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