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