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.JColorChooser;
  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     wsPrefs = new WsPreferences();
 193     wsTab.add(wsPrefs, BorderLayout.CENTER);
 194     int width = 500, height = 450;
 195     new jalview.util.Platform();
 196     if (Platform.isAMac())
 197     {
 198       width = 570;
 199       height = 480;
 200     }
 201
 202     Desktop.addInternalFrame(frame,
 203             MessageManager.getString("label.preferences"), width, height);
 204     frame.setMinimumSize(new Dimension(width, height));
 205
 206     /*
 207      * Set Visual tab defaults
 208      */
 209     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 210     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 211     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 212     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 213
 214     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 215     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 216     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 217     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 218     showUnconserved
 219             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 220     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 221     showGroupConsensus
 222             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 223     showGroupConservation.setSelected(
 224             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 225     showConsensHistogram.setSelected(
 226             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 227     showConsensLogo
 228             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 229     showNpTooltip
 230             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 231     showDbRefTooltip
 232             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 233
 234     String[] fonts = java.awt.GraphicsEnvironment
 235             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 236     for (int i = 0; i < fonts.length; i++)
 237     {
 238       fontNameCB.addItem(fonts[i]);
 239     }
 240
 241     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 242     {
 243       fontSizeCB.addItem(i + "");
 244     }
 245
 246     fontStyleCB.addItem("plain");
 247     fontStyleCB.addItem("bold");
 248     fontStyleCB.addItem("italic");
 249
 250     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 251     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 252     fontStyleCB.setSelectedItem(
 253             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 254
 255     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 256     scaleProteinToCdna
 257             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 258
 259     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 260
 261     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 262
 263     gapSymbolCB.addItem("-");
 264     gapSymbolCB.addItem(".");
 265
 266     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 267
 268     sortby.addItem("No sort");
 269     sortby.addItem("Id");
 270     sortby.addItem("Pairwise Identity");
 271     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 272
 273     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 278     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 279             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 280                     SequenceAnnotationOrder.NONE.name()));
 281     sortAnnBy.setSelectedItem(savedSort.toString());
 282
 283     sortAutocalc.addItem("Autocalculated first");
 284     sortAutocalc.addItem("Autocalculated last");
 285     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 286     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 287             : sortAutocalc.getItemAt(1));
 288     startupCheckbox
 289             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 290     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 291             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 292                     + "/examples/exampleFile_2_3.jar"));
 293
 294     /*
 295      * Set Colours tab defaults
 296      */
 297     protColour.addItem(ResidueColourScheme.NONE);
 298     nucColour.addItem(ResidueColourScheme.NONE);
 299     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 300     {
 301       String name = cs.getSchemeName();
 302       protColour.addItem(name);
 303       nucColour.addItem(name);
 304     }
 305     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 306             ResidueColourScheme.NONE);
 307     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 308     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 309     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 310     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     minColour.setBackground(
 312             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 313     maxColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 315
 316     /*
 317      * Set overview panel defaults
 318      */
 319     gapColour.setBackground(
 320             Cache.getDefaultColour(GAP_COLOUR,
 321                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 322     hiddenColour.setBackground(
 323             Cache.getDefaultColour(HIDDEN_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 325     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 326     gapLabel.setEnabled(!useLegacyGap.isSelected());
 327     gapColour.setEnabled(!useLegacyGap.isSelected());
 328     showHiddenAtStart
 329             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 330
 331     /*
 332      * Set Structure tab defaults.
 333      */
 334     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 335     structFromPdb.setSelected(structSelected);
 336     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 337     useRnaView.setEnabled(structSelected);
 338     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 339     addSecondaryStructure.setEnabled(structSelected);
 340     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 341     addTempFactor.setEnabled(structSelected);
 342     structViewer.setSelectedItem(
 343             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 344     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 345     chimeraPath.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         validateChimeraPath();
 351       }
 352     });
 353
 354     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 355     {
 356       siftsMapping.setSelected(true);
 357     }
 358     else
 359     {
 360       nwMapping.setSelected(true);
 361     }
 362
 363     SiftsSettings
 364             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 365
 366     /*
 367      * Set Connections tab defaults
 368      */
 369
 370     // set up sorting
 371     linkUrlTable.setModel(dataModel);
 372     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 373             linkUrlTable.getModel());
 374     linkUrlTable.setRowSorter(sorter);
 375     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 376
 377     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 378     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(
 383             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 384
 385     sorter.setSortKeys(sortKeys);
 386     sorter.sort();
 387
 388     // set up filtering
 389     ActionListener onReset;
 390     onReset = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         filterTB.setText("");
 396         sorter.setRowFilter(RowFilter.regexFilter(""));
 397       }
 398
 399     };
 400     doReset.addActionListener(onReset);
 401
 402     // filter to display only custom urls
 403     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 404     {
 405       @Override
 406       public boolean include(
 407               Entry<? extends TableModel, ? extends Object> entry)
 408       {
 409         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 410       }
 411     };
 412
 413     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 414             linkUrlTable.getModel());
 415     customSorter.setRowFilter(customUrlFilter);
 416
 417     ActionListener onCustomOnly;
 418     onCustomOnly = new ActionListener()
 419     {
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         filterTB.setText("");
 424         sorter.setRowFilter(customUrlFilter);
 425       }
 426     };
 427     userOnly.addActionListener(onCustomOnly);
 428
 429     filterTB.getDocument().addDocumentListener(new DocumentListener()
 430     {
 431       String caseInsensitiveFlag = "(?i)";
 432
 433       @Override
 434       public void changedUpdate(DocumentEvent e)
 435       {
 436         sorter.setRowFilter(RowFilter
 437                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 438       }
 439
 440       @Override
 441       public void removeUpdate(DocumentEvent e)
 442       {
 443         sorter.setRowFilter(RowFilter
 444                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 445       }
 446
 447       @Override
 448       public void insertUpdate(DocumentEvent e)
 449       {
 450         sorter.setRowFilter(RowFilter
 451                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 452       }
 453     });
 454
 455     // set up list selection functionality
 456     linkUrlTable.getSelectionModel()
 457             .addListSelectionListener(new UrlListSelectionHandler());
 458
 459     // set up radio buttons
 460     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 461             .getPrimaryColumn();
 462     String onClickName = linkUrlTable.getColumnName(onClickCol);
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellRenderer(new RadioButtonRenderer());
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellEditor(new RadioButtonEditor());
 467
 468     // get boolean columns and resize those to min possible
 469     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 470     {
 471       if (linkUrlTable.getModel().getColumnClass(column)
 472               .equals(Boolean.class))
 473       {
 474         TableColumn tableColumn = linkUrlTable.getColumnModel()
 475                 .getColumn(column);
 476         int preferredWidth = tableColumn.getMinWidth();
 477
 478         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 479                 column);
 480         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 481         int cwidth = c.getPreferredSize().width
 482                 + linkUrlTable.getIntercellSpacing().width;
 483         preferredWidth = Math.max(preferredWidth, cwidth);
 484
 485         tableColumn.setPreferredWidth(preferredWidth);
 486       }
 487     }
 488
 489     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 490     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 491     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 492     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 493
 494     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 495
 496     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 497     // note antisense here: default is true
 498     questionnaire
 499             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 500     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 501
 502     /*
 503      * Set Output tab defaults
 504      */
 505     epsRendering.addItem(promptEachTimeOpt);
 506     epsRendering.addItem(lineArtOpt);
 507     epsRendering.addItem(textOpt);
 508     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 509             "Prompt each time");
 510     if (defaultEPS.equalsIgnoreCase("Text"))
 511     {
 512       epsRendering.setSelectedItem(textOpt);
 513     }
 514     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 515     {
 516       epsRendering.setSelectedItem(lineArtOpt);
 517     }
 518     else
 519     {
 520       epsRendering.setSelectedItem(promptEachTimeOpt);
 521     }
 522     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 523     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 524     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 525     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 526     userIdWidth.setText(wi == null ? "" : wi.toString());
 527     // TODO: refactor to use common enum via FormatAdapter and allow extension
 528     // for new flat file formats
 529     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 530     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 531     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 532     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 533     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 534     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 535     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 536     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 537     embbedBioJSON
 538             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 539
 540     /*
 541      * Set Editing tab defaults
 542      */
 543     autoCalculateConsCheck
 544             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 545     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 546     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 547
 548     annotations_actionPerformed(null); // update the display of the annotation
 549                                        // settings
 550
 551
 552     /*
 553      * Set Backups tab defaults
 554      */
 555     enableBackupFiles
 556             .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
 557     suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
 558             ".v" + BackupFiles.NUM_PLACEHOLDER));
 559     suffixDigitsSpinner
 560             .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
 561     suffixReverse.setSelected(
 562             Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
 563     backupfilesKeepAll
 564             .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
 565     backupfilesRollMaxSpinner
 566             .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4));
 567     backupfilesConfirmDelete.setSelected(
 568             Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
 569     setComboIntStringKey(backupfilesPresetsCombo, Cache.getDefault(BackupFiles.NS+"_PRESET", 0));
 570     backupsOptionsSetEnabled(enableBackupFiles.isSelected());
 571
 572     updateBackupFilesExampleLabel();
 573     /*
 574     suffixPanel.setPreferredSize(
 575             new Dimension(width, suffixPanel.getHeight()));
 576     keepfilesPanel.setPreferredSize(
 577             new Dimension(width, keepfilesPanel.getHeight()));
 578     exampleFilesPanel.setPreferredSize(
 579             new Dimension(width, exampleFilesPanel.getHeight()));
 580             */
 581
 582   }
 583
 584   /**
 585    * Save user selections on the Preferences tabs to the Cache and write out to
 586    * file.
 587    *
 588    * @param e
 589    */
 590   @Override
 591   public void ok_actionPerformed(ActionEvent e)
 592   {
 593     if (!validateSettings())
 594     {
 595       return;
 596     }
 597
 598     /*
 599      * Save Visual settings
 600      */
 601     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 602             Boolean.toString(seqLimit.isSelected()));
 603     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 604             Boolean.toString(rightAlign.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 606             Boolean.toString(fullScreen.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 608             Boolean.toString(openoverv.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 610             Boolean.toString(annotations.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 612             Boolean.toString(conservation.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 614             Boolean.toString(quality.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 616             Boolean.toString(identity.isSelected()));
 617
 618     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 619             gapSymbolCB.getSelectedItem().toString());
 620
 621     Cache.applicationProperties.setProperty("FONT_NAME",
 622             fontNameCB.getSelectedItem().toString());
 623     Cache.applicationProperties.setProperty("FONT_STYLE",
 624             fontStyleCB.getSelectedItem().toString());
 625     Cache.applicationProperties.setProperty("FONT_SIZE",
 626             fontSizeCB.getSelectedItem().toString());
 627
 628     Cache.applicationProperties.setProperty("ID_ITALICS",
 629             Boolean.toString(idItalics.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 631             Boolean.toString(showUnconserved.isSelected()));
 632     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 633             Boolean.toString(showOccupancy.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 635             Boolean.toString(showGroupConsensus.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 637             Boolean.toString(showGroupConservation.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 639             Boolean.toString(showConsensHistogram.isSelected()));
 640     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 641             Boolean.toString(showConsensLogo.isSelected()));
 642     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 643             Boolean.toString(smoothFont.isSelected()));
 644     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 645             Boolean.toString(scaleProteinToCdna.isSelected()));
 646     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 647             Boolean.toString(showNpTooltip.isSelected()));
 648     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 649             Boolean.toString(showDbRefTooltip.isSelected()));
 650
 651     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 652             Boolean.toString(wrap.isSelected()));
 653
 654     Cache.applicationProperties.setProperty("STARTUP_FILE",
 655             startupFileTextfield.getText());
 656     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 657             Boolean.toString(startupCheckbox.isSelected()));
 658
 659     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 660             sortby.getSelectedItem().toString());
 661
 662     // convert description of sort order to enum name for save
 663     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 664             .forDescription(sortAnnBy.getSelectedItem().toString());
 665     if (annSortOrder != null)
 666     {
 667       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 668               annSortOrder.name());
 669     }
 670
 671     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 672     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 673             Boolean.valueOf(showAutocalcFirst).toString());
 674
 675     /*
 676      * Save Colours settings
 677      */
 678     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 679             protColour.getSelectedItem().toString());
 680     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 681             nucColour.getSelectedItem().toString());
 682     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 683             minColour.getBackground());
 684     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 685             maxColour.getBackground());
 686
 687     /*
 688      * Save Overview settings
 689      */
 690     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 691     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 692     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 693             Boolean.toString(useLegacyGap.isSelected()));
 694     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 695             Boolean.toString(showHiddenAtStart.isSelected()));
 696
 697     /*
 698      * Save Structure settings
 699      */
 700     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 701             Boolean.toString(addTempFactor.isSelected()));
 702     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 703             Boolean.toString(addSecondaryStructure.isSelected()));
 704     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 705             Boolean.toString(useRnaView.isSelected()));
 706     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 707             Boolean.toString(structFromPdb.isSelected()));
 708     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 709             structViewer.getSelectedItem().toString());
 710     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 711     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 712             Boolean.toString(siftsMapping.isSelected()));
 713     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 714
 715     /*
 716      * Save Output settings
 717      */
 718     Cache.applicationProperties.setProperty("EPS_RENDERING",
 719             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 720
 721     /*
 722      * Save Connections settings
 723      */
 724     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 725
 726     jalview.util.BrowserLauncher.resetBrowser();
 727
 728     // save user-defined and selected links
 729     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 730     if (menuLinks.isEmpty())
 731     {
 732       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 733     }
 734     else
 735     {
 736       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 737               menuLinks.toString());
 738     }
 739
 740     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 741     if (nonMenuLinks.isEmpty())
 742     {
 743       Cache.applicationProperties.remove("STORED_LINKS");
 744     }
 745     else
 746     {
 747       Cache.applicationProperties.setProperty("STORED_LINKS",
 748               nonMenuLinks.toString());
 749     }
 750
 751     Cache.applicationProperties.setProperty("DEFAULT_URL",
 752             sequenceUrlLinks.getPrimaryUrlId());
 753
 754     Cache.applicationProperties.setProperty("USE_PROXY",
 755             Boolean.toString(useProxy.isSelected()));
 756
 757     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 758
 759     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 760
 761     if (useProxy.isSelected())
 762     {
 763       System.setProperty("http.proxyHost", proxyServerTB.getText());
 764       System.setProperty("http.proxyPort", proxyPortTB.getText());
 765     }
 766     else
 767     {
 768       System.setProperty("http.proxyHost", "");
 769       System.setProperty("http.proxyPort", "");
 770     }
 771     Cache.setProperty("VERSION_CHECK",
 772             Boolean.toString(versioncheck.isSelected()));
 773     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 774     {
 775       // default is false - we only set this if the user has actively agreed
 776       Cache.setProperty("USAGESTATS",
 777               Boolean.toString(usagestats.isSelected()));
 778     }
 779     if (!questionnaire.isSelected())
 780     {
 781       Cache.setProperty("NOQUESTIONNAIRES", "true");
 782     }
 783     else
 784     {
 785       // special - made easy to edit a property file to disable questionnaires
 786       // by just adding the given line
 787       Cache.removeProperty("NOQUESTIONNAIRES");
 788     }
 789
 790     /*
 791      * Save Output settings
 792      */
 793     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 794             Boolean.toString(blcjv.isSelected()));
 795     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 796             Boolean.toString(clustaljv.isSelected()));
 797     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 798             Boolean.toString(fastajv.isSelected()));
 799     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 800             Boolean.toString(msfjv.isSelected()));
 801     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 802             Boolean.toString(pfamjv.isSelected()));
 803     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 804             Boolean.toString(pileupjv.isSelected()));
 805     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 806             Boolean.toString(pirjv.isSelected()));
 807     Cache.applicationProperties.setProperty("PIR_MODELLER",
 808             Boolean.toString(modellerOutput.isSelected()));
 809     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 810             Boolean.toString(embbedBioJSON.isSelected()));
 811     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 812
 813     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 814             Boolean.toString(autoIdWidth.isSelected()));
 815     userIdWidth_actionPerformed();
 816     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 817             userIdWidth.getText());
 818
 819     /*
 820      * Save Editing settings
 821      */
 822     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 823             Boolean.toString(autoCalculateConsCheck.isSelected()));
 824     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 825             Boolean.toString(sortByTree.isSelected()));
 826     Cache.applicationProperties.setProperty("PAD_GAPS",
 827             Boolean.toString(padGaps.isSelected()));
 828
 829     wsPrefs.updateAndRefreshWsMenuConfig(false);
 830
 831     /*
 832      * Save Backups settings
 833      */
 834     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 835             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 836     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 837             Boolean.toString(enableBackupFiles.isSelected()));
 838     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 839             Boolean.toString(backupfilesKeepAll.isSelected()));
 840     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 841             Boolean.toString(suffixReverse.isSelected()));
 842     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 843             suffixTemplate.getText());
 844     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 845             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 846     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 847             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 848     Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
 849             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 850
 851     Cache.saveProperties();
 852     Desktop.instance.doConfigureStructurePrefs();
 853     try
 854     {
 855       frame.setClosed(true);
 856     } catch (Exception ex)
 857     {
 858     }
 859   }
 860
 861   /**
 862    * Do any necessary validation before saving settings. Return focus to the
 863    * first tab which fails validation.
 864    *
 865    * @return
 866    */
 867   private boolean validateSettings()
 868   {
 869     if (!validateStructure())
 870     {
 871       structureTab.requestFocusInWindow();
 872       return false;
 873     }
 874     return true;
 875   }
 876
 877   @Override
 878   protected boolean validateStructure()
 879   {
 880     return validateChimeraPath();
 881
 882   }
 883
 884   /**
 885    * DOCUMENT ME!
 886    */
 887   @Override
 888   public void startupFileTextfield_mouseClicked()
 889   {
 890     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 891     JalviewFileChooser chooser = JalviewFileChooser
 892             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 893     chooser.setFileView(new JalviewFileView());
 894     chooser.setDialogTitle(
 895             MessageManager.getString("label.select_startup_file"));
 896
 897     int value = chooser.showOpenDialog(this);
 898
 899     if (value == JalviewFileChooser.APPROVE_OPTION)
 900     {
 901       FileFormatI format = chooser.getSelectedFormat();
 902       if (format != null)
 903       {
 904         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 905                 format.getName());
 906       }
 907       startupFileTextfield
 908               .setText(chooser.getSelectedFile().getAbsolutePath());
 909     }
 910   }
 911
 912   /**
 913    * DOCUMENT ME!
 914    *
 915    * @param e
 916    *          DOCUMENT ME!
 917    */
 918   @Override
 919   public void cancel_actionPerformed(ActionEvent e)
 920   {
 921     try
 922     {
 923       wsPrefs.updateWsMenuConfig(true);
 924       wsPrefs.refreshWs_actionPerformed(e);
 925       frame.setClosed(true);
 926     } catch (Exception ex)
 927     {
 928     }
 929   }
 930
 931   /**
 932    * DOCUMENT ME!
 933    *
 934    * @param e
 935    *          DOCUMENT ME!
 936    */
 937   @Override
 938   public void annotations_actionPerformed(ActionEvent e)
 939   {
 940     conservation.setEnabled(annotations.isSelected());
 941     quality.setEnabled(annotations.isSelected());
 942     identity.setEnabled(annotations.isSelected());
 943     showOccupancy.setEnabled(annotations.isSelected());
 944     showGroupConsensus.setEnabled(annotations.isSelected());
 945     showGroupConservation.setEnabled(annotations.isSelected());
 946     showConsensHistogram.setEnabled(annotations.isSelected()
 947             && (identity.isSelected() || showGroupConsensus.isSelected()));
 948     showConsensLogo.setEnabled(annotations.isSelected()
 949             && (identity.isSelected() || showGroupConsensus.isSelected()));
 950   }
 951
 952   @Override
 953   public void newLink_actionPerformed(ActionEvent e)
 954   {
 955     GSequenceLink link = new GSequenceLink();
 956     boolean valid = false;
 957     while (!valid)
 958     {
 959       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 960               MessageManager.getString("label.new_sequence_url_link"),
 961               JvOptionPane.OK_CANCEL_OPTION, -1,
 962               null) == JvOptionPane.OK_OPTION)
 963       {
 964         if (link.checkValid())
 965         {
 966           if (((UrlLinkTableModel) linkUrlTable.getModel())
 967                   .isUniqueName(link.getName()))
 968           {
 969             ((UrlLinkTableModel) linkUrlTable.getModel())
 970                     .insertRow(link.getName(), link.getURL());
 971             valid = true;
 972           }
 973           else
 974           {
 975             link.notifyDuplicate();
 976             continue;
 977           }
 978         }
 979       }
 980       else
 981       {
 982         break;
 983       }
 984     }
 985   }
 986
 987   @Override
 988   public void editLink_actionPerformed(ActionEvent e)
 989   {
 990     GSequenceLink link = new GSequenceLink();
 991
 992     int index = linkUrlTable.getSelectedRow();
 993     if (index == -1)
 994     {
 995       // button no longer enabled if row is not selected
 996       Cache.log.debug("Edit with no row selected in linkUrlTable");
 997       return;
 998     }
 999
1000     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1001             .getNameColumn();
1002     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1003             .getUrlColumn();
1004     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1005     link.setName(oldName);
1006     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1007
1008     boolean valid = false;
1009     while (!valid)
1010     {
1011       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1012               MessageManager.getString("label.edit_sequence_url_link"),
1013               JvOptionPane.OK_CANCEL_OPTION, -1,
1014               null) == JvOptionPane.OK_OPTION)
1015       {
1016         if (link.checkValid())
1017         {
1018           if ((oldName.equals(link.getName()))
1019                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1020                           .isUniqueName(link.getName())))
1021           {
1022             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1023             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1024             valid = true;
1025           }
1026           else
1027           {
1028             link.notifyDuplicate();
1029             continue;
1030           }
1031         }
1032       }
1033       else
1034       {
1035         break;
1036       }
1037     }
1038   }
1039
1040   @Override
1041   public void deleteLink_actionPerformed(ActionEvent e)
1042   {
1043     int index = linkUrlTable.getSelectedRow();
1044     int modelIndex = -1;
1045     if (index == -1)
1046     {
1047       // button no longer enabled if row is not selected
1048       Cache.log.debug("Delete with no row selected in linkUrlTable");
1049       return;
1050     }
1051     else
1052     {
1053       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1054     }
1055
1056     // make sure we use the model index to delete, and not the table index
1057     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1058   }
1059
1060   @Override
1061   public void defaultBrowser_mouseClicked(MouseEvent e)
1062   {
1063     JFileChooser chooser = new JFileChooser(".");
1064     chooser.setDialogTitle(
1065             MessageManager.getString("label.select_default_browser"));
1066
1067     int value = chooser.showOpenDialog(this);
1068
1069     if (value == JFileChooser.APPROVE_OPTION)
1070     {
1071       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1072     }
1073
1074   }
1075
1076   /*
1077    * (non-Javadoc)
1078    *
1079    * @see
1080    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1081    * .ActionEvent)
1082    */
1083   @Override
1084   protected void showunconserved_actionPerformed(ActionEvent e)
1085   {
1086     // TODO Auto-generated method stub
1087     super.showunconserved_actionPerformed(e);
1088   }
1089
1090   public static List<String> getGroupURLLinks()
1091   {
1092     return groupURLLinks;
1093   }
1094
1095   @Override
1096   public void minColour_actionPerformed(JPanel panel)
1097   {
1098     Color col = JColorChooser.showDialog(this,
1099             MessageManager.getString("label.select_colour_minimum_value"),
1100             minColour.getBackground());
1101     if (col != null)
1102     {
1103       panel.setBackground(col);
1104     }
1105     panel.repaint();
1106   }
1107
1108   @Override
1109   public void maxColour_actionPerformed(JPanel panel)
1110   {
1111     Color col = JColorChooser.showDialog(this,
1112             MessageManager.getString("label.select_colour_maximum_value"),
1113             maxColour.getBackground());
1114     if (col != null)
1115     {
1116       panel.setBackground(col);
1117     }
1118     panel.repaint();
1119   }
1120
1121   @Override
1122   public void gapColour_actionPerformed(JPanel gap)
1123   {
1124     if (!useLegacyGap.isSelected())
1125     {
1126       Color col = JColorChooser.showDialog(this,
1127               MessageManager.getString("label.select_gap_colour"),
1128               gapColour.getBackground());
1129       if (col != null)
1130       {
1131         gap.setBackground(col);
1132       }
1133       gap.repaint();
1134     }
1135   }
1136
1137   @Override
1138   public void hiddenColour_actionPerformed(JPanel hidden)
1139   {
1140     Color col = JColorChooser.showDialog(this,
1141             MessageManager.getString("label.select_hidden_colour"),
1142             hiddenColour.getBackground());
1143     if (col != null)
1144     {
1145       hidden.setBackground(col);
1146     }
1147     hidden.repaint();
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(true);
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       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1196               MessageManager
1197                       .getString("warn.user_defined_width_requirements"),
1198               MessageManager.getString("label.invalid_id_column_width"),
1199               JvOptionPane.WARNING_MESSAGE);
1200       userIdWidth.setText("");
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 }