src/jalview/gui/Preferences.java

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