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.JButton;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.RowFilter;
  64 import javax.swing.RowSorter;
  65 import javax.swing.SortOrder;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70 import javax.swing.table.TableCellRenderer;
  71 import javax.swing.table.TableColumn;
  72 import javax.swing.table.TableModel;
  73 import javax.swing.table.TableRowSorter;
  74
  75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   private static final int MIN_FONT_SIZE = 1;
 114
 115   private static final int MAX_FONT_SIZE = 30;
 116
 117   /**
 118    * Holds name and link separated with | character. Sequence ID must be
 119    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 120    */
 121   public static UrlProviderI sequenceUrlLinks;
 122
 123   public static UrlLinkTableModel dataModel;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence IDS and Sequences
 127    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 128    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 129    * for first and second token specified after a pipe character at end |,|.
 130    * (TODO: proper escape for using | to separate ids or sequences
 131    */
 132
 133   public static List<String> groupURLLinks;
 134   static
 135   {
 136     // get links selected to be in the menu (SEQUENCE_LINKS)
 137     // and links entered by the user but not selected (STORED_LINKS)
 138     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 139     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 140     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 141             UrlConstants.DEFAULT_LABEL);
 142
 143     // if both links lists are empty, add the DEFAULT_URL link
 144     // otherwise we assume the default link is in one of the lists
 145     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 146     {
 147       inMenuString = UrlConstants.DEFAULT_STRING;
 148     }
 149     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 150             inMenuString, notInMenuString);
 151     sequenceUrlLinks = factory.createUrlProvider();
 152     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 153
 154     /**
 155      * TODO: reformulate groupURL encoding so two or more can be stored in the
 156      * .properties file as '|' separated strings
 157      */
 158
 159     groupURLLinks = new ArrayList<>();
 160   }
 161
 162   JInternalFrame frame;
 163
 164   DasSourceBrowser dasSource;
 165
 166   private WsPreferences wsPrefs;
 167
 168   private OptionsParam promptEachTimeOpt = new OptionsParam(
 169           MessageManager.getString("label.prompt_each_time"),
 170           "Prompt each time");
 171
 172   private OptionsParam lineArtOpt = new OptionsParam(
 173           MessageManager.getString("label.lineart"), "Lineart");
 174
 175   private OptionsParam textOpt = new OptionsParam(
 176           MessageManager.getString("action.text"), "Text");
 177
 178   /**
 179    * Creates a new Preferences object.
 180    */
 181   public Preferences()
 182   {
 183     super();
 184     frame = new JInternalFrame();
 185     frame.setContentPane(this);
 186     dasSource = new DasSourceBrowser();
 187     dasTab.add(dasSource, BorderLayout.CENTER);
 188     wsPrefs = new WsPreferences();
 189     wsTab.add(wsPrefs, BorderLayout.CENTER);
 190     int width = 500, height = 450;
 191     new jalview.util.Platform();
 192     if (Platform.isAMac())
 193     {
 194       width = 570;
 195       height = 480;
 196     }
 197
 198     Desktop.addInternalFrame(frame,
 199             MessageManager.getString("label.preferences"), width, height);
 200     frame.setMinimumSize(new Dimension(width, height));
 201
 202     /*
 203      * Set Visual tab defaults
 204      */
 205     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 206     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 207     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 208     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 209
 210     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 211     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 212     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 213     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 214     showUnconserved
 215             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 216     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 217     showGroupConsensus
 218             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 219     showGroupConservation.setSelected(
 220             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 221     showConsensHistogram.setSelected(
 222             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 223     showConsensLogo
 224             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 225     showNpTooltip
 226             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 227     showDbRefTooltip
 228             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 229
 230     String[] fonts = java.awt.GraphicsEnvironment
 231             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 232     for (int i = 0; i < fonts.length; i++)
 233     {
 234       fontNameCB.addItem(fonts[i]);
 235     }
 236
 237     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 238     {
 239       fontSizeCB.addItem(i + "");
 240     }
 241
 242     fontStyleCB.addItem("plain");
 243     fontStyleCB.addItem("bold");
 244     fontStyleCB.addItem("italic");
 245
 246     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 247     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 248     fontStyleCB.setSelectedItem(
 249             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 250
 251     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 252     scaleProteinToCdna
 253             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 254
 255     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 256
 257     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 258
 259     gapSymbolCB.addItem("-");
 260     gapSymbolCB.addItem(".");
 261
 262     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 263
 264     sortby.addItem("No sort");
 265     sortby.addItem("Id");
 266     sortby.addItem("Pairwise Identity");
 267     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 268
 269     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 270     sortAnnBy
 271             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 272     sortAnnBy
 273             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 274     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 275             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 276                     SequenceAnnotationOrder.NONE.name()));
 277     sortAnnBy.setSelectedItem(savedSort.toString());
 278
 279     sortAutocalc.addItem("Autocalculated first");
 280     sortAutocalc.addItem("Autocalculated last");
 281     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 282     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 283             : sortAutocalc.getItemAt(1));
 284     startupCheckbox
 285             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 286     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 287             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 288                     + "/examples/exampleFile_2_3.jar"));
 289
 290     /*
 291      * Set Colours tab defaults
 292      */
 293     protColour.addItem(ResidueColourScheme.NONE);
 294     nucColour.addItem(ResidueColourScheme.NONE);
 295     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 296     {
 297       String name = cs.getSchemeName();
 298       protColour.addItem(name);
 299       nucColour.addItem(name);
 300     }
 301     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 302             ResidueColourScheme.NONE);
 303     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 304     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 305     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 306     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 307     minColour.setBackground(
 308             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 309     maxColour.setBackground(
 310             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 311     gapColour.setBackground(
 312             Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
 313     hiddenColour.setBackground(
 314             Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
 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(
 328             Cache.getDefault(STRUCTURE_DISPLAY, 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(
 368             new RowSorter.SortKey(m.getNameColumn(), 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
 422                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 423       }
 424
 425       @Override
 426       public void removeUpdate(DocumentEvent e)
 427       {
 428         sorter.setRowFilter(RowFilter
 429                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 430       }
 431
 432       @Override
 433       public void insertUpdate(DocumentEvent e)
 434       {
 435         sorter.setRowFilter(RowFilter
 436                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 437       }
 438     });
 439
 440     // set up list selection functionality
 441     linkUrlTable.getSelectionModel()
 442             .addListSelectionListener(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)
 449             .setCellRenderer(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()
 460                 .getColumn(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
 521             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 522
 523     /*
 524      * Set Editing tab defaults
 525      */
 526     autoCalculateConsCheck
 527             .setSelected(Cache.getDefault("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",
 570             gapSymbolCB.getSelectedItem().toString());
 571
 572     Cache.applicationProperties.setProperty("FONT_NAME",
 573             fontNameCB.getSelectedItem().toString());
 574     Cache.applicationProperties.setProperty("FONT_STYLE",
 575             fontStyleCB.getSelectedItem().toString());
 576     Cache.applicationProperties.setProperty("FONT_SIZE",
 577             fontSizeCB.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("ANTI_ALIAS",
 594             Boolean.toString(smoothFont.isSelected()));
 595     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 596             Boolean.toString(scaleProteinToCdna.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 598             Boolean.toString(showNpTooltip.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 600             Boolean.toString(showDbRefTooltip.isSelected()));
 601
 602     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 603             Boolean.toString(wrap.isSelected()));
 604
 605     Cache.applicationProperties.setProperty("STARTUP_FILE",
 606             startupFileTextfield.getText());
 607     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 608             Boolean.toString(startupCheckbox.isSelected()));
 609
 610     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 611             sortby.getSelectedItem().toString());
 612
 613     // convert description of sort order to enum name for save
 614     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 615             .forDescription(sortAnnBy.getSelectedItem().toString());
 616     if (annSortOrder != null)
 617     {
 618       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 619               annSortOrder.name());
 620     }
 621
 622     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 623     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 624             Boolean.valueOf(showAutocalcFirst).toString());
 625
 626     /*
 627      * Save Colours settings
 628      */
 629     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 630             protColour.getSelectedItem().toString());
 631     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 632             nucColour.getSelectedItem().toString());
 633     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 634             minColour.getBackground());
 635     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 636             maxColour.getBackground());
 637
 638     /*
 639      * Save Structure settings
 640      */
 641     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 642             Boolean.toString(addTempFactor.isSelected()));
 643     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 644             Boolean.toString(addSecondaryStructure.isSelected()));
 645     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 646             Boolean.toString(useRnaView.isSelected()));
 647     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 648             Boolean.toString(structFromPdb.isSelected()));
 649     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 650             structViewer.getSelectedItem().toString());
 651     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 652     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 653             Boolean.toString(siftsMapping.isSelected()));
 654     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 655
 656     /*
 657      * Save Output settings
 658      */
 659     Cache.applicationProperties.setProperty("EPS_RENDERING",
 660             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 661
 662     /*
 663      * Save Connections settings
 664      */
 665     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 666
 667     jalview.util.BrowserLauncher.resetBrowser();
 668
 669     // save user-defined and selected links
 670     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 671     if (menuLinks.isEmpty())
 672     {
 673       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 674     }
 675     else
 676     {
 677       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 678               menuLinks.toString());
 679     }
 680
 681     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 682     if (nonMenuLinks.isEmpty())
 683     {
 684       Cache.applicationProperties.remove("STORED_LINKS");
 685     }
 686     else
 687     {
 688       Cache.applicationProperties.setProperty("STORED_LINKS",
 689               nonMenuLinks.toString());
 690     }
 691
 692     Cache.applicationProperties.setProperty("DEFAULT_URL",
 693             sequenceUrlLinks.getPrimaryUrlId());
 694
 695     Cache.applicationProperties.setProperty("USE_PROXY",
 696             Boolean.toString(useProxy.isSelected()));
 697
 698     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 699
 700     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 701
 702     if (useProxy.isSelected())
 703     {
 704       System.setProperty("http.proxyHost", proxyServerTB.getText());
 705       System.setProperty("http.proxyPort", proxyPortTB.getText());
 706     }
 707     else
 708     {
 709       System.setProperty("http.proxyHost", "");
 710       System.setProperty("http.proxyPort", "");
 711     }
 712     Cache.setProperty("VERSION_CHECK",
 713             Boolean.toString(versioncheck.isSelected()));
 714     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 715     {
 716       // default is false - we only set this if the user has actively agreed
 717       Cache.setProperty("USAGESTATS",
 718               Boolean.toString(usagestats.isSelected()));
 719     }
 720     if (!questionnaire.isSelected())
 721     {
 722       Cache.setProperty("NOQUESTIONNAIRES", "true");
 723     }
 724     else
 725     {
 726       // special - made easy to edit a property file to disable questionnaires
 727       // by just adding the given line
 728       Cache.removeProperty("NOQUESTIONNAIRES");
 729     }
 730
 731     /*
 732      * Save Output settings
 733      */
 734     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 735             Boolean.toString(blcjv.isSelected()));
 736     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 737             Boolean.toString(clustaljv.isSelected()));
 738     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 739             Boolean.toString(fastajv.isSelected()));
 740     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 741             Boolean.toString(msfjv.isSelected()));
 742     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 743             Boolean.toString(pfamjv.isSelected()));
 744     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 745             Boolean.toString(pileupjv.isSelected()));
 746     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 747             Boolean.toString(pirjv.isSelected()));
 748     Cache.applicationProperties.setProperty("PIR_MODELLER",
 749             Boolean.toString(modellerOutput.isSelected()));
 750     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 751             Boolean.toString(embbedBioJSON.isSelected()));
 752     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 753
 754     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 755             Boolean.toString(autoIdWidth.isSelected()));
 756     userIdWidth_actionPerformed();
 757     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 758             userIdWidth.getText());
 759
 760     /*
 761      * Save Editing settings
 762      */
 763     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 764             Boolean.toString(autoCalculateConsCheck.isSelected()));
 765     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 766             Boolean.toString(sortByTree.isSelected()));
 767     Cache.applicationProperties.setProperty("PAD_GAPS",
 768             Boolean.toString(padGaps.isSelected()));
 769
 770     dasSource.saveProperties(Cache.applicationProperties);
 771     wsPrefs.updateAndRefreshWsMenuConfig(false);
 772     Cache.saveProperties();
 773     Desktop.instance.doConfigureStructurePrefs();
 774     try
 775     {
 776       frame.setClosed(true);
 777     } catch (Exception ex)
 778     {
 779     }
 780   }
 781
 782   /**
 783    * Do any necessary validation before saving settings. Return focus to the
 784    * first tab which fails validation.
 785    *
 786    * @return
 787    */
 788   private boolean validateSettings()
 789   {
 790     if (!validateStructure())
 791     {
 792       structureTab.requestFocusInWindow();
 793       return false;
 794     }
 795     return true;
 796   }
 797
 798   @Override
 799   protected boolean validateStructure()
 800   {
 801     return validateChimeraPath();
 802
 803   }
 804
 805   /**
 806    * DOCUMENT ME!
 807    */
 808   @Override
 809   public void startupFileTextfield_mouseClicked()
 810   {
 811     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 812     JalviewFileChooser chooser = JalviewFileChooser
 813             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 814     chooser.setFileView(new JalviewFileView());
 815     chooser.setDialogTitle(
 816             MessageManager.getString("label.select_startup_file"));
 817
 818     int value = chooser.showOpenDialog(this);
 819
 820     if (value == JalviewFileChooser.APPROVE_OPTION)
 821     {
 822       FileFormatI format = chooser.getSelectedFormat();
 823       if (format != null)
 824       {
 825         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 826                 format.getName());
 827       }
 828       startupFileTextfield
 829               .setText(chooser.getSelectedFile().getAbsolutePath());
 830     }
 831   }
 832
 833   /**
 834    * DOCUMENT ME!
 835    *
 836    * @param e
 837    *          DOCUMENT ME!
 838    */
 839   @Override
 840   public void cancel_actionPerformed(ActionEvent e)
 841   {
 842     try
 843     {
 844       wsPrefs.updateWsMenuConfig(true);
 845       wsPrefs.refreshWs_actionPerformed(e);
 846       frame.setClosed(true);
 847     } catch (Exception ex)
 848     {
 849     }
 850   }
 851
 852   /**
 853    * DOCUMENT ME!
 854    *
 855    * @param e
 856    *          DOCUMENT ME!
 857    */
 858   @Override
 859   public void annotations_actionPerformed(ActionEvent e)
 860   {
 861     conservation.setEnabled(annotations.isSelected());
 862     quality.setEnabled(annotations.isSelected());
 863     identity.setEnabled(annotations.isSelected());
 864     showOccupancy.setEnabled(annotations.isSelected());
 865     showGroupConsensus.setEnabled(annotations.isSelected());
 866     showGroupConservation.setEnabled(annotations.isSelected());
 867     showConsensHistogram.setEnabled(annotations.isSelected()
 868             && (identity.isSelected() || showGroupConsensus.isSelected()));
 869     showConsensLogo.setEnabled(annotations.isSelected()
 870             && (identity.isSelected() || showGroupConsensus.isSelected()));
 871   }
 872
 873   @Override
 874   public void newLink_actionPerformed(ActionEvent e)
 875   {
 876     GSequenceLink link = new GSequenceLink();
 877     boolean valid = false;
 878     while (!valid)
 879     {
 880       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 881               MessageManager.getString("label.new_sequence_url_link"),
 882               JvOptionPane.OK_CANCEL_OPTION, -1,
 883               null) == JvOptionPane.OK_OPTION)
 884       {
 885         if (link.checkValid())
 886         {
 887           if (((UrlLinkTableModel) linkUrlTable.getModel())
 888                   .isUniqueName(link.getName()))
 889           {
 890             ((UrlLinkTableModel) linkUrlTable.getModel())
 891                     .insertRow(link.getName(), link.getURL());
 892             valid = true;
 893           }
 894           else
 895           {
 896             link.notifyDuplicate();
 897             continue;
 898           }
 899         }
 900       }
 901       else
 902       {
 903         break;
 904       }
 905     }
 906   }
 907
 908   @Override
 909   public void editLink_actionPerformed(ActionEvent e)
 910   {
 911     GSequenceLink link = new GSequenceLink();
 912
 913     int index = linkUrlTable.getSelectedRow();
 914     if (index == -1)
 915     {
 916       // button no longer enabled if row is not selected
 917       Cache.log.debug("Edit with no row selected in linkUrlTable");
 918       return;
 919     }
 920
 921     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 922             .getNameColumn();
 923     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 924             .getUrlColumn();
 925     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 926     link.setName(oldName);
 927     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 928
 929     boolean valid = false;
 930     while (!valid)
 931     {
 932       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 933               MessageManager.getString("label.edit_sequence_url_link"),
 934               JvOptionPane.OK_CANCEL_OPTION, -1,
 935               null) == JvOptionPane.OK_OPTION)
 936       {
 937         if (link.checkValid())
 938         {
 939           if ((oldName.equals(link.getName()))
 940                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 941                           .isUniqueName(link.getName())))
 942           {
 943             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 944             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 945             valid = true;
 946           }
 947           else
 948           {
 949             link.notifyDuplicate();
 950             continue;
 951           }
 952         }
 953       }
 954       else
 955       {
 956         break;
 957       }
 958     }
 959   }
 960
 961   @Override
 962   public void deleteLink_actionPerformed(ActionEvent e)
 963   {
 964     int index = linkUrlTable.getSelectedRow();
 965     int modelIndex = -1;
 966     if (index == -1)
 967     {
 968       // button no longer enabled if row is not selected
 969       Cache.log.debug("Delete with no row selected in linkUrlTable");
 970       return;
 971     }
 972     else
 973     {
 974       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 975     }
 976
 977     // make sure we use the model index to delete, and not the table index
 978     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 979   }
 980
 981   @Override
 982   public void defaultBrowser_mouseClicked(MouseEvent e)
 983   {
 984     JFileChooser chooser = new JFileChooser(".");
 985     chooser.setDialogTitle(
 986             MessageManager.getString("label.select_default_browser"));
 987
 988     int value = chooser.showOpenDialog(this);
 989
 990     if (value == JFileChooser.APPROVE_OPTION)
 991     {
 992       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 993     }
 994
 995   }
 996
 997   /*
 998    * (non-Javadoc)
 999    *
1000    * @see
1001    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1002    * .ActionEvent)
1003    */
1004   @Override
1005   protected void showunconserved_actionPerformed(ActionEvent e)
1006   {
1007     // TODO Auto-generated method stub
1008     super.showunconserved_actionPerformed(e);
1009   }
1010
1011   public static List<String> getGroupURLLinks()
1012   {
1013     return groupURLLinks;
1014   }
1015
1016   @Override
1017   public void minColour_actionPerformed(JPanel panel)
1018   {
1019     Color col = JColorChooser.showDialog(this,
1020             MessageManager.getString("label.select_colour_minimum_value"),
1021             minColour.getBackground());
1022     if (col != null)
1023     {
1024       panel.setBackground(col);
1025     }
1026     panel.repaint();
1027   }
1028
1029   @Override
1030   public void maxColour_actionPerformed(JPanel panel)
1031   {
1032     Color col = JColorChooser.showDialog(this,
1033             MessageManager.getString("label.select_colour_maximum_value"),
1034             maxColour.getBackground());
1035     if (col != null)
1036     {
1037       panel.setBackground(col);
1038     }
1039     panel.repaint();
1040   }
1041
1042   @Override
1043   public void gapColour_actionPerformed(JButton btn)
1044   {
1045     Color col = JColorChooser.showDialog(this,
1046             MessageManager.getString("label.select_gap_colour"),
1047             gapColour.getForeground());
1048     if (col != null)
1049     {
1050       btn.setForeground(col);
1051     }
1052     btn.repaint();
1053   }
1054
1055   @Override
1056   public void hiddenColour_actionPerformed(JButton btn)
1057   {
1058     Color col = JColorChooser.showDialog(this,
1059             MessageManager.getString("label.select_hidden_colour"),
1060             hiddenColour.getForeground());
1061     if (col != null)
1062     {
1063       btn.setForeground(col);
1064     }
1065     btn.repaint();
1066   }
1067
1068   @Override
1069   protected void userIdWidth_actionPerformed()
1070   {
1071     try
1072     {
1073       String val = userIdWidth.getText().trim();
1074       if (val.length() > 0)
1075       {
1076         Integer iw = Integer.parseInt(val);
1077         if (iw.intValue() < 12)
1078         {
1079           throw new NumberFormatException();
1080         }
1081         userIdWidth.setText(iw.toString());
1082       }
1083     } catch (NumberFormatException x)
1084     {
1085       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1086               MessageManager
1087                       .getString("warn.user_defined_width_requirements"),
1088               MessageManager.getString("label.invalid_id_column_width"),
1089               JvOptionPane.WARNING_MESSAGE);
1090       userIdWidth.setText("");
1091     }
1092   }
1093
1094   @Override
1095   protected void autoIdWidth_actionPerformed()
1096   {
1097     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1098     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1099   }
1100
1101   /**
1102    * Returns true if chimera path is to a valid executable, else show an error
1103    * dialog.
1104    */
1105   private boolean validateChimeraPath()
1106   {
1107     if (chimeraPath.getText().trim().length() > 0)
1108     {
1109       File f = new File(chimeraPath.getText());
1110       if (!f.canExecute())
1111       {
1112         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1113                 MessageManager.getString("label.invalid_chimera_path"),
1114                 MessageManager.getString("label.invalid_name"),
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(Desktop.desktop,
1152               JvSwingUtils.wrapTooltip(true,
1153                       MessageManager.getString("label.chimera_missing")),
1154               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1155               null, options, options[0]);
1156       if (showHelp == JvOptionPane.NO_OPTION)
1157       {
1158         try
1159         {
1160           Help.showHelpWindow(HelpId.StructureViewer);
1161         } catch (HelpSetException e)
1162         {
1163           e.printStackTrace();
1164         }
1165       }
1166     }
1167   }
1168
1169   public class OptionsParam
1170   {
1171     private String name;
1172
1173     private String code;
1174
1175     public OptionsParam(String name, String code)
1176     {
1177       this.name = name;
1178       this.code = code;
1179     }
1180
1181     public String getName()
1182     {
1183       return name;
1184     }
1185
1186     public void setName(String name)
1187     {
1188       this.name = name;
1189     }
1190
1191     public String getCode()
1192     {
1193       return code;
1194     }
1195
1196     public void setCode(String code)
1197     {
1198       this.code = code;
1199     }
1200
1201     @Override
1202     public String toString()
1203     {
1204       return name;
1205     }
1206
1207     @Override
1208     public boolean equals(Object that)
1209     {
1210       if (!(that instanceof OptionsParam))
1211       {
1212         return false;
1213       }
1214       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1215     }
1216
1217     @Override
1218     public int hashCode()
1219     {
1220       return name.hashCode() + code.hashCode();
1221     }
1222   }
1223
1224   private class UrlListSelectionHandler implements ListSelectionListener
1225   {
1226
1227     @Override
1228     public void valueChanged(ListSelectionEvent e)
1229     {
1230       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1231
1232       int index = lsm.getMinSelectionIndex();
1233       if (index == -1)
1234       {
1235         // no selection, so disable delete/edit buttons
1236         editLink.setEnabled(false);
1237         deleteLink.setEnabled(false);
1238         return;
1239       }
1240       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1241
1242       // enable/disable edit and delete link buttons
1243       if (((UrlLinkTableModel) linkUrlTable.getModel())
1244               .isRowDeletable(modelIndex))
1245       {
1246         deleteLink.setEnabled(true);
1247       }
1248       else
1249       {
1250         deleteLink.setEnabled(false);
1251       }
1252
1253       if (((UrlLinkTableModel) linkUrlTable.getModel())
1254               .isRowEditable(modelIndex))
1255       {
1256         editLink.setEnabled(true);
1257       }
1258       else
1259       {
1260         editLink.setEnabled(false);
1261       }
1262     }
1263   }
1264 }