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.JComboBox;
  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   public static final String GAP_COLOUR = "GAP_COLOUR";
 117
 118   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 119
 120   private static final int MIN_FONT_SIZE = 1;
 121
 122   private static final int MAX_FONT_SIZE = 30;
 123
 124   /**
 125    * Holds name and link separated with | character. Sequence ID must be
 126    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 127    */
 128   public static UrlProviderI sequenceUrlLinks;
 129
 130   public static UrlLinkTableModel dataModel;
 131
 132   /**
 133    * Holds name and link separated with | character. Sequence IDS and Sequences
 134    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 135    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 136    * for first and second token specified after a pipe character at end |,|.
 137    * (TODO: proper escape for using | to separate ids or sequences
 138    */
 139
 140   public static List<String> groupURLLinks;
 141   static
 142   {
 143     // get links selected to be in the menu (SEQUENCE_LINKS)
 144     // and links entered by the user but not selected (STORED_LINKS)
 145     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 146     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 147     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 148             UrlConstants.DEFAULT_LABEL);
 149
 150     // if both links lists are empty, add the DEFAULT_URL link
 151     // otherwise we assume the default link is in one of the lists
 152     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 153     {
 154       inMenuString = UrlConstants.DEFAULT_STRING;
 155     }
 156     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 157             inMenuString, notInMenuString);
 158     sequenceUrlLinks = factory.createUrlProvider();
 159     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 160
 161     /**
 162      * TODO: reformulate groupURL encoding so two or more can be stored in the
 163      * .properties file as '|' separated strings
 164      */
 165
 166     groupURLLinks = new ArrayList<>();
 167   }
 168
 169   JInternalFrame frame;
 170
 171   private WsPreferences wsPrefs;
 172
 173   private OptionsParam promptEachTimeOpt = new OptionsParam(
 174           MessageManager.getString("label.prompt_each_time"),
 175           "Prompt each time");
 176
 177   private OptionsParam lineArtOpt = new OptionsParam(
 178           MessageManager.getString("label.lineart"), "Lineart");
 179
 180   private OptionsParam textOpt = new OptionsParam(
 181           MessageManager.getString("action.text"), "Text");
 182
 183   /**
 184    * Creates a new Preferences object.
 185    */
 186   public Preferences()
 187   {
 188     super();
 189     frame = new JInternalFrame();
 190     frame.setContentPane(this);
 191     if (!Platform.isJS())
 192     {
 193       wsPrefs = new WsPreferences();
 194       wsTab.add(wsPrefs, BorderLayout.CENTER);
 195     }
 196     int width = 500, height = 450;
 197     if (Platform.isAMacAndNotJS())
 198     {
 199       width = 570;
 200       height = 480;
 201     }
 202
 203     Desktop.addInternalFrame(frame,
 204             MessageManager.getString("label.preferences"), width, height);
 205     frame.setMinimumSize(new Dimension(width, height));
 206
 207     /*
 208      * Set Visual tab defaults
 209      */
 210     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 211     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 212     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 213     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 214
 215     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 216     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 217     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 218     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 219     showUnconserved
 220             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 221     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 222     showGroupConsensus
 223             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 224     showGroupConservation.setSelected(
 225             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 226     showConsensHistogram.setSelected(
 227             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 228     showConsensLogo
 229             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 230     showNpTooltip
 231             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 232     showDbRefTooltip
 233             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 234
 235     String[] fonts = java.awt.GraphicsEnvironment
 236             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 237     for (int i = 0; i < fonts.length; i++)
 238     {
 239       fontNameCB.addItem(fonts[i]);
 240     }
 241
 242     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 243     {
 244       fontSizeCB.addItem(i + "");
 245     }
 246
 247     fontStyleCB.addItem("plain");
 248     fontStyleCB.addItem("bold");
 249     fontStyleCB.addItem("italic");
 250
 251     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 252     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 253     fontStyleCB.setSelectedItem(
 254             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 255
 256     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 257     scaleProteinToCdna
 258             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 259
 260     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 261
 262     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 263
 264     gapSymbolCB.addItem("-");
 265     gapSymbolCB.addItem(".");
 266
 267     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 268
 269     sortby.addItem("No sort");
 270     sortby.addItem("Id");
 271     sortby.addItem("Pairwise Identity");
 272     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 273
 274     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 275     sortAnnBy
 276             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 277     sortAnnBy
 278             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 279     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 280             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 281                     SequenceAnnotationOrder.NONE.name()));
 282     sortAnnBy.setSelectedItem(savedSort.toString());
 283
 284     sortAutocalc.addItem("Autocalculated first");
 285     sortAutocalc.addItem("Autocalculated last");
 286     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 287     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 288             : sortAutocalc.getItemAt(1));
 289     startupCheckbox
 290             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 291     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 292             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 293                     + "/examples/exampleFile_2_3.jar"));
 294
 295     /*
 296      * Set Colours tab defaults
 297      */
 298     protColour.addItem(ResidueColourScheme.NONE);
 299     nucColour.addItem(ResidueColourScheme.NONE);
 300     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 301     {
 302       String name = cs.getSchemeName();
 303       protColour.addItem(name);
 304       nucColour.addItem(name);
 305     }
 306     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 307             ResidueColourScheme.NONE);
 308     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 309     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 310     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 311     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 312     minColour.setBackground(
 313             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 314     maxColour.setBackground(
 315             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 316
 317     /*
 318      * Set overview panel defaults
 319      */
 320     gapColour.setBackground(
 321             Cache.getDefaultColour(GAP_COLOUR,
 322                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 323     hiddenColour.setBackground(
 324             Cache.getDefaultColour(HIDDEN_COLOUR,
 325                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 326     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 327     gapLabel.setEnabled(!useLegacyGap.isSelected());
 328     gapColour.setEnabled(!useLegacyGap.isSelected());
 329     showHiddenAtStart
 330             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 331
 332     /*
 333      * Set Structure tab defaults.
 334      */
 335     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 336     structFromPdb.setSelected(structSelected);
 337     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 338     useRnaView.setEnabled(structSelected);
 339     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 340     addSecondaryStructure.setEnabled(structSelected);
 341     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 342     addTempFactor.setEnabled(structSelected);
 343     structViewer.setSelectedItem(
 344             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 345     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 346     chimeraPath.addActionListener(new ActionListener()
 347     {
 348       @Override
 349       public void actionPerformed(ActionEvent e)
 350       {
 351         validateChimeraPath();
 352       }
 353     });
 354
 355     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 356     {
 357       siftsMapping.setSelected(true);
 358     }
 359     else
 360     {
 361       nwMapping.setSelected(true);
 362     }
 363
 364     SiftsSettings
 365             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 366
 367     /*
 368      * Set Connections tab defaults
 369      */
 370
 371     // set up sorting
 372     linkUrlTable.setModel(dataModel);
 373     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 374             linkUrlTable.getModel());
 375     linkUrlTable.setRowSorter(sorter);
 376     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 377
 378     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 379     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 380             SortOrder.DESCENDING));
 381     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 382             SortOrder.DESCENDING));
 383     sortKeys.add(
 384             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 385
 386     sorter.setSortKeys(sortKeys);
 387     // BH 2018 setSortKeys will do the sort
 388     // sorter.sort();
 389
 390     // set up filtering
 391     ActionListener onReset;
 392     onReset = new ActionListener()
 393     {
 394       @Override
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         filterTB.setText("");
 398         sorter.setRowFilter(RowFilter.regexFilter(""));
 399       }
 400
 401     };
 402     doReset.addActionListener(onReset);
 403
 404     // filter to display only custom urls
 405     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 406     {
 407       @Override
 408       public boolean include(
 409               Entry<? extends TableModel, ? extends Object> entry)
 410       {
 411         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 412       }
 413     };
 414
 415     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 416             linkUrlTable.getModel());
 417     customSorter.setRowFilter(customUrlFilter);
 418
 419     ActionListener onCustomOnly;
 420     onCustomOnly = new ActionListener()
 421     {
 422       @Override
 423       public void actionPerformed(ActionEvent e)
 424       {
 425         filterTB.setText("");
 426         sorter.setRowFilter(customUrlFilter);
 427       }
 428     };
 429     userOnly.addActionListener(onCustomOnly);
 430
 431     filterTB.getDocument().addDocumentListener(new DocumentListener()
 432     {
 433       String caseInsensitiveFlag = "(?i)";
 434
 435       @Override
 436       public void changedUpdate(DocumentEvent e)
 437       {
 438         sorter.setRowFilter(RowFilter
 439                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 440       }
 441
 442       @Override
 443       public void removeUpdate(DocumentEvent e)
 444       {
 445         sorter.setRowFilter(RowFilter
 446                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 447       }
 448
 449       @Override
 450       public void insertUpdate(DocumentEvent e)
 451       {
 452         sorter.setRowFilter(RowFilter
 453                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 454       }
 455     });
 456
 457     // set up list selection functionality
 458     linkUrlTable.getSelectionModel()
 459             .addListSelectionListener(new UrlListSelectionHandler());
 460
 461     // set up radio buttons
 462     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 463             .getPrimaryColumn();
 464     String onClickName = linkUrlTable.getColumnName(onClickCol);
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellRenderer(new RadioButtonRenderer());
 467     linkUrlTable.getColumn(onClickName)
 468             .setCellEditor(new RadioButtonEditor());
 469
 470     // get boolean columns and resize those to min possible
 471     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 472     {
 473       if (linkUrlTable.getModel().getColumnClass(column)
 474               .equals(Boolean.class))
 475       {
 476         TableColumn tableColumn = linkUrlTable.getColumnModel()
 477                 .getColumn(column);
 478         int preferredWidth = tableColumn.getMinWidth();
 479
 480         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 481                 column);
 482         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 483         int cwidth = c.getPreferredSize().width
 484                 + linkUrlTable.getIntercellSpacing().width;
 485         preferredWidth = Math.max(preferredWidth, cwidth);
 486
 487         tableColumn.setPreferredWidth(preferredWidth);
 488       }
 489     }
 490
 491     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 492     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 493     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 494     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 495
 496     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 497
 498     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 499     // note antisense here: default is true
 500     questionnaire
 501             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 502     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 503
 504     /*
 505      * Set Output tab defaults
 506      */
 507     setupOutputCombo(epsRendering, "EPS_RENDERING");
 508     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 509     setupOutputCombo(svgRendering, "SVG_RENDERING");
 510     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 511     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 512     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 513     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 514     userIdWidth.setText(wi == null ? "" : wi.toString());
 515     // TODO: refactor to use common enum via FormatAdapter and allow extension
 516     // for new flat file formats
 517     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 518     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 519     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 520     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 521     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 522     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 523     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 524     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 525     embbedBioJSON
 526             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 527
 528     /*
 529      * Set Editing tab defaults
 530      */
 531     autoCalculateConsCheck
 532             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 533     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 534     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 535
 536     annotations_actionPerformed(null); // update the display of the annotation
 537                                        // settings
 538   }
 539
 540   /**
 541    * A helper method that sets the items and initial selection in a character
 542    * rendering option list (Prompt each time/Lineart/Text)
 543    *
 544    * @param comboBox
 545    * @param propertyKey
 546    */
 547   protected void setupOutputCombo(JComboBox<Object> comboBox,
 548           String propertyKey)
 549   {
 550     comboBox.addItem(promptEachTimeOpt);
 551     comboBox.addItem(lineArtOpt);
 552     comboBox.addItem(textOpt);
 553
 554     /*
 555      * JalviewJS doesn't support Lineart so force it to Text
 556      */
 557     String defaultOption = Platform.isJS() ? "Text"
 558             : Cache.getDefault(propertyKey, "Prompt each time");
 559     if (defaultOption.equalsIgnoreCase("Text"))
 560     {
 561       comboBox.setSelectedItem(textOpt);
 562     }
 563     else if (defaultOption.equalsIgnoreCase("Lineart"))
 564     {
 565       comboBox.setSelectedItem(lineArtOpt);
 566     }
 567     else
 568     {
 569       comboBox.setSelectedItem(promptEachTimeOpt);
 570     }
 571   }
 572
 573   /**
 574    * Save user selections on the Preferences tabs to the Cache and write out to
 575    * file.
 576    *
 577    * @param e
 578    */
 579   @Override
 580   public void ok_actionPerformed(ActionEvent e)
 581   {
 582     if (!validateSettings())
 583     {
 584       return;
 585     }
 586
 587     /*
 588      * Save Visual settings
 589      */
 590     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 591             Boolean.toString(seqLimit.isSelected()));
 592     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 593             Boolean.toString(rightAlign.isSelected()));
 594     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 595             Boolean.toString(fullScreen.isSelected()));
 596     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 597             Boolean.toString(openoverv.isSelected()));
 598     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 599             Boolean.toString(annotations.isSelected()));
 600     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 601             Boolean.toString(conservation.isSelected()));
 602     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 603             Boolean.toString(quality.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 605             Boolean.toString(identity.isSelected()));
 606
 607     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 608             gapSymbolCB.getSelectedItem().toString());
 609
 610     Cache.applicationProperties.setProperty("FONT_NAME",
 611             fontNameCB.getSelectedItem().toString());
 612     Cache.applicationProperties.setProperty("FONT_STYLE",
 613             fontStyleCB.getSelectedItem().toString());
 614     Cache.applicationProperties.setProperty("FONT_SIZE",
 615             fontSizeCB.getSelectedItem().toString());
 616
 617     Cache.applicationProperties.setProperty("ID_ITALICS",
 618             Boolean.toString(idItalics.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 620             Boolean.toString(showUnconserved.isSelected()));
 621     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 622             Boolean.toString(showOccupancy.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 624             Boolean.toString(showGroupConsensus.isSelected()));
 625     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 626             Boolean.toString(showGroupConservation.isSelected()));
 627     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 628             Boolean.toString(showConsensHistogram.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 630             Boolean.toString(showConsensLogo.isSelected()));
 631     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 632             Boolean.toString(smoothFont.isSelected()));
 633     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 634             Boolean.toString(scaleProteinToCdna.isSelected()));
 635     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 636             Boolean.toString(showNpTooltip.isSelected()));
 637     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 638             Boolean.toString(showDbRefTooltip.isSelected()));
 639
 640     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 641             Boolean.toString(wrap.isSelected()));
 642
 643     Cache.applicationProperties.setProperty("STARTUP_FILE",
 644             startupFileTextfield.getText());
 645     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 646             Boolean.toString(startupCheckbox.isSelected()));
 647
 648     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 649             sortby.getSelectedItem().toString());
 650
 651     // convert description of sort order to enum name for save
 652     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 653             .forDescription(sortAnnBy.getSelectedItem().toString());
 654     if (annSortOrder != null)
 655     {
 656       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 657               annSortOrder.name());
 658     }
 659
 660     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 661     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 662             Boolean.valueOf(showAutocalcFirst).toString());
 663
 664     /*
 665      * Save Colours settings
 666      */
 667     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 668             protColour.getSelectedItem().toString());
 669     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 670             nucColour.getSelectedItem().toString());
 671     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 672             minColour.getBackground());
 673     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 674             maxColour.getBackground());
 675
 676     /*
 677      * Save Overview settings
 678      */
 679     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 680     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 681     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 682             Boolean.toString(useLegacyGap.isSelected()));
 683     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 684             Boolean.toString(showHiddenAtStart.isSelected()));
 685
 686     /*
 687      * Save Structure settings
 688      */
 689     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 690             Boolean.toString(addTempFactor.isSelected()));
 691     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 692             Boolean.toString(addSecondaryStructure.isSelected()));
 693     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 694             Boolean.toString(useRnaView.isSelected()));
 695     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 696             Boolean.toString(structFromPdb.isSelected()));
 697     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 698             structViewer.getSelectedItem().toString());
 699     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 700     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 701             Boolean.toString(siftsMapping.isSelected()));
 702     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 703
 704     /*
 705      * Save Output settings
 706      */
 707     Cache.applicationProperties.setProperty("EPS_RENDERING",
 708             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 709     Cache.applicationProperties.setProperty("HTML_RENDERING",
 710             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 711     Cache.applicationProperties.setProperty("SVG_RENDERING",
 712             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 713
 714     /*
 715      * Save Connections settings
 716      */
 717     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 718
 719     jalview.util.BrowserLauncher.resetBrowser();
 720
 721     // save user-defined and selected links
 722     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 723     if (menuLinks.isEmpty())
 724     {
 725       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 726     }
 727     else
 728     {
 729       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 730               menuLinks.toString());
 731     }
 732
 733     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 734     if (nonMenuLinks.isEmpty())
 735     {
 736       Cache.applicationProperties.remove("STORED_LINKS");
 737     }
 738     else
 739     {
 740       Cache.applicationProperties.setProperty("STORED_LINKS",
 741               nonMenuLinks.toString());
 742     }
 743
 744     Cache.applicationProperties.setProperty("DEFAULT_URL",
 745             sequenceUrlLinks.getPrimaryUrlId());
 746
 747     Cache.applicationProperties.setProperty("USE_PROXY",
 748             Boolean.toString(useProxy.isSelected()));
 749
 750     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 751
 752     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 753
 754     if (useProxy.isSelected())
 755     {
 756       System.setProperty("http.proxyHost", proxyServerTB.getText());
 757       System.setProperty("http.proxyPort", proxyPortTB.getText());
 758     }
 759     else
 760     {
 761       System.setProperty("http.proxyHost", "");
 762       System.setProperty("http.proxyPort", "");
 763     }
 764     Cache.setProperty("VERSION_CHECK",
 765             Boolean.toString(versioncheck.isSelected()));
 766     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 767     {
 768       // default is false - we only set this if the user has actively agreed
 769       Cache.setProperty("USAGESTATS",
 770               Boolean.toString(usagestats.isSelected()));
 771     }
 772     if (!questionnaire.isSelected())
 773     {
 774       Cache.setProperty("NOQUESTIONNAIRES", "true");
 775     }
 776     else
 777     {
 778       // special - made easy to edit a property file to disable questionnaires
 779       // by just adding the given line
 780       Cache.removeProperty("NOQUESTIONNAIRES");
 781     }
 782
 783     /*
 784      * Save Output settings
 785      */
 786     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 787             Boolean.toString(blcjv.isSelected()));
 788     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 789             Boolean.toString(clustaljv.isSelected()));
 790     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 791             Boolean.toString(fastajv.isSelected()));
 792     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 793             Boolean.toString(msfjv.isSelected()));
 794     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 795             Boolean.toString(pfamjv.isSelected()));
 796     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 797             Boolean.toString(pileupjv.isSelected()));
 798     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 799             Boolean.toString(pirjv.isSelected()));
 800     Cache.applicationProperties.setProperty("PIR_MODELLER",
 801             Boolean.toString(modellerOutput.isSelected()));
 802     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 803             Boolean.toString(embbedBioJSON.isSelected()));
 804     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 805
 806     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 807             Boolean.toString(autoIdWidth.isSelected()));
 808     userIdWidth_actionPerformed();
 809     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 810             userIdWidth.getText());
 811
 812     /*
 813      * Save Editing settings
 814      */
 815     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 816             Boolean.toString(autoCalculateConsCheck.isSelected()));
 817     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 818             Boolean.toString(sortByTree.isSelected()));
 819     Cache.applicationProperties.setProperty("PAD_GAPS",
 820             Boolean.toString(padGaps.isSelected()));
 821
 822     if (!Platform.isJS())
 823     {
 824       wsPrefs.updateAndRefreshWsMenuConfig(false);
 825     }
 826     Cache.saveProperties();
 827     Desktop.instance.doConfigureStructurePrefs();
 828     try
 829     {
 830       frame.setClosed(true);
 831     } catch (Exception ex)
 832     {
 833     }
 834   }
 835
 836   /**
 837    * Do any necessary validation before saving settings. Return focus to the
 838    * first tab which fails validation.
 839    *
 840    * @return
 841    */
 842   private boolean validateSettings()
 843   {
 844     if (!validateStructure())
 845     {
 846       structureTab.requestFocusInWindow();
 847       return false;
 848     }
 849     return true;
 850   }
 851
 852   @Override
 853   protected boolean validateStructure()
 854   {
 855     return validateChimeraPath();
 856
 857   }
 858
 859   /**
 860    * DOCUMENT ME!
 861    */
 862   @Override
 863   public void startupFileTextfield_mouseClicked()
 864   {
 865     // TODO: JAL-3048 not needed for Jalview-JS
 866     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 867     JalviewFileChooser chooser = JalviewFileChooser
 868             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 869     chooser.setFileView(new JalviewFileView());
 870     chooser.setDialogTitle(
 871             MessageManager.getString("label.select_startup_file"));
 872
 873     int value = chooser.showOpenDialog(this);
 874
 875     if (value == JalviewFileChooser.APPROVE_OPTION)
 876     {
 877       FileFormatI format = chooser.getSelectedFormat();
 878       if (format != null)
 879       {
 880         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 881                 format.getName());
 882       }
 883       startupFileTextfield
 884               .setText(chooser.getSelectedFile().getAbsolutePath());
 885     }
 886   }
 887
 888   /**
 889    * DOCUMENT ME!
 890    *
 891    * @param e
 892    *          DOCUMENT ME!
 893    */
 894   @Override
 895   public void cancel_actionPerformed(ActionEvent e)
 896   {
 897     try
 898     {
 899       if (!Platform.isJS())
 900       {
 901         wsPrefs.updateWsMenuConfig(true);
 902         wsPrefs.refreshWs_actionPerformed(e);
 903       }
 904       frame.setClosed(true);
 905     } catch (Exception ex)
 906     {
 907     }
 908   }
 909
 910   /**
 911    * DOCUMENT ME!
 912    *
 913    * @param e
 914    *          DOCUMENT ME!
 915    */
 916   @Override
 917   public void annotations_actionPerformed(ActionEvent e)
 918   {
 919     conservation.setEnabled(annotations.isSelected());
 920     quality.setEnabled(annotations.isSelected());
 921     identity.setEnabled(annotations.isSelected());
 922     showOccupancy.setEnabled(annotations.isSelected());
 923     showGroupConsensus.setEnabled(annotations.isSelected());
 924     showGroupConservation.setEnabled(annotations.isSelected());
 925     showConsensHistogram.setEnabled(annotations.isSelected()
 926             && (identity.isSelected() || showGroupConsensus.isSelected()));
 927     showConsensLogo.setEnabled(annotations.isSelected()
 928             && (identity.isSelected() || showGroupConsensus.isSelected()));
 929   }
 930
 931   @Override
 932   public void newLink_actionPerformed(ActionEvent e)
 933   {
 934     GSequenceLink link = new GSequenceLink();
 935     boolean valid = false;
 936     while (!valid)
 937     {
 938       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 939               MessageManager.getString("label.new_sequence_url_link"),
 940               JvOptionPane.OK_CANCEL_OPTION, -1,
 941               null) == JvOptionPane.OK_OPTION)
 942       {
 943         if (link.checkValid())
 944         {
 945           if (((UrlLinkTableModel) linkUrlTable.getModel())
 946                   .isUniqueName(link.getName()))
 947           {
 948             ((UrlLinkTableModel) linkUrlTable.getModel())
 949                     .insertRow(link.getName(), link.getURL());
 950             valid = true;
 951           }
 952           else
 953           {
 954             link.notifyDuplicate();
 955             continue;
 956           }
 957         }
 958       }
 959       else
 960       {
 961         break;
 962       }
 963     }
 964   }
 965
 966   @Override
 967   public void editLink_actionPerformed(ActionEvent e)
 968   {
 969     GSequenceLink link = new GSequenceLink();
 970
 971     int index = linkUrlTable.getSelectedRow();
 972     if (index == -1)
 973     {
 974       // button no longer enabled if row is not selected
 975       Cache.log.debug("Edit with no row selected in linkUrlTable");
 976       return;
 977     }
 978
 979     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 980             .getNameColumn();
 981     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 982             .getUrlColumn();
 983     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 984     link.setName(oldName);
 985     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 986
 987     boolean valid = false;
 988     while (!valid)
 989     {
 990       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 991               MessageManager.getString("label.edit_sequence_url_link"),
 992               JvOptionPane.OK_CANCEL_OPTION, -1,
 993               null) == JvOptionPane.OK_OPTION)
 994       {
 995         if (link.checkValid())
 996         {
 997           if ((oldName.equals(link.getName()))
 998                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 999                           .isUniqueName(link.getName())))
1000           {
1001             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1002             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1003             valid = true;
1004           }
1005           else
1006           {
1007             link.notifyDuplicate();
1008             continue;
1009           }
1010         }
1011       }
1012       else
1013       {
1014         break;
1015       }
1016     }
1017   }
1018
1019   @Override
1020   public void deleteLink_actionPerformed(ActionEvent e)
1021   {
1022     int index = linkUrlTable.getSelectedRow();
1023     int modelIndex = -1;
1024     if (index == -1)
1025     {
1026       // button no longer enabled if row is not selected
1027       Cache.log.debug("Delete with no row selected in linkUrlTable");
1028       return;
1029     }
1030     else
1031     {
1032       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1033     }
1034
1035     // make sure we use the model index to delete, and not the table index
1036     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1037   }
1038
1039   @Override
1040   public void defaultBrowser_mouseClicked(MouseEvent e)
1041   {
1042     // TODO: JAL-3048 not needed for j2s
1043         if (Platform.isJS())
1044                 return;
1045     /*
1046      * @j2sNative
1047      */
1048     {
1049       JFileChooser chooser = new JFileChooser(".");
1050       chooser.setDialogTitle(
1051               MessageManager.getString("label.select_default_browser"));
1052
1053       int value = chooser.showOpenDialog(this);
1054
1055       if (value == JFileChooser.APPROVE_OPTION)
1056       {
1057         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1058       }
1059     }
1060   }
1061
1062   /*
1063    * (non-Javadoc)
1064    *
1065    * @see
1066    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1067    * .ActionEvent)
1068    */
1069   @Override
1070   protected void showunconserved_actionPerformed(ActionEvent e)
1071   {
1072     // TODO Auto-generated method stub
1073     super.showunconserved_actionPerformed(e);
1074   }
1075
1076   public static List<String> getGroupURLLinks()
1077   {
1078     return groupURLLinks;
1079   }
1080
1081   @Override
1082   public void minColour_actionPerformed(JPanel panel)
1083   {
1084     JalviewColourChooser.showColourChooser(this,
1085             MessageManager.getString("label.select_colour_minimum_value"),
1086             panel);
1087   }
1088
1089   @Override
1090   public void maxColour_actionPerformed(JPanel panel)
1091   {
1092     JalviewColourChooser.showColourChooser(this,
1093             MessageManager.getString("label.select_colour_maximum_value"),
1094             panel);
1095   }
1096
1097   @Override
1098   public void gapColour_actionPerformed(JPanel gap)
1099   {
1100     if (!useLegacyGap.isSelected())
1101     {
1102       JalviewColourChooser.showColourChooser(this,
1103               MessageManager.getString("label.select_gap_colour"),
1104               gap);
1105     }
1106   }
1107
1108   @Override
1109   public void hiddenColour_actionPerformed(JPanel hidden)
1110   {
1111     JalviewColourChooser.showColourChooser(this,
1112             MessageManager.getString("label.select_hidden_colour"),
1113             hidden);
1114   }
1115
1116   @Override
1117   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1118   {
1119     boolean enabled = useLegacyGap.isSelected();
1120     if (enabled)
1121     {
1122       gapColour.setBackground(
1123               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1124     }
1125     else
1126     {
1127       gapColour.setBackground(
1128               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1129     }
1130     gapColour.setEnabled(!enabled);
1131     gapLabel.setEnabled(!enabled);
1132   }
1133
1134   @Override
1135   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1136   {
1137     useLegacyGap.setSelected(false);
1138     useLegacyGaps_actionPerformed(null);
1139     showHiddenAtStart.setSelected(true);
1140     hiddenColour.setBackground(
1141             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1142   }
1143
1144   @Override
1145   protected void userIdWidth_actionPerformed()
1146   {
1147     try
1148     {
1149       String val = userIdWidth.getText().trim();
1150       if (val.length() > 0)
1151       {
1152         Integer iw = Integer.parseInt(val);
1153         if (iw.intValue() < 12)
1154         {
1155           throw new NumberFormatException();
1156         }
1157         userIdWidth.setText(iw.toString());
1158       }
1159     } catch (NumberFormatException x)
1160     {
1161       userIdWidth.setText("");
1162       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1163               MessageManager
1164                       .getString("warn.user_defined_width_requirements"),
1165               MessageManager.getString("label.invalid_id_column_width"),
1166               JvOptionPane.WARNING_MESSAGE);
1167     }
1168   }
1169
1170   @Override
1171   protected void autoIdWidth_actionPerformed()
1172   {
1173     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1174     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1175   }
1176
1177   /**
1178    * Returns true if chimera path is to a valid executable, else show an error
1179    * dialog.
1180    */
1181   private boolean validateChimeraPath()
1182   {
1183     if (chimeraPath.getText().trim().length() > 0)
1184     {
1185       File f = new File(chimeraPath.getText());
1186       if (!f.canExecute())
1187       {
1188         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1189                 MessageManager.getString("label.invalid_chimera_path"),
1190                 MessageManager.getString("label.invalid_name"),
1191                 JvOptionPane.ERROR_MESSAGE);
1192         return false;
1193       }
1194     }
1195     return true;
1196   }
1197
1198   /**
1199    * If Chimera is selected, check it can be found on default or user-specified
1200    * path, if not show a warning/help dialog.
1201    */
1202   @Override
1203   protected void structureViewer_actionPerformed(String selectedItem)
1204   {
1205     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1206     {
1207       return;
1208     }
1209     boolean found = false;
1210
1211     /*
1212      * Try user-specified and standard paths for Chimera executable.
1213      */
1214     List<String> paths = StructureManager.getChimeraPaths();
1215     paths.add(0, chimeraPath.getText());
1216     for (String path : paths)
1217     {
1218       if (new File(path.trim()).canExecute())
1219       {
1220         found = true;
1221         break;
1222       }
1223     }
1224     if (!found)
1225     {
1226       String[] options = { "OK", "Help" };
1227       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1228               JvSwingUtils.wrapTooltip(true,
1229                       MessageManager.getString("label.chimera_missing")),
1230               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1231               null, options, options[0]);
1232       if (showHelp == JvOptionPane.NO_OPTION)
1233       {
1234         try
1235         {
1236           Help.showHelpWindow(HelpId.StructureViewer);
1237         } catch (HelpSetException e)
1238         {
1239           e.printStackTrace();
1240         }
1241       }
1242     }
1243   }
1244
1245   public class OptionsParam
1246   {
1247     private String name;
1248
1249     private String code;
1250
1251     public OptionsParam(String name, String code)
1252     {
1253       this.name = name;
1254       this.code = code;
1255     }
1256
1257     public String getName()
1258     {
1259       return name;
1260     }
1261
1262     public void setName(String name)
1263     {
1264       this.name = name;
1265     }
1266
1267     public String getCode()
1268     {
1269       return code;
1270     }
1271
1272     public void setCode(String code)
1273     {
1274       this.code = code;
1275     }
1276
1277     @Override
1278     public String toString()
1279     {
1280       return name;
1281     }
1282
1283     @Override
1284     public boolean equals(Object that)
1285     {
1286       if (!(that instanceof OptionsParam))
1287       {
1288         return false;
1289       }
1290       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1291     }
1292
1293     @Override
1294     public int hashCode()
1295     {
1296       return name.hashCode() + code.hashCode();
1297     }
1298   }
1299
1300   private class UrlListSelectionHandler implements ListSelectionListener
1301   {
1302
1303     @Override
1304     public void valueChanged(ListSelectionEvent e)
1305     {
1306       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1307
1308       int index = lsm.getMinSelectionIndex();
1309       if (index == -1)
1310       {
1311         // no selection, so disable delete/edit buttons
1312         editLink.setEnabled(false);
1313         deleteLink.setEnabled(false);
1314         return;
1315       }
1316       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1317
1318       // enable/disable edit and delete link buttons
1319       if (((UrlLinkTableModel) linkUrlTable.getModel())
1320               .isRowDeletable(modelIndex))
1321       {
1322         deleteLink.setEnabled(true);
1323       }
1324       else
1325       {
1326         deleteLink.setEnabled(false);
1327       }
1328
1329       if (((UrlLinkTableModel) linkUrlTable.getModel())
1330               .isRowEditable(modelIndex))
1331       {
1332         editLink.setEnabled(true);
1333       }
1334       else
1335       {
1336         editLink.setEnabled(false);
1337       }
1338     }
1339   }
1340 }