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.JColorChooser;
  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.gui.Help.HelpId;
  57 import jalview.gui.StructureViewer.ViewerType;
  58 import jalview.io.BackupFiles;
  59 import jalview.io.BackupFilesPresetEntry;
  60 import jalview.io.FileFormatI;
  61 import jalview.io.JalviewFileChooser;
  62 import jalview.io.JalviewFileView;
  63 import jalview.jbgui.GPreferences;
  64 import jalview.jbgui.GSequenceLink;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.ColourSchemes;
  67 import jalview.schemes.ResidueColourScheme;
  68 import jalview.urls.UrlLinkTableModel;
  69 import jalview.urls.api.UrlProviderFactoryI;
  70 import jalview.urls.api.UrlProviderI;
  71 import jalview.urls.desktop.DesktopUrlProviderFactory;
  72 import jalview.util.MessageManager;
  73 import jalview.util.Platform;
  74 import jalview.util.UrlConstants;
  75 import jalview.ws.sifts.SiftsSettings;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   private String previousProxyType;
 126
 127   private static Preferences INSTANCE = null; // add "final"
 128
 129   /**
 130    * Holds name and link separated with | character. Sequence ID must be
 131    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 132    */
 133   public static UrlProviderI sequenceUrlLinks;
 134
 135   public static UrlLinkTableModel dataModel;
 136
 137   /**
 138    * Holds name and link separated with | character. Sequence IDS and Sequences
 139    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 140    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 141    * for first and second token specified after a pipe character at end |,|.
 142    * (TODO: proper escape for using | to separate ids or sequences
 143    */
 144
 145   public static List<String> groupURLLinks;
 146   static
 147   {
 148     // get links selected to be in the menu (SEQUENCE_LINKS)
 149     // and links entered by the user but not selected (STORED_LINKS)
 150     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 151     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 152     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 153             UrlConstants.DEFAULT_LABEL);
 154
 155     // if both links lists are empty, add the DEFAULT_URL link
 156     // otherwise we assume the default link is in one of the lists
 157     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 158     {
 159       inMenuString = UrlConstants.DEFAULT_STRING;
 160     }
 161     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 162             inMenuString, notInMenuString);
 163     sequenceUrlLinks = factory.createUrlProvider();
 164     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 165
 166     /**
 167      * TODO: reformulate groupURL encoding so two or more can be stored in the
 168      * .properties file as '|' separated strings
 169      */
 170
 171     groupURLLinks = new ArrayList<>();
 172   }
 173
 174   JInternalFrame frame;
 175
 176   private WsPreferences wsPrefs;
 177
 178   private OptionsParam promptEachTimeOpt = new OptionsParam(
 179           MessageManager.getString("label.prompt_each_time"),
 180           "Prompt each time");
 181
 182   private OptionsParam lineArtOpt = new OptionsParam(
 183           MessageManager.getString("label.lineart"), "Lineart");
 184
 185   private OptionsParam textOpt = new OptionsParam(
 186           MessageManager.getString("action.text"), "Text");
 187
 188   // get singleton Preferences instance
 189   public static Preferences getPreferences()
 190   {
 191     return getPreferences(0, null);
 192   }
 193
 194   public static Preferences getPreferences(int selectTab, String message)
 195   {
 196     if (INSTANCE == null || INSTANCE.frame == null
 197             || INSTANCE.frame.isClosed())
 198     {
 199       INSTANCE = new Preferences();
 200     }
 201     INSTANCE.selectTab(selectTab);
 202     INSTANCE.setMessage(message);
 203     return INSTANCE;
 204   }
 205
 206   public static void openPreferences()
 207   {
 208     openPreferences(0, null);
 209   }
 210
 211   public static void openPreferences(int selectTab, String message)
 212   {
 213     Preferences p = getPreferences(selectTab, message);
 214     p.frame.show();
 215     p.frame.moveToFront();
 216     p.frame.grabFocus();
 217   }
 218
 219   /**
 220    * Creates a new Preferences object.
 221    */
 222   private Preferences()
 223   {
 224     super();
 225     frame = new JInternalFrame();
 226     frame.setContentPane(this);
 227     wsPrefs = new WsPreferences();
 228     wsTab.add(wsPrefs, BorderLayout.CENTER);
 229     int width = 500, height = 450;
 230     new jalview.util.Platform();
 231     if (Platform.isAMac())
 232     {
 233       width = 570;
 234       height = 480;
 235     }
 236
 237     Desktop.addInternalFrame(frame,
 238             MessageManager.getString("label.preferences"), width, height);
 239     frame.setMinimumSize(new Dimension(width, height));
 240
 241     /*
 242      * Set Visual tab defaults
 243      */
 244     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 245     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 246     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 247     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 248
 249     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 250     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 251     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 252     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 253     showUnconserved
 254             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 255     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 256     showGroupConsensus
 257             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 258     showGroupConservation.setSelected(
 259             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 260     showConsensHistogram.setSelected(
 261             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 262     showConsensLogo
 263             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 264     showNpTooltip
 265             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 266     showDbRefTooltip
 267             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 268
 269     String[] fonts = java.awt.GraphicsEnvironment
 270             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 271     for (int i = 0; i < fonts.length; i++)
 272     {
 273       fontNameCB.addItem(fonts[i]);
 274     }
 275
 276     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 277     {
 278       fontSizeCB.addItem(i + "");
 279     }
 280
 281     fontStyleCB.addItem("plain");
 282     fontStyleCB.addItem("bold");
 283     fontStyleCB.addItem("italic");
 284
 285     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 286     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 287     fontStyleCB.setSelectedItem(
 288             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 289
 290     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 291     scaleProteinToCdna
 292             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 293
 294     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 295
 296     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 297
 298     gapSymbolCB.addItem("-");
 299     gapSymbolCB.addItem(".");
 300
 301     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 302
 303     sortby.addItem("No sort");
 304     sortby.addItem("Id");
 305     sortby.addItem("Pairwise Identity");
 306     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 307
 308     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 309     sortAnnBy
 310             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 311     sortAnnBy
 312             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 313     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 314             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 315                     SequenceAnnotationOrder.NONE.name()));
 316     sortAnnBy.setSelectedItem(savedSort.toString());
 317
 318     sortAutocalc.addItem("Autocalculated first");
 319     sortAutocalc.addItem("Autocalculated last");
 320     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 321     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 322             : sortAutocalc.getItemAt(1));
 323     startupCheckbox
 324             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 325     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 326             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 327                     + "/examples/exampleFile_2_3.jar"));
 328
 329     /*
 330      * Set Colours tab defaults
 331      */
 332     protColour.addItem(ResidueColourScheme.NONE);
 333     nucColour.addItem(ResidueColourScheme.NONE);
 334     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 335     {
 336       String name = cs.getSchemeName();
 337       protColour.addItem(name);
 338       nucColour.addItem(name);
 339     }
 340     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 341             ResidueColourScheme.NONE);
 342     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 343     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 344     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 345     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 346     minColour.setBackground(
 347             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 348     maxColour.setBackground(
 349             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 350
 351     /*
 352      * Set overview panel defaults
 353      */
 354     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 355             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 356     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 357             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 358     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 359     gapLabel.setEnabled(!useLegacyGap.isSelected());
 360     gapColour.setEnabled(!useLegacyGap.isSelected());
 361     showHiddenAtStart
 362             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 363
 364     /*
 365      * Set Structure tab defaults.
 366      */
 367     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 368     structFromPdb.setSelected(structSelected);
 369     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 370     useRnaView.setEnabled(structSelected);
 371     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 372     addSecondaryStructure.setEnabled(structSelected);
 373     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 374     addTempFactor.setEnabled(structSelected);
 375     structViewer.setSelectedItem(
 376             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 377     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 378     chimeraPath.addActionListener(new ActionListener()
 379     {
 380       @Override
 381       public void actionPerformed(ActionEvent e)
 382       {
 383         validateChimeraPath();
 384       }
 385     });
 386
 387     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 388     {
 389       siftsMapping.setSelected(true);
 390     }
 391     else
 392     {
 393       nwMapping.setSelected(true);
 394     }
 395
 396     SiftsSettings
 397             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 398
 399     /*
 400      * Set Connections tab defaults
 401      */
 402
 403     // set up sorting
 404     linkUrlTable.setModel(dataModel);
 405     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 406             linkUrlTable.getModel());
 407     linkUrlTable.setRowSorter(sorter);
 408     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 409
 410     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 411     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 412             SortOrder.DESCENDING));
 413     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 414             SortOrder.DESCENDING));
 415     sortKeys.add(
 416             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 417
 418     sorter.setSortKeys(sortKeys);
 419     sorter.sort();
 420
 421     // set up filtering
 422     ActionListener onReset;
 423     onReset = new ActionListener()
 424     {
 425       @Override
 426       public void actionPerformed(ActionEvent e)
 427       {
 428         filterTB.setText("");
 429         sorter.setRowFilter(RowFilter.regexFilter(""));
 430       }
 431
 432     };
 433     doReset.addActionListener(onReset);
 434
 435     // filter to display only custom urls
 436     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 437     {
 438       @Override
 439       public boolean include(
 440               Entry<? extends TableModel, ? extends Object> entry)
 441       {
 442         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 443       }
 444     };
 445
 446     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 447             linkUrlTable.getModel());
 448     customSorter.setRowFilter(customUrlFilter);
 449
 450     ActionListener onCustomOnly;
 451     onCustomOnly = new ActionListener()
 452     {
 453       @Override
 454       public void actionPerformed(ActionEvent e)
 455       {
 456         filterTB.setText("");
 457         sorter.setRowFilter(customUrlFilter);
 458       }
 459     };
 460     userOnly.addActionListener(onCustomOnly);
 461
 462     filterTB.getDocument().addDocumentListener(new DocumentListener()
 463     {
 464       String caseInsensitiveFlag = "(?i)";
 465
 466       @Override
 467       public void changedUpdate(DocumentEvent e)
 468       {
 469         sorter.setRowFilter(RowFilter
 470                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 471       }
 472
 473       @Override
 474       public void removeUpdate(DocumentEvent e)
 475       {
 476         sorter.setRowFilter(RowFilter
 477                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 478       }
 479
 480       @Override
 481       public void insertUpdate(DocumentEvent e)
 482       {
 483         sorter.setRowFilter(RowFilter
 484                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 485       }
 486     });
 487
 488     // set up list selection functionality
 489     linkUrlTable.getSelectionModel()
 490             .addListSelectionListener(new UrlListSelectionHandler());
 491
 492     // set up radio buttons
 493     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 494             .getPrimaryColumn();
 495     String onClickName = linkUrlTable.getColumnName(onClickCol);
 496     linkUrlTable.getColumn(onClickName)
 497             .setCellRenderer(new RadioButtonRenderer());
 498     linkUrlTable.getColumn(onClickName)
 499             .setCellEditor(new RadioButtonEditor());
 500
 501     // get boolean columns and resize those to min possible
 502     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 503     {
 504       if (linkUrlTable.getModel().getColumnClass(column)
 505               .equals(Boolean.class))
 506       {
 507         TableColumn tableColumn = linkUrlTable.getColumnModel()
 508                 .getColumn(column);
 509         int preferredWidth = tableColumn.getMinWidth();
 510
 511         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 512                 column);
 513         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 514         int cwidth = c.getPreferredSize().width
 515                 + linkUrlTable.getIntercellSpacing().width;
 516         preferredWidth = Math.max(preferredWidth, cwidth);
 517
 518         tableColumn.setPreferredWidth(preferredWidth);
 519       }
 520     }
 521
 522     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 523     previousProxyType = proxyTypeString;
 524     switch (proxyTypeString)
 525     {
 526     case Cache.PROXYTYPE_NONE:
 527       proxyType.setSelected(noProxy.getModel(), true);
 528       break;
 529     case Cache.PROXYTYPE_SYSTEM:
 530       proxyType.setSelected(systemProxy.getModel(), true);
 531       break;
 532     case Cache.PROXYTYPE_CUSTOM:
 533       proxyType.setSelected(customProxy.getModel(), true);
 534       break;
 535     default:
 536       Cache.log.warn(
 537               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 538                       + proxyTypeString);
 539     }
 540     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 541     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 542     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 543     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 544     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 545     proxyAuthUsernameTB
 546             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 547     // we are not storing or retrieving proxy password from .jalview_properties
 548     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 549             : new String(Cache.proxyAuthPassword));
 550     setCustomProxyEnabled();
 551
 552     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 553
 554     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 555     // note antisense here: default is true
 556     questionnaire
 557             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 558     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 559
 560     /*
 561      * Set Output tab defaults
 562      */
 563     epsRendering.addItem(promptEachTimeOpt);
 564     epsRendering.addItem(lineArtOpt);
 565     epsRendering.addItem(textOpt);
 566     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 567             "Prompt each time");
 568     if (defaultEPS.equalsIgnoreCase("Text"))
 569     {
 570       epsRendering.setSelectedItem(textOpt);
 571     }
 572     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 573     {
 574       epsRendering.setSelectedItem(lineArtOpt);
 575     }
 576     else
 577     {
 578       epsRendering.setSelectedItem(promptEachTimeOpt);
 579     }
 580     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 581     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 582     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 583     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 584     userIdWidth.setText(wi == null ? "" : wi.toString());
 585     // TODO: refactor to use common enum via FormatAdapter and allow extension
 586     // for new flat file formats
 587     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 588     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 589     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 590     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 591     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 592     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 593     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 594     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 595     embbedBioJSON
 596             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 597
 598     /*
 599      * Set Editing tab defaults
 600      */
 601     autoCalculateConsCheck
 602             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 603     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 604     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 605
 606     annotations_actionPerformed(null); // update the display of the annotation
 607                                        // settings
 608
 609     /*
 610      * Set Backups tab defaults
 611      */
 612     loadLastSavedBackupsOptions();
 613   }
 614
 615   /**
 616    * Save user selections on the Preferences tabs to the Cache and write out to
 617    * file.
 618    *
 619    * @param e
 620    */
 621   @Override
 622   public void ok_actionPerformed(ActionEvent e)
 623   {
 624     if (!validateSettings())
 625     {
 626       return;
 627     }
 628
 629     /*
 630      * Set proxy settings first (to be before web services refresh)
 631      */
 632     saveProxySettings();
 633
 634     /*
 635      * Save Visual settings
 636      */
 637     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 638             Boolean.toString(seqLimit.isSelected()));
 639     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 640             Boolean.toString(rightAlign.isSelected()));
 641     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 642             Boolean.toString(fullScreen.isSelected()));
 643     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 644             Boolean.toString(openoverv.isSelected()));
 645     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 646             Boolean.toString(annotations.isSelected()));
 647     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 648             Boolean.toString(conservation.isSelected()));
 649     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 650             Boolean.toString(quality.isSelected()));
 651     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 652             Boolean.toString(identity.isSelected()));
 653
 654     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 655             gapSymbolCB.getSelectedItem().toString());
 656
 657     Cache.applicationProperties.setProperty("FONT_NAME",
 658             fontNameCB.getSelectedItem().toString());
 659     Cache.applicationProperties.setProperty("FONT_STYLE",
 660             fontStyleCB.getSelectedItem().toString());
 661     Cache.applicationProperties.setProperty("FONT_SIZE",
 662             fontSizeCB.getSelectedItem().toString());
 663
 664     Cache.applicationProperties.setProperty("ID_ITALICS",
 665             Boolean.toString(idItalics.isSelected()));
 666     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 667             Boolean.toString(showUnconserved.isSelected()));
 668     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 669             Boolean.toString(showOccupancy.isSelected()));
 670     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 671             Boolean.toString(showGroupConsensus.isSelected()));
 672     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 673             Boolean.toString(showGroupConservation.isSelected()));
 674     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 675             Boolean.toString(showConsensHistogram.isSelected()));
 676     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 677             Boolean.toString(showConsensLogo.isSelected()));
 678     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 679             Boolean.toString(smoothFont.isSelected()));
 680     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 681             Boolean.toString(scaleProteinToCdna.isSelected()));
 682     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 683             Boolean.toString(showNpTooltip.isSelected()));
 684     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 685             Boolean.toString(showDbRefTooltip.isSelected()));
 686
 687     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 688             Boolean.toString(wrap.isSelected()));
 689
 690     Cache.applicationProperties.setProperty("STARTUP_FILE",
 691             startupFileTextfield.getText());
 692     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 693             Boolean.toString(startupCheckbox.isSelected()));
 694
 695     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 696             sortby.getSelectedItem().toString());
 697
 698     // convert description of sort order to enum name for save
 699     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 700             .forDescription(sortAnnBy.getSelectedItem().toString());
 701     if (annSortOrder != null)
 702     {
 703       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 704               annSortOrder.name());
 705     }
 706
 707     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 708     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 709             Boolean.valueOf(showAutocalcFirst).toString());
 710
 711     /*
 712      * Save Colours settings
 713      */
 714     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 715             protColour.getSelectedItem().toString());
 716     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 717             nucColour.getSelectedItem().toString());
 718     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 719             minColour.getBackground());
 720     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 721             maxColour.getBackground());
 722
 723     /*
 724      * Save Overview settings
 725      */
 726     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 727     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 728     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 729             Boolean.toString(useLegacyGap.isSelected()));
 730     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 731             Boolean.toString(showHiddenAtStart.isSelected()));
 732
 733     /*
 734      * Save Structure settings
 735      */
 736     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 737             Boolean.toString(addTempFactor.isSelected()));
 738     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 739             Boolean.toString(addSecondaryStructure.isSelected()));
 740     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 741             Boolean.toString(useRnaView.isSelected()));
 742     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 743             Boolean.toString(structFromPdb.isSelected()));
 744     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 745             structViewer.getSelectedItem().toString());
 746     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 747     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 748             Boolean.toString(siftsMapping.isSelected()));
 749     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 750
 751     /*
 752      * Save Output settings
 753      */
 754     Cache.applicationProperties.setProperty("EPS_RENDERING",
 755             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 756
 757     /*
 758      * Save Connections settings
 759      */
 760     // Proxy settings set first (to catch web services)
 761
 762     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 763
 764     jalview.util.BrowserLauncher.resetBrowser();
 765
 766     // save user-defined and selected links
 767     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 768     if (menuLinks.isEmpty())
 769     {
 770       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 771     }
 772     else
 773     {
 774       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 775               menuLinks.toString());
 776     }
 777
 778     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 779     if (nonMenuLinks.isEmpty())
 780     {
 781       Cache.applicationProperties.remove("STORED_LINKS");
 782     }
 783     else
 784     {
 785       Cache.applicationProperties.setProperty("STORED_LINKS",
 786               nonMenuLinks.toString());
 787     }
 788
 789     Cache.applicationProperties.setProperty("DEFAULT_URL",
 790             sequenceUrlLinks.getPrimaryUrlId());
 791
 792     Cache.setProperty("VERSION_CHECK",
 793             Boolean.toString(versioncheck.isSelected()));
 794     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 795     {
 796       // default is false - we only set this if the user has actively agreed
 797       Cache.setProperty("USAGESTATS",
 798               Boolean.toString(usagestats.isSelected()));
 799     }
 800     if (!questionnaire.isSelected())
 801     {
 802       Cache.setProperty("NOQUESTIONNAIRES", "true");
 803     }
 804     else
 805     {
 806       // special - made easy to edit a property file to disable questionnaires
 807       // by just adding the given line
 808       Cache.removeProperty("NOQUESTIONNAIRES");
 809     }
 810
 811     /*
 812      * Save Output settings
 813      */
 814     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 815             Boolean.toString(blcjv.isSelected()));
 816     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 817             Boolean.toString(clustaljv.isSelected()));
 818     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 819             Boolean.toString(fastajv.isSelected()));
 820     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 821             Boolean.toString(msfjv.isSelected()));
 822     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 823             Boolean.toString(pfamjv.isSelected()));
 824     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 825             Boolean.toString(pileupjv.isSelected()));
 826     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 827             Boolean.toString(pirjv.isSelected()));
 828     Cache.applicationProperties.setProperty("PIR_MODELLER",
 829             Boolean.toString(modellerOutput.isSelected()));
 830     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 831             Boolean.toString(embbedBioJSON.isSelected()));
 832     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 833
 834     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 835             Boolean.toString(autoIdWidth.isSelected()));
 836     userIdWidth_actionPerformed();
 837     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 838             userIdWidth.getText());
 839
 840     /*
 841      * Save Editing settings
 842      */
 843     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 844             Boolean.toString(autoCalculateConsCheck.isSelected()));
 845     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 846             Boolean.toString(sortByTree.isSelected()));
 847     Cache.applicationProperties.setProperty("PAD_GAPS",
 848             Boolean.toString(padGaps.isSelected()));
 849
 850     wsPrefs.updateAndRefreshWsMenuConfig(false);
 851
 852     /*
 853      * Save Backups settings
 854      */
 855     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 856             Boolean.toString(enableBackupFiles.isSelected()));
 857     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 858     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 859             Integer.toString(preset));
 860
 861     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 862     {
 863       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 864       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 865               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 866       Cache.applicationProperties.setProperty(
 867               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 868     }
 869
 870     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 871             .get(preset);
 872     Cache.applicationProperties.setProperty(
 873             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 874
 875     Cache.saveProperties();
 876     Desktop.instance.doConfigureStructurePrefs();
 877     try
 878     {
 879       frame.setClosed(true);
 880     } catch (Exception ex)
 881     {
 882     }
 883   }
 884
 885   public void saveProxySettings()
 886   {
 887     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 888             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 889                     : Cache.PROXYTYPE_SYSTEM;
 890     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
 891     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 892     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 893     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 894     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 895     Cache.setOrRemove("PROXY_AUTH",
 896             Boolean.toString(proxyAuth.isSelected()));
 897     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
 898     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
 899     Cache.setProxyPropertiesFromPreferences(previousProxyType);
 900     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
 901             || !newProxyType.equals(previousProxyType))
 902     {
 903       // force a re-lookup of ws if proxytype is custom or has changed
 904       wsPrefs.update++;
 905     }
 906     previousProxyType = newProxyType;
 907   }
 908
 909   /**
 910    * Do any necessary validation before saving settings. Return focus to the
 911    * first tab which fails validation.
 912    *
 913    * @return
 914    */
 915   private boolean validateSettings()
 916   {
 917     if (!validateStructure())
 918     {
 919       structureTab.requestFocusInWindow();
 920       return false;
 921     }
 922     return true;
 923   }
 924
 925   @Override
 926   protected boolean validateStructure()
 927   {
 928     return validateChimeraPath();
 929
 930   }
 931
 932   /**
 933    * DOCUMENT ME!
 934    */
 935   @Override
 936   public void startupFileTextfield_mouseClicked()
 937   {
 938     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 939     JalviewFileChooser chooser = JalviewFileChooser
 940             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 941     chooser.setFileView(new JalviewFileView());
 942     chooser.setDialogTitle(
 943             MessageManager.getString("label.select_startup_file"));
 944
 945     int value = chooser.showOpenDialog(this);
 946
 947     if (value == JalviewFileChooser.APPROVE_OPTION)
 948     {
 949       FileFormatI format = chooser.getSelectedFormat();
 950       if (format != null)
 951       {
 952         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 953                 format.getName());
 954       }
 955       startupFileTextfield
 956               .setText(chooser.getSelectedFile().getAbsolutePath());
 957     }
 958   }
 959
 960   /**
 961    * DOCUMENT ME!
 962    *
 963    * @param e
 964    *          DOCUMENT ME!
 965    */
 966   @Override
 967   public void cancel_actionPerformed(ActionEvent e)
 968   {
 969     try
 970     {
 971       wsPrefs.updateWsMenuConfig(true);
 972       wsPrefs.refreshWs_actionPerformed(e);
 973       frame.setClosed(true);
 974     } catch (Exception ex)
 975     {
 976     }
 977   }
 978
 979   /**
 980    * DOCUMENT ME!
 981    *
 982    * @param e
 983    *          DOCUMENT ME!
 984    */
 985   @Override
 986   public void annotations_actionPerformed(ActionEvent e)
 987   {
 988     conservation.setEnabled(annotations.isSelected());
 989     quality.setEnabled(annotations.isSelected());
 990     identity.setEnabled(annotations.isSelected());
 991     showOccupancy.setEnabled(annotations.isSelected());
 992     showGroupConsensus.setEnabled(annotations.isSelected());
 993     showGroupConservation.setEnabled(annotations.isSelected());
 994     showConsensHistogram.setEnabled(annotations.isSelected()
 995             && (identity.isSelected() || showGroupConsensus.isSelected()));
 996     showConsensLogo.setEnabled(annotations.isSelected()
 997             && (identity.isSelected() || showGroupConsensus.isSelected()));
 998   }
 999
1000   @Override
1001   public void newLink_actionPerformed(ActionEvent e)
1002   {
1003     GSequenceLink link = new GSequenceLink();
1004     boolean valid = false;
1005     while (!valid)
1006     {
1007       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1008               MessageManager.getString("label.new_sequence_url_link"),
1009               JvOptionPane.OK_CANCEL_OPTION, -1,
1010               null) == JvOptionPane.OK_OPTION)
1011       {
1012         if (link.checkValid())
1013         {
1014           if (((UrlLinkTableModel) linkUrlTable.getModel())
1015                   .isUniqueName(link.getName()))
1016           {
1017             ((UrlLinkTableModel) linkUrlTable.getModel())
1018                     .insertRow(link.getName(), link.getURL());
1019             valid = true;
1020           }
1021           else
1022           {
1023             link.notifyDuplicate();
1024             continue;
1025           }
1026         }
1027       }
1028       else
1029       {
1030         break;
1031       }
1032     }
1033   }
1034
1035   @Override
1036   public void editLink_actionPerformed(ActionEvent e)
1037   {
1038     GSequenceLink link = new GSequenceLink();
1039
1040     int index = linkUrlTable.getSelectedRow();
1041     if (index == -1)
1042     {
1043       // button no longer enabled if row is not selected
1044       Cache.log.debug("Edit with no row selected in linkUrlTable");
1045       return;
1046     }
1047
1048     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1049             .getNameColumn();
1050     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1051             .getUrlColumn();
1052     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1053     link.setName(oldName);
1054     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1055
1056     boolean valid = false;
1057     while (!valid)
1058     {
1059       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1060               MessageManager.getString("label.edit_sequence_url_link"),
1061               JvOptionPane.OK_CANCEL_OPTION, -1,
1062               null) == JvOptionPane.OK_OPTION)
1063       {
1064         if (link.checkValid())
1065         {
1066           if ((oldName.equals(link.getName()))
1067                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1068                           .isUniqueName(link.getName())))
1069           {
1070             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1071             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1072             valid = true;
1073           }
1074           else
1075           {
1076             link.notifyDuplicate();
1077             continue;
1078           }
1079         }
1080       }
1081       else
1082       {
1083         break;
1084       }
1085     }
1086   }
1087
1088   @Override
1089   public void deleteLink_actionPerformed(ActionEvent e)
1090   {
1091     int index = linkUrlTable.getSelectedRow();
1092     int modelIndex = -1;
1093     if (index == -1)
1094     {
1095       // button no longer enabled if row is not selected
1096       Cache.log.debug("Delete with no row selected in linkUrlTable");
1097       return;
1098     }
1099     else
1100     {
1101       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1102     }
1103
1104     // make sure we use the model index to delete, and not the table index
1105     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1106   }
1107
1108   @Override
1109   public void defaultBrowser_mouseClicked(MouseEvent e)
1110   {
1111     JFileChooser chooser = new JFileChooser(".");
1112     chooser.setDialogTitle(
1113             MessageManager.getString("label.select_default_browser"));
1114
1115     int value = chooser.showOpenDialog(this);
1116
1117     if (value == JFileChooser.APPROVE_OPTION)
1118     {
1119       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1120     }
1121
1122   }
1123
1124   /*
1125    * (non-Javadoc)
1126    *
1127    * @see
1128    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1129    * .ActionEvent)
1130    */
1131   @Override
1132   protected void showunconserved_actionPerformed(ActionEvent e)
1133   {
1134     // TODO Auto-generated method stub
1135     super.showunconserved_actionPerformed(e);
1136   }
1137
1138   public static List<String> getGroupURLLinks()
1139   {
1140     return groupURLLinks;
1141   }
1142
1143   @Override
1144   public void minColour_actionPerformed(JPanel panel)
1145   {
1146     Color col = JColorChooser.showDialog(this,
1147             MessageManager.getString("label.select_colour_minimum_value"),
1148             minColour.getBackground());
1149     if (col != null)
1150     {
1151       panel.setBackground(col);
1152     }
1153     panel.repaint();
1154   }
1155
1156   @Override
1157   public void maxColour_actionPerformed(JPanel panel)
1158   {
1159     Color col = JColorChooser.showDialog(this,
1160             MessageManager.getString("label.select_colour_maximum_value"),
1161             maxColour.getBackground());
1162     if (col != null)
1163     {
1164       panel.setBackground(col);
1165     }
1166     panel.repaint();
1167   }
1168
1169   @Override
1170   public void gapColour_actionPerformed(JPanel gap)
1171   {
1172     if (!useLegacyGap.isSelected())
1173     {
1174       Color col = JColorChooser.showDialog(this,
1175               MessageManager.getString("label.select_gap_colour"),
1176               gapColour.getBackground());
1177       if (col != null)
1178       {
1179         gap.setBackground(col);
1180       }
1181       gap.repaint();
1182     }
1183   }
1184
1185   @Override
1186   public void hiddenColour_actionPerformed(JPanel hidden)
1187   {
1188     Color col = JColorChooser.showDialog(this,
1189             MessageManager.getString("label.select_hidden_colour"),
1190             hiddenColour.getBackground());
1191     if (col != null)
1192     {
1193       hidden.setBackground(col);
1194     }
1195     hidden.repaint();
1196   }
1197
1198   @Override
1199   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1200   {
1201     boolean enabled = useLegacyGap.isSelected();
1202     if (enabled)
1203     {
1204       gapColour.setBackground(
1205               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1206     }
1207     else
1208     {
1209       gapColour.setBackground(
1210               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1211     }
1212     gapColour.setEnabled(!enabled);
1213     gapLabel.setEnabled(!enabled);
1214   }
1215
1216   @Override
1217   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1218   {
1219     useLegacyGap.setSelected(false);
1220     useLegacyGaps_actionPerformed(null);
1221     showHiddenAtStart.setSelected(false);
1222     hiddenColour.setBackground(
1223             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1224   }
1225
1226   @Override
1227   protected void userIdWidth_actionPerformed()
1228   {
1229     try
1230     {
1231       String val = userIdWidth.getText().trim();
1232       if (val.length() > 0)
1233       {
1234         Integer iw = Integer.parseInt(val);
1235         if (iw.intValue() < 12)
1236         {
1237           throw new NumberFormatException();
1238         }
1239         userIdWidth.setText(iw.toString());
1240       }
1241     } catch (NumberFormatException x)
1242     {
1243       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1244               MessageManager
1245                       .getString("warn.user_defined_width_requirements"),
1246               MessageManager.getString("label.invalid_id_column_width"),
1247               JvOptionPane.WARNING_MESSAGE);
1248       userIdWidth.setText("");
1249     }
1250   }
1251
1252   @Override
1253   protected void autoIdWidth_actionPerformed()
1254   {
1255     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1256     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1257   }
1258
1259   /**
1260    * Returns true if chimera path is to a valid executable, else show an error
1261    * dialog.
1262    */
1263   private boolean validateChimeraPath()
1264   {
1265     if (chimeraPath.getText().trim().length() > 0)
1266     {
1267       File f = new File(chimeraPath.getText());
1268       if (!f.canExecute())
1269       {
1270         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1271                 MessageManager.getString("label.invalid_chimera_path"),
1272                 MessageManager.getString("label.invalid_name"),
1273                 JvOptionPane.ERROR_MESSAGE);
1274         return false;
1275       }
1276     }
1277     return true;
1278   }
1279
1280   /**
1281    * If Chimera is selected, check it can be found on default or user-specified
1282    * path, if not show a warning/help dialog.
1283    */
1284   @Override
1285   protected void structureViewer_actionPerformed(String selectedItem)
1286   {
1287     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1288     {
1289       return;
1290     }
1291     boolean found = false;
1292
1293     /*
1294      * Try user-specified and standard paths for Chimera executable.
1295      */
1296     List<String> paths = StructureManager.getChimeraPaths();
1297     paths.add(0, chimeraPath.getText());
1298     for (String path : paths)
1299     {
1300       if (new File(path.trim()).canExecute())
1301       {
1302         found = true;
1303         break;
1304       }
1305     }
1306     if (!found)
1307     {
1308       String[] options = { "OK", "Help" };
1309       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1310               JvSwingUtils.wrapTooltip(true,
1311                       MessageManager.getString("label.chimera_missing")),
1312               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1313               null, options, options[0]);
1314       if (showHelp == JvOptionPane.NO_OPTION)
1315       {
1316         try
1317         {
1318           Help.showHelpWindow(HelpId.StructureViewer);
1319         } catch (HelpSetException e)
1320         {
1321           e.printStackTrace();
1322         }
1323       }
1324     }
1325   }
1326
1327   public class OptionsParam
1328   {
1329     private String name;
1330
1331     private String code;
1332
1333     public OptionsParam(String name, String code)
1334     {
1335       this.name = name;
1336       this.code = code;
1337     }
1338
1339     public String getName()
1340     {
1341       return name;
1342     }
1343
1344     public void setName(String name)
1345     {
1346       this.name = name;
1347     }
1348
1349     public String getCode()
1350     {
1351       return code;
1352     }
1353
1354     public void setCode(String code)
1355     {
1356       this.code = code;
1357     }
1358
1359     @Override
1360     public String toString()
1361     {
1362       return name;
1363     }
1364
1365     @Override
1366     public boolean equals(Object that)
1367     {
1368       if (!(that instanceof OptionsParam))
1369       {
1370         return false;
1371       }
1372       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1373     }
1374
1375     @Override
1376     public int hashCode()
1377     {
1378       return name.hashCode() + code.hashCode();
1379     }
1380   }
1381
1382   private class UrlListSelectionHandler implements ListSelectionListener
1383   {
1384
1385     @Override
1386     public void valueChanged(ListSelectionEvent e)
1387     {
1388       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1389
1390       int index = lsm.getMinSelectionIndex();
1391       if (index == -1)
1392       {
1393         // no selection, so disable delete/edit buttons
1394         editLink.setEnabled(false);
1395         deleteLink.setEnabled(false);
1396         return;
1397       }
1398       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1399
1400       // enable/disable edit and delete link buttons
1401       if (((UrlLinkTableModel) linkUrlTable.getModel())
1402               .isRowDeletable(modelIndex))
1403       {
1404         deleteLink.setEnabled(true);
1405       }
1406       else
1407       {
1408         deleteLink.setEnabled(false);
1409       }
1410
1411       if (((UrlLinkTableModel) linkUrlTable.getModel())
1412               .isRowEditable(modelIndex))
1413       {
1414         editLink.setEnabled(true);
1415       }
1416       else
1417       {
1418         editLink.setEnabled(false);
1419       }
1420     }
1421   }
1422
1423 }