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, false));
 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     loadLastSavedBackupsOptions();
 556   }
 557
 558   /**
 559    * Save user selections on the Preferences tabs to the Cache and write out to
 560    * file.
 561    *
 562    * @param e
 563    */
 564   @Override
 565   public void ok_actionPerformed(ActionEvent e)
 566   {
 567     if (!validateSettings())
 568     {
 569       return;
 570     }
 571
 572     /*
 573      * Save Visual settings
 574      */
 575     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 576             Boolean.toString(seqLimit.isSelected()));
 577     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 578             Boolean.toString(rightAlign.isSelected()));
 579     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 580             Boolean.toString(fullScreen.isSelected()));
 581     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 582             Boolean.toString(openoverv.isSelected()));
 583     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 584             Boolean.toString(annotations.isSelected()));
 585     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 586             Boolean.toString(conservation.isSelected()));
 587     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 588             Boolean.toString(quality.isSelected()));
 589     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 590             Boolean.toString(identity.isSelected()));
 591
 592     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 593             gapSymbolCB.getSelectedItem().toString());
 594
 595     Cache.applicationProperties.setProperty("FONT_NAME",
 596             fontNameCB.getSelectedItem().toString());
 597     Cache.applicationProperties.setProperty("FONT_STYLE",
 598             fontStyleCB.getSelectedItem().toString());
 599     Cache.applicationProperties.setProperty("FONT_SIZE",
 600             fontSizeCB.getSelectedItem().toString());
 601
 602     Cache.applicationProperties.setProperty("ID_ITALICS",
 603             Boolean.toString(idItalics.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 605             Boolean.toString(showUnconserved.isSelected()));
 606     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 607             Boolean.toString(showOccupancy.isSelected()));
 608     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 609             Boolean.toString(showGroupConsensus.isSelected()));
 610     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 611             Boolean.toString(showGroupConservation.isSelected()));
 612     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 613             Boolean.toString(showConsensHistogram.isSelected()));
 614     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 615             Boolean.toString(showConsensLogo.isSelected()));
 616     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 617             Boolean.toString(smoothFont.isSelected()));
 618     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 619             Boolean.toString(scaleProteinToCdna.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 621             Boolean.toString(showNpTooltip.isSelected()));
 622     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 623             Boolean.toString(showDbRefTooltip.isSelected()));
 624
 625     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 626             Boolean.toString(wrap.isSelected()));
 627
 628     Cache.applicationProperties.setProperty("STARTUP_FILE",
 629             startupFileTextfield.getText());
 630     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 631             Boolean.toString(startupCheckbox.isSelected()));
 632
 633     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 634             sortby.getSelectedItem().toString());
 635
 636     // convert description of sort order to enum name for save
 637     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 638             .forDescription(sortAnnBy.getSelectedItem().toString());
 639     if (annSortOrder != null)
 640     {
 641       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 642               annSortOrder.name());
 643     }
 644
 645     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 646     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 647             Boolean.valueOf(showAutocalcFirst).toString());
 648
 649     /*
 650      * Save Colours settings
 651      */
 652     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 653             protColour.getSelectedItem().toString());
 654     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 655             nucColour.getSelectedItem().toString());
 656     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 657             minColour.getBackground());
 658     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 659             maxColour.getBackground());
 660
 661     /*
 662      * Save Overview settings
 663      */
 664     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 665     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 666     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 667             Boolean.toString(useLegacyGap.isSelected()));
 668     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 669             Boolean.toString(showHiddenAtStart.isSelected()));
 670
 671     /*
 672      * Save Structure settings
 673      */
 674     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 675             Boolean.toString(addTempFactor.isSelected()));
 676     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 677             Boolean.toString(addSecondaryStructure.isSelected()));
 678     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 679             Boolean.toString(useRnaView.isSelected()));
 680     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 681             Boolean.toString(structFromPdb.isSelected()));
 682     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 683             structViewer.getSelectedItem().toString());
 684     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 685     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 686             Boolean.toString(siftsMapping.isSelected()));
 687     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 688
 689     /*
 690      * Save Output settings
 691      */
 692     Cache.applicationProperties.setProperty("EPS_RENDERING",
 693             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 694
 695     /*
 696      * Save Connections settings
 697      */
 698     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 699
 700     jalview.util.BrowserLauncher.resetBrowser();
 701
 702     // save user-defined and selected links
 703     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 704     if (menuLinks.isEmpty())
 705     {
 706       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 707     }
 708     else
 709     {
 710       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 711               menuLinks.toString());
 712     }
 713
 714     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 715     if (nonMenuLinks.isEmpty())
 716     {
 717       Cache.applicationProperties.remove("STORED_LINKS");
 718     }
 719     else
 720     {
 721       Cache.applicationProperties.setProperty("STORED_LINKS",
 722               nonMenuLinks.toString());
 723     }
 724
 725     Cache.applicationProperties.setProperty("DEFAULT_URL",
 726             sequenceUrlLinks.getPrimaryUrlId());
 727
 728     Cache.applicationProperties.setProperty("USE_PROXY",
 729             Boolean.toString(useProxy.isSelected()));
 730
 731     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 732
 733     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 734
 735     if (useProxy.isSelected())
 736     {
 737       System.setProperty("http.proxyHost", proxyServerTB.getText());
 738       System.setProperty("http.proxyPort", proxyPortTB.getText());
 739     }
 740     else
 741     {
 742       System.setProperty("http.proxyHost", "");
 743       System.setProperty("http.proxyPort", "");
 744     }
 745     Cache.setProperty("VERSION_CHECK",
 746             Boolean.toString(versioncheck.isSelected()));
 747     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 748     {
 749       // default is false - we only set this if the user has actively agreed
 750       Cache.setProperty("USAGESTATS",
 751               Boolean.toString(usagestats.isSelected()));
 752     }
 753     if (!questionnaire.isSelected())
 754     {
 755       Cache.setProperty("NOQUESTIONNAIRES", "true");
 756     }
 757     else
 758     {
 759       // special - made easy to edit a property file to disable questionnaires
 760       // by just adding the given line
 761       Cache.removeProperty("NOQUESTIONNAIRES");
 762     }
 763
 764     /*
 765      * Save Output settings
 766      */
 767     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 768             Boolean.toString(blcjv.isSelected()));
 769     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 770             Boolean.toString(clustaljv.isSelected()));
 771     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 772             Boolean.toString(fastajv.isSelected()));
 773     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 774             Boolean.toString(msfjv.isSelected()));
 775     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 776             Boolean.toString(pfamjv.isSelected()));
 777     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 778             Boolean.toString(pileupjv.isSelected()));
 779     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 780             Boolean.toString(pirjv.isSelected()));
 781     Cache.applicationProperties.setProperty("PIR_MODELLER",
 782             Boolean.toString(modellerOutput.isSelected()));
 783     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 784             Boolean.toString(embbedBioJSON.isSelected()));
 785     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 786
 787     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 788             Boolean.toString(autoIdWidth.isSelected()));
 789     userIdWidth_actionPerformed();
 790     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 791             userIdWidth.getText());
 792
 793     /*
 794      * Save Editing settings
 795      */
 796     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 797             Boolean.toString(autoCalculateConsCheck.isSelected()));
 798     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 799             Boolean.toString(sortByTree.isSelected()));
 800     Cache.applicationProperties.setProperty("PAD_GAPS",
 801             Boolean.toString(padGaps.isSelected()));
 802
 803     wsPrefs.updateAndRefreshWsMenuConfig(false);
 804
 805     /*
 806      * Save Backups settings
 807      */
 808     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 809             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 810     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 811             Boolean.toString(enableBackupFiles.isSelected()));
 812     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 813             Boolean.toString(backupfilesKeepAll.isSelected()));
 814     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 815             Boolean.toString(suffixReverse.isSelected()));
 816     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 817             suffixTemplate.getText());
 818     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 819             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 820     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 821             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 822     Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
 823             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 824
 825     Cache.saveProperties();
 826     Desktop.instance.doConfigureStructurePrefs();
 827     try
 828     {
 829       frame.setClosed(true);
 830     } catch (Exception ex)
 831     {
 832     }
 833   }
 834
 835   /**
 836    * Do any necessary validation before saving settings. Return focus to the
 837    * first tab which fails validation.
 838    *
 839    * @return
 840    */
 841   private boolean validateSettings()
 842   {
 843     if (!validateStructure())
 844     {
 845       structureTab.requestFocusInWindow();
 846       return false;
 847     }
 848     return true;
 849   }
 850
 851   @Override
 852   protected boolean validateStructure()
 853   {
 854     return validateChimeraPath();
 855
 856   }
 857
 858   /**
 859    * DOCUMENT ME!
 860    */
 861   @Override
 862   public void startupFileTextfield_mouseClicked()
 863   {
 864     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 865     JalviewFileChooser chooser = JalviewFileChooser
 866             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 867     chooser.setFileView(new JalviewFileView());
 868     chooser.setDialogTitle(
 869             MessageManager.getString("label.select_startup_file"));
 870
 871     int value = chooser.showOpenDialog(this);
 872
 873     if (value == JalviewFileChooser.APPROVE_OPTION)
 874     {
 875       FileFormatI format = chooser.getSelectedFormat();
 876       if (format != null)
 877       {
 878         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 879                 format.getName());
 880       }
 881       startupFileTextfield
 882               .setText(chooser.getSelectedFile().getAbsolutePath());
 883     }
 884   }
 885
 886   /**
 887    * DOCUMENT ME!
 888    *
 889    * @param e
 890    *          DOCUMENT ME!
 891    */
 892   @Override
 893   public void cancel_actionPerformed(ActionEvent e)
 894   {
 895     try
 896     {
 897       wsPrefs.updateWsMenuConfig(true);
 898       wsPrefs.refreshWs_actionPerformed(e);
 899       frame.setClosed(true);
 900     } catch (Exception ex)
 901     {
 902     }
 903   }
 904
 905   /**
 906    * DOCUMENT ME!
 907    *
 908    * @param e
 909    *          DOCUMENT ME!
 910    */
 911   @Override
 912   public void annotations_actionPerformed(ActionEvent e)
 913   {
 914     conservation.setEnabled(annotations.isSelected());
 915     quality.setEnabled(annotations.isSelected());
 916     identity.setEnabled(annotations.isSelected());
 917     showOccupancy.setEnabled(annotations.isSelected());
 918     showGroupConsensus.setEnabled(annotations.isSelected());
 919     showGroupConservation.setEnabled(annotations.isSelected());
 920     showConsensHistogram.setEnabled(annotations.isSelected()
 921             && (identity.isSelected() || showGroupConsensus.isSelected()));
 922     showConsensLogo.setEnabled(annotations.isSelected()
 923             && (identity.isSelected() || showGroupConsensus.isSelected()));
 924   }
 925
 926   @Override
 927   public void newLink_actionPerformed(ActionEvent e)
 928   {
 929     GSequenceLink link = new GSequenceLink();
 930     boolean valid = false;
 931     while (!valid)
 932     {
 933       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 934               MessageManager.getString("label.new_sequence_url_link"),
 935               JvOptionPane.OK_CANCEL_OPTION, -1,
 936               null) == JvOptionPane.OK_OPTION)
 937       {
 938         if (link.checkValid())
 939         {
 940           if (((UrlLinkTableModel) linkUrlTable.getModel())
 941                   .isUniqueName(link.getName()))
 942           {
 943             ((UrlLinkTableModel) linkUrlTable.getModel())
 944                     .insertRow(link.getName(), link.getURL());
 945             valid = true;
 946           }
 947           else
 948           {
 949             link.notifyDuplicate();
 950             continue;
 951           }
 952         }
 953       }
 954       else
 955       {
 956         break;
 957       }
 958     }
 959   }
 960
 961   @Override
 962   public void editLink_actionPerformed(ActionEvent e)
 963   {
 964     GSequenceLink link = new GSequenceLink();
 965
 966     int index = linkUrlTable.getSelectedRow();
 967     if (index == -1)
 968     {
 969       // button no longer enabled if row is not selected
 970       Cache.log.debug("Edit with no row selected in linkUrlTable");
 971       return;
 972     }
 973
 974     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 975             .getNameColumn();
 976     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 977             .getUrlColumn();
 978     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 979     link.setName(oldName);
 980     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 981
 982     boolean valid = false;
 983     while (!valid)
 984     {
 985       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 986               MessageManager.getString("label.edit_sequence_url_link"),
 987               JvOptionPane.OK_CANCEL_OPTION, -1,
 988               null) == JvOptionPane.OK_OPTION)
 989       {
 990         if (link.checkValid())
 991         {
 992           if ((oldName.equals(link.getName()))
 993                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 994                           .isUniqueName(link.getName())))
 995           {
 996             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 997             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 998             valid = true;
 999           }
1000           else
1001           {
1002             link.notifyDuplicate();
1003             continue;
1004           }
1005         }
1006       }
1007       else
1008       {
1009         break;
1010       }
1011     }
1012   }
1013
1014   @Override
1015   public void deleteLink_actionPerformed(ActionEvent e)
1016   {
1017     int index = linkUrlTable.getSelectedRow();
1018     int modelIndex = -1;
1019     if (index == -1)
1020     {
1021       // button no longer enabled if row is not selected
1022       Cache.log.debug("Delete with no row selected in linkUrlTable");
1023       return;
1024     }
1025     else
1026     {
1027       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1028     }
1029
1030     // make sure we use the model index to delete, and not the table index
1031     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1032   }
1033
1034   @Override
1035   public void defaultBrowser_mouseClicked(MouseEvent e)
1036   {
1037     JFileChooser chooser = new JFileChooser(".");
1038     chooser.setDialogTitle(
1039             MessageManager.getString("label.select_default_browser"));
1040
1041     int value = chooser.showOpenDialog(this);
1042
1043     if (value == JFileChooser.APPROVE_OPTION)
1044     {
1045       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1046     }
1047
1048   }
1049
1050   /*
1051    * (non-Javadoc)
1052    *
1053    * @see
1054    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1055    * .ActionEvent)
1056    */
1057   @Override
1058   protected void showunconserved_actionPerformed(ActionEvent e)
1059   {
1060     // TODO Auto-generated method stub
1061     super.showunconserved_actionPerformed(e);
1062   }
1063
1064   public static List<String> getGroupURLLinks()
1065   {
1066     return groupURLLinks;
1067   }
1068
1069   @Override
1070   public void minColour_actionPerformed(JPanel panel)
1071   {
1072     Color col = JColorChooser.showDialog(this,
1073             MessageManager.getString("label.select_colour_minimum_value"),
1074             minColour.getBackground());
1075     if (col != null)
1076     {
1077       panel.setBackground(col);
1078     }
1079     panel.repaint();
1080   }
1081
1082   @Override
1083   public void maxColour_actionPerformed(JPanel panel)
1084   {
1085     Color col = JColorChooser.showDialog(this,
1086             MessageManager.getString("label.select_colour_maximum_value"),
1087             maxColour.getBackground());
1088     if (col != null)
1089     {
1090       panel.setBackground(col);
1091     }
1092     panel.repaint();
1093   }
1094
1095   @Override
1096   public void gapColour_actionPerformed(JPanel gap)
1097   {
1098     if (!useLegacyGap.isSelected())
1099     {
1100       Color col = JColorChooser.showDialog(this,
1101               MessageManager.getString("label.select_gap_colour"),
1102               gapColour.getBackground());
1103       if (col != null)
1104       {
1105         gap.setBackground(col);
1106       }
1107       gap.repaint();
1108     }
1109   }
1110
1111   @Override
1112   public void hiddenColour_actionPerformed(JPanel hidden)
1113   {
1114     Color col = JColorChooser.showDialog(this,
1115             MessageManager.getString("label.select_hidden_colour"),
1116             hiddenColour.getBackground());
1117     if (col != null)
1118     {
1119       hidden.setBackground(col);
1120     }
1121     hidden.repaint();
1122   }
1123
1124   @Override
1125   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1126   {
1127     boolean enabled = useLegacyGap.isSelected();
1128     if (enabled)
1129     {
1130       gapColour.setBackground(
1131               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1132     }
1133     else
1134     {
1135       gapColour.setBackground(
1136               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1137     }
1138     gapColour.setEnabled(!enabled);
1139     gapLabel.setEnabled(!enabled);
1140   }
1141
1142   @Override
1143   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1144   {
1145     useLegacyGap.setSelected(false);
1146     useLegacyGaps_actionPerformed(null);
1147     showHiddenAtStart.setSelected(false);
1148     hiddenColour.setBackground(
1149             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1150   }
1151
1152   @Override
1153   protected void userIdWidth_actionPerformed()
1154   {
1155     try
1156     {
1157       String val = userIdWidth.getText().trim();
1158       if (val.length() > 0)
1159       {
1160         Integer iw = Integer.parseInt(val);
1161         if (iw.intValue() < 12)
1162         {
1163           throw new NumberFormatException();
1164         }
1165         userIdWidth.setText(iw.toString());
1166       }
1167     } catch (NumberFormatException x)
1168     {
1169       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1170               MessageManager
1171                       .getString("warn.user_defined_width_requirements"),
1172               MessageManager.getString("label.invalid_id_column_width"),
1173               JvOptionPane.WARNING_MESSAGE);
1174       userIdWidth.setText("");
1175     }
1176   }
1177
1178   @Override
1179   protected void autoIdWidth_actionPerformed()
1180   {
1181     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1182     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1183   }
1184
1185   /**
1186    * Returns true if chimera path is to a valid executable, else show an error
1187    * dialog.
1188    */
1189   private boolean validateChimeraPath()
1190   {
1191     if (chimeraPath.getText().trim().length() > 0)
1192     {
1193       File f = new File(chimeraPath.getText());
1194       if (!f.canExecute())
1195       {
1196         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1197                 MessageManager.getString("label.invalid_chimera_path"),
1198                 MessageManager.getString("label.invalid_name"),
1199                 JvOptionPane.ERROR_MESSAGE);
1200         return false;
1201       }
1202     }
1203     return true;
1204   }
1205
1206   /**
1207    * If Chimera is selected, check it can be found on default or user-specified
1208    * path, if not show a warning/help dialog.
1209    */
1210   @Override
1211   protected void structureViewer_actionPerformed(String selectedItem)
1212   {
1213     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1214     {
1215       return;
1216     }
1217     boolean found = false;
1218
1219     /*
1220      * Try user-specified and standard paths for Chimera executable.
1221      */
1222     List<String> paths = StructureManager.getChimeraPaths();
1223     paths.add(0, chimeraPath.getText());
1224     for (String path : paths)
1225     {
1226       if (new File(path.trim()).canExecute())
1227       {
1228         found = true;
1229         break;
1230       }
1231     }
1232     if (!found)
1233     {
1234       String[] options = { "OK", "Help" };
1235       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1236               JvSwingUtils.wrapTooltip(true,
1237                       MessageManager.getString("label.chimera_missing")),
1238               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1239               null, options, options[0]);
1240       if (showHelp == JvOptionPane.NO_OPTION)
1241       {
1242         try
1243         {
1244           Help.showHelpWindow(HelpId.StructureViewer);
1245         } catch (HelpSetException e)
1246         {
1247           e.printStackTrace();
1248         }
1249       }
1250     }
1251   }
1252
1253   public class OptionsParam
1254   {
1255     private String name;
1256
1257     private String code;
1258
1259     public OptionsParam(String name, String code)
1260     {
1261       this.name = name;
1262       this.code = code;
1263     }
1264
1265     public String getName()
1266     {
1267       return name;
1268     }
1269
1270     public void setName(String name)
1271     {
1272       this.name = name;
1273     }
1274
1275     public String getCode()
1276     {
1277       return code;
1278     }
1279
1280     public void setCode(String code)
1281     {
1282       this.code = code;
1283     }
1284
1285     @Override
1286     public String toString()
1287     {
1288       return name;
1289     }
1290
1291     @Override
1292     public boolean equals(Object that)
1293     {
1294       if (!(that instanceof OptionsParam))
1295       {
1296         return false;
1297       }
1298       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1299     }
1300
1301     @Override
1302     public int hashCode()
1303     {
1304       return name.hashCode() + code.hashCode();
1305     }
1306   }
1307
1308   private class UrlListSelectionHandler implements ListSelectionListener
1309   {
1310
1311     @Override
1312     public void valueChanged(ListSelectionEvent e)
1313     {
1314       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1315
1316       int index = lsm.getMinSelectionIndex();
1317       if (index == -1)
1318       {
1319         // no selection, so disable delete/edit buttons
1320         editLink.setEnabled(false);
1321         deleteLink.setEnabled(false);
1322         return;
1323       }
1324       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1325
1326       // enable/disable edit and delete link buttons
1327       if (((UrlLinkTableModel) linkUrlTable.getModel())
1328               .isRowDeletable(modelIndex))
1329       {
1330         deleteLink.setEnabled(true);
1331       }
1332       else
1333       {
1334         deleteLink.setEnabled(false);
1335       }
1336
1337       if (((UrlLinkTableModel) linkUrlTable.getModel())
1338               .isRowEditable(modelIndex))
1339       {
1340         editLink.setEnabled(true);
1341       }
1342       else
1343       {
1344         editLink.setEnabled(false);
1345       }
1346     }
1347   }
1348 }