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