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(Cache.getDefaultColour(GAP_COLOUR,
 332             OverviewCanvas.OVERVIEW_DEFAULT_GAP));
 333     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 334             OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
 335     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 336     gapLabel.setEnabled(!useLegacyGap.isSelected());
 337     gapColour.setEnabled(!useLegacyGap.isSelected());
 338     showHiddenAtStart
 339             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 340
 341     /*
 342      * Set Structure tab defaults
 343      */
 344     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 345     structFromPdb.setSelected(structSelected);
 346     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 347     useRnaView.setEnabled(structSelected);
 348     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 349     addSecondaryStructure.setEnabled(structSelected);
 350     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 351     addTempFactor.setEnabled(structSelected);
 352
 353     /*
 354      * set choice of structure viewer, and path if saved as a preference;
 355      * default to Jmol (first choice) if an unexpected value is found
 356      */
 357     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 358             ViewerType.JMOL.name());
 359     structViewer.setSelectedItem(viewerType);
 360     String viewerPath = "";
 361     ViewerType type = null;
 362     try
 363     {
 364       type = ViewerType.valueOf(viewerType);
 365       switch (type)
 366       {
 367       case JMOL:
 368         break;
 369       case CHIMERA:
 370         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 371         break;
 372       case CHIMERAX:
 373         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 374         break;
 375       case PYMOL:
 376         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 377         break;
 378       }
 379     } catch (IllegalArgumentException e)
 380     {
 381       Cache.log.error("Unknown structure viewer type: " + viewerType
 382               + ", defaulting to Jmol");
 383       type = ViewerType.JMOL;
 384     }
 385     structureViewerPath.setText(viewerPath);
 386
 387     structureViewerPath.addActionListener(new ActionListener()
 388     {
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         if (validateViewerPath())
 393         {
 394           Cache.setProperty(
 395                   structViewer.getSelectedItem().equals(
 396                           ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
 397                                   : CHIMERA_PATH,
 398                   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      * Set Backups tab defaults
 589      */
 590     loadLastSavedBackupsOptions();
 591   }
 592
 593   /**
 594    * A helper method that sets the items and initial selection in a character
 595    * rendering option list (Prompt each time/Lineart/Text)
 596    *
 597    * @param comboBox
 598    * @param propertyKey
 599    */
 600   protected void setupOutputCombo(JComboBox<Object> comboBox,
 601           String propertyKey)
 602   {
 603     comboBox.addItem(promptEachTimeOpt);
 604     comboBox.addItem(lineArtOpt);
 605     comboBox.addItem(textOpt);
 606
 607     /*
 608      * JalviewJS doesn't support Lineart so force it to Text
 609      */
 610     String defaultOption = Platform.isJS() ? "Text"
 611             : Cache.getDefault(propertyKey, "Prompt each time");
 612     if (defaultOption.equalsIgnoreCase("Text"))
 613     {
 614       comboBox.setSelectedItem(textOpt);
 615     }
 616     else if (defaultOption.equalsIgnoreCase("Lineart"))
 617     {
 618       comboBox.setSelectedItem(lineArtOpt);
 619     }
 620     else
 621     {
 622       comboBox.setSelectedItem(promptEachTimeOpt);
 623     }
 624   }
 625
 626   /**
 627    * Save user selections on the Preferences tabs to the Cache and write out to
 628    * file.
 629    *
 630    * @param e
 631    */
 632   @Override
 633   public void ok_actionPerformed(ActionEvent e)
 634   {
 635     if (!validateSettings())
 636     {
 637       return;
 638     }
 639
 640     /*
 641      * Save Visual settings
 642      */
 643     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 644             Boolean.toString(seqLimit.isSelected()));
 645     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 646             Boolean.toString(rightAlign.isSelected()));
 647     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 648             Boolean.toString(fullScreen.isSelected()));
 649     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 650             Boolean.toString(openoverv.isSelected()));
 651     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 652             Boolean.toString(annotations.isSelected()));
 653     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 654             Boolean.toString(conservation.isSelected()));
 655     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 656             Boolean.toString(quality.isSelected()));
 657     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 658             Boolean.toString(identity.isSelected()));
 659
 660     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 661             gapSymbolCB.getSelectedItem().toString());
 662
 663     Cache.applicationProperties.setProperty("FONT_NAME",
 664             fontNameCB.getSelectedItem().toString());
 665     Cache.applicationProperties.setProperty("FONT_STYLE",
 666             fontStyleCB.getSelectedItem().toString());
 667     Cache.applicationProperties.setProperty("FONT_SIZE",
 668             fontSizeCB.getSelectedItem().toString());
 669
 670     Cache.applicationProperties.setProperty("ID_ITALICS",
 671             Boolean.toString(idItalics.isSelected()));
 672     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 673             Boolean.toString(showUnconserved.isSelected()));
 674     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 675             Boolean.toString(showOccupancy.isSelected()));
 676     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 677             Boolean.toString(showGroupConsensus.isSelected()));
 678     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 679             Boolean.toString(showGroupConservation.isSelected()));
 680     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 681             Boolean.toString(showConsensHistogram.isSelected()));
 682     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 683             Boolean.toString(showConsensLogo.isSelected()));
 684     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 685             Boolean.toString(smoothFont.isSelected()));
 686     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 687             Boolean.toString(scaleProteinToCdna.isSelected()));
 688     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 689             Boolean.toString(showNpTooltip.isSelected()));
 690     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 691             Boolean.toString(showDbRefTooltip.isSelected()));
 692
 693     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 694             Boolean.toString(wrap.isSelected()));
 695
 696     Cache.applicationProperties.setProperty("STARTUP_FILE",
 697             startupFileTextfield.getText());
 698     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 699             Boolean.toString(startupCheckbox.isSelected()));
 700
 701     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 702             sortby.getSelectedItem().toString());
 703
 704     // convert description of sort order to enum name for save
 705     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 706             .forDescription(sortAnnBy.getSelectedItem().toString());
 707     if (annSortOrder != null)
 708     {
 709       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 710               annSortOrder.name());
 711     }
 712
 713     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 714     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 715             Boolean.valueOf(showAutocalcFirst).toString());
 716
 717     /*
 718      * Save Colours settings
 719      */
 720     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 721             protColour.getSelectedItem().toString());
 722     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 723             nucColour.getSelectedItem().toString());
 724     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 725             minColour.getBackground());
 726     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 727             maxColour.getBackground());
 728
 729     /*
 730      * Save Overview settings
 731      */
 732     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 733     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 734     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 735             Boolean.toString(useLegacyGap.isSelected()));
 736     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 737             Boolean.toString(showHiddenAtStart.isSelected()));
 738
 739     /*
 740      * Save Structure settings
 741      */
 742     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 743             Boolean.toString(addTempFactor.isSelected()));
 744     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 745             Boolean.toString(addSecondaryStructure.isSelected()));
 746     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 747             Boolean.toString(useRnaView.isSelected()));
 748     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 749             Boolean.toString(structFromPdb.isSelected()));
 750     String viewer = structViewer.getSelectedItem().toString();
 751     String viewerPath = structureViewerPath.getText();
 752     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 753     if (viewer.equals(ViewerType.CHIMERA.name()))
 754     {
 755       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 756     }
 757     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 758     {
 759       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 760     }
 761     else if (viewer.equals(ViewerType.PYMOL.name()))
 762     {
 763       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 764     }
 765     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 766             Boolean.toString(siftsMapping.isSelected()));
 767     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 768
 769     /*
 770      * Save Output settings
 771      */
 772     Cache.applicationProperties.setProperty("EPS_RENDERING",
 773             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 774     Cache.applicationProperties.setProperty("HTML_RENDERING",
 775             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 776     Cache.applicationProperties.setProperty("SVG_RENDERING",
 777             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 778
 779     /*
 780      * Save Connections settings
 781      */
 782     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 783
 784     jalview.util.BrowserLauncher.resetBrowser();
 785
 786     // save user-defined and selected links
 787     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 788     if (menuLinks.isEmpty())
 789     {
 790       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 791     }
 792     else
 793     {
 794       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 795               menuLinks.toString());
 796     }
 797
 798     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 799     if (nonMenuLinks.isEmpty())
 800     {
 801       Cache.applicationProperties.remove("STORED_LINKS");
 802     }
 803     else
 804     {
 805       Cache.applicationProperties.setProperty("STORED_LINKS",
 806               nonMenuLinks.toString());
 807     }
 808
 809     Cache.applicationProperties.setProperty("DEFAULT_URL",
 810             sequenceUrlLinks.getPrimaryUrlId());
 811
 812     Cache.applicationProperties.setProperty("USE_PROXY",
 813             Boolean.toString(useProxy.isSelected()));
 814
 815     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 816
 817     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 818
 819     if (useProxy.isSelected())
 820     {
 821       System.setProperty("http.proxyHost", proxyServerTB.getText());
 822       System.setProperty("http.proxyPort", proxyPortTB.getText());
 823     }
 824     else
 825     {
 826       System.setProperty("http.proxyHost", "");
 827       System.setProperty("http.proxyPort", "");
 828     }
 829     Cache.setProperty("VERSION_CHECK",
 830             Boolean.toString(versioncheck.isSelected()));
 831     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 832     {
 833       // default is false - we only set this if the user has actively agreed
 834       Cache.setProperty("USAGESTATS",
 835               Boolean.toString(usagestats.isSelected()));
 836     }
 837     if (!questionnaire.isSelected())
 838     {
 839       Cache.setProperty("NOQUESTIONNAIRES", "true");
 840     }
 841     else
 842     {
 843       // special - made easy to edit a property file to disable questionnaires
 844       // by just adding the given line
 845       Cache.removeProperty("NOQUESTIONNAIRES");
 846     }
 847
 848     /*
 849      * Save Output settings
 850      */
 851     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 852             Boolean.toString(blcjv.isSelected()));
 853     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 854             Boolean.toString(clustaljv.isSelected()));
 855     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 856             Boolean.toString(fastajv.isSelected()));
 857     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 858             Boolean.toString(msfjv.isSelected()));
 859     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 860             Boolean.toString(pfamjv.isSelected()));
 861     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 862             Boolean.toString(pileupjv.isSelected()));
 863     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 864             Boolean.toString(pirjv.isSelected()));
 865     Cache.applicationProperties.setProperty("PIR_MODELLER",
 866             Boolean.toString(modellerOutput.isSelected()));
 867     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 868             Boolean.toString(embbedBioJSON.isSelected()));
 869     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 870
 871     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 872             Boolean.toString(autoIdWidth.isSelected()));
 873     userIdWidth_actionPerformed();
 874     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 875             userIdWidth.getText());
 876
 877     /*
 878      * Save Editing settings
 879      */
 880     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 881             Boolean.toString(autoCalculateConsCheck.isSelected()));
 882     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 883             Boolean.toString(sortByTree.isSelected()));
 884     Cache.applicationProperties.setProperty("PAD_GAPS",
 885             Boolean.toString(padGaps.isSelected()));
 886
 887     if (!Platform.isJS())
 888     {
 889       wsPrefs.updateAndRefreshWsMenuConfig(false);
 890     }
 891
 892     /*
 893      * Save Backups settings
 894      */
 895     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 896             Boolean.toString(enableBackupFiles.isSelected()));
 897     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 898     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 899             Integer.toString(preset));
 900
 901     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 902     {
 903       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 904       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 905               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 906       Cache.applicationProperties.setProperty(
 907               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 908     }
 909
 910     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 911             .get(preset);
 912     Cache.applicationProperties.setProperty(
 913             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 914
 915     Cache.saveProperties();
 916     Desktop.instance.doConfigureStructurePrefs();
 917     try
 918     {
 919       frame.setClosed(true);
 920     } catch (Exception ex)
 921     {
 922     }
 923   }
 924
 925   /**
 926    * Do any necessary validation before saving settings. Return focus to the
 927    * first tab which fails validation.
 928    *
 929    * @return
 930    */
 931   private boolean validateSettings()
 932   {
 933     if (!validateStructure())
 934     {
 935       structureTab.requestFocusInWindow();
 936       return false;
 937     }
 938     return true;
 939   }
 940
 941   @Override
 942   protected boolean validateStructure()
 943   {
 944     return validateViewerPath();
 945
 946   }
 947
 948   /**
 949    * DOCUMENT ME!
 950    */
 951   @Override
 952   public void startupFileTextfield_mouseClicked()
 953   {
 954     // TODO: JAL-3048 not needed for Jalview-JS
 955     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 956     JalviewFileChooser chooser = JalviewFileChooser
 957             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 958     chooser.setFileView(new JalviewFileView());
 959     chooser.setDialogTitle(
 960             MessageManager.getString("label.select_startup_file"));
 961
 962     int value = chooser.showOpenDialog(this);
 963
 964     if (value == JalviewFileChooser.APPROVE_OPTION)
 965     {
 966       FileFormatI format = chooser.getSelectedFormat();
 967       if (format != null)
 968       {
 969         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 970                 format.getName());
 971       }
 972       startupFileTextfield
 973               .setText(chooser.getSelectedFile().getAbsolutePath());
 974     }
 975   }
 976
 977   /**
 978    * DOCUMENT ME!
 979    *
 980    * @param e
 981    *          DOCUMENT ME!
 982    */
 983   @Override
 984   public void cancel_actionPerformed(ActionEvent e)
 985   {
 986     try
 987     {
 988       if (!Platform.isJS())
 989       {
 990         wsPrefs.updateWsMenuConfig(true);
 991         wsPrefs.refreshWs_actionPerformed(e);
 992       }
 993       frame.setClosed(true);
 994     } catch (Exception ex)
 995     {
 996     }
 997   }
 998
 999   /**
1000    * DOCUMENT ME!
1001    *
1002    * @param e
1003    *          DOCUMENT ME!
1004    */
1005   @Override
1006   public void annotations_actionPerformed(ActionEvent e)
1007   {
1008     conservation.setEnabled(annotations.isSelected());
1009     quality.setEnabled(annotations.isSelected());
1010     identity.setEnabled(annotations.isSelected());
1011     showOccupancy.setEnabled(annotations.isSelected());
1012     showGroupConsensus.setEnabled(annotations.isSelected());
1013     showGroupConservation.setEnabled(annotations.isSelected());
1014     showConsensHistogram.setEnabled(annotations.isSelected()
1015             && (identity.isSelected() || showGroupConsensus.isSelected()));
1016     showConsensLogo.setEnabled(annotations.isSelected()
1017             && (identity.isSelected() || showGroupConsensus.isSelected()));
1018   }
1019
1020   @Override
1021   public void newLink_actionPerformed(ActionEvent e)
1022   {
1023     GSequenceLink link = new GSequenceLink();
1024     boolean valid = false;
1025     while (!valid)
1026     {
1027       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1028               MessageManager.getString("label.new_sequence_url_link"),
1029               JvOptionPane.OK_CANCEL_OPTION, -1,
1030               null) == JvOptionPane.OK_OPTION)
1031       {
1032         if (link.checkValid())
1033         {
1034           if (((UrlLinkTableModel) linkUrlTable.getModel())
1035                   .isUniqueName(link.getName()))
1036           {
1037             ((UrlLinkTableModel) linkUrlTable.getModel())
1038                     .insertRow(link.getName(), link.getURL());
1039             valid = true;
1040           }
1041           else
1042           {
1043             link.notifyDuplicate();
1044             continue;
1045           }
1046         }
1047       }
1048       else
1049       {
1050         break;
1051       }
1052     }
1053   }
1054
1055   @Override
1056   public void editLink_actionPerformed(ActionEvent e)
1057   {
1058     GSequenceLink link = new GSequenceLink();
1059
1060     int index = linkUrlTable.getSelectedRow();
1061     if (index == -1)
1062     {
1063       // button no longer enabled if row is not selected
1064       Cache.log.debug("Edit with no row selected in linkUrlTable");
1065       return;
1066     }
1067
1068     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1069             .getNameColumn();
1070     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1071             .getUrlColumn();
1072     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1073     link.setName(oldName);
1074     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1075
1076     boolean valid = false;
1077     while (!valid)
1078     {
1079       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1080               MessageManager.getString("label.edit_sequence_url_link"),
1081               JvOptionPane.OK_CANCEL_OPTION, -1,
1082               null) == JvOptionPane.OK_OPTION)
1083       {
1084         if (link.checkValid())
1085         {
1086           if ((oldName.equals(link.getName()))
1087                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1088                           .isUniqueName(link.getName())))
1089           {
1090             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1091             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1092             valid = true;
1093           }
1094           else
1095           {
1096             link.notifyDuplicate();
1097             continue;
1098           }
1099         }
1100       }
1101       else
1102       {
1103         break;
1104       }
1105     }
1106   }
1107
1108   @Override
1109   public void deleteLink_actionPerformed(ActionEvent e)
1110   {
1111     int index = linkUrlTable.getSelectedRow();
1112     int modelIndex = -1;
1113     if (index == -1)
1114     {
1115       // button no longer enabled if row is not selected
1116       Cache.log.debug("Delete with no row selected in linkUrlTable");
1117       return;
1118     }
1119     else
1120     {
1121       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1122     }
1123
1124     // make sure we use the model index to delete, and not the table index
1125     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1126   }
1127
1128   @Override
1129   public void defaultBrowser_mouseClicked(MouseEvent e)
1130   {
1131     // TODO: JAL-3048 not needed for j2s
1132     if (!Platform.isJS()) // BH 2019
1133     /**
1134      * Java only
1135      *
1136      * @j2sIgnore
1137      */
1138     {
1139       JFileChooser chooser = new JFileChooser(".");
1140       chooser.setDialogTitle(
1141               MessageManager.getString("label.select_default_browser"));
1142
1143       int value = chooser.showOpenDialog(this);
1144
1145       if (value == JFileChooser.APPROVE_OPTION)
1146       {
1147         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1148       }
1149     }
1150   }
1151
1152   /*
1153    * (non-Javadoc)
1154    *
1155    * @see
1156    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1157    * .ActionEvent)
1158    */
1159   @Override
1160   protected void showunconserved_actionPerformed(ActionEvent e)
1161   {
1162     // TODO Auto-generated method stub
1163     super.showunconserved_actionPerformed(e);
1164   }
1165
1166   public static List<String> getGroupURLLinks()
1167   {
1168     return groupURLLinks;
1169   }
1170
1171   @Override
1172   public void minColour_actionPerformed(JPanel panel)
1173   {
1174     JalviewColourChooser.showColourChooser(this,
1175             MessageManager.getString("label.select_colour_minimum_value"),
1176             panel);
1177   }
1178
1179   @Override
1180   public void maxColour_actionPerformed(JPanel panel)
1181   {
1182     JalviewColourChooser.showColourChooser(this,
1183             MessageManager.getString("label.select_colour_maximum_value"),
1184             panel);
1185   }
1186
1187   @Override
1188   public void gapColour_actionPerformed(JPanel gap)
1189   {
1190     if (!useLegacyGap.isSelected())
1191     {
1192       JalviewColourChooser.showColourChooser(this,
1193               MessageManager.getString("label.select_gap_colour"), gap);
1194     }
1195   }
1196
1197   @Override
1198   public void hiddenColour_actionPerformed(JPanel hidden)
1199   {
1200     JalviewColourChooser.showColourChooser(this,
1201             MessageManager.getString("label.select_hidden_colour"), hidden);
1202   }
1203
1204   @Override
1205   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1206   {
1207     boolean enabled = useLegacyGap.isSelected();
1208     if (enabled)
1209     {
1210       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
1211     }
1212     else
1213     {
1214       gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
1215     }
1216     gapColour.setEnabled(!enabled);
1217     gapLabel.setEnabled(!enabled);
1218   }
1219
1220   @Override
1221   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1222   {
1223     useLegacyGap.setSelected(false);
1224     useLegacyGaps_actionPerformed(null);
1225     showHiddenAtStart.setSelected(false);
1226     hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
1227   }
1228
1229   @Override
1230   protected void userIdWidth_actionPerformed()
1231   {
1232     try
1233     {
1234       String val = userIdWidth.getText().trim();
1235       if (val.length() > 0)
1236       {
1237         Integer iw = Integer.parseInt(val);
1238         if (iw.intValue() < 12)
1239         {
1240           throw new NumberFormatException();
1241         }
1242         userIdWidth.setText(iw.toString());
1243       }
1244     } catch (NumberFormatException x)
1245     {
1246       userIdWidth.setText("");
1247       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1248               MessageManager
1249                       .getString("warn.user_defined_width_requirements"),
1250               MessageManager.getString("label.invalid_id_column_width"),
1251               JvOptionPane.WARNING_MESSAGE);
1252     }
1253   }
1254
1255   @Override
1256   protected void autoIdWidth_actionPerformed()
1257   {
1258     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1259     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1260   }
1261
1262   /**
1263    * Returns true if structure viewer path is to a valid executable, else shows
1264    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1265    * (built in to Jalview) or when Jalview is left to try default paths.
1266    */
1267   private boolean validateViewerPath()
1268   {
1269     if (structureViewerPath.getText().trim().length() > 0)
1270     {
1271       File f = new File(structureViewerPath.getText());
1272       if (!f.canExecute())
1273       {
1274         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1275                 MessageManager.getString("label.invalid_viewer_path"),
1276                 MessageManager.getString("label.invalid_viewer_path"),
1277                 JvOptionPane.ERROR_MESSAGE);
1278         return false;
1279       }
1280     }
1281     return true;
1282   }
1283
1284   /**
1285    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1286    * default or user-specified path, if not show a warning/help dialog
1287    */
1288   @Override
1289   protected void structureViewer_actionPerformed(String selectedItem)
1290   {
1291     if (selectedItem.equals(ViewerType.JMOL.name()))
1292     {
1293       structureViewerPath.setEnabled(false);
1294       structureViewerPathLabel.setEnabled(false);
1295       return;
1296     }
1297     boolean found = false;
1298     structureViewerPath.setEnabled(true);
1299     structureViewerPathLabel.setEnabled(true);
1300     structureViewerPathLabel.setText(MessageManager
1301             .formatMessage("label.viewer_path", selectedItem));
1302
1303     /*
1304      * Try user-specified and standard paths for structure viewer executable
1305      */
1306     String viewerPath = "";
1307     List<String> paths = null;
1308     try
1309     {
1310       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1311       switch (viewerType)
1312       {
1313       case JMOL:
1314         // dealt with above
1315         break;
1316       case CHIMERA:
1317         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1318         paths = StructureManager.getChimeraPaths(false);
1319         break;
1320       case CHIMERAX:
1321         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1322         paths = StructureManager.getChimeraPaths(true);
1323         break;
1324       case PYMOL:
1325         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1326         paths = PymolManager.getPymolPaths();
1327         break;
1328       }
1329     } catch (IllegalArgumentException e)
1330     {
1331       // only valid entries should be in the drop-down
1332     }
1333     structureViewerPath.setText(viewerPath);
1334
1335     paths.add(0, structureViewerPath.getText());
1336     for (String path : paths)
1337     {
1338       if (new File(path.trim()).canExecute())
1339       {
1340         found = true;
1341         break;
1342       }
1343     }
1344
1345     if (!found)
1346     {
1347       String[] options = { "OK", "Help" };
1348       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1349               JvSwingUtils.wrapTooltip(true,
1350                       MessageManager.getString("label.viewer_missing")),
1351               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1352               null, options, options[0]);
1353       if (showHelp == JvOptionPane.NO_OPTION)
1354       {
1355         try
1356         {
1357           Help.showHelpWindow(HelpId.StructureViewer);
1358         } catch (HelpSetException e)
1359         {
1360           e.printStackTrace();
1361         }
1362       }
1363     }
1364   }
1365
1366   public class OptionsParam
1367   {
1368     private String name;
1369
1370     private String code;
1371
1372     public OptionsParam(String name, String code)
1373     {
1374       this.name = name;
1375       this.code = code;
1376     }
1377
1378     public String getName()
1379     {
1380       return name;
1381     }
1382
1383     public void setName(String name)
1384     {
1385       this.name = name;
1386     }
1387
1388     public String getCode()
1389     {
1390       return code;
1391     }
1392
1393     public void setCode(String code)
1394     {
1395       this.code = code;
1396     }
1397
1398     @Override
1399     public String toString()
1400     {
1401       return name;
1402     }
1403
1404     @Override
1405     public boolean equals(Object that)
1406     {
1407       if (!(that instanceof OptionsParam))
1408       {
1409         return false;
1410       }
1411       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1412     }
1413
1414     @Override
1415     public int hashCode()
1416     {
1417       return name.hashCode() + code.hashCode();
1418     }
1419   }
1420
1421   private class UrlListSelectionHandler implements ListSelectionListener
1422   {
1423
1424     @Override
1425     public void valueChanged(ListSelectionEvent e)
1426     {
1427       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1428
1429       int index = lsm.getMinSelectionIndex();
1430       if (index == -1)
1431       {
1432         // no selection, so disable delete/edit buttons
1433         editLink.setEnabled(false);
1434         deleteLink.setEnabled(false);
1435         return;
1436       }
1437       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1438
1439       // enable/disable edit and delete link buttons
1440       if (((UrlLinkTableModel) linkUrlTable.getModel())
1441               .isRowDeletable(modelIndex))
1442       {
1443         deleteLink.setEnabled(true);
1444       }
1445       else
1446       {
1447         deleteLink.setEnabled(false);
1448       }
1449
1450       if (((UrlLinkTableModel) linkUrlTable.getModel())
1451               .isRowEditable(modelIndex))
1452       {
1453         editLink.setEnabled(true);
1454       }
1455       else
1456       {
1457         editLink.setEnabled(false);
1458       }
1459     }
1460   }
1461 }