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     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 645
 646     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 647     // note antisense here: default is true
 648     questionnaire
 649             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 650     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 651
 652     /*
 653      * Set Output tab defaults
 654      */
 655     setupOutputCombo(epsRendering, "EPS_RENDERING");
 656     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 657     setupOutputCombo(svgRendering, "SVG_RENDERING");
 658     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 659     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 660     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 661     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 662     userIdWidth.setText(wi == null ? "" : wi.toString());
 663     // TODO: refactor to use common enum via FormatAdapter and allow extension
 664     // for new flat file formats
 665     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 666     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 667     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 668     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 669     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 670     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 671     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 672     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 673     embbedBioJSON
 674             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 675
 676     /*
 677      * Set Editing tab defaults
 678      */
 679     autoCalculateConsCheck
 680             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 681     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 682     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 683
 684     annotations_actionPerformed(null); // update the display of the annotation
 685                                        // settings
 686
 687     /*
 688      * Set Backups tab defaults
 689      */
 690     loadLastSavedBackupsOptions();
 691
 692     /*
 693      * Set Startup tab defaults
 694      */
 695
 696   }
 697
 698   /**
 699    * A helper method that sets the items and initial selection in a character
 700    * rendering option list (Prompt each time/Lineart/Text)
 701    *
 702    * @param comboBox
 703    * @param propertyKey
 704    */
 705   protected void setupOutputCombo(JComboBox<Object> comboBox,
 706           String propertyKey)
 707   {
 708     comboBox.addItem(promptEachTimeOpt);
 709     comboBox.addItem(lineArtOpt);
 710     comboBox.addItem(textOpt);
 711
 712     /*
 713      * JalviewJS doesn't support Lineart so force it to Text
 714      */
 715     String defaultOption = Platform.isJS() ? "Text"
 716             : Cache.getDefault(propertyKey, "Prompt each time");
 717     if (defaultOption.equalsIgnoreCase("Text"))
 718     {
 719       comboBox.setSelectedItem(textOpt);
 720     }
 721     else if (defaultOption.equalsIgnoreCase("Lineart"))
 722     {
 723       comboBox.setSelectedItem(lineArtOpt);
 724     }
 725     else
 726     {
 727       comboBox.setSelectedItem(promptEachTimeOpt);
 728     }
 729   }
 730
 731   /**
 732    * Save user selections on the Preferences tabs to the Cache and write out to
 733    * file.
 734    *
 735    * @param e
 736    */
 737   @Override
 738   public void ok_actionPerformed(ActionEvent e)
 739   {
 740     if (!validateSettings())
 741     {
 742       return;
 743     }
 744
 745     /*
 746      * Set proxy settings first (to be before web services refresh)
 747      */
 748     saveProxySettings();
 749
 750     /*
 751      * Save Visual settings
 752      */
 753     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 754             Boolean.toString(seqLimit.isSelected()));
 755     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 756             Boolean.toString(rightAlign.isSelected()));
 757     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 758             Boolean.toString(fullScreen.isSelected()));
 759     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 760             Boolean.toString(openoverv.isSelected()));
 761     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 762             Boolean.toString(annotations.isSelected()));
 763     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 764             Boolean.toString(conservation.isSelected()));
 765     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 766             Boolean.toString(quality.isSelected()));
 767     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 768             Boolean.toString(identity.isSelected()));
 769
 770     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 771             gapSymbolCB.getSelectedItem().toString());
 772
 773     Cache.applicationProperties.setProperty("FONT_NAME",
 774             fontNameCB.getSelectedItem().toString());
 775     Cache.applicationProperties.setProperty("FONT_STYLE",
 776             fontStyleCB.getSelectedItem().toString());
 777     Cache.applicationProperties.setProperty("FONT_SIZE",
 778             fontSizeCB.getSelectedItem().toString());
 779
 780     Cache.applicationProperties.setProperty("ID_ITALICS",
 781             Boolean.toString(idItalics.isSelected()));
 782     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 783             Boolean.toString(showUnconserved.isSelected()));
 784     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 785             Boolean.toString(showOccupancy.isSelected()));
 786     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 787             Boolean.toString(showGroupConsensus.isSelected()));
 788     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 789             Boolean.toString(showGroupConservation.isSelected()));
 790     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 791             Boolean.toString(showConsensHistogram.isSelected()));
 792     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 793             Boolean.toString(showConsensLogo.isSelected()));
 794     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 795             Boolean.toString(smoothFont.isSelected()));
 796     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 797             Boolean.toString(scaleProteinToCdna.isSelected()));
 798     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 799             Boolean.toString(showNpTooltip.isSelected()));
 800     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 801             Boolean.toString(showDbRefTooltip.isSelected()));
 802
 803     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 804             Boolean.toString(wrap.isSelected()));
 805
 806     Cache.applicationProperties.setProperty("STARTUP_FILE",
 807             startupFileTextfield.getText());
 808     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 809             Boolean.toString(startupCheckbox.isSelected()));
 810
 811     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 812             sortby.getSelectedItem().toString());
 813
 814     // convert description of sort order to enum name for save
 815     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 816             .forDescription(sortAnnBy.getSelectedItem().toString());
 817     if (annSortOrder != null)
 818     {
 819       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 820               annSortOrder.name());
 821     }
 822
 823     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 824     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 825             Boolean.valueOf(showAutocalcFirst).toString());
 826
 827     /*
 828      * Save Colours settings
 829      */
 830     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 831             protColour.getSelectedItem().toString());
 832     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 833             nucColour.getSelectedItem().toString());
 834     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 835             minColour.getBackground());
 836     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 837             maxColour.getBackground());
 838
 839     /*
 840      * Save Overview settings
 841      */
 842     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 843     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 844     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 845             Boolean.toString(useLegacyGap.isSelected()));
 846     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 847             Boolean.toString(showHiddenAtStart.isSelected()));
 848
 849     /*
 850      * Save Structure settings
 851      */
 852     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 853             Boolean.toString(addTempFactor.isSelected()));
 854     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 855             Boolean.toString(addSecondaryStructure.isSelected()));
 856     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 857             Boolean.toString(structFromPdb.isSelected()));
 858     String viewer = structViewer.getSelectedItem().toString();
 859     String viewerPath = structureViewerPath.getText();
 860     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 861     if (viewer.equals(ViewerType.CHIMERA.name()))
 862     {
 863       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 864     }
 865     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 866     {
 867       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 868     }
 869     else if (viewer.equals(ViewerType.PYMOL.name()))
 870     {
 871       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 872     }
 873     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 874             Boolean.toString(siftsMapping.isSelected()));
 875     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 876
 877     /*
 878      * Save Output settings
 879      */
 880     Cache.applicationProperties.setProperty("EPS_RENDERING",
 881             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 882     Cache.applicationProperties.setProperty("HTML_RENDERING",
 883             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 884     Cache.applicationProperties.setProperty("SVG_RENDERING",
 885             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 886
 887     /*
 888      * Save Connections settings
 889      */
 890     // Proxy settings set first (to catch web services)
 891
 892     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 893     if (Cache.getProperty("DEFAULT_BROWSER") != null)
 894     {
 895       System.setProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY,
 896               Cache.getProperty("DEFAULT_BROWSER"));
 897     }
 898     else
 899     {
 900       System.clearProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY);
 901     }
 902     BrowserLauncher.resetBrowser();
 903
 904     // save user-defined and selected links
 905     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 906     if (menuLinks.isEmpty())
 907     {
 908       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 909     }
 910     else
 911     {
 912       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 913               menuLinks.toString());
 914     }
 915
 916     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 917     if (nonMenuLinks.isEmpty())
 918     {
 919       Cache.applicationProperties.remove("STORED_LINKS");
 920     }
 921     else
 922     {
 923       Cache.applicationProperties.setProperty("STORED_LINKS",
 924               nonMenuLinks.toString());
 925     }
 926
 927     Cache.applicationProperties.setProperty("DEFAULT_URL",
 928             sequenceUrlLinks.getPrimaryUrlId());
 929
 930     Cache.setProperty("VERSION_CHECK",
 931             Boolean.toString(versioncheck.isSelected()));
 932     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 933     {
 934       // default is false - we only set this if the user has actively agreed
 935       Cache.setProperty("USAGESTATS",
 936               Boolean.toString(usagestats.isSelected()));
 937     }
 938     if (!questionnaire.isSelected())
 939     {
 940       Cache.setProperty("NOQUESTIONNAIRES", "true");
 941     }
 942     else
 943     {
 944       // special - made easy to edit a property file to disable questionnaires
 945       // by just adding the given line
 946       Cache.removeProperty("NOQUESTIONNAIRES");
 947     }
 948
 949     /*
 950      * Save Output settings
 951      */
 952     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 953             Boolean.toString(blcjv.isSelected()));
 954     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 955             Boolean.toString(clustaljv.isSelected()));
 956     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 957             Boolean.toString(fastajv.isSelected()));
 958     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 959             Boolean.toString(msfjv.isSelected()));
 960     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 961             Boolean.toString(pfamjv.isSelected()));
 962     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 963             Boolean.toString(pileupjv.isSelected()));
 964     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 965             Boolean.toString(pirjv.isSelected()));
 966     Cache.applicationProperties.setProperty("PIR_MODELLER",
 967             Boolean.toString(modellerOutput.isSelected()));
 968     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 969             Boolean.toString(embbedBioJSON.isSelected()));
 970     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 971
 972     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 973             Boolean.toString(autoIdWidth.isSelected()));
 974     userIdWidth_actionPerformed();
 975     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 976             userIdWidth.getText());
 977
 978     /*
 979      * Save Editing settings
 980      */
 981     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 982             Boolean.toString(autoCalculateConsCheck.isSelected()));
 983     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 984             Boolean.toString(sortByTree.isSelected()));
 985     Cache.applicationProperties.setProperty("PAD_GAPS",
 986             Boolean.toString(padGaps.isSelected()));
 987
 988     if (!Platform.isJS())
 989     {
 990       wsPrefs.updateAndRefreshWsMenuConfig(false);
 991     }
 992
 993     /*
 994      * Save Backups settings
 995      */
 996     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 997             Boolean.toString(enableBackupFiles.isSelected()));
 998     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 999     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
1000             Integer.toString(preset));
1001
1002     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
1003     {
1004       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
1005       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
1006               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
1007       Cache.applicationProperties.setProperty(
1008               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
1009     }
1010
1011     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1012             .get(preset);
1013     Cache.applicationProperties.setProperty(
1014             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1015
1016     /*
1017      * Save Memory Settings
1018      */
1019     Cache.applicationProperties.setProperty(
1020             MemorySetting.CUSTOMISED_SETTINGS,
1021             Boolean.toString(customiseMemorySetting.isSelected()));
1022     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
1023             Integer.toString(jvmMemoryPercentSlider.getValue()));
1024     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
1025             jvmMemoryMaxTextField.getText());
1026
1027     /*
1028      * save and close Preferences
1029      */
1030
1031     Cache.saveProperties();
1032     Desktop.instance.doConfigureStructurePrefs();
1033     try
1034     {
1035       frame.setClosed(true);
1036     } catch (Exception ex)
1037     {
1038     }
1039   }
1040
1041   public void saveProxySettings()
1042   {
1043     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1044             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1045                     : Cache.PROXYTYPE_SYSTEM;
1046     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1047     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1048     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1049     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1050     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1051     Cache.setOrRemove("PROXY_AUTH",
1052             Boolean.toString(proxyAuth.isSelected()));
1053     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1054     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1055     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1056     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1057             || !newProxyType.equals(previousProxyType))
1058     {
1059       // force a re-lookup of ws if proxytype is custom or has changed
1060       wsPrefs.update++;
1061     }
1062     previousProxyType = newProxyType;
1063   }
1064
1065   /**
1066    * Do any necessary validation before saving settings. Return focus to the
1067    * first tab which fails validation.
1068    *
1069    * @return
1070    */
1071   private boolean validateSettings()
1072   {
1073     if (!validateStructure())
1074     {
1075       structureTab.requestFocusInWindow();
1076       return false;
1077     }
1078     return true;
1079   }
1080
1081   @Override
1082   protected boolean validateStructure()
1083   {
1084     return validateViewerPath();
1085
1086   }
1087
1088   /**
1089    * DOCUMENT ME!
1090    */
1091   @Override
1092   public void startupFileTextfield_mouseClicked()
1093   {
1094     // TODO: JAL-3048 not needed for Jalview-JS
1095     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1096     JalviewFileChooser chooser = JalviewFileChooser
1097             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1098     chooser.setFileView(new JalviewFileView());
1099     chooser.setDialogTitle(
1100             MessageManager.getString("label.select_startup_file"));
1101
1102     int value = chooser.showOpenDialog(this);
1103
1104     if (value == JalviewFileChooser.APPROVE_OPTION)
1105     {
1106       FileFormatI format = chooser.getSelectedFormat();
1107       if (format != null)
1108       {
1109         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1110                 format.getName());
1111       }
1112       startupFileTextfield
1113               .setText(chooser.getSelectedFile().getAbsolutePath());
1114     }
1115   }
1116
1117   /**
1118    * DOCUMENT ME!
1119    *
1120    * @param e
1121    *          DOCUMENT ME!
1122    */
1123   @Override
1124   public void cancel_actionPerformed(ActionEvent e)
1125   {
1126     try
1127     {
1128       if (!Platform.isJS())
1129       {
1130         wsPrefs.updateWsMenuConfig(true);
1131         wsPrefs.refreshWs_actionPerformed(e);
1132       }
1133       frame.setClosed(true);
1134     } catch (Exception ex)
1135     {
1136     }
1137   }
1138
1139   /**
1140    * DOCUMENT ME!
1141    *
1142    * @param e
1143    *          DOCUMENT ME!
1144    */
1145   @Override
1146   public void annotations_actionPerformed(ActionEvent e)
1147   {
1148     conservation.setEnabled(annotations.isSelected());
1149     quality.setEnabled(annotations.isSelected());
1150     identity.setEnabled(annotations.isSelected());
1151     showOccupancy.setEnabled(annotations.isSelected());
1152     showGroupConsensus.setEnabled(annotations.isSelected());
1153     showGroupConservation.setEnabled(annotations.isSelected());
1154     showConsensHistogram.setEnabled(annotations.isSelected()
1155             && (identity.isSelected() || showGroupConsensus.isSelected()));
1156     showConsensLogo.setEnabled(annotations.isSelected()
1157             && (identity.isSelected() || showGroupConsensus.isSelected()));
1158   }
1159
1160   @Override
1161   public void newLink_actionPerformed(ActionEvent e)
1162   {
1163     GSequenceLink link = new GSequenceLink();
1164     boolean valid = false;
1165     while (!valid)
1166     {
1167       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1168               MessageManager.getString("label.new_sequence_url_link"),
1169               JvOptionPane.OK_CANCEL_OPTION, -1,
1170               null) == JvOptionPane.OK_OPTION)
1171       {
1172         if (link.checkValid())
1173         {
1174           if (((UrlLinkTableModel) linkUrlTable.getModel())
1175                   .isUniqueName(link.getName()))
1176           {
1177             ((UrlLinkTableModel) linkUrlTable.getModel())
1178                     .insertRow(link.getName(), link.getURL());
1179             valid = true;
1180           }
1181           else
1182           {
1183             link.notifyDuplicate();
1184             continue;
1185           }
1186         }
1187       }
1188       else
1189       {
1190         break;
1191       }
1192     }
1193   }
1194
1195   @Override
1196   public void editLink_actionPerformed(ActionEvent e)
1197   {
1198     GSequenceLink link = new GSequenceLink();
1199
1200     int index = linkUrlTable.getSelectedRow();
1201     if (index == -1)
1202     {
1203       // button no longer enabled if row is not selected
1204       Console.debug("Edit with no row selected in linkUrlTable");
1205       return;
1206     }
1207
1208     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1209             .getNameColumn();
1210     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1211             .getUrlColumn();
1212     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1213     link.setName(oldName);
1214     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1215
1216     boolean valid = false;
1217     while (!valid)
1218     {
1219       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1220               MessageManager.getString("label.edit_sequence_url_link"),
1221               JvOptionPane.OK_CANCEL_OPTION, -1,
1222               null) == JvOptionPane.OK_OPTION)
1223       {
1224         if (link.checkValid())
1225         {
1226           if ((oldName.equals(link.getName()))
1227                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1228                           .isUniqueName(link.getName())))
1229           {
1230             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1231             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1232             valid = true;
1233           }
1234           else
1235           {
1236             link.notifyDuplicate();
1237             continue;
1238           }
1239         }
1240       }
1241       else
1242       {
1243         break;
1244       }
1245     }
1246   }
1247
1248   @Override
1249   public void deleteLink_actionPerformed(ActionEvent e)
1250   {
1251     int index = linkUrlTable.getSelectedRow();
1252     int modelIndex = -1;
1253     if (index == -1)
1254     {
1255       // button no longer enabled if row is not selected
1256       Console.debug("Delete with no row selected in linkUrlTable");
1257       return;
1258     }
1259     else
1260     {
1261       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1262     }
1263
1264     // make sure we use the model index to delete, and not the table index
1265     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1266   }
1267
1268   @Override
1269   public void defaultBrowser_mouseClicked(MouseEvent e)
1270   {
1271     // TODO: JAL-3048 not needed for j2s
1272     if (!Platform.isJS()) // BH 2019
1273     /**
1274      * Java only
1275      *
1276      * @j2sIgnore
1277      */
1278     {
1279       JFileChooser chooser = new JFileChooser(".");
1280       chooser.setDialogTitle(
1281               MessageManager.getString("label.select_default_browser"));
1282
1283       int value = chooser.showOpenDialog(this);
1284
1285       if (value == JFileChooser.APPROVE_OPTION)
1286       {
1287         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1288       }
1289     }
1290   }
1291
1292   /*
1293    * (non-Javadoc)
1294    *
1295    * @see
1296    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1297    * .ActionEvent)
1298    */
1299   @Override
1300   protected void showunconserved_actionPerformed(ActionEvent e)
1301   {
1302     // TODO Auto-generated method stub
1303     super.showunconserved_actionPerformed(e);
1304   }
1305
1306   public static List<String> getGroupURLLinks()
1307   {
1308     return groupURLLinks;
1309   }
1310
1311   @Override
1312   public void minColour_actionPerformed(JPanel panel)
1313   {
1314     JalviewColourChooser.showColourChooser(this,
1315             MessageManager.getString("label.select_colour_minimum_value"),
1316             panel);
1317   }
1318
1319   @Override
1320   public void maxColour_actionPerformed(JPanel panel)
1321   {
1322     JalviewColourChooser.showColourChooser(this,
1323             MessageManager.getString("label.select_colour_maximum_value"),
1324             panel);
1325   }
1326
1327   @Override
1328   public void gapColour_actionPerformed(JPanel gap)
1329   {
1330     if (!useLegacyGap.isSelected())
1331     {
1332       JalviewColourChooser.showColourChooser(this,
1333               MessageManager.getString("label.select_gap_colour"), gap);
1334     }
1335   }
1336
1337   @Override
1338   public void hiddenColour_actionPerformed(JPanel hidden)
1339   {
1340     JalviewColourChooser.showColourChooser(this,
1341             MessageManager.getString("label.select_hidden_colour"), hidden);
1342   }
1343
1344   @Override
1345   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1346   {
1347     boolean enabled = useLegacyGap.isSelected();
1348     if (enabled)
1349     {
1350       gapColour.setBackground(
1351               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1352     }
1353     else
1354     {
1355       gapColour.setBackground(
1356               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1357     }
1358     gapColour.setEnabled(!enabled);
1359     gapLabel.setEnabled(!enabled);
1360   }
1361
1362   @Override
1363   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1364   {
1365     useLegacyGap.setSelected(false);
1366     useLegacyGaps_actionPerformed(null);
1367     showHiddenAtStart.setSelected(false);
1368     hiddenColour.setBackground(
1369             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1370   }
1371
1372   @Override
1373   protected void userIdWidth_actionPerformed()
1374   {
1375     try
1376     {
1377       String val = userIdWidth.getText().trim();
1378       if (val.length() > 0)
1379       {
1380         Integer iw = Integer.parseInt(val);
1381         if (iw.intValue() < 12)
1382         {
1383           throw new NumberFormatException();
1384         }
1385         userIdWidth.setText(iw.toString());
1386       }
1387     } catch (NumberFormatException x)
1388     {
1389       userIdWidth.setText("");
1390       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1391               MessageManager
1392                       .getString("warn.user_defined_width_requirements"),
1393               MessageManager.getString("label.invalid_id_column_width"),
1394               JvOptionPane.WARNING_MESSAGE);
1395     }
1396   }
1397
1398   @Override
1399   protected void autoIdWidth_actionPerformed()
1400   {
1401     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1402     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1403   }
1404
1405   /**
1406    * Returns true if structure viewer path is to a valid executable, else shows
1407    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1408    * (built in to Jalview) or when Jalview is left to try default paths.
1409    */
1410   private boolean validateViewerPath()
1411   {
1412     if (structureViewerPath.getText().trim().length() > 0)
1413     {
1414       File f = new File(structureViewerPath.getText());
1415       if (!f.canExecute())
1416       {
1417         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1418                 MessageManager.getString("label.invalid_viewer_path"),
1419                 MessageManager.getString("label.invalid_viewer_path"),
1420                 JvOptionPane.ERROR_MESSAGE);
1421         return false;
1422       }
1423     }
1424     return true;
1425   }
1426
1427   /**
1428    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1429    * default or user-specified path, if not show a warning/help dialog
1430    */
1431   @Override
1432   protected void structureViewer_actionPerformed(String selectedItem)
1433   {
1434     if (selectedItem.equals(ViewerType.JMOL.name()))
1435     {
1436       structureViewerPath.setEnabled(false);
1437       structureViewerPathLabel.setEnabled(false);
1438       return;
1439     }
1440     boolean found = false;
1441     structureViewerPath.setEnabled(true);
1442     structureViewerPathLabel.setEnabled(true);
1443     structureViewerPathLabel.setText(MessageManager
1444             .formatMessage("label.viewer_path", selectedItem));
1445
1446     /*
1447      * Try user-specified and standard paths for structure viewer executable
1448      */
1449     String viewerPath = "";
1450     List<String> paths = null;
1451     try
1452     {
1453       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1454       switch (viewerType)
1455       {
1456       case JMOL:
1457         // dealt with above
1458         break;
1459       case CHIMERA:
1460         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1461         paths = StructureManager.getChimeraPaths(false);
1462         break;
1463       case CHIMERAX:
1464         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1465         paths = StructureManager.getChimeraPaths(true);
1466         break;
1467       case PYMOL:
1468         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1469         paths = PymolManager.getPymolPaths();
1470         break;
1471       }
1472     } catch (IllegalArgumentException e)
1473     {
1474       // only valid entries should be in the drop-down
1475     }
1476     structureViewerPath.setText(viewerPath);
1477
1478     paths.add(0, structureViewerPath.getText());
1479     for (String path : paths)
1480     {
1481       if (new File(path.trim()).canExecute())
1482       {
1483         found = true;
1484         break;
1485       }
1486     }
1487
1488     if (!found)
1489     {
1490       String[] options = { "OK", "Help" };
1491       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1492               JvSwingUtils.wrapTooltip(true,
1493                       MessageManager.getString("label.viewer_missing")),
1494               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1495               null, options, options[0]);
1496
1497       if (showHelp == JvOptionPane.NO_OPTION)
1498       {
1499         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1500         try
1501         {
1502           Help.showHelpWindow(HelpId.StructureViewer);
1503         } catch (HelpSetException e)
1504         {
1505           e.printStackTrace();
1506         }
1507       }
1508       else if (showHelp == JvOptionPane.OK_OPTION)
1509       {
1510         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1511         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1512           try
1513           {
1514             for (int i = 0; i < 3; i++)
1515             {
1516               structureViewerPath.setBackground(Color.PINK);
1517               Thread.sleep(500);
1518               structureViewerPath.setBackground(Color.WHITE);
1519               Thread.sleep(500);
1520             }
1521           } catch (InterruptedException e)
1522           {
1523           }
1524         });
1525       }
1526     }
1527   }
1528
1529   public class OptionsParam
1530   {
1531     private String name;
1532
1533     private String code;
1534
1535     public OptionsParam(String name, String code)
1536     {
1537       this.name = name;
1538       this.code = code;
1539     }
1540
1541     public String getName()
1542     {
1543       return name;
1544     }
1545
1546     public void setName(String name)
1547     {
1548       this.name = name;
1549     }
1550
1551     public String getCode()
1552     {
1553       return code;
1554     }
1555
1556     public void setCode(String code)
1557     {
1558       this.code = code;
1559     }
1560
1561     @Override
1562     public String toString()
1563     {
1564       return name;
1565     }
1566
1567     @Override
1568     public boolean equals(Object that)
1569     {
1570       if (!(that instanceof OptionsParam))
1571       {
1572         return false;
1573       }
1574       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1575     }
1576
1577     @Override
1578     public int hashCode()
1579     {
1580       return name.hashCode() + code.hashCode();
1581     }
1582   }
1583
1584   private class UrlListSelectionHandler implements ListSelectionListener
1585   {
1586
1587     @Override
1588     public void valueChanged(ListSelectionEvent e)
1589     {
1590       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1591
1592       int index = lsm.getMinSelectionIndex();
1593       if (index == -1)
1594       {
1595         // no selection, so disable delete/edit buttons
1596         editLink.setEnabled(false);
1597         deleteLink.setEnabled(false);
1598         return;
1599       }
1600       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1601
1602       // enable/disable edit and delete link buttons
1603       if (((UrlLinkTableModel) linkUrlTable.getModel())
1604               .isRowDeletable(modelIndex))
1605       {
1606         deleteLink.setEnabled(true);
1607       }
1608       else
1609       {
1610         deleteLink.setEnabled(false);
1611       }
1612
1613       if (((UrlLinkTableModel) linkUrlTable.getModel())
1614               .isRowEditable(modelIndex))
1615       {
1616         editLink.setEnabled(true);
1617       }
1618       else
1619       {
1620         editLink.setEnabled(false);
1621       }
1622     }
1623   }
1624 }