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