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