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 ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  55 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  56 import jalview.bin.Cache;
  57 import jalview.ext.pymol.PymolManager;
  58 import jalview.gui.Help.HelpId;
  59 import jalview.gui.StructureViewer.ViewerType;
  60 import jalview.io.BackupFiles;
  61 import jalview.io.BackupFilesPresetEntry;
  62 import jalview.io.FileFormatI;
  63 import jalview.io.JalviewFileChooser;
  64 import jalview.io.JalviewFileView;
  65 import jalview.jbgui.GPreferences;
  66 import jalview.jbgui.GSequenceLink;
  67 import jalview.schemes.ColourSchemeI;
  68 import jalview.schemes.ColourSchemes;
  69 import jalview.schemes.ResidueColourScheme;
  70 import jalview.urls.UrlLinkTableModel;
  71 import jalview.urls.api.UrlProviderFactoryI;
  72 import jalview.urls.api.UrlProviderI;
  73 import jalview.urls.desktop.DesktopUrlProviderFactory;
  74 import jalview.util.MessageManager;
  75 import jalview.util.Platform;
  76 import jalview.util.UrlConstants;
  77 import jalview.ws.sifts.SiftsSettings;
  78
  79 /**
  80  * DOCUMENT ME!
  81  *
  82  * @author $author$
  83  * @version $Revision$
  84  */
  85 /*
  86  * for merge with Jalview-JS
  87  public class Preferences extends GPreferences implements ApplicationSingletonI
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  92
  93   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  94
  95   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  96
  97   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  98
  99   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 100
 101   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 102
 103   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 104
 105   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 106
 107   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 108
 109   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 110
 111   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 112
 113   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 114
 115   public static final String PYMOL_PATH = "PYMOL_PATH";
 116
 117   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 118
 119   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 120
 121   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 122
 123   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 124
 125   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 126
 127   public static final String GAP_COLOUR = "GAP_COLOUR";
 128
 129   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 130
 131   private static final int MIN_FONT_SIZE = 1;
 132
 133   private static final int MAX_FONT_SIZE = 30;
 134
 135   private String previousProxyType;
 136
 137   private static Preferences INSTANCE = null; // add "final"
 138
 139   /**
 140    * Holds name and link separated with | character. Sequence ID must be
 141    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 142    */
 143   public static UrlProviderI sequenceUrlLinks;
 144
 145   public static UrlLinkTableModel dataModel;
 146
 147   /**
 148    * Holds name and link separated with | character. Sequence IDS and Sequences
 149    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
 150    * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
 151    * second token specified after a pipe character at end |,|. (TODO: proper
 152    * escape for using | to separate ids or sequences
 153    */
 154
 155   public static List<String> groupURLLinks;
 156   static
 157   {
 158     // get links selected to be in the menu (SEQUENCE_LINKS)
 159     // and links entered by the user but not selected (STORED_LINKS)
 160     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 161     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 162     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 163             UrlConstants.DEFAULT_LABEL);
 164
 165     // if both links lists are empty, add the DEFAULT_URL link
 166     // otherwise we assume the default link is in one of the lists
 167     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 168     {
 169       inMenuString = UrlConstants.DEFAULT_STRING;
 170     }
 171     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 172             inMenuString, notInMenuString);
 173     sequenceUrlLinks = factory.createUrlProvider();
 174     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 175
 176     /**
 177      * TODO: reformulate groupURL encoding so two or more can be stored in the
 178      * .properties file as '|' separated strings
 179      */
 180
 181     groupURLLinks = new ArrayList<>();
 182   }
 183
 184   JInternalFrame frame;
 185
 186   private WsPreferences wsPrefs;
 187
 188   private OptionsParam promptEachTimeOpt = new OptionsParam(
 189           MessageManager.getString("label.prompt_each_time"),
 190           "Prompt each time");
 191
 192   private OptionsParam lineArtOpt = new OptionsParam(
 193           MessageManager.getString("label.lineart"), "Lineart");
 194
 195   private OptionsParam textOpt = new OptionsParam(
 196           MessageManager.getString("action.text"), "Text");
 197
 198   // get singleton Preferences instance
 199   public static Preferences getInstance()
 200   {
 201     if (INSTANCE == null || INSTANCE.frame == null
 202             || INSTANCE.frame.isClosed())
 203     {
 204       INSTANCE = new Preferences();
 205     }
 206     return INSTANCE;
 207
 208     /*
 209      * Replace code with the following for Jalvew-JS
 210     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 211     if (INSTANCE == null || INSTANCE.frame == null
 212             || INSTANCE.frame.isClosed())
 213     {
 214       ApplicationSingletonProvider.remove(Preferences.class);
 215       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 216     }
 217     return INSTANCE;
 218     */
 219   }
 220
 221   public static void openPreferences()
 222   {
 223     openPreferences(null, null);
 224   }
 225
 226   public static void openPreferences(TabRef selectTab, String message)
 227   {
 228     Preferences p = getInstance();
 229     if (selectTab != null)
 230       p.selectTab(selectTab, message);
 231     p.frame.show();
 232     p.frame.moveToFront();
 233     p.frame.grabFocus();
 234   }
 235
 236   public void selectTab(TabRef selectTab, String message)
 237   {
 238     this.selectTab(selectTab);
 239     if (message != null)
 240       this.setMessage(message);
 241     this.frame.show();
 242   }
 243
 244   /**
 245    * Creates a new Preferences object.
 246    */
 247   private Preferences()
 248   {
 249     super();
 250     frame = new JInternalFrame();
 251     frame.setContentPane(this);
 252     if (!Platform.isJS())
 253     /**
 254      * Java only
 255      *
 256      * @j2sIgnore
 257      */
 258     {
 259       wsPrefs = new WsPreferences();
 260       wsTab.add(wsPrefs, BorderLayout.CENTER);
 261     }
 262     int width = 500, height = 450;
 263     if (Platform.isAMacAndNotJS())
 264     {
 265       width = 570;
 266       height = 480;
 267     }
 268
 269     Desktop.addInternalFrame(frame,
 270             MessageManager.getString("label.preferences"), width, height);
 271     frame.setMinimumSize(new Dimension(width, height));
 272
 273     /*
 274      * Set Visual tab defaults
 275      */
 276     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 277     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 278     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 279     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 280
 281     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 282     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 283     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 284     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 285     showUnconserved
 286             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 287     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 288     showGroupConsensus
 289             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 290     showGroupConservation.setSelected(
 291             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 292     showConsensHistogram.setSelected(
 293             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 294     showConsensLogo
 295             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 296     showNpTooltip
 297             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 298     showDbRefTooltip
 299             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 300
 301     String[] fonts = java.awt.GraphicsEnvironment
 302             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 303     for (int i = 0; i < fonts.length; i++)
 304     {
 305       fontNameCB.addItem(fonts[i]);
 306     }
 307
 308     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 309     {
 310       fontSizeCB.addItem(i + "");
 311     }
 312
 313     fontStyleCB.addItem("plain");
 314     fontStyleCB.addItem("bold");
 315     fontStyleCB.addItem("italic");
 316
 317     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 318     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 319     fontStyleCB.setSelectedItem(
 320             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 321
 322     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 323     scaleProteinToCdna
 324             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 325
 326     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 327
 328     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 329
 330     gapSymbolCB.addItem("-");
 331     gapSymbolCB.addItem(".");
 332
 333     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 334
 335     sortby.addItem("No sort");
 336     sortby.addItem("Id");
 337     sortby.addItem("Pairwise Identity");
 338     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 339
 340     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 341     sortAnnBy
 342             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 343     sortAnnBy
 344             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 345     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 346             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 347                     SequenceAnnotationOrder.NONE.name()));
 348     sortAnnBy.setSelectedItem(savedSort.toString());
 349
 350     sortAutocalc.addItem("Autocalculated first");
 351     sortAutocalc.addItem("Autocalculated last");
 352     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 353     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 354             : sortAutocalc.getItemAt(1));
 355     startupCheckbox
 356             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 357     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 358             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 359                     + "/examples/exampleFile_2_7.jvp"));
 360
 361     /*
 362      * Set Colours tab defaults
 363      */
 364     protColour.addItem(ResidueColourScheme.NONE);
 365     nucColour.addItem(ResidueColourScheme.NONE);
 366     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 367     {
 368       String name = cs.getSchemeName();
 369       protColour.addItem(name);
 370       nucColour.addItem(name);
 371     }
 372     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 373             ResidueColourScheme.NONE);
 374     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 375     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 376     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 377     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 378     minColour.setBackground(
 379             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 380     maxColour.setBackground(
 381             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 382
 383     /*
 384      * Set overview panel defaults
 385      */
 386     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 387             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 388     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 389             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 390     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 391     gapLabel.setEnabled(!useLegacyGap.isSelected());
 392     gapColour.setEnabled(!useLegacyGap.isSelected());
 393     showHiddenAtStart
 394             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 395
 396     /*
 397      * Set Structure tab defaults
 398      */
 399     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 400     structFromPdb.setSelected(structSelected);
 401     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 402     useRnaView.setEnabled(structSelected);
 403     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 404     addSecondaryStructure.setEnabled(structSelected);
 405     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 406     addTempFactor.setEnabled(structSelected);
 407
 408     /*
 409      * set choice of structure viewer, and path if saved as a preference;
 410      * default to Jmol (first choice) if an unexpected value is found
 411      */
 412     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 413             ViewerType.JMOL.name());
 414     structViewer.setSelectedItem(viewerType);
 415     String viewerPath = "";
 416     ViewerType type = null;
 417     try
 418     {
 419       type = ViewerType.valueOf(viewerType);
 420       switch (type)
 421       {
 422       case JMOL:
 423         break;
 424       case CHIMERA:
 425         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 426         break;
 427       case CHIMERAX:
 428         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 429         break;
 430       case PYMOL:
 431         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 432         break;
 433       }
 434     } catch (IllegalArgumentException e)
 435     {
 436       Cache.log.error("Unknown structure viewer type: " + viewerType
 437               + ", defaulting to Jmol");
 438       type = ViewerType.JMOL;
 439     }
 440     structureViewerPath.setText(viewerPath);
 441
 442     structureViewerPath.addActionListener(new ActionListener()
 443     {
 444       @Override
 445       public void actionPerformed(ActionEvent e)
 446       {
 447         if (validateViewerPath())
 448         {
 449           Cache.setProperty(
 450                   structViewer.getSelectedItem().equals(
 451                           ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
 452                                   : CHIMERA_PATH,
 453                   structureViewerPath.getText());
 454         }
 455       }
 456     });
 457
 458     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 459     {
 460       siftsMapping.setSelected(true);
 461     }
 462     else
 463     {
 464       nwMapping.setSelected(true);
 465     }
 466
 467     SiftsSettings
 468             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 469
 470     /*
 471      * Set Connections tab defaults
 472      */
 473
 474     // set up sorting
 475     linkUrlTable.setModel(dataModel);
 476     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 477             linkUrlTable.getModel());
 478     linkUrlTable.setRowSorter(sorter);
 479     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 480
 481     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 482     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 483             SortOrder.DESCENDING));
 484     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 485             SortOrder.DESCENDING));
 486     sortKeys.add(
 487             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 488
 489     sorter.setSortKeys(sortKeys);
 490     // BH 2018 setSortKeys will do the sort
 491     // sorter.sort();
 492
 493     // set up filtering
 494     ActionListener onReset;
 495     onReset = new ActionListener()
 496     {
 497       @Override
 498       public void actionPerformed(ActionEvent e)
 499       {
 500         filterTB.setText("");
 501         sorter.setRowFilter(RowFilter.regexFilter(""));
 502       }
 503
 504     };
 505     doReset.addActionListener(onReset);
 506
 507     // filter to display only custom urls
 508     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 509     {
 510       @Override
 511       public boolean include(
 512               Entry<? extends TableModel, ? extends Object> entry)
 513       {
 514         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 515       }
 516     };
 517
 518     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 519             linkUrlTable.getModel());
 520     customSorter.setRowFilter(customUrlFilter);
 521
 522     ActionListener onCustomOnly;
 523     onCustomOnly = new ActionListener()
 524     {
 525       @Override
 526       public void actionPerformed(ActionEvent e)
 527       {
 528         filterTB.setText("");
 529         sorter.setRowFilter(customUrlFilter);
 530       }
 531     };
 532     userOnly.addActionListener(onCustomOnly);
 533
 534     filterTB.getDocument().addDocumentListener(new DocumentListener()
 535     {
 536       String caseInsensitiveFlag = "(?i)";
 537
 538       @Override
 539       public void changedUpdate(DocumentEvent e)
 540       {
 541         sorter.setRowFilter(RowFilter
 542                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 543       }
 544
 545       @Override
 546       public void removeUpdate(DocumentEvent e)
 547       {
 548         sorter.setRowFilter(RowFilter
 549                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 550       }
 551
 552       @Override
 553       public void insertUpdate(DocumentEvent e)
 554       {
 555         sorter.setRowFilter(RowFilter
 556                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 557       }
 558     });
 559
 560     // set up list selection functionality
 561     linkUrlTable.getSelectionModel()
 562             .addListSelectionListener(new UrlListSelectionHandler());
 563
 564     // set up radio buttons
 565     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 566             .getPrimaryColumn();
 567     String onClickName = linkUrlTable.getColumnName(onClickCol);
 568     linkUrlTable.getColumn(onClickName)
 569             .setCellRenderer(new RadioButtonRenderer());
 570     linkUrlTable.getColumn(onClickName)
 571             .setCellEditor(new RadioButtonEditor());
 572
 573     // get boolean columns and resize those to min possible
 574     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 575     {
 576       if (linkUrlTable.getModel().getColumnClass(column)
 577               .equals(Boolean.class))
 578       {
 579         TableColumn tableColumn = linkUrlTable.getColumnModel()
 580                 .getColumn(column);
 581         int preferredWidth = tableColumn.getMinWidth();
 582
 583         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 584                 column);
 585         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 586         int cwidth = c.getPreferredSize().width
 587                 + linkUrlTable.getIntercellSpacing().width;
 588         preferredWidth = Math.max(preferredWidth, cwidth);
 589
 590         tableColumn.setPreferredWidth(preferredWidth);
 591       }
 592     }
 593
 594     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 595     previousProxyType = proxyTypeString;
 596     switch (proxyTypeString)
 597     {
 598     case Cache.PROXYTYPE_NONE:
 599       proxyType.setSelected(noProxy.getModel(), true);
 600       break;
 601     case Cache.PROXYTYPE_SYSTEM:
 602       proxyType.setSelected(systemProxy.getModel(), true);
 603       break;
 604     case Cache.PROXYTYPE_CUSTOM:
 605       proxyType.setSelected(customProxy.getModel(), true);
 606       break;
 607     default:
 608       Cache.log.warn(
 609               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 610                       + proxyTypeString);
 611     }
 612     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 613     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 614     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 615     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 616     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 617     proxyAuthUsernameTB
 618             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 619     // we are not storing or retrieving proxy password from .jalview_properties
 620     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 621             : new String(Cache.proxyAuthPassword));
 622     setCustomProxyEnabled();
 623     applyProxyButtonEnabled(false);
 624
 625     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 626
 627     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 628     // note antisense here: default is true
 629     questionnaire
 630             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 631     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 632
 633     /*
 634      * Set Output tab defaults
 635      */
 636     setupOutputCombo(epsRendering, "EPS_RENDERING");
 637     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 638     setupOutputCombo(svgRendering, "SVG_RENDERING");
 639     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 640     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 641     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 642     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 643     userIdWidth.setText(wi == null ? "" : wi.toString());
 644     // TODO: refactor to use common enum via FormatAdapter and allow extension
 645     // for new flat file formats
 646     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 647     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 648     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 649     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 650     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 651     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 652     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 653     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 654     embbedBioJSON
 655             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 656
 657     /*
 658      * Set Editing tab defaults
 659      */
 660     autoCalculateConsCheck
 661             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 662     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 663     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 664
 665     annotations_actionPerformed(null); // update the display of the annotation
 666                                        // settings
 667
 668     /*
 669      * Set Backups tab defaults
 670      */
 671     loadLastSavedBackupsOptions();
 672   }
 673
 674   /**
 675    * A helper method that sets the items and initial selection in a character
 676    * rendering option list (Prompt each time/Lineart/Text)
 677    *
 678    * @param comboBox
 679    * @param propertyKey
 680    */
 681   protected void setupOutputCombo(JComboBox<Object> comboBox,
 682           String propertyKey)
 683   {
 684     comboBox.addItem(promptEachTimeOpt);
 685     comboBox.addItem(lineArtOpt);
 686     comboBox.addItem(textOpt);
 687
 688     /*
 689      * JalviewJS doesn't support Lineart so force it to Text
 690      */
 691     String defaultOption = Platform.isJS() ? "Text"
 692             : Cache.getDefault(propertyKey, "Prompt each time");
 693     if (defaultOption.equalsIgnoreCase("Text"))
 694     {
 695       comboBox.setSelectedItem(textOpt);
 696     }
 697     else if (defaultOption.equalsIgnoreCase("Lineart"))
 698     {
 699       comboBox.setSelectedItem(lineArtOpt);
 700     }
 701     else
 702     {
 703       comboBox.setSelectedItem(promptEachTimeOpt);
 704     }
 705   }
 706
 707   /**
 708    * Save user selections on the Preferences tabs to the Cache and write out to
 709    * file.
 710    *
 711    * @param e
 712    */
 713   @Override
 714   public void ok_actionPerformed(ActionEvent e)
 715   {
 716     if (!validateSettings())
 717     {
 718       return;
 719     }
 720
 721     /*
 722      * Set proxy settings first (to be before web services refresh)
 723      */
 724     saveProxySettings();
 725
 726     /*
 727      * Save Visual settings
 728      */
 729     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 730             Boolean.toString(seqLimit.isSelected()));
 731     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 732             Boolean.toString(rightAlign.isSelected()));
 733     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 734             Boolean.toString(fullScreen.isSelected()));
 735     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 736             Boolean.toString(openoverv.isSelected()));
 737     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 738             Boolean.toString(annotations.isSelected()));
 739     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 740             Boolean.toString(conservation.isSelected()));
 741     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 742             Boolean.toString(quality.isSelected()));
 743     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 744             Boolean.toString(identity.isSelected()));
 745
 746     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 747             gapSymbolCB.getSelectedItem().toString());
 748
 749     Cache.applicationProperties.setProperty("FONT_NAME",
 750             fontNameCB.getSelectedItem().toString());
 751     Cache.applicationProperties.setProperty("FONT_STYLE",
 752             fontStyleCB.getSelectedItem().toString());
 753     Cache.applicationProperties.setProperty("FONT_SIZE",
 754             fontSizeCB.getSelectedItem().toString());
 755
 756     Cache.applicationProperties.setProperty("ID_ITALICS",
 757             Boolean.toString(idItalics.isSelected()));
 758     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 759             Boolean.toString(showUnconserved.isSelected()));
 760     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 761             Boolean.toString(showOccupancy.isSelected()));
 762     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 763             Boolean.toString(showGroupConsensus.isSelected()));
 764     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 765             Boolean.toString(showGroupConservation.isSelected()));
 766     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 767             Boolean.toString(showConsensHistogram.isSelected()));
 768     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 769             Boolean.toString(showConsensLogo.isSelected()));
 770     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 771             Boolean.toString(smoothFont.isSelected()));
 772     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 773             Boolean.toString(scaleProteinToCdna.isSelected()));
 774     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 775             Boolean.toString(showNpTooltip.isSelected()));
 776     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 777             Boolean.toString(showDbRefTooltip.isSelected()));
 778
 779     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 780             Boolean.toString(wrap.isSelected()));
 781
 782     Cache.applicationProperties.setProperty("STARTUP_FILE",
 783             startupFileTextfield.getText());
 784     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 785             Boolean.toString(startupCheckbox.isSelected()));
 786
 787     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 788             sortby.getSelectedItem().toString());
 789
 790     // convert description of sort order to enum name for save
 791     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 792             .forDescription(sortAnnBy.getSelectedItem().toString());
 793     if (annSortOrder != null)
 794     {
 795       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 796               annSortOrder.name());
 797     }
 798
 799     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 800     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 801             Boolean.valueOf(showAutocalcFirst).toString());
 802
 803     /*
 804      * Save Colours settings
 805      */
 806     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 807             protColour.getSelectedItem().toString());
 808     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 809             nucColour.getSelectedItem().toString());
 810     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 811             minColour.getBackground());
 812     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 813             maxColour.getBackground());
 814
 815     /*
 816      * Save Overview settings
 817      */
 818     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 819     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 820     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 821             Boolean.toString(useLegacyGap.isSelected()));
 822     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 823             Boolean.toString(showHiddenAtStart.isSelected()));
 824
 825     /*
 826      * Save Structure settings
 827      */
 828     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 829             Boolean.toString(addTempFactor.isSelected()));
 830     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 831             Boolean.toString(addSecondaryStructure.isSelected()));
 832     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 833             Boolean.toString(useRnaView.isSelected()));
 834     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 835             Boolean.toString(structFromPdb.isSelected()));
 836     String viewer = structViewer.getSelectedItem().toString();
 837     String viewerPath = structureViewerPath.getText();
 838     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 839     if (viewer.equals(ViewerType.CHIMERA.name()))
 840     {
 841       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 842     }
 843     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 844     {
 845       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 846     }
 847     else if (viewer.equals(ViewerType.PYMOL.name()))
 848     {
 849       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 850     }
 851     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 852             Boolean.toString(siftsMapping.isSelected()));
 853     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 854
 855     /*
 856      * Save Output settings
 857      */
 858     Cache.applicationProperties.setProperty("EPS_RENDERING",
 859             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 860     Cache.applicationProperties.setProperty("HTML_RENDERING",
 861             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 862     Cache.applicationProperties.setProperty("SVG_RENDERING",
 863             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 864
 865     /*
 866      * Save Connections settings
 867      */
 868     // Proxy settings set first (to catch web services)
 869
 870     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 871
 872     jalview.util.BrowserLauncher.resetBrowser();
 873
 874     // save user-defined and selected links
 875     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 876     if (menuLinks.isEmpty())
 877     {
 878       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 879     }
 880     else
 881     {
 882       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 883               menuLinks.toString());
 884     }
 885
 886     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 887     if (nonMenuLinks.isEmpty())
 888     {
 889       Cache.applicationProperties.remove("STORED_LINKS");
 890     }
 891     else
 892     {
 893       Cache.applicationProperties.setProperty("STORED_LINKS",
 894               nonMenuLinks.toString());
 895     }
 896
 897     Cache.applicationProperties.setProperty("DEFAULT_URL",
 898             sequenceUrlLinks.getPrimaryUrlId());
 899
 900     Cache.setProperty("VERSION_CHECK",
 901             Boolean.toString(versioncheck.isSelected()));
 902     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 903     {
 904       // default is false - we only set this if the user has actively agreed
 905       Cache.setProperty("USAGESTATS",
 906               Boolean.toString(usagestats.isSelected()));
 907     }
 908     if (!questionnaire.isSelected())
 909     {
 910       Cache.setProperty("NOQUESTIONNAIRES", "true");
 911     }
 912     else
 913     {
 914       // special - made easy to edit a property file to disable questionnaires
 915       // by just adding the given line
 916       Cache.removeProperty("NOQUESTIONNAIRES");
 917     }
 918
 919     /*
 920      * Save Output settings
 921      */
 922     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 923             Boolean.toString(blcjv.isSelected()));
 924     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 925             Boolean.toString(clustaljv.isSelected()));
 926     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 927             Boolean.toString(fastajv.isSelected()));
 928     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 929             Boolean.toString(msfjv.isSelected()));
 930     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 931             Boolean.toString(pfamjv.isSelected()));
 932     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 933             Boolean.toString(pileupjv.isSelected()));
 934     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 935             Boolean.toString(pirjv.isSelected()));
 936     Cache.applicationProperties.setProperty("PIR_MODELLER",
 937             Boolean.toString(modellerOutput.isSelected()));
 938     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 939             Boolean.toString(embbedBioJSON.isSelected()));
 940     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 941
 942     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 943             Boolean.toString(autoIdWidth.isSelected()));
 944     userIdWidth_actionPerformed();
 945     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 946             userIdWidth.getText());
 947
 948     /*
 949      * Save Editing settings
 950      */
 951     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 952             Boolean.toString(autoCalculateConsCheck.isSelected()));
 953     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 954             Boolean.toString(sortByTree.isSelected()));
 955     Cache.applicationProperties.setProperty("PAD_GAPS",
 956             Boolean.toString(padGaps.isSelected()));
 957
 958     if (!Platform.isJS())
 959     {
 960       wsPrefs.updateAndRefreshWsMenuConfig(false);
 961     }
 962
 963     /*
 964      * Save Backups settings
 965      */
 966     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 967             Boolean.toString(enableBackupFiles.isSelected()));
 968     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 969     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 970             Integer.toString(preset));
 971
 972     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 973     {
 974       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 975       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 976               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 977       Cache.applicationProperties.setProperty(
 978               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 979     }
 980
 981     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 982             .get(preset);
 983     Cache.applicationProperties.setProperty(
 984             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 985
 986     Cache.saveProperties();
 987     Desktop.instance.doConfigureStructurePrefs();
 988     try
 989     {
 990       frame.setClosed(true);
 991     } catch (Exception ex)
 992     {
 993     }
 994   }
 995
 996   public void saveProxySettings()
 997   {
 998     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 999             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1000                     : Cache.PROXYTYPE_SYSTEM;
1001     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1002     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1003     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1004     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1005     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1006     Cache.setOrRemove("PROXY_AUTH",
1007             Boolean.toString(proxyAuth.isSelected()));
1008     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1009     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1010     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1011     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1012             || !newProxyType.equals(previousProxyType))
1013     {
1014       // force a re-lookup of ws if proxytype is custom or has changed
1015       wsPrefs.update++;
1016     }
1017     previousProxyType = newProxyType;
1018   }
1019
1020   /**
1021    * Do any necessary validation before saving settings. Return focus to the first
1022    * tab which fails validation.
1023    *
1024    * @return
1025    */
1026   private boolean validateSettings()
1027   {
1028     if (!validateStructure())
1029     {
1030       structureTab.requestFocusInWindow();
1031       return false;
1032     }
1033     return true;
1034   }
1035
1036   @Override
1037   protected boolean validateStructure()
1038   {
1039     return validateViewerPath();
1040
1041   }
1042
1043   /**
1044    * DOCUMENT ME!
1045    */
1046   @Override
1047   public void startupFileTextfield_mouseClicked()
1048   {
1049     // TODO: JAL-3048 not needed for Jalview-JS
1050     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1051     JalviewFileChooser chooser = JalviewFileChooser
1052             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1053     chooser.setFileView(new JalviewFileView());
1054     chooser.setDialogTitle(
1055             MessageManager.getString("label.select_startup_file"));
1056
1057     int value = chooser.showOpenDialog(this);
1058
1059     if (value == JalviewFileChooser.APPROVE_OPTION)
1060     {
1061       FileFormatI format = chooser.getSelectedFormat();
1062       if (format != null)
1063       {
1064         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1065                 format.getName());
1066       }
1067       startupFileTextfield
1068               .setText(chooser.getSelectedFile().getAbsolutePath());
1069     }
1070   }
1071
1072   /**
1073    * DOCUMENT ME!
1074    *
1075    * @param e
1076    *            DOCUMENT ME!
1077    */
1078   @Override
1079   public void cancel_actionPerformed(ActionEvent e)
1080   {
1081     try
1082     {
1083       if (!Platform.isJS())
1084       {
1085         wsPrefs.updateWsMenuConfig(true);
1086         wsPrefs.refreshWs_actionPerformed(e);
1087       }
1088       frame.setClosed(true);
1089     } catch (Exception ex)
1090     {
1091     }
1092   }
1093
1094   /**
1095    * DOCUMENT ME!
1096    *
1097    * @param e
1098    *            DOCUMENT ME!
1099    */
1100   @Override
1101   public void annotations_actionPerformed(ActionEvent e)
1102   {
1103     conservation.setEnabled(annotations.isSelected());
1104     quality.setEnabled(annotations.isSelected());
1105     identity.setEnabled(annotations.isSelected());
1106     showOccupancy.setEnabled(annotations.isSelected());
1107     showGroupConsensus.setEnabled(annotations.isSelected());
1108     showGroupConservation.setEnabled(annotations.isSelected());
1109     showConsensHistogram.setEnabled(annotations.isSelected()
1110             && (identity.isSelected() || showGroupConsensus.isSelected()));
1111     showConsensLogo.setEnabled(annotations.isSelected()
1112             && (identity.isSelected() || showGroupConsensus.isSelected()));
1113   }
1114
1115   @Override
1116   public void newLink_actionPerformed(ActionEvent e)
1117   {
1118     GSequenceLink link = new GSequenceLink();
1119     boolean valid = false;
1120     while (!valid)
1121     {
1122       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1123               MessageManager.getString("label.new_sequence_url_link"),
1124               JvOptionPane.OK_CANCEL_OPTION, -1,
1125               null) == JvOptionPane.OK_OPTION)
1126       {
1127         if (link.checkValid())
1128         {
1129           if (((UrlLinkTableModel) linkUrlTable.getModel())
1130                   .isUniqueName(link.getName()))
1131           {
1132             ((UrlLinkTableModel) linkUrlTable.getModel())
1133                     .insertRow(link.getName(), link.getURL());
1134             valid = true;
1135           }
1136           else
1137           {
1138             link.notifyDuplicate();
1139             continue;
1140           }
1141         }
1142       }
1143       else
1144       {
1145         break;
1146       }
1147     }
1148   }
1149
1150   @Override
1151   public void editLink_actionPerformed(ActionEvent e)
1152   {
1153     GSequenceLink link = new GSequenceLink();
1154
1155     int index = linkUrlTable.getSelectedRow();
1156     if (index == -1)
1157     {
1158       // button no longer enabled if row is not selected
1159       Cache.log.debug("Edit with no row selected in linkUrlTable");
1160       return;
1161     }
1162
1163     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1164             .getNameColumn();
1165     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1166             .getUrlColumn();
1167     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1168     link.setName(oldName);
1169     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1170
1171     boolean valid = false;
1172     while (!valid)
1173     {
1174       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1175               MessageManager.getString("label.edit_sequence_url_link"),
1176               JvOptionPane.OK_CANCEL_OPTION, -1,
1177               null) == JvOptionPane.OK_OPTION)
1178       {
1179         if (link.checkValid())
1180         {
1181           if ((oldName.equals(link.getName()))
1182                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1183                           .isUniqueName(link.getName())))
1184           {
1185             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1186             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1187             valid = true;
1188           }
1189           else
1190           {
1191             link.notifyDuplicate();
1192             continue;
1193           }
1194         }
1195       }
1196       else
1197       {
1198         break;
1199       }
1200     }
1201   }
1202
1203   @Override
1204   public void deleteLink_actionPerformed(ActionEvent e)
1205   {
1206     int index = linkUrlTable.getSelectedRow();
1207     int modelIndex = -1;
1208     if (index == -1)
1209     {
1210       // button no longer enabled if row is not selected
1211       Cache.log.debug("Delete with no row selected in linkUrlTable");
1212       return;
1213     }
1214     else
1215     {
1216       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1217     }
1218
1219     // make sure we use the model index to delete, and not the table index
1220     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1221   }
1222
1223   @Override
1224   public void defaultBrowser_mouseClicked(MouseEvent e)
1225   {
1226     // TODO: JAL-3048 not needed for j2s
1227     if (!Platform.isJS()) // BH 2019
1228     /**
1229      * Java only
1230      *
1231      * @j2sIgnore
1232      */
1233     {
1234       JFileChooser chooser = new JFileChooser(".");
1235       chooser.setDialogTitle(
1236               MessageManager.getString("label.select_default_browser"));
1237
1238       int value = chooser.showOpenDialog(this);
1239
1240       if (value == JFileChooser.APPROVE_OPTION)
1241       {
1242         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1243       }
1244     }
1245   }
1246
1247   /*
1248    * (non-Javadoc)
1249    *
1250    * @see
1251    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1252    * .ActionEvent)
1253    */
1254   @Override
1255   protected void showunconserved_actionPerformed(ActionEvent e)
1256   {
1257     // TODO Auto-generated method stub
1258     super.showunconserved_actionPerformed(e);
1259   }
1260
1261   public static List<String> getGroupURLLinks()
1262   {
1263     return groupURLLinks;
1264   }
1265
1266   @Override
1267   public void minColour_actionPerformed(JPanel panel)
1268   {
1269     JalviewColourChooser.showColourChooser(this,
1270             MessageManager.getString("label.select_colour_minimum_value"),
1271             panel);
1272   }
1273
1274   @Override
1275   public void maxColour_actionPerformed(JPanel panel)
1276   {
1277     JalviewColourChooser.showColourChooser(this,
1278             MessageManager.getString("label.select_colour_maximum_value"),
1279             panel);
1280   }
1281
1282   @Override
1283   public void gapColour_actionPerformed(JPanel gap)
1284   {
1285     if (!useLegacyGap.isSelected())
1286     {
1287       JalviewColourChooser.showColourChooser(this,
1288               MessageManager.getString("label.select_gap_colour"), gap);
1289     }
1290   }
1291
1292   @Override
1293   public void hiddenColour_actionPerformed(JPanel hidden)
1294   {
1295     JalviewColourChooser.showColourChooser(this,
1296             MessageManager.getString("label.select_hidden_colour"), hidden);
1297   }
1298
1299   @Override
1300   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1301   {
1302     boolean enabled = useLegacyGap.isSelected();
1303     if (enabled)
1304     {
1305       gapColour.setBackground(
1306               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1307     }
1308     else
1309     {
1310       gapColour.setBackground(
1311               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1312     }
1313     gapColour.setEnabled(!enabled);
1314     gapLabel.setEnabled(!enabled);
1315   }
1316
1317   @Override
1318   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1319   {
1320     useLegacyGap.setSelected(false);
1321     useLegacyGaps_actionPerformed(null);
1322     showHiddenAtStart.setSelected(false);
1323     hiddenColour.setBackground(
1324             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1325   }
1326
1327   @Override
1328   protected void userIdWidth_actionPerformed()
1329   {
1330     try
1331     {
1332       String val = userIdWidth.getText().trim();
1333       if (val.length() > 0)
1334       {
1335         Integer iw = Integer.parseInt(val);
1336         if (iw.intValue() < 12)
1337         {
1338           throw new NumberFormatException();
1339         }
1340         userIdWidth.setText(iw.toString());
1341       }
1342     } catch (NumberFormatException x)
1343     {
1344       userIdWidth.setText("");
1345       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1346               MessageManager
1347                       .getString("warn.user_defined_width_requirements"),
1348               MessageManager.getString("label.invalid_id_column_width"),
1349               JvOptionPane.WARNING_MESSAGE);
1350     }
1351   }
1352
1353   @Override
1354   protected void autoIdWidth_actionPerformed()
1355   {
1356     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1357     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1358   }
1359
1360   /**
1361    * Returns true if structure viewer path is to a valid executable, else shows an
1362    * error dialog. Does nothing if the path is empty, as is the case for Jmol
1363    * (built in to Jalview) or when Jalview is left to try default paths.
1364    */
1365   private boolean validateViewerPath()
1366   {
1367     if (structureViewerPath.getText().trim().length() > 0)
1368     {
1369       File f = new File(structureViewerPath.getText());
1370       if (!f.canExecute())
1371       {
1372         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1373                 MessageManager.getString("label.invalid_viewer_path"),
1374                 MessageManager.getString("label.invalid_viewer_path"),
1375                 JvOptionPane.ERROR_MESSAGE);
1376         return false;
1377       }
1378     }
1379     return true;
1380   }
1381
1382   /**
1383    * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
1384    * or user-specified path, if not show a warning/help dialog
1385    */
1386   @Override
1387   protected void structureViewer_actionPerformed(String selectedItem)
1388   {
1389     if (selectedItem.equals(ViewerType.JMOL.name()))
1390     {
1391       structureViewerPath.setEnabled(false);
1392       structureViewerPathLabel.setEnabled(false);
1393       return;
1394     }
1395     boolean found = false;
1396     structureViewerPath.setEnabled(true);
1397     structureViewerPathLabel.setEnabled(true);
1398     structureViewerPathLabel.setText(MessageManager
1399             .formatMessage("label.viewer_path", selectedItem));
1400
1401     /*
1402      * Try user-specified and standard paths for structure viewer executable
1403      */
1404     String viewerPath = "";
1405     List<String> paths = null;
1406     try
1407     {
1408       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1409       switch (viewerType)
1410       {
1411       case JMOL:
1412         // dealt with above
1413         break;
1414       case CHIMERA:
1415         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1416         paths = StructureManager.getChimeraPaths(false);
1417         break;
1418       case CHIMERAX:
1419         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1420         paths = StructureManager.getChimeraPaths(true);
1421         break;
1422       case PYMOL:
1423         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1424         paths = PymolManager.getPymolPaths();
1425         break;
1426       }
1427     } catch (IllegalArgumentException e)
1428     {
1429       // only valid entries should be in the drop-down
1430     }
1431     structureViewerPath.setText(viewerPath);
1432
1433     paths.add(0, structureViewerPath.getText());
1434     for (String path : paths)
1435     {
1436       if (new File(path.trim()).canExecute())
1437       {
1438         found = true;
1439         break;
1440       }
1441     }
1442
1443     if (!found)
1444     {
1445       String[] options = { "OK", "Help" };
1446       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1447               JvSwingUtils.wrapTooltip(true,
1448                       MessageManager.getString("label.viewer_missing")),
1449               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1450               null, options, options[0]);
1451
1452       if (showHelp == JvOptionPane.NO_OPTION)
1453       {
1454         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1455         try
1456         {
1457           Help.showHelpWindow(HelpId.StructureViewer);
1458         } catch (HelpSetException e)
1459         {
1460           e.printStackTrace();
1461         }
1462       }
1463       else if (showHelp == JvOptionPane.OK_OPTION)
1464       {
1465         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1466         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1467           try
1468           {
1469             for (int i = 0; i < 3; i++)
1470             {
1471               structureViewerPath.setBackground(Color.PINK);
1472               Thread.sleep(500);
1473               structureViewerPath.setBackground(Color.WHITE);
1474               Thread.sleep(500);
1475             }
1476           } catch (InterruptedException e)
1477           {
1478           }
1479         });
1480       }
1481     }
1482   }
1483
1484   public class OptionsParam
1485   {
1486     private String name;
1487
1488     private String code;
1489
1490     public OptionsParam(String name, String code)
1491     {
1492       this.name = name;
1493       this.code = code;
1494     }
1495
1496     public String getName()
1497     {
1498       return name;
1499     }
1500
1501     public void setName(String name)
1502     {
1503       this.name = name;
1504     }
1505
1506     public String getCode()
1507     {
1508       return code;
1509     }
1510
1511     public void setCode(String code)
1512     {
1513       this.code = code;
1514     }
1515
1516     @Override
1517     public String toString()
1518     {
1519       return name;
1520     }
1521
1522     @Override
1523     public boolean equals(Object that)
1524     {
1525       if (!(that instanceof OptionsParam))
1526       {
1527         return false;
1528       }
1529       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1530     }
1531
1532     @Override
1533     public int hashCode()
1534     {
1535       return name.hashCode() + code.hashCode();
1536     }
1537   }
1538
1539   private class UrlListSelectionHandler implements ListSelectionListener
1540   {
1541
1542     @Override
1543     public void valueChanged(ListSelectionEvent e)
1544     {
1545       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1546
1547       int index = lsm.getMinSelectionIndex();
1548       if (index == -1)
1549       {
1550         // no selection, so disable delete/edit buttons
1551         editLink.setEnabled(false);
1552         deleteLink.setEnabled(false);
1553         return;
1554       }
1555       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1556
1557       // enable/disable edit and delete link buttons
1558       if (((UrlLinkTableModel) linkUrlTable.getModel())
1559               .isRowDeletable(modelIndex))
1560       {
1561         deleteLink.setEnabled(true);
1562       }
1563       else
1564       {
1565         deleteLink.setEnabled(false);
1566       }
1567
1568       if (((UrlLinkTableModel) linkUrlTable.getModel())
1569               .isRowEditable(modelIndex))
1570       {
1571         editLink.setEnabled(true);
1572       }
1573       else
1574       {
1575         editLink.setEnabled(false);
1576       }
1577     }
1578   }
1579 }