src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.ext.pymol.PymolManager;
  57 import jalview.gui.Help.HelpId;
  58 import jalview.gui.StructureViewer.ViewerType;
  59 import jalview.io.BackupFiles;
  60 import jalview.io.BackupFilesPresetEntry;
  61 import jalview.io.FileFormatI;
  62 import jalview.io.JalviewFileChooser;
  63 import jalview.io.JalviewFileView;
  64 import jalview.jbgui.GPreferences;
  65 import jalview.jbgui.GSequenceLink;
  66 import jalview.schemes.ColourSchemeI;
  67 import jalview.schemes.ColourSchemes;
  68 import jalview.schemes.ResidueColourScheme;
  69 import jalview.urls.UrlLinkTableModel;
  70 import jalview.urls.api.UrlProviderFactoryI;
  71 import jalview.urls.api.UrlProviderI;
  72 import jalview.urls.desktop.DesktopUrlProviderFactory;
  73 import jalview.util.MessageManager;
  74 import jalview.util.Platform;
  75 import jalview.util.UrlConstants;
  76 import jalview.ws.sifts.SiftsSettings;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 109
 110   public static final String PYMOL_PATH = "PYMOL_PATH";
 111
 112   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 113
 114   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 115
 116   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 117
 118   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 119
 120   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 121
 122   public static final String GAP_COLOUR = "GAP_COLOUR";
 123
 124   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 125
 126   private static final int MIN_FONT_SIZE = 1;
 127
 128   private static final int MAX_FONT_SIZE = 30;
 129
 130   private String previousProxyType;
 131
 132   private static Preferences INSTANCE = null; // add "final"
 133
 134   /**
 135    * Holds name and link separated with | character. Sequence ID must be
 136    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 137    */
 138   public static UrlProviderI sequenceUrlLinks;
 139
 140   public static UrlLinkTableModel dataModel;
 141
 142   /**
 143    * Holds name and link separated with | character. Sequence IDS and Sequences
 144    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 145    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 146    * for first and second token specified after a pipe character at end |,|.
 147    * (TODO: proper escape for using | to separate ids or sequences
 148    */
 149
 150   public static List<String> groupURLLinks;
 151   static
 152   {
 153     // get links selected to be in the menu (SEQUENCE_LINKS)
 154     // and links entered by the user but not selected (STORED_LINKS)
 155     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 156     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 157     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 158             UrlConstants.DEFAULT_LABEL);
 159
 160     // if both links lists are empty, add the DEFAULT_URL link
 161     // otherwise we assume the default link is in one of the lists
 162     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 163     {
 164       inMenuString = UrlConstants.DEFAULT_STRING;
 165     }
 166     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 167             inMenuString, notInMenuString);
 168     sequenceUrlLinks = factory.createUrlProvider();
 169     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 170
 171     /**
 172      * TODO: reformulate groupURL encoding so two or more can be stored in the
 173      * .properties file as '|' separated strings
 174      */
 175
 176     groupURLLinks = new ArrayList<>();
 177   }
 178
 179   JInternalFrame frame;
 180
 181   private WsPreferences wsPrefs;
 182
 183   private OptionsParam promptEachTimeOpt = new OptionsParam(
 184           MessageManager.getString("label.prompt_each_time"),
 185           "Prompt each time");
 186
 187   private OptionsParam lineArtOpt = new OptionsParam(
 188           MessageManager.getString("label.lineart"), "Lineart");
 189
 190   private OptionsParam textOpt = new OptionsParam(
 191           MessageManager.getString("action.text"), "Text");
 192
 193   // get singleton Preferences instance
 194   public static Preferences getPreferences()
 195   {
 196     return getPreferences(0, null);
 197   }
 198
 199   public static Preferences getPreferences(int selectTab, String message)
 200   {
 201     if (INSTANCE == null || INSTANCE.frame == null
 202             || INSTANCE.frame.isClosed())
 203     {
 204       INSTANCE = new Preferences();
 205     }
 206     INSTANCE.selectTab(selectTab);
 207     INSTANCE.setMessage(message);
 208     return INSTANCE;
 209   }
 210
 211   public static void openPreferences()
 212   {
 213     openPreferences(0, null);
 214   }
 215
 216   public static void openPreferences(int selectTab, String message)
 217   {
 218     Preferences p = getPreferences(selectTab, message);
 219     p.frame.show();
 220     p.frame.moveToFront();
 221     p.frame.grabFocus();
 222   }
 223
 224   /**
 225    * Creates a new Preferences object.
 226    */
 227   private Preferences()
 228   {
 229     super();
 230     frame = new JInternalFrame();
 231     frame.setContentPane(this);
 232     if (!Platform.isJS())
 233     /**
 234      * Java only
 235      *
 236      * @j2sIgnore
 237      */
 238     {
 239       wsPrefs = new WsPreferences();
 240       wsTab.add(wsPrefs, BorderLayout.CENTER);
 241     }
 242     int width = 500, height = 450;
 243     if (Platform.isAMacAndNotJS())
 244     {
 245       width = 570;
 246       height = 480;
 247     }
 248
 249     Desktop.addInternalFrame(frame,
 250             MessageManager.getString("label.preferences"), width, height);
 251     frame.setMinimumSize(new Dimension(width, height));
 252
 253     /*
 254      * Set Visual tab defaults
 255      */
 256     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 257     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 258     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 259     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 260
 261     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 262     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 263     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 264     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 265     showUnconserved
 266             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 267     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 268     showGroupConsensus
 269             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 270     showGroupConservation.setSelected(
 271             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 272     showConsensHistogram.setSelected(
 273             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 274     showConsensLogo
 275             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 276     showNpTooltip
 277             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 278     showDbRefTooltip
 279             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 280
 281     String[] fonts = java.awt.GraphicsEnvironment
 282             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 283     for (int i = 0; i < fonts.length; i++)
 284     {
 285       fontNameCB.addItem(fonts[i]);
 286     }
 287
 288     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 289     {
 290       fontSizeCB.addItem(i + "");
 291     }
 292
 293     fontStyleCB.addItem("plain");
 294     fontStyleCB.addItem("bold");
 295     fontStyleCB.addItem("italic");
 296
 297     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 298     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 299     fontStyleCB.setSelectedItem(
 300             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 301
 302     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 303     scaleProteinToCdna
 304             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 305
 306     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 307
 308     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 309
 310     gapSymbolCB.addItem("-");
 311     gapSymbolCB.addItem(".");
 312
 313     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 314
 315     sortby.addItem("No sort");
 316     sortby.addItem("Id");
 317     sortby.addItem("Pairwise Identity");
 318     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 319
 320     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 321     sortAnnBy
 322             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 323     sortAnnBy
 324             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 325     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 326             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 327                     SequenceAnnotationOrder.NONE.name()));
 328     sortAnnBy.setSelectedItem(savedSort.toString());
 329
 330     sortAutocalc.addItem("Autocalculated first");
 331     sortAutocalc.addItem("Autocalculated last");
 332     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 333     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 334             : sortAutocalc.getItemAt(1));
 335     startupCheckbox
 336             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 337     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 338             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 339                     + "/examples/exampleFile_2_3.jar"));
 340
 341     /*
 342      * Set Colours tab defaults
 343      */
 344     protColour.addItem(ResidueColourScheme.NONE);
 345     nucColour.addItem(ResidueColourScheme.NONE);
 346     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 347     {
 348       String name = cs.getSchemeName();
 349       protColour.addItem(name);
 350       nucColour.addItem(name);
 351     }
 352     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 353             ResidueColourScheme.NONE);
 354     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 355     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 356     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 357     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 358     minColour.setBackground(
 359             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 360     maxColour.setBackground(
 361             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 362
 363     /*
 364      * Set overview panel defaults
 365      */
 366     gapColour.setBackground(
 367             Cache.getDefaultColour(GAP_COLOUR,
 368                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 369     hiddenColour.setBackground(
 370             Cache.getDefaultColour(HIDDEN_COLOUR,
 371                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 372     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 373     gapLabel.setEnabled(!useLegacyGap.isSelected());
 374     gapColour.setEnabled(!useLegacyGap.isSelected());
 375     showHiddenAtStart
 376             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 377
 378     /*
 379      * Set Structure tab defaults
 380      */
 381     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 382     structFromPdb.setSelected(structSelected);
 383     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 384     useRnaView.setEnabled(structSelected);
 385     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 386     addSecondaryStructure.setEnabled(structSelected);
 387     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 388     addTempFactor.setEnabled(structSelected);
 389
 390     /*
 391      * set choice of structure viewer, and path if saved as a preference;
 392      * default to Jmol (first choice) if an unexpected value is found
 393      */
 394     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 395     structViewer.setSelectedItem(viewerType);
 396     String viewerPath = "";
 397     ViewerType type = null;
 398     try
 399     {
 400       type = ViewerType.valueOf(viewerType);
 401       switch (type)
 402       {
 403       case JMOL:
 404         break;
 405       case CHIMERA:
 406         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 407         break;
 408       case CHIMERAX:
 409         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 410         break;
 411       case PYMOL:
 412         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 413         break;
 414       }
 415     } catch (IllegalArgumentException e)
 416     {
 417       Cache.log.error("Unknown structure viewer type: " + viewerType
 418               + ", defaulting to Jmol");
 419       type = ViewerType.JMOL;
 420     }
 421     structureViewerPath.setText(viewerPath);
 422
 423     structureViewerPath.addActionListener(new ActionListener()
 424     {
 425       @Override
 426       public void actionPerformed(ActionEvent e)
 427       {
 428         if (validateViewerPath())
 429         {
 430           Cache.setProperty(structViewer.getSelectedItem()
 431                   .equals(ViewerType.CHIMERAX.name())
 432                   ? CHIMERAX_PATH
 433                   : CHIMERA_PATH, structureViewerPath.getText());
 434         }
 435       }
 436     });
 437
 438     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 439     {
 440       siftsMapping.setSelected(true);
 441     }
 442     else
 443     {
 444       nwMapping.setSelected(true);
 445     }
 446
 447     SiftsSettings
 448             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 449
 450     /*
 451      * Set Connections tab defaults
 452      */
 453
 454     // set up sorting
 455     linkUrlTable.setModel(dataModel);
 456     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 457             linkUrlTable.getModel());
 458     linkUrlTable.setRowSorter(sorter);
 459     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 460
 461     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 462     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 463             SortOrder.DESCENDING));
 464     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 465             SortOrder.DESCENDING));
 466     sortKeys.add(
 467             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 468
 469     sorter.setSortKeys(sortKeys);
 470     // BH 2018 setSortKeys will do the sort
 471     // sorter.sort();
 472
 473     // set up filtering
 474     ActionListener onReset;
 475     onReset = new ActionListener()
 476     {
 477       @Override
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         filterTB.setText("");
 481         sorter.setRowFilter(RowFilter.regexFilter(""));
 482       }
 483
 484     };
 485     doReset.addActionListener(onReset);
 486
 487     // filter to display only custom urls
 488     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 489     {
 490       @Override
 491       public boolean include(
 492               Entry<? extends TableModel, ? extends Object> entry)
 493       {
 494         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 495       }
 496     };
 497
 498     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 499             linkUrlTable.getModel());
 500     customSorter.setRowFilter(customUrlFilter);
 501
 502     ActionListener onCustomOnly;
 503     onCustomOnly = new ActionListener()
 504     {
 505       @Override
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         filterTB.setText("");
 509         sorter.setRowFilter(customUrlFilter);
 510       }
 511     };
 512     userOnly.addActionListener(onCustomOnly);
 513
 514     filterTB.getDocument().addDocumentListener(new DocumentListener()
 515     {
 516       String caseInsensitiveFlag = "(?i)";
 517
 518       @Override
 519       public void changedUpdate(DocumentEvent e)
 520       {
 521         sorter.setRowFilter(RowFilter
 522                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 523       }
 524
 525       @Override
 526       public void removeUpdate(DocumentEvent e)
 527       {
 528         sorter.setRowFilter(RowFilter
 529                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 530       }
 531
 532       @Override
 533       public void insertUpdate(DocumentEvent e)
 534       {
 535         sorter.setRowFilter(RowFilter
 536                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 537       }
 538     });
 539
 540     // set up list selection functionality
 541     linkUrlTable.getSelectionModel()
 542             .addListSelectionListener(new UrlListSelectionHandler());
 543
 544     // set up radio buttons
 545     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 546             .getPrimaryColumn();
 547     String onClickName = linkUrlTable.getColumnName(onClickCol);
 548     linkUrlTable.getColumn(onClickName)
 549             .setCellRenderer(new RadioButtonRenderer());
 550     linkUrlTable.getColumn(onClickName)
 551             .setCellEditor(new RadioButtonEditor());
 552
 553     // get boolean columns and resize those to min possible
 554     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 555     {
 556       if (linkUrlTable.getModel().getColumnClass(column)
 557               .equals(Boolean.class))
 558       {
 559         TableColumn tableColumn = linkUrlTable.getColumnModel()
 560                 .getColumn(column);
 561         int preferredWidth = tableColumn.getMinWidth();
 562
 563         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 564                 column);
 565         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 566         int cwidth = c.getPreferredSize().width
 567                 + linkUrlTable.getIntercellSpacing().width;
 568         preferredWidth = Math.max(preferredWidth, cwidth);
 569
 570         tableColumn.setPreferredWidth(preferredWidth);
 571       }
 572     }
 573
 574     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 575     previousProxyType = proxyTypeString;
 576     switch (proxyTypeString)
 577     {
 578     case Cache.PROXYTYPE_NONE:
 579       proxyType.setSelected(noProxy.getModel(), true);
 580       break;
 581     case Cache.PROXYTYPE_SYSTEM:
 582       proxyType.setSelected(systemProxy.getModel(), true);
 583       break;
 584     case Cache.PROXYTYPE_CUSTOM:
 585       proxyType.setSelected(customProxy.getModel(), true);
 586       break;
 587     default:
 588       Cache.log.warn(
 589               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 590                       + proxyTypeString);
 591     }
 592     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 593     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 594     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 595     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 596     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 597     proxyAuthUsernameTB
 598             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 599     // we are not storing or retrieving proxy password from .jalview_properties
 600     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 601             : new String(Cache.proxyAuthPassword));
 602     setCustomProxyEnabled();
 603
 604     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 605
 606     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 607     // note antisense here: default is true
 608     questionnaire
 609             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 610     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 611
 612     /*
 613      * Set Output tab defaults
 614      */
 615     setupOutputCombo(epsRendering, "EPS_RENDERING");
 616     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 617     setupOutputCombo(svgRendering, "SVG_RENDERING");
 618     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 619     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 620     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 621     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 622     userIdWidth.setText(wi == null ? "" : wi.toString());
 623     // TODO: refactor to use common enum via FormatAdapter and allow extension
 624     // for new flat file formats
 625     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 626     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 627     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 628     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 629     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 630     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 631     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 632     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 633     embbedBioJSON
 634             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 635
 636     /*
 637      * Set Editing tab defaults
 638      */
 639     autoCalculateConsCheck
 640             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 641     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 642     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 643
 644     annotations_actionPerformed(null); // update the display of the annotation
 645                                        // settings
 646
 647
 648     /*
 649      * Set Backups tab defaults
 650      */
 651     loadLastSavedBackupsOptions();
 652   }
 653
 654   /**
 655    * A helper method that sets the items and initial selection in a character
 656    * rendering option list (Prompt each time/Lineart/Text)
 657    *
 658    * @param comboBox
 659    * @param propertyKey
 660    */
 661   protected void setupOutputCombo(JComboBox<Object> comboBox,
 662           String propertyKey)
 663   {
 664     comboBox.addItem(promptEachTimeOpt);
 665     comboBox.addItem(lineArtOpt);
 666     comboBox.addItem(textOpt);
 667
 668     /*
 669      * JalviewJS doesn't support Lineart so force it to Text
 670      */
 671     String defaultOption = Platform.isJS() ? "Text"
 672             : Cache.getDefault(propertyKey, "Prompt each time");
 673     if (defaultOption.equalsIgnoreCase("Text"))
 674     {
 675       comboBox.setSelectedItem(textOpt);
 676     }
 677     else if (defaultOption.equalsIgnoreCase("Lineart"))
 678     {
 679       comboBox.setSelectedItem(lineArtOpt);
 680     }
 681     else
 682     {
 683       comboBox.setSelectedItem(promptEachTimeOpt);
 684     }
 685   }
 686
 687   /**
 688    * Save user selections on the Preferences tabs to the Cache and write out to
 689    * file.
 690    *
 691    * @param e
 692    */
 693   @Override
 694   public void ok_actionPerformed(ActionEvent e)
 695   {
 696     if (!validateSettings())
 697     {
 698       return;
 699     }
 700
 701     /*
 702      * Set proxy settings first (to be before web services refresh)
 703      */
 704     saveProxySettings();
 705
 706     /*
 707      * Save Visual settings
 708      */
 709     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 710             Boolean.toString(seqLimit.isSelected()));
 711     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 712             Boolean.toString(rightAlign.isSelected()));
 713     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 714             Boolean.toString(fullScreen.isSelected()));
 715     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 716             Boolean.toString(openoverv.isSelected()));
 717     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 718             Boolean.toString(annotations.isSelected()));
 719     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 720             Boolean.toString(conservation.isSelected()));
 721     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 722             Boolean.toString(quality.isSelected()));
 723     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 724             Boolean.toString(identity.isSelected()));
 725
 726     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 727             gapSymbolCB.getSelectedItem().toString());
 728
 729     Cache.applicationProperties.setProperty("FONT_NAME",
 730             fontNameCB.getSelectedItem().toString());
 731     Cache.applicationProperties.setProperty("FONT_STYLE",
 732             fontStyleCB.getSelectedItem().toString());
 733     Cache.applicationProperties.setProperty("FONT_SIZE",
 734             fontSizeCB.getSelectedItem().toString());
 735
 736     Cache.applicationProperties.setProperty("ID_ITALICS",
 737             Boolean.toString(idItalics.isSelected()));
 738     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 739             Boolean.toString(showUnconserved.isSelected()));
 740     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 741             Boolean.toString(showOccupancy.isSelected()));
 742     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 743             Boolean.toString(showGroupConsensus.isSelected()));
 744     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 745             Boolean.toString(showGroupConservation.isSelected()));
 746     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 747             Boolean.toString(showConsensHistogram.isSelected()));
 748     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 749             Boolean.toString(showConsensLogo.isSelected()));
 750     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 751             Boolean.toString(smoothFont.isSelected()));
 752     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 753             Boolean.toString(scaleProteinToCdna.isSelected()));
 754     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 755             Boolean.toString(showNpTooltip.isSelected()));
 756     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 757             Boolean.toString(showDbRefTooltip.isSelected()));
 758
 759     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 760             Boolean.toString(wrap.isSelected()));
 761
 762     Cache.applicationProperties.setProperty("STARTUP_FILE",
 763             startupFileTextfield.getText());
 764     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 765             Boolean.toString(startupCheckbox.isSelected()));
 766
 767     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 768             sortby.getSelectedItem().toString());
 769
 770     // convert description of sort order to enum name for save
 771     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 772             .forDescription(sortAnnBy.getSelectedItem().toString());
 773     if (annSortOrder != null)
 774     {
 775       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 776               annSortOrder.name());
 777     }
 778
 779     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 780     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 781             Boolean.valueOf(showAutocalcFirst).toString());
 782
 783     /*
 784      * Save Colours settings
 785      */
 786     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 787             protColour.getSelectedItem().toString());
 788     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 789             nucColour.getSelectedItem().toString());
 790     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 791             minColour.getBackground());
 792     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 793             maxColour.getBackground());
 794
 795     /*
 796      * Save Overview settings
 797      */
 798     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 799     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 800     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 801             Boolean.toString(useLegacyGap.isSelected()));
 802     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 803             Boolean.toString(showHiddenAtStart.isSelected()));
 804
 805     /*
 806      * Save Structure settings
 807      */
 808     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 809             Boolean.toString(addTempFactor.isSelected()));
 810     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 811             Boolean.toString(addSecondaryStructure.isSelected()));
 812     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 813             Boolean.toString(useRnaView.isSelected()));
 814     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 815             Boolean.toString(structFromPdb.isSelected()));
 816     String viewer = structViewer.getSelectedItem().toString();
 817     String viewerPath = structureViewerPath.getText();
 818     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 819             viewer);
 820     if (viewer.equals(ViewerType.CHIMERA.name()))
 821     {
 822       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 823     }
 824     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 825     {
 826       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 827     }
 828     else if (viewer.equals(ViewerType.PYMOL.name()))
 829     {
 830       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 831     }
 832     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 833             Boolean.toString(siftsMapping.isSelected()));
 834     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 835
 836     /*
 837      * Save Output settings
 838      */
 839     Cache.applicationProperties.setProperty("EPS_RENDERING",
 840             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 841     Cache.applicationProperties.setProperty("HTML_RENDERING",
 842             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 843     Cache.applicationProperties.setProperty("SVG_RENDERING",
 844             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 845
 846     /*
 847      * Save Connections settings
 848      */
 849     // Proxy settings set first (to catch web services)
 850
 851     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 852
 853     jalview.util.BrowserLauncher.resetBrowser();
 854
 855     // save user-defined and selected links
 856     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 857     if (menuLinks.isEmpty())
 858     {
 859       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 860     }
 861     else
 862     {
 863       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 864               menuLinks.toString());
 865     }
 866
 867     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 868     if (nonMenuLinks.isEmpty())
 869     {
 870       Cache.applicationProperties.remove("STORED_LINKS");
 871     }
 872     else
 873     {
 874       Cache.applicationProperties.setProperty("STORED_LINKS",
 875               nonMenuLinks.toString());
 876     }
 877
 878     Cache.applicationProperties.setProperty("DEFAULT_URL",
 879             sequenceUrlLinks.getPrimaryUrlId());
 880
 881     Cache.setProperty("VERSION_CHECK",
 882             Boolean.toString(versioncheck.isSelected()));
 883     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 884     {
 885       // default is false - we only set this if the user has actively agreed
 886       Cache.setProperty("USAGESTATS",
 887               Boolean.toString(usagestats.isSelected()));
 888     }
 889     if (!questionnaire.isSelected())
 890     {
 891       Cache.setProperty("NOQUESTIONNAIRES", "true");
 892     }
 893     else
 894     {
 895       // special - made easy to edit a property file to disable questionnaires
 896       // by just adding the given line
 897       Cache.removeProperty("NOQUESTIONNAIRES");
 898     }
 899
 900     /*
 901      * Save Output settings
 902      */
 903     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 904             Boolean.toString(blcjv.isSelected()));
 905     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 906             Boolean.toString(clustaljv.isSelected()));
 907     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 908             Boolean.toString(fastajv.isSelected()));
 909     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 910             Boolean.toString(msfjv.isSelected()));
 911     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 912             Boolean.toString(pfamjv.isSelected()));
 913     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 914             Boolean.toString(pileupjv.isSelected()));
 915     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 916             Boolean.toString(pirjv.isSelected()));
 917     Cache.applicationProperties.setProperty("PIR_MODELLER",
 918             Boolean.toString(modellerOutput.isSelected()));
 919     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 920             Boolean.toString(embbedBioJSON.isSelected()));
 921     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 922
 923     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 924             Boolean.toString(autoIdWidth.isSelected()));
 925     userIdWidth_actionPerformed();
 926     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 927             userIdWidth.getText());
 928
 929     /*
 930      * Save Editing settings
 931      */
 932     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 933             Boolean.toString(autoCalculateConsCheck.isSelected()));
 934     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 935             Boolean.toString(sortByTree.isSelected()));
 936     Cache.applicationProperties.setProperty("PAD_GAPS",
 937             Boolean.toString(padGaps.isSelected()));
 938
 939     if (!Platform.isJS())
 940     {
 941       wsPrefs.updateAndRefreshWsMenuConfig(false);
 942     }
 943
 944     /*
 945      * Save Backups settings
 946      */
 947     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 948             Boolean.toString(enableBackupFiles.isSelected()));
 949     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 950     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 951
 952     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 953     {
 954       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 955       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 956               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 957       Cache.applicationProperties
 958               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 959                       customBFPE.toString());
 960     }
 961
 962     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 963             .get(preset);
 964     Cache.applicationProperties.setProperty(
 965             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 966
 967     Cache.saveProperties();
 968     Desktop.instance.doConfigureStructurePrefs();
 969     try
 970     {
 971       frame.setClosed(true);
 972     } catch (Exception ex)
 973     {
 974     }
 975   }
 976
 977   public void saveProxySettings()
 978   {
 979     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 980             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 981                     : Cache.PROXYTYPE_SYSTEM;
 982     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
 983     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 984     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 985     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 986     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 987     Cache.setOrRemove("PROXY_AUTH",
 988             Boolean.toString(proxyAuth.isSelected()));
 989     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
 990     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
 991     Cache.setProxyPropertiesFromPreferences(previousProxyType);
 992     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
 993             || !newProxyType.equals(previousProxyType))
 994     {
 995       // force a re-lookup of ws if proxytype is custom or has changed
 996       wsPrefs.update++;
 997     }
 998     previousProxyType = newProxyType;
 999   }
1000
1001   /**
1002    * Do any necessary validation before saving settings. Return focus to the
1003    * first tab which fails validation.
1004    *
1005    * @return
1006    */
1007   private boolean validateSettings()
1008   {
1009     if (!validateStructure())
1010     {
1011       structureTab.requestFocusInWindow();
1012       return false;
1013     }
1014     return true;
1015   }
1016
1017   @Override
1018   protected boolean validateStructure()
1019   {
1020     return validateViewerPath();
1021
1022   }
1023
1024   /**
1025    * DOCUMENT ME!
1026    */
1027   @Override
1028   public void startupFileTextfield_mouseClicked()
1029   {
1030     // TODO: JAL-3048 not needed for Jalview-JS
1031     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1032     JalviewFileChooser chooser = JalviewFileChooser
1033             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1034     chooser.setFileView(new JalviewFileView());
1035     chooser.setDialogTitle(
1036             MessageManager.getString("label.select_startup_file"));
1037
1038     int value = chooser.showOpenDialog(this);
1039
1040     if (value == JalviewFileChooser.APPROVE_OPTION)
1041     {
1042       FileFormatI format = chooser.getSelectedFormat();
1043       if (format != null)
1044       {
1045         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1046                 format.getName());
1047       }
1048       startupFileTextfield
1049               .setText(chooser.getSelectedFile().getAbsolutePath());
1050     }
1051   }
1052
1053   /**
1054    * DOCUMENT ME!
1055    *
1056    * @param e
1057    *          DOCUMENT ME!
1058    */
1059   @Override
1060   public void cancel_actionPerformed(ActionEvent e)
1061   {
1062     try
1063     {
1064       if (!Platform.isJS())
1065       {
1066         wsPrefs.updateWsMenuConfig(true);
1067         wsPrefs.refreshWs_actionPerformed(e);
1068       }
1069       frame.setClosed(true);
1070     } catch (Exception ex)
1071     {
1072     }
1073   }
1074
1075   /**
1076    * DOCUMENT ME!
1077    *
1078    * @param e
1079    *          DOCUMENT ME!
1080    */
1081   @Override
1082   public void annotations_actionPerformed(ActionEvent e)
1083   {
1084     conservation.setEnabled(annotations.isSelected());
1085     quality.setEnabled(annotations.isSelected());
1086     identity.setEnabled(annotations.isSelected());
1087     showOccupancy.setEnabled(annotations.isSelected());
1088     showGroupConsensus.setEnabled(annotations.isSelected());
1089     showGroupConservation.setEnabled(annotations.isSelected());
1090     showConsensHistogram.setEnabled(annotations.isSelected()
1091             && (identity.isSelected() || showGroupConsensus.isSelected()));
1092     showConsensLogo.setEnabled(annotations.isSelected()
1093             && (identity.isSelected() || showGroupConsensus.isSelected()));
1094   }
1095
1096   @Override
1097   public void newLink_actionPerformed(ActionEvent e)
1098   {
1099     GSequenceLink link = new GSequenceLink();
1100     boolean valid = false;
1101     while (!valid)
1102     {
1103       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1104               MessageManager.getString("label.new_sequence_url_link"),
1105               JvOptionPane.OK_CANCEL_OPTION, -1,
1106               null) == JvOptionPane.OK_OPTION)
1107       {
1108         if (link.checkValid())
1109         {
1110           if (((UrlLinkTableModel) linkUrlTable.getModel())
1111                   .isUniqueName(link.getName()))
1112           {
1113             ((UrlLinkTableModel) linkUrlTable.getModel())
1114                     .insertRow(link.getName(), link.getURL());
1115             valid = true;
1116           }
1117           else
1118           {
1119             link.notifyDuplicate();
1120             continue;
1121           }
1122         }
1123       }
1124       else
1125       {
1126         break;
1127       }
1128     }
1129   }
1130
1131   @Override
1132   public void editLink_actionPerformed(ActionEvent e)
1133   {
1134     GSequenceLink link = new GSequenceLink();
1135
1136     int index = linkUrlTable.getSelectedRow();
1137     if (index == -1)
1138     {
1139       // button no longer enabled if row is not selected
1140       Cache.log.debug("Edit with no row selected in linkUrlTable");
1141       return;
1142     }
1143
1144     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1145             .getNameColumn();
1146     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1147             .getUrlColumn();
1148     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1149     link.setName(oldName);
1150     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1151
1152     boolean valid = false;
1153     while (!valid)
1154     {
1155       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1156               MessageManager.getString("label.edit_sequence_url_link"),
1157               JvOptionPane.OK_CANCEL_OPTION, -1,
1158               null) == JvOptionPane.OK_OPTION)
1159       {
1160         if (link.checkValid())
1161         {
1162           if ((oldName.equals(link.getName()))
1163                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1164                           .isUniqueName(link.getName())))
1165           {
1166             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1167             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1168             valid = true;
1169           }
1170           else
1171           {
1172             link.notifyDuplicate();
1173             continue;
1174           }
1175         }
1176       }
1177       else
1178       {
1179         break;
1180       }
1181     }
1182   }
1183
1184   @Override
1185   public void deleteLink_actionPerformed(ActionEvent e)
1186   {
1187     int index = linkUrlTable.getSelectedRow();
1188     int modelIndex = -1;
1189     if (index == -1)
1190     {
1191       // button no longer enabled if row is not selected
1192       Cache.log.debug("Delete with no row selected in linkUrlTable");
1193       return;
1194     }
1195     else
1196     {
1197       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1198     }
1199
1200     // make sure we use the model index to delete, and not the table index
1201     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1202   }
1203
1204   @Override
1205   public void defaultBrowser_mouseClicked(MouseEvent e)
1206   {
1207     // TODO: JAL-3048 not needed for j2s
1208     if (!Platform.isJS()) // BH 2019
1209     /**
1210      * Java only
1211      *
1212      * @j2sIgnore
1213      */
1214     {
1215       JFileChooser chooser = new JFileChooser(".");
1216       chooser.setDialogTitle(
1217               MessageManager.getString("label.select_default_browser"));
1218
1219       int value = chooser.showOpenDialog(this);
1220
1221       if (value == JFileChooser.APPROVE_OPTION)
1222       {
1223         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1224       }
1225     }
1226   }
1227
1228   /*
1229    * (non-Javadoc)
1230    *
1231    * @see
1232    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1233    * .ActionEvent)
1234    */
1235   @Override
1236   protected void showunconserved_actionPerformed(ActionEvent e)
1237   {
1238     // TODO Auto-generated method stub
1239     super.showunconserved_actionPerformed(e);
1240   }
1241
1242   public static List<String> getGroupURLLinks()
1243   {
1244     return groupURLLinks;
1245   }
1246
1247   @Override
1248   public void minColour_actionPerformed(JPanel panel)
1249   {
1250     JalviewColourChooser.showColourChooser(this,
1251             MessageManager.getString("label.select_colour_minimum_value"),
1252             panel);
1253   }
1254
1255   @Override
1256   public void maxColour_actionPerformed(JPanel panel)
1257   {
1258     JalviewColourChooser.showColourChooser(this,
1259             MessageManager.getString("label.select_colour_maximum_value"),
1260             panel);
1261   }
1262
1263   @Override
1264   public void gapColour_actionPerformed(JPanel gap)
1265   {
1266     if (!useLegacyGap.isSelected())
1267     {
1268       JalviewColourChooser.showColourChooser(this,
1269               MessageManager.getString("label.select_gap_colour"),
1270               gap);
1271     }
1272   }
1273
1274   @Override
1275   public void hiddenColour_actionPerformed(JPanel hidden)
1276   {
1277     JalviewColourChooser.showColourChooser(this,
1278             MessageManager.getString("label.select_hidden_colour"),
1279             hidden);
1280   }
1281
1282   @Override
1283   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1284   {
1285     boolean enabled = useLegacyGap.isSelected();
1286     if (enabled)
1287     {
1288       gapColour.setBackground(
1289               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1290     }
1291     else
1292     {
1293       gapColour.setBackground(
1294               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1295     }
1296     gapColour.setEnabled(!enabled);
1297     gapLabel.setEnabled(!enabled);
1298   }
1299
1300   @Override
1301   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1302   {
1303     useLegacyGap.setSelected(false);
1304     useLegacyGaps_actionPerformed(null);
1305     showHiddenAtStart.setSelected(false);
1306     hiddenColour.setBackground(
1307             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1308   }
1309
1310   @Override
1311   protected void userIdWidth_actionPerformed()
1312   {
1313     try
1314     {
1315       String val = userIdWidth.getText().trim();
1316       if (val.length() > 0)
1317       {
1318         Integer iw = Integer.parseInt(val);
1319         if (iw.intValue() < 12)
1320         {
1321           throw new NumberFormatException();
1322         }
1323         userIdWidth.setText(iw.toString());
1324       }
1325     } catch (NumberFormatException x)
1326     {
1327       userIdWidth.setText("");
1328       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1329               MessageManager
1330                       .getString("warn.user_defined_width_requirements"),
1331               MessageManager.getString("label.invalid_id_column_width"),
1332               JvOptionPane.WARNING_MESSAGE);
1333     }
1334   }
1335
1336   @Override
1337   protected void autoIdWidth_actionPerformed()
1338   {
1339     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1340     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1341   }
1342
1343   /**
1344    * Returns true if structure viewer path is to a valid executable, else shows
1345    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1346    * (built in to Jalview) or when Jalview is left to try default paths.
1347    */
1348   private boolean validateViewerPath()
1349   {
1350     if (structureViewerPath.getText().trim().length() > 0)
1351     {
1352       File f = new File(structureViewerPath.getText());
1353       if (!f.canExecute())
1354       {
1355         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1356                 MessageManager.getString("label.invalid_viewer_path"),
1357                 MessageManager.getString("label.invalid_viewer_path"),
1358                 JvOptionPane.ERROR_MESSAGE);
1359         return false;
1360       }
1361     }
1362     return true;
1363   }
1364
1365   /**
1366    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1367    * default or user-specified path, if not show a warning/help dialog
1368    */
1369   @Override
1370   protected void structureViewer_actionPerformed(String selectedItem)
1371   {
1372     if (selectedItem.equals(ViewerType.JMOL.name()))
1373     {
1374       structureViewerPath.setEnabled(false);
1375       structureViewerPathLabel.setEnabled(false);
1376       return;
1377     }
1378     boolean found = false;
1379     structureViewerPath.setEnabled(true);
1380     structureViewerPathLabel.setEnabled(true);
1381     structureViewerPathLabel.setText(MessageManager
1382             .formatMessage("label.viewer_path", selectedItem));
1383
1384     /*
1385      * Try user-specified and standard paths for structure viewer executable
1386      */
1387     String viewerPath = "";
1388     List<String> paths = null;
1389     try
1390     {
1391       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1392       switch (viewerType)
1393       {
1394       case JMOL:
1395         // dealt with above
1396         break;
1397       case CHIMERA:
1398         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1399         paths = StructureManager.getChimeraPaths(false);
1400         break;
1401       case CHIMERAX:
1402         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1403         paths = StructureManager.getChimeraPaths(true);
1404         break;
1405       case PYMOL:
1406         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1407         paths = PymolManager.getPymolPaths();
1408         break;
1409       }
1410     } catch (IllegalArgumentException e)
1411     {
1412       // only valid entries should be in the drop-down
1413     }
1414     structureViewerPath.setText(viewerPath);
1415
1416     paths.add(0, structureViewerPath.getText());
1417     for (String path : paths)
1418     {
1419       if (new File(path.trim()).canExecute())
1420       {
1421         found = true;
1422         break;
1423       }
1424     }
1425
1426     if (!found)
1427     {
1428       String[] options = { "OK", "Help" };
1429       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1430               JvSwingUtils.wrapTooltip(true,
1431                       MessageManager.getString("label.viewer_missing")),
1432               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1433               null, options, options[0]);
1434       if (showHelp == JvOptionPane.NO_OPTION)
1435       {
1436         try
1437         {
1438           Help.showHelpWindow(HelpId.StructureViewer);
1439         } catch (HelpSetException e)
1440         {
1441           e.printStackTrace();
1442         }
1443       }
1444     }
1445   }
1446
1447   public class OptionsParam
1448   {
1449     private String name;
1450
1451     private String code;
1452
1453     public OptionsParam(String name, String code)
1454     {
1455       this.name = name;
1456       this.code = code;
1457     }
1458
1459     public String getName()
1460     {
1461       return name;
1462     }
1463
1464     public void setName(String name)
1465     {
1466       this.name = name;
1467     }
1468
1469     public String getCode()
1470     {
1471       return code;
1472     }
1473
1474     public void setCode(String code)
1475     {
1476       this.code = code;
1477     }
1478
1479     @Override
1480     public String toString()
1481     {
1482       return name;
1483     }
1484
1485     @Override
1486     public boolean equals(Object that)
1487     {
1488       if (!(that instanceof OptionsParam))
1489       {
1490         return false;
1491       }
1492       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1493     }
1494
1495     @Override
1496     public int hashCode()
1497     {
1498       return name.hashCode() + code.hashCode();
1499     }
1500   }
1501
1502   private class UrlListSelectionHandler implements ListSelectionListener
1503   {
1504
1505     @Override
1506     public void valueChanged(ListSelectionEvent e)
1507     {
1508       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1509
1510       int index = lsm.getMinSelectionIndex();
1511       if (index == -1)
1512       {
1513         // no selection, so disable delete/edit buttons
1514         editLink.setEnabled(false);
1515         deleteLink.setEnabled(false);
1516         return;
1517       }
1518       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1519
1520       // enable/disable edit and delete link buttons
1521       if (((UrlLinkTableModel) linkUrlTable.getModel())
1522               .isRowDeletable(modelIndex))
1523       {
1524         deleteLink.setEnabled(true);
1525       }
1526       else
1527       {
1528         deleteLink.setEnabled(false);
1529       }
1530
1531       if (((UrlLinkTableModel) linkUrlTable.getModel())
1532               .isRowEditable(modelIndex))
1533       {
1534         editLink.setEnabled(true);
1535       }
1536       else
1537       {
1538         editLink.setEnabled(false);
1539       }
1540     }
1541   }
1542 }