src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.ext.pymol.PymolManager;
  57 import jalview.gui.Help.HelpId;
  58 import jalview.gui.StructureViewer.ViewerType;
  59 import jalview.io.BackupFiles;
  60 import jalview.io.BackupFilesPresetEntry;
  61 import jalview.io.FileFormatI;
  62 import jalview.io.JalviewFileChooser;
  63 import jalview.io.JalviewFileView;
  64 import jalview.jbgui.GPreferences;
  65 import jalview.jbgui.GSequenceLink;
  66 import jalview.schemes.ColourSchemeI;
  67 import jalview.schemes.ColourSchemes;
  68 import jalview.schemes.ResidueColourScheme;
  69 import jalview.urls.UrlLinkTableModel;
  70 import jalview.urls.api.UrlProviderFactoryI;
  71 import jalview.urls.api.UrlProviderI;
  72 import jalview.urls.desktop.DesktopUrlProviderFactory;
  73 import jalview.util.MessageManager;
  74 import jalview.util.Platform;
  75 import jalview.util.UrlConstants;
  76 import jalview.ws.sifts.SiftsSettings;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 109
 110   public static final String PYMOL_PATH = "PYMOL_PATH";
 111
 112   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 113
 114   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 115
 116   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 117
 118   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 119
 120   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 121
 122   public static final String GAP_COLOUR = "GAP_COLOUR";
 123
 124   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 125
 126   private static final int MIN_FONT_SIZE = 1;
 127
 128   private static final int MAX_FONT_SIZE = 30;
 129
 130   /**
 131    * Holds name and link separated with | character. Sequence ID must be
 132    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 133    */
 134   public static UrlProviderI sequenceUrlLinks;
 135
 136   public static UrlLinkTableModel dataModel;
 137
 138   /**
 139    * Holds name and link separated with | character. Sequence IDS and Sequences
 140    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 141    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 142    * for first and second token specified after a pipe character at end |,|.
 143    * (TODO: proper escape for using | to separate ids or sequences
 144    */
 145
 146   public static List<String> groupURLLinks;
 147   static
 148   {
 149     // get links selected to be in the menu (SEQUENCE_LINKS)
 150     // and links entered by the user but not selected (STORED_LINKS)
 151     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 152     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 153     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 154             UrlConstants.DEFAULT_LABEL);
 155
 156     // if both links lists are empty, add the DEFAULT_URL link
 157     // otherwise we assume the default link is in one of the lists
 158     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 159     {
 160       inMenuString = UrlConstants.DEFAULT_STRING;
 161     }
 162     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 163             inMenuString, notInMenuString);
 164     sequenceUrlLinks = factory.createUrlProvider();
 165     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 166
 167     /**
 168      * TODO: reformulate groupURL encoding so two or more can be stored in the
 169      * .properties file as '|' separated strings
 170      */
 171
 172     groupURLLinks = new ArrayList<>();
 173   }
 174
 175   JInternalFrame frame;
 176
 177   private WsPreferences wsPrefs;
 178
 179   private OptionsParam promptEachTimeOpt = new OptionsParam(
 180           MessageManager.getString("label.prompt_each_time"),
 181           "Prompt each time");
 182
 183   private OptionsParam lineArtOpt = new OptionsParam(
 184           MessageManager.getString("label.lineart"), "Lineart");
 185
 186   private OptionsParam textOpt = new OptionsParam(
 187           MessageManager.getString("action.text"), "Text");
 188
 189   /**
 190    * Creates a new Preferences object.
 191    */
 192   public Preferences()
 193   {
 194     super();
 195     frame = new JInternalFrame();
 196     frame.setContentPane(this);
 197     if (!Platform.isJS())
 198     /**
 199      * Java only
 200      *
 201      * @j2sIgnore
 202      */
 203     {
 204       wsPrefs = new WsPreferences();
 205       wsTab.add(wsPrefs, BorderLayout.CENTER);
 206     }
 207     int width = 500, height = 450;
 208     if (Platform.isAMacAndNotJS())
 209     {
 210       width = 570;
 211       height = 480;
 212     }
 213
 214     Desktop.addInternalFrame(frame,
 215             MessageManager.getString("label.preferences"), width, height);
 216     frame.setMinimumSize(new Dimension(width, height));
 217
 218     /*
 219      * Set Visual tab defaults
 220      */
 221     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 222     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 223     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 224     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 225
 226     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 227     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 228     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 229     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 230     showUnconserved
 231             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 232     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 233     showGroupConsensus
 234             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 235     showGroupConservation.setSelected(
 236             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 237     showConsensHistogram.setSelected(
 238             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 239     showConsensLogo
 240             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 241     showNpTooltip
 242             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 243     showDbRefTooltip
 244             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 245
 246     String[] fonts = java.awt.GraphicsEnvironment
 247             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 248     for (int i = 0; i < fonts.length; i++)
 249     {
 250       fontNameCB.addItem(fonts[i]);
 251     }
 252
 253     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 254     {
 255       fontSizeCB.addItem(i + "");
 256     }
 257
 258     fontStyleCB.addItem("plain");
 259     fontStyleCB.addItem("bold");
 260     fontStyleCB.addItem("italic");
 261
 262     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 263     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 264     fontStyleCB.setSelectedItem(
 265             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 266
 267     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 268     scaleProteinToCdna
 269             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 270
 271     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 272
 273     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 274
 275     gapSymbolCB.addItem("-");
 276     gapSymbolCB.addItem(".");
 277
 278     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 279
 280     sortby.addItem("No sort");
 281     sortby.addItem("Id");
 282     sortby.addItem("Pairwise Identity");
 283     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 284
 285     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 286     sortAnnBy
 287             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 288     sortAnnBy
 289             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 290     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 291             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 292                     SequenceAnnotationOrder.NONE.name()));
 293     sortAnnBy.setSelectedItem(savedSort.toString());
 294
 295     sortAutocalc.addItem("Autocalculated first");
 296     sortAutocalc.addItem("Autocalculated last");
 297     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 298     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 299             : sortAutocalc.getItemAt(1));
 300     startupCheckbox
 301             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 302     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 303             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 304                     + "/examples/exampleFile_2_3.jar"));
 305
 306     /*
 307      * Set Colours tab defaults
 308      */
 309     protColour.addItem(ResidueColourScheme.NONE);
 310     nucColour.addItem(ResidueColourScheme.NONE);
 311     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 312     {
 313       String name = cs.getSchemeName();
 314       protColour.addItem(name);
 315       nucColour.addItem(name);
 316     }
 317     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 318             ResidueColourScheme.NONE);
 319     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 320     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 321     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 322     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 323     minColour.setBackground(
 324             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 325     maxColour.setBackground(
 326             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 327
 328     /*
 329      * Set overview panel defaults
 330      */
 331     gapColour.setBackground(
 332             Cache.getDefaultColour(GAP_COLOUR,
 333                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 334     hiddenColour.setBackground(
 335             Cache.getDefaultColour(HIDDEN_COLOUR,
 336                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 337     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 338     gapLabel.setEnabled(!useLegacyGap.isSelected());
 339     gapColour.setEnabled(!useLegacyGap.isSelected());
 340     showHiddenAtStart
 341             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 342
 343     /*
 344      * Set Structure tab defaults
 345      */
 346     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 347     structFromPdb.setSelected(structSelected);
 348     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 349     useRnaView.setEnabled(structSelected);
 350     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 351     addSecondaryStructure.setEnabled(structSelected);
 352     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 353     addTempFactor.setEnabled(structSelected);
 354
 355     /*
 356      * set choice of structure viewer, and path if saved as a preference;
 357      * default to Jmol (first choice) if an unexpected value is found
 358      */
 359     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 360     structViewer.setSelectedItem(viewerType);
 361     String viewerPath = "";
 362     ViewerType type = null;
 363     try
 364     {
 365       type = ViewerType.valueOf(viewerType);
 366       switch (type)
 367       {
 368       case JMOL:
 369         break;
 370       case CHIMERA:
 371         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 372         break;
 373       case CHIMERAX:
 374         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 375         break;
 376       case PYMOL:
 377         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 378         break;
 379       }
 380     } catch (IllegalArgumentException e)
 381     {
 382       Cache.log.error("Unknown structure viewer type: " + viewerType
 383               + ", defaulting to Jmol");
 384       type = ViewerType.JMOL;
 385     }
 386     structureViewerPath.setText(viewerPath);
 387
 388     structureViewerPath.addActionListener(new ActionListener()
 389     {
 390       @Override
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         if (validateViewerPath())
 394         {
 395           Cache.setProperty(structViewer.getSelectedItem()
 396                   .equals(ViewerType.CHIMERAX.name())
 397                   ? CHIMERAX_PATH
 398                   : CHIMERA_PATH, structureViewerPath.getText());
 399         }
 400       }
 401     });
 402
 403     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 404     {
 405       siftsMapping.setSelected(true);
 406     }
 407     else
 408     {
 409       nwMapping.setSelected(true);
 410     }
 411
 412     SiftsSettings
 413             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 414
 415     /*
 416      * Set Connections tab defaults
 417      */
 418
 419     // set up sorting
 420     linkUrlTable.setModel(dataModel);
 421     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 422             linkUrlTable.getModel());
 423     linkUrlTable.setRowSorter(sorter);
 424     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 425
 426     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 427     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 428             SortOrder.DESCENDING));
 429     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 430             SortOrder.DESCENDING));
 431     sortKeys.add(
 432             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 433
 434     sorter.setSortKeys(sortKeys);
 435     // BH 2018 setSortKeys will do the sort
 436     // sorter.sort();
 437
 438     // set up filtering
 439     ActionListener onReset;
 440     onReset = new ActionListener()
 441     {
 442       @Override
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         filterTB.setText("");
 446         sorter.setRowFilter(RowFilter.regexFilter(""));
 447       }
 448
 449     };
 450     doReset.addActionListener(onReset);
 451
 452     // filter to display only custom urls
 453     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 454     {
 455       @Override
 456       public boolean include(
 457               Entry<? extends TableModel, ? extends Object> entry)
 458       {
 459         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 460       }
 461     };
 462
 463     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 464             linkUrlTable.getModel());
 465     customSorter.setRowFilter(customUrlFilter);
 466
 467     ActionListener onCustomOnly;
 468     onCustomOnly = new ActionListener()
 469     {
 470       @Override
 471       public void actionPerformed(ActionEvent e)
 472       {
 473         filterTB.setText("");
 474         sorter.setRowFilter(customUrlFilter);
 475       }
 476     };
 477     userOnly.addActionListener(onCustomOnly);
 478
 479     filterTB.getDocument().addDocumentListener(new DocumentListener()
 480     {
 481       String caseInsensitiveFlag = "(?i)";
 482
 483       @Override
 484       public void changedUpdate(DocumentEvent e)
 485       {
 486         sorter.setRowFilter(RowFilter
 487                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 488       }
 489
 490       @Override
 491       public void removeUpdate(DocumentEvent e)
 492       {
 493         sorter.setRowFilter(RowFilter
 494                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 495       }
 496
 497       @Override
 498       public void insertUpdate(DocumentEvent e)
 499       {
 500         sorter.setRowFilter(RowFilter
 501                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 502       }
 503     });
 504
 505     // set up list selection functionality
 506     linkUrlTable.getSelectionModel()
 507             .addListSelectionListener(new UrlListSelectionHandler());
 508
 509     // set up radio buttons
 510     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 511             .getPrimaryColumn();
 512     String onClickName = linkUrlTable.getColumnName(onClickCol);
 513     linkUrlTable.getColumn(onClickName)
 514             .setCellRenderer(new RadioButtonRenderer());
 515     linkUrlTable.getColumn(onClickName)
 516             .setCellEditor(new RadioButtonEditor());
 517
 518     // get boolean columns and resize those to min possible
 519     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 520     {
 521       if (linkUrlTable.getModel().getColumnClass(column)
 522               .equals(Boolean.class))
 523       {
 524         TableColumn tableColumn = linkUrlTable.getColumnModel()
 525                 .getColumn(column);
 526         int preferredWidth = tableColumn.getMinWidth();
 527
 528         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 529                 column);
 530         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 531         int cwidth = c.getPreferredSize().width
 532                 + linkUrlTable.getIntercellSpacing().width;
 533         preferredWidth = Math.max(preferredWidth, cwidth);
 534
 535         tableColumn.setPreferredWidth(preferredWidth);
 536       }
 537     }
 538
 539     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 540     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 541     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 542     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 543
 544     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 545
 546     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 547     // note antisense here: default is true
 548     questionnaire
 549             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 550     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 551
 552     /*
 553      * Set Output tab defaults
 554      */
 555     setupOutputCombo(epsRendering, "EPS_RENDERING");
 556     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 557     setupOutputCombo(svgRendering, "SVG_RENDERING");
 558     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 559     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 560     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 561     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 562     userIdWidth.setText(wi == null ? "" : wi.toString());
 563     // TODO: refactor to use common enum via FormatAdapter and allow extension
 564     // for new flat file formats
 565     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 566     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 567     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 568     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 569     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 570     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 571     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 572     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 573     embbedBioJSON
 574             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 575
 576     /*
 577      * Set Editing tab defaults
 578      */
 579     autoCalculateConsCheck
 580             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 581     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 582     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 583
 584     annotations_actionPerformed(null); // update the display of the annotation
 585                                        // settings
 586
 587
 588     /*
 589      * Set Backups tab defaults
 590      */
 591     loadLastSavedBackupsOptions();
 592   }
 593
 594   /**
 595    * A helper method that sets the items and initial selection in a character
 596    * rendering option list (Prompt each time/Lineart/Text)
 597    *
 598    * @param comboBox
 599    * @param propertyKey
 600    */
 601   protected void setupOutputCombo(JComboBox<Object> comboBox,
 602           String propertyKey)
 603   {
 604     comboBox.addItem(promptEachTimeOpt);
 605     comboBox.addItem(lineArtOpt);
 606     comboBox.addItem(textOpt);
 607
 608     /*
 609      * JalviewJS doesn't support Lineart so force it to Text
 610      */
 611     String defaultOption = Platform.isJS() ? "Text"
 612             : Cache.getDefault(propertyKey, "Prompt each time");
 613     if (defaultOption.equalsIgnoreCase("Text"))
 614     {
 615       comboBox.setSelectedItem(textOpt);
 616     }
 617     else if (defaultOption.equalsIgnoreCase("Lineart"))
 618     {
 619       comboBox.setSelectedItem(lineArtOpt);
 620     }
 621     else
 622     {
 623       comboBox.setSelectedItem(promptEachTimeOpt);
 624     }
 625   }
 626
 627   /**
 628    * Save user selections on the Preferences tabs to the Cache and write out to
 629    * file.
 630    *
 631    * @param e
 632    */
 633   @Override
 634   public void ok_actionPerformed(ActionEvent e)
 635   {
 636     if (!validateSettings())
 637     {
 638       return;
 639     }
 640
 641     /*
 642      * Save Visual settings
 643      */
 644     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 645             Boolean.toString(seqLimit.isSelected()));
 646     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 647             Boolean.toString(rightAlign.isSelected()));
 648     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 649             Boolean.toString(fullScreen.isSelected()));
 650     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 651             Boolean.toString(openoverv.isSelected()));
 652     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 653             Boolean.toString(annotations.isSelected()));
 654     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 655             Boolean.toString(conservation.isSelected()));
 656     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 657             Boolean.toString(quality.isSelected()));
 658     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 659             Boolean.toString(identity.isSelected()));
 660
 661     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 662             gapSymbolCB.getSelectedItem().toString());
 663
 664     Cache.applicationProperties.setProperty("FONT_NAME",
 665             fontNameCB.getSelectedItem().toString());
 666     Cache.applicationProperties.setProperty("FONT_STYLE",
 667             fontStyleCB.getSelectedItem().toString());
 668     Cache.applicationProperties.setProperty("FONT_SIZE",
 669             fontSizeCB.getSelectedItem().toString());
 670
 671     Cache.applicationProperties.setProperty("ID_ITALICS",
 672             Boolean.toString(idItalics.isSelected()));
 673     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 674             Boolean.toString(showUnconserved.isSelected()));
 675     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 676             Boolean.toString(showOccupancy.isSelected()));
 677     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 678             Boolean.toString(showGroupConsensus.isSelected()));
 679     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 680             Boolean.toString(showGroupConservation.isSelected()));
 681     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 682             Boolean.toString(showConsensHistogram.isSelected()));
 683     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 684             Boolean.toString(showConsensLogo.isSelected()));
 685     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 686             Boolean.toString(smoothFont.isSelected()));
 687     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 688             Boolean.toString(scaleProteinToCdna.isSelected()));
 689     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 690             Boolean.toString(showNpTooltip.isSelected()));
 691     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 692             Boolean.toString(showDbRefTooltip.isSelected()));
 693
 694     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 695             Boolean.toString(wrap.isSelected()));
 696
 697     Cache.applicationProperties.setProperty("STARTUP_FILE",
 698             startupFileTextfield.getText());
 699     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 700             Boolean.toString(startupCheckbox.isSelected()));
 701
 702     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 703             sortby.getSelectedItem().toString());
 704
 705     // convert description of sort order to enum name for save
 706     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 707             .forDescription(sortAnnBy.getSelectedItem().toString());
 708     if (annSortOrder != null)
 709     {
 710       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 711               annSortOrder.name());
 712     }
 713
 714     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 715     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 716             Boolean.valueOf(showAutocalcFirst).toString());
 717
 718     /*
 719      * Save Colours settings
 720      */
 721     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 722             protColour.getSelectedItem().toString());
 723     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 724             nucColour.getSelectedItem().toString());
 725     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 726             minColour.getBackground());
 727     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 728             maxColour.getBackground());
 729
 730     /*
 731      * Save Overview settings
 732      */
 733     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 734     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 735     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 736             Boolean.toString(useLegacyGap.isSelected()));
 737     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 738             Boolean.toString(showHiddenAtStart.isSelected()));
 739
 740     /*
 741      * Save Structure settings
 742      */
 743     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 744             Boolean.toString(addTempFactor.isSelected()));
 745     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 746             Boolean.toString(addSecondaryStructure.isSelected()));
 747     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 748             Boolean.toString(useRnaView.isSelected()));
 749     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 750             Boolean.toString(structFromPdb.isSelected()));
 751     String viewer = structViewer.getSelectedItem().toString();
 752     String viewerPath = structureViewerPath.getText();
 753     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 754             viewer);
 755     if (viewer.equals(ViewerType.CHIMERA.name()))
 756     {
 757       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 758     }
 759     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 760     {
 761       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 762     }
 763     else if (viewer.equals(ViewerType.PYMOL.name()))
 764     {
 765       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 766     }
 767     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 768             Boolean.toString(siftsMapping.isSelected()));
 769     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 770
 771     /*
 772      * Save Output settings
 773      */
 774     Cache.applicationProperties.setProperty("EPS_RENDERING",
 775             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 776     Cache.applicationProperties.setProperty("HTML_RENDERING",
 777             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 778     Cache.applicationProperties.setProperty("SVG_RENDERING",
 779             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 780
 781     /*
 782      * Save Connections settings
 783      */
 784     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 785
 786     jalview.util.BrowserLauncher.resetBrowser();
 787
 788     // save user-defined and selected links
 789     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 790     if (menuLinks.isEmpty())
 791     {
 792       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 793     }
 794     else
 795     {
 796       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 797               menuLinks.toString());
 798     }
 799
 800     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 801     if (nonMenuLinks.isEmpty())
 802     {
 803       Cache.applicationProperties.remove("STORED_LINKS");
 804     }
 805     else
 806     {
 807       Cache.applicationProperties.setProperty("STORED_LINKS",
 808               nonMenuLinks.toString());
 809     }
 810
 811     Cache.applicationProperties.setProperty("DEFAULT_URL",
 812             sequenceUrlLinks.getPrimaryUrlId());
 813
 814     Cache.applicationProperties.setProperty("USE_PROXY",
 815             Boolean.toString(useProxy.isSelected()));
 816
 817     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 818
 819     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 820
 821     if (useProxy.isSelected())
 822     {
 823       System.setProperty("http.proxyHost", proxyServerTB.getText());
 824       System.setProperty("http.proxyPort", proxyPortTB.getText());
 825     }
 826     else
 827     {
 828       System.setProperty("http.proxyHost", "");
 829       System.setProperty("http.proxyPort", "");
 830     }
 831     Cache.setProperty("VERSION_CHECK",
 832             Boolean.toString(versioncheck.isSelected()));
 833     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 834     {
 835       // default is false - we only set this if the user has actively agreed
 836       Cache.setProperty("USAGESTATS",
 837               Boolean.toString(usagestats.isSelected()));
 838     }
 839     if (!questionnaire.isSelected())
 840     {
 841       Cache.setProperty("NOQUESTIONNAIRES", "true");
 842     }
 843     else
 844     {
 845       // special - made easy to edit a property file to disable questionnaires
 846       // by just adding the given line
 847       Cache.removeProperty("NOQUESTIONNAIRES");
 848     }
 849
 850     /*
 851      * Save Output settings
 852      */
 853     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 854             Boolean.toString(blcjv.isSelected()));
 855     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 856             Boolean.toString(clustaljv.isSelected()));
 857     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 858             Boolean.toString(fastajv.isSelected()));
 859     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 860             Boolean.toString(msfjv.isSelected()));
 861     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 862             Boolean.toString(pfamjv.isSelected()));
 863     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 864             Boolean.toString(pileupjv.isSelected()));
 865     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 866             Boolean.toString(pirjv.isSelected()));
 867     Cache.applicationProperties.setProperty("PIR_MODELLER",
 868             Boolean.toString(modellerOutput.isSelected()));
 869     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 870             Boolean.toString(embbedBioJSON.isSelected()));
 871     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 872
 873     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 874             Boolean.toString(autoIdWidth.isSelected()));
 875     userIdWidth_actionPerformed();
 876     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 877             userIdWidth.getText());
 878
 879     /*
 880      * Save Editing settings
 881      */
 882     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 883             Boolean.toString(autoCalculateConsCheck.isSelected()));
 884     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 885             Boolean.toString(sortByTree.isSelected()));
 886     Cache.applicationProperties.setProperty("PAD_GAPS",
 887             Boolean.toString(padGaps.isSelected()));
 888
 889     if (!Platform.isJS())
 890     {
 891       wsPrefs.updateAndRefreshWsMenuConfig(false);
 892     }
 893
 894     /*
 895      * Save Backups settings
 896      */
 897     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 898             Boolean.toString(enableBackupFiles.isSelected()));
 899     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 900     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 901
 902     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 903     {
 904       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 905       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 906               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 907       Cache.applicationProperties
 908               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 909                       customBFPE.toString());
 910     }
 911
 912     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 913             .get(preset);
 914     Cache.applicationProperties.setProperty(
 915             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 916
 917     Cache.saveProperties();
 918     Desktop.instance.doConfigureStructurePrefs();
 919     try
 920     {
 921       frame.setClosed(true);
 922     } catch (Exception ex)
 923     {
 924     }
 925   }
 926
 927   /**
 928    * Do any necessary validation before saving settings. Return focus to the
 929    * first tab which fails validation.
 930    *
 931    * @return
 932    */
 933   private boolean validateSettings()
 934   {
 935     if (!validateStructure())
 936     {
 937       structureTab.requestFocusInWindow();
 938       return false;
 939     }
 940     return true;
 941   }
 942
 943   @Override
 944   protected boolean validateStructure()
 945   {
 946     return validateViewerPath();
 947
 948   }
 949
 950   /**
 951    * DOCUMENT ME!
 952    */
 953   @Override
 954   public void startupFileTextfield_mouseClicked()
 955   {
 956     // TODO: JAL-3048 not needed for Jalview-JS
 957     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 958     JalviewFileChooser chooser = JalviewFileChooser
 959             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 960     chooser.setFileView(new JalviewFileView());
 961     chooser.setDialogTitle(
 962             MessageManager.getString("label.select_startup_file"));
 963
 964     int value = chooser.showOpenDialog(this);
 965
 966     if (value == JalviewFileChooser.APPROVE_OPTION)
 967     {
 968       FileFormatI format = chooser.getSelectedFormat();
 969       if (format != null)
 970       {
 971         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 972                 format.getName());
 973       }
 974       startupFileTextfield
 975               .setText(chooser.getSelectedFile().getAbsolutePath());
 976     }
 977   }
 978
 979   /**
 980    * DOCUMENT ME!
 981    *
 982    * @param e
 983    *          DOCUMENT ME!
 984    */
 985   @Override
 986   public void cancel_actionPerformed(ActionEvent e)
 987   {
 988     try
 989     {
 990       if (!Platform.isJS())
 991       {
 992         wsPrefs.updateWsMenuConfig(true);
 993         wsPrefs.refreshWs_actionPerformed(e);
 994       }
 995       frame.setClosed(true);
 996     } catch (Exception ex)
 997     {
 998     }
 999   }
1000
1001   /**
1002    * DOCUMENT ME!
1003    *
1004    * @param e
1005    *          DOCUMENT ME!
1006    */
1007   @Override
1008   public void annotations_actionPerformed(ActionEvent e)
1009   {
1010     conservation.setEnabled(annotations.isSelected());
1011     quality.setEnabled(annotations.isSelected());
1012     identity.setEnabled(annotations.isSelected());
1013     showOccupancy.setEnabled(annotations.isSelected());
1014     showGroupConsensus.setEnabled(annotations.isSelected());
1015     showGroupConservation.setEnabled(annotations.isSelected());
1016     showConsensHistogram.setEnabled(annotations.isSelected()
1017             && (identity.isSelected() || showGroupConsensus.isSelected()));
1018     showConsensLogo.setEnabled(annotations.isSelected()
1019             && (identity.isSelected() || showGroupConsensus.isSelected()));
1020   }
1021
1022   @Override
1023   public void newLink_actionPerformed(ActionEvent e)
1024   {
1025     GSequenceLink link = new GSequenceLink();
1026     boolean valid = false;
1027     while (!valid)
1028     {
1029       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1030               MessageManager.getString("label.new_sequence_url_link"),
1031               JvOptionPane.OK_CANCEL_OPTION, -1,
1032               null) == JvOptionPane.OK_OPTION)
1033       {
1034         if (link.checkValid())
1035         {
1036           if (((UrlLinkTableModel) linkUrlTable.getModel())
1037                   .isUniqueName(link.getName()))
1038           {
1039             ((UrlLinkTableModel) linkUrlTable.getModel())
1040                     .insertRow(link.getName(), link.getURL());
1041             valid = true;
1042           }
1043           else
1044           {
1045             link.notifyDuplicate();
1046             continue;
1047           }
1048         }
1049       }
1050       else
1051       {
1052         break;
1053       }
1054     }
1055   }
1056
1057   @Override
1058   public void editLink_actionPerformed(ActionEvent e)
1059   {
1060     GSequenceLink link = new GSequenceLink();
1061
1062     int index = linkUrlTable.getSelectedRow();
1063     if (index == -1)
1064     {
1065       // button no longer enabled if row is not selected
1066       Cache.log.debug("Edit with no row selected in linkUrlTable");
1067       return;
1068     }
1069
1070     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1071             .getNameColumn();
1072     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1073             .getUrlColumn();
1074     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1075     link.setName(oldName);
1076     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1077
1078     boolean valid = false;
1079     while (!valid)
1080     {
1081       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1082               MessageManager.getString("label.edit_sequence_url_link"),
1083               JvOptionPane.OK_CANCEL_OPTION, -1,
1084               null) == JvOptionPane.OK_OPTION)
1085       {
1086         if (link.checkValid())
1087         {
1088           if ((oldName.equals(link.getName()))
1089                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1090                           .isUniqueName(link.getName())))
1091           {
1092             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1093             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1094             valid = true;
1095           }
1096           else
1097           {
1098             link.notifyDuplicate();
1099             continue;
1100           }
1101         }
1102       }
1103       else
1104       {
1105         break;
1106       }
1107     }
1108   }
1109
1110   @Override
1111   public void deleteLink_actionPerformed(ActionEvent e)
1112   {
1113     int index = linkUrlTable.getSelectedRow();
1114     int modelIndex = -1;
1115     if (index == -1)
1116     {
1117       // button no longer enabled if row is not selected
1118       Cache.log.debug("Delete with no row selected in linkUrlTable");
1119       return;
1120     }
1121     else
1122     {
1123       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1124     }
1125
1126     // make sure we use the model index to delete, and not the table index
1127     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1128   }
1129
1130   @Override
1131   public void defaultBrowser_mouseClicked(MouseEvent e)
1132   {
1133     // TODO: JAL-3048 not needed for j2s
1134     if (!Platform.isJS()) // BH 2019
1135     /**
1136      * Java only
1137      *
1138      * @j2sIgnore
1139      */
1140     {
1141       JFileChooser chooser = new JFileChooser(".");
1142       chooser.setDialogTitle(
1143               MessageManager.getString("label.select_default_browser"));
1144
1145       int value = chooser.showOpenDialog(this);
1146
1147       if (value == JFileChooser.APPROVE_OPTION)
1148       {
1149         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1150       }
1151     }
1152   }
1153
1154   /*
1155    * (non-Javadoc)
1156    *
1157    * @see
1158    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1159    * .ActionEvent)
1160    */
1161   @Override
1162   protected void showunconserved_actionPerformed(ActionEvent e)
1163   {
1164     // TODO Auto-generated method stub
1165     super.showunconserved_actionPerformed(e);
1166   }
1167
1168   public static List<String> getGroupURLLinks()
1169   {
1170     return groupURLLinks;
1171   }
1172
1173   @Override
1174   public void minColour_actionPerformed(JPanel panel)
1175   {
1176     JalviewColourChooser.showColourChooser(this,
1177             MessageManager.getString("label.select_colour_minimum_value"),
1178             panel);
1179   }
1180
1181   @Override
1182   public void maxColour_actionPerformed(JPanel panel)
1183   {
1184     JalviewColourChooser.showColourChooser(this,
1185             MessageManager.getString("label.select_colour_maximum_value"),
1186             panel);
1187   }
1188
1189   @Override
1190   public void gapColour_actionPerformed(JPanel gap)
1191   {
1192     if (!useLegacyGap.isSelected())
1193     {
1194       JalviewColourChooser.showColourChooser(this,
1195               MessageManager.getString("label.select_gap_colour"),
1196               gap);
1197     }
1198   }
1199
1200   @Override
1201   public void hiddenColour_actionPerformed(JPanel hidden)
1202   {
1203     JalviewColourChooser.showColourChooser(this,
1204             MessageManager.getString("label.select_hidden_colour"),
1205             hidden);
1206   }
1207
1208   @Override
1209   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1210   {
1211     boolean enabled = useLegacyGap.isSelected();
1212     if (enabled)
1213     {
1214       gapColour.setBackground(
1215               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1216     }
1217     else
1218     {
1219       gapColour.setBackground(
1220               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1221     }
1222     gapColour.setEnabled(!enabled);
1223     gapLabel.setEnabled(!enabled);
1224   }
1225
1226   @Override
1227   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1228   {
1229     useLegacyGap.setSelected(false);
1230     useLegacyGaps_actionPerformed(null);
1231     showHiddenAtStart.setSelected(false);
1232     hiddenColour.setBackground(
1233             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1234   }
1235
1236   @Override
1237   protected void userIdWidth_actionPerformed()
1238   {
1239     try
1240     {
1241       String val = userIdWidth.getText().trim();
1242       if (val.length() > 0)
1243       {
1244         Integer iw = Integer.parseInt(val);
1245         if (iw.intValue() < 12)
1246         {
1247           throw new NumberFormatException();
1248         }
1249         userIdWidth.setText(iw.toString());
1250       }
1251     } catch (NumberFormatException x)
1252     {
1253       userIdWidth.setText("");
1254       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1255               MessageManager
1256                       .getString("warn.user_defined_width_requirements"),
1257               MessageManager.getString("label.invalid_id_column_width"),
1258               JvOptionPane.WARNING_MESSAGE);
1259     }
1260   }
1261
1262   @Override
1263   protected void autoIdWidth_actionPerformed()
1264   {
1265     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1266     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1267   }
1268
1269   /**
1270    * Returns true if structure viewer path is to a valid executable, else shows
1271    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1272    * (built in to Jalview) or when Jalview is left to try default paths.
1273    */
1274   private boolean validateViewerPath()
1275   {
1276     if (structureViewerPath.getText().trim().length() > 0)
1277     {
1278       File f = new File(structureViewerPath.getText());
1279       if (!f.canExecute())
1280       {
1281         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1282                 MessageManager.getString("label.invalid_viewer_path"),
1283                 MessageManager.getString("label.invalid_viewer_path"),
1284                 JvOptionPane.ERROR_MESSAGE);
1285         return false;
1286       }
1287     }
1288     return true;
1289   }
1290
1291   /**
1292    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1293    * default or user-specified path, if not show a warning/help dialog
1294    */
1295   @Override
1296   protected void structureViewer_actionPerformed(String selectedItem)
1297   {
1298     if (selectedItem.equals(ViewerType.JMOL.name()))
1299     {
1300       structureViewerPath.setEnabled(false);
1301       structureViewerPathLabel.setEnabled(false);
1302       return;
1303     }
1304     boolean found = false;
1305     structureViewerPath.setEnabled(true);
1306     structureViewerPathLabel.setEnabled(true);
1307     structureViewerPathLabel.setText(MessageManager
1308             .formatMessage("label.viewer_path", selectedItem));
1309
1310     /*
1311      * Try user-specified and standard paths for structure viewer executable
1312      */
1313     String viewerPath = "";
1314     List<String> paths = null;
1315     try
1316     {
1317       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1318       switch (viewerType)
1319       {
1320       case JMOL:
1321         // dealt with above
1322         break;
1323       case CHIMERA:
1324         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1325         paths = StructureManager.getChimeraPaths(false);
1326         break;
1327       case CHIMERAX:
1328         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1329         paths = StructureManager.getChimeraPaths(true);
1330         break;
1331       case PYMOL:
1332         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1333         paths = PymolManager.getPymolPaths();
1334         break;
1335       }
1336     } catch (IllegalArgumentException e)
1337     {
1338       // only valid entries should be in the drop-down
1339     }
1340     structureViewerPath.setText(viewerPath);
1341
1342     paths.add(0, structureViewerPath.getText());
1343     for (String path : paths)
1344     {
1345       if (new File(path.trim()).canExecute())
1346       {
1347         found = true;
1348         break;
1349       }
1350     }
1351
1352     if (!found)
1353     {
1354       String[] options = { "OK", "Help" };
1355       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1356               JvSwingUtils.wrapTooltip(true,
1357                       MessageManager.getString("label.viewer_missing")),
1358               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1359               null, options, options[0]);
1360       if (showHelp == JvOptionPane.NO_OPTION)
1361       {
1362         try
1363         {
1364           Help.showHelpWindow(HelpId.StructureViewer);
1365         } catch (HelpSetException e)
1366         {
1367           e.printStackTrace();
1368         }
1369       }
1370     }
1371   }
1372
1373   public class OptionsParam
1374   {
1375     private String name;
1376
1377     private String code;
1378
1379     public OptionsParam(String name, String code)
1380     {
1381       this.name = name;
1382       this.code = code;
1383     }
1384
1385     public String getName()
1386     {
1387       return name;
1388     }
1389
1390     public void setName(String name)
1391     {
1392       this.name = name;
1393     }
1394
1395     public String getCode()
1396     {
1397       return code;
1398     }
1399
1400     public void setCode(String code)
1401     {
1402       this.code = code;
1403     }
1404
1405     @Override
1406     public String toString()
1407     {
1408       return name;
1409     }
1410
1411     @Override
1412     public boolean equals(Object that)
1413     {
1414       if (!(that instanceof OptionsParam))
1415       {
1416         return false;
1417       }
1418       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1419     }
1420
1421     @Override
1422     public int hashCode()
1423     {
1424       return name.hashCode() + code.hashCode();
1425     }
1426   }
1427
1428   private class UrlListSelectionHandler implements ListSelectionListener
1429   {
1430
1431     @Override
1432     public void valueChanged(ListSelectionEvent e)
1433     {
1434       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1435
1436       int index = lsm.getMinSelectionIndex();
1437       if (index == -1)
1438       {
1439         // no selection, so disable delete/edit buttons
1440         editLink.setEnabled(false);
1441         deleteLink.setEnabled(false);
1442         return;
1443       }
1444       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1445
1446       // enable/disable edit and delete link buttons
1447       if (((UrlLinkTableModel) linkUrlTable.getModel())
1448               .isRowDeletable(modelIndex))
1449       {
1450         deleteLink.setEnabled(true);
1451       }
1452       else
1453       {
1454         deleteLink.setEnabled(false);
1455       }
1456
1457       if (((UrlLinkTableModel) linkUrlTable.getModel())
1458               .isRowEditable(modelIndex))
1459       {
1460         editLink.setEnabled(true);
1461       }
1462       else
1463       {
1464         editLink.setEnabled(false);
1465       }
1466     }
1467   }
1468 }