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.bin.Jalview;
  26 import jalview.gui.Help.HelpId;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.io.FileFormatI;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeI;
  34 import jalview.schemes.ColourSchemes;
  35 import jalview.schemes.ResidueColourScheme;
  36 import jalview.urls.UrlLinkTableModel;
  37 import jalview.urls.api.UrlProviderFactoryI;
  38 import jalview.urls.api.UrlProviderI;
  39 import jalview.urls.desktop.DesktopUrlProviderFactory;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.util.UrlConstants;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.BorderLayout;
  46 import java.awt.Color;
  47 import java.awt.Component;
  48 import java.awt.Dimension;
  49 import java.awt.Font;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.MouseEvent;
  53 import java.io.File;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56
  57 import javax.help.HelpSetException;
  58 import javax.swing.JComboBox;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.RowFilter;
  64 import javax.swing.RowSorter;
  65 import javax.swing.SortOrder;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70 import javax.swing.table.TableCellRenderer;
  71 import javax.swing.table.TableColumn;
  72 import javax.swing.table.TableModel;
  73 import javax.swing.table.TableRowSorter;
  74
  75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence ID must be
 127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 128    */
 129   public static UrlProviderI sequenceUrlLinks;
 130
 131   public static UrlLinkTableModel dataModel;
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence IDS and Sequences
 135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 137    * for first and second token specified after a pipe character at end |,|.
 138    * (TODO: proper escape for using | to separate ids or sequences
 139    */
 140
 141   public static List<String> groupURLLinks;
 142   static
 143   {
 144     // get links selected to be in the menu (SEQUENCE_LINKS)
 145     // and links entered by the user but not selected (STORED_LINKS)
 146     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 147     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 148     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 149             UrlConstants.DEFAULT_LABEL);
 150
 151     // if both links lists are empty, add the DEFAULT_URL link
 152     // otherwise we assume the default link is in one of the lists
 153     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 154     {
 155       inMenuString = UrlConstants.DEFAULT_STRING;
 156     }
 157     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 158             inMenuString, notInMenuString);
 159     sequenceUrlLinks = factory.createUrlProvider();
 160     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 161
 162     /**
 163      * TODO: reformulate groupURL encoding so two or more can be stored in the
 164      * .properties file as '|' separated strings
 165      */
 166
 167     groupURLLinks = new ArrayList<>();
 168   }
 169
 170   JInternalFrame frame;
 171
 172   private WsPreferences wsPrefs;
 173
 174   private OptionsParam promptEachTimeOpt = new OptionsParam(
 175           MessageManager.getString("label.prompt_each_time"),
 176           "Prompt each time");
 177
 178   private OptionsParam lineArtOpt = new OptionsParam(
 179           MessageManager.getString("label.lineart"), "Lineart");
 180
 181   private OptionsParam textOpt = new OptionsParam(
 182           MessageManager.getString("action.text"), "Text");
 183
 184   /**
 185    * Creates a new Preferences object.
 186    */
 187   public Preferences()
 188   {
 189     super();
 190     frame = new JInternalFrame();
 191     frame.setContentPane(this);
 192     if (!Jalview.isJS())
 193     {
 194       wsPrefs = new WsPreferences();
 195       wsTab.add(wsPrefs, BorderLayout.CENTER);
 196     }
 197     int width = 500, height = 450;
 198     if (Platform.isAMacAndNotJS())
 199     {
 200       width = 570;
 201       height = 480;
 202     }
 203
 204     Desktop.addInternalFrame(frame,
 205             MessageManager.getString("label.preferences"), width, height);
 206     frame.setMinimumSize(new Dimension(width, height));
 207
 208     /*
 209      * Set Visual tab defaults
 210      */
 211     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 212     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 213     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 214     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 215
 216     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 217     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 218     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 219     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 220     showUnconserved
 221             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 222     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 223     showGroupConsensus
 224             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 225     showGroupConservation.setSelected(
 226             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 227     showConsensHistogram.setSelected(
 228             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 229     showConsensLogo
 230             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 231     showNpTooltip
 232             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 233     showDbRefTooltip
 234             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 235
 236     String[] fonts = java.awt.GraphicsEnvironment
 237             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 238     for (int i = 0; i < fonts.length; i++)
 239     {
 240       fontNameCB.addItem(fonts[i]);
 241     }
 242
 243     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 244     {
 245       fontSizeCB.addItem(i + "");
 246     }
 247
 248     fontStyleCB.addItem("plain");
 249     fontStyleCB.addItem("bold");
 250     fontStyleCB.addItem("italic");
 251
 252     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 253     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 254     fontStyleCB.setSelectedItem(
 255             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 256
 257     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 258     scaleProteinToCdna
 259             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 260
 261     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 262
 263     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 264
 265     gapSymbolCB.addItem("-");
 266     gapSymbolCB.addItem(".");
 267
 268     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 269
 270     sortby.addItem("No sort");
 271     sortby.addItem("Id");
 272     sortby.addItem("Pairwise Identity");
 273     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 274
 275     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 278     sortAnnBy
 279             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 280     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 281             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 282                     SequenceAnnotationOrder.NONE.name()));
 283     sortAnnBy.setSelectedItem(savedSort.toString());
 284
 285     sortAutocalc.addItem("Autocalculated first");
 286     sortAutocalc.addItem("Autocalculated last");
 287     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 288     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 289             : sortAutocalc.getItemAt(1));
 290     startupCheckbox
 291             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 292     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 293             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 294                     + "/examples/exampleFile_2_3.jar"));
 295
 296     /*
 297      * Set Colours tab defaults
 298      */
 299     protColour.addItem(ResidueColourScheme.NONE);
 300     nucColour.addItem(ResidueColourScheme.NONE);
 301     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 302     {
 303       String name = cs.getSchemeName();
 304       protColour.addItem(name);
 305       nucColour.addItem(name);
 306     }
 307     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 308             ResidueColourScheme.NONE);
 309     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 310     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 312     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 313     minColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 315     maxColour.setBackground(
 316             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 317
 318     /*
 319      * Set overview panel defaults
 320      */
 321     gapColour.setBackground(
 322             Cache.getDefaultColour(GAP_COLOUR,
 323                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 324     hiddenColour.setBackground(
 325             Cache.getDefaultColour(HIDDEN_COLOUR,
 326                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 327     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 328     gapLabel.setEnabled(!useLegacyGap.isSelected());
 329     gapColour.setEnabled(!useLegacyGap.isSelected());
 330     showHiddenAtStart
 331             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 332
 333     /*
 334      * Set Structure tab defaults.
 335      */
 336     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 337     structFromPdb.setSelected(structSelected);
 338     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 339     useRnaView.setEnabled(structSelected);
 340     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 341     addSecondaryStructure.setEnabled(structSelected);
 342     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 343     addTempFactor.setEnabled(structSelected);
 344     structViewer.setSelectedItem(
 345             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 346     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 347     chimeraPath.addActionListener(new ActionListener()
 348     {
 349       @Override
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         validateChimeraPath();
 353       }
 354     });
 355
 356     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 357     {
 358       siftsMapping.setSelected(true);
 359     }
 360     else
 361     {
 362       nwMapping.setSelected(true);
 363     }
 364
 365     SiftsSettings
 366             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 367
 368     /*
 369      * Set Connections tab defaults
 370      */
 371
 372     // set up sorting
 373     linkUrlTable.setModel(dataModel);
 374     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 375             linkUrlTable.getModel());
 376     linkUrlTable.setRowSorter(sorter);
 377     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 378
 379     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 380     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 383             SortOrder.DESCENDING));
 384     sortKeys.add(
 385             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 386
 387     sorter.setSortKeys(sortKeys);
 388     // BH 2018 setSortKeys will do the sort
 389     // sorter.sort();
 390
 391     // set up filtering
 392     ActionListener onReset;
 393     onReset = new ActionListener()
 394     {
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         filterTB.setText("");
 399         sorter.setRowFilter(RowFilter.regexFilter(""));
 400       }
 401
 402     };
 403     doReset.addActionListener(onReset);
 404
 405     // filter to display only custom urls
 406     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 407     {
 408       @Override
 409       public boolean include(
 410               Entry<? extends TableModel, ? extends Object> entry)
 411       {
 412         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 413       }
 414     };
 415
 416     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 417             linkUrlTable.getModel());
 418     customSorter.setRowFilter(customUrlFilter);
 419
 420     ActionListener onCustomOnly;
 421     onCustomOnly = new ActionListener()
 422     {
 423       @Override
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         filterTB.setText("");
 427         sorter.setRowFilter(customUrlFilter);
 428       }
 429     };
 430     userOnly.addActionListener(onCustomOnly);
 431
 432     filterTB.getDocument().addDocumentListener(new DocumentListener()
 433     {
 434       String caseInsensitiveFlag = "(?i)";
 435
 436       @Override
 437       public void changedUpdate(DocumentEvent e)
 438       {
 439         sorter.setRowFilter(RowFilter
 440                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 441       }
 442
 443       @Override
 444       public void removeUpdate(DocumentEvent e)
 445       {
 446         sorter.setRowFilter(RowFilter
 447                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 448       }
 449
 450       @Override
 451       public void insertUpdate(DocumentEvent e)
 452       {
 453         sorter.setRowFilter(RowFilter
 454                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 455       }
 456     });
 457
 458     // set up list selection functionality
 459     linkUrlTable.getSelectionModel()
 460             .addListSelectionListener(new UrlListSelectionHandler());
 461
 462     // set up radio buttons
 463     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 464             .getPrimaryColumn();
 465     String onClickName = linkUrlTable.getColumnName(onClickCol);
 466     linkUrlTable.getColumn(onClickName)
 467             .setCellRenderer(new RadioButtonRenderer());
 468     linkUrlTable.getColumn(onClickName)
 469             .setCellEditor(new RadioButtonEditor());
 470
 471     // get boolean columns and resize those to min possible
 472     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 473     {
 474       if (linkUrlTable.getModel().getColumnClass(column)
 475               .equals(Boolean.class))
 476       {
 477         TableColumn tableColumn = linkUrlTable.getColumnModel()
 478                 .getColumn(column);
 479         int preferredWidth = tableColumn.getMinWidth();
 480
 481         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 482                 column);
 483         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 484         int cwidth = c.getPreferredSize().width
 485                 + linkUrlTable.getIntercellSpacing().width;
 486         preferredWidth = Math.max(preferredWidth, cwidth);
 487
 488         tableColumn.setPreferredWidth(preferredWidth);
 489       }
 490     }
 491
 492     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 493     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 494     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 495     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 496
 497     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 498
 499     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 500     // note antisense here: default is true
 501     questionnaire
 502             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 503     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 504
 505     /*
 506      * Set Output tab defaults
 507      */
 508     setupOutputCombo(epsRendering, "EPS_RENDERING");
 509     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 510     setupOutputCombo(svgRendering, "SVG_RENDERING");
 511     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 512     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 513     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 514     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 515     userIdWidth.setText(wi == null ? "" : wi.toString());
 516     // TODO: refactor to use common enum via FormatAdapter and allow extension
 517     // for new flat file formats
 518     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 519     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 520     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 521     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 522     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 523     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 524     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 525     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 526     embbedBioJSON
 527             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 528
 529     /*
 530      * Set Editing tab defaults
 531      */
 532     autoCalculateConsCheck
 533             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 534     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 535     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 536
 537     annotations_actionPerformed(null); // update the display of the annotation
 538                                        // settings
 539   }
 540
 541   /**
 542    * A helper method that sets the items and initial selection in a character
 543    * rendering option list (Prompt each time/Lineart/Text)
 544    *
 545    * @param comboBox
 546    * @param propertyKey
 547    */
 548   protected void setupOutputCombo(JComboBox<Object> comboBox,
 549           String propertyKey)
 550   {
 551     comboBox.addItem(promptEachTimeOpt);
 552     comboBox.addItem(lineArtOpt);
 553     comboBox.addItem(textOpt);
 554
 555     /*
 556      * JalviewJS doesn't support Lineart so force it to Text
 557      */
 558     String defaultOption = Jalview.isJS() ? "Text"
 559             : Cache.getDefault(propertyKey, "Prompt each time");
 560     if (defaultOption.equalsIgnoreCase("Text"))
 561     {
 562       comboBox.setSelectedItem(textOpt);
 563     }
 564     else if (defaultOption.equalsIgnoreCase("Lineart"))
 565     {
 566       comboBox.setSelectedItem(lineArtOpt);
 567     }
 568     else
 569     {
 570       comboBox.setSelectedItem(promptEachTimeOpt);
 571     }
 572   }
 573
 574   /**
 575    * Save user selections on the Preferences tabs to the Cache and write out to
 576    * file.
 577    *
 578    * @param e
 579    */
 580   @Override
 581   public void ok_actionPerformed(ActionEvent e)
 582   {
 583     if (!validateSettings())
 584     {
 585       return;
 586     }
 587
 588     /*
 589      * Save Visual settings
 590      */
 591     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 592             Boolean.toString(seqLimit.isSelected()));
 593     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 594             Boolean.toString(rightAlign.isSelected()));
 595     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 596             Boolean.toString(fullScreen.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 598             Boolean.toString(openoverv.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 600             Boolean.toString(annotations.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 602             Boolean.toString(conservation.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 604             Boolean.toString(quality.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 606             Boolean.toString(identity.isSelected()));
 607
 608     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 609             gapSymbolCB.getSelectedItem().toString());
 610
 611     Cache.applicationProperties.setProperty("FONT_NAME",
 612             fontNameCB.getSelectedItem().toString());
 613     Cache.applicationProperties.setProperty("FONT_STYLE",
 614             fontStyleCB.getSelectedItem().toString());
 615     Cache.applicationProperties.setProperty("FONT_SIZE",
 616             fontSizeCB.getSelectedItem().toString());
 617
 618     Cache.applicationProperties.setProperty("ID_ITALICS",
 619             Boolean.toString(idItalics.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 621             Boolean.toString(showUnconserved.isSelected()));
 622     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 623             Boolean.toString(showOccupancy.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 625             Boolean.toString(showGroupConsensus.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 627             Boolean.toString(showGroupConservation.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 629             Boolean.toString(showConsensHistogram.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 631             Boolean.toString(showConsensLogo.isSelected()));
 632     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 633             Boolean.toString(smoothFont.isSelected()));
 634     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 635             Boolean.toString(scaleProteinToCdna.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 637             Boolean.toString(showNpTooltip.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 639             Boolean.toString(showDbRefTooltip.isSelected()));
 640
 641     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 642             Boolean.toString(wrap.isSelected()));
 643
 644     Cache.applicationProperties.setProperty("STARTUP_FILE",
 645             startupFileTextfield.getText());
 646     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 647             Boolean.toString(startupCheckbox.isSelected()));
 648
 649     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 650             sortby.getSelectedItem().toString());
 651
 652     // convert description of sort order to enum name for save
 653     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 654             .forDescription(sortAnnBy.getSelectedItem().toString());
 655     if (annSortOrder != null)
 656     {
 657       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 658               annSortOrder.name());
 659     }
 660
 661     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 662     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 663             Boolean.valueOf(showAutocalcFirst).toString());
 664
 665     /*
 666      * Save Colours settings
 667      */
 668     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 669             protColour.getSelectedItem().toString());
 670     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 671             nucColour.getSelectedItem().toString());
 672     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 673             minColour.getBackground());
 674     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 675             maxColour.getBackground());
 676
 677     /*
 678      * Save Overview settings
 679      */
 680     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 681     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 682     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 683             Boolean.toString(useLegacyGap.isSelected()));
 684     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 685             Boolean.toString(showHiddenAtStart.isSelected()));
 686
 687     /*
 688      * Save Structure settings
 689      */
 690     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 691             Boolean.toString(addTempFactor.isSelected()));
 692     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 693             Boolean.toString(addSecondaryStructure.isSelected()));
 694     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 695             Boolean.toString(useRnaView.isSelected()));
 696     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 697             Boolean.toString(structFromPdb.isSelected()));
 698     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 699             structViewer.getSelectedItem().toString());
 700     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 701     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 702             Boolean.toString(siftsMapping.isSelected()));
 703     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 704
 705     /*
 706      * Save Output settings
 707      */
 708     Cache.applicationProperties.setProperty("EPS_RENDERING",
 709             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 710     Cache.applicationProperties.setProperty("HTML_RENDERING",
 711             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 712     Cache.applicationProperties.setProperty("SVG_RENDERING",
 713             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 714
 715     /*
 716      * Save Connections settings
 717      */
 718     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 719
 720     jalview.util.BrowserLauncher.resetBrowser();
 721
 722     // save user-defined and selected links
 723     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 724     if (menuLinks.isEmpty())
 725     {
 726       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 727     }
 728     else
 729     {
 730       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 731               menuLinks.toString());
 732     }
 733
 734     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 735     if (nonMenuLinks.isEmpty())
 736     {
 737       Cache.applicationProperties.remove("STORED_LINKS");
 738     }
 739     else
 740     {
 741       Cache.applicationProperties.setProperty("STORED_LINKS",
 742               nonMenuLinks.toString());
 743     }
 744
 745     Cache.applicationProperties.setProperty("DEFAULT_URL",
 746             sequenceUrlLinks.getPrimaryUrlId());
 747
 748     Cache.applicationProperties.setProperty("USE_PROXY",
 749             Boolean.toString(useProxy.isSelected()));
 750
 751     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 752
 753     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 754
 755     if (useProxy.isSelected())
 756     {
 757       System.setProperty("http.proxyHost", proxyServerTB.getText());
 758       System.setProperty("http.proxyPort", proxyPortTB.getText());
 759     }
 760     else
 761     {
 762       System.setProperty("http.proxyHost", "");
 763       System.setProperty("http.proxyPort", "");
 764     }
 765     Cache.setProperty("VERSION_CHECK",
 766             Boolean.toString(versioncheck.isSelected()));
 767     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 768     {
 769       // default is false - we only set this if the user has actively agreed
 770       Cache.setProperty("USAGESTATS",
 771               Boolean.toString(usagestats.isSelected()));
 772     }
 773     if (!questionnaire.isSelected())
 774     {
 775       Cache.setProperty("NOQUESTIONNAIRES", "true");
 776     }
 777     else
 778     {
 779       // special - made easy to edit a property file to disable questionnaires
 780       // by just adding the given line
 781       Cache.removeProperty("NOQUESTIONNAIRES");
 782     }
 783
 784     /*
 785      * Save Output settings
 786      */
 787     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 788             Boolean.toString(blcjv.isSelected()));
 789     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 790             Boolean.toString(clustaljv.isSelected()));
 791     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 792             Boolean.toString(fastajv.isSelected()));
 793     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 794             Boolean.toString(msfjv.isSelected()));
 795     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 796             Boolean.toString(pfamjv.isSelected()));
 797     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 798             Boolean.toString(pileupjv.isSelected()));
 799     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 800             Boolean.toString(pirjv.isSelected()));
 801     Cache.applicationProperties.setProperty("PIR_MODELLER",
 802             Boolean.toString(modellerOutput.isSelected()));
 803     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 804             Boolean.toString(embbedBioJSON.isSelected()));
 805     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 806
 807     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 808             Boolean.toString(autoIdWidth.isSelected()));
 809     userIdWidth_actionPerformed();
 810     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 811             userIdWidth.getText());
 812
 813     /*
 814      * Save Editing settings
 815      */
 816     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 817             Boolean.toString(autoCalculateConsCheck.isSelected()));
 818     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 819             Boolean.toString(sortByTree.isSelected()));
 820     Cache.applicationProperties.setProperty("PAD_GAPS",
 821             Boolean.toString(padGaps.isSelected()));
 822
 823     if (!Jalview.isJS())
 824     {
 825       wsPrefs.updateAndRefreshWsMenuConfig(false);
 826     }
 827     Cache.saveProperties();
 828     Desktop.instance.doConfigureStructurePrefs();
 829     try
 830     {
 831       frame.setClosed(true);
 832     } catch (Exception ex)
 833     {
 834     }
 835   }
 836
 837   /**
 838    * Do any necessary validation before saving settings. Return focus to the
 839    * first tab which fails validation.
 840    *
 841    * @return
 842    */
 843   private boolean validateSettings()
 844   {
 845     if (!validateStructure())
 846     {
 847       structureTab.requestFocusInWindow();
 848       return false;
 849     }
 850     return true;
 851   }
 852
 853   @Override
 854   protected boolean validateStructure()
 855   {
 856     return validateChimeraPath();
 857
 858   }
 859
 860   /**
 861    * DOCUMENT ME!
 862    */
 863   @Override
 864   public void startupFileTextfield_mouseClicked()
 865   {
 866     // TODO: JAL-3048 not needed for Jalview-JS
 867     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 868     JalviewFileChooser chooser = JalviewFileChooser
 869             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 870     chooser.setFileView(new JalviewFileView());
 871     chooser.setDialogTitle(
 872             MessageManager.getString("label.select_startup_file"));
 873
 874     int value = chooser.showOpenDialog(this);
 875
 876     if (value == JalviewFileChooser.APPROVE_OPTION)
 877     {
 878       FileFormatI format = chooser.getSelectedFormat();
 879       if (format != null)
 880       {
 881         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 882                 format.getName());
 883       }
 884       startupFileTextfield
 885               .setText(chooser.getSelectedFile().getAbsolutePath());
 886     }
 887   }
 888
 889   /**
 890    * DOCUMENT ME!
 891    *
 892    * @param e
 893    *          DOCUMENT ME!
 894    */
 895   @Override
 896   public void cancel_actionPerformed(ActionEvent e)
 897   {
 898     try
 899     {
 900       if (!Jalview.isJS())
 901       {
 902         wsPrefs.updateWsMenuConfig(true);
 903         wsPrefs.refreshWs_actionPerformed(e);
 904       }
 905       frame.setClosed(true);
 906     } catch (Exception ex)
 907     {
 908     }
 909   }
 910
 911   /**
 912    * DOCUMENT ME!
 913    *
 914    * @param e
 915    *          DOCUMENT ME!
 916    */
 917   @Override
 918   public void annotations_actionPerformed(ActionEvent e)
 919   {
 920     conservation.setEnabled(annotations.isSelected());
 921     quality.setEnabled(annotations.isSelected());
 922     identity.setEnabled(annotations.isSelected());
 923     showOccupancy.setEnabled(annotations.isSelected());
 924     showGroupConsensus.setEnabled(annotations.isSelected());
 925     showGroupConservation.setEnabled(annotations.isSelected());
 926     showConsensHistogram.setEnabled(annotations.isSelected()
 927             && (identity.isSelected() || showGroupConsensus.isSelected()));
 928     showConsensLogo.setEnabled(annotations.isSelected()
 929             && (identity.isSelected() || showGroupConsensus.isSelected()));
 930   }
 931
 932   @Override
 933   public void newLink_actionPerformed(ActionEvent e)
 934   {
 935     GSequenceLink link = new GSequenceLink();
 936     boolean valid = false;
 937     while (!valid)
 938     {
 939       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 940               MessageManager.getString("label.new_sequence_url_link"),
 941               JvOptionPane.OK_CANCEL_OPTION, -1,
 942               null) == JvOptionPane.OK_OPTION)
 943       {
 944         if (link.checkValid())
 945         {
 946           if (((UrlLinkTableModel) linkUrlTable.getModel())
 947                   .isUniqueName(link.getName()))
 948           {
 949             ((UrlLinkTableModel) linkUrlTable.getModel())
 950                     .insertRow(link.getName(), link.getURL());
 951             valid = true;
 952           }
 953           else
 954           {
 955             link.notifyDuplicate();
 956             continue;
 957           }
 958         }
 959       }
 960       else
 961       {
 962         break;
 963       }
 964     }
 965   }
 966
 967   @Override
 968   public void editLink_actionPerformed(ActionEvent e)
 969   {
 970     GSequenceLink link = new GSequenceLink();
 971
 972     int index = linkUrlTable.getSelectedRow();
 973     if (index == -1)
 974     {
 975       // button no longer enabled if row is not selected
 976       Cache.log.debug("Edit with no row selected in linkUrlTable");
 977       return;
 978     }
 979
 980     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 981             .getNameColumn();
 982     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 983             .getUrlColumn();
 984     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 985     link.setName(oldName);
 986     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 987
 988     boolean valid = false;
 989     while (!valid)
 990     {
 991       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 992               MessageManager.getString("label.edit_sequence_url_link"),
 993               JvOptionPane.OK_CANCEL_OPTION, -1,
 994               null) == JvOptionPane.OK_OPTION)
 995       {
 996         if (link.checkValid())
 997         {
 998           if ((oldName.equals(link.getName()))
 999                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1000                           .isUniqueName(link.getName())))
1001           {
1002             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1003             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1004             valid = true;
1005           }
1006           else
1007           {
1008             link.notifyDuplicate();
1009             continue;
1010           }
1011         }
1012       }
1013       else
1014       {
1015         break;
1016       }
1017     }
1018   }
1019
1020   @Override
1021   public void deleteLink_actionPerformed(ActionEvent e)
1022   {
1023     int index = linkUrlTable.getSelectedRow();
1024     int modelIndex = -1;
1025     if (index == -1)
1026     {
1027       // button no longer enabled if row is not selected
1028       Cache.log.debug("Delete with no row selected in linkUrlTable");
1029       return;
1030     }
1031     else
1032     {
1033       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1034     }
1035
1036     // make sure we use the model index to delete, and not the table index
1037     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1038   }
1039
1040   @Override
1041   public void defaultBrowser_mouseClicked(MouseEvent e)
1042   {
1043     // TODO: JAL-3048 not needed for j2s
1044     /*
1045      * @j2sNative
1046      */
1047     {
1048       JFileChooser chooser = new JFileChooser(".");
1049       chooser.setDialogTitle(
1050               MessageManager.getString("label.select_default_browser"));
1051
1052       int value = chooser.showOpenDialog(this);
1053
1054       if (value == JFileChooser.APPROVE_OPTION)
1055       {
1056         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1057       }
1058     }
1059   }
1060
1061   /*
1062    * (non-Javadoc)
1063    *
1064    * @see
1065    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1066    * .ActionEvent)
1067    */
1068   @Override
1069   protected void showunconserved_actionPerformed(ActionEvent e)
1070   {
1071     // TODO Auto-generated method stub
1072     super.showunconserved_actionPerformed(e);
1073   }
1074
1075   public static List<String> getGroupURLLinks()
1076   {
1077     return groupURLLinks;
1078   }
1079
1080   @Override
1081   public void minColour_actionPerformed(JPanel panel)
1082   {
1083     JalviewColourChooser.showColourChooser(this,
1084             MessageManager.getString("label.select_colour_minimum_value"),
1085             panel);
1086   }
1087
1088   @Override
1089   public void maxColour_actionPerformed(JPanel panel)
1090   {
1091     JalviewColourChooser.showColourChooser(this,
1092             MessageManager.getString("label.select_colour_maximum_value"),
1093             panel);
1094   }
1095
1096   @Override
1097   public void gapColour_actionPerformed(JPanel gap)
1098   {
1099     if (!useLegacyGap.isSelected())
1100     {
1101       JalviewColourChooser.showColourChooser(this,
1102               MessageManager.getString("label.select_gap_colour"),
1103               gap);
1104     }
1105   }
1106
1107   @Override
1108   public void hiddenColour_actionPerformed(JPanel hidden)
1109   {
1110     JalviewColourChooser.showColourChooser(this,
1111             MessageManager.getString("label.select_hidden_colour"),
1112             hidden);
1113   }
1114
1115   @Override
1116   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1117   {
1118     boolean enabled = useLegacyGap.isSelected();
1119     if (enabled)
1120     {
1121       gapColour.setBackground(
1122               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1123     }
1124     else
1125     {
1126       gapColour.setBackground(
1127               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1128     }
1129     gapColour.setEnabled(!enabled);
1130     gapLabel.setEnabled(!enabled);
1131   }
1132
1133   @Override
1134   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1135   {
1136     useLegacyGap.setSelected(false);
1137     useLegacyGaps_actionPerformed(null);
1138     showHiddenAtStart.setSelected(true);
1139     hiddenColour.setBackground(
1140             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1141   }
1142
1143   @Override
1144   protected void userIdWidth_actionPerformed()
1145   {
1146     try
1147     {
1148       String val = userIdWidth.getText().trim();
1149       if (val.length() > 0)
1150       {
1151         Integer iw = Integer.parseInt(val);
1152         if (iw.intValue() < 12)
1153         {
1154           throw new NumberFormatException();
1155         }
1156         userIdWidth.setText(iw.toString());
1157       }
1158     } catch (NumberFormatException x)
1159     {
1160       userIdWidth.setText("");
1161       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1162               MessageManager
1163                       .getString("warn.user_defined_width_requirements"),
1164               MessageManager.getString("label.invalid_id_column_width"),
1165               JvOptionPane.WARNING_MESSAGE);
1166     }
1167   }
1168
1169   @Override
1170   protected void autoIdWidth_actionPerformed()
1171   {
1172     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1173     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1174   }
1175
1176   /**
1177    * Returns true if chimera path is to a valid executable, else show an error
1178    * dialog.
1179    */
1180   private boolean validateChimeraPath()
1181   {
1182     if (chimeraPath.getText().trim().length() > 0)
1183     {
1184       File f = new File(chimeraPath.getText());
1185       if (!f.canExecute())
1186       {
1187         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1188                 MessageManager.getString("label.invalid_chimera_path"),
1189                 MessageManager.getString("label.invalid_name"),
1190                 JvOptionPane.ERROR_MESSAGE);
1191         return false;
1192       }
1193     }
1194     return true;
1195   }
1196
1197   /**
1198    * If Chimera is selected, check it can be found on default or user-specified
1199    * path, if not show a warning/help dialog.
1200    */
1201   @Override
1202   protected void structureViewer_actionPerformed(String selectedItem)
1203   {
1204     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1205     {
1206       return;
1207     }
1208     boolean found = false;
1209
1210     /*
1211      * Try user-specified and standard paths for Chimera executable.
1212      */
1213     List<String> paths = StructureManager.getChimeraPaths();
1214     paths.add(0, chimeraPath.getText());
1215     for (String path : paths)
1216     {
1217       if (new File(path.trim()).canExecute())
1218       {
1219         found = true;
1220         break;
1221       }
1222     }
1223     if (!found)
1224     {
1225       String[] options = { "OK", "Help" };
1226       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1227               JvSwingUtils.wrapTooltip(true,
1228                       MessageManager.getString("label.chimera_missing")),
1229               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1230               null, options, options[0]);
1231       if (showHelp == JvOptionPane.NO_OPTION)
1232       {
1233         try
1234         {
1235           Help.showHelpWindow(HelpId.StructureViewer);
1236         } catch (HelpSetException e)
1237         {
1238           e.printStackTrace();
1239         }
1240       }
1241     }
1242   }
1243
1244   public class OptionsParam
1245   {
1246     private String name;
1247
1248     private String code;
1249
1250     public OptionsParam(String name, String code)
1251     {
1252       this.name = name;
1253       this.code = code;
1254     }
1255
1256     public String getName()
1257     {
1258       return name;
1259     }
1260
1261     public void setName(String name)
1262     {
1263       this.name = name;
1264     }
1265
1266     public String getCode()
1267     {
1268       return code;
1269     }
1270
1271     public void setCode(String code)
1272     {
1273       this.code = code;
1274     }
1275
1276     @Override
1277     public String toString()
1278     {
1279       return name;
1280     }
1281
1282     @Override
1283     public boolean equals(Object that)
1284     {
1285       if (!(that instanceof OptionsParam))
1286       {
1287         return false;
1288       }
1289       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1290     }
1291
1292     @Override
1293     public int hashCode()
1294     {
1295       return name.hashCode() + code.hashCode();
1296     }
1297   }
1298
1299   private class UrlListSelectionHandler implements ListSelectionListener
1300   {
1301
1302     @Override
1303     public void valueChanged(ListSelectionEvent e)
1304     {
1305       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1306
1307       int index = lsm.getMinSelectionIndex();
1308       if (index == -1)
1309       {
1310         // no selection, so disable delete/edit buttons
1311         editLink.setEnabled(false);
1312         deleteLink.setEnabled(false);
1313         return;
1314       }
1315       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1316
1317       // enable/disable edit and delete link buttons
1318       if (((UrlLinkTableModel) linkUrlTable.getModel())
1319               .isRowDeletable(modelIndex))
1320       {
1321         deleteLink.setEnabled(true);
1322       }
1323       else
1324       {
1325         deleteLink.setEnabled(false);
1326       }
1327
1328       if (((UrlLinkTableModel) linkUrlTable.getModel())
1329               .isRowEditable(modelIndex))
1330       {
1331         editLink.setEnabled(true);
1332       }
1333       else
1334       {
1335         editLink.setEnabled(false);
1336       }
1337     }
1338   }
1339 }