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.BackupFilesPresetEntry;
  29 import jalview.io.FileFormatI;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32 import jalview.jbgui.GPreferences;
  33 import jalview.jbgui.GSequenceLink;
  34 import jalview.schemes.ColourSchemeI;
  35 import jalview.schemes.ColourSchemes;
  36 import jalview.schemes.ResidueColourScheme;
  37 import jalview.urls.UrlLinkTableModel;
  38 import jalview.urls.api.UrlProviderFactoryI;
  39 import jalview.urls.api.UrlProviderI;
  40 import jalview.urls.desktop.DesktopUrlProviderFactory;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JColorChooser;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 109
 110   public static final String PYMOL_PATH = "PYMOL_PATH";
 111
 112   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 113
 114   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 115
 116   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 117
 118   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 119
 120   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 121
 122   public static final String GAP_COLOUR = "GAP_COLOUR";
 123
 124   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 125
 126   private static final int MIN_FONT_SIZE = 1;
 127
 128   private static final int MAX_FONT_SIZE = 30;
 129
 130   /**
 131    * Holds name and link separated with | character. Sequence ID must be
 132    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 133    */
 134   public static UrlProviderI sequenceUrlLinks;
 135
 136   public static UrlLinkTableModel dataModel;
 137
 138   /**
 139    * Holds name and link separated with | character. Sequence IDS and Sequences
 140    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 141    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 142    * for first and second token specified after a pipe character at end |,|.
 143    * (TODO: proper escape for using | to separate ids or sequences
 144    */
 145
 146   public static List<String> groupURLLinks;
 147   static
 148   {
 149     // get links selected to be in the menu (SEQUENCE_LINKS)
 150     // and links entered by the user but not selected (STORED_LINKS)
 151     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 152     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 153     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 154             UrlConstants.DEFAULT_LABEL);
 155
 156     // if both links lists are empty, add the DEFAULT_URL link
 157     // otherwise we assume the default link is in one of the lists
 158     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 159     {
 160       inMenuString = UrlConstants.DEFAULT_STRING;
 161     }
 162     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 163             inMenuString, notInMenuString);
 164     sequenceUrlLinks = factory.createUrlProvider();
 165     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 166
 167     /**
 168      * TODO: reformulate groupURL encoding so two or more can be stored in the
 169      * .properties file as '|' separated strings
 170      */
 171
 172     groupURLLinks = new ArrayList<>();
 173   }
 174
 175   JInternalFrame frame;
 176
 177   private WsPreferences wsPrefs;
 178
 179   private OptionsParam promptEachTimeOpt = new OptionsParam(
 180           MessageManager.getString("label.prompt_each_time"),
 181           "Prompt each time");
 182
 183   private OptionsParam lineArtOpt = new OptionsParam(
 184           MessageManager.getString("label.lineart"), "Lineart");
 185
 186   private OptionsParam textOpt = new OptionsParam(
 187           MessageManager.getString("action.text"), "Text");
 188
 189   /**
 190    * Creates a new Preferences object.
 191    */
 192   public Preferences()
 193   {
 194     super();
 195     frame = new JInternalFrame();
 196     frame.setContentPane(this);
 197     wsPrefs = new WsPreferences();
 198     wsTab.add(wsPrefs, BorderLayout.CENTER);
 199     int width = 500, height = 450;
 200     new jalview.util.Platform();
 201     if (Platform.isAMac())
 202     {
 203       width = 570;
 204       height = 480;
 205     }
 206
 207     Desktop.addInternalFrame(frame,
 208             MessageManager.getString("label.preferences"), width, height);
 209     frame.setMinimumSize(new Dimension(width, height));
 210
 211     /*
 212      * Set Visual tab defaults
 213      */
 214     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 215     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 216     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 217     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 218
 219     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 220     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 221     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 222     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 223     showUnconserved
 224             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 225     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 226     showGroupConsensus
 227             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 228     showGroupConservation.setSelected(
 229             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 230     showConsensHistogram.setSelected(
 231             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 232     showConsensLogo
 233             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 234     showNpTooltip
 235             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 236     showDbRefTooltip
 237             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 238
 239     String[] fonts = java.awt.GraphicsEnvironment
 240             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 241     for (int i = 0; i < fonts.length; i++)
 242     {
 243       fontNameCB.addItem(fonts[i]);
 244     }
 245
 246     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 247     {
 248       fontSizeCB.addItem(i + "");
 249     }
 250
 251     fontStyleCB.addItem("plain");
 252     fontStyleCB.addItem("bold");
 253     fontStyleCB.addItem("italic");
 254
 255     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 256     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 257     fontStyleCB.setSelectedItem(
 258             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 259
 260     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 261     scaleProteinToCdna
 262             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 263
 264     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 265
 266     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 267
 268     gapSymbolCB.addItem("-");
 269     gapSymbolCB.addItem(".");
 270
 271     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 272
 273     sortby.addItem("No sort");
 274     sortby.addItem("Id");
 275     sortby.addItem("Pairwise Identity");
 276     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 277
 278     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 279     sortAnnBy
 280             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 281     sortAnnBy
 282             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 283     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 284             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 285                     SequenceAnnotationOrder.NONE.name()));
 286     sortAnnBy.setSelectedItem(savedSort.toString());
 287
 288     sortAutocalc.addItem("Autocalculated first");
 289     sortAutocalc.addItem("Autocalculated last");
 290     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 291     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 292             : sortAutocalc.getItemAt(1));
 293     startupCheckbox
 294             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 295     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 296             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 297                     + "/examples/exampleFile_2_3.jar"));
 298
 299     /*
 300      * Set Colours tab defaults
 301      */
 302     protColour.addItem(ResidueColourScheme.NONE);
 303     nucColour.addItem(ResidueColourScheme.NONE);
 304     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 305     {
 306       String name = cs.getSchemeName();
 307       protColour.addItem(name);
 308       nucColour.addItem(name);
 309     }
 310     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 311             ResidueColourScheme.NONE);
 312     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 313     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 314     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 315     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 316     minColour.setBackground(
 317             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 318     maxColour.setBackground(
 319             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 320
 321     /*
 322      * Set overview panel defaults
 323      */
 324     gapColour.setBackground(
 325             Cache.getDefaultColour(GAP_COLOUR,
 326                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 327     hiddenColour.setBackground(
 328             Cache.getDefaultColour(HIDDEN_COLOUR,
 329                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 330     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 331     gapLabel.setEnabled(!useLegacyGap.isSelected());
 332     gapColour.setEnabled(!useLegacyGap.isSelected());
 333     showHiddenAtStart
 334             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 335
 336     /*
 337      * Set Structure tab defaults.
 338      */
 339     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 340     structFromPdb.setSelected(structSelected);
 341     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 342     useRnaView.setEnabled(structSelected);
 343     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 344     addSecondaryStructure.setEnabled(structSelected);
 345     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 346     addTempFactor.setEnabled(structSelected);
 347     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 348     structViewer.setSelectedItem(viewerType);
 349     boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name());
 350     if (viewerType.equals(ViewerType.JMOL.name()))
 351     {
 352       structureViewerPath.setText("");
 353     }
 354     else
 355     {
 356       structureViewerPath.setText(Cache
 357               .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
 358     }
 359     structureViewerPath.addActionListener(new ActionListener()
 360     {
 361       @Override
 362       public void actionPerformed(ActionEvent e)
 363       {
 364         if (validateChimeraPath())
 365         {
 366           Cache.setProperty(structViewer.getSelectedItem()
 367                   .equals(ViewerType.CHIMERAX.name())
 368                   ? CHIMERAX_PATH
 369                   : CHIMERA_PATH, structureViewerPath.getText());
 370         }
 371       }
 372     });
 373
 374     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 375     {
 376       siftsMapping.setSelected(true);
 377     }
 378     else
 379     {
 380       nwMapping.setSelected(true);
 381     }
 382
 383     SiftsSettings
 384             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 385
 386     /*
 387      * Set Connections tab defaults
 388      */
 389
 390     // set up sorting
 391     linkUrlTable.setModel(dataModel);
 392     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 393             linkUrlTable.getModel());
 394     linkUrlTable.setRowSorter(sorter);
 395     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 396
 397     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 398     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 399             SortOrder.DESCENDING));
 400     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 401             SortOrder.DESCENDING));
 402     sortKeys.add(
 403             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 404
 405     sorter.setSortKeys(sortKeys);
 406     sorter.sort();
 407
 408     // set up filtering
 409     ActionListener onReset;
 410     onReset = new ActionListener()
 411     {
 412       @Override
 413       public void actionPerformed(ActionEvent e)
 414       {
 415         filterTB.setText("");
 416         sorter.setRowFilter(RowFilter.regexFilter(""));
 417       }
 418
 419     };
 420     doReset.addActionListener(onReset);
 421
 422     // filter to display only custom urls
 423     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 424     {
 425       @Override
 426       public boolean include(
 427               Entry<? extends TableModel, ? extends Object> entry)
 428       {
 429         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 430       }
 431     };
 432
 433     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 434             linkUrlTable.getModel());
 435     customSorter.setRowFilter(customUrlFilter);
 436
 437     ActionListener onCustomOnly;
 438     onCustomOnly = new ActionListener()
 439     {
 440       @Override
 441       public void actionPerformed(ActionEvent e)
 442       {
 443         filterTB.setText("");
 444         sorter.setRowFilter(customUrlFilter);
 445       }
 446     };
 447     userOnly.addActionListener(onCustomOnly);
 448
 449     filterTB.getDocument().addDocumentListener(new DocumentListener()
 450     {
 451       String caseInsensitiveFlag = "(?i)";
 452
 453       @Override
 454       public void changedUpdate(DocumentEvent e)
 455       {
 456         sorter.setRowFilter(RowFilter
 457                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 458       }
 459
 460       @Override
 461       public void removeUpdate(DocumentEvent e)
 462       {
 463         sorter.setRowFilter(RowFilter
 464                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 465       }
 466
 467       @Override
 468       public void insertUpdate(DocumentEvent e)
 469       {
 470         sorter.setRowFilter(RowFilter
 471                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 472       }
 473     });
 474
 475     // set up list selection functionality
 476     linkUrlTable.getSelectionModel()
 477             .addListSelectionListener(new UrlListSelectionHandler());
 478
 479     // set up radio buttons
 480     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 481             .getPrimaryColumn();
 482     String onClickName = linkUrlTable.getColumnName(onClickCol);
 483     linkUrlTable.getColumn(onClickName)
 484             .setCellRenderer(new RadioButtonRenderer());
 485     linkUrlTable.getColumn(onClickName)
 486             .setCellEditor(new RadioButtonEditor());
 487
 488     // get boolean columns and resize those to min possible
 489     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 490     {
 491       if (linkUrlTable.getModel().getColumnClass(column)
 492               .equals(Boolean.class))
 493       {
 494         TableColumn tableColumn = linkUrlTable.getColumnModel()
 495                 .getColumn(column);
 496         int preferredWidth = tableColumn.getMinWidth();
 497
 498         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 499                 column);
 500         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 501         int cwidth = c.getPreferredSize().width
 502                 + linkUrlTable.getIntercellSpacing().width;
 503         preferredWidth = Math.max(preferredWidth, cwidth);
 504
 505         tableColumn.setPreferredWidth(preferredWidth);
 506       }
 507     }
 508
 509     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 510     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 511     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 512     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 513
 514     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 515
 516     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 517     // note antisense here: default is true
 518     questionnaire
 519             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 520     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 521
 522     /*
 523      * Set Output tab defaults
 524      */
 525     epsRendering.addItem(promptEachTimeOpt);
 526     epsRendering.addItem(lineArtOpt);
 527     epsRendering.addItem(textOpt);
 528     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 529             "Prompt each time");
 530     if (defaultEPS.equalsIgnoreCase("Text"))
 531     {
 532       epsRendering.setSelectedItem(textOpt);
 533     }
 534     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 535     {
 536       epsRendering.setSelectedItem(lineArtOpt);
 537     }
 538     else
 539     {
 540       epsRendering.setSelectedItem(promptEachTimeOpt);
 541     }
 542     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 543     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 544     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 545     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 546     userIdWidth.setText(wi == null ? "" : wi.toString());
 547     // TODO: refactor to use common enum via FormatAdapter and allow extension
 548     // for new flat file formats
 549     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 550     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 551     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 552     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 553     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 554     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 555     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 556     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 557     embbedBioJSON
 558             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 559
 560     /*
 561      * Set Editing tab defaults
 562      */
 563     autoCalculateConsCheck
 564             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 565     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 566     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 567
 568     annotations_actionPerformed(null); // update the display of the annotation
 569                                        // settings
 570
 571
 572     /*
 573      * Set Backups tab defaults
 574      */
 575     loadLastSavedBackupsOptions();
 576   }
 577
 578   /**
 579    * Save user selections on the Preferences tabs to the Cache and write out to
 580    * file.
 581    *
 582    * @param e
 583    */
 584   @Override
 585   public void ok_actionPerformed(ActionEvent e)
 586   {
 587     if (!validateSettings())
 588     {
 589       return;
 590     }
 591
 592     /*
 593      * Save Visual settings
 594      */
 595     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 596             Boolean.toString(seqLimit.isSelected()));
 597     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 598             Boolean.toString(rightAlign.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 600             Boolean.toString(fullScreen.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 602             Boolean.toString(openoverv.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 604             Boolean.toString(annotations.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 606             Boolean.toString(conservation.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 608             Boolean.toString(quality.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 610             Boolean.toString(identity.isSelected()));
 611
 612     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 613             gapSymbolCB.getSelectedItem().toString());
 614
 615     Cache.applicationProperties.setProperty("FONT_NAME",
 616             fontNameCB.getSelectedItem().toString());
 617     Cache.applicationProperties.setProperty("FONT_STYLE",
 618             fontStyleCB.getSelectedItem().toString());
 619     Cache.applicationProperties.setProperty("FONT_SIZE",
 620             fontSizeCB.getSelectedItem().toString());
 621
 622     Cache.applicationProperties.setProperty("ID_ITALICS",
 623             Boolean.toString(idItalics.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 625             Boolean.toString(showUnconserved.isSelected()));
 626     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 627             Boolean.toString(showOccupancy.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 629             Boolean.toString(showGroupConsensus.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 631             Boolean.toString(showGroupConservation.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 633             Boolean.toString(showConsensHistogram.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 635             Boolean.toString(showConsensLogo.isSelected()));
 636     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 637             Boolean.toString(smoothFont.isSelected()));
 638     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 639             Boolean.toString(scaleProteinToCdna.isSelected()));
 640     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 641             Boolean.toString(showNpTooltip.isSelected()));
 642     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 643             Boolean.toString(showDbRefTooltip.isSelected()));
 644
 645     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 646             Boolean.toString(wrap.isSelected()));
 647
 648     Cache.applicationProperties.setProperty("STARTUP_FILE",
 649             startupFileTextfield.getText());
 650     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 651             Boolean.toString(startupCheckbox.isSelected()));
 652
 653     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 654             sortby.getSelectedItem().toString());
 655
 656     // convert description of sort order to enum name for save
 657     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 658             .forDescription(sortAnnBy.getSelectedItem().toString());
 659     if (annSortOrder != null)
 660     {
 661       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 662               annSortOrder.name());
 663     }
 664
 665     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 666     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 667             Boolean.valueOf(showAutocalcFirst).toString());
 668
 669     /*
 670      * Save Colours settings
 671      */
 672     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 673             protColour.getSelectedItem().toString());
 674     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 675             nucColour.getSelectedItem().toString());
 676     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 677             minColour.getBackground());
 678     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 679             maxColour.getBackground());
 680
 681     /*
 682      * Save Overview settings
 683      */
 684     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 685     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 686     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 687             Boolean.toString(useLegacyGap.isSelected()));
 688     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 689             Boolean.toString(showHiddenAtStart.isSelected()));
 690
 691     /*
 692      * Save Structure settings
 693      */
 694     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 695             Boolean.toString(addTempFactor.isSelected()));
 696     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 697             Boolean.toString(addSecondaryStructure.isSelected()));
 698     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 699             Boolean.toString(useRnaView.isSelected()));
 700     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 701             Boolean.toString(structFromPdb.isSelected()));
 702     String viewer = structViewer.getSelectedItem().toString();
 703     String viewerPath = structureViewerPath.getText();
 704     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 705             viewer);
 706     if (viewer.equals(ViewerType.CHIMERA.name()))
 707     {
 708       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 709     }
 710     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 711     {
 712       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 713     }
 714     else if (viewer.equals(ViewerType.PYMOL.name()))
 715     {
 716       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 717     }
 718     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 719             Boolean.toString(siftsMapping.isSelected()));
 720     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 721
 722     /*
 723      * Save Output settings
 724      */
 725     Cache.applicationProperties.setProperty("EPS_RENDERING",
 726             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 727
 728     /*
 729      * Save Connections settings
 730      */
 731     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 732
 733     jalview.util.BrowserLauncher.resetBrowser();
 734
 735     // save user-defined and selected links
 736     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 737     if (menuLinks.isEmpty())
 738     {
 739       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 740     }
 741     else
 742     {
 743       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 744               menuLinks.toString());
 745     }
 746
 747     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 748     if (nonMenuLinks.isEmpty())
 749     {
 750       Cache.applicationProperties.remove("STORED_LINKS");
 751     }
 752     else
 753     {
 754       Cache.applicationProperties.setProperty("STORED_LINKS",
 755               nonMenuLinks.toString());
 756     }
 757
 758     Cache.applicationProperties.setProperty("DEFAULT_URL",
 759             sequenceUrlLinks.getPrimaryUrlId());
 760
 761     Cache.applicationProperties.setProperty("USE_PROXY",
 762             Boolean.toString(useProxy.isSelected()));
 763
 764     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 765
 766     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 767
 768     if (useProxy.isSelected())
 769     {
 770       System.setProperty("http.proxyHost", proxyServerTB.getText());
 771       System.setProperty("http.proxyPort", proxyPortTB.getText());
 772     }
 773     else
 774     {
 775       System.setProperty("http.proxyHost", "");
 776       System.setProperty("http.proxyPort", "");
 777     }
 778     Cache.setProperty("VERSION_CHECK",
 779             Boolean.toString(versioncheck.isSelected()));
 780     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 781     {
 782       // default is false - we only set this if the user has actively agreed
 783       Cache.setProperty("USAGESTATS",
 784               Boolean.toString(usagestats.isSelected()));
 785     }
 786     if (!questionnaire.isSelected())
 787     {
 788       Cache.setProperty("NOQUESTIONNAIRES", "true");
 789     }
 790     else
 791     {
 792       // special - made easy to edit a property file to disable questionnaires
 793       // by just adding the given line
 794       Cache.removeProperty("NOQUESTIONNAIRES");
 795     }
 796
 797     /*
 798      * Save Output settings
 799      */
 800     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 801             Boolean.toString(blcjv.isSelected()));
 802     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 803             Boolean.toString(clustaljv.isSelected()));
 804     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 805             Boolean.toString(fastajv.isSelected()));
 806     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 807             Boolean.toString(msfjv.isSelected()));
 808     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 809             Boolean.toString(pfamjv.isSelected()));
 810     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 811             Boolean.toString(pileupjv.isSelected()));
 812     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 813             Boolean.toString(pirjv.isSelected()));
 814     Cache.applicationProperties.setProperty("PIR_MODELLER",
 815             Boolean.toString(modellerOutput.isSelected()));
 816     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 817             Boolean.toString(embbedBioJSON.isSelected()));
 818     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 819
 820     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 821             Boolean.toString(autoIdWidth.isSelected()));
 822     userIdWidth_actionPerformed();
 823     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 824             userIdWidth.getText());
 825
 826     /*
 827      * Save Editing settings
 828      */
 829     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 830             Boolean.toString(autoCalculateConsCheck.isSelected()));
 831     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 832             Boolean.toString(sortByTree.isSelected()));
 833     Cache.applicationProperties.setProperty("PAD_GAPS",
 834             Boolean.toString(padGaps.isSelected()));
 835
 836     wsPrefs.updateAndRefreshWsMenuConfig(false);
 837
 838     /*
 839      * Save Backups settings
 840      */
 841     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 842             Boolean.toString(enableBackupFiles.isSelected()));
 843     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 844     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 845
 846     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 847     {
 848       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 849       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 850               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 851       Cache.applicationProperties
 852               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 853                       customBFPE.toString());
 854     }
 855
 856     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 857             .get(preset);
 858     Cache.applicationProperties.setProperty(
 859             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 860
 861     Cache.saveProperties();
 862     Desktop.instance.doConfigureStructurePrefs();
 863     try
 864     {
 865       frame.setClosed(true);
 866     } catch (Exception ex)
 867     {
 868     }
 869   }
 870
 871   /**
 872    * Do any necessary validation before saving settings. Return focus to the
 873    * first tab which fails validation.
 874    *
 875    * @return
 876    */
 877   private boolean validateSettings()
 878   {
 879     if (!validateStructure())
 880     {
 881       structureTab.requestFocusInWindow();
 882       return false;
 883     }
 884     return true;
 885   }
 886
 887   @Override
 888   protected boolean validateStructure()
 889   {
 890     return validateChimeraPath();
 891
 892   }
 893
 894   /**
 895    * DOCUMENT ME!
 896    */
 897   @Override
 898   public void startupFileTextfield_mouseClicked()
 899   {
 900     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 901     JalviewFileChooser chooser = JalviewFileChooser
 902             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 903     chooser.setFileView(new JalviewFileView());
 904     chooser.setDialogTitle(
 905             MessageManager.getString("label.select_startup_file"));
 906
 907     int value = chooser.showOpenDialog(this);
 908
 909     if (value == JalviewFileChooser.APPROVE_OPTION)
 910     {
 911       FileFormatI format = chooser.getSelectedFormat();
 912       if (format != null)
 913       {
 914         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 915                 format.getName());
 916       }
 917       startupFileTextfield
 918               .setText(chooser.getSelectedFile().getAbsolutePath());
 919     }
 920   }
 921
 922   /**
 923    * DOCUMENT ME!
 924    *
 925    * @param e
 926    *          DOCUMENT ME!
 927    */
 928   @Override
 929   public void cancel_actionPerformed(ActionEvent e)
 930   {
 931     try
 932     {
 933       wsPrefs.updateWsMenuConfig(true);
 934       wsPrefs.refreshWs_actionPerformed(e);
 935       frame.setClosed(true);
 936     } catch (Exception ex)
 937     {
 938     }
 939   }
 940
 941   /**
 942    * DOCUMENT ME!
 943    *
 944    * @param e
 945    *          DOCUMENT ME!
 946    */
 947   @Override
 948   public void annotations_actionPerformed(ActionEvent e)
 949   {
 950     conservation.setEnabled(annotations.isSelected());
 951     quality.setEnabled(annotations.isSelected());
 952     identity.setEnabled(annotations.isSelected());
 953     showOccupancy.setEnabled(annotations.isSelected());
 954     showGroupConsensus.setEnabled(annotations.isSelected());
 955     showGroupConservation.setEnabled(annotations.isSelected());
 956     showConsensHistogram.setEnabled(annotations.isSelected()
 957             && (identity.isSelected() || showGroupConsensus.isSelected()));
 958     showConsensLogo.setEnabled(annotations.isSelected()
 959             && (identity.isSelected() || showGroupConsensus.isSelected()));
 960   }
 961
 962   @Override
 963   public void newLink_actionPerformed(ActionEvent e)
 964   {
 965     GSequenceLink link = new GSequenceLink();
 966     boolean valid = false;
 967     while (!valid)
 968     {
 969       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 970               MessageManager.getString("label.new_sequence_url_link"),
 971               JvOptionPane.OK_CANCEL_OPTION, -1,
 972               null) == JvOptionPane.OK_OPTION)
 973       {
 974         if (link.checkValid())
 975         {
 976           if (((UrlLinkTableModel) linkUrlTable.getModel())
 977                   .isUniqueName(link.getName()))
 978           {
 979             ((UrlLinkTableModel) linkUrlTable.getModel())
 980                     .insertRow(link.getName(), link.getURL());
 981             valid = true;
 982           }
 983           else
 984           {
 985             link.notifyDuplicate();
 986             continue;
 987           }
 988         }
 989       }
 990       else
 991       {
 992         break;
 993       }
 994     }
 995   }
 996
 997   @Override
 998   public void editLink_actionPerformed(ActionEvent e)
 999   {
1000     GSequenceLink link = new GSequenceLink();
1001
1002     int index = linkUrlTable.getSelectedRow();
1003     if (index == -1)
1004     {
1005       // button no longer enabled if row is not selected
1006       Cache.log.debug("Edit with no row selected in linkUrlTable");
1007       return;
1008     }
1009
1010     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1011             .getNameColumn();
1012     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1013             .getUrlColumn();
1014     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1015     link.setName(oldName);
1016     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1017
1018     boolean valid = false;
1019     while (!valid)
1020     {
1021       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1022               MessageManager.getString("label.edit_sequence_url_link"),
1023               JvOptionPane.OK_CANCEL_OPTION, -1,
1024               null) == JvOptionPane.OK_OPTION)
1025       {
1026         if (link.checkValid())
1027         {
1028           if ((oldName.equals(link.getName()))
1029                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1030                           .isUniqueName(link.getName())))
1031           {
1032             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1033             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1034             valid = true;
1035           }
1036           else
1037           {
1038             link.notifyDuplicate();
1039             continue;
1040           }
1041         }
1042       }
1043       else
1044       {
1045         break;
1046       }
1047     }
1048   }
1049
1050   @Override
1051   public void deleteLink_actionPerformed(ActionEvent e)
1052   {
1053     int index = linkUrlTable.getSelectedRow();
1054     int modelIndex = -1;
1055     if (index == -1)
1056     {
1057       // button no longer enabled if row is not selected
1058       Cache.log.debug("Delete with no row selected in linkUrlTable");
1059       return;
1060     }
1061     else
1062     {
1063       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1064     }
1065
1066     // make sure we use the model index to delete, and not the table index
1067     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1068   }
1069
1070   @Override
1071   public void defaultBrowser_mouseClicked(MouseEvent e)
1072   {
1073     JFileChooser chooser = new JFileChooser(".");
1074     chooser.setDialogTitle(
1075             MessageManager.getString("label.select_default_browser"));
1076
1077     int value = chooser.showOpenDialog(this);
1078
1079     if (value == JFileChooser.APPROVE_OPTION)
1080     {
1081       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1082     }
1083
1084   }
1085
1086   /*
1087    * (non-Javadoc)
1088    *
1089    * @see
1090    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1091    * .ActionEvent)
1092    */
1093   @Override
1094   protected void showunconserved_actionPerformed(ActionEvent e)
1095   {
1096     // TODO Auto-generated method stub
1097     super.showunconserved_actionPerformed(e);
1098   }
1099
1100   public static List<String> getGroupURLLinks()
1101   {
1102     return groupURLLinks;
1103   }
1104
1105   @Override
1106   public void minColour_actionPerformed(JPanel panel)
1107   {
1108     Color col = JColorChooser.showDialog(this,
1109             MessageManager.getString("label.select_colour_minimum_value"),
1110             minColour.getBackground());
1111     if (col != null)
1112     {
1113       panel.setBackground(col);
1114     }
1115     panel.repaint();
1116   }
1117
1118   @Override
1119   public void maxColour_actionPerformed(JPanel panel)
1120   {
1121     Color col = JColorChooser.showDialog(this,
1122             MessageManager.getString("label.select_colour_maximum_value"),
1123             maxColour.getBackground());
1124     if (col != null)
1125     {
1126       panel.setBackground(col);
1127     }
1128     panel.repaint();
1129   }
1130
1131   @Override
1132   public void gapColour_actionPerformed(JPanel gap)
1133   {
1134     if (!useLegacyGap.isSelected())
1135     {
1136       Color col = JColorChooser.showDialog(this,
1137               MessageManager.getString("label.select_gap_colour"),
1138               gapColour.getBackground());
1139       if (col != null)
1140       {
1141         gap.setBackground(col);
1142       }
1143       gap.repaint();
1144     }
1145   }
1146
1147   @Override
1148   public void hiddenColour_actionPerformed(JPanel hidden)
1149   {
1150     Color col = JColorChooser.showDialog(this,
1151             MessageManager.getString("label.select_hidden_colour"),
1152             hiddenColour.getBackground());
1153     if (col != null)
1154     {
1155       hidden.setBackground(col);
1156     }
1157     hidden.repaint();
1158   }
1159
1160   @Override
1161   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1162   {
1163     boolean enabled = useLegacyGap.isSelected();
1164     if (enabled)
1165     {
1166       gapColour.setBackground(
1167               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1168     }
1169     else
1170     {
1171       gapColour.setBackground(
1172               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1173     }
1174     gapColour.setEnabled(!enabled);
1175     gapLabel.setEnabled(!enabled);
1176   }
1177
1178   @Override
1179   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1180   {
1181     useLegacyGap.setSelected(false);
1182     useLegacyGaps_actionPerformed(null);
1183     showHiddenAtStart.setSelected(false);
1184     hiddenColour.setBackground(
1185             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1186   }
1187
1188   @Override
1189   protected void userIdWidth_actionPerformed()
1190   {
1191     try
1192     {
1193       String val = userIdWidth.getText().trim();
1194       if (val.length() > 0)
1195       {
1196         Integer iw = Integer.parseInt(val);
1197         if (iw.intValue() < 12)
1198         {
1199           throw new NumberFormatException();
1200         }
1201         userIdWidth.setText(iw.toString());
1202       }
1203     } catch (NumberFormatException x)
1204     {
1205       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1206               MessageManager
1207                       .getString("warn.user_defined_width_requirements"),
1208               MessageManager.getString("label.invalid_id_column_width"),
1209               JvOptionPane.WARNING_MESSAGE);
1210       userIdWidth.setText("");
1211     }
1212   }
1213
1214   @Override
1215   protected void autoIdWidth_actionPerformed()
1216   {
1217     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1218     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1219   }
1220
1221   /**
1222    * Returns true if chimera path is to a valid executable, else show an error
1223    * dialog.
1224    */
1225   private boolean validateChimeraPath()
1226   {
1227     if (structureViewerPath.getText().trim().length() > 0)
1228     {
1229       File f = new File(structureViewerPath.getText());
1230       if (!f.canExecute())
1231       {
1232         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1233                 MessageManager.getString("label.invalid_chimera_path"),
1234                 MessageManager.getString("label.invalid_name"),
1235                 JvOptionPane.ERROR_MESSAGE);
1236         return false;
1237       }
1238     }
1239     return true;
1240   }
1241
1242   /**
1243    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1244    * default or user-specified path, if not show a warning/help dialog
1245    */
1246   @Override
1247   protected void structureViewer_actionPerformed(String selectedItem)
1248   {
1249     if (selectedItem.equals(ViewerType.JMOL.name()))
1250     {
1251       structureViewerPath.setEnabled(false);
1252       structureViewerPathLabel.setEnabled(false);
1253       return;
1254     }
1255     boolean found = false;
1256     structureViewerPath.setEnabled(true);
1257     structureViewerPathLabel.setEnabled(true);
1258     structureViewerPathLabel.setText(MessageManager
1259             .formatMessage("label.chimera_path", selectedItem));
1260
1261     /*
1262      * Try user-specified and standard paths for Chimera executable
1263      */
1264     boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name());
1265     structureViewerPath.setText(Cache
1266             .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
1267
1268     List<String> paths = StructureManager.getChimeraPaths(isChimeraX);
1269     paths.add(0, structureViewerPath.getText());
1270     for (String path : paths)
1271     {
1272       if (new File(path.trim()).canExecute())
1273       {
1274         found = true;
1275         break;
1276       }
1277     }
1278     if (!found)
1279     {
1280       String[] options = { "OK", "Help" };
1281       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1282               JvSwingUtils.wrapTooltip(true,
1283                       MessageManager.getString("label.chimera_missing")),
1284               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1285               null, options, options[0]);
1286       if (showHelp == JvOptionPane.NO_OPTION)
1287       {
1288         try
1289         {
1290           Help.showHelpWindow(HelpId.StructureViewer);
1291         } catch (HelpSetException e)
1292         {
1293           e.printStackTrace();
1294         }
1295       }
1296     }
1297   }
1298
1299   public class OptionsParam
1300   {
1301     private String name;
1302
1303     private String code;
1304
1305     public OptionsParam(String name, String code)
1306     {
1307       this.name = name;
1308       this.code = code;
1309     }
1310
1311     public String getName()
1312     {
1313       return name;
1314     }
1315
1316     public void setName(String name)
1317     {
1318       this.name = name;
1319     }
1320
1321     public String getCode()
1322     {
1323       return code;
1324     }
1325
1326     public void setCode(String code)
1327     {
1328       this.code = code;
1329     }
1330
1331     @Override
1332     public String toString()
1333     {
1334       return name;
1335     }
1336
1337     @Override
1338     public boolean equals(Object that)
1339     {
1340       if (!(that instanceof OptionsParam))
1341       {
1342         return false;
1343       }
1344       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1345     }
1346
1347     @Override
1348     public int hashCode()
1349     {
1350       return name.hashCode() + code.hashCode();
1351     }
1352   }
1353
1354   private class UrlListSelectionHandler implements ListSelectionListener
1355   {
1356
1357     @Override
1358     public void valueChanged(ListSelectionEvent e)
1359     {
1360       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1361
1362       int index = lsm.getMinSelectionIndex();
1363       if (index == -1)
1364       {
1365         // no selection, so disable delete/edit buttons
1366         editLink.setEnabled(false);
1367         deleteLink.setEnabled(false);
1368         return;
1369       }
1370       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1371
1372       // enable/disable edit and delete link buttons
1373       if (((UrlLinkTableModel) linkUrlTable.getModel())
1374               .isRowDeletable(modelIndex))
1375       {
1376         deleteLink.setEnabled(true);
1377       }
1378       else
1379       {
1380         deleteLink.setEnabled(false);
1381       }
1382
1383       if (((UrlLinkTableModel) linkUrlTable.getModel())
1384               .isRowEditable(modelIndex))
1385       {
1386         editLink.setEnabled(true);
1387       }
1388       else
1389       {
1390         editLink.setEnabled(false);
1391       }
1392     }
1393   }
1394 }