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
  35 import javax.help.HelpSetException;
  36 import javax.swing.JComboBox;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.bin.MemorySetting;
  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
 150    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 151    * for first and second token specified after a pipe character at end |,|.
 152    * (TODO: proper 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(0, null);
 224   }
 225
 226   public static void openPreferences(int selectTab, String message)
 227   {
 228     Preferences p = getInstance();
 229     p.selectTab(selectTab);
 230     p.setMessage(message);
 231     p.frame.show();
 232     p.frame.moveToFront();
 233     p.frame.grabFocus();
 234   }
 235
 236   /**
 237    * Creates a new Preferences object.
 238    */
 239   private Preferences()
 240   {
 241     super();
 242     frame = new JInternalFrame();
 243     frame.setContentPane(this);
 244     if (!Platform.isJS())
 245     /**
 246      * Java only
 247      *
 248      * @j2sIgnore
 249      */
 250     {
 251       wsPrefs = new WsPreferences();
 252       wsTab.add(wsPrefs, BorderLayout.CENTER);
 253     }
 254     int width = 500, height = 450;
 255     if (Platform.isAMacAndNotJS())
 256     {
 257       width = 570;
 258       height = 480;
 259     }
 260
 261     Desktop.addInternalFrame(frame,
 262             MessageManager.getString("label.preferences"), width, height);
 263     frame.setMinimumSize(new Dimension(width, height));
 264
 265     /*
 266      * Set Visual tab defaults
 267      */
 268     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 269     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 270     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 271     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 272
 273     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 274     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 275     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 276     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 277     showUnconserved
 278             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 279     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 280     showGroupConsensus
 281             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 282     showGroupConservation.setSelected(
 283             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 284     showConsensHistogram.setSelected(
 285             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 286     showConsensLogo
 287             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 288     showNpTooltip
 289             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 290     showDbRefTooltip
 291             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 292
 293     String[] fonts = java.awt.GraphicsEnvironment
 294             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 295     for (int i = 0; i < fonts.length; i++)
 296     {
 297       fontNameCB.addItem(fonts[i]);
 298     }
 299
 300     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 301     {
 302       fontSizeCB.addItem(i + "");
 303     }
 304
 305     fontStyleCB.addItem("plain");
 306     fontStyleCB.addItem("bold");
 307     fontStyleCB.addItem("italic");
 308
 309     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 310     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 311     fontStyleCB.setSelectedItem(
 312             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 313
 314     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 315     scaleProteinToCdna
 316             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 317
 318     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 319
 320     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 321
 322     gapSymbolCB.addItem("-");
 323     gapSymbolCB.addItem(".");
 324
 325     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 326
 327     sortby.addItem("No sort");
 328     sortby.addItem("Id");
 329     sortby.addItem("Pairwise Identity");
 330     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 331
 332     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 333     sortAnnBy
 334             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 335     sortAnnBy
 336             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 337     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 338             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 339                     SequenceAnnotationOrder.NONE.name()));
 340     sortAnnBy.setSelectedItem(savedSort.toString());
 341
 342     sortAutocalc.addItem("Autocalculated first");
 343     sortAutocalc.addItem("Autocalculated last");
 344     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 345     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 346             : sortAutocalc.getItemAt(1));
 347     startupCheckbox
 348             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 349     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 350             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 351                     + "/examples/exampleFile_2_3.jar"));
 352
 353     /*
 354      * Set Colours tab defaults
 355      */
 356     protColour.addItem(ResidueColourScheme.NONE);
 357     nucColour.addItem(ResidueColourScheme.NONE);
 358     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 359     {
 360       String name = cs.getSchemeName();
 361       protColour.addItem(name);
 362       nucColour.addItem(name);
 363     }
 364     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 365             ResidueColourScheme.NONE);
 366     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 367     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 368     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 369     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 370     minColour.setBackground(
 371             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 372     maxColour.setBackground(
 373             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 374
 375     /*
 376      * Set overview panel defaults
 377      */
 378     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 379             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 380     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 381             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 382     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 383     gapLabel.setEnabled(!useLegacyGap.isSelected());
 384     gapColour.setEnabled(!useLegacyGap.isSelected());
 385     showHiddenAtStart
 386             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 387
 388     /*
 389      * Set Structure tab defaults
 390      */
 391     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 392     structFromPdb.setSelected(structSelected);
 393     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 394     useRnaView.setEnabled(structSelected);
 395     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 396     addSecondaryStructure.setEnabled(structSelected);
 397     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 398     addTempFactor.setEnabled(structSelected);
 399
 400     /*
 401      * set choice of structure viewer, and path if saved as a preference;
 402      * default to Jmol (first choice) if an unexpected value is found
 403      */
 404     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 405             ViewerType.JMOL.name());
 406     structViewer.setSelectedItem(viewerType);
 407     String viewerPath = "";
 408     ViewerType type = null;
 409     try
 410     {
 411       type = ViewerType.valueOf(viewerType);
 412       switch (type)
 413       {
 414       case JMOL:
 415         break;
 416       case CHIMERA:
 417         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 418         break;
 419       case CHIMERAX:
 420         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 421         break;
 422       case PYMOL:
 423         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 424         break;
 425       }
 426     } catch (IllegalArgumentException e)
 427     {
 428       Cache.log.error("Unknown structure viewer type: " + viewerType
 429               + ", defaulting to Jmol");
 430       type = ViewerType.JMOL;
 431     }
 432     structureViewerPath.setText(viewerPath);
 433
 434     structureViewerPath.addActionListener(new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         if (validateViewerPath())
 440         {
 441           Cache.setProperty(
 442                   structViewer.getSelectedItem().equals(
 443                           ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
 444                                   : CHIMERA_PATH,
 445                   structureViewerPath.getText());
 446         }
 447       }
 448     });
 449
 450     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 451     {
 452       siftsMapping.setSelected(true);
 453     }
 454     else
 455     {
 456       nwMapping.setSelected(true);
 457     }
 458
 459     SiftsSettings
 460             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 461
 462     /*
 463      * Set Connections tab defaults
 464      */
 465
 466     // set up sorting
 467     linkUrlTable.setModel(dataModel);
 468     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 469             linkUrlTable.getModel());
 470     linkUrlTable.setRowSorter(sorter);
 471     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 472
 473     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 474     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 475             SortOrder.DESCENDING));
 476     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 477             SortOrder.DESCENDING));
 478     sortKeys.add(
 479             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 480
 481     sorter.setSortKeys(sortKeys);
 482     // BH 2018 setSortKeys will do the sort
 483     // sorter.sort();
 484
 485     // set up filtering
 486     ActionListener onReset;
 487     onReset = new ActionListener()
 488     {
 489       @Override
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         filterTB.setText("");
 493         sorter.setRowFilter(RowFilter.regexFilter(""));
 494       }
 495
 496     };
 497     doReset.addActionListener(onReset);
 498
 499     // filter to display only custom urls
 500     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 501     {
 502       @Override
 503       public boolean include(
 504               Entry<? extends TableModel, ? extends Object> entry)
 505       {
 506         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 507       }
 508     };
 509
 510     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 511             linkUrlTable.getModel());
 512     customSorter.setRowFilter(customUrlFilter);
 513
 514     ActionListener onCustomOnly;
 515     onCustomOnly = new ActionListener()
 516     {
 517       @Override
 518       public void actionPerformed(ActionEvent e)
 519       {
 520         filterTB.setText("");
 521         sorter.setRowFilter(customUrlFilter);
 522       }
 523     };
 524     userOnly.addActionListener(onCustomOnly);
 525
 526     filterTB.getDocument().addDocumentListener(new DocumentListener()
 527     {
 528       String caseInsensitiveFlag = "(?i)";
 529
 530       @Override
 531       public void changedUpdate(DocumentEvent e)
 532       {
 533         sorter.setRowFilter(RowFilter
 534                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 535       }
 536
 537       @Override
 538       public void removeUpdate(DocumentEvent e)
 539       {
 540         sorter.setRowFilter(RowFilter
 541                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 542       }
 543
 544       @Override
 545       public void insertUpdate(DocumentEvent e)
 546       {
 547         sorter.setRowFilter(RowFilter
 548                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 549       }
 550     });
 551
 552     // set up list selection functionality
 553     linkUrlTable.getSelectionModel()
 554             .addListSelectionListener(new UrlListSelectionHandler());
 555
 556     // set up radio buttons
 557     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 558             .getPrimaryColumn();
 559     String onClickName = linkUrlTable.getColumnName(onClickCol);
 560     linkUrlTable.getColumn(onClickName)
 561             .setCellRenderer(new RadioButtonRenderer());
 562     linkUrlTable.getColumn(onClickName)
 563             .setCellEditor(new RadioButtonEditor());
 564
 565     // get boolean columns and resize those to min possible
 566     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 567     {
 568       if (linkUrlTable.getModel().getColumnClass(column)
 569               .equals(Boolean.class))
 570       {
 571         TableColumn tableColumn = linkUrlTable.getColumnModel()
 572                 .getColumn(column);
 573         int preferredWidth = tableColumn.getMinWidth();
 574
 575         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 576                 column);
 577         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 578         int cwidth = c.getPreferredSize().width
 579                 + linkUrlTable.getIntercellSpacing().width;
 580         preferredWidth = Math.max(preferredWidth, cwidth);
 581
 582         tableColumn.setPreferredWidth(preferredWidth);
 583       }
 584     }
 585
 586     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 587     previousProxyType = proxyTypeString;
 588     switch (proxyTypeString)
 589     {
 590     case Cache.PROXYTYPE_NONE:
 591       proxyType.setSelected(noProxy.getModel(), true);
 592       break;
 593     case Cache.PROXYTYPE_SYSTEM:
 594       proxyType.setSelected(systemProxy.getModel(), true);
 595       break;
 596     case Cache.PROXYTYPE_CUSTOM:
 597       proxyType.setSelected(customProxy.getModel(), true);
 598       break;
 599     default:
 600       Cache.log.warn(
 601               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 602                       + proxyTypeString);
 603     }
 604     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 605     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 606     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 607     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 608     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 609     proxyAuthUsernameTB
 610             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 611     // we are not storing or retrieving proxy password from .jalview_properties
 612     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 613             : new String(Cache.proxyAuthPassword));
 614     setCustomProxyEnabled();
 615     applyProxyButtonEnabled(false);
 616
 617     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 618
 619     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 620     // note antisense here: default is true
 621     questionnaire
 622             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 623     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 624
 625     /*
 626      * Set Output tab defaults
 627      */
 628     setupOutputCombo(epsRendering, "EPS_RENDERING");
 629     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 630     setupOutputCombo(svgRendering, "SVG_RENDERING");
 631     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 632     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 633     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 634     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 635     userIdWidth.setText(wi == null ? "" : wi.toString());
 636     // TODO: refactor to use common enum via FormatAdapter and allow extension
 637     // for new flat file formats
 638     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 639     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 640     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 641     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 642     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 643     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 644     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 645     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 646     embbedBioJSON
 647             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 648
 649     /*
 650      * Set Editing tab defaults
 651      */
 652     autoCalculateConsCheck
 653             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 654     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 655     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 656
 657     annotations_actionPerformed(null); // update the display of the annotation
 658                                        // settings
 659
 660     /*
 661      * Set Backups tab defaults
 662      */
 663     loadLastSavedBackupsOptions();
 664
 665     /*
 666      * Set Startup tab defaults
 667      */
 668
 669   }
 670
 671   /**
 672    * A helper method that sets the items and initial selection in a character
 673    * rendering option list (Prompt each time/Lineart/Text)
 674    *
 675    * @param comboBox
 676    * @param propertyKey
 677    */
 678   protected void setupOutputCombo(JComboBox<Object> comboBox,
 679           String propertyKey)
 680   {
 681     comboBox.addItem(promptEachTimeOpt);
 682     comboBox.addItem(lineArtOpt);
 683     comboBox.addItem(textOpt);
 684
 685     /*
 686      * JalviewJS doesn't support Lineart so force it to Text
 687      */
 688     String defaultOption = Platform.isJS() ? "Text"
 689             : Cache.getDefault(propertyKey, "Prompt each time");
 690     if (defaultOption.equalsIgnoreCase("Text"))
 691     {
 692       comboBox.setSelectedItem(textOpt);
 693     }
 694     else if (defaultOption.equalsIgnoreCase("Lineart"))
 695     {
 696       comboBox.setSelectedItem(lineArtOpt);
 697     }
 698     else
 699     {
 700       comboBox.setSelectedItem(promptEachTimeOpt);
 701     }
 702   }
 703
 704   /**
 705    * Save user selections on the Preferences tabs to the Cache and write out to
 706    * file.
 707    *
 708    * @param e
 709    */
 710   @Override
 711   public void ok_actionPerformed(ActionEvent e)
 712   {
 713     if (!validateSettings())
 714     {
 715       return;
 716     }
 717
 718     /*
 719      * Set proxy settings first (to be before web services refresh)
 720      */
 721     saveProxySettings();
 722
 723     /*
 724      * Save Visual settings
 725      */
 726     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 727             Boolean.toString(seqLimit.isSelected()));
 728     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 729             Boolean.toString(rightAlign.isSelected()));
 730     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 731             Boolean.toString(fullScreen.isSelected()));
 732     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 733             Boolean.toString(openoverv.isSelected()));
 734     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 735             Boolean.toString(annotations.isSelected()));
 736     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 737             Boolean.toString(conservation.isSelected()));
 738     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 739             Boolean.toString(quality.isSelected()));
 740     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 741             Boolean.toString(identity.isSelected()));
 742
 743     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 744             gapSymbolCB.getSelectedItem().toString());
 745
 746     Cache.applicationProperties.setProperty("FONT_NAME",
 747             fontNameCB.getSelectedItem().toString());
 748     Cache.applicationProperties.setProperty("FONT_STYLE",
 749             fontStyleCB.getSelectedItem().toString());
 750     Cache.applicationProperties.setProperty("FONT_SIZE",
 751             fontSizeCB.getSelectedItem().toString());
 752
 753     Cache.applicationProperties.setProperty("ID_ITALICS",
 754             Boolean.toString(idItalics.isSelected()));
 755     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 756             Boolean.toString(showUnconserved.isSelected()));
 757     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 758             Boolean.toString(showOccupancy.isSelected()));
 759     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 760             Boolean.toString(showGroupConsensus.isSelected()));
 761     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 762             Boolean.toString(showGroupConservation.isSelected()));
 763     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 764             Boolean.toString(showConsensHistogram.isSelected()));
 765     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 766             Boolean.toString(showConsensLogo.isSelected()));
 767     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 768             Boolean.toString(smoothFont.isSelected()));
 769     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 770             Boolean.toString(scaleProteinToCdna.isSelected()));
 771     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 772             Boolean.toString(showNpTooltip.isSelected()));
 773     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 774             Boolean.toString(showDbRefTooltip.isSelected()));
 775
 776     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 777             Boolean.toString(wrap.isSelected()));
 778
 779     Cache.applicationProperties.setProperty("STARTUP_FILE",
 780             startupFileTextfield.getText());
 781     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 782             Boolean.toString(startupCheckbox.isSelected()));
 783
 784     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 785             sortby.getSelectedItem().toString());
 786
 787     // convert description of sort order to enum name for save
 788     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 789             .forDescription(sortAnnBy.getSelectedItem().toString());
 790     if (annSortOrder != null)
 791     {
 792       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 793               annSortOrder.name());
 794     }
 795
 796     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 797     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 798             Boolean.valueOf(showAutocalcFirst).toString());
 799
 800     /*
 801      * Save Colours settings
 802      */
 803     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 804             protColour.getSelectedItem().toString());
 805     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 806             nucColour.getSelectedItem().toString());
 807     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 808             minColour.getBackground());
 809     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 810             maxColour.getBackground());
 811
 812     /*
 813      * Save Overview settings
 814      */
 815     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 816     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 817     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 818             Boolean.toString(useLegacyGap.isSelected()));
 819     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 820             Boolean.toString(showHiddenAtStart.isSelected()));
 821
 822     /*
 823      * Save Structure settings
 824      */
 825     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 826             Boolean.toString(addTempFactor.isSelected()));
 827     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 828             Boolean.toString(addSecondaryStructure.isSelected()));
 829     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 830             Boolean.toString(useRnaView.isSelected()));
 831     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 832             Boolean.toString(structFromPdb.isSelected()));
 833     String viewer = structViewer.getSelectedItem().toString();
 834     String viewerPath = structureViewerPath.getText();
 835     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 836     if (viewer.equals(ViewerType.CHIMERA.name()))
 837     {
 838       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 839     }
 840     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 841     {
 842       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 843     }
 844     else if (viewer.equals(ViewerType.PYMOL.name()))
 845     {
 846       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 847     }
 848     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 849             Boolean.toString(siftsMapping.isSelected()));
 850     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 851
 852     /*
 853      * Save Output settings
 854      */
 855     Cache.applicationProperties.setProperty("EPS_RENDERING",
 856             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 857     Cache.applicationProperties.setProperty("HTML_RENDERING",
 858             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 859     Cache.applicationProperties.setProperty("SVG_RENDERING",
 860             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 861
 862     /*
 863      * Save Connections settings
 864      */
 865     // Proxy settings set first (to catch web services)
 866
 867     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 868
 869     jalview.util.BrowserLauncher.resetBrowser();
 870
 871     // save user-defined and selected links
 872     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 873     if (menuLinks.isEmpty())
 874     {
 875       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 876     }
 877     else
 878     {
 879       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 880               menuLinks.toString());
 881     }
 882
 883     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 884     if (nonMenuLinks.isEmpty())
 885     {
 886       Cache.applicationProperties.remove("STORED_LINKS");
 887     }
 888     else
 889     {
 890       Cache.applicationProperties.setProperty("STORED_LINKS",
 891               nonMenuLinks.toString());
 892     }
 893
 894     Cache.applicationProperties.setProperty("DEFAULT_URL",
 895             sequenceUrlLinks.getPrimaryUrlId());
 896
 897     Cache.setProperty("VERSION_CHECK",
 898             Boolean.toString(versioncheck.isSelected()));
 899     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 900     {
 901       // default is false - we only set this if the user has actively agreed
 902       Cache.setProperty("USAGESTATS",
 903               Boolean.toString(usagestats.isSelected()));
 904     }
 905     if (!questionnaire.isSelected())
 906     {
 907       Cache.setProperty("NOQUESTIONNAIRES", "true");
 908     }
 909     else
 910     {
 911       // special - made easy to edit a property file to disable questionnaires
 912       // by just adding the given line
 913       Cache.removeProperty("NOQUESTIONNAIRES");
 914     }
 915
 916     /*
 917      * Save Output settings
 918      */
 919     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 920             Boolean.toString(blcjv.isSelected()));
 921     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 922             Boolean.toString(clustaljv.isSelected()));
 923     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 924             Boolean.toString(fastajv.isSelected()));
 925     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 926             Boolean.toString(msfjv.isSelected()));
 927     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 928             Boolean.toString(pfamjv.isSelected()));
 929     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 930             Boolean.toString(pileupjv.isSelected()));
 931     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 932             Boolean.toString(pirjv.isSelected()));
 933     Cache.applicationProperties.setProperty("PIR_MODELLER",
 934             Boolean.toString(modellerOutput.isSelected()));
 935     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 936             Boolean.toString(embbedBioJSON.isSelected()));
 937     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 938
 939     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 940             Boolean.toString(autoIdWidth.isSelected()));
 941     userIdWidth_actionPerformed();
 942     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 943             userIdWidth.getText());
 944
 945     /*
 946      * Save Editing settings
 947      */
 948     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 949             Boolean.toString(autoCalculateConsCheck.isSelected()));
 950     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 951             Boolean.toString(sortByTree.isSelected()));
 952     Cache.applicationProperties.setProperty("PAD_GAPS",
 953             Boolean.toString(padGaps.isSelected()));
 954
 955     if (!Platform.isJS())
 956     {
 957       wsPrefs.updateAndRefreshWsMenuConfig(false);
 958     }
 959
 960     /*
 961      * Save Backups settings
 962      */
 963     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 964             Boolean.toString(enableBackupFiles.isSelected()));
 965     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 966     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 967             Integer.toString(preset));
 968
 969     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 970     {
 971       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 972       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 973               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 974       Cache.applicationProperties.setProperty(
 975               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 976     }
 977
 978     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 979             .get(preset);
 980     Cache.applicationProperties.setProperty(
 981             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 982
 983     /*
 984      * Save Memory Settings
 985      */
 986     Cache.applicationProperties.setProperty(
 987             MemorySetting.CUSTOMISED_SETTINGS,
 988             Boolean.toString(customiseMemorySetting.isSelected()));
 989     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
 990             Integer.toString(jvmMemoryPercentSlider.getValue()));
 991     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
 992             jvmMemoryMaxTextField.getText());
 993
 994     /*
 995      * save and close Preferences
 996      */
 997
 998     Cache.saveProperties();
 999     Desktop.instance.doConfigureStructurePrefs();
1000     try
1001     {
1002       frame.setClosed(true);
1003     } catch (Exception ex)
1004     {
1005     }
1006   }
1007
1008   public void saveProxySettings()
1009   {
1010     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1011             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1012                     : Cache.PROXYTYPE_SYSTEM;
1013     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1014     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1015     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1016     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1017     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1018     Cache.setOrRemove("PROXY_AUTH",
1019             Boolean.toString(proxyAuth.isSelected()));
1020     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1021     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1022     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1023     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1024             || !newProxyType.equals(previousProxyType))
1025     {
1026       // force a re-lookup of ws if proxytype is custom or has changed
1027       wsPrefs.update++;
1028     }
1029     previousProxyType = newProxyType;
1030   }
1031
1032   /**
1033    * Do any necessary validation before saving settings. Return focus to the
1034    * first tab which fails validation.
1035    *
1036    * @return
1037    */
1038   private boolean validateSettings()
1039   {
1040     if (!validateStructure())
1041     {
1042       structureTab.requestFocusInWindow();
1043       return false;
1044     }
1045     return true;
1046   }
1047
1048   @Override
1049   protected boolean validateStructure()
1050   {
1051     return validateViewerPath();
1052
1053   }
1054
1055   /**
1056    * DOCUMENT ME!
1057    */
1058   @Override
1059   public void startupFileTextfield_mouseClicked()
1060   {
1061     // TODO: JAL-3048 not needed for Jalview-JS
1062     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1063     JalviewFileChooser chooser = JalviewFileChooser
1064             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1065     chooser.setFileView(new JalviewFileView());
1066     chooser.setDialogTitle(
1067             MessageManager.getString("label.select_startup_file"));
1068
1069     int value = chooser.showOpenDialog(this);
1070
1071     if (value == JalviewFileChooser.APPROVE_OPTION)
1072     {
1073       FileFormatI format = chooser.getSelectedFormat();
1074       if (format != null)
1075       {
1076         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1077                 format.getName());
1078       }
1079       startupFileTextfield
1080               .setText(chooser.getSelectedFile().getAbsolutePath());
1081     }
1082   }
1083
1084   /**
1085    * DOCUMENT ME!
1086    *
1087    * @param e
1088    *          DOCUMENT ME!
1089    */
1090   @Override
1091   public void cancel_actionPerformed(ActionEvent e)
1092   {
1093     try
1094     {
1095       if (!Platform.isJS())
1096       {
1097         wsPrefs.updateWsMenuConfig(true);
1098         wsPrefs.refreshWs_actionPerformed(e);
1099       }
1100       frame.setClosed(true);
1101     } catch (Exception ex)
1102     {
1103     }
1104   }
1105
1106   /**
1107    * DOCUMENT ME!
1108    *
1109    * @param e
1110    *          DOCUMENT ME!
1111    */
1112   @Override
1113   public void annotations_actionPerformed(ActionEvent e)
1114   {
1115     conservation.setEnabled(annotations.isSelected());
1116     quality.setEnabled(annotations.isSelected());
1117     identity.setEnabled(annotations.isSelected());
1118     showOccupancy.setEnabled(annotations.isSelected());
1119     showGroupConsensus.setEnabled(annotations.isSelected());
1120     showGroupConservation.setEnabled(annotations.isSelected());
1121     showConsensHistogram.setEnabled(annotations.isSelected()
1122             && (identity.isSelected() || showGroupConsensus.isSelected()));
1123     showConsensLogo.setEnabled(annotations.isSelected()
1124             && (identity.isSelected() || showGroupConsensus.isSelected()));
1125   }
1126
1127   @Override
1128   public void newLink_actionPerformed(ActionEvent e)
1129   {
1130     GSequenceLink link = new GSequenceLink();
1131     boolean valid = false;
1132     while (!valid)
1133     {
1134       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1135               MessageManager.getString("label.new_sequence_url_link"),
1136               JvOptionPane.OK_CANCEL_OPTION, -1,
1137               null) == JvOptionPane.OK_OPTION)
1138       {
1139         if (link.checkValid())
1140         {
1141           if (((UrlLinkTableModel) linkUrlTable.getModel())
1142                   .isUniqueName(link.getName()))
1143           {
1144             ((UrlLinkTableModel) linkUrlTable.getModel())
1145                     .insertRow(link.getName(), link.getURL());
1146             valid = true;
1147           }
1148           else
1149           {
1150             link.notifyDuplicate();
1151             continue;
1152           }
1153         }
1154       }
1155       else
1156       {
1157         break;
1158       }
1159     }
1160   }
1161
1162   @Override
1163   public void editLink_actionPerformed(ActionEvent e)
1164   {
1165     GSequenceLink link = new GSequenceLink();
1166
1167     int index = linkUrlTable.getSelectedRow();
1168     if (index == -1)
1169     {
1170       // button no longer enabled if row is not selected
1171       Cache.log.debug("Edit with no row selected in linkUrlTable");
1172       return;
1173     }
1174
1175     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1176             .getNameColumn();
1177     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1178             .getUrlColumn();
1179     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1180     link.setName(oldName);
1181     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1182
1183     boolean valid = false;
1184     while (!valid)
1185     {
1186       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1187               MessageManager.getString("label.edit_sequence_url_link"),
1188               JvOptionPane.OK_CANCEL_OPTION, -1,
1189               null) == JvOptionPane.OK_OPTION)
1190       {
1191         if (link.checkValid())
1192         {
1193           if ((oldName.equals(link.getName()))
1194                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1195                           .isUniqueName(link.getName())))
1196           {
1197             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1198             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1199             valid = true;
1200           }
1201           else
1202           {
1203             link.notifyDuplicate();
1204             continue;
1205           }
1206         }
1207       }
1208       else
1209       {
1210         break;
1211       }
1212     }
1213   }
1214
1215   @Override
1216   public void deleteLink_actionPerformed(ActionEvent e)
1217   {
1218     int index = linkUrlTable.getSelectedRow();
1219     int modelIndex = -1;
1220     if (index == -1)
1221     {
1222       // button no longer enabled if row is not selected
1223       Cache.log.debug("Delete with no row selected in linkUrlTable");
1224       return;
1225     }
1226     else
1227     {
1228       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1229     }
1230
1231     // make sure we use the model index to delete, and not the table index
1232     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1233   }
1234
1235   @Override
1236   public void defaultBrowser_mouseClicked(MouseEvent e)
1237   {
1238     // TODO: JAL-3048 not needed for j2s
1239     if (!Platform.isJS()) // BH 2019
1240     /**
1241      * Java only
1242      *
1243      * @j2sIgnore
1244      */
1245     {
1246       JFileChooser chooser = new JFileChooser(".");
1247       chooser.setDialogTitle(
1248               MessageManager.getString("label.select_default_browser"));
1249
1250       int value = chooser.showOpenDialog(this);
1251
1252       if (value == JFileChooser.APPROVE_OPTION)
1253       {
1254         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1255       }
1256     }
1257   }
1258
1259   /*
1260    * (non-Javadoc)
1261    *
1262    * @see
1263    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1264    * .ActionEvent)
1265    */
1266   @Override
1267   protected void showunconserved_actionPerformed(ActionEvent e)
1268   {
1269     // TODO Auto-generated method stub
1270     super.showunconserved_actionPerformed(e);
1271   }
1272
1273   public static List<String> getGroupURLLinks()
1274   {
1275     return groupURLLinks;
1276   }
1277
1278   @Override
1279   public void minColour_actionPerformed(JPanel panel)
1280   {
1281     JalviewColourChooser.showColourChooser(this,
1282             MessageManager.getString("label.select_colour_minimum_value"),
1283             panel);
1284   }
1285
1286   @Override
1287   public void maxColour_actionPerformed(JPanel panel)
1288   {
1289     JalviewColourChooser.showColourChooser(this,
1290             MessageManager.getString("label.select_colour_maximum_value"),
1291             panel);
1292   }
1293
1294   @Override
1295   public void gapColour_actionPerformed(JPanel gap)
1296   {
1297     if (!useLegacyGap.isSelected())
1298     {
1299       JalviewColourChooser.showColourChooser(this,
1300               MessageManager.getString("label.select_gap_colour"), gap);
1301     }
1302   }
1303
1304   @Override
1305   public void hiddenColour_actionPerformed(JPanel hidden)
1306   {
1307     JalviewColourChooser.showColourChooser(this,
1308             MessageManager.getString("label.select_hidden_colour"), hidden);
1309   }
1310
1311   @Override
1312   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1313   {
1314     boolean enabled = useLegacyGap.isSelected();
1315     if (enabled)
1316     {
1317       gapColour.setBackground(
1318               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1319     }
1320     else
1321     {
1322       gapColour.setBackground(
1323               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1324     }
1325     gapColour.setEnabled(!enabled);
1326     gapLabel.setEnabled(!enabled);
1327   }
1328
1329   @Override
1330   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1331   {
1332     useLegacyGap.setSelected(false);
1333     useLegacyGaps_actionPerformed(null);
1334     showHiddenAtStart.setSelected(false);
1335     hiddenColour.setBackground(
1336             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1337   }
1338
1339   @Override
1340   protected void userIdWidth_actionPerformed()
1341   {
1342     try
1343     {
1344       String val = userIdWidth.getText().trim();
1345       if (val.length() > 0)
1346       {
1347         Integer iw = Integer.parseInt(val);
1348         if (iw.intValue() < 12)
1349         {
1350           throw new NumberFormatException();
1351         }
1352         userIdWidth.setText(iw.toString());
1353       }
1354     } catch (NumberFormatException x)
1355     {
1356       userIdWidth.setText("");
1357       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1358               MessageManager
1359                       .getString("warn.user_defined_width_requirements"),
1360               MessageManager.getString("label.invalid_id_column_width"),
1361               JvOptionPane.WARNING_MESSAGE);
1362     }
1363   }
1364
1365   @Override
1366   protected void autoIdWidth_actionPerformed()
1367   {
1368     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1369     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1370   }
1371
1372   /**
1373    * Returns true if structure viewer path is to a valid executable, else shows
1374    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1375    * (built in to Jalview) or when Jalview is left to try default paths.
1376    */
1377   private boolean validateViewerPath()
1378   {
1379     if (structureViewerPath.getText().trim().length() > 0)
1380     {
1381       File f = new File(structureViewerPath.getText());
1382       if (!f.canExecute())
1383       {
1384         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1385                 MessageManager.getString("label.invalid_viewer_path"),
1386                 MessageManager.getString("label.invalid_viewer_path"),
1387                 JvOptionPane.ERROR_MESSAGE);
1388         return false;
1389       }
1390     }
1391     return true;
1392   }
1393
1394   /**
1395    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1396    * default or user-specified path, if not show a warning/help dialog
1397    */
1398   @Override
1399   protected void structureViewer_actionPerformed(String selectedItem)
1400   {
1401     if (selectedItem.equals(ViewerType.JMOL.name()))
1402     {
1403       structureViewerPath.setEnabled(false);
1404       structureViewerPathLabel.setEnabled(false);
1405       return;
1406     }
1407     boolean found = false;
1408     structureViewerPath.setEnabled(true);
1409     structureViewerPathLabel.setEnabled(true);
1410     structureViewerPathLabel.setText(MessageManager
1411             .formatMessage("label.viewer_path", selectedItem));
1412
1413     /*
1414      * Try user-specified and standard paths for structure viewer executable
1415      */
1416     String viewerPath = "";
1417     List<String> paths = null;
1418     try
1419     {
1420       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1421       switch (viewerType)
1422       {
1423       case JMOL:
1424         // dealt with above
1425         break;
1426       case CHIMERA:
1427         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1428         paths = StructureManager.getChimeraPaths(false);
1429         break;
1430       case CHIMERAX:
1431         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1432         paths = StructureManager.getChimeraPaths(true);
1433         break;
1434       case PYMOL:
1435         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1436         paths = PymolManager.getPymolPaths();
1437         break;
1438       }
1439     } catch (IllegalArgumentException e)
1440     {
1441       // only valid entries should be in the drop-down
1442     }
1443     structureViewerPath.setText(viewerPath);
1444
1445     paths.add(0, structureViewerPath.getText());
1446     for (String path : paths)
1447     {
1448       if (new File(path.trim()).canExecute())
1449       {
1450         found = true;
1451         break;
1452       }
1453     }
1454
1455     if (!found)
1456     {
1457       String[] options = { "OK", "Help" };
1458       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1459               JvSwingUtils.wrapTooltip(true,
1460                       MessageManager.getString("label.viewer_missing")),
1461               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1462               null, options, options[0]);
1463       if (showHelp == JvOptionPane.NO_OPTION)
1464       {
1465         try
1466         {
1467           Help.showHelpWindow(HelpId.StructureViewer);
1468         } catch (HelpSetException e)
1469         {
1470           e.printStackTrace();
1471         }
1472       }
1473     }
1474   }
1475
1476   public class OptionsParam
1477   {
1478     private String name;
1479
1480     private String code;
1481
1482     public OptionsParam(String name, String code)
1483     {
1484       this.name = name;
1485       this.code = code;
1486     }
1487
1488     public String getName()
1489     {
1490       return name;
1491     }
1492
1493     public void setName(String name)
1494     {
1495       this.name = name;
1496     }
1497
1498     public String getCode()
1499     {
1500       return code;
1501     }
1502
1503     public void setCode(String code)
1504     {
1505       this.code = code;
1506     }
1507
1508     @Override
1509     public String toString()
1510     {
1511       return name;
1512     }
1513
1514     @Override
1515     public boolean equals(Object that)
1516     {
1517       if (!(that instanceof OptionsParam))
1518       {
1519         return false;
1520       }
1521       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1522     }
1523
1524     @Override
1525     public int hashCode()
1526     {
1527       return name.hashCode() + code.hashCode();
1528     }
1529   }
1530
1531   private class UrlListSelectionHandler implements ListSelectionListener
1532   {
1533
1534     @Override
1535     public void valueChanged(ListSelectionEvent e)
1536     {
1537       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1538
1539       int index = lsm.getMinSelectionIndex();
1540       if (index == -1)
1541       {
1542         // no selection, so disable delete/edit buttons
1543         editLink.setEnabled(false);
1544         deleteLink.setEnabled(false);
1545         return;
1546       }
1547       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1548
1549       // enable/disable edit and delete link buttons
1550       if (((UrlLinkTableModel) linkUrlTable.getModel())
1551               .isRowDeletable(modelIndex))
1552       {
1553         deleteLink.setEnabled(true);
1554       }
1555       else
1556       {
1557         deleteLink.setEnabled(false);
1558       }
1559
1560       if (((UrlLinkTableModel) linkUrlTable.getModel())
1561               .isRowEditable(modelIndex))
1562       {
1563         editLink.setEnabled(true);
1564       }
1565       else
1566       {
1567         editLink.setEnabled(false);
1568       }
1569     }
1570   }
1571 }