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