src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.FocusAdapter;
  31 import java.awt.event.FocusEvent;
  32 import java.awt.event.MouseEvent;
  33 import java.io.File;
  34 import java.util.ArrayList;
  35 import java.util.List;
  36 import java.util.concurrent.CompletableFuture;
  37
  38 import javax.help.HelpSetException;
  39 import javax.swing.JComboBox;
  40 import javax.swing.JFileChooser;
  41 import javax.swing.JInternalFrame;
  42 import javax.swing.JPanel;
  43 import javax.swing.JTabbedPane;
  44 import javax.swing.JTextField;
  45 import javax.swing.ListSelectionModel;
  46 import javax.swing.RowFilter;
  47 import javax.swing.RowSorter;
  48 import javax.swing.SortOrder;
  49 import javax.swing.event.DocumentEvent;
  50 import javax.swing.event.DocumentListener;
  51 import javax.swing.event.ListSelectionEvent;
  52 import javax.swing.event.ListSelectionListener;
  53 import javax.swing.table.TableCellRenderer;
  54 import javax.swing.table.TableColumn;
  55 import javax.swing.table.TableModel;
  56 import javax.swing.table.TableRowSorter;
  57
  58 import jalview.hmmer.HmmerCommand;
  59 import jalview.util.FileUtils;
  60 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  61 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  62 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
  63 import jalview.bin.Cache;
  64 import jalview.bin.Console;
  65 import jalview.bin.MemorySetting;
  66 import jalview.ext.pymol.PymolManager;
  67 import jalview.gui.Help.HelpId;
  68 import jalview.gui.StructureViewer.ViewerType;
  69 import jalview.io.BackupFiles;
  70 import jalview.io.BackupFilesPresetEntry;
  71 import jalview.io.FileFormatI;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.jbgui.GPreferences;
  75 import jalview.jbgui.GSequenceLink;
  76 import jalview.schemes.ColourSchemeI;
  77 import jalview.schemes.ColourSchemes;
  78 import jalview.schemes.ResidueColourScheme;
  79 import jalview.urls.UrlLinkTableModel;
  80 import jalview.urls.api.UrlProviderFactoryI;
  81 import jalview.urls.api.UrlProviderI;
  82 import jalview.urls.desktop.DesktopUrlProviderFactory;
  83 import jalview.util.MessageManager;
  84 import jalview.util.Platform;
  85 import jalview.util.UrlConstants;
  86 import jalview.ws.sifts.SiftsSettings;
  87 import jalview.ws2.client.api.WebServiceDiscovererI;
  88 import jalview.ws2.client.ebi.JobDispatcherWSDiscoverer;
  89 import jalview.ws2.client.jpred4.JPred4WSDiscoverer;
  90 import jalview.ws2.client.slivka.SlivkaWSDiscoverer;
  91
  92 /**
  93  * DOCUMENT ME!
  94  *
  95  * @author $author$
  96  * @version $Revision$
  97  */
  98 public class Preferences extends GPreferences implements ApplicationSingletonI
  99 {
 100   // suggested list delimiter character
 101   public static final String COMMA = ",";
 102
 103   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
 104
 105   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
 106
 107   public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
 108
 109   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 110
 111   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 112
 113   public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
 114
 115   public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
 116
 117   public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
 118
 119   public static final String ANTI_ALIAS = "ANTI_ALIAS";
 120
 121   public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
 122
 123   public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
 124
 125   public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
 126
 127   public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
 128
 129   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 130
 131   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 132
 133   public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
 134
 135   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 136
 137   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 138   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 139
 140   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 141
 142   public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
 143
 144   public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
 145
 146   public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
 147
 148   public static final String FONT_NAME = "FONT_NAME";
 149
 150   public static final String FONT_SIZE = "FONT_SIZE";
 151
 152   public static final String FONT_STYLE = "FONT_STYLE";
 153
 154   public static final String HMMER_PATH = "HMMER_PATH";
 155
 156   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 157
 158   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 159
 160   public static final String GAP_COLOUR = "GAP_COLOUR";
 161
 162   public static final String GAP_SYMBOL = "GAP_SYMBOL";
 163
 164   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 165
 166   public static final String HIDE_INTRONS = "HIDE_INTRONS";
 167
 168   public static final String ID_ITALICS = "ID_ITALICS";
 169
 170   public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
 171
 172   public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
 173
 174   public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
 175
 176   public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
 177
 178   public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
 179
 180   public static final String PAD_GAPS = "PAD_GAPS";
 181
 182   public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
 183   public static final String PYMOL_PATH = "PYMOL_PATH";
 184
 185   public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
 186
 187   public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
 188
 189   public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
 190
 191   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 192
 193   public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
 194
 195   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 196
 197   public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
 198
 199   public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
 200
 201   public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
 202
 203   public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
 204
 205   public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
 206
 207   public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
 208
 209   public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
 210
 211   public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
 212
 213   public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
 214   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 215
 216   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 217
 218   public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
 219
 220   public static final String SHOW_QUALITY = "SHOW_QUALITY";
 221
 222   public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
 223
 224   public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
 225
 226   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 227
 228   public static final String SORT_BY_TREE = "SORT_BY_TREE";
 229
 230   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 231
 232   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 233
 234   public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
 235
 236   public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
 237
 238   public static final String USE_FULL_SO = "USE_FULL_SO";
 239   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 240
 241   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 242
 243   public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
 244
 245   public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
 246
 247   private static final int MIN_FONT_SIZE = 1;
 248
 249   private static final int MAX_FONT_SIZE = 30;
 250
 251   private String previousProxyType;
 252
 253   private static Preferences INSTANCE = null; // add "final"
 254
 255   /**
 256    * Holds name and link separated with | character. Sequence ID must be
 257    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 258    */
 259   public static UrlProviderI sequenceUrlLinks;
 260
 261   public static UrlLinkTableModel dataModel;
 262
 263   /**
 264    * Holds name and link separated with | character. Sequence IDS and Sequences
 265    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
 266    * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
 267    * second token specified after a pipe character at end |,|. (TODO: proper
 268    * escape for using | to separate ids or sequences
 269    */
 270
 271   public static List<String> groupURLLinks;
 272   static
 273   {
 274     // get links selected to be in the menu (SEQUENCE_LINKS)
 275     // and links entered by the user but not selected (STORED_LINKS)
 276     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 277     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 278     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 279             UrlConstants.DEFAULT_LABEL);
 280
 281     // if both links lists are empty, add the DEFAULT_URL link
 282     // otherwise we assume the default link is in one of the lists
 283     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 284     {
 285       inMenuString = UrlConstants.DEFAULT_STRING;
 286     }
 287     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 288             inMenuString, notInMenuString);
 289     sequenceUrlLinks = factory.createUrlProvider();
 290     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 291
 292     /**
 293      * TODO: reformulate groupURL encoding so two or more can be stored in the
 294      * .properties file as '|' separated strings
 295      */
 296
 297     groupURLLinks = new ArrayList<>();
 298   }
 299
 300   JInternalFrame frame;
 301
 302   private WsPreferences wsPrefs;
 303
 304   private OptionsParam promptEachTimeOpt = new OptionsParam(
 305           MessageManager.getString("label.prompt_each_time"),
 306           "Prompt each time");
 307
 308   private OptionsParam lineArtOpt = new OptionsParam(
 309           MessageManager.getString("label.lineart"), "Lineart");
 310
 311   private OptionsParam textOpt = new OptionsParam(
 312           MessageManager.getString("action.text"), "Text");
 313
 314   // get singleton Preferences instance
 315   public static Preferences getInstance()
 316   {
 317     if (INSTANCE == null || INSTANCE.frame == null
 318             || INSTANCE.frame.isClosed())
 319     {
 320       INSTANCE = new Preferences();
 321     }
 322     return INSTANCE;
 323
 324     /*
 325      * Replace code with the following for Jalvew-JS
 326     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 327     if (INSTANCE == null || INSTANCE.frame == null
 328             || INSTANCE.frame.isClosed())
 329     {
 330       ApplicationSingletonProvider.remove(Preferences.class);
 331       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 332     }
 333     return INSTANCE;
 334     */
 335   }
 336
 337   public static void openPreferences()
 338   {
 339     openPreferences(null, null);
 340   }
 341
 342   public static void openPreferences(TabRef selectTab, String message)
 343   {
 344     Preferences p = getInstance();
 345     if (selectTab != null)
 346       p.selectTab(selectTab, message);
 347     p.frame.show();
 348     p.frame.moveToFront();
 349     p.frame.grabFocus();
 350   }
 351
 352   public void selectTab(TabRef selectTab, String message)
 353   {
 354     this.selectTab(selectTab);
 355     if (message != null)
 356       this.setMessage(message);
 357     this.frame.show();
 358   }
 359
 360   /**
 361    * Creates a new Preferences object.
 362    */
 363   private Preferences()
 364   {
 365     super();
 366     frame = new JInternalFrame();
 367     frame.setContentPane(this);
 368     if (!Platform.isJS())
 369     /**
 370      * Java only
 371      *
 372      * @j2sIgnore
 373      */
 374     {
 375       wsPrefs = new WsPreferences();
 376       wsTab.add(wsPrefs, BorderLayout.CENTER);
 377     }
 378
 379     if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
 380       addWebServiceTab(tabbedPane, SlivkaWSDiscoverer.getInstance());
 381     if (Cache.getDefault("SHOW_EBI_SERVICES", true))
 382       addWebServiceTab(tabbedPane, JobDispatcherWSDiscoverer.getInstance());
 383     if (Cache.getDefault("SHOW_JPRED4_SERVICES", true))
 384       addWebServiceTab(tabbedPane, JPred4WSDiscoverer.getInstance());
 385
 386     int width = 500, height = 450;
 387     if (Platform.isAMacAndNotJS())
 388     {
 389       width = 570;
 390       height = 480;
 391     }
 392
 393     Desktop.addInternalFrame(frame,
 394             MessageManager.getString("label.preferences"), width, height);
 395     frame.setMinimumSize(new Dimension(width, height));
 396
 397     /*
 398      * Set HMMER tab defaults
 399      */
 400     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 401     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 402     {
 403       hmmerBackgroundUniprot.setSelected(true);
 404     }
 405     else
 406     {
 407       hmmerBackgroundAlignment.setSelected(true);
 408     }
 409     hmmerSequenceCount
 410             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 411     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 412     hmmerPath.addActionListener(new ActionListener()
 413     {
 414       @Override
 415       public void actionPerformed(ActionEvent e)
 416       {
 417         validateHmmerPath();
 418       }
 419     });
 420     hmmerPath.addFocusListener(new FocusAdapter()
 421     {
 422       @Override
 423       public void focusLost(FocusEvent e)
 424       {
 425         validateHmmerPath();
 426       }
 427     });
 428     if (cygwinPath != null)
 429     {
 430       String path = Cache.getProperty(CYGWIN_PATH);
 431       if (path == null)
 432       {
 433         path = FileUtils.getPathTo("bash");
 434       }
 435       cygwinPath.setText(path);
 436       cygwinPath.addActionListener(new ActionListener()
 437       {
 438         @Override
 439         public void actionPerformed(ActionEvent e)
 440         {
 441           validateCygwinPath();
 442         }
 443       });
 444       cygwinPath.addFocusListener(new FocusAdapter()
 445       {
 446         @Override
 447         public void focusLost(FocusEvent e)
 448         {
 449           validateCygwinPath();
 450         }
 451       });
 452     }
 453
 454     /*
 455      * Set Visual tab defaults
 456      */
 457     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 458     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 459     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 460     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 461
 462     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 463     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 464     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 465     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 466     showUnconserved
 467             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 468     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 469     showGroupConsensus
 470             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 471     showGroupConservation.setSelected(
 472             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 473     showConsensHistogram.setSelected(
 474             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 475     showConsensLogo
 476             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 477     showInformationHistogram.setSelected(
 478             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 479     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 480     showNpTooltip
 481             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 482     showDbRefTooltip
 483             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 484
 485     String[] fonts = java.awt.GraphicsEnvironment
 486             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 487     for (int i = 0; i < fonts.length; i++)
 488     {
 489       fontNameCB.addItem(fonts[i]);
 490     }
 491
 492     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 493     {
 494       fontSizeCB.addItem(i + "");
 495     }
 496
 497     fontStyleCB.addItem("plain");
 498     fontStyleCB.addItem("bold");
 499     fontStyleCB.addItem("italic");
 500
 501     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 502     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 503     fontStyleCB.setSelectedItem(
 504             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 505
 506     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 507     scaleProteinToCdna
 508             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 509
 510     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 511
 512     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 513
 514     gapSymbolCB.addItem("-");
 515     gapSymbolCB.addItem(".");
 516
 517     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 518
 519     sortby.addItem("No sort");
 520     sortby.addItem("Id");
 521     sortby.addItem("Pairwise Identity");
 522     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 523
 524     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 525     sortAnnBy
 526             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 527     sortAnnBy
 528             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 529     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 530             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 531                     SequenceAnnotationOrder.NONE.name()));
 532     sortAnnBy.setSelectedItem(savedSort.toString());
 533
 534     sortAutocalc.addItem("Autocalculated first");
 535     sortAutocalc.addItem("Autocalculated last");
 536     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 537     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 538             : sortAutocalc.getItemAt(1));
 539     startupCheckbox
 540             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 541     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 542             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 543                     + "/examples/exampleFile_2_7.jvp"));
 544
 545     /*
 546      * Set Colours tab defaults
 547      */
 548     protColour.addItem(ResidueColourScheme.NONE);
 549     nucColour.addItem(ResidueColourScheme.NONE);
 550     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 551     {
 552       String name = cs.getSchemeName();
 553       protColour.addItem(name);
 554       nucColour.addItem(name);
 555     }
 556     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 557             ResidueColourScheme.NONE);
 558     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 559     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 560     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 561     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 562     minColour.setBackground(
 563             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 564     maxColour.setBackground(
 565             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 566
 567     /*
 568      * Set overview panel defaults
 569      */
 570     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 571             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 572     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 573             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 574     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 575     gapLabel.setEnabled(!useLegacyGap.isSelected());
 576     gapColour.setEnabled(!useLegacyGap.isSelected());
 577     showHiddenAtStart
 578             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 579
 580     /*
 581      * Set Structure tab defaults
 582      */
 583     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
 584     structFromPdb.setSelected(structSelected);
 585     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
 586     addSecondaryStructure.setEnabled(structSelected);
 587     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
 588     addTempFactor.setEnabled(structSelected);
 589
 590     /*
 591      * set choice of structure viewer, and path if saved as a preference;
 592      * default to Jmol (first choice) if an unexpected value is found
 593      */
 594     String viewerType = ViewerType.JMOL.name();
 595     if (!Platform.isJS())
 596     {
 597       Cache.getDefault(STRUCTURE_DISPLAY,
 598             ViewerType.JMOL.name());
 599     }
 600     // TODO - disable external viewers for JS
 601     structViewer.setSelectedItem(viewerType);
 602     String viewerPath = "";
 603     ViewerType type = null;
 604     try
 605     {
 606       type = ViewerType.valueOf(viewerType);
 607       switch (type)
 608       {
 609       case JMOL:
 610         break;
 611       case CHIMERA:
 612         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 613         break;
 614       case CHIMERAX:
 615         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 616         break;
 617       case PYMOL:
 618         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 619         break;
 620       }
 621     } catch (IllegalArgumentException e)
 622     {
 623       Console.error("Unknown structure viewer type: " + viewerType
 624               + ", defaulting to Jmol");
 625       type = ViewerType.JMOL;
 626     }
 627     structureViewerPath.setText(viewerPath);
 628
 629     structureViewerPath.addActionListener(new ActionListener()
 630     {
 631       @Override
 632       public void actionPerformed(ActionEvent e)
 633       {
 634         if (validateViewerPath())
 635         {
 636           String path = structureViewerPath.getText();
 637           try
 638           {
 639             ViewerType type = ViewerType.valueOf(viewerType);
 640             switch (type)
 641             {
 642             case JMOL:
 643               break;
 644             case CHIMERA:
 645               Cache.setProperty(CHIMERA_PATH, path);
 646               break;
 647             case CHIMERAX:
 648               Cache.setProperty(CHIMERAX_PATH, path);
 649               break;
 650             case PYMOL:
 651               Cache.setProperty(PYMOL_PATH, path);
 652               break;
 653             }
 654           } catch (IllegalArgumentException x)
 655           {
 656             Console.error("Failed to set path - unknown viewer type", x);
 657           }
 658         }
 659       }
 660     });
 661
 662     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 663     {
 664       siftsMapping.setSelected(true);
 665     }
 666     else
 667     {
 668       nwMapping.setSelected(true);
 669     }
 670
 671     SiftsSettings
 672             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 673
 674     /*
 675      * Set Connections tab defaults
 676      */
 677
 678     // set up sorting
 679     linkUrlTable.setModel(dataModel);
 680     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 681             linkUrlTable.getModel());
 682     linkUrlTable.setRowSorter(sorter);
 683     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 684
 685     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 686     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 687             SortOrder.DESCENDING));
 688     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 689             SortOrder.DESCENDING));
 690     sortKeys.add(
 691             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 692
 693     sorter.setSortKeys(sortKeys);
 694     // BH 2018 setSortKeys will do the sort
 695     // sorter.sort();
 696
 697     // set up filtering
 698     ActionListener onReset;
 699     onReset = new ActionListener()
 700     {
 701       @Override
 702       public void actionPerformed(ActionEvent e)
 703       {
 704         filterTB.setText("");
 705         sorter.setRowFilter(RowFilter.regexFilter(""));
 706       }
 707
 708     };
 709     doReset.addActionListener(onReset);
 710
 711     // filter to display only custom urls
 712     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 713     {
 714       @Override
 715       public boolean include(
 716               Entry<? extends TableModel, ? extends Object> entry)
 717       {
 718         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 719       }
 720     };
 721
 722     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 723             linkUrlTable.getModel());
 724     customSorter.setRowFilter(customUrlFilter);
 725
 726     ActionListener onCustomOnly;
 727     onCustomOnly = new ActionListener()
 728     {
 729       @Override
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         filterTB.setText("");
 733         sorter.setRowFilter(customUrlFilter);
 734       }
 735     };
 736     userOnly.addActionListener(onCustomOnly);
 737
 738     filterTB.getDocument().addDocumentListener(new DocumentListener()
 739     {
 740       String caseInsensitiveFlag = "(?i)";
 741
 742       @Override
 743       public void changedUpdate(DocumentEvent e)
 744       {
 745         sorter.setRowFilter(RowFilter
 746                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 747       }
 748
 749       @Override
 750       public void removeUpdate(DocumentEvent e)
 751       {
 752         sorter.setRowFilter(RowFilter
 753                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 754       }
 755
 756       @Override
 757       public void insertUpdate(DocumentEvent e)
 758       {
 759         sorter.setRowFilter(RowFilter
 760                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 761       }
 762     });
 763
 764     // set up list selection functionality
 765     linkUrlTable.getSelectionModel()
 766             .addListSelectionListener(new UrlListSelectionHandler());
 767
 768     // set up radio buttons
 769     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 770             .getPrimaryColumn();
 771     String onClickName = linkUrlTable.getColumnName(onClickCol);
 772     linkUrlTable.getColumn(onClickName)
 773             .setCellRenderer(new RadioButtonRenderer());
 774     linkUrlTable.getColumn(onClickName)
 775             .setCellEditor(new RadioButtonEditor());
 776
 777     // get boolean columns and resize those to min possible
 778     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 779     {
 780       if (linkUrlTable.getModel().getColumnClass(column)
 781               .equals(Boolean.class))
 782       {
 783         TableColumn tableColumn = linkUrlTable.getColumnModel()
 784                 .getColumn(column);
 785         int preferredWidth = tableColumn.getMinWidth();
 786
 787         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 788                 column);
 789         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 790         int cwidth = c.getPreferredSize().width
 791                 + linkUrlTable.getIntercellSpacing().width;
 792         preferredWidth = Math.max(preferredWidth, cwidth);
 793
 794         tableColumn.setPreferredWidth(preferredWidth);
 795       }
 796     }
 797
 798     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 799     previousProxyType = proxyTypeString;
 800     switch (proxyTypeString)
 801     {
 802     case Cache.PROXYTYPE_NONE:
 803       proxyType.setSelected(noProxy.getModel(), true);
 804       break;
 805     case Cache.PROXYTYPE_SYSTEM:
 806       proxyType.setSelected(systemProxy.getModel(), true);
 807       break;
 808     case Cache.PROXYTYPE_CUSTOM:
 809       proxyType.setSelected(customProxy.getModel(), true);
 810       break;
 811     default:
 812       Console.warn(
 813               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 814                       + proxyTypeString);
 815     }
 816     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 817     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 818     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 819     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 820     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 821     proxyAuthUsernameTB
 822             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 823     // we are not storing or retrieving proxy password from .jalview_properties
 824     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 825             : new String(Cache.proxyAuthPassword));
 826     setCustomProxyEnabled();
 827     applyProxyButtonEnabled(false);
 828
 829     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 830
 831     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 832     // note antisense here: default is true
 833     questionnaire
 834             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 835     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 836
 837     /*
 838      * Set Output tab defaults
 839      */
 840     setupOutputCombo(epsRendering, "EPS_RENDERING");
 841     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 842     setupOutputCombo(svgRendering, "SVG_RENDERING");
 843     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 844     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 845     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 846     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 847     userIdWidth.setText(wi == null ? "" : wi.toString());
 848     // TODO: refactor to use common enum via FormatAdapter and allow extension
 849     // for new flat file formats
 850     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 851     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 852     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 853     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 854     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 855     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 856     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 857     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 858     embbedBioJSON
 859             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 860
 861     /*
 862      * Set Editing tab defaults
 863      */
 864     autoCalculateConsCheck
 865             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 866     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 867     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 868
 869     annotations_actionPerformed(null); // update the display of the annotation
 870                                        // settings
 871
 872
 873
 874     /*
 875      * Set Backups tab defaults
 876      */
 877     loadLastSavedBackupsOptions();
 878   }
 879
 880
 881   private void addWebServiceTab(JTabbedPane tabs, WebServiceDiscovererI discoverer)
 882   {
 883     String name = discoverer.getName();
 884     JPanel tab = new JPanel();
 885     tab.setLayout(new BorderLayout());
 886     tab.add(new WS2PreferencesPanel(discoverer), BorderLayout.CENTER);
 887     tabs.add(tab, name + " services");
 888   }
 889
 890   /**
 891    * A helper method that sets the items and initial selection in a character
 892    * rendering option list (Prompt each time/Lineart/Text)
 893    *
 894    * @param comboBox
 895    * @param propertyKey
 896    */
 897   protected void setupOutputCombo(JComboBox<Object> comboBox,
 898           String propertyKey)
 899   {
 900     comboBox.addItem(promptEachTimeOpt);
 901     comboBox.addItem(lineArtOpt);
 902     comboBox.addItem(textOpt);
 903
 904
 905     /*
 906      * JalviewJS doesn't support Lineart so force it to Text
 907      */
 908     String defaultOption = Platform.isJS() ? "Text"
 909             : Cache.getDefault(propertyKey, "Prompt each time");
 910     if (defaultOption.equalsIgnoreCase("Text"))
 911     {
 912       comboBox.setSelectedItem(textOpt);
 913     }
 914     else if (defaultOption.equalsIgnoreCase("Lineart"))
 915     {
 916       comboBox.setSelectedItem(lineArtOpt);
 917     }
 918     else
 919     {
 920       comboBox.setSelectedItem(promptEachTimeOpt);
 921     }
 922   }
 923
 924   /**
 925    * Save user selections on the Preferences tabs to the Cache and write out to
 926    * file.
 927    *
 928    * @param e
 929    */
 930   @Override
 931   public void ok_actionPerformed(ActionEvent e)
 932   {
 933     if (!validateSettings())
 934     {
 935       return;
 936     }
 937
 938     /*
 939      * Set proxy settings first (to be before web services refresh)
 940      */
 941     saveProxySettings();
 942
 943     /*
 944      * Save Visual settings
 945      */
 946     Cache.setPropertyNoSave("SHOW_JVSUFFIX",
 947             Boolean.toString(seqLimit.isSelected()));
 948     Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
 949             Boolean.toString(rightAlign.isSelected()));
 950     Cache.setPropertyNoSave("SHOW_FULLSCREEN",
 951             Boolean.toString(fullScreen.isSelected()));
 952     Cache.setPropertyNoSave("SHOW_OVERVIEW",
 953             Boolean.toString(openoverv.isSelected()));
 954     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
 955             Boolean.toString(annotations.isSelected()));
 956     Cache.setPropertyNoSave("SHOW_CONSERVATION",
 957             Boolean.toString(conservation.isSelected()));
 958     Cache.setPropertyNoSave("SHOW_QUALITY",
 959             Boolean.toString(quality.isSelected()));
 960     Cache.setPropertyNoSave("SHOW_IDENTITY",
 961             Boolean.toString(identity.isSelected()));
 962
 963     Cache.setPropertyNoSave("GAP_SYMBOL",
 964             gapSymbolCB.getSelectedItem().toString());
 965
 966     Cache.setPropertyNoSave("FONT_NAME",
 967             fontNameCB.getSelectedItem().toString());
 968     Cache.setPropertyNoSave("FONT_STYLE",
 969             fontStyleCB.getSelectedItem().toString());
 970     Cache.setPropertyNoSave("FONT_SIZE",
 971             fontSizeCB.getSelectedItem().toString());
 972
 973     Cache.setPropertyNoSave("ID_ITALICS",
 974             Boolean.toString(idItalics.isSelected()));
 975     Cache.setPropertyNoSave("SHOW_UNCONSERVED",
 976             Boolean.toString(showUnconserved.isSelected()));
 977     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
 978             Boolean.toString(showOccupancy.isSelected()));
 979     Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
 980             Boolean.toString(showGroupConsensus.isSelected()));
 981     Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
 982             Boolean.toString(showGroupConservation.isSelected()));
 983     Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
 984             Boolean.toString(showConsensHistogram.isSelected()));
 985     Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
 986             Boolean.toString(showConsensLogo.isSelected()));
 987     Cache.setPropertyNoSave("SHOW_INFORMATION_HISTOGRAM",
 988             Boolean.toString(showConsensHistogram.isSelected()));
 989     Cache.setPropertyNoSave("SHOW_HMM_LOGO",
 990             Boolean.toString(showHMMLogo.isSelected()));
 991     Cache.setPropertyNoSave("ANTI_ALIAS",
 992             Boolean.toString(smoothFont.isSelected()));
 993     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
 994             Boolean.toString(scaleProteinToCdna.isSelected()));
 995     Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
 996             Boolean.toString(showNpTooltip.isSelected()));
 997     Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
 998             Boolean.toString(showDbRefTooltip.isSelected()));
 999
1000     Cache.setPropertyNoSave("WRAP_ALIGNMENT",
1001             Boolean.toString(wrap.isSelected()));
1002
1003     Cache.setPropertyNoSave("STARTUP_FILE",
1004             startupFileTextfield.getText());
1005     Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
1006             Boolean.toString(startupCheckbox.isSelected()));
1007
1008     Cache.setPropertyNoSave("SORT_ALIGNMENT",
1009             sortby.getSelectedItem().toString());
1010
1011     // convert description of sort order to enum name for save
1012     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
1013             .forDescription(sortAnnBy.getSelectedItem().toString());
1014     if (annSortOrder != null)
1015     {
1016       Cache.setPropertyNoSave(SORT_ANNOTATIONS,
1017               annSortOrder.name());
1018     }
1019
1020     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
1021     Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
1022             Boolean.valueOf(showAutocalcFirst).toString());
1023
1024     /*
1025      * Save Colours settings
1026      */
1027     Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
1028             protColour.getSelectedItem().toString());
1029     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
1030             nucColour.getSelectedItem().toString());
1031     Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MIN",
1032             minColour.getBackground());
1033     Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MAX",
1034             maxColour.getBackground());
1035
1036     /*
1037      * Save HMMER settings
1038      */
1039     Cache.setPropertyNoSave(HMMALIGN_TRIM_TERMINI,
1040             Boolean.toString(hmmrTrimTermini.isSelected()));
1041     Cache.setPropertyNoSave(HMMINFO_GLOBAL_BACKGROUND,
1042             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
1043     Cache.setPropertyNoSave(HMMSEARCH_SEQCOUNT,
1044             hmmerSequenceCount.getText());
1045     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
1046     if (cygwinPath != null)
1047     {
1048       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
1049     }
1050     AlignFrame[] frames = Desktop.getAlignFrames();
1051     if (frames != null && frames.length > 0)
1052     {
1053       for (AlignFrame f : frames)
1054       {
1055         f.updateHMMERStatus();
1056       }
1057     }
1058
1059     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
1060     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
1061     {
1062       hmmerBackgroundUniprot.setSelected(true);
1063     }
1064     else
1065     {
1066       hmmerBackgroundAlignment.setSelected(true);
1067     }
1068     hmmerSequenceCount
1069             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
1070     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
1071
1072     /*
1073      * Save Overview settings
1074      */
1075     Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
1076     Cache.setColourPropertyNoSave(HIDDEN_COLOUR, hiddenColour.getBackground());
1077     Cache.setPropertyNoSave(USE_LEGACY_GAP,
1078             Boolean.toString(useLegacyGap.isSelected()));
1079     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
1080             Boolean.toString(showHiddenAtStart.isSelected()));
1081
1082     /*
1083      * Save Structure settings
1084      */
1085     Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
1086             Boolean.toString(addTempFactor.isSelected()));
1087     Cache.setPropertyNoSave(ADD_SS_ANN,
1088             Boolean.toString(addSecondaryStructure.isSelected()));
1089     Cache.setPropertyNoSave(STRUCT_FROM_PDB,
1090             Boolean.toString(structFromPdb.isSelected()));
1091     if (!Platform.isJS()) {
1092     String viewer = structViewer.getSelectedItem().toString();
1093     String viewerPath = structureViewerPath.getText();
1094     Cache.setPropertyNoSave(STRUCTURE_DISPLAY, viewer);
1095     if (viewer.equals(ViewerType.CHIMERA.name()))
1096     {
1097       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
1098     }
1099     else if (viewer.equals(ViewerType.CHIMERAX.name()))
1100     {
1101       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
1102     }
1103     else if (viewer.equals(ViewerType.PYMOL.name()))
1104     {
1105       Cache.setOrRemove(PYMOL_PATH, viewerPath);
1106     }
1107     } // nojs
1108     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
1109             Boolean.toString(siftsMapping.isSelected()));
1110     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
1111
1112     /*
1113      * Save Output settings
1114      */
1115     Cache.setPropertyNoSave("EPS_RENDERING",
1116             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
1117     Cache.setPropertyNoSave("HTML_RENDERING",
1118             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
1119     Cache.setPropertyNoSave("SVG_RENDERING",
1120             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
1121
1122     /*
1123      * Save Connections settings
1124      */
1125     // Proxy settings were already set first (to catch web services)
1126     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
1127
1128     jalview.util.BrowserLauncher.resetBrowser();
1129
1130     // save user-defined and selected links
1131     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
1132     if (menuLinks.isEmpty())
1133     {
1134       Cache.removePropertyNoSave("SEQUENCE_LINKS");
1135     }
1136     else
1137     {
1138       Cache.setPropertyNoSave("SEQUENCE_LINKS",
1139               menuLinks.toString());
1140     }
1141
1142     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
1143     if (nonMenuLinks.isEmpty())
1144     {
1145       Cache.removePropertyNoSave("STORED_LINKS");
1146     }
1147     else
1148     {
1149       Cache.setPropertyNoSave("STORED_LINKS",
1150               nonMenuLinks.toString());
1151     }
1152
1153     Cache.setPropertyNoSave("DEFAULT_URL",
1154             sequenceUrlLinks.getPrimaryUrlId());
1155
1156     Cache.setProperty("VERSION_CHECK",
1157             Boolean.toString(versioncheck.isSelected()));
1158     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
1159     {
1160       // default is false - we only set this if the user has actively agreed
1161       Cache.setProperty("USAGESTATS",
1162               Boolean.toString(usagestats.isSelected()));
1163     }
1164     if (!questionnaire.isSelected())
1165     {
1166       Cache.setProperty("NOQUESTIONNAIRES", "true");
1167     }
1168     else
1169     {
1170       // special - made easy to edit a property file to disable questionnaires
1171       // by just adding the given line
1172       Cache.removeProperty("NOQUESTIONNAIRES");
1173     }
1174
1175     /*
1176      * Save Output settings
1177      */
1178     Cache.setPropertyNoSave("BLC_JVSUFFIX",
1179             Boolean.toString(blcjv.isSelected()));
1180     Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
1181             Boolean.toString(clustaljv.isSelected()));
1182     Cache.setPropertyNoSave("FASTA_JVSUFFIX",
1183             Boolean.toString(fastajv.isSelected()));
1184     Cache.setPropertyNoSave("MSF_JVSUFFIX",
1185             Boolean.toString(msfjv.isSelected()));
1186     Cache.setPropertyNoSave("PFAM_JVSUFFIX",
1187             Boolean.toString(pfamjv.isSelected()));
1188     Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
1189             Boolean.toString(pileupjv.isSelected()));
1190     Cache.setPropertyNoSave("PIR_JVSUFFIX",
1191             Boolean.toString(pirjv.isSelected()));
1192     Cache.setPropertyNoSave("PIR_MODELLER",
1193             Boolean.toString(modellerOutput.isSelected()));
1194     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
1195             Boolean.toString(embbedBioJSON.isSelected()));
1196     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
1197
1198     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
1199             Boolean.toString(autoIdWidth.isSelected()));
1200     userIdWidth_actionPerformed();
1201     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
1202             userIdWidth.getText());
1203
1204     /*
1205      * Save Editing settings
1206      */
1207     Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
1208             Boolean.toString(autoCalculateConsCheck.isSelected()));
1209     Cache.setPropertyNoSave("SORT_BY_TREE",
1210             Boolean.toString(sortByTree.isSelected()));
1211     Cache.setPropertyNoSave("PAD_GAPS",
1212             Boolean.toString(padGaps.isSelected()));
1213
1214     if (!Platform.isJS())
1215     {
1216       wsPrefs.updateAndRefreshWsMenuConfig(false);
1217     }
1218
1219     /*
1220      * Save Backups settings
1221      */
1222     Cache.setPropertyNoSave(BackupFiles.ENABLED,
1223             Boolean.toString(enableBackupFiles.isSelected()));
1224     int preset = getComboIntStringKey(backupfilesPresetsCombo);
1225     Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset));
1226
1227     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1228     {
1229       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1230       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1231               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1232       Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
1233                       customBFPE.toString());
1234     }
1235
1236     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1237             .get(preset);
1238     Cache.setPropertyNoSave(
1239             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1240
1241     /*
1242      * Save Memory Settings
1243      */
1244     Cache.setPropertyNoSave(
1245             MemorySetting.CUSTOMISED_SETTINGS,
1246             Boolean.toString(customiseMemorySetting.isSelected()));
1247     Cache.setPropertyNoSave(MemorySetting.MEMORY_JVMMEMPC,
1248             Integer.toString(jvmMemoryPercentSlider.getValue()));
1249     Cache.setPropertyNoSave(MemorySetting.MEMORY_JVMMEMMAX,
1250             jvmMemoryMaxTextField.getText());
1251
1252     /*
1253      * save and close Preferences
1254      */
1255     Cache.saveProperties();
1256     Desktop.getInstance().doConfigureStructurePrefs();
1257     try
1258     {
1259       frame.setClosed(true);
1260     } catch (Exception ex)
1261     {
1262     }
1263   }
1264
1265   public void saveProxySettings()
1266   {
1267     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1268             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1269                     : Cache.PROXYTYPE_SYSTEM;
1270     Cache.setPropertyNoSave("USE_PROXY", newProxyType);
1271     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1272     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1273     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1274     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1275     Cache.setOrRemove("PROXY_AUTH",
1276             Boolean.toString(proxyAuth.isSelected()));
1277     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1278     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1279     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1280     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1281             || !newProxyType.equals(previousProxyType))
1282     {
1283       // force a re-lookup of ws if proxytype is custom or has changed
1284       wsPrefs.refreshWs_actionPerformed(null);
1285     }
1286     previousProxyType = newProxyType;
1287   }
1288
1289   public static void setAppletDefaults()
1290   {
1291
1292     // http://www.jalview.org/old/v2_8/examples/appletParameters.html
1293
1294     // showConservation true or false Default is true.
1295     // showQuality true or false Default is true.
1296     // showConsensus true or false Default is true.
1297     // showFeatureSettings true or false Shows the feature settings window when
1298     // startin
1299     // showTreeBootstraps true or false (default is true) show or hide branch
1300     // bootstraps
1301     // showTreeDistances true or false (default is true) show or hide branch
1302     // lengths
1303     // showUnlinkedTreeNodes true or false (default is false) indicate if
1304     // unassociated nodes should be highlighted in the tree view
1305     // showUnconserved true of false (default is false) When true, only gaps and
1306     // symbols different to the consensus sequence ions of the alignment
1307     // showGroupConsensus true of false (default is false) When true, shows
1308     // consensus annotation row for any groups on the alignment. (since 2.7)
1309     // showGroupConservation true of false (default is false) When true, shows
1310     // amino-acid property conservation annotation row for any groups on the
1311     // showConsensusHistogram true of false (default is true) When true, shows
1312     // the percentage occurence of the consensus symbol for each column as a
1313     // showSequenceLogo true of false (default is false) When true, shows a
1314     // sequence logo above the consensus sequence (overlaid above the Consensus
1315
1316     Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
1317     Cache.setPropertyNoSave(SHOW_QUALITY, "false");
1318     Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
1319     Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
1320     Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
1321     Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
1322
1323     // TODO -- just a start here
1324   }
1325  /**
1326    * Do any necessary validation before saving settings. Return focus to the
1327    * first tab which fails validation.
1328    *
1329    * @return
1330    */
1331   private boolean validateSettings()
1332   {
1333     if (!validateStructure())
1334     {
1335       structureTab.requestFocusInWindow();
1336       return false;
1337     }
1338     return true;
1339   }
1340
1341   @Override
1342   protected boolean validateStructure()
1343   {
1344     return validateViewerPath();
1345
1346   }
1347
1348   /**
1349    * DOCUMENT ME!
1350    */
1351   @Override
1352   public void startupFileTextfield_mouseClicked()
1353   {
1354     // TODO: JAL-3048 not needed for Jalview-JS
1355     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1356     JalviewFileChooser chooser = JalviewFileChooser
1357             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1358     chooser.setFileView(new JalviewFileView());
1359     chooser.setDialogTitle(
1360             MessageManager.getString("label.select_startup_file"));
1361
1362     int value = chooser.showOpenDialog(this);
1363
1364     if (value == JalviewFileChooser.APPROVE_OPTION)
1365     {
1366       FileFormatI format = chooser.getSelectedFormat();
1367       if (format != null)
1368       {
1369         Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
1370                 format.getName());
1371       }
1372       startupFileTextfield
1373               .setText(chooser.getSelectedFile().getAbsolutePath());
1374     }
1375   }
1376
1377   /**
1378    * DOCUMENT ME!
1379    *
1380    * @param e
1381    *          DOCUMENT ME!
1382    */
1383   @Override
1384   public void cancel_actionPerformed(ActionEvent e)
1385   {
1386     try
1387     {
1388       if (!Platform.isJS())
1389       {
1390         wsPrefs.updateWsMenuConfig(true);
1391         wsPrefs.refreshWs_actionPerformed(e);
1392       }
1393       frame.setClosed(true);
1394     } catch (Exception ex)
1395     {
1396     }
1397   }
1398
1399   /**
1400    * DOCUMENT ME!
1401    *
1402    * @param e
1403    *          DOCUMENT ME!
1404    */
1405   @Override
1406   public void annotations_actionPerformed(ActionEvent e)
1407   {
1408     conservation.setEnabled(annotations.isSelected());
1409     quality.setEnabled(annotations.isSelected());
1410     identity.setEnabled(annotations.isSelected());
1411     showOccupancy.setEnabled(annotations.isSelected());
1412     showGroupConsensus.setEnabled(annotations.isSelected());
1413     showGroupConservation.setEnabled(annotations.isSelected());
1414     showConsensHistogram.setEnabled(annotations.isSelected()
1415             && (identity.isSelected() || showGroupConsensus.isSelected()));
1416     showConsensLogo.setEnabled(annotations.isSelected()
1417             && (identity.isSelected() || showGroupConsensus.isSelected()));
1418     showInformationHistogram.setEnabled(annotations.isSelected());
1419     showHMMLogo.setEnabled(annotations.isSelected());
1420   }
1421
1422   @Override
1423   public void newLink_actionPerformed(ActionEvent e)
1424   {
1425     GSequenceLink link = new GSequenceLink();
1426     boolean valid = false;
1427     while (!valid)
1428     {
1429       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1430               MessageManager.getString("label.new_sequence_url_link"),
1431               JvOptionPane.OK_CANCEL_OPTION, -1,
1432               null) == JvOptionPane.OK_OPTION)
1433       {
1434         if (link.checkValid())
1435         {
1436           if (((UrlLinkTableModel) linkUrlTable.getModel())
1437                   .isUniqueName(link.getName()))
1438           {
1439             ((UrlLinkTableModel) linkUrlTable.getModel())
1440                     .insertRow(link.getName(), link.getURL());
1441             valid = true;
1442           }
1443           else
1444           {
1445             link.notifyDuplicate();
1446             continue;
1447           }
1448         }
1449       }
1450       else
1451       {
1452         break;
1453       }
1454     }
1455   }
1456
1457   @Override
1458   public void editLink_actionPerformed(ActionEvent e)
1459   {
1460     GSequenceLink link = new GSequenceLink();
1461
1462     int index = linkUrlTable.getSelectedRow();
1463     if (index == -1)
1464     {
1465       // button no longer enabled if row is not selected
1466       Console.debug("Edit with no row selected in linkUrlTable");
1467       return;
1468     }
1469
1470     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1471             .getNameColumn();
1472     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1473             .getUrlColumn();
1474     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1475     link.setName(oldName);
1476     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1477
1478     boolean valid = false;
1479     while (!valid)
1480     {
1481       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1482               MessageManager.getString("label.edit_sequence_url_link"),
1483               JvOptionPane.OK_CANCEL_OPTION, -1,
1484               null) == JvOptionPane.OK_OPTION)
1485       {
1486         if (link.checkValid())
1487         {
1488           if ((oldName.equals(link.getName()))
1489                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1490                           .isUniqueName(link.getName())))
1491           {
1492             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1493             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1494             valid = true;
1495           }
1496           else
1497           {
1498             link.notifyDuplicate();
1499             continue;
1500           }
1501         }
1502       }
1503       else
1504       {
1505         break;
1506       }
1507     }
1508   }
1509
1510   @Override
1511   public void deleteLink_actionPerformed(ActionEvent e)
1512   {
1513     int index = linkUrlTable.getSelectedRow();
1514     int modelIndex = -1;
1515     if (index == -1)
1516     {
1517       // button no longer enabled if row is not selected
1518       Console.debug("Delete with no row selected in linkUrlTable");
1519       return;
1520     }
1521     else
1522     {
1523       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1524     }
1525
1526     // make sure we use the model index to delete, and not the table index
1527     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1528   }
1529
1530   @Override
1531   public void defaultBrowser_mouseClicked(MouseEvent e)
1532   {
1533     // TODO: JAL-3048 not needed for j2s
1534     if (!Platform.isJS()) // BH 2019
1535     /**
1536      * Java only
1537      *
1538      * @j2sIgnore
1539      */
1540     {
1541       JFileChooser chooser = new JFileChooser(".");
1542       chooser.setDialogTitle(
1543               MessageManager.getString("label.select_default_browser"));
1544
1545       int value = chooser.showOpenDialog(this);
1546
1547       if (value == JFileChooser.APPROVE_OPTION)
1548       {
1549         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1550       }
1551     }
1552   }
1553
1554   /*
1555    * (non-Javadoc)
1556    *
1557    * @see
1558    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1559    * .ActionEvent)
1560    */
1561   @Override
1562   protected void showunconserved_actionPerformed(ActionEvent e)
1563   {
1564     // TODO Auto-generated method stub
1565     super.showunconserved_actionPerformed(e);
1566   }
1567
1568   public static List<String> getGroupURLLinks()
1569   {
1570     return groupURLLinks;
1571   }
1572
1573   @Override
1574   public void minColour_actionPerformed(JPanel panel)
1575   {
1576     JalviewColourChooser.showColourChooser(this,
1577             MessageManager.getString("label.select_colour_minimum_value"),
1578             panel);
1579   }
1580
1581   @Override
1582   public void maxColour_actionPerformed(JPanel panel)
1583   {
1584     JalviewColourChooser.showColourChooser(this,
1585             MessageManager.getString("label.select_colour_maximum_value"),
1586             panel);
1587   }
1588
1589   @Override
1590   public void gapColour_actionPerformed(JPanel gap)
1591   {
1592     if (!useLegacyGap.isSelected())
1593     {
1594       JalviewColourChooser.showColourChooser(this,
1595               MessageManager.getString("label.select_gap_colour"),
1596               gap);
1597     }
1598   }
1599
1600   @Override
1601   public void hiddenColour_actionPerformed(JPanel hidden)
1602   {
1603     JalviewColourChooser.showColourChooser(this,
1604             MessageManager.getString("label.select_hidden_colour"),
1605             hidden);
1606   }
1607
1608   @Override
1609   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1610   {
1611     boolean enabled = useLegacyGap.isSelected();
1612     if (enabled)
1613     {
1614       gapColour.setBackground(
1615               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1616     }
1617     else
1618     {
1619       gapColour.setBackground(
1620               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1621     }
1622     gapColour.setEnabled(!enabled);
1623     gapLabel.setEnabled(!enabled);
1624   }
1625
1626   @Override
1627   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1628   {
1629     useLegacyGap.setSelected(false);
1630     useLegacyGaps_actionPerformed(null);
1631     showHiddenAtStart.setSelected(false);
1632     hiddenColour.setBackground(
1633             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1634   }
1635
1636   @Override
1637   protected void userIdWidth_actionPerformed()
1638   {
1639     try
1640     {
1641       String val = userIdWidth.getText().trim();
1642       if (val.length() > 0)
1643       {
1644         Integer iw = Integer.parseInt(val);
1645         if (iw.intValue() < 12)
1646         {
1647           throw new NumberFormatException();
1648         }
1649         userIdWidth.setText(iw.toString());
1650       }
1651     } catch (NumberFormatException x)
1652     {
1653       userIdWidth.setText("");
1654       JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1655               MessageManager
1656                       .getString("warn.user_defined_width_requirements"),
1657               MessageManager.getString("label.invalid_id_column_width"),
1658               JvOptionPane.WARNING_MESSAGE);
1659     }
1660   }
1661
1662   @Override
1663   protected void autoIdWidth_actionPerformed()
1664   {
1665     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1666     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1667   }
1668
1669   /**
1670    * Returns true if structure viewer path is to a valid executable, else shows an
1671    * error dialog. Does nothing if the path is empty, as is the case for Jmol
1672    * (built in to Jalview) or when Jalview is left to try default paths.
1673    */
1674   private boolean validateViewerPath()
1675   {
1676     if (structureViewerPath.getText().trim().length() > 0)
1677     {
1678       File f = new File(structureViewerPath.getText());
1679       if (!f.canExecute())
1680       {
1681         JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1682                 MessageManager.getString("label.invalid_viewer_path"),
1683                 MessageManager.getString("label.invalid_viewer_path"),
1684                 JvOptionPane.ERROR_MESSAGE);
1685         return false;
1686       }
1687     }
1688     return true;
1689   }
1690
1691   /**
1692    * Returns true if the given text field contains a path to a folder that
1693    * contains an executable with the given name, else false (after showing a
1694    * warning dialog). The executable name will be tried with .exe appended if not
1695    * found.
1696    *
1697    * @param textField
1698    * @param executable
1699    */
1700   protected boolean validateExecutablePath(JTextField textField, String executable)
1701   {
1702     String folder = textField.getText().trim();
1703
1704     if (FileUtils.getExecutable(executable, folder) != null)
1705     {
1706       return true;
1707     }
1708     if (folder.length() > 0)
1709     {
1710       JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
1711               MessageManager.formatMessage("label.executable_not_found",
1712                       executable),
1713               MessageManager.getString("label.invalid_folder"),
1714               JvOptionPane.ERROR_MESSAGE);
1715     }
1716     return false;
1717   }
1718
1719   /**
1720    * Checks if a file can be executed
1721    *
1722    * @param path
1723    *          the path to the file
1724    * @return
1725    */
1726   public boolean canExecute(String path)
1727   {
1728     File file = new File(path);
1729     if (!file.canExecute())
1730     {
1731       file = new File(path + ".exe");
1732       {
1733         if (!file.canExecute())
1734         {
1735           return false;
1736         }
1737       }
1738     }
1739     return true;
1740   }
1741
1742   /**
1743    * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
1744    * or user-specified path, if not show a warning/help dialog
1745    */
1746   @Override
1747   protected void structureViewer_actionPerformed(String selectedItem)
1748   {
1749     if (selectedItem.equals(ViewerType.JMOL.name()))
1750     {
1751       structureViewerPath.setEnabled(false);
1752       structureViewerPathLabel.setEnabled(false);
1753       return;
1754     }
1755     boolean found = false;
1756     structureViewerPath.setEnabled(true);
1757     structureViewerPathLabel.setEnabled(true);
1758     structureViewerPathLabel.setText(MessageManager
1759             .formatMessage("label.viewer_path", selectedItem));
1760
1761     /*
1762      * Try user-specified and standard paths for structure viewer executable
1763      */
1764     String viewerPath = "";
1765     List<String> paths = null;
1766     try
1767     {
1768       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1769       switch (viewerType)
1770       {
1771       case JMOL:
1772         // dealt with above
1773         break;
1774       case CHIMERA:
1775         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1776         paths = StructureManager.getChimeraPaths(false);
1777         break;
1778       case CHIMERAX:
1779         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1780         paths = StructureManager.getChimeraPaths(true);
1781         break;
1782       case PYMOL:
1783         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1784         paths = PymolManager.getPymolPaths();
1785         break;
1786       }
1787     } catch (IllegalArgumentException e)
1788     {
1789       // only valid entries should be in the drop-down
1790     }
1791     structureViewerPath.setText(viewerPath);
1792
1793     paths.add(0, structureViewerPath.getText());
1794     for (String path : paths)
1795     {
1796       if (new File(path.trim()).canExecute())
1797       {
1798         found = true;
1799         break;
1800       }
1801     }
1802
1803     if (!found)
1804     {
1805       String[] options = { "OK", "Help" };
1806       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
1807               JvSwingUtils.wrapTooltip(true,
1808                       MessageManager.getString("label.viewer_missing")),
1809               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1810               null, options, options[0]);
1811
1812       if (showHelp == JvOptionPane.NO_OPTION)
1813       {
1814         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1815         try
1816         {
1817           Help.showHelpWindow(HelpId.StructureViewer);
1818         } catch (HelpSetException e)
1819         {
1820           e.printStackTrace();
1821         }
1822       }
1823       else if (showHelp == JvOptionPane.OK_OPTION)
1824       {
1825         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1826         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1827           try
1828           {
1829             for (int i = 0; i < 3; i++)
1830             {
1831               structureViewerPath.setBackground(Color.PINK);
1832               Thread.sleep(500);
1833               structureViewerPath.setBackground(Color.WHITE);
1834               Thread.sleep(500);
1835             }
1836           } catch (InterruptedException e)
1837           {
1838           }
1839         });
1840       }
1841      }
1842   }
1843
1844   @Override
1845   protected void validateHmmerPath()
1846   {
1847     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1848   }
1849
1850   @Override
1851   protected void validateCygwinPath()
1852   {
1853     validateExecutablePath(cygwinPath, "run");
1854   }
1855
1856   public class OptionsParam
1857   {
1858     private String name;
1859
1860     private String code;
1861
1862     public OptionsParam(String name, String code)
1863     {
1864       this.name = name;
1865       this.code = code;
1866     }
1867
1868     public String getName()
1869     {
1870       return name;
1871     }
1872
1873     public void setName(String name)
1874     {
1875       this.name = name;
1876     }
1877
1878     public String getCode()
1879     {
1880       return code;
1881     }
1882
1883     public void setCode(String code)
1884     {
1885       this.code = code;
1886     }
1887
1888     @Override
1889     public String toString()
1890     {
1891       return name;
1892     }
1893
1894     @Override
1895     public boolean equals(Object that)
1896     {
1897       if (!(that instanceof OptionsParam))
1898       {
1899         return false;
1900       }
1901       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1902     }
1903
1904     @Override
1905     public int hashCode()
1906     {
1907       return name.hashCode() + code.hashCode();
1908     }
1909   }
1910
1911   private class UrlListSelectionHandler implements ListSelectionListener
1912   {
1913
1914     @Override
1915     public void valueChanged(ListSelectionEvent e)
1916     {
1917       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1918
1919       int index = lsm.getMinSelectionIndex();
1920       if (index == -1)
1921       {
1922         // no selection, so disable delete/edit buttons
1923         editLink.setEnabled(false);
1924         deleteLink.setEnabled(false);
1925         return;
1926       }
1927       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1928
1929       // enable/disable edit and delete link buttons
1930       if (((UrlLinkTableModel) linkUrlTable.getModel())
1931               .isRowDeletable(modelIndex))
1932       {
1933         deleteLink.setEnabled(true);
1934       }
1935       else
1936       {
1937         deleteLink.setEnabled(false);
1938       }
1939
1940       if (((UrlLinkTableModel) linkUrlTable.getModel())
1941               .isRowEditable(modelIndex))
1942       {
1943         editLink.setEnabled(true);
1944       }
1945       else
1946       {
1947         editLink.setEnabled(false);
1948       }
1949     }
1950   }
1951 }