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
  37 import javax.help.HelpSetException;
  38 import javax.swing.JComboBox;
  39 import javax.swing.JFileChooser;
  40 import javax.swing.JInternalFrame;
  41 import javax.swing.JPanel;
  42 import javax.swing.JTextField;
  43 import javax.swing.ListSelectionModel;
  44 import javax.swing.RowFilter;
  45 import javax.swing.RowSorter;
  46 import javax.swing.SortOrder;
  47 import javax.swing.event.DocumentEvent;
  48 import javax.swing.event.DocumentListener;
  49 import javax.swing.event.ListSelectionEvent;
  50 import javax.swing.event.ListSelectionListener;
  51 import javax.swing.table.TableCellRenderer;
  52 import javax.swing.table.TableColumn;
  53 import javax.swing.table.TableModel;
  54 import javax.swing.table.TableRowSorter;
  55
  56 import jalview.hmmer.HmmerCommand;
  57 import jalview.util.FileUtils;
  58
  59 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  60 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  61 import jalview.bin.Cache;
  62 import jalview.gui.Help.HelpId;
  63 import jalview.gui.StructureViewer.ViewerType;
  64 import jalview.io.BackupFiles;
  65 import jalview.io.BackupFilesPresetEntry;
  66 import jalview.io.FileFormatI;
  67 import jalview.io.JalviewFileChooser;
  68 import jalview.io.JalviewFileView;
  69 import jalview.jbgui.GPreferences;
  70 import jalview.jbgui.GSequenceLink;
  71 import jalview.schemes.ColourSchemeI;
  72 import jalview.schemes.ColourSchemes;
  73 import jalview.schemes.ResidueColourScheme;
  74 import jalview.urls.UrlLinkTableModel;
  75 import jalview.urls.api.UrlProviderFactoryI;
  76 import jalview.urls.api.UrlProviderI;
  77 import jalview.urls.desktop.DesktopUrlProviderFactory;
  78 import jalview.util.MessageManager;
  79 import jalview.util.Platform;
  80 import jalview.util.UrlConstants;
  81 import jalview.ws.sifts.SiftsSettings;
  82
  83 /**
  84  * DOCUMENT ME!
  85  *
  86  * @author $author$
  87  * @version $Revision$
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   // suggested list delimiter character
  92   public static final String COMMA = ",";
  93
  94   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
  95
  96   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
  97
  98   public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
  99
 100   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 101
 102   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 103
 104   public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
 105
 106   public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
 107
 108   public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
 109
 110   public static final String ANTI_ALIAS = "ANTI_ALIAS";
 111
 112   public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
 113
 114   public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
 115
 116   public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
 117
 118   public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
 119
 120   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 121
 122   public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
 123
 124   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 125
 126   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 127
 128   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 129
 130   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 131
 132   public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
 133
 134   public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
 135
 136   public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
 137
 138   public static final String FONT_NAME = "FONT_NAME";
 139
 140   public static final String FONT_SIZE = "FONT_SIZE";
 141
 142   public static final String FONT_STYLE = "FONT_STYLE";
 143
 144   public static final String HMMER_PATH = "HMMER_PATH";
 145
 146   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 147
 148   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 149
 150   public static final String GAP_COLOUR = "GAP_COLOUR";
 151
 152   public static final String GAP_SYMBOL = "GAP_SYMBOL";
 153
 154   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 155
 156   public static final String HIDE_INTRONS = "HIDE_INTRONS";
 157
 158   public static final String ID_ITALICS = "ID_ITALICS";
 159
 160   public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
 161
 162   public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
 163
 164   public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
 165
 166   public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
 167
 168   public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
 169
 170   public static final String PAD_GAPS = "PAD_GAPS";
 171
 172   public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
 173
 174   public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
 175
 176   public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
 177
 178   public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
 179
 180   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 181
 182   public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
 183
 184   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 185
 186   public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
 187
 188   public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
 189
 190   public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
 191
 192   public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
 193
 194   public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
 195
 196   public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
 197
 198   public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
 199
 200   public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
 201
 202   public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
 203
 204   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 205
 206   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 207
 208   public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
 209
 210   public static final String SHOW_QUALITY = "SHOW_QUALITY";
 211
 212   public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
 213
 214   public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
 215
 216   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 217
 218   public static final String SORT_BY_TREE = "SORT_BY_TREE";
 219
 220   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 221
 222   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 223
 224   public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
 225
 226   public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
 227
 228   public static final String USE_FULL_SO = "USE_FULL_SO";
 229
 230   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 231
 232   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 233
 234   public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
 235
 236   public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
 237
 238
 239   private static final int MIN_FONT_SIZE = 1;
 240
 241   private static final int MAX_FONT_SIZE = 30;
 242
 243   /**
 244    * Holds name and link separated with | character. Sequence ID must be
 245    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 246    */
 247   public static UrlProviderI sequenceUrlLinks;
 248
 249   public static UrlLinkTableModel dataModel;
 250
 251   /**
 252    * Holds name and link separated with | character. Sequence IDS and Sequences
 253    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 254    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 255    * for first and second token specified after a pipe character at end |,|.
 256    * (TODO: proper escape for using | to separate ids or sequences
 257    */
 258
 259   public static List<String> groupURLLinks;
 260   static
 261   {
 262     // get links selected to be in the menu (SEQUENCE_LINKS)
 263     // and links entered by the user but not selected (STORED_LINKS)
 264     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 265     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 266     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 267             UrlConstants.DEFAULT_LABEL);
 268
 269     // if both links lists are empty, add the DEFAULT_URL link
 270     // otherwise we assume the default link is in one of the lists
 271     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 272     {
 273       inMenuString = UrlConstants.DEFAULT_STRING;
 274     }
 275     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 276             inMenuString, notInMenuString);
 277     sequenceUrlLinks = factory.createUrlProvider();
 278     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 279
 280     /**
 281      * TODO: reformulate groupURL encoding so two or more can be stored in the
 282      * .properties file as '|' separated strings
 283      */
 284
 285     groupURLLinks = new ArrayList<>();
 286   }
 287
 288   JInternalFrame frame;
 289
 290   private WsPreferences wsPrefs;
 291
 292   private SlivkaPreferences slivkaPrefs;
 293
 294   private OptionsParam promptEachTimeOpt = new OptionsParam(
 295           MessageManager.getString("label.prompt_each_time"),
 296           "Prompt each time");
 297
 298   private OptionsParam lineArtOpt = new OptionsParam(
 299           MessageManager.getString("label.lineart"), "Lineart");
 300
 301   private OptionsParam textOpt = new OptionsParam(
 302           MessageManager.getString("action.text"), "Text");
 303
 304   /**
 305    * Creates a new Preferences object.
 306    */
 307   public Preferences()
 308   {
 309     super();
 310     frame = new JInternalFrame();
 311     frame.setContentPane(this);
 312     if (!Platform.isJS())
 313     /**
 314      * Java only
 315      *
 316      * @j2sIgnore
 317      */
 318     {
 319       wsPrefs = new WsPreferences();
 320       wsTab.add(wsPrefs, BorderLayout.CENTER);
 321     }
 322
 323     slivkaPrefs = new SlivkaPreferences();
 324     slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
 325
 326     int width = 500, height = 450;
 327     if (Platform.isAMacAndNotJS())
 328     {
 329       width = 570;
 330       height = 480;
 331     }
 332
 333     Desktop.addInternalFrame(frame,
 334             MessageManager.getString("label.preferences"), width, height);
 335     frame.setMinimumSize(new Dimension(width, height));
 336
 337     /*
 338      * Set HMMER tab defaults
 339      */
 340     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 341     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 342     {
 343       hmmerBackgroundUniprot.setSelected(true);
 344     }
 345     else
 346     {
 347       hmmerBackgroundAlignment.setSelected(true);
 348     }
 349     hmmerSequenceCount
 350             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 351     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 352     hmmerPath.addActionListener(new ActionListener()
 353     {
 354       @Override
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         validateHmmerPath();
 358       }
 359     });
 360     hmmerPath.addFocusListener(new FocusAdapter()
 361     {
 362       @Override
 363       public void focusLost(FocusEvent e)
 364       {
 365         validateHmmerPath();
 366       }
 367     });
 368     if (cygwinPath != null)
 369     {
 370       String path = Cache.getProperty(CYGWIN_PATH);
 371       if (path == null)
 372       {
 373         path = FileUtils.getPathTo("bash");
 374       }
 375       cygwinPath.setText(path);
 376       cygwinPath.addActionListener(new ActionListener()
 377       {
 378         @Override
 379         public void actionPerformed(ActionEvent e)
 380         {
 381           validateCygwinPath();
 382         }
 383       });
 384       cygwinPath.addFocusListener(new FocusAdapter()
 385       {
 386         @Override
 387         public void focusLost(FocusEvent e)
 388         {
 389           validateCygwinPath();
 390         }
 391       });
 392     }
 393
 394     /*
 395      * Set Visual tab defaults
 396      */
 397     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 398     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 399     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 400     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 401
 402     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 403     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 404     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 405     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 406     showUnconserved
 407             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 408     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 409     showGroupConsensus
 410             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 411     showGroupConservation.setSelected(
 412             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 413     showConsensHistogram.setSelected(
 414             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 415     showConsensLogo
 416             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 417     showInformationHistogram.setSelected(
 418             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 419     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 420     showNpTooltip
 421             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 422     showDbRefTooltip
 423             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 424
 425     String[] fonts = java.awt.GraphicsEnvironment
 426             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 427     for (int i = 0; i < fonts.length; i++)
 428     {
 429       fontNameCB.addItem(fonts[i]);
 430     }
 431
 432     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 433     {
 434       fontSizeCB.addItem(i + "");
 435     }
 436
 437     fontStyleCB.addItem("plain");
 438     fontStyleCB.addItem("bold");
 439     fontStyleCB.addItem("italic");
 440
 441     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 442     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 443     fontStyleCB.setSelectedItem(
 444             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 445
 446     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 447     scaleProteinToCdna
 448             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 449
 450     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 451
 452     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 453
 454     gapSymbolCB.addItem("-");
 455     gapSymbolCB.addItem(".");
 456
 457     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 458
 459     sortby.addItem("No sort");
 460     sortby.addItem("Id");
 461     sortby.addItem("Pairwise Identity");
 462     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 463
 464     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 465     sortAnnBy
 466             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 467     sortAnnBy
 468             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 469     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 470             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 471                     SequenceAnnotationOrder.NONE.name()));
 472     sortAnnBy.setSelectedItem(savedSort.toString());
 473
 474     sortAutocalc.addItem("Autocalculated first");
 475     sortAutocalc.addItem("Autocalculated last");
 476     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 477     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 478             : sortAutocalc.getItemAt(1));
 479     startupCheckbox
 480             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 481     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 482             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 483                     + "/examples/exampleFile_2_3.jar"));
 484
 485     /*
 486      * Set Colours tab defaults
 487      */
 488     protColour.addItem(ResidueColourScheme.NONE);
 489     nucColour.addItem(ResidueColourScheme.NONE);
 490     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 491     {
 492       String name = cs.getSchemeName();
 493       protColour.addItem(name);
 494       nucColour.addItem(name);
 495     }
 496     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 497             ResidueColourScheme.NONE);
 498     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 499     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 500     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 501     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 502     minColour.setBackground(
 503             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 504     maxColour.setBackground(
 505             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 506
 507     /*
 508      * Set overview panel defaults
 509      */
 510     gapColour.setBackground(
 511             Cache.getDefaultColour(GAP_COLOUR,
 512                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 513     hiddenColour.setBackground(
 514             Cache.getDefaultColour(HIDDEN_COLOUR,
 515                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 516     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 517     gapLabel.setEnabled(!useLegacyGap.isSelected());
 518     gapColour.setEnabled(!useLegacyGap.isSelected());
 519     showHiddenAtStart
 520             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 521
 522     /*
 523      * Set Structure tab defaults.
 524      */
 525     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 526     structFromPdb.setSelected(structSelected);
 527     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 528     useRnaView.setEnabled(structSelected);
 529     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 530     addSecondaryStructure.setEnabled(structSelected);
 531     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 532     addTempFactor.setEnabled(structSelected);
 533     if (!Platform.isJS())
 534     {
 535       structViewer.setSelectedItem(
 536             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 537     }
 538     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 539     chimeraPath.addActionListener(new ActionListener()
 540     {
 541       @Override
 542       public void actionPerformed(ActionEvent e)
 543       {
 544         validateChimeraPath();
 545       }
 546     });
 547
 548     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 549     {
 550       siftsMapping.setSelected(true);
 551     }
 552     else
 553     {
 554       nwMapping.setSelected(true);
 555     }
 556
 557     SiftsSettings
 558             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 559
 560     /*
 561      * Set Connections tab defaults
 562      */
 563
 564     // set up sorting
 565     linkUrlTable.setModel(dataModel);
 566     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 567             linkUrlTable.getModel());
 568     linkUrlTable.setRowSorter(sorter);
 569     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 570
 571     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 572     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 573             SortOrder.DESCENDING));
 574     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 575             SortOrder.DESCENDING));
 576     sortKeys.add(
 577             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 578
 579     sorter.setSortKeys(sortKeys);
 580     // BH 2018 setSortKeys will do the sort
 581     // sorter.sort();
 582
 583     // set up filtering
 584     ActionListener onReset;
 585     onReset = new ActionListener()
 586     {
 587       @Override
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         filterTB.setText("");
 591         sorter.setRowFilter(RowFilter.regexFilter(""));
 592       }
 593
 594     };
 595     doReset.addActionListener(onReset);
 596
 597     // filter to display only custom urls
 598     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 599     {
 600       @Override
 601       public boolean include(
 602               Entry<? extends TableModel, ? extends Object> entry)
 603       {
 604         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 605       }
 606     };
 607
 608     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 609             linkUrlTable.getModel());
 610     customSorter.setRowFilter(customUrlFilter);
 611
 612     ActionListener onCustomOnly;
 613     onCustomOnly = new ActionListener()
 614     {
 615       @Override
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         filterTB.setText("");
 619         sorter.setRowFilter(customUrlFilter);
 620       }
 621     };
 622     userOnly.addActionListener(onCustomOnly);
 623
 624     filterTB.getDocument().addDocumentListener(new DocumentListener()
 625     {
 626       String caseInsensitiveFlag = "(?i)";
 627
 628       @Override
 629       public void changedUpdate(DocumentEvent e)
 630       {
 631         sorter.setRowFilter(RowFilter
 632                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 633       }
 634
 635       @Override
 636       public void removeUpdate(DocumentEvent e)
 637       {
 638         sorter.setRowFilter(RowFilter
 639                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 640       }
 641
 642       @Override
 643       public void insertUpdate(DocumentEvent e)
 644       {
 645         sorter.setRowFilter(RowFilter
 646                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 647       }
 648     });
 649
 650     // set up list selection functionality
 651     linkUrlTable.getSelectionModel()
 652             .addListSelectionListener(new UrlListSelectionHandler());
 653
 654     // set up radio buttons
 655     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 656             .getPrimaryColumn();
 657     String onClickName = linkUrlTable.getColumnName(onClickCol);
 658     linkUrlTable.getColumn(onClickName)
 659             .setCellRenderer(new RadioButtonRenderer());
 660     linkUrlTable.getColumn(onClickName)
 661             .setCellEditor(new RadioButtonEditor());
 662
 663     // get boolean columns and resize those to min possible
 664     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 665     {
 666       if (linkUrlTable.getModel().getColumnClass(column)
 667               .equals(Boolean.class))
 668       {
 669         TableColumn tableColumn = linkUrlTable.getColumnModel()
 670                 .getColumn(column);
 671         int preferredWidth = tableColumn.getMinWidth();
 672
 673         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 674                 column);
 675         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 676         int cwidth = c.getPreferredSize().width
 677                 + linkUrlTable.getIntercellSpacing().width;
 678         preferredWidth = Math.max(preferredWidth, cwidth);
 679
 680         tableColumn.setPreferredWidth(preferredWidth);
 681       }
 682     }
 683
 684     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 685     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 686     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 687     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 688
 689     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 690
 691     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 692     // note antisense here: default is true
 693     questionnaire
 694             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 695     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 696
 697     /*
 698      * Set Output tab defaults
 699      */
 700     setupOutputCombo(epsRendering, "EPS_RENDERING");
 701     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 702     setupOutputCombo(svgRendering, "SVG_RENDERING");
 703     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 704     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 705     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 706     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 707     userIdWidth.setText(wi == null ? "" : wi.toString());
 708     // TODO: refactor to use common enum via FormatAdapter and allow extension
 709     // for new flat file formats
 710     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 711     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 712     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 713     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 714     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 715     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 716     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 717     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 718     embbedBioJSON
 719             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 720
 721     /*
 722      * Set Editing tab defaults
 723      */
 724     autoCalculateConsCheck
 725             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 726     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 727     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 728
 729     annotations_actionPerformed(null); // update the display of the annotation
 730                                        // settings
 731
 732
 733     /*
 734      * Set Backups tab defaults
 735      */
 736     loadLastSavedBackupsOptions();
 737   }
 738
 739   /**
 740    * A helper method that sets the items and initial selection in a character
 741    * rendering option list (Prompt each time/Lineart/Text)
 742    *
 743    * @param comboBox
 744    * @param propertyKey
 745    */
 746   protected void setupOutputCombo(JComboBox<Object> comboBox,
 747           String propertyKey)
 748   {
 749     comboBox.addItem(promptEachTimeOpt);
 750     comboBox.addItem(lineArtOpt);
 751     comboBox.addItem(textOpt);
 752
 753     /*
 754      * JalviewJS doesn't support Lineart so force it to Text
 755      */
 756     String defaultOption = Platform.isJS() ? "Text"
 757             : Cache.getDefault(propertyKey, "Prompt each time");
 758     if (defaultOption.equalsIgnoreCase("Text"))
 759     {
 760       comboBox.setSelectedItem(textOpt);
 761     }
 762     else if (defaultOption.equalsIgnoreCase("Lineart"))
 763     {
 764       comboBox.setSelectedItem(lineArtOpt);
 765     }
 766     else
 767     {
 768       comboBox.setSelectedItem(promptEachTimeOpt);
 769     }
 770   }
 771
 772   /**
 773    * Save user selections on the Preferences tabs to the Cache and write out to
 774    * file.
 775    *
 776    * @param e
 777    */
 778   @Override
 779   public void ok_actionPerformed(ActionEvent e)
 780   {
 781     if (!validateSettings())
 782     {
 783       return;
 784     }
 785
 786     /*
 787      * Save Visual settings
 788      */
 789     Cache.setPropertyNoSave("SHOW_JVSUFFIX",
 790             Boolean.toString(seqLimit.isSelected()));
 791     Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
 792             Boolean.toString(rightAlign.isSelected()));
 793     Cache.setPropertyNoSave("SHOW_FULLSCREEN",
 794             Boolean.toString(fullScreen.isSelected()));
 795     Cache.setPropertyNoSave("SHOW_OVERVIEW",
 796             Boolean.toString(openoverv.isSelected()));
 797     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
 798             Boolean.toString(annotations.isSelected()));
 799     Cache.setPropertyNoSave("SHOW_CONSERVATION",
 800             Boolean.toString(conservation.isSelected()));
 801     Cache.setPropertyNoSave("SHOW_QUALITY",
 802             Boolean.toString(quality.isSelected()));
 803     Cache.setPropertyNoSave("SHOW_IDENTITY",
 804             Boolean.toString(identity.isSelected()));
 805
 806     Cache.setPropertyNoSave("GAP_SYMBOL",
 807             gapSymbolCB.getSelectedItem().toString());
 808
 809     Cache.setPropertyNoSave("FONT_NAME",
 810             fontNameCB.getSelectedItem().toString());
 811     Cache.setPropertyNoSave("FONT_STYLE",
 812             fontStyleCB.getSelectedItem().toString());
 813     Cache.setPropertyNoSave("FONT_SIZE",
 814             fontSizeCB.getSelectedItem().toString());
 815
 816     Cache.setPropertyNoSave("ID_ITALICS",
 817             Boolean.toString(idItalics.isSelected()));
 818     Cache.setPropertyNoSave("SHOW_UNCONSERVED",
 819             Boolean.toString(showUnconserved.isSelected()));
 820     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
 821             Boolean.toString(showOccupancy.isSelected()));
 822     Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
 823             Boolean.toString(showGroupConsensus.isSelected()));
 824     Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
 825             Boolean.toString(showGroupConservation.isSelected()));
 826     Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
 827             Boolean.toString(showConsensHistogram.isSelected()));
 828     Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
 829             Boolean.toString(showConsensLogo.isSelected()));
 830     Cache.setPropertyNoSave("SHOW_INFORMATION_HISTOGRAM",
 831             Boolean.toString(showConsensHistogram.isSelected()));
 832     Cache.setPropertyNoSave("SHOW_HMM_LOGO",
 833             Boolean.toString(showHMMLogo.isSelected()));
 834     Cache.setPropertyNoSave("ANTI_ALIAS",
 835             Boolean.toString(smoothFont.isSelected()));
 836     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
 837             Boolean.toString(scaleProteinToCdna.isSelected()));
 838     Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
 839             Boolean.toString(showNpTooltip.isSelected()));
 840     Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
 841             Boolean.toString(showDbRefTooltip.isSelected()));
 842
 843     Cache.setPropertyNoSave("WRAP_ALIGNMENT",
 844             Boolean.toString(wrap.isSelected()));
 845
 846     Cache.setPropertyNoSave("STARTUP_FILE",
 847             startupFileTextfield.getText());
 848     Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
 849             Boolean.toString(startupCheckbox.isSelected()));
 850
 851     Cache.setPropertyNoSave("SORT_ALIGNMENT",
 852             sortby.getSelectedItem().toString());
 853
 854     // convert description of sort order to enum name for save
 855     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 856             .forDescription(sortAnnBy.getSelectedItem().toString());
 857     if (annSortOrder != null)
 858     {
 859       Cache.setPropertyNoSave(SORT_ANNOTATIONS,
 860               annSortOrder.name());
 861     }
 862
 863     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 864     Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
 865             Boolean.valueOf(showAutocalcFirst).toString());
 866
 867     /*
 868      * Save Colours settings
 869      */
 870     Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
 871             protColour.getSelectedItem().toString());
 872     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
 873             nucColour.getSelectedItem().toString());
 874     Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MIN",
 875             minColour.getBackground());
 876     Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MAX",
 877             maxColour.getBackground());
 878
 879     /*
 880      * Save HMMER settings
 881      */
 882     Cache.setPropertyNoSave(HMMALIGN_TRIM_TERMINI,
 883             Boolean.toString(hmmrTrimTermini.isSelected()));
 884     Cache.setPropertyNoSave(HMMINFO_GLOBAL_BACKGROUND,
 885             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 886     Cache.setPropertyNoSave(HMMSEARCH_SEQCOUNT,
 887             hmmerSequenceCount.getText());
 888     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
 889     if (cygwinPath != null)
 890     {
 891       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
 892     }
 893     AlignFrame[] frames = Desktop.getAlignFrames();
 894     if (frames != null && frames.length > 0)
 895     {
 896       for (AlignFrame f : frames)
 897       {
 898         f.updateHMMERStatus();
 899       }
 900     }
 901
 902     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 903     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 904     {
 905       hmmerBackgroundUniprot.setSelected(true);
 906     }
 907     else
 908     {
 909       hmmerBackgroundAlignment.setSelected(true);
 910     }
 911     hmmerSequenceCount
 912             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 913     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 914
 915     /*
 916      * Save Overview settings
 917      */
 918     Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
 919     Cache.setColourPropertyNoSave(HIDDEN_COLOUR, hiddenColour.getBackground());
 920     Cache.setPropertyNoSave(USE_LEGACY_GAP,
 921             Boolean.toString(useLegacyGap.isSelected()));
 922     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
 923             Boolean.toString(showHiddenAtStart.isSelected()));
 924
 925     /*
 926      * Save Structure settings
 927      */
 928     Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
 929             Boolean.toString(addTempFactor.isSelected()));
 930     Cache.setPropertyNoSave(ADD_SS_ANN,
 931             Boolean.toString(addSecondaryStructure.isSelected()));
 932     Cache.setPropertyNoSave(USE_RNAVIEW,
 933             Boolean.toString(useRnaView.isSelected()));
 934     Cache.setPropertyNoSave(STRUCT_FROM_PDB,
 935             Boolean.toString(structFromPdb.isSelected()));
 936     if (!Platform.isJS())
 937     {
 938       Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
 939               structViewer.getSelectedItem().toString());
 940     }
 941     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 942     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
 943             Boolean.toString(siftsMapping.isSelected()));
 944     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 945
 946     /*
 947      * Save Output settings
 948      */
 949     Cache.setPropertyNoSave("EPS_RENDERING",
 950             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 951     Cache.setPropertyNoSave("HTML_RENDERING",
 952             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 953     Cache.setPropertyNoSave("SVG_RENDERING",
 954             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 955
 956     /*
 957      * Save Connections settings
 958      */
 959     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 960
 961     jalview.util.BrowserLauncher.resetBrowser();
 962
 963     // save user-defined and selected links
 964     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 965     if (menuLinks.isEmpty())
 966     {
 967       Cache.removePropertyNoSave("SEQUENCE_LINKS");
 968     }
 969     else
 970     {
 971       Cache.setPropertyNoSave("SEQUENCE_LINKS",
 972               menuLinks.toString());
 973     }
 974
 975     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 976     if (nonMenuLinks.isEmpty())
 977     {
 978       Cache.removePropertyNoSave("STORED_LINKS");
 979     }
 980     else
 981     {
 982       Cache.setPropertyNoSave("STORED_LINKS",
 983               nonMenuLinks.toString());
 984     }
 985
 986     Cache.setPropertyNoSave("DEFAULT_URL",
 987             sequenceUrlLinks.getPrimaryUrlId());
 988
 989     Cache.setPropertyNoSave("USE_PROXY",
 990             Boolean.toString(useProxy.isSelected()));
 991
 992     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 993
 994     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 995
 996     if (useProxy.isSelected())
 997     {
 998       System.setProperty("http.proxyHost", proxyServerTB.getText());
 999       System.setProperty("http.proxyPort", proxyPortTB.getText());
1000     }
1001     else
1002     {
1003       System.setProperty("http.proxyHost", "");
1004       System.setProperty("http.proxyPort", "");
1005     }
1006     Cache.setProperty("VERSION_CHECK",
1007             Boolean.toString(versioncheck.isSelected()));
1008     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
1009     {
1010       // default is false - we only set this if the user has actively agreed
1011       Cache.setProperty("USAGESTATS",
1012               Boolean.toString(usagestats.isSelected()));
1013     }
1014     if (!questionnaire.isSelected())
1015     {
1016       Cache.setProperty("NOQUESTIONNAIRES", "true");
1017     }
1018     else
1019     {
1020       // special - made easy to edit a property file to disable questionnaires
1021       // by just adding the given line
1022       Cache.removeProperty("NOQUESTIONNAIRES");
1023     }
1024
1025     /*
1026      * Save Output settings
1027      */
1028     Cache.setPropertyNoSave("BLC_JVSUFFIX",
1029             Boolean.toString(blcjv.isSelected()));
1030     Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
1031             Boolean.toString(clustaljv.isSelected()));
1032     Cache.setPropertyNoSave("FASTA_JVSUFFIX",
1033             Boolean.toString(fastajv.isSelected()));
1034     Cache.setPropertyNoSave("MSF_JVSUFFIX",
1035             Boolean.toString(msfjv.isSelected()));
1036     Cache.setPropertyNoSave("PFAM_JVSUFFIX",
1037             Boolean.toString(pfamjv.isSelected()));
1038     Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
1039             Boolean.toString(pileupjv.isSelected()));
1040     Cache.setPropertyNoSave("PIR_JVSUFFIX",
1041             Boolean.toString(pirjv.isSelected()));
1042     Cache.setPropertyNoSave("PIR_MODELLER",
1043             Boolean.toString(modellerOutput.isSelected()));
1044     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
1045             Boolean.toString(embbedBioJSON.isSelected()));
1046     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
1047
1048     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
1049             Boolean.toString(autoIdWidth.isSelected()));
1050     userIdWidth_actionPerformed();
1051     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
1052             userIdWidth.getText());
1053
1054     /*
1055      * Save Editing settings
1056      */
1057     Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
1058             Boolean.toString(autoCalculateConsCheck.isSelected()));
1059     Cache.setPropertyNoSave("SORT_BY_TREE",
1060             Boolean.toString(sortByTree.isSelected()));
1061     Cache.setPropertyNoSave("PAD_GAPS",
1062             Boolean.toString(padGaps.isSelected()));
1063
1064     if (!Platform.isJS())
1065     {
1066       wsPrefs.updateAndRefreshWsMenuConfig(false);
1067     }
1068
1069     /*
1070      * Save Backups settings
1071      */
1072     Cache.setPropertyNoSave(BackupFiles.ENABLED,
1073             Boolean.toString(enableBackupFiles.isSelected()));
1074     int preset = getComboIntStringKey(backupfilesPresetsCombo);
1075     Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset));
1076
1077     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1078     {
1079       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1080       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1081               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1082       Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
1083                       customBFPE.toString());
1084     }
1085
1086     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1087             .get(preset);
1088     Cache.setPropertyNoSave(
1089             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1090
1091     Cache.saveProperties();
1092     Desktop.getInstance().doConfigureStructurePrefs();
1093     try
1094     {
1095       frame.setClosed(true);
1096     } catch (Exception ex)
1097     {
1098     }
1099   }
1100
1101   public static void setAppletDefaults()
1102   {
1103
1104     // http://www.jalview.org/old/v2_8/examples/appletParameters.html
1105
1106     // showConservation true or false Default is true.
1107     // showQuality true or false Default is true.
1108     // showConsensus true or false Default is true.
1109     // showFeatureSettings true or false Shows the feature settings window when
1110     // startin
1111     // showTreeBootstraps true or false (default is true) show or hide branch
1112     // bootstraps
1113     // showTreeDistances true or false (default is true) show or hide branch
1114     // lengths
1115     // showUnlinkedTreeNodes true or false (default is false) indicate if
1116     // unassociated nodes should be highlighted in the tree view
1117     // showUnconserved true of false (default is false) When true, only gaps and
1118     // symbols different to the consensus sequence ions of the alignment
1119     // showGroupConsensus true of false (default is false) When true, shows
1120     // consensus annotation row for any groups on the alignment. (since 2.7)
1121     // showGroupConservation true of false (default is false) When true, shows
1122     // amino-acid property conservation annotation row for any groups on the
1123     // showConsensusHistogram true of false (default is true) When true, shows
1124     // the percentage occurence of the consensus symbol for each column as a
1125     // showSequenceLogo true of false (default is false) When true, shows a
1126     // sequence logo above the consensus sequence (overlaid above the Consensus
1127
1128     Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
1129     Cache.setPropertyNoSave(SHOW_QUALITY, "false");
1130     Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
1131     Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
1132     Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
1133     Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
1134
1135     // TODO -- just a start here
1136   }
1137  /**
1138    * Do any necessary validation before saving settings. Return focus to the
1139    * first tab which fails validation.
1140    *
1141    * @return
1142    */
1143   private boolean validateSettings()
1144   {
1145     if (!validateStructure())
1146     {
1147       structureTab.requestFocusInWindow();
1148       return false;
1149     }
1150     return true;
1151   }
1152
1153   @Override
1154   protected boolean validateStructure()
1155   {
1156     return validateChimeraPath();
1157
1158   }
1159
1160   /**
1161    * DOCUMENT ME!
1162    */
1163   @Override
1164   public void startupFileTextfield_mouseClicked()
1165   {
1166     // TODO: JAL-3048 not needed for Jalview-JS
1167     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1168     JalviewFileChooser chooser = JalviewFileChooser
1169             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1170     chooser.setFileView(new JalviewFileView());
1171     chooser.setDialogTitle(
1172             MessageManager.getString("label.select_startup_file"));
1173
1174     int value = chooser.showOpenDialog(this);
1175
1176     if (value == JalviewFileChooser.APPROVE_OPTION)
1177     {
1178       FileFormatI format = chooser.getSelectedFormat();
1179       if (format != null)
1180       {
1181         Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
1182                 format.getName());
1183       }
1184       startupFileTextfield
1185               .setText(chooser.getSelectedFile().getAbsolutePath());
1186     }
1187   }
1188
1189   /**
1190    * DOCUMENT ME!
1191    *
1192    * @param e
1193    *          DOCUMENT ME!
1194    */
1195   @Override
1196   public void cancel_actionPerformed(ActionEvent e)
1197   {
1198     try
1199     {
1200       if (!Platform.isJS())
1201       {
1202         wsPrefs.updateWsMenuConfig(true);
1203         wsPrefs.refreshWs_actionPerformed(e);
1204       }
1205       frame.setClosed(true);
1206     } catch (Exception ex)
1207     {
1208     }
1209   }
1210
1211   /**
1212    * DOCUMENT ME!
1213    *
1214    * @param e
1215    *          DOCUMENT ME!
1216    */
1217   @Override
1218   public void annotations_actionPerformed(ActionEvent e)
1219   {
1220     conservation.setEnabled(annotations.isSelected());
1221     quality.setEnabled(annotations.isSelected());
1222     identity.setEnabled(annotations.isSelected());
1223     showOccupancy.setEnabled(annotations.isSelected());
1224     showGroupConsensus.setEnabled(annotations.isSelected());
1225     showGroupConservation.setEnabled(annotations.isSelected());
1226     showConsensHistogram.setEnabled(annotations.isSelected()
1227             && (identity.isSelected() || showGroupConsensus.isSelected()));
1228     showConsensLogo.setEnabled(annotations.isSelected()
1229             && (identity.isSelected() || showGroupConsensus.isSelected()));
1230     showInformationHistogram.setEnabled(annotations.isSelected());
1231     showHMMLogo.setEnabled(annotations.isSelected());
1232   }
1233
1234   @Override
1235   public void newLink_actionPerformed(ActionEvent e)
1236   {
1237     GSequenceLink link = new GSequenceLink();
1238     boolean valid = false;
1239     while (!valid)
1240     {
1241       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1242               MessageManager.getString("label.new_sequence_url_link"),
1243               JvOptionPane.OK_CANCEL_OPTION, -1,
1244               null) == JvOptionPane.OK_OPTION)
1245       {
1246         if (link.checkValid())
1247         {
1248           if (((UrlLinkTableModel) linkUrlTable.getModel())
1249                   .isUniqueName(link.getName()))
1250           {
1251             ((UrlLinkTableModel) linkUrlTable.getModel())
1252                     .insertRow(link.getName(), link.getURL());
1253             valid = true;
1254           }
1255           else
1256           {
1257             link.notifyDuplicate();
1258             continue;
1259           }
1260         }
1261       }
1262       else
1263       {
1264         break;
1265       }
1266     }
1267   }
1268
1269   @Override
1270   public void editLink_actionPerformed(ActionEvent e)
1271   {
1272     GSequenceLink link = new GSequenceLink();
1273
1274     int index = linkUrlTable.getSelectedRow();
1275     if (index == -1)
1276     {
1277       // button no longer enabled if row is not selected
1278       Cache.log.debug("Edit with no row selected in linkUrlTable");
1279       return;
1280     }
1281
1282     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1283             .getNameColumn();
1284     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1285             .getUrlColumn();
1286     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1287     link.setName(oldName);
1288     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1289
1290     boolean valid = false;
1291     while (!valid)
1292     {
1293       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1294               MessageManager.getString("label.edit_sequence_url_link"),
1295               JvOptionPane.OK_CANCEL_OPTION, -1,
1296               null) == JvOptionPane.OK_OPTION)
1297       {
1298         if (link.checkValid())
1299         {
1300           if ((oldName.equals(link.getName()))
1301                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1302                           .isUniqueName(link.getName())))
1303           {
1304             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1305             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1306             valid = true;
1307           }
1308           else
1309           {
1310             link.notifyDuplicate();
1311             continue;
1312           }
1313         }
1314       }
1315       else
1316       {
1317         break;
1318       }
1319     }
1320   }
1321
1322   @Override
1323   public void deleteLink_actionPerformed(ActionEvent e)
1324   {
1325     int index = linkUrlTable.getSelectedRow();
1326     int modelIndex = -1;
1327     if (index == -1)
1328     {
1329       // button no longer enabled if row is not selected
1330       Cache.log.debug("Delete with no row selected in linkUrlTable");
1331       return;
1332     }
1333     else
1334     {
1335       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1336     }
1337
1338     // make sure we use the model index to delete, and not the table index
1339     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1340   }
1341
1342   @Override
1343   public void defaultBrowser_mouseClicked(MouseEvent e)
1344   {
1345     // TODO: JAL-3048 not needed for j2s
1346     if (!Platform.isJS()) // BH 2019
1347     /**
1348      * Java only
1349      *
1350      * @j2sIgnore
1351      */
1352     {
1353       JFileChooser chooser = new JFileChooser(".");
1354       chooser.setDialogTitle(
1355               MessageManager.getString("label.select_default_browser"));
1356
1357       int value = chooser.showOpenDialog(this);
1358
1359       if (value == JFileChooser.APPROVE_OPTION)
1360       {
1361         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1362       }
1363     }
1364   }
1365
1366   /*
1367    * (non-Javadoc)
1368    *
1369    * @see
1370    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1371    * .ActionEvent)
1372    */
1373   @Override
1374   protected void showunconserved_actionPerformed(ActionEvent e)
1375   {
1376     // TODO Auto-generated method stub
1377     super.showunconserved_actionPerformed(e);
1378   }
1379
1380   public static List<String> getGroupURLLinks()
1381   {
1382     return groupURLLinks;
1383   }
1384
1385   @Override
1386   public void minColour_actionPerformed(JPanel panel)
1387   {
1388     JalviewColourChooser.showColourChooser(this,
1389             MessageManager.getString("label.select_colour_minimum_value"),
1390             panel);
1391   }
1392
1393   @Override
1394   public void maxColour_actionPerformed(JPanel panel)
1395   {
1396     JalviewColourChooser.showColourChooser(this,
1397             MessageManager.getString("label.select_colour_maximum_value"),
1398             panel);
1399   }
1400
1401   @Override
1402   public void gapColour_actionPerformed(JPanel gap)
1403   {
1404     if (!useLegacyGap.isSelected())
1405     {
1406       JalviewColourChooser.showColourChooser(this,
1407               MessageManager.getString("label.select_gap_colour"),
1408               gap);
1409     }
1410   }
1411
1412   @Override
1413   public void hiddenColour_actionPerformed(JPanel hidden)
1414   {
1415     JalviewColourChooser.showColourChooser(this,
1416             MessageManager.getString("label.select_hidden_colour"),
1417             hidden);
1418   }
1419
1420   @Override
1421   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1422   {
1423     boolean enabled = useLegacyGap.isSelected();
1424     if (enabled)
1425     {
1426       gapColour.setBackground(
1427               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1428     }
1429     else
1430     {
1431       gapColour.setBackground(
1432               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1433     }
1434     gapColour.setEnabled(!enabled);
1435     gapLabel.setEnabled(!enabled);
1436   }
1437
1438   @Override
1439   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1440   {
1441     useLegacyGap.setSelected(false);
1442     useLegacyGaps_actionPerformed(null);
1443     showHiddenAtStart.setSelected(false);
1444     hiddenColour.setBackground(
1445             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1446   }
1447
1448   @Override
1449   protected void userIdWidth_actionPerformed()
1450   {
1451     try
1452     {
1453       String val = userIdWidth.getText().trim();
1454       if (val.length() > 0)
1455       {
1456         Integer iw = Integer.parseInt(val);
1457         if (iw.intValue() < 12)
1458         {
1459           throw new NumberFormatException();
1460         }
1461         userIdWidth.setText(iw.toString());
1462       }
1463     } catch (NumberFormatException x)
1464     {
1465       userIdWidth.setText("");
1466       JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1467               MessageManager
1468                       .getString("warn.user_defined_width_requirements"),
1469               MessageManager.getString("label.invalid_id_column_width"),
1470               JvOptionPane.WARNING_MESSAGE);
1471     }
1472   }
1473
1474   @Override
1475   protected void autoIdWidth_actionPerformed()
1476   {
1477     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1478     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1479   }
1480
1481   /**
1482    * Returns true if chimera path is to a valid executable, else show an error
1483    * dialog.
1484    */
1485   private boolean validateChimeraPath()
1486   {
1487     if (chimeraPath.getText().trim().length() > 0)
1488     {
1489       File f = new File(chimeraPath.getText());
1490       if (!f.canExecute())
1491       {
1492         JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1493                 MessageManager.getString("label.invalid_chimera_path"),
1494                 MessageManager.getString("label.invalid_name"),
1495                 JvOptionPane.ERROR_MESSAGE);
1496         return false;
1497       }
1498     }
1499     return true;
1500   }
1501
1502   /**
1503    * Returns true if the given text field contains a path to a folder that
1504    * contains an executable with the given name, else false (after showing a
1505    * warning dialog). The executable name will be tried with .exe appended if not
1506    * found.
1507    *
1508    * @param textField
1509    * @param executable
1510    */
1511   protected boolean validateExecutablePath(JTextField textField, String executable)
1512   {
1513     String folder = textField.getText().trim();
1514
1515     if (FileUtils.getExecutable(executable, folder) != null)
1516     {
1517       return true;
1518     }
1519     if (folder.length() > 0)
1520     {
1521       JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
1522               MessageManager.formatMessage("label.executable_not_found",
1523                       executable),
1524               MessageManager.getString("label.invalid_folder"),
1525               JvOptionPane.ERROR_MESSAGE);
1526     }
1527     return false;
1528   }
1529
1530   /**
1531    * Checks if a file can be executed
1532    *
1533    * @param path
1534    *          the path to the file
1535    * @return
1536    */
1537   public boolean canExecute(String path)
1538   {
1539     File file = new File(path);
1540     if (!file.canExecute())
1541     {
1542       file = new File(path + ".exe");
1543       {
1544         if (!file.canExecute())
1545         {
1546           return false;
1547         }
1548       }
1549     }
1550     return true;
1551   }
1552
1553   /**
1554    * If Chimera is selected, check it can be found on default or user-specified
1555    * path, if not show a warning/help dialog.
1556    */
1557   @Override
1558   protected void structureViewer_actionPerformed(String selectedItem)
1559   {
1560     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1561     {
1562       return;
1563     }
1564     boolean found = false;
1565
1566     /*
1567      * Try user-specified and standard paths for Chimera executable.
1568      */
1569     List<String> paths = StructureManager.getChimeraPaths();
1570     paths.add(0, chimeraPath.getText());
1571     for (String path : paths)
1572     {
1573       if (new File(path.trim()).canExecute())
1574       {
1575         found = true;
1576         break;
1577       }
1578     }
1579     if (!found)
1580     {
1581       String[] options = { "OK", "Help" };
1582       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
1583               JvSwingUtils.wrapTooltip(true,
1584                       MessageManager.getString("label.chimera_missing")),
1585               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1586               null, options, options[0]);
1587       if (showHelp == JvOptionPane.NO_OPTION)
1588       {
1589         try
1590         {
1591           Help.showHelpWindow(HelpId.StructureViewer);
1592         } catch (HelpSetException e)
1593         {
1594           e.printStackTrace();
1595         }
1596       }
1597     }
1598   }
1599
1600   @Override
1601   protected void validateHmmerPath()
1602   {
1603     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1604   }
1605
1606   @Override
1607   protected void validateCygwinPath()
1608   {
1609     validateExecutablePath(cygwinPath, "run");
1610   }
1611
1612   public class OptionsParam
1613   {
1614     private String name;
1615
1616     private String code;
1617
1618     public OptionsParam(String name, String code)
1619     {
1620       this.name = name;
1621       this.code = code;
1622     }
1623
1624     public String getName()
1625     {
1626       return name;
1627     }
1628
1629     public void setName(String name)
1630     {
1631       this.name = name;
1632     }
1633
1634     public String getCode()
1635     {
1636       return code;
1637     }
1638
1639     public void setCode(String code)
1640     {
1641       this.code = code;
1642     }
1643
1644     @Override
1645     public String toString()
1646     {
1647       return name;
1648     }
1649
1650     @Override
1651     public boolean equals(Object that)
1652     {
1653       if (!(that instanceof OptionsParam))
1654       {
1655         return false;
1656       }
1657       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1658     }
1659
1660     @Override
1661     public int hashCode()
1662     {
1663       return name.hashCode() + code.hashCode();
1664     }
1665   }
1666
1667   private class UrlListSelectionHandler implements ListSelectionListener
1668   {
1669
1670     @Override
1671     public void valueChanged(ListSelectionEvent e)
1672     {
1673       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1674
1675       int index = lsm.getMinSelectionIndex();
1676       if (index == -1)
1677       {
1678         // no selection, so disable delete/edit buttons
1679         editLink.setEnabled(false);
1680         deleteLink.setEnabled(false);
1681         return;
1682       }
1683       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1684
1685       // enable/disable edit and delete link buttons
1686       if (((UrlLinkTableModel) linkUrlTable.getModel())
1687               .isRowDeletable(modelIndex))
1688       {
1689         deleteLink.setEnabled(true);
1690       }
1691       else
1692       {
1693         deleteLink.setEnabled(false);
1694       }
1695
1696       if (((UrlLinkTableModel) linkUrlTable.getModel())
1697               .isRowEditable(modelIndex))
1698       {
1699         editLink.setEnabled(true);
1700       }
1701       else
1702       {
1703         editLink.setEnabled(false);
1704       }
1705     }
1706   }
1707 }