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