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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  28 import jalview.io.BackupFilesPresetEntry;
  29 import jalview.io.FileFormatI;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32 import jalview.jbgui.GPreferences;
  33 import jalview.jbgui.GSequenceLink;
  34 import jalview.schemes.ColourSchemeI;
  35 import jalview.schemes.ColourSchemes;
  36 import jalview.schemes.ResidueColourScheme;
  37 import jalview.urls.UrlLinkTableModel;
  38 import jalview.urls.api.UrlProviderFactoryI;
  39 import jalview.urls.api.UrlProviderI;
  40 import jalview.urls.desktop.DesktopUrlProviderFactory;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JComboBox;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86
  87   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  88
  89   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  90
  91   public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
  92
  93   public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
  94
  95   public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
  96
  97   public static final String ANTI_ALIAS = "ANTI_ALIAS";
  98
  99   public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
 100
 101   public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
 102
 103   public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
 104
 105   public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
 106
 107   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 108
 109   public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
 110
 111   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 112
 113   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 114
 115   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 116
 117   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 118
 119   public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
 120
 121   public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
 122
 123   public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
 124
 125   public static final String FONT_NAME = "FONT_NAME";
 126
 127   public static final String FONT_SIZE = "FONT_SIZE";
 128
 129   public static final String FONT_STYLE = "FONT_STYLE";
 130
 131   public static final String GAP_COLOUR = "GAP_COLOUR";
 132
 133   public static final String GAP_SYMBOL = "GAP_SYMBOL";
 134
 135   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 136
 137   public static final String HIDE_INTRONS = "HIDE_INTRONS";
 138
 139   public static final String ID_ITALICS = "ID_ITALICS";
 140
 141   public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
 142
 143   public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
 144
 145   public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
 146
 147   public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
 148
 149   public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
 150
 151   public static final String PAD_GAPS = "PAD_GAPS";
 152
 153   public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
 154
 155   public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
 156
 157   public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
 158
 159   public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
 160
 161   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 162
 163   public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
 164
 165   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 166
 167   public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
 168
 169   public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
 170
 171   public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
 172
 173   public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
 174
 175   public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
 176
 177   public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
 178
 179   public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
 180
 181   public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
 182
 183   public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
 184
 185   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 186
 187   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 188
 189   public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
 190
 191   public static final String SHOW_QUALITY = "SHOW_QUALITY";
 192
 193   public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
 194
 195   public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
 196
 197   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 198
 199   public static final String SORT_BY_TREE = "SORT_BY_TREE";
 200
 201   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 202
 203   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 204
 205   public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
 206
 207   public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
 208
 209   public static final String USE_FULL_SO = "USE_FULL_SO";
 210
 211   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 212
 213   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 214
 215   public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
 216
 217   public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
 218
 219
 220   private static final int MIN_FONT_SIZE = 1;
 221
 222   private static final int MAX_FONT_SIZE = 30;
 223
 224   /**
 225    * Holds name and link separated with | character. Sequence ID must be
 226    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 227    */
 228   public static UrlProviderI sequenceUrlLinks;
 229
 230   public static UrlLinkTableModel dataModel;
 231
 232   /**
 233    * Holds name and link separated with | character. Sequence IDS and Sequences
 234    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 235    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 236    * for first and second token specified after a pipe character at end |,|.
 237    * (TODO: proper escape for using | to separate ids or sequences
 238    */
 239
 240   public static List<String> groupURLLinks;
 241   static
 242   {
 243     // get links selected to be in the menu (SEQUENCE_LINKS)
 244     // and links entered by the user but not selected (STORED_LINKS)
 245     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 246     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 247     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 248             UrlConstants.DEFAULT_LABEL);
 249
 250     // if both links lists are empty, add the DEFAULT_URL link
 251     // otherwise we assume the default link is in one of the lists
 252     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 253     {
 254       inMenuString = UrlConstants.DEFAULT_STRING;
 255     }
 256     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 257             inMenuString, notInMenuString);
 258     sequenceUrlLinks = factory.createUrlProvider();
 259     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 260
 261     /**
 262      * TODO: reformulate groupURL encoding so two or more can be stored in the
 263      * .properties file as '|' separated strings
 264      */
 265
 266     groupURLLinks = new ArrayList<>();
 267   }
 268
 269   JInternalFrame frame;
 270
 271   private WsPreferences wsPrefs;
 272
 273   private OptionsParam promptEachTimeOpt = new OptionsParam(
 274           MessageManager.getString("label.prompt_each_time"),
 275           "Prompt each time");
 276
 277   private OptionsParam lineArtOpt = new OptionsParam(
 278           MessageManager.getString("label.lineart"), "Lineart");
 279
 280   private OptionsParam textOpt = new OptionsParam(
 281           MessageManager.getString("action.text"), "Text");
 282
 283   /**
 284    * Creates a new Preferences object.
 285    */
 286   public Preferences()
 287   {
 288     super();
 289     frame = new JInternalFrame();
 290     frame.setContentPane(this);
 291     if (!Platform.isJS())
 292     /**
 293      * Java only
 294      *
 295      * @j2sIgnore
 296      */
 297     {
 298       wsPrefs = new WsPreferences();
 299       wsTab.add(wsPrefs, BorderLayout.CENTER);
 300     }
 301     int width = 500, height = 450;
 302     if (Platform.isAMacAndNotJS())
 303     {
 304       width = 570;
 305       height = 480;
 306     }
 307
 308     Desktop.addInternalFrame(frame,
 309             MessageManager.getString("label.preferences"), width, height);
 310     frame.setMinimumSize(new Dimension(width, height));
 311
 312     /*
 313      * Set Visual tab defaults
 314      */
 315     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 316     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 317     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 318     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 319
 320     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 321     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 322     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 323     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 324     showUnconserved
 325             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 326     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 327     showGroupConsensus
 328             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 329     showGroupConservation.setSelected(
 330             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 331     showConsensHistogram.setSelected(
 332             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 333     showConsensLogo
 334             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 335     showNpTooltip
 336             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 337     showDbRefTooltip
 338             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 339
 340     String[] fonts = java.awt.GraphicsEnvironment
 341             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 342     for (int i = 0; i < fonts.length; i++)
 343     {
 344       fontNameCB.addItem(fonts[i]);
 345     }
 346
 347     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 348     {
 349       fontSizeCB.addItem(i + "");
 350     }
 351
 352     fontStyleCB.addItem("plain");
 353     fontStyleCB.addItem("bold");
 354     fontStyleCB.addItem("italic");
 355
 356     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 357     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 358     fontStyleCB.setSelectedItem(
 359             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 360
 361     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 362     scaleProteinToCdna
 363             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 364
 365     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 366
 367     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 368
 369     gapSymbolCB.addItem("-");
 370     gapSymbolCB.addItem(".");
 371
 372     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 373
 374     sortby.addItem("No sort");
 375     sortby.addItem("Id");
 376     sortby.addItem("Pairwise Identity");
 377     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 378
 379     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 380     sortAnnBy
 381             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 382     sortAnnBy
 383             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 384     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 385             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 386                     SequenceAnnotationOrder.NONE.name()));
 387     sortAnnBy.setSelectedItem(savedSort.toString());
 388
 389     sortAutocalc.addItem("Autocalculated first");
 390     sortAutocalc.addItem("Autocalculated last");
 391     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 392     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 393             : sortAutocalc.getItemAt(1));
 394     startupCheckbox
 395             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 396     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 397             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 398                     + "/examples/exampleFile_2_3.jar"));
 399
 400     /*
 401      * Set Colours tab defaults
 402      */
 403     protColour.addItem(ResidueColourScheme.NONE);
 404     nucColour.addItem(ResidueColourScheme.NONE);
 405     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 406     {
 407       String name = cs.getSchemeName();
 408       protColour.addItem(name);
 409       nucColour.addItem(name);
 410     }
 411     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 412             ResidueColourScheme.NONE);
 413     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 414     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 415     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 416     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 417     minColour.setBackground(
 418             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 419     maxColour.setBackground(
 420             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 421
 422     /*
 423      * Set overview panel defaults
 424      */
 425     gapColour.setBackground(
 426             Cache.getDefaultColour(GAP_COLOUR,
 427                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 428     hiddenColour.setBackground(
 429             Cache.getDefaultColour(HIDDEN_COLOUR,
 430                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 431     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 432     gapLabel.setEnabled(!useLegacyGap.isSelected());
 433     gapColour.setEnabled(!useLegacyGap.isSelected());
 434     showHiddenAtStart
 435             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 436
 437     /*
 438      * Set Structure tab defaults.
 439      */
 440     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 441     structFromPdb.setSelected(structSelected);
 442     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 443     useRnaView.setEnabled(structSelected);
 444     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 445     addSecondaryStructure.setEnabled(structSelected);
 446     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 447     addTempFactor.setEnabled(structSelected);
 448     structViewer.setSelectedItem(
 449             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 450     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 451     chimeraPath.addActionListener(new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         validateChimeraPath();
 457       }
 458     });
 459
 460     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 461     {
 462       siftsMapping.setSelected(true);
 463     }
 464     else
 465     {
 466       nwMapping.setSelected(true);
 467     }
 468
 469     SiftsSettings
 470             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 471
 472     /*
 473      * Set Connections tab defaults
 474      */
 475
 476     // set up sorting
 477     linkUrlTable.setModel(dataModel);
 478     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 479             linkUrlTable.getModel());
 480     linkUrlTable.setRowSorter(sorter);
 481     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 482
 483     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 484     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 485             SortOrder.DESCENDING));
 486     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 487             SortOrder.DESCENDING));
 488     sortKeys.add(
 489             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 490
 491     sorter.setSortKeys(sortKeys);
 492     // BH 2018 setSortKeys will do the sort
 493     // sorter.sort();
 494
 495     // set up filtering
 496     ActionListener onReset;
 497     onReset = new ActionListener()
 498     {
 499       @Override
 500       public void actionPerformed(ActionEvent e)
 501       {
 502         filterTB.setText("");
 503         sorter.setRowFilter(RowFilter.regexFilter(""));
 504       }
 505
 506     };
 507     doReset.addActionListener(onReset);
 508
 509     // filter to display only custom urls
 510     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 511     {
 512       @Override
 513       public boolean include(
 514               Entry<? extends TableModel, ? extends Object> entry)
 515       {
 516         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 517       }
 518     };
 519
 520     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 521             linkUrlTable.getModel());
 522     customSorter.setRowFilter(customUrlFilter);
 523
 524     ActionListener onCustomOnly;
 525     onCustomOnly = new ActionListener()
 526     {
 527       @Override
 528       public void actionPerformed(ActionEvent e)
 529       {
 530         filterTB.setText("");
 531         sorter.setRowFilter(customUrlFilter);
 532       }
 533     };
 534     userOnly.addActionListener(onCustomOnly);
 535
 536     filterTB.getDocument().addDocumentListener(new DocumentListener()
 537     {
 538       String caseInsensitiveFlag = "(?i)";
 539
 540       @Override
 541       public void changedUpdate(DocumentEvent e)
 542       {
 543         sorter.setRowFilter(RowFilter
 544                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 545       }
 546
 547       @Override
 548       public void removeUpdate(DocumentEvent e)
 549       {
 550         sorter.setRowFilter(RowFilter
 551                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 552       }
 553
 554       @Override
 555       public void insertUpdate(DocumentEvent e)
 556       {
 557         sorter.setRowFilter(RowFilter
 558                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 559       }
 560     });
 561
 562     // set up list selection functionality
 563     linkUrlTable.getSelectionModel()
 564             .addListSelectionListener(new UrlListSelectionHandler());
 565
 566     // set up radio buttons
 567     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 568             .getPrimaryColumn();
 569     String onClickName = linkUrlTable.getColumnName(onClickCol);
 570     linkUrlTable.getColumn(onClickName)
 571             .setCellRenderer(new RadioButtonRenderer());
 572     linkUrlTable.getColumn(onClickName)
 573             .setCellEditor(new RadioButtonEditor());
 574
 575     // get boolean columns and resize those to min possible
 576     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 577     {
 578       if (linkUrlTable.getModel().getColumnClass(column)
 579               .equals(Boolean.class))
 580       {
 581         TableColumn tableColumn = linkUrlTable.getColumnModel()
 582                 .getColumn(column);
 583         int preferredWidth = tableColumn.getMinWidth();
 584
 585         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 586                 column);
 587         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 588         int cwidth = c.getPreferredSize().width
 589                 + linkUrlTable.getIntercellSpacing().width;
 590         preferredWidth = Math.max(preferredWidth, cwidth);
 591
 592         tableColumn.setPreferredWidth(preferredWidth);
 593       }
 594     }
 595
 596     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 597     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 598     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 599     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 600
 601     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 602
 603     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 604     // note antisense here: default is true
 605     questionnaire
 606             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 607     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 608
 609     /*
 610      * Set Output tab defaults
 611      */
 612     setupOutputCombo(epsRendering, "EPS_RENDERING");
 613     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 614     setupOutputCombo(svgRendering, "SVG_RENDERING");
 615     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 616     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 617     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 618     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 619     userIdWidth.setText(wi == null ? "" : wi.toString());
 620     // TODO: refactor to use common enum via FormatAdapter and allow extension
 621     // for new flat file formats
 622     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 623     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 624     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 625     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 626     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 627     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 628     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 629     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 630     embbedBioJSON
 631             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 632
 633     /*
 634      * Set Editing tab defaults
 635      */
 636     autoCalculateConsCheck
 637             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 638     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 639     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 640
 641     annotations_actionPerformed(null); // update the display of the annotation
 642                                        // settings
 643
 644
 645     /*
 646      * Set Backups tab defaults
 647      */
 648     loadLastSavedBackupsOptions();
 649   }
 650
 651   /**
 652    * A helper method that sets the items and initial selection in a character
 653    * rendering option list (Prompt each time/Lineart/Text)
 654    *
 655    * @param comboBox
 656    * @param propertyKey
 657    */
 658   protected void setupOutputCombo(JComboBox<Object> comboBox,
 659           String propertyKey)
 660   {
 661     comboBox.addItem(promptEachTimeOpt);
 662     comboBox.addItem(lineArtOpt);
 663     comboBox.addItem(textOpt);
 664
 665     /*
 666      * JalviewJS doesn't support Lineart so force it to Text
 667      */
 668     String defaultOption = Platform.isJS() ? "Text"
 669             : Cache.getDefault(propertyKey, "Prompt each time");
 670     if (defaultOption.equalsIgnoreCase("Text"))
 671     {
 672       comboBox.setSelectedItem(textOpt);
 673     }
 674     else if (defaultOption.equalsIgnoreCase("Lineart"))
 675     {
 676       comboBox.setSelectedItem(lineArtOpt);
 677     }
 678     else
 679     {
 680       comboBox.setSelectedItem(promptEachTimeOpt);
 681     }
 682   }
 683
 684   /**
 685    * Save user selections on the Preferences tabs to the Cache and write out to
 686    * file.
 687    *
 688    * @param e
 689    */
 690   @Override
 691   public void ok_actionPerformed(ActionEvent e)
 692   {
 693     if (!validateSettings())
 694     {
 695       return;
 696     }
 697
 698     /*
 699      * Save Visual settings
 700      */
 701     Cache.setPropertyNoSave("SHOW_JVSUFFIX",
 702             Boolean.toString(seqLimit.isSelected()));
 703     Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
 704             Boolean.toString(rightAlign.isSelected()));
 705     Cache.setPropertyNoSave("SHOW_FULLSCREEN",
 706             Boolean.toString(fullScreen.isSelected()));
 707     Cache.setPropertyNoSave("SHOW_OVERVIEW",
 708             Boolean.toString(openoverv.isSelected()));
 709     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
 710             Boolean.toString(annotations.isSelected()));
 711     Cache.setPropertyNoSave("SHOW_CONSERVATION",
 712             Boolean.toString(conservation.isSelected()));
 713     Cache.setPropertyNoSave("SHOW_QUALITY",
 714             Boolean.toString(quality.isSelected()));
 715     Cache.setPropertyNoSave("SHOW_IDENTITY",
 716             Boolean.toString(identity.isSelected()));
 717
 718     Cache.setPropertyNoSave("GAP_SYMBOL",
 719             gapSymbolCB.getSelectedItem().toString());
 720
 721     Cache.setPropertyNoSave("FONT_NAME",
 722             fontNameCB.getSelectedItem().toString());
 723     Cache.setPropertyNoSave("FONT_STYLE",
 724             fontStyleCB.getSelectedItem().toString());
 725     Cache.setPropertyNoSave("FONT_SIZE",
 726             fontSizeCB.getSelectedItem().toString());
 727
 728     Cache.setPropertyNoSave("ID_ITALICS",
 729             Boolean.toString(idItalics.isSelected()));
 730     Cache.setPropertyNoSave("SHOW_UNCONSERVED",
 731             Boolean.toString(showUnconserved.isSelected()));
 732     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
 733             Boolean.toString(showOccupancy.isSelected()));
 734     Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
 735             Boolean.toString(showGroupConsensus.isSelected()));
 736     Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
 737             Boolean.toString(showGroupConservation.isSelected()));
 738     Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
 739             Boolean.toString(showConsensHistogram.isSelected()));
 740     Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
 741             Boolean.toString(showConsensLogo.isSelected()));
 742     Cache.setPropertyNoSave("ANTI_ALIAS",
 743             Boolean.toString(smoothFont.isSelected()));
 744     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
 745             Boolean.toString(scaleProteinToCdna.isSelected()));
 746     Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
 747             Boolean.toString(showNpTooltip.isSelected()));
 748     Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
 749             Boolean.toString(showDbRefTooltip.isSelected()));
 750
 751     Cache.setPropertyNoSave("WRAP_ALIGNMENT",
 752             Boolean.toString(wrap.isSelected()));
 753
 754     Cache.setPropertyNoSave("STARTUP_FILE",
 755             startupFileTextfield.getText());
 756     Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
 757             Boolean.toString(startupCheckbox.isSelected()));
 758
 759     Cache.setPropertyNoSave("SORT_ALIGNMENT",
 760             sortby.getSelectedItem().toString());
 761
 762     // convert description of sort order to enum name for save
 763     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 764             .forDescription(sortAnnBy.getSelectedItem().toString());
 765     if (annSortOrder != null)
 766     {
 767       Cache.setPropertyNoSave(SORT_ANNOTATIONS,
 768               annSortOrder.name());
 769     }
 770
 771     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 772     Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
 773             Boolean.valueOf(showAutocalcFirst).toString());
 774
 775     /*
 776      * Save Colours settings
 777      */
 778     Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
 779             protColour.getSelectedItem().toString());
 780     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
 781             nucColour.getSelectedItem().toString());
 782     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 783             minColour.getBackground());
 784     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 785             maxColour.getBackground());
 786
 787     /*
 788      * Save Overview settings
 789      */
 790     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 791     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 792     Cache.setPropertyNoSave(USE_LEGACY_GAP,
 793             Boolean.toString(useLegacyGap.isSelected()));
 794     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
 795             Boolean.toString(showHiddenAtStart.isSelected()));
 796
 797     /*
 798      * Save Structure settings
 799      */
 800     Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
 801             Boolean.toString(addTempFactor.isSelected()));
 802     Cache.setPropertyNoSave(ADD_SS_ANN,
 803             Boolean.toString(addSecondaryStructure.isSelected()));
 804     Cache.setPropertyNoSave(USE_RNAVIEW,
 805             Boolean.toString(useRnaView.isSelected()));
 806     Cache.setPropertyNoSave(STRUCT_FROM_PDB,
 807             Boolean.toString(structFromPdb.isSelected()));
 808     Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
 809             structViewer.getSelectedItem().toString());
 810     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 811     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
 812             Boolean.toString(siftsMapping.isSelected()));
 813     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 814
 815     /*
 816      * Save Output settings
 817      */
 818     Cache.setPropertyNoSave("EPS_RENDERING",
 819             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 820     Cache.setPropertyNoSave("HTML_RENDERING",
 821             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 822     Cache.setPropertyNoSave("SVG_RENDERING",
 823             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 824
 825     /*
 826      * Save Connections settings
 827      */
 828     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 829
 830     jalview.util.BrowserLauncher.resetBrowser();
 831
 832     // save user-defined and selected links
 833     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 834     if (menuLinks.isEmpty())
 835     {
 836       Cache.removeNoSave("SEQUENCE_LINKS");
 837     }
 838     else
 839     {
 840       Cache.setPropertyNoSave("SEQUENCE_LINKS",
 841               menuLinks.toString());
 842     }
 843
 844     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 845     if (nonMenuLinks.isEmpty())
 846     {
 847       Cache.removeNoSave("STORED_LINKS");
 848     }
 849     else
 850     {
 851       Cache.setPropertyNoSave("STORED_LINKS",
 852               nonMenuLinks.toString());
 853     }
 854
 855     Cache.setPropertyNoSave("DEFAULT_URL",
 856             sequenceUrlLinks.getPrimaryUrlId());
 857
 858     Cache.setPropertyNoSave("USE_PROXY",
 859             Boolean.toString(useProxy.isSelected()));
 860
 861     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 862
 863     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 864
 865     if (useProxy.isSelected())
 866     {
 867       System.setProperty("http.proxyHost", proxyServerTB.getText());
 868       System.setProperty("http.proxyPort", proxyPortTB.getText());
 869     }
 870     else
 871     {
 872       System.setProperty("http.proxyHost", "");
 873       System.setProperty("http.proxyPort", "");
 874     }
 875     Cache.setProperty("VERSION_CHECK",
 876             Boolean.toString(versioncheck.isSelected()));
 877     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 878     {
 879       // default is false - we only set this if the user has actively agreed
 880       Cache.setProperty("USAGESTATS",
 881               Boolean.toString(usagestats.isSelected()));
 882     }
 883     if (!questionnaire.isSelected())
 884     {
 885       Cache.setProperty("NOQUESTIONNAIRES", "true");
 886     }
 887     else
 888     {
 889       // special - made easy to edit a property file to disable questionnaires
 890       // by just adding the given line
 891       Cache.removeProperty("NOQUESTIONNAIRES");
 892     }
 893
 894     /*
 895      * Save Output settings
 896      */
 897     Cache.setPropertyNoSave("BLC_JVSUFFIX",
 898             Boolean.toString(blcjv.isSelected()));
 899     Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
 900             Boolean.toString(clustaljv.isSelected()));
 901     Cache.setPropertyNoSave("FASTA_JVSUFFIX",
 902             Boolean.toString(fastajv.isSelected()));
 903     Cache.setPropertyNoSave("MSF_JVSUFFIX",
 904             Boolean.toString(msfjv.isSelected()));
 905     Cache.setPropertyNoSave("PFAM_JVSUFFIX",
 906             Boolean.toString(pfamjv.isSelected()));
 907     Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
 908             Boolean.toString(pileupjv.isSelected()));
 909     Cache.setPropertyNoSave("PIR_JVSUFFIX",
 910             Boolean.toString(pirjv.isSelected()));
 911     Cache.setPropertyNoSave("PIR_MODELLER",
 912             Boolean.toString(modellerOutput.isSelected()));
 913     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
 914             Boolean.toString(embbedBioJSON.isSelected()));
 915     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 916
 917     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
 918             Boolean.toString(autoIdWidth.isSelected()));
 919     userIdWidth_actionPerformed();
 920     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
 921             userIdWidth.getText());
 922
 923     /*
 924      * Save Editing settings
 925      */
 926     Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
 927             Boolean.toString(autoCalculateConsCheck.isSelected()));
 928     Cache.setPropertyNoSave("SORT_BY_TREE",
 929             Boolean.toString(sortByTree.isSelected()));
 930     Cache.setPropertyNoSave("PAD_GAPS",
 931             Boolean.toString(padGaps.isSelected()));
 932
 933     if (!Platform.isJS())
 934     {
 935       wsPrefs.updateAndRefreshWsMenuConfig(false);
 936     }
 937
 938     /*
 939      * Save Backups settings
 940      */
 941     Cache.setPropertyNoSave(BackupFiles.ENABLED,
 942             Boolean.toString(enableBackupFiles.isSelected()));
 943     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 944     Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 945
 946     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 947     {
 948       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 949       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 950               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 951       Cache.applicationProperties
 952               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 953                       customBFPE.toString());
 954     }
 955
 956     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 957             .get(preset);
 958     Cache.setPropertyNoSave(
 959             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 960
 961     Cache.saveProperties();
 962     Desktop.instance.doConfigureStructurePrefs();
 963     try
 964     {
 965       frame.setClosed(true);
 966     } catch (Exception ex)
 967     {
 968     }
 969   }
 970
 971   /**
 972    * Do any necessary validation before saving settings. Return focus to the
 973    * first tab which fails validation.
 974    *
 975    * @return
 976    */
 977   private boolean validateSettings()
 978   {
 979     if (!validateStructure())
 980     {
 981       structureTab.requestFocusInWindow();
 982       return false;
 983     }
 984     return true;
 985   }
 986
 987   @Override
 988   protected boolean validateStructure()
 989   {
 990     return validateChimeraPath();
 991
 992   }
 993
 994   /**
 995    * DOCUMENT ME!
 996    */
 997   @Override
 998   public void startupFileTextfield_mouseClicked()
 999   {
1000     // TODO: JAL-3048 not needed for Jalview-JS
1001     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1002     JalviewFileChooser chooser = JalviewFileChooser
1003             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1004     chooser.setFileView(new JalviewFileView());
1005     chooser.setDialogTitle(
1006             MessageManager.getString("label.select_startup_file"));
1007
1008     int value = chooser.showOpenDialog(this);
1009
1010     if (value == JalviewFileChooser.APPROVE_OPTION)
1011     {
1012       FileFormatI format = chooser.getSelectedFormat();
1013       if (format != null)
1014       {
1015         Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
1016                 format.getName());
1017       }
1018       startupFileTextfield
1019               .setText(chooser.getSelectedFile().getAbsolutePath());
1020     }
1021   }
1022
1023   /**
1024    * DOCUMENT ME!
1025    *
1026    * @param e
1027    *          DOCUMENT ME!
1028    */
1029   @Override
1030   public void cancel_actionPerformed(ActionEvent e)
1031   {
1032     try
1033     {
1034       if (!Platform.isJS())
1035       {
1036         wsPrefs.updateWsMenuConfig(true);
1037         wsPrefs.refreshWs_actionPerformed(e);
1038       }
1039       frame.setClosed(true);
1040     } catch (Exception ex)
1041     {
1042     }
1043   }
1044
1045   /**
1046    * DOCUMENT ME!
1047    *
1048    * @param e
1049    *          DOCUMENT ME!
1050    */
1051   @Override
1052   public void annotations_actionPerformed(ActionEvent e)
1053   {
1054     conservation.setEnabled(annotations.isSelected());
1055     quality.setEnabled(annotations.isSelected());
1056     identity.setEnabled(annotations.isSelected());
1057     showOccupancy.setEnabled(annotations.isSelected());
1058     showGroupConsensus.setEnabled(annotations.isSelected());
1059     showGroupConservation.setEnabled(annotations.isSelected());
1060     showConsensHistogram.setEnabled(annotations.isSelected()
1061             && (identity.isSelected() || showGroupConsensus.isSelected()));
1062     showConsensLogo.setEnabled(annotations.isSelected()
1063             && (identity.isSelected() || showGroupConsensus.isSelected()));
1064   }
1065
1066   @Override
1067   public void newLink_actionPerformed(ActionEvent e)
1068   {
1069     GSequenceLink link = new GSequenceLink();
1070     boolean valid = false;
1071     while (!valid)
1072     {
1073       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1074               MessageManager.getString("label.new_sequence_url_link"),
1075               JvOptionPane.OK_CANCEL_OPTION, -1,
1076               null) == JvOptionPane.OK_OPTION)
1077       {
1078         if (link.checkValid())
1079         {
1080           if (((UrlLinkTableModel) linkUrlTable.getModel())
1081                   .isUniqueName(link.getName()))
1082           {
1083             ((UrlLinkTableModel) linkUrlTable.getModel())
1084                     .insertRow(link.getName(), link.getURL());
1085             valid = true;
1086           }
1087           else
1088           {
1089             link.notifyDuplicate();
1090             continue;
1091           }
1092         }
1093       }
1094       else
1095       {
1096         break;
1097       }
1098     }
1099   }
1100
1101   @Override
1102   public void editLink_actionPerformed(ActionEvent e)
1103   {
1104     GSequenceLink link = new GSequenceLink();
1105
1106     int index = linkUrlTable.getSelectedRow();
1107     if (index == -1)
1108     {
1109       // button no longer enabled if row is not selected
1110       Cache.log.debug("Edit with no row selected in linkUrlTable");
1111       return;
1112     }
1113
1114     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1115             .getNameColumn();
1116     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1117             .getUrlColumn();
1118     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1119     link.setName(oldName);
1120     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1121
1122     boolean valid = false;
1123     while (!valid)
1124     {
1125       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1126               MessageManager.getString("label.edit_sequence_url_link"),
1127               JvOptionPane.OK_CANCEL_OPTION, -1,
1128               null) == JvOptionPane.OK_OPTION)
1129       {
1130         if (link.checkValid())
1131         {
1132           if ((oldName.equals(link.getName()))
1133                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1134                           .isUniqueName(link.getName())))
1135           {
1136             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1137             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1138             valid = true;
1139           }
1140           else
1141           {
1142             link.notifyDuplicate();
1143             continue;
1144           }
1145         }
1146       }
1147       else
1148       {
1149         break;
1150       }
1151     }
1152   }
1153
1154   @Override
1155   public void deleteLink_actionPerformed(ActionEvent e)
1156   {
1157     int index = linkUrlTable.getSelectedRow();
1158     int modelIndex = -1;
1159     if (index == -1)
1160     {
1161       // button no longer enabled if row is not selected
1162       Cache.log.debug("Delete with no row selected in linkUrlTable");
1163       return;
1164     }
1165     else
1166     {
1167       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1168     }
1169
1170     // make sure we use the model index to delete, and not the table index
1171     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1172   }
1173
1174   @Override
1175   public void defaultBrowser_mouseClicked(MouseEvent e)
1176   {
1177     // TODO: JAL-3048 not needed for j2s
1178     if (!Platform.isJS()) // BH 2019
1179     /**
1180      * Java only
1181      *
1182      * @j2sIgnore
1183      */
1184     {
1185       JFileChooser chooser = new JFileChooser(".");
1186       chooser.setDialogTitle(
1187               MessageManager.getString("label.select_default_browser"));
1188
1189       int value = chooser.showOpenDialog(this);
1190
1191       if (value == JFileChooser.APPROVE_OPTION)
1192       {
1193         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1194       }
1195     }
1196   }
1197
1198   /*
1199    * (non-Javadoc)
1200    *
1201    * @see
1202    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1203    * .ActionEvent)
1204    */
1205   @Override
1206   protected void showunconserved_actionPerformed(ActionEvent e)
1207   {
1208     // TODO Auto-generated method stub
1209     super.showunconserved_actionPerformed(e);
1210   }
1211
1212   public static List<String> getGroupURLLinks()
1213   {
1214     return groupURLLinks;
1215   }
1216
1217   @Override
1218   public void minColour_actionPerformed(JPanel panel)
1219   {
1220     JalviewColourChooser.showColourChooser(this,
1221             MessageManager.getString("label.select_colour_minimum_value"),
1222             panel);
1223   }
1224
1225   @Override
1226   public void maxColour_actionPerformed(JPanel panel)
1227   {
1228     JalviewColourChooser.showColourChooser(this,
1229             MessageManager.getString("label.select_colour_maximum_value"),
1230             panel);
1231   }
1232
1233   @Override
1234   public void gapColour_actionPerformed(JPanel gap)
1235   {
1236     if (!useLegacyGap.isSelected())
1237     {
1238       JalviewColourChooser.showColourChooser(this,
1239               MessageManager.getString("label.select_gap_colour"),
1240               gap);
1241     }
1242   }
1243
1244   @Override
1245   public void hiddenColour_actionPerformed(JPanel hidden)
1246   {
1247     JalviewColourChooser.showColourChooser(this,
1248             MessageManager.getString("label.select_hidden_colour"),
1249             hidden);
1250   }
1251
1252   @Override
1253   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1254   {
1255     boolean enabled = useLegacyGap.isSelected();
1256     if (enabled)
1257     {
1258       gapColour.setBackground(
1259               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1260     }
1261     else
1262     {
1263       gapColour.setBackground(
1264               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1265     }
1266     gapColour.setEnabled(!enabled);
1267     gapLabel.setEnabled(!enabled);
1268   }
1269
1270   @Override
1271   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1272   {
1273     useLegacyGap.setSelected(false);
1274     useLegacyGaps_actionPerformed(null);
1275     showHiddenAtStart.setSelected(false);
1276     hiddenColour.setBackground(
1277             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1278   }
1279
1280   @Override
1281   protected void userIdWidth_actionPerformed()
1282   {
1283     try
1284     {
1285       String val = userIdWidth.getText().trim();
1286       if (val.length() > 0)
1287       {
1288         Integer iw = Integer.parseInt(val);
1289         if (iw.intValue() < 12)
1290         {
1291           throw new NumberFormatException();
1292         }
1293         userIdWidth.setText(iw.toString());
1294       }
1295     } catch (NumberFormatException x)
1296     {
1297       userIdWidth.setText("");
1298       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1299               MessageManager
1300                       .getString("warn.user_defined_width_requirements"),
1301               MessageManager.getString("label.invalid_id_column_width"),
1302               JvOptionPane.WARNING_MESSAGE);
1303     }
1304   }
1305
1306   @Override
1307   protected void autoIdWidth_actionPerformed()
1308   {
1309     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1310     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1311   }
1312
1313   /**
1314    * Returns true if chimera path is to a valid executable, else show an error
1315    * dialog.
1316    */
1317   private boolean validateChimeraPath()
1318   {
1319     if (chimeraPath.getText().trim().length() > 0)
1320     {
1321       File f = new File(chimeraPath.getText());
1322       if (!f.canExecute())
1323       {
1324         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1325                 MessageManager.getString("label.invalid_chimera_path"),
1326                 MessageManager.getString("label.invalid_name"),
1327                 JvOptionPane.ERROR_MESSAGE);
1328         return false;
1329       }
1330     }
1331     return true;
1332   }
1333
1334   /**
1335    * If Chimera is selected, check it can be found on default or user-specified
1336    * path, if not show a warning/help dialog.
1337    */
1338   @Override
1339   protected void structureViewer_actionPerformed(String selectedItem)
1340   {
1341     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1342     {
1343       return;
1344     }
1345     boolean found = false;
1346
1347     /*
1348      * Try user-specified and standard paths for Chimera executable.
1349      */
1350     List<String> paths = StructureManager.getChimeraPaths();
1351     paths.add(0, chimeraPath.getText());
1352     for (String path : paths)
1353     {
1354       if (new File(path.trim()).canExecute())
1355       {
1356         found = true;
1357         break;
1358       }
1359     }
1360     if (!found)
1361     {
1362       String[] options = { "OK", "Help" };
1363       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1364               JvSwingUtils.wrapTooltip(true,
1365                       MessageManager.getString("label.chimera_missing")),
1366               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1367               null, options, options[0]);
1368       if (showHelp == JvOptionPane.NO_OPTION)
1369       {
1370         try
1371         {
1372           Help.showHelpWindow(HelpId.StructureViewer);
1373         } catch (HelpSetException e)
1374         {
1375           e.printStackTrace();
1376         }
1377       }
1378     }
1379   }
1380
1381   public class OptionsParam
1382   {
1383     private String name;
1384
1385     private String code;
1386
1387     public OptionsParam(String name, String code)
1388     {
1389       this.name = name;
1390       this.code = code;
1391     }
1392
1393     public String getName()
1394     {
1395       return name;
1396     }
1397
1398     public void setName(String name)
1399     {
1400       this.name = name;
1401     }
1402
1403     public String getCode()
1404     {
1405       return code;
1406     }
1407
1408     public void setCode(String code)
1409     {
1410       this.code = code;
1411     }
1412
1413     @Override
1414     public String toString()
1415     {
1416       return name;
1417     }
1418
1419     @Override
1420     public boolean equals(Object that)
1421     {
1422       if (!(that instanceof OptionsParam))
1423       {
1424         return false;
1425       }
1426       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1427     }
1428
1429     @Override
1430     public int hashCode()
1431     {
1432       return name.hashCode() + code.hashCode();
1433     }
1434   }
1435
1436   private class UrlListSelectionHandler implements ListSelectionListener
1437   {
1438
1439     @Override
1440     public void valueChanged(ListSelectionEvent e)
1441     {
1442       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1443
1444       int index = lsm.getMinSelectionIndex();
1445       if (index == -1)
1446       {
1447         // no selection, so disable delete/edit buttons
1448         editLink.setEnabled(false);
1449         deleteLink.setEnabled(false);
1450         return;
1451       }
1452       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1453
1454       // enable/disable edit and delete link buttons
1455       if (((UrlLinkTableModel) linkUrlTable.getModel())
1456               .isRowDeletable(modelIndex))
1457       {
1458         deleteLink.setEnabled(true);
1459       }
1460       else
1461       {
1462         deleteLink.setEnabled(false);
1463       }
1464
1465       if (((UrlLinkTableModel) linkUrlTable.getModel())
1466               .isRowEditable(modelIndex))
1467       {
1468         editLink.setEnabled(true);
1469       }
1470       else
1471       {
1472         editLink.setEnabled(false);
1473       }
1474     }
1475   }
1476 }