src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.bin.Instance;
  26 import jalview.gui.Help.HelpId;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.io.BackupFiles;
  29 import jalview.io.FileFormatI;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32 import jalview.jbgui.GPreferences;
  33 import jalview.jbgui.GSequenceLink;
  34 import jalview.schemes.ColourSchemeI;
  35 import jalview.schemes.ColourSchemes;
  36 import jalview.schemes.ResidueColourScheme;
  37 import jalview.urls.UrlLinkTableModel;
  38 import jalview.urls.api.UrlProviderFactoryI;
  39 import jalview.urls.api.UrlProviderI;
  40 import jalview.urls.desktop.DesktopUrlProviderFactory;
  41 import jalview.util.BrowserLauncher;
  42 import jalview.util.MessageManager;
  43 import jalview.util.Platform;
  44 import jalview.util.UrlConstants;
  45 import jalview.ws.sifts.SiftsSettings;
  46
  47 import java.awt.BorderLayout;
  48 import java.awt.Color;
  49 import java.awt.Component;
  50 import java.awt.Dimension;
  51 import java.awt.Font;
  52 import java.awt.event.ActionEvent;
  53 import java.awt.event.ActionListener;
  54 import java.awt.event.MouseEvent;
  55 import java.io.File;
  56 import java.util.ArrayList;
  57 import java.util.List;
  58
  59 import javax.help.HelpSetException;
  60 import javax.swing.JComboBox;
  61 import javax.swing.JFileChooser;
  62 import javax.swing.JInternalFrame;
  63 import javax.swing.JPanel;
  64 import javax.swing.ListSelectionModel;
  65 import javax.swing.RowFilter;
  66 import javax.swing.RowSorter;
  67 import javax.swing.SortOrder;
  68 import javax.swing.event.DocumentEvent;
  69 import javax.swing.event.DocumentListener;
  70 import javax.swing.event.ListSelectionEvent;
  71 import javax.swing.event.ListSelectionListener;
  72 import javax.swing.table.TableCellRenderer;
  73 import javax.swing.table.TableColumn;
  74 import javax.swing.table.TableModel;
  75 import javax.swing.table.TableRowSorter;
  76
  77 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  78
  79 /**
  80  * DOCUMENT ME!
  81  *
  82  * @author $author$
  83  * @version $Revision$
  84  */
  85 @SuppressWarnings("serial")
  86 public class Preferences extends GPreferences
  87 {
  88   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  89
  90   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  91
  92   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  93
  94   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  95
  96   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  97
  98   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  99
 100   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 101
 102   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 103
 104   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 105
 106   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 107
 108   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 109
 110   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 111
 112   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 113
 114   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 115
 116   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 117
 118   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 119
 120   public static final String GAP_COLOUR = "GAP_COLOUR";
 121
 122   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 123
 124   private static final int MIN_FONT_SIZE = 1;
 125
 126   private static final int MAX_FONT_SIZE = 30;
 127
 128   /**
 129    * Holds name and link separated with | character. Sequence ID must be
 130    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 131    */
 132   public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
 133
 134   public final static UrlLinkTableModel dataModel;
 135
 136   /**
 137    * Holds name and link separated with | character. Sequence IDS and Sequences
 138    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 139    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 140    * for first and second token specified after a pipe character at end |,|.
 141    * (TODO: proper escape for using | to separate ids or sequences
 142    */
 143
 144   public static final List<String> groupURLLinks; // not implemented
 145
 146   static
 147   {
 148     // get links selected to be in the menu (SEQUENCE_LINKS)
 149     // and links entered by the user but not selected (STORED_LINKS)
 150     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 151     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 152     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 153             UrlConstants.DEFAULT_LABEL);
 154
 155     // if both links lists are empty, add the DEFAULT_URL link
 156     // otherwise we assume the default link is in one of the lists
 157     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 158     {
 159       inMenuString = UrlConstants.DEFAULT_STRING;
 160     }
 161     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 162             inMenuString, notInMenuString);
 163     sequenceUrlLinks = factory.createUrlProvider();
 164     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 165
 166     /**
 167      * TODO: reformulate groupURL encoding so two or more can be stored in the
 168      * .properties file as '|' separated strings
 169      */
 170
 171     groupURLLinks = new ArrayList<>(); // not implemented
 172   }
 173
 174   JInternalFrame frame;
 175
 176   private WsPreferences wsPrefs;
 177
 178   private OptionsParam promptEachTimeOpt = new OptionsParam(
 179           MessageManager.getString("label.prompt_each_time"),
 180           "Prompt each time");
 181
 182   private OptionsParam lineArtOpt = new OptionsParam(
 183           MessageManager.getString("label.lineart"), "Lineart");
 184
 185   private OptionsParam textOpt = new OptionsParam(
 186           MessageManager.getString("action.text"), "Text");
 187
 188   /**
 189    * Creates a new Preferences object.
 190    */
 191   public Preferences()
 192   {
 193     super();
 194     frame = new JInternalFrame();
 195     frame.setContentPane(this);
 196     if (!Platform.isJS())
 197     /**
 198      * Java only
 199      *
 200      * @j2sIgnore
 201      */
 202     {
 203       wsPrefs = new WsPreferences();
 204       wsTab.add(wsPrefs, BorderLayout.CENTER);
 205     }
 206     int width = 500, height = 450;
 207     if (Platform.isAMacAndNotJS())
 208     {
 209       width = 570;
 210       height = 480;
 211     }
 212
 213     Desktop.addInternalFrame(frame,
 214             MessageManager.getString("label.preferences"), width, height);
 215     frame.setMinimumSize(new Dimension(width, height));
 216
 217     /*
 218      * Set Visual tab defaults
 219      */
 220     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 221     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 222     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 223     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 224
 225     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 226     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 227     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 228     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 229     showUnconserved
 230             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 231     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 232     showGroupConsensus
 233             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 234     showGroupConservation.setSelected(
 235             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 236     showConsensHistogram.setSelected(
 237             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 238     showConsensLogo
 239             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 240     showNpTooltip
 241             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 242     showDbRefTooltip
 243             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 244
 245     String[] fonts = java.awt.GraphicsEnvironment
 246             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 247     for (int i = 0; i < fonts.length; i++)
 248     {
 249       fontNameCB.addItem(fonts[i]);
 250     }
 251
 252     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 253     {
 254       fontSizeCB.addItem(i + "");
 255     }
 256
 257     fontStyleCB.addItem("plain");
 258     fontStyleCB.addItem("bold");
 259     fontStyleCB.addItem("italic");
 260
 261     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 262     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 263     fontStyleCB.setSelectedItem(
 264             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 265
 266     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 267     scaleProteinToCdna
 268             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 269
 270     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 271
 272     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 273
 274     gapSymbolCB.addItem("-");
 275     gapSymbolCB.addItem(".");
 276
 277     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 278
 279     sortby.addItem("No sort");
 280     sortby.addItem("Id");
 281     sortby.addItem("Pairwise Identity");
 282     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 283
 284     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 285     sortAnnBy
 286             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 287     sortAnnBy
 288             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 289     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 290             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 291                     SequenceAnnotationOrder.NONE.name()));
 292     sortAnnBy.setSelectedItem(savedSort.toString());
 293
 294     sortAutocalc.addItem("Autocalculated first");
 295     sortAutocalc.addItem("Autocalculated last");
 296     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 297     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 298             : sortAutocalc.getItemAt(1));
 299     startupCheckbox
 300             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 301     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 302             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 303                     + "/examples/exampleFile_2_3.jar"));
 304
 305     /*
 306      * Set Colours tab defaults
 307      */
 308     protColour.addItem(ResidueColourScheme.NONE);
 309     nucColour.addItem(ResidueColourScheme.NONE);
 310     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 311     {
 312       String name = cs.getSchemeName();
 313       protColour.addItem(name);
 314       nucColour.addItem(name);
 315     }
 316     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 317             ResidueColourScheme.NONE);
 318     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 319     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 320     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 321     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 322     minColour.setBackground(
 323             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 324     maxColour.setBackground(
 325             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 326
 327     /*
 328      * Set overview panel defaults
 329      */
 330     gapColour.setBackground(
 331             Cache.getDefaultColour(GAP_COLOUR,
 332                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 333     hiddenColour.setBackground(
 334             Cache.getDefaultColour(HIDDEN_COLOUR,
 335                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 336     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 337     gapLabel.setEnabled(!useLegacyGap.isSelected());
 338     gapColour.setEnabled(!useLegacyGap.isSelected());
 339     showHiddenAtStart
 340             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 341
 342     /*
 343      * Set Structure tab defaults.
 344      */
 345     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 346     structFromPdb.setSelected(structSelected);
 347     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 348     useRnaView.setEnabled(structSelected);
 349     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 350     addSecondaryStructure.setEnabled(structSelected);
 351     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 352     addTempFactor.setEnabled(structSelected);
 353     structViewer.setSelectedItem(
 354             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 355     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 356     chimeraPath.addActionListener(new ActionListener()
 357     {
 358       @Override
 359       public void actionPerformed(ActionEvent e)
 360       {
 361         validateChimeraPath();
 362       }
 363     });
 364
 365     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 366     {
 367       siftsMapping.setSelected(true);
 368     }
 369     else
 370     {
 371       nwMapping.setSelected(true);
 372     }
 373
 374     SiftsSettings
 375             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 376
 377     /*
 378      * Set Connections tab defaults
 379      */
 380
 381     // set up sorting
 382     linkUrlTable.setModel(dataModel);
 383     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 384             linkUrlTable.getModel());
 385     linkUrlTable.setRowSorter(sorter);
 386     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 387
 388     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 389     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 390             SortOrder.DESCENDING));
 391     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 392             SortOrder.DESCENDING));
 393     sortKeys.add(
 394             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 395
 396     sorter.setSortKeys(sortKeys);
 397     // BH 2018 setSortKeys will do the sort
 398     // sorter.sort();
 399
 400     // set up filtering
 401     ActionListener onReset;
 402     onReset = new ActionListener()
 403     {
 404       @Override
 405       public void actionPerformed(ActionEvent e)
 406       {
 407         filterTB.setText("");
 408         sorter.setRowFilter(RowFilter.regexFilter(""));
 409       }
 410
 411     };
 412     doReset.addActionListener(onReset);
 413
 414     // filter to display only custom urls
 415     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 416     {
 417       @Override
 418       public boolean include(
 419               Entry<? extends TableModel, ? extends Object> entry)
 420       {
 421         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 422       }
 423     };
 424
 425     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 426             linkUrlTable.getModel());
 427     customSorter.setRowFilter(customUrlFilter);
 428
 429     ActionListener onCustomOnly;
 430     onCustomOnly = new ActionListener()
 431     {
 432       @Override
 433       public void actionPerformed(ActionEvent e)
 434       {
 435         filterTB.setText("");
 436         sorter.setRowFilter(customUrlFilter);
 437       }
 438     };
 439     userOnly.addActionListener(onCustomOnly);
 440
 441     filterTB.getDocument().addDocumentListener(new DocumentListener()
 442     {
 443       String caseInsensitiveFlag = "(?i)";
 444
 445       @Override
 446       public void changedUpdate(DocumentEvent e)
 447       {
 448         sorter.setRowFilter(RowFilter
 449                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 450       }
 451
 452       @Override
 453       public void removeUpdate(DocumentEvent e)
 454       {
 455         sorter.setRowFilter(RowFilter
 456                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 457       }
 458
 459       @Override
 460       public void insertUpdate(DocumentEvent e)
 461       {
 462         sorter.setRowFilter(RowFilter
 463                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 464       }
 465     });
 466
 467     // set up list selection functionality
 468     linkUrlTable.getSelectionModel()
 469             .addListSelectionListener(new UrlListSelectionHandler());
 470
 471     // set up radio buttons
 472     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 473             .getPrimaryColumn();
 474     String onClickName = linkUrlTable.getColumnName(onClickCol);
 475     linkUrlTable.getColumn(onClickName)
 476             .setCellRenderer(new RadioButtonRenderer());
 477     linkUrlTable.getColumn(onClickName)
 478             .setCellEditor(new RadioButtonEditor());
 479
 480     // get boolean columns and resize those to min possible
 481     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 482     {
 483       if (linkUrlTable.getModel().getColumnClass(column)
 484               .equals(Boolean.class))
 485       {
 486         TableColumn tableColumn = linkUrlTable.getColumnModel()
 487                 .getColumn(column);
 488         int preferredWidth = tableColumn.getMinWidth();
 489
 490         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 491                 column);
 492         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 493         int cwidth = c.getPreferredSize().width
 494                 + linkUrlTable.getIntercellSpacing().width;
 495         preferredWidth = Math.max(preferredWidth, cwidth);
 496
 497         tableColumn.setPreferredWidth(preferredWidth);
 498       }
 499     }
 500
 501     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 502     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 503     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 504     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 505
 506     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 507
 508     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 509     // note antisense here: default is true
 510     questionnaire
 511             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 512     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 513
 514     /*
 515      * Set Output tab defaults
 516      */
 517     setupOutputCombo(epsRendering, "EPS_RENDERING");
 518     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 519     setupOutputCombo(svgRendering, "SVG_RENDERING");
 520     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 521     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 522     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 523     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 524     userIdWidth.setText(wi == null ? "" : wi.toString());
 525     // TODO: refactor to use common enum via FormatAdapter and allow extension
 526     // for new flat file formats
 527     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 528     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 529     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 530     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 531     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 532     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 533     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 534     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 535     embbedBioJSON
 536             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 537
 538     /*
 539      * Set Editing tab defaults
 540      */
 541     autoCalculateConsCheck
 542             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 543     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 544     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 545
 546     annotations_actionPerformed(null); // update the display of the annotation
 547                                        // settings
 548
 549
 550     /*
 551      * Set Backups tab defaults
 552      */
 553     loadLastSavedBackupsOptions();
 554   }
 555
 556   /**
 557    * A helper method that sets the items and initial selection in a character
 558    * rendering option list (Prompt each time/Lineart/Text)
 559    *
 560    * @param comboBox
 561    * @param propertyKey
 562    */
 563   protected void setupOutputCombo(JComboBox<Object> comboBox,
 564           String propertyKey)
 565   {
 566     comboBox.addItem(promptEachTimeOpt);
 567     comboBox.addItem(lineArtOpt);
 568     comboBox.addItem(textOpt);
 569
 570     /*
 571      * JalviewJS doesn't support Lineart so force it to Text
 572      */
 573     String defaultOption = Platform.isJS() ? "Text"
 574             : Cache.getDefault(propertyKey, "Prompt each time");
 575     if (defaultOption.equalsIgnoreCase("Text"))
 576     {
 577       comboBox.setSelectedItem(textOpt);
 578     }
 579     else if (defaultOption.equalsIgnoreCase("Lineart"))
 580     {
 581       comboBox.setSelectedItem(lineArtOpt);
 582     }
 583     else
 584     {
 585       comboBox.setSelectedItem(promptEachTimeOpt);
 586     }
 587   }
 588
 589   /**
 590    * Save user selections on the Preferences tabs to the Cache and write out to
 591    * file.
 592    *
 593    * @param e
 594    */
 595   @Override
 596   public void ok_actionPerformed(ActionEvent e)
 597   {
 598     if (!validateSettings())
 599     {
 600       return;
 601     }
 602
 603     /*
 604      * Save Visual settings
 605      */
 606     Cache.setPropertyNoSave("SHOW_JVSUFFIX",
 607             Boolean.toString(seqLimit.isSelected()));
 608     Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
 609             Boolean.toString(rightAlign.isSelected()));
 610     Cache.setPropertyNoSave("SHOW_FULLSCREEN",
 611             Boolean.toString(fullScreen.isSelected()));
 612     Cache.setPropertyNoSave("SHOW_OVERVIEW",
 613             Boolean.toString(openoverv.isSelected()));
 614     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
 615             Boolean.toString(annotations.isSelected()));
 616     Cache.setPropertyNoSave("SHOW_CONSERVATION",
 617             Boolean.toString(conservation.isSelected()));
 618     Cache.setPropertyNoSave("SHOW_QUALITY",
 619             Boolean.toString(quality.isSelected()));
 620     Cache.setPropertyNoSave("SHOW_IDENTITY",
 621             Boolean.toString(identity.isSelected()));
 622
 623     Cache.setPropertyNoSave("GAP_SYMBOL",
 624             gapSymbolCB.getSelectedItem().toString());
 625
 626     Cache.setPropertyNoSave("FONT_NAME",
 627             fontNameCB.getSelectedItem().toString());
 628     Cache.setPropertyNoSave("FONT_STYLE",
 629             fontStyleCB.getSelectedItem().toString());
 630     Cache.setPropertyNoSave("FONT_SIZE",
 631             fontSizeCB.getSelectedItem().toString());
 632
 633     Cache.setPropertyNoSave("ID_ITALICS",
 634             Boolean.toString(idItalics.isSelected()));
 635     Cache.setPropertyNoSave("SHOW_UNCONSERVED",
 636             Boolean.toString(showUnconserved.isSelected()));
 637     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
 638             Boolean.toString(showOccupancy.isSelected()));
 639     Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
 640             Boolean.toString(showGroupConsensus.isSelected()));
 641     Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
 642             Boolean.toString(showGroupConservation.isSelected()));
 643     Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
 644             Boolean.toString(showConsensHistogram.isSelected()));
 645     Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
 646             Boolean.toString(showConsensLogo.isSelected()));
 647     Cache.setPropertyNoSave("ANTI_ALIAS",
 648             Boolean.toString(smoothFont.isSelected()));
 649     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
 650             Boolean.toString(scaleProteinToCdna.isSelected()));
 651     Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
 652             Boolean.toString(showNpTooltip.isSelected()));
 653     Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
 654             Boolean.toString(showDbRefTooltip.isSelected()));
 655
 656     Cache.setPropertyNoSave("WRAP_ALIGNMENT",
 657             Boolean.toString(wrap.isSelected()));
 658
 659     Cache.setPropertyNoSave("STARTUP_FILE",
 660             startupFileTextfield.getText());
 661     Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
 662             Boolean.toString(startupCheckbox.isSelected()));
 663
 664     Cache.setPropertyNoSave("SORT_ALIGNMENT",
 665             sortby.getSelectedItem().toString());
 666
 667     // convert description of sort order to enum name for save
 668     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 669             .forDescription(sortAnnBy.getSelectedItem().toString());
 670     if (annSortOrder != null)
 671     {
 672       Cache.setPropertyNoSave(SORT_ANNOTATIONS,
 673               annSortOrder.name());
 674     }
 675
 676     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 677     Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
 678             Boolean.valueOf(showAutocalcFirst).toString());
 679
 680     /*
 681      * Save Colours settings
 682      */
 683     Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
 684             protColour.getSelectedItem().toString());
 685     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
 686             nucColour.getSelectedItem().toString());
 687     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 688             minColour.getBackground());
 689     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 690             maxColour.getBackground());
 691
 692     /*
 693      * Save Overview settings
 694      */
 695     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 696     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 697     Cache.setPropertyNoSave(USE_LEGACY_GAP,
 698             Boolean.toString(useLegacyGap.isSelected()));
 699     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
 700             Boolean.toString(showHiddenAtStart.isSelected()));
 701
 702     /*
 703      * Save Structure settings
 704      */
 705     Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
 706             Boolean.toString(addTempFactor.isSelected()));
 707     Cache.setPropertyNoSave(ADD_SS_ANN,
 708             Boolean.toString(addSecondaryStructure.isSelected()));
 709     Cache.setPropertyNoSave(USE_RNAVIEW,
 710             Boolean.toString(useRnaView.isSelected()));
 711     Cache.setPropertyNoSave(STRUCT_FROM_PDB,
 712             Boolean.toString(structFromPdb.isSelected()));
 713     Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
 714             structViewer.getSelectedItem().toString());
 715     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 716     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
 717             Boolean.toString(siftsMapping.isSelected()));
 718     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 719
 720     /*
 721      * Save Output settings
 722      */
 723     Cache.setPropertyNoSave("EPS_RENDERING",
 724             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 725     Cache.setPropertyNoSave("HTML_RENDERING",
 726             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 727     Cache.setPropertyNoSave("SVG_RENDERING",
 728             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 729
 730     if (!Platform.isJS())
 731     /**
 732      * @j2sNative
 733      */
 734     {
 735       // Java only
 736       // Save Connections settings
 737       Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 738       BrowserLauncher.resetBrowser();
 739     }
 740
 741     // save user-defined and selected links
 742     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 743     if (menuLinks.isEmpty())
 744     {
 745       Cache.removePropertyNoSave("SEQUENCE_LINKS");
 746     }
 747     else
 748     {
 749       Cache.setPropertyNoSave("SEQUENCE_LINKS",
 750               menuLinks.toString());
 751     }
 752
 753     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 754     if (nonMenuLinks.isEmpty())
 755     {
 756       Cache.removePropertyNoSave("STORED_LINKS");
 757     }
 758     else
 759     {
 760       Cache.setPropertyNoSave("STORED_LINKS",
 761               nonMenuLinks.toString());
 762     }
 763
 764     Cache.setPropertyNoSave("DEFAULT_URL",
 765             sequenceUrlLinks.getPrimaryUrlId());
 766
 767     Cache.setPropertyNoSave("USE_PROXY",
 768             Boolean.toString(useProxy.isSelected()));
 769
 770     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 771
 772     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 773
 774     if (useProxy.isSelected())
 775     {
 776       System.setProperty("http.proxyHost", proxyServerTB.getText());
 777       System.setProperty("http.proxyPort", proxyPortTB.getText());
 778     }
 779     else
 780     {
 781       System.setProperty("http.proxyHost", "");
 782       System.setProperty("http.proxyPort", "");
 783     }
 784     Cache.setProperty("VERSION_CHECK",
 785             Boolean.toString(versioncheck.isSelected()));
 786     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 787     {
 788       // default is false - we only set this if the user has actively agreed
 789       Cache.setProperty("USAGESTATS",
 790               Boolean.toString(usagestats.isSelected()));
 791     }
 792     if (!questionnaire.isSelected())
 793     {
 794       Cache.setProperty("NOQUESTIONNAIRES", "true");
 795     }
 796     else
 797     {
 798       // special - made easy to edit a property file to disable questionnaires
 799       // by just adding the given line
 800       Cache.removeProperty("NOQUESTIONNAIRES");
 801     }
 802
 803     /*
 804      * Save Output settings
 805      */
 806     Cache.setPropertyNoSave("BLC_JVSUFFIX",
 807             Boolean.toString(blcjv.isSelected()));
 808     Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
 809             Boolean.toString(clustaljv.isSelected()));
 810     Cache.setPropertyNoSave("FASTA_JVSUFFIX",
 811             Boolean.toString(fastajv.isSelected()));
 812     Cache.setPropertyNoSave("MSF_JVSUFFIX",
 813             Boolean.toString(msfjv.isSelected()));
 814     Cache.setPropertyNoSave("PFAM_JVSUFFIX",
 815             Boolean.toString(pfamjv.isSelected()));
 816     Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
 817             Boolean.toString(pileupjv.isSelected()));
 818     Cache.setPropertyNoSave("PIR_JVSUFFIX",
 819             Boolean.toString(pirjv.isSelected()));
 820     Cache.setPropertyNoSave("PIR_MODELLER",
 821             Boolean.toString(modellerOutput.isSelected()));
 822     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
 823             Boolean.toString(embbedBioJSON.isSelected()));
 824     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
 825             Boolean.toString(autoIdWidth.isSelected()));
 826     userIdWidth_actionPerformed();
 827     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
 828             userIdWidth.getText());
 829
 830     /*
 831      * Save Editing settings
 832      */
 833     Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
 834             Boolean.toString(autoCalculateConsCheck.isSelected()));
 835     Cache.setPropertyNoSave("SORT_BY_TREE",
 836             Boolean.toString(sortByTree.isSelected()));
 837     Cache.setPropertyNoSave("PAD_GAPS",
 838             Boolean.toString(padGaps.isSelected()));
 839
 840     if (!Platform.isJS())
 841     {
 842       wsPrefs.updateAndRefreshWsMenuConfig(false);
 843     }
 844
 845     /*
 846      * Save Backups settings
 847      */
 848     Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
 849             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 850     Cache.setPropertyNoSave(BackupFiles.ENABLED,
 851             Boolean.toString(enableBackupFiles.isSelected()));
 852     Cache.setPropertyNoSave(BackupFiles.NO_MAX,
 853             Boolean.toString(backupfilesKeepAll.isSelected()));
 854     Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
 855             Boolean.toString(suffixReverse.isSelected()));
 856     Cache.setPropertyNoSave(BackupFiles.SUFFIX,
 857             suffixTemplate.getText());
 858     Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
 859             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 860     Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
 861             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 862     Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
 863             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 864
 865     Cache.saveProperties();
 866     Instance.getDesktop().doConfigureStructurePrefs();
 867     try
 868     {
 869       frame.setClosed(true);
 870     } catch (Exception ex)
 871     {
 872     }
 873   }
 874
 875   /**
 876    * Do any necessary validation before saving settings. Return focus to the
 877    * first tab which fails validation.
 878    *
 879    * @return
 880    */
 881   private boolean validateSettings()
 882   {
 883     if (!validateStructure())
 884     {
 885       structureTab.requestFocusInWindow();
 886       return false;
 887     }
 888     return true;
 889   }
 890
 891   @Override
 892   protected boolean validateStructure()
 893   {
 894     return validateChimeraPath();
 895
 896   }
 897
 898   /**
 899    * DOCUMENT ME!
 900    */
 901   @Override
 902   public void startupFileTextfield_mouseClicked()
 903   {
 904     // TODO: JAL-3048 not needed for Jalview-JS
 905     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 906     JalviewFileChooser chooser = JalviewFileChooser
 907             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 908     chooser.setFileView(new JalviewFileView());
 909     chooser.setDialogTitle(
 910             MessageManager.getString("label.select_startup_file"));
 911
 912     int value = chooser.showOpenDialog(this);
 913
 914     if (value == JalviewFileChooser.APPROVE_OPTION)
 915     {
 916       FileFormatI format = chooser.getSelectedFormat();
 917       if (format != null)
 918       {
 919         Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
 920                 format.getName());
 921       }
 922       startupFileTextfield
 923               .setText(chooser.getSelectedFile().getAbsolutePath());
 924     }
 925   }
 926
 927   /**
 928    * DOCUMENT ME!
 929    *
 930    * @param e
 931    *          DOCUMENT ME!
 932    */
 933   @Override
 934   public void cancel_actionPerformed(ActionEvent e)
 935   {
 936     try
 937     {
 938       if (!Platform.isJS())
 939       {
 940         wsPrefs.updateWsMenuConfig(true);
 941         wsPrefs.refreshWs_actionPerformed(e);
 942       }
 943       frame.setClosed(true);
 944     } catch (Exception ex)
 945     {
 946     }
 947   }
 948
 949   /**
 950    * DOCUMENT ME!
 951    *
 952    * @param e
 953    *          DOCUMENT ME!
 954    */
 955   @Override
 956   public void annotations_actionPerformed(ActionEvent e)
 957   {
 958     conservation.setEnabled(annotations.isSelected());
 959     quality.setEnabled(annotations.isSelected());
 960     identity.setEnabled(annotations.isSelected());
 961     showOccupancy.setEnabled(annotations.isSelected());
 962     showGroupConsensus.setEnabled(annotations.isSelected());
 963     showGroupConservation.setEnabled(annotations.isSelected());
 964     showConsensHistogram.setEnabled(annotations.isSelected()
 965             && (identity.isSelected() || showGroupConsensus.isSelected()));
 966     showConsensLogo.setEnabled(annotations.isSelected()
 967             && (identity.isSelected() || showGroupConsensus.isSelected()));
 968   }
 969
 970   @Override
 971   public void newLink_actionPerformed(ActionEvent e)
 972   {
 973     GSequenceLink link = new GSequenceLink();
 974     boolean valid = false;
 975     while (!valid)
 976     {
 977       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
 978               MessageManager.getString("label.new_sequence_url_link"),
 979               JvOptionPane.OK_CANCEL_OPTION, -1,
 980               null) == JvOptionPane.OK_OPTION)
 981       {
 982         if (link.checkValid())
 983         {
 984           if (((UrlLinkTableModel) linkUrlTable.getModel())
 985                   .isUniqueName(link.getName()))
 986           {
 987             ((UrlLinkTableModel) linkUrlTable.getModel())
 988                     .insertRow(link.getName(), link.getURL());
 989             valid = true;
 990           }
 991           else
 992           {
 993             link.notifyDuplicate();
 994             continue;
 995           }
 996         }
 997       }
 998       else
 999       {
1000         break;
1001       }
1002     }
1003   }
1004
1005   @Override
1006   public void editLink_actionPerformed(ActionEvent e)
1007   {
1008     GSequenceLink link = new GSequenceLink();
1009
1010     int index = linkUrlTable.getSelectedRow();
1011     if (index == -1)
1012     {
1013       // button no longer enabled if row is not selected
1014       Cache.log.debug("Edit with no row selected in linkUrlTable");
1015       return;
1016     }
1017
1018     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1019             .getNameColumn();
1020     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1021             .getUrlColumn();
1022     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1023     link.setName(oldName);
1024     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1025
1026     boolean valid = false;
1027     while (!valid)
1028     {
1029       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1030               MessageManager.getString("label.edit_sequence_url_link"),
1031               JvOptionPane.OK_CANCEL_OPTION, -1,
1032               null) == JvOptionPane.OK_OPTION)
1033       {
1034         if (link.checkValid())
1035         {
1036           if ((oldName.equals(link.getName()))
1037                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1038                           .isUniqueName(link.getName())))
1039           {
1040             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1041             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1042             valid = true;
1043           }
1044           else
1045           {
1046             link.notifyDuplicate();
1047             continue;
1048           }
1049         }
1050       }
1051       else
1052       {
1053         break;
1054       }
1055     }
1056   }
1057
1058   @Override
1059   public void deleteLink_actionPerformed(ActionEvent e)
1060   {
1061     int index = linkUrlTable.getSelectedRow();
1062     int modelIndex = -1;
1063     if (index == -1)
1064     {
1065       // button no longer enabled if row is not selected
1066       Cache.log.debug("Delete with no row selected in linkUrlTable");
1067       return;
1068     }
1069     else
1070     {
1071       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1072     }
1073
1074     // make sure we use the model index to delete, and not the table index
1075     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1076   }
1077
1078   @Override
1079   public void defaultBrowser_mouseClicked(MouseEvent e)
1080   {
1081     // TODO: JAL-3048 not needed for j2s
1082     if (!Platform.isJS()) // BH 2019
1083     /**
1084      * Java only
1085      *
1086      * @j2sIgnore
1087      */
1088     {
1089       JFileChooser chooser = new JFileChooser(".");
1090       chooser.setDialogTitle(
1091               MessageManager.getString("label.select_default_browser"));
1092
1093       int value = chooser.showOpenDialog(this);
1094
1095       if (value == JFileChooser.APPROVE_OPTION)
1096       {
1097         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1098       }
1099     }
1100   }
1101
1102   /*
1103    * (non-Javadoc)
1104    *
1105    * @see
1106    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1107    * .ActionEvent)
1108    */
1109   @Override
1110   protected void showunconserved_actionPerformed(ActionEvent e)
1111   {
1112     // TODO Auto-generated method stub
1113     super.showunconserved_actionPerformed(e);
1114   }
1115
1116   /**
1117    * not implemented -- returns empty list
1118    *
1119    * @return
1120    */
1121   public static List<String> getGroupURLLinks()
1122   {
1123     return groupURLLinks;
1124   }
1125
1126   @Override
1127   public void minColour_actionPerformed(JPanel panel)
1128   {
1129     JalviewColourChooser.showColourChooser(this,
1130             MessageManager.getString("label.select_colour_minimum_value"),
1131             panel);
1132   }
1133
1134   @Override
1135   public void maxColour_actionPerformed(JPanel panel)
1136   {
1137     JalviewColourChooser.showColourChooser(this,
1138             MessageManager.getString("label.select_colour_maximum_value"),
1139             panel);
1140   }
1141
1142   @Override
1143   public void gapColour_actionPerformed(JPanel gap)
1144   {
1145     if (!useLegacyGap.isSelected())
1146     {
1147       JalviewColourChooser.showColourChooser(this,
1148               MessageManager.getString("label.select_gap_colour"),
1149               gap);
1150     }
1151   }
1152
1153   @Override
1154   public void hiddenColour_actionPerformed(JPanel hidden)
1155   {
1156     JalviewColourChooser.showColourChooser(this,
1157             MessageManager.getString("label.select_hidden_colour"),
1158             hidden);
1159   }
1160
1161   @Override
1162   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1163   {
1164     boolean enabled = useLegacyGap.isSelected();
1165     if (enabled)
1166     {
1167       gapColour.setBackground(
1168               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1169     }
1170     else
1171     {
1172       gapColour.setBackground(
1173               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1174     }
1175     gapColour.setEnabled(!enabled);
1176     gapLabel.setEnabled(!enabled);
1177   }
1178
1179   @Override
1180   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1181   {
1182     useLegacyGap.setSelected(false);
1183     useLegacyGaps_actionPerformed(null);
1184     showHiddenAtStart.setSelected(false);
1185     hiddenColour.setBackground(
1186             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1187   }
1188
1189   @Override
1190   protected void userIdWidth_actionPerformed()
1191   {
1192     try
1193     {
1194       String val = userIdWidth.getText().trim();
1195       if (val.length() > 0)
1196       {
1197         Integer iw = Integer.parseInt(val);
1198         if (iw.intValue() < 12)
1199         {
1200           throw new NumberFormatException();
1201         }
1202         userIdWidth.setText(iw.toString());
1203       }
1204     } catch (NumberFormatException x)
1205     {
1206       userIdWidth.setText("");
1207       JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1208               MessageManager
1209                       .getString("warn.user_defined_width_requirements"),
1210               MessageManager.getString("label.invalid_id_column_width"),
1211               JvOptionPane.WARNING_MESSAGE);
1212     }
1213   }
1214
1215   @Override
1216   protected void autoIdWidth_actionPerformed()
1217   {
1218     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1219     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1220   }
1221
1222   /**
1223    * Returns true if chimera path is to a valid executable, else show an error
1224    * dialog.
1225    */
1226   protected boolean validateChimeraPath()
1227   {
1228     if (chimeraPath.getText().trim().length() > 0)
1229     {
1230       File f = new File(chimeraPath.getText());
1231       if (!f.canExecute())
1232       {
1233         JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1234                 MessageManager.getString("label.invalid_chimera_path"),
1235                 MessageManager.getString("label.invalid_name"),
1236                 JvOptionPane.ERROR_MESSAGE);
1237         return false;
1238       }
1239     }
1240     return true;
1241   }
1242
1243   /**
1244    * If Chimera is selected, check it can be found on default or user-specified
1245    * path, if not show a warning/help dialog.
1246    */
1247   @Override
1248   protected void structureViewer_actionPerformed(String selectedItem)
1249   {
1250     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1251     {
1252       return;
1253     }
1254     boolean found = false;
1255
1256     /*
1257      * Try user-specified and standard paths for Chimera executable.
1258      */
1259     List<String> paths = StructureManager.getChimeraPaths();
1260     paths.add(0, chimeraPath.getText());
1261     for (String path : paths)
1262     {
1263       if (new File(path.trim()).canExecute())
1264       {
1265         found = true;
1266         break;
1267       }
1268     }
1269     if (!found)
1270     {
1271       String[] options = { "OK", "Help" };
1272       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
1273               JvSwingUtils.wrapTooltip(true,
1274                       MessageManager.getString("label.chimera_missing")),
1275               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1276               null, options, options[0]);
1277       if (showHelp == JvOptionPane.NO_OPTION)
1278       {
1279         try
1280         {
1281           Help.showHelpWindow(HelpId.StructureViewer);
1282         } catch (HelpSetException e)
1283         {
1284           e.printStackTrace();
1285         }
1286       }
1287     }
1288   }
1289
1290   public class OptionsParam
1291   {
1292     private String name;
1293
1294     private String code;
1295
1296     public OptionsParam(String name, String code)
1297     {
1298       this.name = name;
1299       this.code = code;
1300     }
1301
1302     public String getName()
1303     {
1304       return name;
1305     }
1306
1307     public void setName(String name)
1308     {
1309       this.name = name;
1310     }
1311
1312     public String getCode()
1313     {
1314       return code;
1315     }
1316
1317     public void setCode(String code)
1318     {
1319       this.code = code;
1320     }
1321
1322     @Override
1323     public String toString()
1324     {
1325       return name;
1326     }
1327
1328     @Override
1329     public boolean equals(Object that)
1330     {
1331       if (!(that instanceof OptionsParam))
1332       {
1333         return false;
1334       }
1335       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1336     }
1337
1338     @Override
1339     public int hashCode()
1340     {
1341       return name.hashCode() + code.hashCode();
1342     }
1343   }
1344
1345   protected class UrlListSelectionHandler implements ListSelectionListener
1346   {
1347
1348     @Override
1349     public void valueChanged(ListSelectionEvent e)
1350     {
1351       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1352
1353       int index = lsm.getMinSelectionIndex();
1354       if (index == -1)
1355       {
1356         // no selection, so disable delete/edit buttons
1357         editLink.setEnabled(false);
1358         deleteLink.setEnabled(false);
1359         return;
1360       }
1361       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1362
1363       // enable/disable edit and delete link buttons
1364       if (((UrlLinkTableModel) linkUrlTable.getModel())
1365               .isRowDeletable(modelIndex))
1366       {
1367         deleteLink.setEnabled(true);
1368       }
1369       else
1370       {
1371         deleteLink.setEnabled(false);
1372       }
1373
1374       if (((UrlLinkTableModel) linkUrlTable.getModel())
1375               .isRowEditable(modelIndex))
1376       {
1377         editLink.setEnabled(true);
1378       }
1379       else
1380       {
1381         editLink.setEnabled(false);
1382       }
1383     }
1384   }
1385 }