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