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