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.io.File;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33 import java.util.concurrent.CompletableFuture;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JInternalFrame;
  38 import javax.swing.JPanel;
  39 import javax.swing.ListSelectionModel;
  40 import javax.swing.RowFilter;
  41 import javax.swing.RowSorter;
  42 import javax.swing.SortOrder;
  43 import javax.swing.event.DocumentEvent;
  44 import javax.swing.event.DocumentListener;
  45 import javax.swing.event.ListSelectionEvent;
  46 import javax.swing.event.ListSelectionListener;
  47 import javax.swing.table.TableCellRenderer;
  48 import javax.swing.table.TableColumn;
  49 import javax.swing.table.TableModel;
  50 import javax.swing.table.TableRowSorter;
  51
  52 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.bin.Console;
  57 import jalview.bin.MemorySetting;
  58 import jalview.ext.pymol.PymolManager;
  59 import jalview.gui.Help.HelpId;
  60 import jalview.gui.StructureViewer.ViewerType;
  61 import jalview.io.BackupFiles;
  62 import jalview.io.BackupFilesPresetEntry;
  63 import jalview.io.FileFormatI;
  64 import jalview.io.JalviewFileChooser;
  65 import jalview.io.JalviewFileView;
  66 import jalview.jbgui.GPreferences;
  67 import jalview.jbgui.GSequenceLink;
  68 import jalview.schemes.ColourSchemeI;
  69 import jalview.schemes.ColourSchemes;
  70 import jalview.schemes.ResidueColourScheme;
  71 import jalview.urls.UrlLinkTableModel;
  72 import jalview.urls.api.UrlProviderFactoryI;
  73 import jalview.urls.api.UrlProviderI;
  74 import jalview.urls.desktop.DesktopUrlProviderFactory;
  75 import jalview.util.MessageManager;
  76 import jalview.util.Platform;
  77 import jalview.util.UrlConstants;
  78 import jalview.ws.sifts.SiftsSettings;
  79
  80 /**
  81  * DOCUMENT ME!
  82  *
  83  * @author $author$
  84  * @version $Revision$
  85  */
  86 /*
  87  * for merge with Jalview-JS
  88  public class Preferences extends GPreferences implements ApplicationSingletonI
  89  */
  90 public class Preferences extends GPreferences
  91 {
  92   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  93
  94   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  95
  96   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  97
  98   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  99
 100   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 101
 102   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 103
 104   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 105
 106   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 107
 108   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 109
 110   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 111
 112   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 113
 114   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 115
 116   public static final String PYMOL_PATH = "PYMOL_PATH";
 117
 118   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 119
 120   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 121
 122   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 123
 124   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 125
 126   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 127
 128   public static final String GAP_COLOUR = "GAP_COLOUR";
 129
 130   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 131
 132   private static final int MIN_FONT_SIZE = 1;
 133
 134   private static final int MAX_FONT_SIZE = 30;
 135
 136   private String previousProxyType;
 137
 138   private static Preferences INSTANCE = null; // add "final"
 139
 140   /**
 141    * Holds name and link separated with | character. Sequence ID must be
 142    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 143    */
 144   public static UrlProviderI sequenceUrlLinks;
 145
 146   public static UrlLinkTableModel dataModel;
 147
 148   /**
 149    * Holds name and link separated with | character. Sequence IDS and Sequences
 150    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 151    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 152    * for first and second token specified after a pipe character at end |,|.
 153    * (TODO: proper escape for using | to separate ids or sequences
 154    */
 155
 156   public static List<String> groupURLLinks;
 157   static
 158   {
 159     // don't populate with session properties
 160     Cache.disableSessionProperties();
 161
 162     // get links selected to be in the menu (SEQUENCE_LINKS)
 163     // and links entered by the user but not selected (STORED_LINKS)
 164     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 165     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 166     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 167             UrlConstants.DEFAULT_LABEL);
 168
 169     // if both links lists are empty, add the DEFAULT_URL link
 170     // otherwise we assume the default link is in one of the lists
 171     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 172     {
 173       inMenuString = UrlConstants.DEFAULT_STRING;
 174     }
 175     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 176             inMenuString, notInMenuString);
 177     sequenceUrlLinks = factory.createUrlProvider();
 178     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 179
 180     /**
 181      * TODO: reformulate groupURL encoding so two or more can be stored in the
 182      * .properties file as '|' separated strings
 183      */
 184
 185     groupURLLinks = new ArrayList<>();
 186
 187     // reenable
 188     Cache.enableSessionProperties();
 189   }
 190
 191   JInternalFrame frame;
 192
 193   private WsPreferences wsPrefs;
 194
 195   private OptionsParam promptEachTimeOpt = new OptionsParam(
 196           MessageManager.getString("label.prompt_each_time"),
 197           LineartOptions.PROMPT_EACH_TIME);
 198
 199   private OptionsParam lineArtOpt = new OptionsParam(
 200           MessageManager.getString("label.lineart"), "Lineart");
 201
 202   private OptionsParam textOpt = new OptionsParam(
 203           MessageManager.getString("action.text"), "Text");
 204
 205   // get singleton Preferences instance
 206   public static Preferences getInstance()
 207   {
 208     if (INSTANCE == null || INSTANCE.frame == null
 209             || INSTANCE.frame.isClosed())
 210     {
 211       INSTANCE = new Preferences();
 212     }
 213     return INSTANCE;
 214
 215     /*
 216      * Replace code with the following for Jalvew-JS
 217     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 218     if (INSTANCE == null || INSTANCE.frame == null
 219             || INSTANCE.frame.isClosed())
 220     {
 221       ApplicationSingletonProvider.remove(Preferences.class);
 222       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 223     }
 224     return INSTANCE;
 225     */
 226   }
 227
 228   public static void openPreferences()
 229   {
 230     openPreferences(null, null);
 231   }
 232
 233   public static void openPreferences(TabRef selectTab, String message)
 234   {
 235     Preferences p = getInstance();
 236     if (selectTab != null)
 237       p.selectTab(selectTab, message);
 238     p.frame.show();
 239     p.frame.moveToFront();
 240     p.frame.grabFocus();
 241   }
 242
 243   public void selectTab(TabRef selectTab, String message)
 244   {
 245     this.selectTab(selectTab);
 246     if (message != null)
 247       this.setMessage(message);
 248     this.frame.show();
 249   }
 250
 251   /**
 252    * Creates a new Preferences object.
 253    */
 254   private Preferences()
 255   {
 256     super();
 257     // don't populate with session properties
 258     Cache.disableSessionProperties();
 259
 260     frame = new JInternalFrame();
 261     frame.setFrameIcon(null);
 262     frame.setContentPane(this);
 263     if (!Platform.isJS())
 264     /**
 265      * Java only
 266      *
 267      * @j2sIgnore
 268      */
 269     {
 270       wsPrefs = new WsPreferences();
 271       wsTab.add(wsPrefs, BorderLayout.CENTER);
 272     }
 273     int width = 500, height = 450;
 274     if (Platform.isAMacAndNotJS())
 275     {
 276       width = 570;
 277       height = 480;
 278     }
 279
 280     Desktop.addInternalFrame(frame,
 281             MessageManager.getString("label.preferences"), width, height);
 282     frame.setMinimumSize(new Dimension(width, height));
 283
 284     /*
 285      * Set Visual tab defaults
 286      */
 287     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 288     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 289     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 290     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 291
 292     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 293     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 294     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 295     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 296     showUnconserved
 297             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 298     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 299     showGroupConsensus
 300             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 301     showGroupConservation.setSelected(
 302             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 303     showConsensHistogram.setSelected(
 304             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 305     showConsensLogo
 306             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 307     showNpTooltip
 308             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 309     showDbRefTooltip
 310             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 311
 312     String[] fonts = java.awt.GraphicsEnvironment
 313             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 314     for (int i = 0; i < fonts.length; i++)
 315     {
 316       fontNameCB.addItem(fonts[i]);
 317     }
 318
 319     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 320     {
 321       fontSizeCB.addItem(i + "");
 322     }
 323
 324     fontStyleCB.addItem("plain");
 325     fontStyleCB.addItem("bold");
 326     fontStyleCB.addItem("italic");
 327
 328     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 329     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 330     fontStyleCB.setSelectedItem(
 331             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 332
 333     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 334     scaleProteinToCdna
 335             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 336
 337     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 338
 339     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 340
 341     gapSymbolCB.addItem("-");
 342     gapSymbolCB.addItem(".");
 343
 344     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 345
 346     sortby.addItem("No sort");
 347     sortby.addItem("Id");
 348     sortby.addItem("Pairwise Identity");
 349     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 350
 351     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 352     sortAnnBy
 353             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 354     sortAnnBy
 355             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 356     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 357             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 358                     SequenceAnnotationOrder.NONE.name()));
 359     sortAnnBy.setSelectedItem(savedSort.toString());
 360
 361     sortAutocalc.addItem("Autocalculated first");
 362     sortAutocalc.addItem("Autocalculated last");
 363     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 364     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 365             : sortAutocalc.getItemAt(1));
 366     startupCheckbox
 367             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 368     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 369             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 370                     + "/examples/exampleFile_2_7.jvp"));
 371
 372     /*
 373      * Set Colours tab defaults
 374      */
 375     protColour.addItem(ResidueColourScheme.NONE);
 376     nucColour.addItem(ResidueColourScheme.NONE);
 377     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 378     {
 379       String name = cs.getSchemeName();
 380       protColour.addItem(name);
 381       nucColour.addItem(name);
 382     }
 383     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 384             ResidueColourScheme.NONE);
 385     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 386     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 387     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 388     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 389     minColour.setBackground(
 390             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 391     maxColour.setBackground(
 392             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 393
 394     /*
 395      * Set overview panel defaults
 396      */
 397     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 398             OverviewCanvas.OVERVIEW_DEFAULT_GAP));
 399     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 400             OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
 401     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 402     gapLabel.setEnabled(!useLegacyGap.isSelected());
 403     gapColour.setEnabled(!useLegacyGap.isSelected());
 404     showHiddenAtStart
 405             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 406
 407     /*
 408      * Set Structure tab defaults
 409      */
 410     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
 411     structFromPdb.setSelected(structSelected);
 412     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
 413     addSecondaryStructure.setEnabled(structSelected);
 414     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
 415     addTempFactor.setEnabled(structSelected);
 416
 417     /*
 418      * set choice of structure viewer, and path if saved as a preference;
 419      * default to Jmol (first choice) if an unexpected value is found
 420      */
 421     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 422             ViewerType.JMOL.name());
 423     structViewer.setSelectedItem(viewerType);
 424     String viewerPath = "";
 425     ViewerType type = null;
 426     try
 427     {
 428       type = ViewerType.valueOf(viewerType);
 429       switch (type)
 430       {
 431       case JMOL:
 432         break;
 433       case CHIMERA:
 434         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 435         break;
 436       case CHIMERAX:
 437         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 438         break;
 439       case PYMOL:
 440         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 441         break;
 442       }
 443     } catch (IllegalArgumentException e)
 444     {
 445       Console.error("Unknown structure viewer type: " + viewerType
 446               + ", defaulting to Jmol");
 447       type = ViewerType.JMOL;
 448     }
 449     structureViewerPath.setText(viewerPath);
 450
 451     structureViewerPath.addActionListener(new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         if (validateViewerPath())
 457         {
 458           String path = structureViewerPath.getText();
 459           try
 460           {
 461             ViewerType type = ViewerType.valueOf(viewerType);
 462             switch (type)
 463             {
 464             case JMOL:
 465               break;
 466             case CHIMERA:
 467               Cache.setProperty(CHIMERA_PATH, path);
 468               break;
 469             case CHIMERAX:
 470               Cache.setProperty(CHIMERAX_PATH, path);
 471               break;
 472             case PYMOL:
 473               Cache.setProperty(PYMOL_PATH, path);
 474               break;
 475             }
 476           } catch (IllegalArgumentException x)
 477           {
 478             Console.error("Failed to set path - unknown viewer type", x);
 479           }
 480         }
 481       }
 482     });
 483
 484     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 485     {
 486       siftsMapping.setSelected(true);
 487     }
 488     else
 489     {
 490       nwMapping.setSelected(true);
 491     }
 492
 493     SiftsSettings
 494             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 495
 496     /*
 497      * Set Connections tab defaults
 498      */
 499
 500     // set up sorting
 501     linkUrlTable.setModel(dataModel);
 502     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 503             linkUrlTable.getModel());
 504     linkUrlTable.setRowSorter(sorter);
 505     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 506
 507     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 508     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 509             SortOrder.DESCENDING));
 510     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 511             SortOrder.DESCENDING));
 512     sortKeys.add(
 513             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 514
 515     sorter.setSortKeys(sortKeys);
 516     // BH 2018 setSortKeys will do the sort
 517     // sorter.sort();
 518
 519     // set up filtering
 520     ActionListener onReset;
 521     onReset = new ActionListener()
 522     {
 523       @Override
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         filterTB.setText("");
 527         sorter.setRowFilter(RowFilter.regexFilter(""));
 528       }
 529
 530     };
 531     doReset.addActionListener(onReset);
 532
 533     // filter to display only custom urls
 534     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 535     {
 536       @Override
 537       public boolean include(
 538               Entry<? extends TableModel, ? extends Object> entry)
 539       {
 540         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 541       }
 542     };
 543
 544     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 545             linkUrlTable.getModel());
 546     customSorter.setRowFilter(customUrlFilter);
 547
 548     ActionListener onCustomOnly;
 549     onCustomOnly = new ActionListener()
 550     {
 551       @Override
 552       public void actionPerformed(ActionEvent e)
 553       {
 554         filterTB.setText("");
 555         sorter.setRowFilter(customUrlFilter);
 556       }
 557     };
 558     userOnly.addActionListener(onCustomOnly);
 559
 560     filterTB.getDocument().addDocumentListener(new DocumentListener()
 561     {
 562       String caseInsensitiveFlag = "(?i)";
 563
 564       @Override
 565       public void changedUpdate(DocumentEvent e)
 566       {
 567         sorter.setRowFilter(RowFilter
 568                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 569       }
 570
 571       @Override
 572       public void removeUpdate(DocumentEvent e)
 573       {
 574         sorter.setRowFilter(RowFilter
 575                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 576       }
 577
 578       @Override
 579       public void insertUpdate(DocumentEvent e)
 580       {
 581         sorter.setRowFilter(RowFilter
 582                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 583       }
 584     });
 585
 586     // set up list selection functionality
 587     linkUrlTable.getSelectionModel()
 588             .addListSelectionListener(new UrlListSelectionHandler());
 589
 590     // set up radio buttons
 591     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 592             .getPrimaryColumn();
 593     String onClickName = linkUrlTable.getColumnName(onClickCol);
 594     linkUrlTable.getColumn(onClickName)
 595             .setCellRenderer(new RadioButtonRenderer());
 596     linkUrlTable.getColumn(onClickName)
 597             .setCellEditor(new RadioButtonEditor());
 598
 599     // get boolean columns and resize those to min possible
 600     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 601     {
 602       if (linkUrlTable.getModel().getColumnClass(column)
 603               .equals(Boolean.class))
 604       {
 605         TableColumn tableColumn = linkUrlTable.getColumnModel()
 606                 .getColumn(column);
 607         int preferredWidth = tableColumn.getMinWidth();
 608
 609         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 610                 column);
 611         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 612         int cwidth = c.getPreferredSize().width
 613                 + linkUrlTable.getIntercellSpacing().width;
 614         preferredWidth = Math.max(preferredWidth, cwidth);
 615
 616         tableColumn.setPreferredWidth(preferredWidth);
 617       }
 618     }
 619
 620     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 621     previousProxyType = proxyTypeString;
 622     switch (proxyTypeString)
 623     {
 624     case Cache.PROXYTYPE_NONE:
 625       proxyType.setSelected(noProxy.getModel(), true);
 626       break;
 627     case Cache.PROXYTYPE_SYSTEM:
 628       proxyType.setSelected(systemProxy.getModel(), true);
 629       break;
 630     case Cache.PROXYTYPE_CUSTOM:
 631       proxyType.setSelected(customProxy.getModel(), true);
 632       break;
 633     default:
 634       Console.warn(
 635               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 636                       + proxyTypeString);
 637     }
 638     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 639     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 640     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 641     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 642     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 643     proxyAuthUsernameTB
 644             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 645     // we are not storing or retrieving proxy password from .jalview_properties
 646     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 647             : new String(Cache.proxyAuthPassword));
 648     setCustomProxyEnabled();
 649     applyProxyButtonEnabled(false);
 650
 651     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 652     // note antisense here: default is true
 653     questionnaire
 654             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 655     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 656
 657     /*
 658      * Set Output tab defaults
 659      */
 660     setupOutputCombo(epsRendering, "EPS_RENDERING");
 661     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 662     setupOutputCombo(svgRendering, "SVG_RENDERING");
 663     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 664     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 665     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 666     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 667     userIdWidth.setText(wi == null ? "" : wi.toString());
 668     // TODO: refactor to use common enum via FormatAdapter and allow extension
 669     // for new flat file formats
 670     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 671     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 672     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 673     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 674     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 675     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 676     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 677     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 678     embbedBioJSON
 679             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 680
 681     /*
 682      * Set Editing tab defaults
 683      */
 684     autoCalculateConsCheck
 685             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 686     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 687     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 688
 689     annotations_actionPerformed(null); // update the display of the annotation
 690                                        // settings
 691
 692     /*
 693      * Set Backups tab defaults
 694      */
 695     loadLastSavedBackupsOptions();
 696
 697     /*
 698      * Set Startup tab defaults
 699      */
 700
 701     // re-enable
 702     Cache.enableSessionProperties();
 703   }
 704
 705   /**
 706    * A helper method that sets the items and initial selection in a character
 707    * rendering option list (Prompt each time/Lineart/Text)
 708    *
 709    * @param comboBox
 710    * @param propertyKey
 711    */
 712   protected void setupOutputCombo(JComboBox<Object> comboBox,
 713           String propertyKey)
 714   {
 715     Cache.disableSessionProperties();
 716
 717     comboBox.addItem(promptEachTimeOpt);
 718     comboBox.addItem(lineArtOpt);
 719     comboBox.addItem(textOpt);
 720
 721     /*
 722      * JalviewJS doesn't support Lineart so force it to Text
 723      */
 724     String defaultOption = Platform.isJS() ? "Text"
 725             : Cache.getDefault(propertyKey, "Prompt each time");
 726     if (defaultOption.equalsIgnoreCase("Text"))
 727     {
 728       comboBox.setSelectedItem(textOpt);
 729     }
 730     else if (defaultOption.equalsIgnoreCase("Lineart"))
 731     {
 732       comboBox.setSelectedItem(lineArtOpt);
 733     }
 734     else
 735     {
 736       comboBox.setSelectedItem(promptEachTimeOpt);
 737     }
 738
 739     Cache.enableSessionProperties();
 740   }
 741
 742   /**
 743    * Save user selections on the Preferences tabs to the Cache and write out to
 744    * file.
 745    *
 746    * @param e
 747    */
 748   @Override
 749   public void ok_actionPerformed(ActionEvent e)
 750   {
 751     Cache.disableSessionProperties();
 752
 753     if (!validateSettings())
 754     {
 755       return;
 756     }
 757
 758     /*
 759      * Set proxy settings first (to be before web services refresh)
 760      */
 761     saveProxySettings();
 762
 763     /*
 764      * Save Visual settings
 765      */
 766
 767     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 768             Boolean.toString(seqLimit.isSelected()));
 769     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 770             Boolean.toString(rightAlign.isSelected()));
 771     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 772             Boolean.toString(fullScreen.isSelected()));
 773     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 774             Boolean.toString(openoverv.isSelected()));
 775     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 776             Boolean.toString(annotations.isSelected()));
 777     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 778             Boolean.toString(conservation.isSelected()));
 779     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 780             Boolean.toString(quality.isSelected()));
 781     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 782             Boolean.toString(identity.isSelected()));
 783
 784     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 785             gapSymbolCB.getSelectedItem().toString());
 786
 787     Cache.applicationProperties.setProperty("FONT_NAME",
 788             fontNameCB.getSelectedItem().toString());
 789     Cache.applicationProperties.setProperty("FONT_STYLE",
 790             fontStyleCB.getSelectedItem().toString());
 791     Cache.applicationProperties.setProperty("FONT_SIZE",
 792             fontSizeCB.getSelectedItem().toString());
 793
 794     Cache.applicationProperties.setProperty("ID_ITALICS",
 795             Boolean.toString(idItalics.isSelected()));
 796     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 797             Boolean.toString(showUnconserved.isSelected()));
 798     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 799             Boolean.toString(showOccupancy.isSelected()));
 800     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 801             Boolean.toString(showGroupConsensus.isSelected()));
 802     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 803             Boolean.toString(showGroupConservation.isSelected()));
 804     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 805             Boolean.toString(showConsensHistogram.isSelected()));
 806     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 807             Boolean.toString(showConsensLogo.isSelected()));
 808     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 809             Boolean.toString(smoothFont.isSelected()));
 810     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 811             Boolean.toString(scaleProteinToCdna.isSelected()));
 812     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 813             Boolean.toString(showNpTooltip.isSelected()));
 814     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 815             Boolean.toString(showDbRefTooltip.isSelected()));
 816
 817     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 818             Boolean.toString(wrap.isSelected()));
 819
 820     Cache.applicationProperties.setProperty("STARTUP_FILE",
 821             startupFileTextfield.getText());
 822     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 823             Boolean.toString(startupCheckbox.isSelected()));
 824
 825     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 826             sortby.getSelectedItem().toString());
 827
 828     // convert description of sort order to enum name for save
 829     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 830             .forDescription(sortAnnBy.getSelectedItem().toString());
 831     if (annSortOrder != null)
 832     {
 833       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 834               annSortOrder.name());
 835     }
 836
 837     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 838     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 839             Boolean.valueOf(showAutocalcFirst).toString());
 840
 841     /*
 842      * Save Colours settings
 843      */
 844     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 845             protColour.getSelectedItem().toString());
 846     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 847             nucColour.getSelectedItem().toString());
 848     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 849             minColour.getBackground());
 850     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 851             maxColour.getBackground());
 852
 853     /*
 854      * Save Overview settings
 855      */
 856     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 857     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 858     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 859             Boolean.toString(useLegacyGap.isSelected()));
 860     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 861             Boolean.toString(showHiddenAtStart.isSelected()));
 862
 863     /*
 864      * Save Structure settings
 865      */
 866     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 867             Boolean.toString(addTempFactor.isSelected()));
 868     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 869             Boolean.toString(addSecondaryStructure.isSelected()));
 870     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 871             Boolean.toString(structFromPdb.isSelected()));
 872     String viewer = structViewer.getSelectedItem().toString();
 873     String viewerPath = structureViewerPath.getText();
 874     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 875     if (viewer.equals(ViewerType.CHIMERA.name()))
 876     {
 877       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 878     }
 879     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 880     {
 881       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 882     }
 883     else if (viewer.equals(ViewerType.PYMOL.name()))
 884     {
 885       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 886     }
 887     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 888             Boolean.toString(siftsMapping.isSelected()));
 889     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 890
 891     /*
 892      * Save Output settings
 893      */
 894     Cache.applicationProperties.setProperty("EPS_RENDERING",
 895             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 896     Cache.applicationProperties.setProperty("HTML_RENDERING",
 897             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 898     Cache.applicationProperties.setProperty("SVG_RENDERING",
 899             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 900
 901     /*
 902      * Save Connections settings
 903      */
 904     // Proxy settings set first (to catch web services)
 905
 906     // save user-defined and selected links
 907     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 908     if (menuLinks.isEmpty())
 909     {
 910       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 911     }
 912     else
 913     {
 914       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 915               menuLinks.toString());
 916     }
 917
 918     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 919     if (nonMenuLinks.isEmpty())
 920     {
 921       Cache.applicationProperties.remove("STORED_LINKS");
 922     }
 923     else
 924     {
 925       Cache.applicationProperties.setProperty("STORED_LINKS",
 926               nonMenuLinks.toString());
 927     }
 928
 929     Cache.applicationProperties.setProperty("DEFAULT_URL",
 930             sequenceUrlLinks.getPrimaryUrlId());
 931
 932     Cache.setProperty("VERSION_CHECK",
 933             Boolean.toString(versioncheck.isSelected()));
 934     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 935     {
 936       // default is false - we only set this if the user has actively agreed
 937       Cache.setProperty("USAGESTATS",
 938               Boolean.toString(usagestats.isSelected()));
 939     }
 940     if (!questionnaire.isSelected())
 941     {
 942       Cache.setProperty("NOQUESTIONNAIRES", "true");
 943     }
 944     else
 945     {
 946       // special - made easy to edit a property file to disable questionnaires
 947       // by just adding the given line
 948       Cache.removeProperty("NOQUESTIONNAIRES");
 949     }
 950
 951     /*
 952      * Save Output settings
 953      */
 954     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 955             Boolean.toString(blcjv.isSelected()));
 956     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 957             Boolean.toString(clustaljv.isSelected()));
 958     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 959             Boolean.toString(fastajv.isSelected()));
 960     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 961             Boolean.toString(msfjv.isSelected()));
 962     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 963             Boolean.toString(pfamjv.isSelected()));
 964     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 965             Boolean.toString(pileupjv.isSelected()));
 966     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 967             Boolean.toString(pirjv.isSelected()));
 968     Cache.applicationProperties.setProperty("PIR_MODELLER",
 969             Boolean.toString(modellerOutput.isSelected()));
 970     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 971             Boolean.toString(embbedBioJSON.isSelected()));
 972     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 973
 974     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 975             Boolean.toString(autoIdWidth.isSelected()));
 976     userIdWidth_actionPerformed();
 977     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 978             userIdWidth.getText());
 979
 980     /*
 981      * Save Editing settings
 982      */
 983     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 984             Boolean.toString(autoCalculateConsCheck.isSelected()));
 985     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 986             Boolean.toString(sortByTree.isSelected()));
 987     Cache.applicationProperties.setProperty("PAD_GAPS",
 988             Boolean.toString(padGaps.isSelected()));
 989
 990     if (!Platform.isJS())
 991     {
 992       wsPrefs.updateAndRefreshWsMenuConfig(false);
 993     }
 994
 995     /*
 996      * Save Backups settings
 997      */
 998     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 999             Boolean.toString(enableBackupFiles.isSelected()));
1000     int preset = getComboIntStringKey(backupfilesPresetsCombo);
1001     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
1002             Integer.toString(preset));
1003
1004     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1005     {
1006       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1007       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1008               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1009       Cache.applicationProperties.setProperty(
1010               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
1011     }
1012
1013     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1014             .get(preset);
1015     Cache.applicationProperties.setProperty(
1016             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1017
1018     /*
1019      * Save Memory Settings
1020      */
1021     Cache.applicationProperties.setProperty(
1022             MemorySetting.CUSTOMISED_SETTINGS,
1023             Boolean.toString(customiseMemorySetting.isSelected()));
1024     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
1025             Integer.toString(jvmMemoryPercentSlider.getValue()));
1026     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
1027             jvmMemoryMaxTextField.getText());
1028
1029     /*
1030      * save and close Preferences
1031      */
1032
1033     Cache.saveProperties();
1034     Desktop.instance.doConfigureStructurePrefs();
1035     try
1036     {
1037       frame.setClosed(true);
1038     } catch (Exception ex)
1039     {
1040     }
1041
1042     Cache.enableSessionProperties();
1043   }
1044
1045   public void saveProxySettings()
1046   {
1047     Cache.disableSessionProperties();
1048
1049     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1050             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1051                     : Cache.PROXYTYPE_SYSTEM;
1052     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1053     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1054     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1055     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1056     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1057     Cache.setOrRemove("PROXY_AUTH",
1058             Boolean.toString(proxyAuth.isSelected()));
1059     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1060     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1061     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1062     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1063             || !newProxyType.equals(previousProxyType))
1064     {
1065       // force a re-lookup of ws if proxytype is custom or has changed
1066       wsPrefs.update++;
1067     }
1068     previousProxyType = newProxyType;
1069
1070     Cache.enableSessionProperties();
1071   }
1072
1073   /**
1074    * Do any necessary validation before saving settings. Return focus to the
1075    * first tab which fails validation.
1076    *
1077    * @return
1078    */
1079   private boolean validateSettings()
1080   {
1081     if (!validateStructure())
1082     {
1083       structureTab.requestFocusInWindow();
1084       return false;
1085     }
1086     return true;
1087   }
1088
1089   @Override
1090   protected boolean validateStructure()
1091   {
1092     return validateViewerPath();
1093
1094   }
1095
1096   /**
1097    * DOCUMENT ME!
1098    */
1099   @Override
1100   public void startupFileTextfield_mouseClicked()
1101   {
1102     Cache.disableSessionProperties();
1103
1104     // TODO: JAL-3048 not needed for Jalview-JS
1105     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1106     JalviewFileChooser chooser = JalviewFileChooser
1107             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1108     chooser.setFileView(new JalviewFileView());
1109     chooser.setDialogTitle(
1110             MessageManager.getString("label.select_startup_file"));
1111
1112     int value = chooser.showOpenDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       FileFormatI format = chooser.getSelectedFormat();
1117       if (format != null)
1118       {
1119         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1120                 format.getName());
1121       }
1122       startupFileTextfield
1123               .setText(chooser.getSelectedFile().getAbsolutePath());
1124     }
1125
1126     Cache.enableSessionProperties();
1127   }
1128
1129   /**
1130    * DOCUMENT ME!
1131    *
1132    * @param e
1133    *          DOCUMENT ME!
1134    */
1135   @Override
1136   public void cancel_actionPerformed(ActionEvent e)
1137   {
1138     try
1139     {
1140       if (!Platform.isJS())
1141       {
1142         wsPrefs.updateWsMenuConfig(true);
1143         wsPrefs.refreshWs_actionPerformed(e);
1144       }
1145       frame.setClosed(true);
1146     } catch (Exception ex)
1147     {
1148     }
1149   }
1150
1151   /**
1152    * DOCUMENT ME!
1153    *
1154    * @param e
1155    *          DOCUMENT ME!
1156    */
1157   @Override
1158   public void annotations_actionPerformed(ActionEvent e)
1159   {
1160     conservation.setEnabled(annotations.isSelected());
1161     quality.setEnabled(annotations.isSelected());
1162     identity.setEnabled(annotations.isSelected());
1163     showOccupancy.setEnabled(annotations.isSelected());
1164     showGroupConsensus.setEnabled(annotations.isSelected());
1165     showGroupConservation.setEnabled(annotations.isSelected());
1166     showConsensHistogram.setEnabled(annotations.isSelected()
1167             && (identity.isSelected() || showGroupConsensus.isSelected()));
1168     showConsensLogo.setEnabled(annotations.isSelected()
1169             && (identity.isSelected() || showGroupConsensus.isSelected()));
1170   }
1171
1172   @Override
1173   public void newLink_actionPerformed(ActionEvent e)
1174   {
1175     GSequenceLink link = new GSequenceLink();
1176     boolean valid = false;
1177     while (!valid)
1178     {
1179       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1180               MessageManager.getString("label.new_sequence_url_link"),
1181               JvOptionPane.OK_CANCEL_OPTION, -1,
1182               null) == JvOptionPane.OK_OPTION)
1183       {
1184         if (link.checkValid())
1185         {
1186           if (((UrlLinkTableModel) linkUrlTable.getModel())
1187                   .isUniqueName(link.getName()))
1188           {
1189             ((UrlLinkTableModel) linkUrlTable.getModel())
1190                     .insertRow(link.getName(), link.getURL());
1191             valid = true;
1192           }
1193           else
1194           {
1195             link.notifyDuplicate();
1196             continue;
1197           }
1198         }
1199       }
1200       else
1201       {
1202         break;
1203       }
1204     }
1205   }
1206
1207   @Override
1208   public void editLink_actionPerformed(ActionEvent e)
1209   {
1210     GSequenceLink link = new GSequenceLink();
1211
1212     int index = linkUrlTable.getSelectedRow();
1213     if (index == -1)
1214     {
1215       // button no longer enabled if row is not selected
1216       Console.debug("Edit with no row selected in linkUrlTable");
1217       return;
1218     }
1219
1220     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1221             .getNameColumn();
1222     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1223             .getUrlColumn();
1224     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1225     link.setName(oldName);
1226     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1227
1228     boolean valid = false;
1229     while (!valid)
1230     {
1231       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1232               MessageManager.getString("label.edit_sequence_url_link"),
1233               JvOptionPane.OK_CANCEL_OPTION, -1,
1234               null) == JvOptionPane.OK_OPTION)
1235       {
1236         if (link.checkValid())
1237         {
1238           if ((oldName.equals(link.getName()))
1239                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1240                           .isUniqueName(link.getName())))
1241           {
1242             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1243             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1244             valid = true;
1245           }
1246           else
1247           {
1248             link.notifyDuplicate();
1249             continue;
1250           }
1251         }
1252       }
1253       else
1254       {
1255         break;
1256       }
1257     }
1258   }
1259
1260   @Override
1261   public void deleteLink_actionPerformed(ActionEvent e)
1262   {
1263     int index = linkUrlTable.getSelectedRow();
1264     int modelIndex = -1;
1265     if (index == -1)
1266     {
1267       // button no longer enabled if row is not selected
1268       Console.debug("Delete with no row selected in linkUrlTable");
1269       return;
1270     }
1271     else
1272     {
1273       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1274     }
1275
1276     // make sure we use the model index to delete, and not the table index
1277     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1278   }
1279
1280   /*
1281    * (non-Javadoc)
1282    *
1283    * @see
1284    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1285    * .ActionEvent)
1286    */
1287   @Override
1288   protected void showunconserved_actionPerformed(ActionEvent e)
1289   {
1290     // TODO Auto-generated method stub
1291     super.showunconserved_actionPerformed(e);
1292   }
1293
1294   public static List<String> getGroupURLLinks()
1295   {
1296     return groupURLLinks;
1297   }
1298
1299   @Override
1300   public void minColour_actionPerformed(JPanel panel)
1301   {
1302     JalviewColourChooser.showColourChooser(this,
1303             MessageManager.getString("label.select_colour_minimum_value"),
1304             panel);
1305   }
1306
1307   @Override
1308   public void maxColour_actionPerformed(JPanel panel)
1309   {
1310     JalviewColourChooser.showColourChooser(this,
1311             MessageManager.getString("label.select_colour_maximum_value"),
1312             panel);
1313   }
1314
1315   @Override
1316   public void gapColour_actionPerformed(JPanel gap)
1317   {
1318     if (!useLegacyGap.isSelected())
1319     {
1320       JalviewColourChooser.showColourChooser(this,
1321               MessageManager.getString("label.select_gap_colour"), gap);
1322     }
1323   }
1324
1325   @Override
1326   public void hiddenColour_actionPerformed(JPanel hidden)
1327   {
1328     JalviewColourChooser.showColourChooser(this,
1329             MessageManager.getString("label.select_hidden_colour"), hidden);
1330   }
1331
1332   @Override
1333   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1334   {
1335     boolean enabled = useLegacyGap.isSelected();
1336     if (enabled)
1337     {
1338       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
1339     }
1340     else
1341     {
1342       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
1343     }
1344     gapColour.setEnabled(!enabled);
1345     gapLabel.setEnabled(!enabled);
1346   }
1347
1348   @Override
1349   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1350   {
1351     useLegacyGap.setSelected(false);
1352     useLegacyGaps_actionPerformed(null);
1353     showHiddenAtStart.setSelected(false);
1354     hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
1355   }
1356
1357   @Override
1358   protected void userIdWidth_actionPerformed()
1359   {
1360     try
1361     {
1362       String val = userIdWidth.getText().trim();
1363       if (val.length() > 0)
1364       {
1365         Integer iw = Integer.parseInt(val);
1366         if (iw.intValue() < 12)
1367         {
1368           throw new NumberFormatException();
1369         }
1370         userIdWidth.setText(iw.toString());
1371       }
1372     } catch (NumberFormatException x)
1373     {
1374       userIdWidth.setText("");
1375       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1376               MessageManager
1377                       .getString("warn.user_defined_width_requirements"),
1378               MessageManager.getString("label.invalid_id_column_width"),
1379               JvOptionPane.WARNING_MESSAGE);
1380     }
1381   }
1382
1383   @Override
1384   protected void autoIdWidth_actionPerformed()
1385   {
1386     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1387     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1388   }
1389
1390   /**
1391    * Returns true if structure viewer path is to a valid executable, else shows
1392    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1393    * (built in to Jalview) or when Jalview is left to try default paths.
1394    */
1395   private boolean validateViewerPath()
1396   {
1397     if (structureViewerPath.getText().trim().length() > 0)
1398     {
1399       File f = new File(structureViewerPath.getText());
1400       if (!f.canExecute())
1401       {
1402         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1403                 MessageManager.getString("label.invalid_viewer_path"),
1404                 MessageManager.getString("label.invalid_viewer_path"),
1405                 JvOptionPane.ERROR_MESSAGE);
1406         return false;
1407       }
1408     }
1409     return true;
1410   }
1411
1412   /**
1413    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1414    * default or user-specified path, if not show a warning/help dialog
1415    */
1416   @Override
1417   protected void structureViewer_actionPerformed(String selectedItem)
1418   {
1419     if (selectedItem.equals(ViewerType.JMOL.name()))
1420     {
1421       structureViewerPath.setEnabled(false);
1422       structureViewerPathLabel.setEnabled(false);
1423       return;
1424     }
1425     boolean found = false;
1426     structureViewerPath.setEnabled(true);
1427     structureViewerPathLabel.setEnabled(true);
1428     structureViewerPathLabel.setText(MessageManager
1429             .formatMessage("label.viewer_path", selectedItem));
1430
1431     /*
1432      * Try user-specified and standard paths for structure viewer executable
1433      */
1434     String viewerPath = "";
1435     List<String> paths = null;
1436     Cache.disableSessionProperties();
1437     try
1438     {
1439       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1440       switch (viewerType)
1441       {
1442       case JMOL:
1443         // dealt with above
1444         break;
1445       case CHIMERA:
1446         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1447         paths = StructureManager.getChimeraPaths(false);
1448         break;
1449       case CHIMERAX:
1450         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1451         paths = StructureManager.getChimeraPaths(true);
1452         break;
1453       case PYMOL:
1454         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1455         paths = PymolManager.getPymolPaths();
1456         break;
1457       }
1458     } catch (IllegalArgumentException e)
1459     {
1460       // only valid entries should be in the drop-down
1461     }
1462     Cache.enableSessionProperties();
1463     structureViewerPath.setText(viewerPath);
1464
1465     paths.add(0, structureViewerPath.getText());
1466     for (String path : paths)
1467     {
1468       if (new File(path.trim()).canExecute())
1469       {
1470         found = true;
1471         break;
1472       }
1473     }
1474
1475     if (!found)
1476     {
1477       String[] options = { "OK", "Help" };
1478       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1479               JvSwingUtils.wrapTooltip(true,
1480                       MessageManager.getString("label.viewer_missing")),
1481               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1482               null, options, options[0]);
1483
1484       if (showHelp == JvOptionPane.NO_OPTION)
1485       {
1486         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1487         try
1488         {
1489           Help.showHelpWindow(HelpId.StructureViewer);
1490         } catch (HelpSetException e)
1491         {
1492           e.printStackTrace();
1493         }
1494       }
1495       else if (showHelp == JvOptionPane.OK_OPTION)
1496       {
1497         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1498         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1499           try
1500           {
1501             for (int i = 0; i < 3; i++)
1502             {
1503               structureViewerPath.setBackground(Color.PINK);
1504               Thread.sleep(500);
1505               structureViewerPath.setBackground(Color.WHITE);
1506               Thread.sleep(500);
1507             }
1508           } catch (InterruptedException e)
1509           {
1510           }
1511         });
1512       }
1513     }
1514   }
1515
1516   public class OptionsParam
1517   {
1518     private String name;
1519
1520     private String code;
1521
1522     public OptionsParam(String name, String code)
1523     {
1524       this.name = name;
1525       this.code = code;
1526     }
1527
1528     public String getName()
1529     {
1530       return name;
1531     }
1532
1533     public void setName(String name)
1534     {
1535       this.name = name;
1536     }
1537
1538     public String getCode()
1539     {
1540       return code;
1541     }
1542
1543     public void setCode(String code)
1544     {
1545       this.code = code;
1546     }
1547
1548     @Override
1549     public String toString()
1550     {
1551       return name;
1552     }
1553
1554     @Override
1555     public boolean equals(Object that)
1556     {
1557       if (!(that instanceof OptionsParam))
1558       {
1559         return false;
1560       }
1561       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1562     }
1563
1564     @Override
1565     public int hashCode()
1566     {
1567       return name.hashCode() + code.hashCode();
1568     }
1569   }
1570
1571   private class UrlListSelectionHandler implements ListSelectionListener
1572   {
1573
1574     @Override
1575     public void valueChanged(ListSelectionEvent e)
1576     {
1577       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1578
1579       int index = lsm.getMinSelectionIndex();
1580       if (index == -1)
1581       {
1582         // no selection, so disable delete/edit buttons
1583         editLink.setEnabled(false);
1584         deleteLink.setEnabled(false);
1585         return;
1586       }
1587       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1588
1589       // enable/disable edit and delete link buttons
1590       if (((UrlLinkTableModel) linkUrlTable.getModel())
1591               .isRowDeletable(modelIndex))
1592       {
1593         deleteLink.setEnabled(true);
1594       }
1595       else
1596       {
1597         deleteLink.setEnabled(false);
1598       }
1599
1600       if (((UrlLinkTableModel) linkUrlTable.getModel())
1601               .isRowEditable(modelIndex))
1602       {
1603         editLink.setEnabled(true);
1604       }
1605       else
1606       {
1607         editLink.setEnabled(false);
1608       }
1609     }
1610   }
1611 }