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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  28 import jalview.io.FileFormatI;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeI;
  34 import jalview.schemes.ColourSchemes;
  35 import jalview.schemes.ResidueColourScheme;
  36 import jalview.urls.UrlLinkTableModel;
  37 import jalview.urls.api.UrlProviderFactoryI;
  38 import jalview.urls.api.UrlProviderI;
  39 import jalview.urls.desktop.DesktopUrlProviderFactory;
  40 import jalview.util.BrowserLauncher;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JComboBox;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 @SuppressWarnings("serial")
  85 public class Preferences extends GPreferences
  86 {
  87   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  88
  89   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  90
  91   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  92
  93   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  94
  95   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  96
  97   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  98
  99   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 100
 101   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 102
 103   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 104
 105   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 106
 107   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 108
 109   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 110
 111   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 112
 113   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 114
 115   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 116
 117   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 118
 119   public static final String GAP_COLOUR = "GAP_COLOUR";
 120
 121   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 122
 123   private static final int MIN_FONT_SIZE = 1;
 124
 125   private static final int MAX_FONT_SIZE = 30;
 126
 127   /**
 128    * Holds name and link separated with | character. Sequence ID must be
 129    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 130    */
 131   public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
 132
 133   public final static UrlLinkTableModel dataModel;
 134
 135   /**
 136    * Holds name and link separated with | character. Sequence IDS and Sequences
 137    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 138    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 139    * for first and second token specified after a pipe character at end |,|.
 140    * (TODO: proper escape for using | to separate ids or sequences
 141    */
 142
 143   public static final List<String> groupURLLinks; // not implemented
 144
 145   static
 146   {
 147     // get links selected to be in the menu (SEQUENCE_LINKS)
 148     // and links entered by the user but not selected (STORED_LINKS)
 149     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 150     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 151     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 152             UrlConstants.DEFAULT_LABEL);
 153
 154     // if both links lists are empty, add the DEFAULT_URL link
 155     // otherwise we assume the default link is in one of the lists
 156     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 157     {
 158       inMenuString = UrlConstants.DEFAULT_STRING;
 159     }
 160     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 161             inMenuString, notInMenuString);
 162     sequenceUrlLinks = factory.createUrlProvider();
 163     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 164
 165     /**
 166      * TODO: reformulate groupURL encoding so two or more can be stored in the
 167      * .properties file as '|' separated strings
 168      */
 169
 170     groupURLLinks = new ArrayList<>(); // not implemented
 171   }
 172
 173   JInternalFrame frame;
 174
 175   private WsPreferences wsPrefs;
 176
 177   private OptionsParam promptEachTimeOpt = new OptionsParam(
 178           MessageManager.getString("label.prompt_each_time"),
 179           "Prompt each time");
 180
 181   private OptionsParam lineArtOpt = new OptionsParam(
 182           MessageManager.getString("label.lineart"), "Lineart");
 183
 184   private OptionsParam textOpt = new OptionsParam(
 185           MessageManager.getString("action.text"), "Text");
 186
 187   /**
 188    * Creates a new Preferences object.
 189    */
 190   public Preferences()
 191   {
 192     super();
 193     frame = new JInternalFrame();
 194     frame.setContentPane(this);
 195     if (!Platform.isJS())
 196     /**
 197      * Java only
 198      *
 199      * @j2sIgnore
 200      */
 201     {
 202       wsPrefs = new WsPreferences();
 203       wsTab.add(wsPrefs, BorderLayout.CENTER);
 204     }
 205     int width = 500, height = 450;
 206     if (Platform.isAMacAndNotJS())
 207     {
 208       width = 570;
 209       height = 480;
 210     }
 211
 212     Desktop.addInternalFrame(frame,
 213             MessageManager.getString("label.preferences"), width, height);
 214     frame.setMinimumSize(new Dimension(width, height));
 215
 216     /*
 217      * Set Visual tab defaults
 218      */
 219     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 220     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 221     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 222     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 223
 224     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 225     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 226     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 227     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 228     showUnconserved
 229             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 230     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 231     showGroupConsensus
 232             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 233     showGroupConservation.setSelected(
 234             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 235     showConsensHistogram.setSelected(
 236             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 237     showConsensLogo
 238             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 239     showNpTooltip
 240             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 241     showDbRefTooltip
 242             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 243
 244     String[] fonts = java.awt.GraphicsEnvironment
 245             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 246     for (int i = 0; i < fonts.length; i++)
 247     {
 248       fontNameCB.addItem(fonts[i]);
 249     }
 250
 251     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 252     {
 253       fontSizeCB.addItem(i + "");
 254     }
 255
 256     fontStyleCB.addItem("plain");
 257     fontStyleCB.addItem("bold");
 258     fontStyleCB.addItem("italic");
 259
 260     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 261     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 262     fontStyleCB.setSelectedItem(
 263             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 264
 265     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 266     scaleProteinToCdna
 267             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 268
 269     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 270
 271     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 272
 273     gapSymbolCB.addItem("-");
 274     gapSymbolCB.addItem(".");
 275
 276     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 277
 278     sortby.addItem("No sort");
 279     sortby.addItem("Id");
 280     sortby.addItem("Pairwise Identity");
 281     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 282
 283     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 284     sortAnnBy
 285             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 286     sortAnnBy
 287             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 288     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 289             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 290                     SequenceAnnotationOrder.NONE.name()));
 291     sortAnnBy.setSelectedItem(savedSort.toString());
 292
 293     sortAutocalc.addItem("Autocalculated first");
 294     sortAutocalc.addItem("Autocalculated last");
 295     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 296     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 297             : sortAutocalc.getItemAt(1));
 298     startupCheckbox
 299             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 300     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 301             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 302                     + "/examples/exampleFile_2_3.jar"));
 303
 304     /*
 305      * Set Colours tab defaults
 306      */
 307     protColour.addItem(ResidueColourScheme.NONE);
 308     nucColour.addItem(ResidueColourScheme.NONE);
 309     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 310     {
 311       String name = cs.getSchemeName();
 312       protColour.addItem(name);
 313       nucColour.addItem(name);
 314     }
 315     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 316             ResidueColourScheme.NONE);
 317     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 318     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 319     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 320     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 321     minColour.setBackground(
 322             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 323     maxColour.setBackground(
 324             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 325
 326     /*
 327      * Set overview panel defaults
 328      */
 329     gapColour.setBackground(
 330             Cache.getDefaultColour(GAP_COLOUR,
 331                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 332     hiddenColour.setBackground(
 333             Cache.getDefaultColour(HIDDEN_COLOUR,
 334                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 335     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 336     gapLabel.setEnabled(!useLegacyGap.isSelected());
 337     gapColour.setEnabled(!useLegacyGap.isSelected());
 338     showHiddenAtStart
 339             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 340
 341     /*
 342      * Set Structure tab defaults.
 343      */
 344     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 345     structFromPdb.setSelected(structSelected);
 346     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 347     useRnaView.setEnabled(structSelected);
 348     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 349     addSecondaryStructure.setEnabled(structSelected);
 350     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 351     addTempFactor.setEnabled(structSelected);
 352     structViewer.setSelectedItem(
 353             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 354     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 355     chimeraPath.addActionListener(new ActionListener()
 356     {
 357       @Override
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         validateChimeraPath();
 361       }
 362     });
 363
 364     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 365     {
 366       siftsMapping.setSelected(true);
 367     }
 368     else
 369     {
 370       nwMapping.setSelected(true);
 371     }
 372
 373     SiftsSettings
 374             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 375
 376     /*
 377      * Set Connections tab defaults
 378      */
 379
 380     // set up sorting
 381     linkUrlTable.setModel(dataModel);
 382     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 383             linkUrlTable.getModel());
 384     linkUrlTable.setRowSorter(sorter);
 385     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 386
 387     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 388     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 389             SortOrder.DESCENDING));
 390     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 391             SortOrder.DESCENDING));
 392     sortKeys.add(
 393             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 394
 395     sorter.setSortKeys(sortKeys);
 396     // BH 2018 setSortKeys will do the sort
 397     // sorter.sort();
 398
 399     // set up filtering
 400     ActionListener onReset;
 401     onReset = new ActionListener()
 402     {
 403       @Override
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         filterTB.setText("");
 407         sorter.setRowFilter(RowFilter.regexFilter(""));
 408       }
 409
 410     };
 411     doReset.addActionListener(onReset);
 412
 413     // filter to display only custom urls
 414     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 415     {
 416       @Override
 417       public boolean include(
 418               Entry<? extends TableModel, ? extends Object> entry)
 419       {
 420         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 421       }
 422     };
 423
 424     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 425             linkUrlTable.getModel());
 426     customSorter.setRowFilter(customUrlFilter);
 427
 428     ActionListener onCustomOnly;
 429     onCustomOnly = new ActionListener()
 430     {
 431       @Override
 432       public void actionPerformed(ActionEvent e)
 433       {
 434         filterTB.setText("");
 435         sorter.setRowFilter(customUrlFilter);
 436       }
 437     };
 438     userOnly.addActionListener(onCustomOnly);
 439
 440     filterTB.getDocument().addDocumentListener(new DocumentListener()
 441     {
 442       String caseInsensitiveFlag = "(?i)";
 443
 444       @Override
 445       public void changedUpdate(DocumentEvent e)
 446       {
 447         sorter.setRowFilter(RowFilter
 448                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 449       }
 450
 451       @Override
 452       public void removeUpdate(DocumentEvent e)
 453       {
 454         sorter.setRowFilter(RowFilter
 455                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 456       }
 457
 458       @Override
 459       public void insertUpdate(DocumentEvent e)
 460       {
 461         sorter.setRowFilter(RowFilter
 462                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 463       }
 464     });
 465
 466     // set up list selection functionality
 467     linkUrlTable.getSelectionModel()
 468             .addListSelectionListener(new UrlListSelectionHandler());
 469
 470     // set up radio buttons
 471     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 472             .getPrimaryColumn();
 473     String onClickName = linkUrlTable.getColumnName(onClickCol);
 474     linkUrlTable.getColumn(onClickName)
 475             .setCellRenderer(new RadioButtonRenderer());
 476     linkUrlTable.getColumn(onClickName)
 477             .setCellEditor(new RadioButtonEditor());
 478
 479     // get boolean columns and resize those to min possible
 480     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 481     {
 482       if (linkUrlTable.getModel().getColumnClass(column)
 483               .equals(Boolean.class))
 484       {
 485         TableColumn tableColumn = linkUrlTable.getColumnModel()
 486                 .getColumn(column);
 487         int preferredWidth = tableColumn.getMinWidth();
 488
 489         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 490                 column);
 491         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 492         int cwidth = c.getPreferredSize().width
 493                 + linkUrlTable.getIntercellSpacing().width;
 494         preferredWidth = Math.max(preferredWidth, cwidth);
 495
 496         tableColumn.setPreferredWidth(preferredWidth);
 497       }
 498     }
 499
 500     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 501     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 502     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 503     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 504
 505     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 506
 507     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 508     // note antisense here: default is true
 509     questionnaire
 510             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 511     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 512
 513     /*
 514      * Set Output tab defaults
 515      */
 516     setupOutputCombo(epsRendering, "EPS_RENDERING");
 517     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 518     setupOutputCombo(svgRendering, "SVG_RENDERING");
 519     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 520     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 521     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 522     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 523     userIdWidth.setText(wi == null ? "" : wi.toString());
 524     // TODO: refactor to use common enum via FormatAdapter and allow extension
 525     // for new flat file formats
 526     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 527     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 528     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 529     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 530     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 531     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 532     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 533     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 534     embbedBioJSON
 535             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 536
 537     /*
 538      * Set Editing tab defaults
 539      */
 540     autoCalculateConsCheck
 541             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 542     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 543     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 544
 545     annotations_actionPerformed(null); // update the display of the annotation
 546                                        // settings
 547
 548
 549     /*
 550      * Set Backups tab defaults
 551      */
 552     loadLastSavedBackupsOptions();
 553   }
 554
 555   /**
 556    * A helper method that sets the items and initial selection in a character
 557    * rendering option list (Prompt each time/Lineart/Text)
 558    *
 559    * @param comboBox
 560    * @param propertyKey
 561    */
 562   protected void setupOutputCombo(JComboBox<Object> comboBox,
 563           String propertyKey)
 564   {
 565     comboBox.addItem(promptEachTimeOpt);
 566     comboBox.addItem(lineArtOpt);
 567     comboBox.addItem(textOpt);
 568
 569     /*
 570      * JalviewJS doesn't support Lineart so force it to Text
 571      */
 572     String defaultOption = Platform.isJS() ? "Text"
 573             : Cache.getDefault(propertyKey, "Prompt each time");
 574     if (defaultOption.equalsIgnoreCase("Text"))
 575     {
 576       comboBox.setSelectedItem(textOpt);
 577     }
 578     else if (defaultOption.equalsIgnoreCase("Lineart"))
 579     {
 580       comboBox.setSelectedItem(lineArtOpt);
 581     }
 582     else
 583     {
 584       comboBox.setSelectedItem(promptEachTimeOpt);
 585     }
 586   }
 587
 588   /**
 589    * Save user selections on the Preferences tabs to the Cache and write out to
 590    * file.
 591    *
 592    * @param e
 593    */
 594   @Override
 595   public void ok_actionPerformed(ActionEvent e)
 596   {
 597     if (!validateSettings())
 598     {
 599       return;
 600     }
 601
 602     /*
 603      * Save Visual settings
 604      */
 605     Cache.setPropertyNoSave("SHOW_JVSUFFIX",
 606             Boolean.toString(seqLimit.isSelected()));
 607     Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
 608             Boolean.toString(rightAlign.isSelected()));
 609     Cache.setPropertyNoSave("SHOW_FULLSCREEN",
 610             Boolean.toString(fullScreen.isSelected()));
 611     Cache.setPropertyNoSave("SHOW_OVERVIEW",
 612             Boolean.toString(openoverv.isSelected()));
 613     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
 614             Boolean.toString(annotations.isSelected()));
 615     Cache.setPropertyNoSave("SHOW_CONSERVATION",
 616             Boolean.toString(conservation.isSelected()));
 617     Cache.setPropertyNoSave("SHOW_QUALITY",
 618             Boolean.toString(quality.isSelected()));
 619     Cache.setPropertyNoSave("SHOW_IDENTITY",
 620             Boolean.toString(identity.isSelected()));
 621
 622     Cache.setPropertyNoSave("GAP_SYMBOL",
 623             gapSymbolCB.getSelectedItem().toString());
 624
 625     Cache.setPropertyNoSave("FONT_NAME",
 626             fontNameCB.getSelectedItem().toString());
 627     Cache.setPropertyNoSave("FONT_STYLE",
 628             fontStyleCB.getSelectedItem().toString());
 629     Cache.setPropertyNoSave("FONT_SIZE",
 630             fontSizeCB.getSelectedItem().toString());
 631
 632     Cache.setPropertyNoSave("ID_ITALICS",
 633             Boolean.toString(idItalics.isSelected()));
 634     Cache.setPropertyNoSave("SHOW_UNCONSERVED",
 635             Boolean.toString(showUnconserved.isSelected()));
 636     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
 637             Boolean.toString(showOccupancy.isSelected()));
 638     Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
 639             Boolean.toString(showGroupConsensus.isSelected()));
 640     Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
 641             Boolean.toString(showGroupConservation.isSelected()));
 642     Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
 643             Boolean.toString(showConsensHistogram.isSelected()));
 644     Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
 645             Boolean.toString(showConsensLogo.isSelected()));
 646     Cache.setPropertyNoSave("ANTI_ALIAS",
 647             Boolean.toString(smoothFont.isSelected()));
 648     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
 649             Boolean.toString(scaleProteinToCdna.isSelected()));
 650     Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
 651             Boolean.toString(showNpTooltip.isSelected()));
 652     Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
 653             Boolean.toString(showDbRefTooltip.isSelected()));
 654
 655     Cache.setPropertyNoSave("WRAP_ALIGNMENT",
 656             Boolean.toString(wrap.isSelected()));
 657
 658     Cache.setPropertyNoSave("STARTUP_FILE",
 659             startupFileTextfield.getText());
 660     Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
 661             Boolean.toString(startupCheckbox.isSelected()));
 662
 663     Cache.setPropertyNoSave("SORT_ALIGNMENT",
 664             sortby.getSelectedItem().toString());
 665
 666     // convert description of sort order to enum name for save
 667     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 668             .forDescription(sortAnnBy.getSelectedItem().toString());
 669     if (annSortOrder != null)
 670     {
 671       Cache.setPropertyNoSave(SORT_ANNOTATIONS,
 672               annSortOrder.name());
 673     }
 674
 675     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 676     Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
 677             Boolean.valueOf(showAutocalcFirst).toString());
 678
 679     /*
 680      * Save Colours settings
 681      */
 682     Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
 683             protColour.getSelectedItem().toString());
 684     Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
 685             nucColour.getSelectedItem().toString());
 686     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 687             minColour.getBackground());
 688     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 689             maxColour.getBackground());
 690
 691     /*
 692      * Save Overview settings
 693      */
 694     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 695     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 696     Cache.setPropertyNoSave(USE_LEGACY_GAP,
 697             Boolean.toString(useLegacyGap.isSelected()));
 698     Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
 699             Boolean.toString(showHiddenAtStart.isSelected()));
 700
 701     /*
 702      * Save Structure settings
 703      */
 704     Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
 705             Boolean.toString(addTempFactor.isSelected()));
 706     Cache.setPropertyNoSave(ADD_SS_ANN,
 707             Boolean.toString(addSecondaryStructure.isSelected()));
 708     Cache.setPropertyNoSave(USE_RNAVIEW,
 709             Boolean.toString(useRnaView.isSelected()));
 710     Cache.setPropertyNoSave(STRUCT_FROM_PDB,
 711             Boolean.toString(structFromPdb.isSelected()));
 712     Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
 713             structViewer.getSelectedItem().toString());
 714     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 715     Cache.setPropertyNoSave("MAP_WITH_SIFTS",
 716             Boolean.toString(siftsMapping.isSelected()));
 717     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 718
 719     /*
 720      * Save Output settings
 721      */
 722     Cache.setPropertyNoSave("EPS_RENDERING",
 723             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 724     Cache.setPropertyNoSave("HTML_RENDERING",
 725             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 726     Cache.setPropertyNoSave("SVG_RENDERING",
 727             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 728
 729     if (!Platform.isJS())
 730     /**
 731      * @j2sNative
 732      */
 733     {
 734       // Java only
 735       // Save Connections settings
 736       Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 737       BrowserLauncher.resetBrowser();
 738     }
 739
 740     // save user-defined and selected links
 741     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 742     if (menuLinks.isEmpty())
 743     {
 744       Cache.removePropertyNoSave("SEQUENCE_LINKS");
 745     }
 746     else
 747     {
 748       Cache.setPropertyNoSave("SEQUENCE_LINKS",
 749               menuLinks.toString());
 750     }
 751
 752     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 753     if (nonMenuLinks.isEmpty())
 754     {
 755       Cache.removePropertyNoSave("STORED_LINKS");
 756     }
 757     else
 758     {
 759       Cache.setPropertyNoSave("STORED_LINKS",
 760               nonMenuLinks.toString());
 761     }
 762
 763     Cache.setPropertyNoSave("DEFAULT_URL",
 764             sequenceUrlLinks.getPrimaryUrlId());
 765
 766     Cache.setPropertyNoSave("USE_PROXY",
 767             Boolean.toString(useProxy.isSelected()));
 768
 769     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 770
 771     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 772
 773     if (useProxy.isSelected())
 774     {
 775       System.setProperty("http.proxyHost", proxyServerTB.getText());
 776       System.setProperty("http.proxyPort", proxyPortTB.getText());
 777     }
 778     else
 779     {
 780       System.setProperty("http.proxyHost", "");
 781       System.setProperty("http.proxyPort", "");
 782     }
 783     Cache.setProperty("VERSION_CHECK",
 784             Boolean.toString(versioncheck.isSelected()));
 785     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 786     {
 787       // default is false - we only set this if the user has actively agreed
 788       Cache.setProperty("USAGESTATS",
 789               Boolean.toString(usagestats.isSelected()));
 790     }
 791     if (!questionnaire.isSelected())
 792     {
 793       Cache.setProperty("NOQUESTIONNAIRES", "true");
 794     }
 795     else
 796     {
 797       // special - made easy to edit a property file to disable questionnaires
 798       // by just adding the given line
 799       Cache.removeProperty("NOQUESTIONNAIRES");
 800     }
 801
 802     /*
 803      * Save Output settings
 804      */
 805     Cache.setPropertyNoSave("BLC_JVSUFFIX",
 806             Boolean.toString(blcjv.isSelected()));
 807     Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
 808             Boolean.toString(clustaljv.isSelected()));
 809     Cache.setPropertyNoSave("FASTA_JVSUFFIX",
 810             Boolean.toString(fastajv.isSelected()));
 811     Cache.setPropertyNoSave("MSF_JVSUFFIX",
 812             Boolean.toString(msfjv.isSelected()));
 813     Cache.setPropertyNoSave("PFAM_JVSUFFIX",
 814             Boolean.toString(pfamjv.isSelected()));
 815     Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
 816             Boolean.toString(pileupjv.isSelected()));
 817     Cache.setPropertyNoSave("PIR_JVSUFFIX",
 818             Boolean.toString(pirjv.isSelected()));
 819     Cache.setPropertyNoSave("PIR_MODELLER",
 820             Boolean.toString(modellerOutput.isSelected()));
 821     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
 822             Boolean.toString(embbedBioJSON.isSelected()));
 823     Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
 824             Boolean.toString(autoIdWidth.isSelected()));
 825     userIdWidth_actionPerformed();
 826     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
 827             userIdWidth.getText());
 828
 829     /*
 830      * Save Editing settings
 831      */
 832     Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
 833             Boolean.toString(autoCalculateConsCheck.isSelected()));
 834     Cache.setPropertyNoSave("SORT_BY_TREE",
 835             Boolean.toString(sortByTree.isSelected()));
 836     Cache.setPropertyNoSave("PAD_GAPS",
 837             Boolean.toString(padGaps.isSelected()));
 838
 839     if (!Platform.isJS())
 840     {
 841       wsPrefs.updateAndRefreshWsMenuConfig(false);
 842     }
 843
 844     /*
 845      * Save Backups settings
 846      */
 847     Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
 848             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 849     Cache.setPropertyNoSave(BackupFiles.ENABLED,
 850             Boolean.toString(enableBackupFiles.isSelected()));
 851     Cache.setPropertyNoSave(BackupFiles.NO_MAX,
 852             Boolean.toString(backupfilesKeepAll.isSelected()));
 853     Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
 854             Boolean.toString(suffixReverse.isSelected()));
 855     Cache.setPropertyNoSave(BackupFiles.SUFFIX,
 856             suffixTemplate.getText());
 857     Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
 858             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 859     Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
 860             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 861     Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
 862             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 863
 864     Cache.saveProperties();
 865     Desktop.getInstance().doConfigureStructurePrefs();
 866     try
 867     {
 868       frame.setClosed(true);
 869     } catch (Exception ex)
 870     {
 871     }
 872   }
 873
 874   /**
 875    * Do any necessary validation before saving settings. Return focus to the
 876    * first tab which fails validation.
 877    *
 878    * @return
 879    */
 880   private boolean validateSettings()
 881   {
 882     if (!validateStructure())
 883     {
 884       structureTab.requestFocusInWindow();
 885       return false;
 886     }
 887     return true;
 888   }
 889
 890   @Override
 891   protected boolean validateStructure()
 892   {
 893     return validateChimeraPath();
 894
 895   }
 896
 897   /**
 898    * DOCUMENT ME!
 899    */
 900   @Override
 901   public void startupFileTextfield_mouseClicked()
 902   {
 903     // TODO: JAL-3048 not needed for Jalview-JS
 904     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 905     JalviewFileChooser chooser = JalviewFileChooser
 906             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 907     chooser.setFileView(new JalviewFileView());
 908     chooser.setDialogTitle(
 909             MessageManager.getString("label.select_startup_file"));
 910
 911     int value = chooser.showOpenDialog(this);
 912
 913     if (value == JalviewFileChooser.APPROVE_OPTION)
 914     {
 915       FileFormatI format = chooser.getSelectedFormat();
 916       if (format != null)
 917       {
 918         Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
 919                 format.getName());
 920       }
 921       startupFileTextfield
 922               .setText(chooser.getSelectedFile().getAbsolutePath());
 923     }
 924   }
 925
 926   /**
 927    * DOCUMENT ME!
 928    *
 929    * @param e
 930    *          DOCUMENT ME!
 931    */
 932   @Override
 933   public void cancel_actionPerformed(ActionEvent e)
 934   {
 935     try
 936     {
 937       if (!Platform.isJS())
 938       {
 939         wsPrefs.updateWsMenuConfig(true);
 940         wsPrefs.refreshWs_actionPerformed(e);
 941       }
 942       frame.setClosed(true);
 943     } catch (Exception ex)
 944     {
 945     }
 946   }
 947
 948   /**
 949    * DOCUMENT ME!
 950    *
 951    * @param e
 952    *          DOCUMENT ME!
 953    */
 954   @Override
 955   public void annotations_actionPerformed(ActionEvent e)
 956   {
 957     conservation.setEnabled(annotations.isSelected());
 958     quality.setEnabled(annotations.isSelected());
 959     identity.setEnabled(annotations.isSelected());
 960     showOccupancy.setEnabled(annotations.isSelected());
 961     showGroupConsensus.setEnabled(annotations.isSelected());
 962     showGroupConservation.setEnabled(annotations.isSelected());
 963     showConsensHistogram.setEnabled(annotations.isSelected()
 964             && (identity.isSelected() || showGroupConsensus.isSelected()));
 965     showConsensLogo.setEnabled(annotations.isSelected()
 966             && (identity.isSelected() || showGroupConsensus.isSelected()));
 967   }
 968
 969   @Override
 970   public void newLink_actionPerformed(ActionEvent e)
 971   {
 972     GSequenceLink link = new GSequenceLink();
 973     boolean valid = false;
 974     while (!valid)
 975     {
 976       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
 977               MessageManager.getString("label.new_sequence_url_link"),
 978               JvOptionPane.OK_CANCEL_OPTION, -1,
 979               null) == JvOptionPane.OK_OPTION)
 980       {
 981         if (link.checkValid())
 982         {
 983           if (((UrlLinkTableModel) linkUrlTable.getModel())
 984                   .isUniqueName(link.getName()))
 985           {
 986             ((UrlLinkTableModel) linkUrlTable.getModel())
 987                     .insertRow(link.getName(), link.getURL());
 988             valid = true;
 989           }
 990           else
 991           {
 992             link.notifyDuplicate();
 993             continue;
 994           }
 995         }
 996       }
 997       else
 998       {
 999         break;
1000       }
1001     }
1002   }
1003
1004   @Override
1005   public void editLink_actionPerformed(ActionEvent e)
1006   {
1007     GSequenceLink link = new GSequenceLink();
1008
1009     int index = linkUrlTable.getSelectedRow();
1010     if (index == -1)
1011     {
1012       // button no longer enabled if row is not selected
1013       Cache.log.debug("Edit with no row selected in linkUrlTable");
1014       return;
1015     }
1016
1017     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1018             .getNameColumn();
1019     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1020             .getUrlColumn();
1021     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1022     link.setName(oldName);
1023     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1024
1025     boolean valid = false;
1026     while (!valid)
1027     {
1028       if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
1029               MessageManager.getString("label.edit_sequence_url_link"),
1030               JvOptionPane.OK_CANCEL_OPTION, -1,
1031               null) == JvOptionPane.OK_OPTION)
1032       {
1033         if (link.checkValid())
1034         {
1035           if ((oldName.equals(link.getName()))
1036                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1037                           .isUniqueName(link.getName())))
1038           {
1039             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1040             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1041             valid = true;
1042           }
1043           else
1044           {
1045             link.notifyDuplicate();
1046             continue;
1047           }
1048         }
1049       }
1050       else
1051       {
1052         break;
1053       }
1054     }
1055   }
1056
1057   @Override
1058   public void deleteLink_actionPerformed(ActionEvent e)
1059   {
1060     int index = linkUrlTable.getSelectedRow();
1061     int modelIndex = -1;
1062     if (index == -1)
1063     {
1064       // button no longer enabled if row is not selected
1065       Cache.log.debug("Delete with no row selected in linkUrlTable");
1066       return;
1067     }
1068     else
1069     {
1070       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1071     }
1072
1073     // make sure we use the model index to delete, and not the table index
1074     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1075   }
1076
1077   @Override
1078   public void defaultBrowser_mouseClicked(MouseEvent e)
1079   {
1080     // TODO: JAL-3048 not needed for j2s
1081     if (!Platform.isJS()) // BH 2019
1082     /**
1083      * Java only
1084      *
1085      * @j2sIgnore
1086      */
1087     {
1088       JFileChooser chooser = new JFileChooser(".");
1089       chooser.setDialogTitle(
1090               MessageManager.getString("label.select_default_browser"));
1091
1092       int value = chooser.showOpenDialog(this);
1093
1094       if (value == JFileChooser.APPROVE_OPTION)
1095       {
1096         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1097       }
1098     }
1099   }
1100
1101   /*
1102    * (non-Javadoc)
1103    *
1104    * @see
1105    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1106    * .ActionEvent)
1107    */
1108   @Override
1109   protected void showunconserved_actionPerformed(ActionEvent e)
1110   {
1111     // TODO Auto-generated method stub
1112     super.showunconserved_actionPerformed(e);
1113   }
1114
1115   /**
1116    * not implemented -- returns empty list
1117    *
1118    * @return
1119    */
1120   public static List<String> getGroupURLLinks()
1121   {
1122     return groupURLLinks;
1123   }
1124
1125   @Override
1126   public void minColour_actionPerformed(JPanel panel)
1127   {
1128     JalviewColourChooser.showColourChooser(this,
1129             MessageManager.getString("label.select_colour_minimum_value"),
1130             panel);
1131   }
1132
1133   @Override
1134   public void maxColour_actionPerformed(JPanel panel)
1135   {
1136     JalviewColourChooser.showColourChooser(this,
1137             MessageManager.getString("label.select_colour_maximum_value"),
1138             panel);
1139   }
1140
1141   @Override
1142   public void gapColour_actionPerformed(JPanel gap)
1143   {
1144     if (!useLegacyGap.isSelected())
1145     {
1146       JalviewColourChooser.showColourChooser(this,
1147               MessageManager.getString("label.select_gap_colour"),
1148               gap);
1149     }
1150   }
1151
1152   @Override
1153   public void hiddenColour_actionPerformed(JPanel hidden)
1154   {
1155     JalviewColourChooser.showColourChooser(this,
1156             MessageManager.getString("label.select_hidden_colour"),
1157             hidden);
1158   }
1159
1160   @Override
1161   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1162   {
1163     boolean enabled = useLegacyGap.isSelected();
1164     if (enabled)
1165     {
1166       gapColour.setBackground(
1167               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1168     }
1169     else
1170     {
1171       gapColour.setBackground(
1172               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1173     }
1174     gapColour.setEnabled(!enabled);
1175     gapLabel.setEnabled(!enabled);
1176   }
1177
1178   @Override
1179   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1180   {
1181     useLegacyGap.setSelected(false);
1182     useLegacyGaps_actionPerformed(null);
1183     showHiddenAtStart.setSelected(false);
1184     hiddenColour.setBackground(
1185             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1186   }
1187
1188   @Override
1189   protected void userIdWidth_actionPerformed()
1190   {
1191     try
1192     {
1193       String val = userIdWidth.getText().trim();
1194       if (val.length() > 0)
1195       {
1196         Integer iw = Integer.parseInt(val);
1197         if (iw.intValue() < 12)
1198         {
1199           throw new NumberFormatException();
1200         }
1201         userIdWidth.setText(iw.toString());
1202       }
1203     } catch (NumberFormatException x)
1204     {
1205       userIdWidth.setText("");
1206       JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1207               MessageManager
1208                       .getString("warn.user_defined_width_requirements"),
1209               MessageManager.getString("label.invalid_id_column_width"),
1210               JvOptionPane.WARNING_MESSAGE);
1211     }
1212   }
1213
1214   @Override
1215   protected void autoIdWidth_actionPerformed()
1216   {
1217     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1218     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1219   }
1220
1221   /**
1222    * Returns true if chimera path is to a valid executable, else show an error
1223    * dialog.
1224    */
1225   protected boolean validateChimeraPath()
1226   {
1227     if (chimeraPath.getText().trim().length() > 0)
1228     {
1229       File f = new File(chimeraPath.getText());
1230       if (!f.canExecute())
1231       {
1232         JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1233                 MessageManager.getString("label.invalid_chimera_path"),
1234                 MessageManager.getString("label.invalid_name"),
1235                 JvOptionPane.ERROR_MESSAGE);
1236         return false;
1237       }
1238     }
1239     return true;
1240   }
1241
1242   /**
1243    * If Chimera is selected, check it can be found on default or user-specified
1244    * path, if not show a warning/help dialog.
1245    */
1246   @Override
1247   protected void structureViewer_actionPerformed(String selectedItem)
1248   {
1249     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1250     {
1251       return;
1252     }
1253     boolean found = false;
1254
1255     /*
1256      * Try user-specified and standard paths for Chimera executable.
1257      */
1258     List<String> paths = StructureManager.getChimeraPaths();
1259     paths.add(0, chimeraPath.getText());
1260     for (String path : paths)
1261     {
1262       if (new File(path.trim()).canExecute())
1263       {
1264         found = true;
1265         break;
1266       }
1267     }
1268     if (!found)
1269     {
1270       String[] options = { "OK", "Help" };
1271       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
1272               JvSwingUtils.wrapTooltip(true,
1273                       MessageManager.getString("label.chimera_missing")),
1274               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1275               null, options, options[0]);
1276       if (showHelp == JvOptionPane.NO_OPTION)
1277       {
1278         try
1279         {
1280           Help.showHelpWindow(HelpId.StructureViewer);
1281         } catch (HelpSetException e)
1282         {
1283           e.printStackTrace();
1284         }
1285       }
1286     }
1287   }
1288
1289   public class OptionsParam
1290   {
1291     private String name;
1292
1293     private String code;
1294
1295     public OptionsParam(String name, String code)
1296     {
1297       this.name = name;
1298       this.code = code;
1299     }
1300
1301     public String getName()
1302     {
1303       return name;
1304     }
1305
1306     public void setName(String name)
1307     {
1308       this.name = name;
1309     }
1310
1311     public String getCode()
1312     {
1313       return code;
1314     }
1315
1316     public void setCode(String code)
1317     {
1318       this.code = code;
1319     }
1320
1321     @Override
1322     public String toString()
1323     {
1324       return name;
1325     }
1326
1327     @Override
1328     public boolean equals(Object that)
1329     {
1330       if (!(that instanceof OptionsParam))
1331       {
1332         return false;
1333       }
1334       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1335     }
1336
1337     @Override
1338     public int hashCode()
1339     {
1340       return name.hashCode() + code.hashCode();
1341     }
1342   }
1343
1344   protected class UrlListSelectionHandler implements ListSelectionListener
1345   {
1346
1347     @Override
1348     public void valueChanged(ListSelectionEvent e)
1349     {
1350       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1351
1352       int index = lsm.getMinSelectionIndex();
1353       if (index == -1)
1354       {
1355         // no selection, so disable delete/edit buttons
1356         editLink.setEnabled(false);
1357         deleteLink.setEnabled(false);
1358         return;
1359       }
1360       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1361
1362       // enable/disable edit and delete link buttons
1363       if (((UrlLinkTableModel) linkUrlTable.getModel())
1364               .isRowDeletable(modelIndex))
1365       {
1366         deleteLink.setEnabled(true);
1367       }
1368       else
1369       {
1370         deleteLink.setEnabled(false);
1371       }
1372
1373       if (((UrlLinkTableModel) linkUrlTable.getModel())
1374               .isRowEditable(modelIndex))
1375       {
1376         editLink.setEnabled(true);
1377       }
1378       else
1379       {
1380         editLink.setEnabled(false);
1381       }
1382     }
1383   }
1384 }