src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.FileFormatI;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeI;
  33 import jalview.schemes.ColourSchemes;
  34 import jalview.schemes.ResidueColourScheme;
  35 import jalview.urls.UrlLinkTableModel;
  36 import jalview.urls.api.UrlProviderFactoryI;
  37 import jalview.urls.api.UrlProviderI;
  38 import jalview.urls.desktop.DesktopUrlProviderFactory;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.util.UrlConstants;
  42 import jalview.ws.sifts.SiftsSettings;
  43
  44 import java.awt.BorderLayout;
  45 import java.awt.Color;
  46 import java.awt.Component;
  47 import java.awt.Dimension;
  48 import java.awt.Font;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseEvent;
  52 import java.io.File;
  53 import java.util.ArrayList;
  54 import java.util.List;
  55
  56 import javax.help.HelpSetException;
  57 import javax.swing.JColorChooser;
  58 import javax.swing.JFileChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JPanel;
  61 import javax.swing.ListSelectionModel;
  62 import javax.swing.RowFilter;
  63 import javax.swing.RowSorter;
  64 import javax.swing.SortOrder;
  65 import javax.swing.event.DocumentEvent;
  66 import javax.swing.event.DocumentListener;
  67 import javax.swing.event.ListSelectionEvent;
  68 import javax.swing.event.ListSelectionListener;
  69 import javax.swing.table.TableCellRenderer;
  70 import javax.swing.table.TableColumn;
  71 import javax.swing.table.TableModel;
  72 import javax.swing.table.TableRowSorter;
  73
  74 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  75
  76 /**
  77  * DOCUMENT ME!
  78  *
  79  * @author $author$
  80  * @version $Revision$
  81  */
  82 public class Preferences extends GPreferences
  83 {
  84   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  85
  86   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  87
  88   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  89
  90   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  91
  92   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  93
  94   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  95
  96   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  97
  98   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  99
 100   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 101
 102   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 103
 104   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 105
 106   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 107
 108   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 109
 110   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 111
 112   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 113
 114   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 115
 116   private static final int MIN_FONT_SIZE = 1;
 117
 118   private static final int MAX_FONT_SIZE = 30;
 119
 120   /**
 121    * Holds name and link separated with | character. Sequence ID must be
 122    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 123    */
 124   public static UrlProviderI sequenceUrlLinks;
 125
 126   public static UrlLinkTableModel dataModel;
 127
 128   /**
 129    * Holds name and link separated with | character. Sequence IDS and Sequences
 130    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 131    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 132    * for first and second token specified after a pipe character at end |,|.
 133    * (TODO: proper escape for using | to separate ids or sequences
 134    */
 135
 136   public static List<String> groupURLLinks;
 137   static
 138   {
 139     // get links selected to be in the menu (SEQUENCE_LINKS)
 140     // and links entered by the user but not selected (STORED_LINKS)
 141     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 142     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 143     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 144             UrlConstants.DEFAULT_LABEL);
 145
 146     // if both links lists are empty, add the DEFAULT_URL link
 147     // otherwise we assume the default link is in one of the lists
 148     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 149     {
 150       inMenuString = UrlConstants.DEFAULT_STRING;
 151     }
 152     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 153             inMenuString, notInMenuString);
 154     sequenceUrlLinks = factory.createUrlProvider();
 155     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 156
 157     /**
 158      * TODO: reformulate groupURL encoding so two or more can be stored in the
 159      * .properties file as '|' separated strings
 160      */
 161
 162     groupURLLinks = new ArrayList<>();
 163   }
 164
 165   JInternalFrame frame;
 166
 167   DasSourceBrowser dasSource;
 168
 169   private WsPreferences wsPrefs;
 170
 171   private OptionsParam promptEachTimeOpt = new OptionsParam(
 172           MessageManager.getString("label.prompt_each_time"),
 173           "Prompt each time");
 174
 175   private OptionsParam lineArtOpt = new OptionsParam(
 176           MessageManager.getString("label.lineart"), "Lineart");
 177
 178   private OptionsParam textOpt = new OptionsParam(
 179           MessageManager.getString("action.text"), "Text");
 180
 181   /**
 182    * Creates a new Preferences object.
 183    */
 184   public Preferences()
 185   {
 186     super();
 187     frame = new JInternalFrame();
 188     frame.setContentPane(this);
 189     dasSource = new DasSourceBrowser();
 190     dasTab.add(dasSource, BorderLayout.CENTER);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set Visual tab defaults
 207      */
 208     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 209     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 210     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 211     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 212
 213     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 214     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 215     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 216     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 217     showUnconserved
 218             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 219     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 220     showGroupConsensus
 221             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 222     showGroupConservation.setSelected(
 223             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 224     showConsensHistogram.setSelected(
 225             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 226     showConsensLogo
 227             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 228     showNpTooltip
 229             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 230     showDbRefTooltip
 231             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 232
 233     String[] fonts = java.awt.GraphicsEnvironment
 234             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 235     for (int i = 0; i < fonts.length; i++)
 236     {
 237       fontNameCB.addItem(fonts[i]);
 238     }
 239
 240     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 241     {
 242       fontSizeCB.addItem(i + "");
 243     }
 244
 245     fontStyleCB.addItem("plain");
 246     fontStyleCB.addItem("bold");
 247     fontStyleCB.addItem("italic");
 248
 249     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 250     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 251     fontStyleCB.setSelectedItem(
 252             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 253
 254     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 255     scaleProteinToCdna
 256             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 257
 258     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 259
 260     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 261
 262     gapSymbolCB.addItem("-");
 263     gapSymbolCB.addItem(".");
 264
 265     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 266
 267     sortby.addItem("No sort");
 268     sortby.addItem("Id");
 269     sortby.addItem("Pairwise Identity");
 270     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 271
 272     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 273     sortAnnBy
 274             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 275     sortAnnBy
 276             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 277     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 278             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 279                     SequenceAnnotationOrder.NONE.name()));
 280     sortAnnBy.setSelectedItem(savedSort.toString());
 281
 282     sortAutocalc.addItem("Autocalculated first");
 283     sortAutocalc.addItem("Autocalculated last");
 284     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 285     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 286             : sortAutocalc.getItemAt(1));
 287     startupCheckbox
 288             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 289     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 290             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 291                     + "/examples/exampleFile_2_3.jar"));
 292
 293     /*
 294      * Set Colours tab defaults
 295      */
 296     protColour.addItem(ResidueColourScheme.NONE);
 297     nucColour.addItem(ResidueColourScheme.NONE);
 298     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 299     {
 300       String name = cs.getSchemeName();
 301       protColour.addItem(name);
 302       nucColour.addItem(name);
 303     }
 304     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 305             ResidueColourScheme.NONE);
 306     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 307     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 308     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 309     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 310     minColour.setBackground(
 311             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 312     maxColour.setBackground(
 313             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 314
 315     /*
 316      * Set overview panel defaults
 317      */
 318     gapColour.setBackground(
 319             Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
 320     hiddenColour.setBackground(
 321             Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
 322     useLegacyGap.setSelected(Cache.getDefault("USE_LEGACY_GAP", false));
 323     gapLabel.setEnabled(!useLegacyGap.isSelected());
 324     gapColour.setEnabled(!useLegacyGap.isSelected());
 325     showHiddenAtStart
 326             .setSelected(Cache.getDefault("SHOW_OV_HIDDEN_AT_START", true));
 327
 328     /*
 329      * Set Structure tab defaults.
 330      */
 331     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 332     structFromPdb.setSelected(structSelected);
 333     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 334     useRnaView.setEnabled(structSelected);
 335     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 336     addSecondaryStructure.setEnabled(structSelected);
 337     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 338     addTempFactor.setEnabled(structSelected);
 339     structViewer.setSelectedItem(
 340             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 341     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 342     chimeraPath.addActionListener(new ActionListener()
 343     {
 344       @Override
 345       public void actionPerformed(ActionEvent e)
 346       {
 347         validateChimeraPath();
 348       }
 349     });
 350
 351     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 352     {
 353       siftsMapping.setSelected(true);
 354     }
 355     else
 356     {
 357       nwMapping.setSelected(true);
 358     }
 359
 360     SiftsSettings
 361             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 362
 363     /*
 364      * Set Connections tab defaults
 365      */
 366
 367     // set up sorting
 368     linkUrlTable.setModel(dataModel);
 369     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 370             linkUrlTable.getModel());
 371     linkUrlTable.setRowSorter(sorter);
 372     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 373
 374     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 375     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 376             SortOrder.DESCENDING));
 377     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 378             SortOrder.DESCENDING));
 379     sortKeys.add(
 380             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 381
 382     sorter.setSortKeys(sortKeys);
 383     sorter.sort();
 384
 385     // set up filtering
 386     ActionListener onReset;
 387     onReset = new ActionListener()
 388     {
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         filterTB.setText("");
 393         sorter.setRowFilter(RowFilter.regexFilter(""));
 394       }
 395
 396     };
 397     doReset.addActionListener(onReset);
 398
 399     // filter to display only custom urls
 400     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 401     {
 402       @Override
 403       public boolean include(
 404               Entry<? extends TableModel, ? extends Object> entry)
 405       {
 406         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 407       }
 408     };
 409
 410     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 411             linkUrlTable.getModel());
 412     customSorter.setRowFilter(customUrlFilter);
 413
 414     ActionListener onCustomOnly;
 415     onCustomOnly = new ActionListener()
 416     {
 417       @Override
 418       public void actionPerformed(ActionEvent e)
 419       {
 420         filterTB.setText("");
 421         sorter.setRowFilter(customUrlFilter);
 422       }
 423     };
 424     userOnly.addActionListener(onCustomOnly);
 425
 426     filterTB.getDocument().addDocumentListener(new DocumentListener()
 427     {
 428       String caseInsensitiveFlag = "(?i)";
 429
 430       @Override
 431       public void changedUpdate(DocumentEvent e)
 432       {
 433         sorter.setRowFilter(RowFilter
 434                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 435       }
 436
 437       @Override
 438       public void removeUpdate(DocumentEvent e)
 439       {
 440         sorter.setRowFilter(RowFilter
 441                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 442       }
 443
 444       @Override
 445       public void insertUpdate(DocumentEvent e)
 446       {
 447         sorter.setRowFilter(RowFilter
 448                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 449       }
 450     });
 451
 452     // set up list selection functionality
 453     linkUrlTable.getSelectionModel()
 454             .addListSelectionListener(new UrlListSelectionHandler());
 455
 456     // set up radio buttons
 457     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 458             .getPrimaryColumn();
 459     String onClickName = linkUrlTable.getColumnName(onClickCol);
 460     linkUrlTable.getColumn(onClickName)
 461             .setCellRenderer(new RadioButtonRenderer());
 462     linkUrlTable.getColumn(onClickName)
 463             .setCellEditor(new RadioButtonEditor());
 464
 465     // get boolean columns and resize those to min possible
 466     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 467     {
 468       if (linkUrlTable.getModel().getColumnClass(column)
 469               .equals(Boolean.class))
 470       {
 471         TableColumn tableColumn = linkUrlTable.getColumnModel()
 472                 .getColumn(column);
 473         int preferredWidth = tableColumn.getMinWidth();
 474
 475         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 476                 column);
 477         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 478         int cwidth = c.getPreferredSize().width
 479                 + linkUrlTable.getIntercellSpacing().width;
 480         preferredWidth = Math.max(preferredWidth, cwidth);
 481
 482         tableColumn.setPreferredWidth(preferredWidth);
 483       }
 484     }
 485
 486     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 487     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 488     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 489     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 490
 491     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 492
 493     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 494     // note antisense here: default is true
 495     questionnaire
 496             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 497     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 498
 499     /*
 500      * Set Output tab defaults
 501      */
 502     epsRendering.addItem(promptEachTimeOpt);
 503     epsRendering.addItem(lineArtOpt);
 504     epsRendering.addItem(textOpt);
 505     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 506             "Prompt each time");
 507     if (defaultEPS.equalsIgnoreCase("Text"))
 508     {
 509       epsRendering.setSelectedItem(textOpt);
 510     }
 511     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 512     {
 513       epsRendering.setSelectedItem(lineArtOpt);
 514     }
 515     else
 516     {
 517       epsRendering.setSelectedItem(promptEachTimeOpt);
 518     }
 519     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 520     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 521     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 522     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 523     userIdWidth.setText(wi == null ? "" : wi.toString());
 524     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 525     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 526     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 527     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 528     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 529     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 530     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 531     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 532     embbedBioJSON
 533             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 534
 535     /*
 536      * Set Editing tab defaults
 537      */
 538     autoCalculateConsCheck
 539             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 540     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 541     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 542
 543     annotations_actionPerformed(null); // update the display of the annotation
 544                                        // settings
 545   }
 546
 547   /**
 548    * Save user selections on the Preferences tabs to the Cache and write out to
 549    * file.
 550    *
 551    * @param e
 552    */
 553   @Override
 554   public void ok_actionPerformed(ActionEvent e)
 555   {
 556     if (!validateSettings())
 557     {
 558       return;
 559     }
 560
 561     /*
 562      * Save Visual settings
 563      */
 564     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 565             Boolean.toString(seqLimit.isSelected()));
 566     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 567             Boolean.toString(rightAlign.isSelected()));
 568     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 569             Boolean.toString(fullScreen.isSelected()));
 570     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 571             Boolean.toString(openoverv.isSelected()));
 572     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 573             Boolean.toString(annotations.isSelected()));
 574     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 575             Boolean.toString(conservation.isSelected()));
 576     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 577             Boolean.toString(quality.isSelected()));
 578     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 579             Boolean.toString(identity.isSelected()));
 580
 581     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 582             gapSymbolCB.getSelectedItem().toString());
 583
 584     Cache.applicationProperties.setProperty("FONT_NAME",
 585             fontNameCB.getSelectedItem().toString());
 586     Cache.applicationProperties.setProperty("FONT_STYLE",
 587             fontStyleCB.getSelectedItem().toString());
 588     Cache.applicationProperties.setProperty("FONT_SIZE",
 589             fontSizeCB.getSelectedItem().toString());
 590
 591     Cache.applicationProperties.setProperty("ID_ITALICS",
 592             Boolean.toString(idItalics.isSelected()));
 593     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 594             Boolean.toString(showUnconserved.isSelected()));
 595     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 596             Boolean.toString(showOccupancy.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 598             Boolean.toString(showGroupConsensus.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 600             Boolean.toString(showGroupConservation.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 602             Boolean.toString(showConsensHistogram.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 604             Boolean.toString(showConsensLogo.isSelected()));
 605     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 606             Boolean.toString(smoothFont.isSelected()));
 607     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 608             Boolean.toString(scaleProteinToCdna.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 610             Boolean.toString(showNpTooltip.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 612             Boolean.toString(showDbRefTooltip.isSelected()));
 613
 614     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 615             Boolean.toString(wrap.isSelected()));
 616
 617     Cache.applicationProperties.setProperty("STARTUP_FILE",
 618             startupFileTextfield.getText());
 619     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 620             Boolean.toString(startupCheckbox.isSelected()));
 621
 622     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 623             sortby.getSelectedItem().toString());
 624
 625     // convert description of sort order to enum name for save
 626     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 627             .forDescription(sortAnnBy.getSelectedItem().toString());
 628     if (annSortOrder != null)
 629     {
 630       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 631               annSortOrder.name());
 632     }
 633
 634     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 635     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 636             Boolean.valueOf(showAutocalcFirst).toString());
 637
 638     /*
 639      * Save Colours settings
 640      */
 641     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 642             protColour.getSelectedItem().toString());
 643     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 644             nucColour.getSelectedItem().toString());
 645     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 646             minColour.getBackground());
 647     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 648             maxColour.getBackground());
 649
 650     /*
 651      * Save Overview settings
 652      */
 653     Cache.setColourProperty("GAP_COLOUR", gapColour.getBackground());
 654     Cache.setColourProperty("HIDDEN_COLOUR", hiddenColour.getBackground());
 655     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 656             Boolean.toString(useLegacyGap.isSelected()));
 657     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 658             Boolean.toString(showHiddenAtStart.isSelected()));
 659
 660     /*
 661      * Save Structure settings
 662      */
 663     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 664             Boolean.toString(addTempFactor.isSelected()));
 665     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 666             Boolean.toString(addSecondaryStructure.isSelected()));
 667     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 668             Boolean.toString(useRnaView.isSelected()));
 669     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 670             Boolean.toString(structFromPdb.isSelected()));
 671     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 672             structViewer.getSelectedItem().toString());
 673     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 674     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 675             Boolean.toString(siftsMapping.isSelected()));
 676     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 677
 678     /*
 679      * Save Output settings
 680      */
 681     Cache.applicationProperties.setProperty("EPS_RENDERING",
 682             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 683
 684     /*
 685      * Save Connections settings
 686      */
 687     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 688
 689     jalview.util.BrowserLauncher.resetBrowser();
 690
 691     // save user-defined and selected links
 692     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 693     if (menuLinks.isEmpty())
 694     {
 695       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 696     }
 697     else
 698     {
 699       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 700               menuLinks.toString());
 701     }
 702
 703     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 704     if (nonMenuLinks.isEmpty())
 705     {
 706       Cache.applicationProperties.remove("STORED_LINKS");
 707     }
 708     else
 709     {
 710       Cache.applicationProperties.setProperty("STORED_LINKS",
 711               nonMenuLinks.toString());
 712     }
 713
 714     Cache.applicationProperties.setProperty("DEFAULT_URL",
 715             sequenceUrlLinks.getPrimaryUrlId());
 716
 717     Cache.applicationProperties.setProperty("USE_PROXY",
 718             Boolean.toString(useProxy.isSelected()));
 719
 720     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 721
 722     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 723
 724     if (useProxy.isSelected())
 725     {
 726       System.setProperty("http.proxyHost", proxyServerTB.getText());
 727       System.setProperty("http.proxyPort", proxyPortTB.getText());
 728     }
 729     else
 730     {
 731       System.setProperty("http.proxyHost", "");
 732       System.setProperty("http.proxyPort", "");
 733     }
 734     Cache.setProperty("VERSION_CHECK",
 735             Boolean.toString(versioncheck.isSelected()));
 736     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 737     {
 738       // default is false - we only set this if the user has actively agreed
 739       Cache.setProperty("USAGESTATS",
 740               Boolean.toString(usagestats.isSelected()));
 741     }
 742     if (!questionnaire.isSelected())
 743     {
 744       Cache.setProperty("NOQUESTIONNAIRES", "true");
 745     }
 746     else
 747     {
 748       // special - made easy to edit a property file to disable questionnaires
 749       // by just adding the given line
 750       Cache.removeProperty("NOQUESTIONNAIRES");
 751     }
 752
 753     /*
 754      * Save Output settings
 755      */
 756     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 757             Boolean.toString(blcjv.isSelected()));
 758     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 759             Boolean.toString(clustaljv.isSelected()));
 760     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 761             Boolean.toString(fastajv.isSelected()));
 762     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 763             Boolean.toString(msfjv.isSelected()));
 764     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 765             Boolean.toString(pfamjv.isSelected()));
 766     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 767             Boolean.toString(pileupjv.isSelected()));
 768     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 769             Boolean.toString(pirjv.isSelected()));
 770     Cache.applicationProperties.setProperty("PIR_MODELLER",
 771             Boolean.toString(modellerOutput.isSelected()));
 772     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 773             Boolean.toString(embbedBioJSON.isSelected()));
 774     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 775
 776     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 777             Boolean.toString(autoIdWidth.isSelected()));
 778     userIdWidth_actionPerformed();
 779     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 780             userIdWidth.getText());
 781
 782     /*
 783      * Save Editing settings
 784      */
 785     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 786             Boolean.toString(autoCalculateConsCheck.isSelected()));
 787     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 788             Boolean.toString(sortByTree.isSelected()));
 789     Cache.applicationProperties.setProperty("PAD_GAPS",
 790             Boolean.toString(padGaps.isSelected()));
 791
 792     dasSource.saveProperties(Cache.applicationProperties);
 793     wsPrefs.updateAndRefreshWsMenuConfig(false);
 794     Cache.saveProperties();
 795     Desktop.instance.doConfigureStructurePrefs();
 796     try
 797     {
 798       frame.setClosed(true);
 799     } catch (Exception ex)
 800     {
 801     }
 802   }
 803
 804   /**
 805    * Do any necessary validation before saving settings. Return focus to the
 806    * first tab which fails validation.
 807    *
 808    * @return
 809    */
 810   private boolean validateSettings()
 811   {
 812     if (!validateStructure())
 813     {
 814       structureTab.requestFocusInWindow();
 815       return false;
 816     }
 817     return true;
 818   }
 819
 820   @Override
 821   protected boolean validateStructure()
 822   {
 823     return validateChimeraPath();
 824
 825   }
 826
 827   /**
 828    * DOCUMENT ME!
 829    */
 830   @Override
 831   public void startupFileTextfield_mouseClicked()
 832   {
 833     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 834     JalviewFileChooser chooser = JalviewFileChooser
 835             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 836     chooser.setFileView(new JalviewFileView());
 837     chooser.setDialogTitle(
 838             MessageManager.getString("label.select_startup_file"));
 839
 840     int value = chooser.showOpenDialog(this);
 841
 842     if (value == JalviewFileChooser.APPROVE_OPTION)
 843     {
 844       FileFormatI format = chooser.getSelectedFormat();
 845       if (format != null)
 846       {
 847         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 848                 format.getName());
 849       }
 850       startupFileTextfield
 851               .setText(chooser.getSelectedFile().getAbsolutePath());
 852     }
 853   }
 854
 855   /**
 856    * DOCUMENT ME!
 857    *
 858    * @param e
 859    *          DOCUMENT ME!
 860    */
 861   @Override
 862   public void cancel_actionPerformed(ActionEvent e)
 863   {
 864     try
 865     {
 866       wsPrefs.updateWsMenuConfig(true);
 867       wsPrefs.refreshWs_actionPerformed(e);
 868       frame.setClosed(true);
 869     } catch (Exception ex)
 870     {
 871     }
 872   }
 873
 874   /**
 875    * DOCUMENT ME!
 876    *
 877    * @param e
 878    *          DOCUMENT ME!
 879    */
 880   @Override
 881   public void annotations_actionPerformed(ActionEvent e)
 882   {
 883     conservation.setEnabled(annotations.isSelected());
 884     quality.setEnabled(annotations.isSelected());
 885     identity.setEnabled(annotations.isSelected());
 886     showOccupancy.setEnabled(annotations.isSelected());
 887     showGroupConsensus.setEnabled(annotations.isSelected());
 888     showGroupConservation.setEnabled(annotations.isSelected());
 889     showConsensHistogram.setEnabled(annotations.isSelected()
 890             && (identity.isSelected() || showGroupConsensus.isSelected()));
 891     showConsensLogo.setEnabled(annotations.isSelected()
 892             && (identity.isSelected() || showGroupConsensus.isSelected()));
 893   }
 894
 895   @Override
 896   public void newLink_actionPerformed(ActionEvent e)
 897   {
 898     GSequenceLink link = new GSequenceLink();
 899     boolean valid = false;
 900     while (!valid)
 901     {
 902       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 903               MessageManager.getString("label.new_sequence_url_link"),
 904               JvOptionPane.OK_CANCEL_OPTION, -1,
 905               null) == JvOptionPane.OK_OPTION)
 906       {
 907         if (link.checkValid())
 908         {
 909           if (((UrlLinkTableModel) linkUrlTable.getModel())
 910                   .isUniqueName(link.getName()))
 911           {
 912             ((UrlLinkTableModel) linkUrlTable.getModel())
 913                     .insertRow(link.getName(), link.getURL());
 914             valid = true;
 915           }
 916           else
 917           {
 918             link.notifyDuplicate();
 919             continue;
 920           }
 921         }
 922       }
 923       else
 924       {
 925         break;
 926       }
 927     }
 928   }
 929
 930   @Override
 931   public void editLink_actionPerformed(ActionEvent e)
 932   {
 933     GSequenceLink link = new GSequenceLink();
 934
 935     int index = linkUrlTable.getSelectedRow();
 936     if (index == -1)
 937     {
 938       // button no longer enabled if row is not selected
 939       Cache.log.debug("Edit with no row selected in linkUrlTable");
 940       return;
 941     }
 942
 943     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 944             .getNameColumn();
 945     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 946             .getUrlColumn();
 947     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 948     link.setName(oldName);
 949     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 950
 951     boolean valid = false;
 952     while (!valid)
 953     {
 954       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 955               MessageManager.getString("label.edit_sequence_url_link"),
 956               JvOptionPane.OK_CANCEL_OPTION, -1,
 957               null) == JvOptionPane.OK_OPTION)
 958       {
 959         if (link.checkValid())
 960         {
 961           if ((oldName.equals(link.getName()))
 962                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 963                           .isUniqueName(link.getName())))
 964           {
 965             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 966             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 967             valid = true;
 968           }
 969           else
 970           {
 971             link.notifyDuplicate();
 972             continue;
 973           }
 974         }
 975       }
 976       else
 977       {
 978         break;
 979       }
 980     }
 981   }
 982
 983   @Override
 984   public void deleteLink_actionPerformed(ActionEvent e)
 985   {
 986     int index = linkUrlTable.getSelectedRow();
 987     int modelIndex = -1;
 988     if (index == -1)
 989     {
 990       // button no longer enabled if row is not selected
 991       Cache.log.debug("Delete with no row selected in linkUrlTable");
 992       return;
 993     }
 994     else
 995     {
 996       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 997     }
 998
 999     // make sure we use the model index to delete, and not the table index
1000     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1001   }
1002
1003   @Override
1004   public void defaultBrowser_mouseClicked(MouseEvent e)
1005   {
1006     JFileChooser chooser = new JFileChooser(".");
1007     chooser.setDialogTitle(
1008             MessageManager.getString("label.select_default_browser"));
1009
1010     int value = chooser.showOpenDialog(this);
1011
1012     if (value == JFileChooser.APPROVE_OPTION)
1013     {
1014       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1015     }
1016
1017   }
1018
1019   /*
1020    * (non-Javadoc)
1021    *
1022    * @see
1023    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1024    * .ActionEvent)
1025    */
1026   @Override
1027   protected void showunconserved_actionPerformed(ActionEvent e)
1028   {
1029     // TODO Auto-generated method stub
1030     super.showunconserved_actionPerformed(e);
1031   }
1032
1033   public static List<String> getGroupURLLinks()
1034   {
1035     return groupURLLinks;
1036   }
1037
1038   @Override
1039   public void minColour_actionPerformed(JPanel panel)
1040   {
1041     Color col = JColorChooser.showDialog(this,
1042             MessageManager.getString("label.select_colour_minimum_value"),
1043             minColour.getBackground());
1044     if (col != null)
1045     {
1046       panel.setBackground(col);
1047     }
1048     panel.repaint();
1049   }
1050
1051   @Override
1052   public void maxColour_actionPerformed(JPanel panel)
1053   {
1054     Color col = JColorChooser.showDialog(this,
1055             MessageManager.getString("label.select_colour_maximum_value"),
1056             maxColour.getBackground());
1057     if (col != null)
1058     {
1059       panel.setBackground(col);
1060     }
1061     panel.repaint();
1062   }
1063
1064   @Override
1065   public void gapColour_actionPerformed(JPanel gap)
1066   {
1067     if (!useLegacyGap.isSelected())
1068     {
1069       Color col = JColorChooser.showDialog(this,
1070               MessageManager.getString("label.select_gap_colour"),
1071               gapColour.getBackground());
1072       if (col != null)
1073       {
1074         gap.setBackground(col);
1075       }
1076       gap.repaint();
1077     }
1078   }
1079
1080   @Override
1081   public void hiddenColour_actionPerformed(JPanel hidden)
1082   {
1083     Color col = JColorChooser.showDialog(this,
1084             MessageManager.getString("label.select_hidden_colour"),
1085             hiddenColour.getBackground());
1086     if (col != null)
1087     {
1088       hidden.setBackground(col);
1089     }
1090     hidden.repaint();
1091   }
1092
1093   @Override
1094   protected void userIdWidth_actionPerformed()
1095   {
1096     try
1097     {
1098       String val = userIdWidth.getText().trim();
1099       if (val.length() > 0)
1100       {
1101         Integer iw = Integer.parseInt(val);
1102         if (iw.intValue() < 12)
1103         {
1104           throw new NumberFormatException();
1105         }
1106         userIdWidth.setText(iw.toString());
1107       }
1108     } catch (NumberFormatException x)
1109     {
1110       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1111               MessageManager
1112                       .getString("warn.user_defined_width_requirements"),
1113               MessageManager.getString("label.invalid_id_column_width"),
1114               JvOptionPane.WARNING_MESSAGE);
1115       userIdWidth.setText("");
1116     }
1117   }
1118
1119   @Override
1120   protected void autoIdWidth_actionPerformed()
1121   {
1122     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1123     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1124   }
1125
1126   /**
1127    * Returns true if chimera path is to a valid executable, else show an error
1128    * dialog.
1129    */
1130   private boolean validateChimeraPath()
1131   {
1132     if (chimeraPath.getText().trim().length() > 0)
1133     {
1134       File f = new File(chimeraPath.getText());
1135       if (!f.canExecute())
1136       {
1137         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1138                 MessageManager.getString("label.invalid_chimera_path"),
1139                 MessageManager.getString("label.invalid_name"),
1140                 JvOptionPane.ERROR_MESSAGE);
1141         return false;
1142       }
1143     }
1144     return true;
1145   }
1146
1147   /**
1148    * If Chimera is selected, check it can be found on default or user-specified
1149    * path, if not show a warning/help dialog.
1150    */
1151   @Override
1152   protected void structureViewer_actionPerformed(String selectedItem)
1153   {
1154     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1155     {
1156       return;
1157     }
1158     boolean found = false;
1159
1160     /*
1161      * Try user-specified and standard paths for Chimera executable.
1162      */
1163     List<String> paths = StructureManager.getChimeraPaths();
1164     paths.add(0, chimeraPath.getText());
1165     for (String path : paths)
1166     {
1167       if (new File(path.trim()).canExecute())
1168       {
1169         found = true;
1170         break;
1171       }
1172     }
1173     if (!found)
1174     {
1175       String[] options = { "OK", "Help" };
1176       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1177               JvSwingUtils.wrapTooltip(true,
1178                       MessageManager.getString("label.chimera_missing")),
1179               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1180               null, options, options[0]);
1181       if (showHelp == JvOptionPane.NO_OPTION)
1182       {
1183         try
1184         {
1185           Help.showHelpWindow(HelpId.StructureViewer);
1186         } catch (HelpSetException e)
1187         {
1188           e.printStackTrace();
1189         }
1190       }
1191     }
1192   }
1193
1194   public class OptionsParam
1195   {
1196     private String name;
1197
1198     private String code;
1199
1200     public OptionsParam(String name, String code)
1201     {
1202       this.name = name;
1203       this.code = code;
1204     }
1205
1206     public String getName()
1207     {
1208       return name;
1209     }
1210
1211     public void setName(String name)
1212     {
1213       this.name = name;
1214     }
1215
1216     public String getCode()
1217     {
1218       return code;
1219     }
1220
1221     public void setCode(String code)
1222     {
1223       this.code = code;
1224     }
1225
1226     @Override
1227     public String toString()
1228     {
1229       return name;
1230     }
1231
1232     @Override
1233     public boolean equals(Object that)
1234     {
1235       if (!(that instanceof OptionsParam))
1236       {
1237         return false;
1238       }
1239       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1240     }
1241
1242     @Override
1243     public int hashCode()
1244     {
1245       return name.hashCode() + code.hashCode();
1246     }
1247   }
1248
1249   private class UrlListSelectionHandler implements ListSelectionListener
1250   {
1251
1252     @Override
1253     public void valueChanged(ListSelectionEvent e)
1254     {
1255       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1256
1257       int index = lsm.getMinSelectionIndex();
1258       if (index == -1)
1259       {
1260         // no selection, so disable delete/edit buttons
1261         editLink.setEnabled(false);
1262         deleteLink.setEnabled(false);
1263         return;
1264       }
1265       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1266
1267       // enable/disable edit and delete link buttons
1268       if (((UrlLinkTableModel) linkUrlTable.getModel())
1269               .isRowDeletable(modelIndex))
1270       {
1271         deleteLink.setEnabled(true);
1272       }
1273       else
1274       {
1275         deleteLink.setEnabled(false);
1276       }
1277
1278       if (((UrlLinkTableModel) linkUrlTable.getModel())
1279               .isRowEditable(modelIndex))
1280       {
1281         editLink.setEnabled(true);
1282       }
1283       else
1284       {
1285         editLink.setEnabled(false);
1286       }
1287     }
1288   }
1289 }