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