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     ssConsensus.setSelected(Cache.getDefault("SHOW_SS_CONSENSUS", false));
 296     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 297     showUnconserved
 298             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 299     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 300     showGroupConsensus
 301             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 302     showGroupConservation.setSelected(
 303             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 304     showConsensHistogram.setSelected(
 305             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 306     showConsensLogo
 307             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 308     showNpTooltip
 309             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 310     showDbRefTooltip
 311             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 312
 313     String[] fonts = java.awt.GraphicsEnvironment
 314             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 315     for (int i = 0; i < fonts.length; i++)
 316     {
 317       fontNameCB.addItem(fonts[i]);
 318     }
 319
 320     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 321     {
 322       fontSizeCB.addItem(i + "");
 323     }
 324
 325     fontStyleCB.addItem("plain");
 326     fontStyleCB.addItem("bold");
 327     fontStyleCB.addItem("italic");
 328
 329     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 330     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 331     fontStyleCB.setSelectedItem(
 332             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 333
 334     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 335     scaleProteinToCdna
 336             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 337
 338     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 339
 340     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 341
 342     gapSymbolCB.addItem("-");
 343     gapSymbolCB.addItem(".");
 344
 345     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 346
 347     sortby.addItem("No sort");
 348     sortby.addItem("Id");
 349     sortby.addItem("Pairwise Identity");
 350     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 351
 352     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 353     sortAnnBy
 354             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 355     sortAnnBy
 356             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 357     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 358             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 359                     SequenceAnnotationOrder.NONE.name()));
 360     sortAnnBy.setSelectedItem(savedSort.toString());
 361
 362     sortAutocalc.addItem("Autocalculated first");
 363     sortAutocalc.addItem("Autocalculated last");
 364     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 365     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 366             : sortAutocalc.getItemAt(1));
 367     startupCheckbox
 368             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 369     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 370             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 371                     + "/examples/exampleFile_2_7.jvp"));
 372
 373     /*
 374      * Set Colours tab defaults
 375      */
 376     protColour.addItem(ResidueColourScheme.NONE);
 377     nucColour.addItem(ResidueColourScheme.NONE);
 378     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 379     {
 380       String name = cs.getSchemeName();
 381       protColour.addItem(name);
 382       nucColour.addItem(name);
 383     }
 384     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 385             ResidueColourScheme.NONE);
 386     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 387     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 388     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 389     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 390     minColour.setBackground(
 391             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 392     maxColour.setBackground(
 393             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 394
 395     /*
 396      * Set overview panel defaults
 397      */
 398     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 399             OverviewCanvas.OVERVIEW_DEFAULT_GAP));
 400     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 401             OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
 402     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 403     gapLabel.setEnabled(!useLegacyGap.isSelected());
 404     gapColour.setEnabled(!useLegacyGap.isSelected());
 405     showHiddenAtStart
 406             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 407
 408     /*
 409      * Set Structure tab defaults
 410      */
 411     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
 412     structFromPdb.setSelected(structSelected);
 413     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
 414     addSecondaryStructure.setEnabled(structSelected);
 415     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
 416     addTempFactor.setEnabled(structSelected);
 417
 418     /*
 419      * set choice of structure viewer, and path if saved as a preference;
 420      * default to Jmol (first choice) if an unexpected value is found
 421      */
 422     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 423             ViewerType.JMOL.name());
 424     structViewer.setSelectedItem(viewerType);
 425     String viewerPath = "";
 426     ViewerType type = null;
 427     try
 428     {
 429       type = ViewerType.valueOf(viewerType);
 430       switch (type)
 431       {
 432       case JMOL:
 433         break;
 434       case CHIMERA:
 435         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 436         break;
 437       case CHIMERAX:
 438         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 439         break;
 440       case PYMOL:
 441         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 442         break;
 443       }
 444     } catch (IllegalArgumentException e)
 445     {
 446       Console.error("Unknown structure viewer type: " + viewerType
 447               + ", defaulting to Jmol");
 448       type = ViewerType.JMOL;
 449     }
 450     structureViewerPath.setText(viewerPath);
 451
 452     structureViewerPath.addActionListener(new ActionListener()
 453     {
 454       @Override
 455       public void actionPerformed(ActionEvent e)
 456       {
 457         if (validateViewerPath())
 458         {
 459           String path = structureViewerPath.getText();
 460           try
 461           {
 462             ViewerType type = ViewerType.valueOf(viewerType);
 463             switch (type)
 464             {
 465             case JMOL:
 466               break;
 467             case CHIMERA:
 468               Cache.setProperty(CHIMERA_PATH, path);
 469               break;
 470             case CHIMERAX:
 471               Cache.setProperty(CHIMERAX_PATH, path);
 472               break;
 473             case PYMOL:
 474               Cache.setProperty(PYMOL_PATH, path);
 475               break;
 476             }
 477           } catch (IllegalArgumentException x)
 478           {
 479             Console.error("Failed to set path - unknown viewer type", x);
 480           }
 481         }
 482       }
 483     });
 484
 485     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 486     {
 487       siftsMapping.setSelected(true);
 488     }
 489     else
 490     {
 491       nwMapping.setSelected(true);
 492     }
 493
 494     SiftsSettings
 495             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 496
 497     /*
 498      * Set Connections tab defaults
 499      */
 500
 501     // set up sorting
 502     linkUrlTable.setModel(dataModel);
 503     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 504             linkUrlTable.getModel());
 505     linkUrlTable.setRowSorter(sorter);
 506     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 507
 508     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 509     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 510             SortOrder.DESCENDING));
 511     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 512             SortOrder.DESCENDING));
 513     sortKeys.add(
 514             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 515
 516     sorter.setSortKeys(sortKeys);
 517     // BH 2018 setSortKeys will do the sort
 518     // sorter.sort();
 519
 520     // set up filtering
 521     ActionListener onReset;
 522     onReset = new ActionListener()
 523     {
 524       @Override
 525       public void actionPerformed(ActionEvent e)
 526       {
 527         filterTB.setText("");
 528         sorter.setRowFilter(RowFilter.regexFilter(""));
 529       }
 530
 531     };
 532     doReset.addActionListener(onReset);
 533
 534     // filter to display only custom urls
 535     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 536     {
 537       @Override
 538       public boolean include(
 539               Entry<? extends TableModel, ? extends Object> entry)
 540       {
 541         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 542       }
 543     };
 544
 545     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 546             linkUrlTable.getModel());
 547     customSorter.setRowFilter(customUrlFilter);
 548
 549     ActionListener onCustomOnly;
 550     onCustomOnly = new ActionListener()
 551     {
 552       @Override
 553       public void actionPerformed(ActionEvent e)
 554       {
 555         filterTB.setText("");
 556         sorter.setRowFilter(customUrlFilter);
 557       }
 558     };
 559     userOnly.addActionListener(onCustomOnly);
 560
 561     filterTB.getDocument().addDocumentListener(new DocumentListener()
 562     {
 563       String caseInsensitiveFlag = "(?i)";
 564
 565       @Override
 566       public void changedUpdate(DocumentEvent e)
 567       {
 568         sorter.setRowFilter(RowFilter
 569                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 570       }
 571
 572       @Override
 573       public void removeUpdate(DocumentEvent e)
 574       {
 575         sorter.setRowFilter(RowFilter
 576                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 577       }
 578
 579       @Override
 580       public void insertUpdate(DocumentEvent e)
 581       {
 582         sorter.setRowFilter(RowFilter
 583                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 584       }
 585     });
 586
 587     // set up list selection functionality
 588     linkUrlTable.getSelectionModel()
 589             .addListSelectionListener(new UrlListSelectionHandler());
 590
 591     // set up radio buttons
 592     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 593             .getPrimaryColumn();
 594     String onClickName = linkUrlTable.getColumnName(onClickCol);
 595     linkUrlTable.getColumn(onClickName)
 596             .setCellRenderer(new RadioButtonRenderer());
 597     linkUrlTable.getColumn(onClickName)
 598             .setCellEditor(new RadioButtonEditor());
 599
 600     // get boolean columns and resize those to min possible
 601     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 602     {
 603       if (linkUrlTable.getModel().getColumnClass(column)
 604               .equals(Boolean.class))
 605       {
 606         TableColumn tableColumn = linkUrlTable.getColumnModel()
 607                 .getColumn(column);
 608         int preferredWidth = tableColumn.getMinWidth();
 609
 610         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 611                 column);
 612         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 613         int cwidth = c.getPreferredSize().width
 614                 + linkUrlTable.getIntercellSpacing().width;
 615         preferredWidth = Math.max(preferredWidth, cwidth);
 616
 617         tableColumn.setPreferredWidth(preferredWidth);
 618       }
 619     }
 620
 621     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 622     previousProxyType = proxyTypeString;
 623     switch (proxyTypeString)
 624     {
 625     case Cache.PROXYTYPE_NONE:
 626       proxyType.setSelected(noProxy.getModel(), true);
 627       break;
 628     case Cache.PROXYTYPE_SYSTEM:
 629       proxyType.setSelected(systemProxy.getModel(), true);
 630       break;
 631     case Cache.PROXYTYPE_CUSTOM:
 632       proxyType.setSelected(customProxy.getModel(), true);
 633       break;
 634     default:
 635       Console.warn(
 636               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 637                       + proxyTypeString);
 638     }
 639     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 640     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 641     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 642     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 643     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 644     proxyAuthUsernameTB
 645             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 646     // we are not storing or retrieving proxy password from .jalview_properties
 647     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 648             : new String(Cache.proxyAuthPassword));
 649     setCustomProxyEnabled();
 650     applyProxyButtonEnabled(false);
 651
 652     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 653     // note antisense here: default is true
 654     questionnaire
 655             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 656     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 657
 658     /*
 659      * Set Output tab defaults
 660      */
 661     setupOutputCombo(epsRendering, "EPS_RENDERING");
 662     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 663     setupOutputCombo(svgRendering, "SVG_RENDERING");
 664     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 665     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 666     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 667     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 668     userIdWidth.setText(wi == null ? "" : wi.toString());
 669     // TODO: refactor to use common enum via FormatAdapter and allow extension
 670     // for new flat file formats
 671     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 672     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 673     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 674     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 675     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 676     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 677     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 678     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 679     embbedBioJSON
 680             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 681
 682     /*
 683      * Set Editing tab defaults
 684      */
 685     autoCalculateConsCheck
 686             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 687     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 688     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 689
 690     annotations_actionPerformed(null); // update the display of the annotation
 691                                        // settings
 692
 693     /*
 694      * Set Backups tab defaults
 695      */
 696     loadLastSavedBackupsOptions();
 697
 698     /*
 699      * Set Startup tab defaults
 700      */
 701
 702     // re-enable
 703     Cache.enableSessionProperties();
 704   }
 705
 706   /**
 707    * A helper method that sets the items and initial selection in a character
 708    * rendering option list (Prompt each time/Lineart/Text)
 709    *
 710    * @param comboBox
 711    * @param propertyKey
 712    */
 713   protected void setupOutputCombo(JComboBox<Object> comboBox,
 714           String propertyKey)
 715   {
 716     Cache.disableSessionProperties();
 717
 718     comboBox.addItem(promptEachTimeOpt);
 719     comboBox.addItem(lineArtOpt);
 720     comboBox.addItem(textOpt);
 721
 722     /*
 723      * JalviewJS doesn't support Lineart so force it to Text
 724      */
 725     String defaultOption = Platform.isJS() ? "Text"
 726             : Cache.getDefault(propertyKey, "Prompt each time");
 727     if (defaultOption.equalsIgnoreCase("Text"))
 728     {
 729       comboBox.setSelectedItem(textOpt);
 730     }
 731     else if (defaultOption.equalsIgnoreCase("Lineart"))
 732     {
 733       comboBox.setSelectedItem(lineArtOpt);
 734     }
 735     else
 736     {
 737       comboBox.setSelectedItem(promptEachTimeOpt);
 738     }
 739
 740     Cache.enableSessionProperties();
 741   }
 742
 743   /**
 744    * Save user selections on the Preferences tabs to the Cache and write out to
 745    * file.
 746    *
 747    * @param e
 748    */
 749   @Override
 750   public void ok_actionPerformed(ActionEvent e)
 751   {
 752     Cache.disableSessionProperties();
 753
 754     if (!validateSettings())
 755     {
 756       return;
 757     }
 758
 759     /*
 760      * Set proxy settings first (to be before web services refresh)
 761      */
 762     saveProxySettings();
 763
 764     /*
 765      * Save Visual settings
 766      */
 767
 768     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 769             Boolean.toString(seqLimit.isSelected()));
 770     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 771             Boolean.toString(rightAlign.isSelected()));
 772     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 773             Boolean.toString(fullScreen.isSelected()));
 774     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 775             Boolean.toString(openoverv.isSelected()));
 776     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 777             Boolean.toString(annotations.isSelected()));
 778     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 779             Boolean.toString(conservation.isSelected()));
 780     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 781             Boolean.toString(quality.isSelected()));
 782     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 783             Boolean.toString(identity.isSelected()));
 784
 785     Cache.applicationProperties.setProperty("SHOW_SS_CONSENSUS",
 786             Boolean.toString(ssConsensus.isSelected()));
 787
 788     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 789             gapSymbolCB.getSelectedItem().toString());
 790
 791     Cache.applicationProperties.setProperty("FONT_NAME",
 792             fontNameCB.getSelectedItem().toString());
 793     Cache.applicationProperties.setProperty("FONT_STYLE",
 794             fontStyleCB.getSelectedItem().toString());
 795     Cache.applicationProperties.setProperty("FONT_SIZE",
 796             fontSizeCB.getSelectedItem().toString());
 797
 798     Cache.applicationProperties.setProperty("ID_ITALICS",
 799             Boolean.toString(idItalics.isSelected()));
 800     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 801             Boolean.toString(showUnconserved.isSelected()));
 802     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 803             Boolean.toString(showOccupancy.isSelected()));
 804     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 805             Boolean.toString(showGroupConsensus.isSelected()));
 806     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 807             Boolean.toString(showGroupConservation.isSelected()));
 808     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 809             Boolean.toString(showConsensHistogram.isSelected()));
 810     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 811             Boolean.toString(showConsensLogo.isSelected()));
 812     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 813             Boolean.toString(smoothFont.isSelected()));
 814     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 815             Boolean.toString(scaleProteinToCdna.isSelected()));
 816     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 817             Boolean.toString(showNpTooltip.isSelected()));
 818     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 819             Boolean.toString(showDbRefTooltip.isSelected()));
 820
 821     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 822             Boolean.toString(wrap.isSelected()));
 823
 824     Cache.applicationProperties.setProperty("STARTUP_FILE",
 825             startupFileTextfield.getText());
 826     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 827             Boolean.toString(startupCheckbox.isSelected()));
 828
 829     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 830             sortby.getSelectedItem().toString());
 831
 832     // convert description of sort order to enum name for save
 833     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 834             .forDescription(sortAnnBy.getSelectedItem().toString());
 835     if (annSortOrder != null)
 836     {
 837       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 838               annSortOrder.name());
 839     }
 840
 841     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 842     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 843             Boolean.valueOf(showAutocalcFirst).toString());
 844
 845     /*
 846      * Save Colours settings
 847      */
 848     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 849             protColour.getSelectedItem().toString());
 850     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 851             nucColour.getSelectedItem().toString());
 852     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 853             minColour.getBackground());
 854     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 855             maxColour.getBackground());
 856
 857     /*
 858      * Save Overview settings
 859      */
 860     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 861     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 862     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 863             Boolean.toString(useLegacyGap.isSelected()));
 864     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 865             Boolean.toString(showHiddenAtStart.isSelected()));
 866
 867     /*
 868      * Save Structure settings
 869      */
 870     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 871             Boolean.toString(addTempFactor.isSelected()));
 872     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 873             Boolean.toString(addSecondaryStructure.isSelected()));
 874     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 875             Boolean.toString(structFromPdb.isSelected()));
 876     String viewer = structViewer.getSelectedItem().toString();
 877     String viewerPath = structureViewerPath.getText();
 878     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 879     if (viewer.equals(ViewerType.CHIMERA.name()))
 880     {
 881       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 882     }
 883     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 884     {
 885       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 886     }
 887     else if (viewer.equals(ViewerType.PYMOL.name()))
 888     {
 889       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 890     }
 891     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 892             Boolean.toString(siftsMapping.isSelected()));
 893     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 894
 895     /*
 896      * Save Output settings
 897      */
 898     Cache.applicationProperties.setProperty("EPS_RENDERING",
 899             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 900     Cache.applicationProperties.setProperty("HTML_RENDERING",
 901             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 902     Cache.applicationProperties.setProperty("SVG_RENDERING",
 903             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 904
 905     /*
 906      * Save Connections settings
 907      */
 908     // Proxy settings set first (to catch web services)
 909
 910     // save user-defined and selected links
 911     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 912     if (menuLinks.isEmpty())
 913     {
 914       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 915     }
 916     else
 917     {
 918       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 919               menuLinks.toString());
 920     }
 921
 922     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 923     if (nonMenuLinks.isEmpty())
 924     {
 925       Cache.applicationProperties.remove("STORED_LINKS");
 926     }
 927     else
 928     {
 929       Cache.applicationProperties.setProperty("STORED_LINKS",
 930               nonMenuLinks.toString());
 931     }
 932
 933     Cache.applicationProperties.setProperty("DEFAULT_URL",
 934             sequenceUrlLinks.getPrimaryUrlId());
 935
 936     Cache.setProperty("VERSION_CHECK",
 937             Boolean.toString(versioncheck.isSelected()));
 938     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 939     {
 940       // default is false - we only set this if the user has actively agreed
 941       Cache.setProperty("USAGESTATS",
 942               Boolean.toString(usagestats.isSelected()));
 943     }
 944     if (!questionnaire.isSelected())
 945     {
 946       Cache.setProperty("NOQUESTIONNAIRES", "true");
 947     }
 948     else
 949     {
 950       // special - made easy to edit a property file to disable questionnaires
 951       // by just adding the given line
 952       Cache.removeProperty("NOQUESTIONNAIRES");
 953     }
 954
 955     /*
 956      * Save Output settings
 957      */
 958     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 959             Boolean.toString(blcjv.isSelected()));
 960     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 961             Boolean.toString(clustaljv.isSelected()));
 962     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 963             Boolean.toString(fastajv.isSelected()));
 964     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 965             Boolean.toString(msfjv.isSelected()));
 966     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 967             Boolean.toString(pfamjv.isSelected()));
 968     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 969             Boolean.toString(pileupjv.isSelected()));
 970     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 971             Boolean.toString(pirjv.isSelected()));
 972     Cache.applicationProperties.setProperty("PIR_MODELLER",
 973             Boolean.toString(modellerOutput.isSelected()));
 974     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 975             Boolean.toString(embbedBioJSON.isSelected()));
 976     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 977
 978     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 979             Boolean.toString(autoIdWidth.isSelected()));
 980     userIdWidth_actionPerformed();
 981     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 982             userIdWidth.getText());
 983
 984     /*
 985      * Save Editing settings
 986      */
 987     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 988             Boolean.toString(autoCalculateConsCheck.isSelected()));
 989     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 990             Boolean.toString(sortByTree.isSelected()));
 991     Cache.applicationProperties.setProperty("PAD_GAPS",
 992             Boolean.toString(padGaps.isSelected()));
 993
 994     if (!Platform.isJS())
 995     {
 996       wsPrefs.updateAndRefreshWsMenuConfig(false);
 997     }
 998
 999     /*
1000      * Save Backups settings
1001      */
1002     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
1003             Boolean.toString(enableBackupFiles.isSelected()));
1004     int preset = getComboIntStringKey(backupfilesPresetsCombo);
1005     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
1006             Integer.toString(preset));
1007
1008     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1009     {
1010       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1011       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1012               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1013       Cache.applicationProperties.setProperty(
1014               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
1015     }
1016
1017     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1018             .get(preset);
1019     Cache.applicationProperties.setProperty(
1020             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1021
1022     /*
1023      * Save Memory Settings
1024      */
1025     Cache.applicationProperties.setProperty(
1026             MemorySetting.CUSTOMISED_SETTINGS,
1027             Boolean.toString(customiseMemorySetting.isSelected()));
1028     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
1029             Integer.toString(jvmMemoryPercentSlider.getValue()));
1030     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
1031             jvmMemoryMaxTextField.getText());
1032
1033     /*
1034      * save and close Preferences
1035      */
1036
1037     Cache.saveProperties();
1038     Desktop.instance.doConfigureStructurePrefs();
1039     try
1040     {
1041       frame.setClosed(true);
1042     } catch (Exception ex)
1043     {
1044     }
1045
1046     Cache.enableSessionProperties();
1047   }
1048
1049   public void saveProxySettings()
1050   {
1051     Cache.disableSessionProperties();
1052
1053     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1054             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1055                     : Cache.PROXYTYPE_SYSTEM;
1056     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1057     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1058     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1059     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1060     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1061     Cache.setOrRemove("PROXY_AUTH",
1062             Boolean.toString(proxyAuth.isSelected()));
1063     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1064     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1065     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1066     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1067             || !newProxyType.equals(previousProxyType))
1068     {
1069       // force a re-lookup of ws if proxytype is custom or has changed
1070       wsPrefs.update++;
1071     }
1072     previousProxyType = newProxyType;
1073
1074     Cache.enableSessionProperties();
1075   }
1076
1077   /**
1078    * Do any necessary validation before saving settings. Return focus to the
1079    * first tab which fails validation.
1080    *
1081    * @return
1082    */
1083   private boolean validateSettings()
1084   {
1085     if (!validateStructure())
1086     {
1087       structureTab.requestFocusInWindow();
1088       return false;
1089     }
1090     return true;
1091   }
1092
1093   @Override
1094   protected boolean validateStructure()
1095   {
1096     return validateViewerPath();
1097
1098   }
1099
1100   /**
1101    * DOCUMENT ME!
1102    */
1103   @Override
1104   public void startupFileTextfield_mouseClicked()
1105   {
1106     Cache.disableSessionProperties();
1107
1108     // TODO: JAL-3048 not needed for Jalview-JS
1109     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1110     JalviewFileChooser chooser = JalviewFileChooser
1111             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1112     chooser.setFileView(new JalviewFileView());
1113     chooser.setDialogTitle(
1114             MessageManager.getString("label.select_startup_file"));
1115
1116     int value = chooser.showOpenDialog(this);
1117
1118     if (value == JalviewFileChooser.APPROVE_OPTION)
1119     {
1120       FileFormatI format = chooser.getSelectedFormat();
1121       if (format != null)
1122       {
1123         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1124                 format.getName());
1125       }
1126       startupFileTextfield
1127               .setText(chooser.getSelectedFile().getAbsolutePath());
1128     }
1129
1130     Cache.enableSessionProperties();
1131   }
1132
1133   /**
1134    * DOCUMENT ME!
1135    *
1136    * @param e
1137    *          DOCUMENT ME!
1138    */
1139   @Override
1140   public void cancel_actionPerformed(ActionEvent e)
1141   {
1142     try
1143     {
1144       if (!Platform.isJS())
1145       {
1146         wsPrefs.updateWsMenuConfig(true);
1147         wsPrefs.refreshWs_actionPerformed(e);
1148       }
1149       frame.setClosed(true);
1150     } catch (Exception ex)
1151     {
1152     }
1153   }
1154
1155   /**
1156    * DOCUMENT ME!
1157    *
1158    * @param e
1159    *          DOCUMENT ME!
1160    */
1161   @Override
1162   public void annotations_actionPerformed(ActionEvent e)
1163   {
1164     conservation.setEnabled(annotations.isSelected());
1165     quality.setEnabled(annotations.isSelected());
1166     identity.setEnabled(annotations.isSelected());
1167     ssConsensus.setEnabled(annotations.isSelected());
1168     showOccupancy.setEnabled(annotations.isSelected());
1169     showGroupConsensus.setEnabled(annotations.isSelected());
1170     showGroupConservation.setEnabled(annotations.isSelected());
1171     showConsensHistogram.setEnabled(annotations.isSelected()
1172             && (identity.isSelected() || showGroupConsensus.isSelected()));
1173     showConsensLogo.setEnabled(annotations.isSelected()
1174             && (identity.isSelected() || showGroupConsensus.isSelected()));
1175   }
1176
1177   @Override
1178   public void newLink_actionPerformed(ActionEvent e)
1179   {
1180     GSequenceLink link = new GSequenceLink();
1181     boolean valid = false;
1182     while (!valid)
1183     {
1184       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1185               MessageManager.getString("label.new_sequence_url_link"),
1186               JvOptionPane.OK_CANCEL_OPTION, -1,
1187               null) == JvOptionPane.OK_OPTION)
1188       {
1189         if (link.checkValid())
1190         {
1191           if (((UrlLinkTableModel) linkUrlTable.getModel())
1192                   .isUniqueName(link.getName()))
1193           {
1194             ((UrlLinkTableModel) linkUrlTable.getModel())
1195                     .insertRow(link.getName(), link.getURL());
1196             valid = true;
1197           }
1198           else
1199           {
1200             link.notifyDuplicate();
1201             continue;
1202           }
1203         }
1204       }
1205       else
1206       {
1207         break;
1208       }
1209     }
1210   }
1211
1212   @Override
1213   public void editLink_actionPerformed(ActionEvent e)
1214   {
1215     GSequenceLink link = new GSequenceLink();
1216
1217     int index = linkUrlTable.getSelectedRow();
1218     if (index == -1)
1219     {
1220       // button no longer enabled if row is not selected
1221       Console.debug("Edit with no row selected in linkUrlTable");
1222       return;
1223     }
1224
1225     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1226             .getNameColumn();
1227     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1228             .getUrlColumn();
1229     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1230     link.setName(oldName);
1231     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1232
1233     boolean valid = false;
1234     while (!valid)
1235     {
1236       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1237               MessageManager.getString("label.edit_sequence_url_link"),
1238               JvOptionPane.OK_CANCEL_OPTION, -1,
1239               null) == JvOptionPane.OK_OPTION)
1240       {
1241         if (link.checkValid())
1242         {
1243           if ((oldName.equals(link.getName()))
1244                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1245                           .isUniqueName(link.getName())))
1246           {
1247             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1248             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1249             valid = true;
1250           }
1251           else
1252           {
1253             link.notifyDuplicate();
1254             continue;
1255           }
1256         }
1257       }
1258       else
1259       {
1260         break;
1261       }
1262     }
1263   }
1264
1265   @Override
1266   public void deleteLink_actionPerformed(ActionEvent e)
1267   {
1268     int index = linkUrlTable.getSelectedRow();
1269     int modelIndex = -1;
1270     if (index == -1)
1271     {
1272       // button no longer enabled if row is not selected
1273       Console.debug("Delete with no row selected in linkUrlTable");
1274       return;
1275     }
1276     else
1277     {
1278       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1279     }
1280
1281     // make sure we use the model index to delete, and not the table index
1282     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1283   }
1284
1285   /*
1286    * (non-Javadoc)
1287    *
1288    * @see
1289    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1290    * .ActionEvent)
1291    */
1292   @Override
1293   protected void showunconserved_actionPerformed(ActionEvent e)
1294   {
1295     // TODO Auto-generated method stub
1296     super.showunconserved_actionPerformed(e);
1297   }
1298
1299   public static List<String> getGroupURLLinks()
1300   {
1301     return groupURLLinks;
1302   }
1303
1304   @Override
1305   public void minColour_actionPerformed(JPanel panel)
1306   {
1307     JalviewColourChooser.showColourChooser(this,
1308             MessageManager.getString("label.select_colour_minimum_value"),
1309             panel);
1310   }
1311
1312   @Override
1313   public void maxColour_actionPerformed(JPanel panel)
1314   {
1315     JalviewColourChooser.showColourChooser(this,
1316             MessageManager.getString("label.select_colour_maximum_value"),
1317             panel);
1318   }
1319
1320   @Override
1321   public void gapColour_actionPerformed(JPanel gap)
1322   {
1323     if (!useLegacyGap.isSelected())
1324     {
1325       JalviewColourChooser.showColourChooser(this,
1326               MessageManager.getString("label.select_gap_colour"), gap);
1327     }
1328   }
1329
1330   @Override
1331   public void hiddenColour_actionPerformed(JPanel hidden)
1332   {
1333     JalviewColourChooser.showColourChooser(this,
1334             MessageManager.getString("label.select_hidden_colour"), hidden);
1335   }
1336
1337   @Override
1338   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1339   {
1340     boolean enabled = useLegacyGap.isSelected();
1341     if (enabled)
1342     {
1343       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
1344     }
1345     else
1346     {
1347       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
1348     }
1349     gapColour.setEnabled(!enabled);
1350     gapLabel.setEnabled(!enabled);
1351   }
1352
1353   @Override
1354   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1355   {
1356     useLegacyGap.setSelected(false);
1357     useLegacyGaps_actionPerformed(null);
1358     showHiddenAtStart.setSelected(false);
1359     hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
1360   }
1361
1362   @Override
1363   protected void userIdWidth_actionPerformed()
1364   {
1365     try
1366     {
1367       String val = userIdWidth.getText().trim();
1368       if (val.length() > 0)
1369       {
1370         Integer iw = Integer.parseInt(val);
1371         if (iw.intValue() < 12)
1372         {
1373           throw new NumberFormatException();
1374         }
1375         userIdWidth.setText(iw.toString());
1376       }
1377     } catch (NumberFormatException x)
1378     {
1379       userIdWidth.setText("");
1380       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1381               MessageManager
1382                       .getString("warn.user_defined_width_requirements"),
1383               MessageManager.getString("label.invalid_id_column_width"),
1384               JvOptionPane.WARNING_MESSAGE);
1385     }
1386   }
1387
1388   @Override
1389   protected void autoIdWidth_actionPerformed()
1390   {
1391     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1392     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1393   }
1394
1395   /**
1396    * Returns true if structure viewer path is to a valid executable, else shows
1397    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1398    * (built in to Jalview) or when Jalview is left to try default paths.
1399    */
1400   private boolean validateViewerPath()
1401   {
1402     if (structureViewerPath.getText().trim().length() > 0)
1403     {
1404       File f = new File(structureViewerPath.getText());
1405       if (!f.canExecute())
1406       {
1407         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1408                 MessageManager.getString("label.invalid_viewer_path"),
1409                 MessageManager.getString("label.invalid_viewer_path"),
1410                 JvOptionPane.ERROR_MESSAGE);
1411         return false;
1412       }
1413     }
1414     return true;
1415   }
1416
1417   /**
1418    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1419    * default or user-specified path, if not show a warning/help dialog
1420    */
1421   @Override
1422   protected void structureViewer_actionPerformed(String selectedItem)
1423   {
1424     if (selectedItem.equals(ViewerType.JMOL.name()))
1425     {
1426       structureViewerPath.setEnabled(false);
1427       structureViewerPathLabel.setEnabled(false);
1428       return;
1429     }
1430     boolean found = false;
1431     structureViewerPath.setEnabled(true);
1432     structureViewerPathLabel.setEnabled(true);
1433     structureViewerPathLabel.setText(MessageManager
1434             .formatMessage("label.viewer_path", selectedItem));
1435
1436     /*
1437      * Try user-specified and standard paths for structure viewer executable
1438      */
1439     String viewerPath = "";
1440     List<String> paths = null;
1441     Cache.disableSessionProperties();
1442     try
1443     {
1444       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1445       switch (viewerType)
1446       {
1447       case JMOL:
1448         // dealt with above
1449         break;
1450       case CHIMERA:
1451         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1452         paths = StructureManager.getChimeraPaths(false);
1453         break;
1454       case CHIMERAX:
1455         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1456         paths = StructureManager.getChimeraPaths(true);
1457         break;
1458       case PYMOL:
1459         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1460         paths = PymolManager.getPymolPaths();
1461         break;
1462       }
1463     } catch (IllegalArgumentException e)
1464     {
1465       // only valid entries should be in the drop-down
1466     }
1467     Cache.enableSessionProperties();
1468     structureViewerPath.setText(viewerPath);
1469
1470     paths.add(0, structureViewerPath.getText());
1471     for (String path : paths)
1472     {
1473       if (new File(path.trim()).canExecute())
1474       {
1475         found = true;
1476         break;
1477       }
1478     }
1479
1480     if (!found)
1481     {
1482       String[] options = { "OK", "Help" };
1483       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1484               JvSwingUtils.wrapTooltip(true,
1485                       MessageManager.getString("label.viewer_missing")),
1486               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1487               null, options, options[0]);
1488
1489       if (showHelp == JvOptionPane.NO_OPTION)
1490       {
1491         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1492         try
1493         {
1494           Help.showHelpWindow(HelpId.StructureViewer);
1495         } catch (HelpSetException e)
1496         {
1497           e.printStackTrace();
1498         }
1499       }
1500       else if (showHelp == JvOptionPane.OK_OPTION)
1501       {
1502         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1503         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1504           try
1505           {
1506             for (int i = 0; i < 3; i++)
1507             {
1508               structureViewerPath.setBackground(Color.PINK);
1509               Thread.sleep(500);
1510               structureViewerPath.setBackground(Color.WHITE);
1511               Thread.sleep(500);
1512             }
1513           } catch (InterruptedException e)
1514           {
1515           }
1516         });
1517       }
1518     }
1519   }
1520
1521   public class OptionsParam
1522   {
1523     private String name;
1524
1525     private String code;
1526
1527     public OptionsParam(String name, String code)
1528     {
1529       this.name = name;
1530       this.code = code;
1531     }
1532
1533     public String getName()
1534     {
1535       return name;
1536     }
1537
1538     public void setName(String name)
1539     {
1540       this.name = name;
1541     }
1542
1543     public String getCode()
1544     {
1545       return code;
1546     }
1547
1548     public void setCode(String code)
1549     {
1550       this.code = code;
1551     }
1552
1553     @Override
1554     public String toString()
1555     {
1556       return name;
1557     }
1558
1559     @Override
1560     public boolean equals(Object that)
1561     {
1562       if (!(that instanceof OptionsParam))
1563       {
1564         return false;
1565       }
1566       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1567     }
1568
1569     @Override
1570     public int hashCode()
1571     {
1572       return name.hashCode() + code.hashCode();
1573     }
1574   }
1575
1576   private class UrlListSelectionHandler implements ListSelectionListener
1577   {
1578
1579     @Override
1580     public void valueChanged(ListSelectionEvent e)
1581     {
1582       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1583
1584       int index = lsm.getMinSelectionIndex();
1585       if (index == -1)
1586       {
1587         // no selection, so disable delete/edit buttons
1588         editLink.setEnabled(false);
1589         deleteLink.setEnabled(false);
1590         return;
1591       }
1592       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1593
1594       // enable/disable edit and delete link buttons
1595       if (((UrlLinkTableModel) linkUrlTable.getModel())
1596               .isRowDeletable(modelIndex))
1597       {
1598         deleteLink.setEnabled(true);
1599       }
1600       else
1601       {
1602         deleteLink.setEnabled(false);
1603       }
1604
1605       if (((UrlLinkTableModel) linkUrlTable.getModel())
1606               .isRowEditable(modelIndex))
1607       {
1608         editLink.setEnabled(true);
1609       }
1610       else
1611       {
1612         editLink.setEnabled(false);
1613       }
1614     }
1615   }
1616 }