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