("label.invalid_id_column_width"),
1340               JvOptionPane.WARNING_MESSAGE);
1341     }
1342   }
1343
1344   @Override
1345   protected void autoIdWidth_actionPerformed()
1346   {
1347     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1348     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1349   }
1350
1351   /**
1352    * Returns true if structure viewer path is to a valid executable, else shows
1353    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1354    * (built in to Jalview) or when Jalview is left to try default paths.
1355    */
1356   private boolean validateViewerPath()
1357   {
1358     if (structureViewerPath.getText().trim().length() > 0)
1359     {
1360       File f = new File(structureViewerPath.getText());
1361       if (!f.canExecute())
1362       {
1363         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1364                 MessageManager.getString("label.invalid_viewer_path"),
1365                 MessageManager.getString("label.invalid_viewer_path"),
1366                 JvOptionPane.ERROR_MESSAGE);
1367         return false;
1368       }
1369     }
1370     return true;
1371   }
1372
1373   /**
1374    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1375    * default or user-specified path, if not show a warning/help dialog
1376    */
1377   @Override
1378   protected void structureViewer_actionPerformed(String selectedItem)
1379   {
1380     if (selectedItem.equals(ViewerType.JMOL.name()))
1381     {
1382       structureViewerPath.setEnabled(false);
1383       structureViewerPathLabel.setEnabled(false);
1384       return;
1385     }
1386     boolean found = false;
1387     structureViewerPath.setEnabled(true);
1388     structureViewerPathLabel.setEnabled(true);
1389     structureViewerPathLabel.setText(MessageManager
1390             .formatMessage("label.viewer_path", selectedItem));
1391
1392     /*
1393      * Try user-specified and standard paths for structure viewer executable
1394      */
1395     String viewerPath = "";
1396     List<String> paths = null;
1397     try
1398     {
1399       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1400       switch (viewerType)
1401       {
1402       case JMOL:
1403         // dealt with above
1404         break;
1405       case CHIMERA:
1406         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1407         paths = StructureManager.getChimeraPaths(false);
1408         break;
1409       case CHIMERAX:
1410         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1411         paths = StructureManager.getChimeraPaths(true);
1412         break;
1413       case PYMOL:
1414         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1415         paths = PymolManager.getPymolPaths();
1416         break;
1417       }
1418     } catch (IllegalArgumentException e)
1419     {
1420       // only valid entries should be in the drop-down
1421     }
1422     structureViewerPath.setText(viewerPath);
1423
1424     paths.add(0, structureViewerPath.getText());
1425     for (String path : paths)
1426     {
1427       if (new File(path.trim()).canExecute())
1428       {
1429         found = true;
1430         break;
1431       }
1432     }
1433
1434     if (!found)
1435     {
1436       String[] options = { "OK", "Help" };
1437       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1438               JvSwingUtils.wrapTooltip(true,
1439                       MessageManager.getString("label.viewer_missing")),
1440               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1441               null, options, options[0]);
1442       if (showHelp == JvOptionPane.NO_OPTION)
1443       {
1444         try
1445         {
1446           Help.showHelpWindow(HelpId.StructureViewer);
1447         } catch (HelpSetException e)
1448         {
1449           e.printStackTrace();
1450         }
1451       }
1452     }
1453   }
1454
1455   public class OptionsParam
1456   {
1457     private String name;
1458
1459     private String code;
1460
1461     public OptionsParam(String name, String code)
1462     {
1463       this.name = name;
1464       this.code = code;
1465     }
1466
1467     public String getName()
1468     {
1469       return name;
1470     }
1471
1472     public void setName(String name)
1473     {
1474       this.name = name;
1475     }
1476
1477     public String getCode()
1478     {
1479       return code;
1480     }
1481
1482     public void setCode(String code)
1483     {
1484       this.code = code;
1485     }
1486
1487     @Override
1488     public String toString()
1489     {
1490       return name;
1491     }
1492
1493     @Override
1494     public boolean equals(Object that)
1495     {
1496       if (!(that instanceof OptionsParam))
1497       {
1498         return false;
1499       }
1500       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1501     }
1502
1503     @Override
1504     public int hashCode()
1505     {
1506       return name.hashCode() + code.hashCode();
1507     }
1508   }
1509
1510   private class UrlListSelectionHandler implements ListSelectionListener
1511   {
1512
1513     @Override
1514     public void valueChanged(ListSelectionEvent e)
1515     {
1516       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1517
1518       int index = lsm.getMinSelectionIndex();
1519       if (index == -1)
1520       {
1521         // no selection, so disable delete/edit buttons
1522         editLink.setEnabled(false);
1523         deleteLink.setEnabled(false);
1524         return;
1525       }
1526       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1527
1528       // enable/disable edit and delete link buttons
1529       if (((UrlLinkTableModel) linkUrlTable.getModel())
1530               .isRowDeletable(modelIndex))
1531       {
1532         deleteLink.setEnabled(true);
1533       }
1534       else
1535       {
1536         deleteLink.setEnabled(false);
1537       }
1538
1539       if (((UrlLinkTableModel) linkUrlTable.getModel())
1540               .isRowEditable(modelIndex))
1541       {
1542         editLink.setEnabled(true);
1543       }
1544       else
1545       {
1546         editLink.setEnabled(false);
1547       }
1548     }
1549   }
1550 }