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