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