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.isAMac())
 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     String defaultOption = Cache.getDefault(propertyKey,
 555             "Prompt each time");
 556     if (defaultOption.equalsIgnoreCase("Text"))
 557     {
 558       comboBox.setSelectedItem(textOpt);
 559     }
 560     else if (defaultOption.equalsIgnoreCase("Lineart"))
 561     {
 562       comboBox.setSelectedItem(lineArtOpt);
 563     }
 564     else
 565     {
 566       comboBox.setSelectedItem(promptEachTimeOpt);
 567     }
 568   }
 569
 570   /**
 571    * Save user selections on the Preferences tabs to the Cache and write out to
 572    * file.
 573    *
 574    * @param e
 575    */
 576   @Override
 577   public void ok_actionPerformed(ActionEvent e)
 578   {
 579     if (!validateSettings())
 580     {
 581       return;
 582     }
 583
 584     /*
 585      * Save Visual settings
 586      */
 587     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 588             Boolean.toString(seqLimit.isSelected()));
 589     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 590             Boolean.toString(rightAlign.isSelected()));
 591     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 592             Boolean.toString(fullScreen.isSelected()));
 593     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 594             Boolean.toString(openoverv.isSelected()));
 595     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 596             Boolean.toString(annotations.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 598             Boolean.toString(conservation.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 600             Boolean.toString(quality.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 602             Boolean.toString(identity.isSelected()));
 603
 604     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 605             gapSymbolCB.getSelectedItem().toString());
 606
 607     Cache.applicationProperties.setProperty("FONT_NAME",
 608             fontNameCB.getSelectedItem().toString());
 609     Cache.applicationProperties.setProperty("FONT_STYLE",
 610             fontStyleCB.getSelectedItem().toString());
 611     Cache.applicationProperties.setProperty("FONT_SIZE",
 612             fontSizeCB.getSelectedItem().toString());
 613
 614     Cache.applicationProperties.setProperty("ID_ITALICS",
 615             Boolean.toString(idItalics.isSelected()));
 616     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 617             Boolean.toString(showUnconserved.isSelected()));
 618     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 619             Boolean.toString(showOccupancy.isSelected()));
 620     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 621             Boolean.toString(showGroupConsensus.isSelected()));
 622     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 623             Boolean.toString(showGroupConservation.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 625             Boolean.toString(showConsensHistogram.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 627             Boolean.toString(showConsensLogo.isSelected()));
 628     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 629             Boolean.toString(smoothFont.isSelected()));
 630     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 631             Boolean.toString(scaleProteinToCdna.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 633             Boolean.toString(showNpTooltip.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 635             Boolean.toString(showDbRefTooltip.isSelected()));
 636
 637     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 638             Boolean.toString(wrap.isSelected()));
 639
 640     Cache.applicationProperties.setProperty("STARTUP_FILE",
 641             startupFileTextfield.getText());
 642     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 643             Boolean.toString(startupCheckbox.isSelected()));
 644
 645     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 646             sortby.getSelectedItem().toString());
 647
 648     // convert description of sort order to enum name for save
 649     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 650             .forDescription(sortAnnBy.getSelectedItem().toString());
 651     if (annSortOrder != null)
 652     {
 653       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 654               annSortOrder.name());
 655     }
 656
 657     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 658     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 659             Boolean.valueOf(showAutocalcFirst).toString());
 660
 661     /*
 662      * Save Colours settings
 663      */
 664     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 665             protColour.getSelectedItem().toString());
 666     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 667             nucColour.getSelectedItem().toString());
 668     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 669             minColour.getBackground());
 670     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 671             maxColour.getBackground());
 672
 673     /*
 674      * Save Overview settings
 675      */
 676     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 677     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 678     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 679             Boolean.toString(useLegacyGap.isSelected()));
 680     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 681             Boolean.toString(showHiddenAtStart.isSelected()));
 682
 683     /*
 684      * Save Structure settings
 685      */
 686     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 687             Boolean.toString(addTempFactor.isSelected()));
 688     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 689             Boolean.toString(addSecondaryStructure.isSelected()));
 690     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 691             Boolean.toString(useRnaView.isSelected()));
 692     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 693             Boolean.toString(structFromPdb.isSelected()));
 694     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 695             structViewer.getSelectedItem().toString());
 696     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 697     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 698             Boolean.toString(siftsMapping.isSelected()));
 699     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 700
 701     /*
 702      * Save Output settings
 703      */
 704     Cache.applicationProperties.setProperty("EPS_RENDERING",
 705             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 706     Cache.applicationProperties.setProperty("HTML_RENDERING",
 707             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 708     Cache.applicationProperties.setProperty("SVG_RENDERING",
 709             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 710
 711     /*
 712      * Save Connections settings
 713      */
 714     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 715
 716     jalview.util.BrowserLauncher.resetBrowser();
 717
 718     // save user-defined and selected links
 719     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 720     if (menuLinks.isEmpty())
 721     {
 722       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 723     }
 724     else
 725     {
 726       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 727               menuLinks.toString());
 728     }
 729
 730     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 731     if (nonMenuLinks.isEmpty())
 732     {
 733       Cache.applicationProperties.remove("STORED_LINKS");
 734     }
 735     else
 736     {
 737       Cache.applicationProperties.setProperty("STORED_LINKS",
 738               nonMenuLinks.toString());
 739     }
 740
 741     Cache.applicationProperties.setProperty("DEFAULT_URL",
 742             sequenceUrlLinks.getPrimaryUrlId());
 743
 744     Cache.applicationProperties.setProperty("USE_PROXY",
 745             Boolean.toString(useProxy.isSelected()));
 746
 747     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 748
 749     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 750
 751     if (useProxy.isSelected())
 752     {
 753       System.setProperty("http.proxyHost", proxyServerTB.getText());
 754       System.setProperty("http.proxyPort", proxyPortTB.getText());
 755     }
 756     else
 757     {
 758       System.setProperty("http.proxyHost", "");
 759       System.setProperty("http.proxyPort", "");
 760     }
 761     Cache.setProperty("VERSION_CHECK",
 762             Boolean.toString(versioncheck.isSelected()));
 763     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 764     {
 765       // default is false - we only set this if the user has actively agreed
 766       Cache.setProperty("USAGESTATS",
 767               Boolean.toString(usagestats.isSelected()));
 768     }
 769     if (!questionnaire.isSelected())
 770     {
 771       Cache.setProperty("NOQUESTIONNAIRES", "true");
 772     }
 773     else
 774     {
 775       // special - made easy to edit a property file to disable questionnaires
 776       // by just adding the given line
 777       Cache.removeProperty("NOQUESTIONNAIRES");
 778     }
 779
 780     /*
 781      * Save Output settings
 782      */
 783     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 784             Boolean.toString(blcjv.isSelected()));
 785     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 786             Boolean.toString(clustaljv.isSelected()));
 787     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 788             Boolean.toString(fastajv.isSelected()));
 789     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 790             Boolean.toString(msfjv.isSelected()));
 791     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 792             Boolean.toString(pfamjv.isSelected()));
 793     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 794             Boolean.toString(pileupjv.isSelected()));
 795     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 796             Boolean.toString(pirjv.isSelected()));
 797     Cache.applicationProperties.setProperty("PIR_MODELLER",
 798             Boolean.toString(modellerOutput.isSelected()));
 799     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 800             Boolean.toString(embbedBioJSON.isSelected()));
 801     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 802
 803     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 804             Boolean.toString(autoIdWidth.isSelected()));
 805     userIdWidth_actionPerformed();
 806     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 807             userIdWidth.getText());
 808
 809     /*
 810      * Save Editing settings
 811      */
 812     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 813             Boolean.toString(autoCalculateConsCheck.isSelected()));
 814     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 815             Boolean.toString(sortByTree.isSelected()));
 816     Cache.applicationProperties.setProperty("PAD_GAPS",
 817             Boolean.toString(padGaps.isSelected()));
 818
 819     if (!Jalview.isJS())
 820     {
 821       wsPrefs.updateAndRefreshWsMenuConfig(false);
 822     }
 823     Cache.saveProperties();
 824     Desktop.instance.doConfigureStructurePrefs();
 825     try
 826     {
 827       frame.setClosed(true);
 828     } catch (Exception ex)
 829     {
 830     }
 831   }
 832
 833   /**
 834    * Do any necessary validation before saving settings. Return focus to the
 835    * first tab which fails validation.
 836    *
 837    * @return
 838    */
 839   private boolean validateSettings()
 840   {
 841     if (!validateStructure())
 842     {
 843       structureTab.requestFocusInWindow();
 844       return false;
 845     }
 846     return true;
 847   }
 848
 849   @Override
 850   protected boolean validateStructure()
 851   {
 852     return validateChimeraPath();
 853
 854   }
 855
 856   /**
 857    * DOCUMENT ME!
 858    */
 859   @Override
 860   public void startupFileTextfield_mouseClicked()
 861   {
 862     // TODO: JAL-3048 not needed for Jalview-JS
 863     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 864     JalviewFileChooser chooser = JalviewFileChooser
 865             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 866     chooser.setFileView(new JalviewFileView());
 867     chooser.setDialogTitle(
 868             MessageManager.getString("label.select_startup_file"));
 869
 870     int value = chooser.showOpenDialog(this);
 871
 872     if (value == JalviewFileChooser.APPROVE_OPTION)
 873     {
 874       FileFormatI format = chooser.getSelectedFormat();
 875       if (format != null)
 876       {
 877         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 878                 format.getName());
 879       }
 880       startupFileTextfield
 881               .setText(chooser.getSelectedFile().getAbsolutePath());
 882     }
 883   }
 884
 885   /**
 886    * DOCUMENT ME!
 887    *
 888    * @param e
 889    *          DOCUMENT ME!
 890    */
 891   @Override
 892   public void cancel_actionPerformed(ActionEvent e)
 893   {
 894     try
 895     {
 896       if (!Jalview.isJS())
 897       {
 898         wsPrefs.updateWsMenuConfig(true);
 899         wsPrefs.refreshWs_actionPerformed(e);
 900       }
 901       frame.setClosed(true);
 902     } catch (Exception ex)
 903     {
 904     }
 905   }
 906
 907   /**
 908    * DOCUMENT ME!
 909    *
 910    * @param e
 911    *          DOCUMENT ME!
 912    */
 913   @Override
 914   public void annotations_actionPerformed(ActionEvent e)
 915   {
 916     conservation.setEnabled(annotations.isSelected());
 917     quality.setEnabled(annotations.isSelected());
 918     identity.setEnabled(annotations.isSelected());
 919     showOccupancy.setEnabled(annotations.isSelected());
 920     showGroupConsensus.setEnabled(annotations.isSelected());
 921     showGroupConservation.setEnabled(annotations.isSelected());
 922     showConsensHistogram.setEnabled(annotations.isSelected()
 923             && (identity.isSelected() || showGroupConsensus.isSelected()));
 924     showConsensLogo.setEnabled(annotations.isSelected()
 925             && (identity.isSelected() || showGroupConsensus.isSelected()));
 926   }
 927
 928   @Override
 929   public void newLink_actionPerformed(ActionEvent e)
 930   {
 931     GSequenceLink link = new GSequenceLink();
 932     boolean valid = false;
 933     while (!valid)
 934     {
 935       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 936               MessageManager.getString("label.new_sequence_url_link"),
 937               JvOptionPane.OK_CANCEL_OPTION, -1,
 938               null) == JvOptionPane.OK_OPTION)
 939       {
 940         if (link.checkValid())
 941         {
 942           if (((UrlLinkTableModel) linkUrlTable.getModel())
 943                   .isUniqueName(link.getName()))
 944           {
 945             ((UrlLinkTableModel) linkUrlTable.getModel())
 946                     .insertRow(link.getName(), link.getURL());
 947             valid = true;
 948           }
 949           else
 950           {
 951             link.notifyDuplicate();
 952             continue;
 953           }
 954         }
 955       }
 956       else
 957       {
 958         break;
 959       }
 960     }
 961   }
 962
 963   @Override
 964   public void editLink_actionPerformed(ActionEvent e)
 965   {
 966     GSequenceLink link = new GSequenceLink();
 967
 968     int index = linkUrlTable.getSelectedRow();
 969     if (index == -1)
 970     {
 971       // button no longer enabled if row is not selected
 972       Cache.log.debug("Edit with no row selected in linkUrlTable");
 973       return;
 974     }
 975
 976     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 977             .getNameColumn();
 978     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 979             .getUrlColumn();
 980     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 981     link.setName(oldName);
 982     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 983
 984     boolean valid = false;
 985     while (!valid)
 986     {
 987       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 988               MessageManager.getString("label.edit_sequence_url_link"),
 989               JvOptionPane.OK_CANCEL_OPTION, -1,
 990               null) == JvOptionPane.OK_OPTION)
 991       {
 992         if (link.checkValid())
 993         {
 994           if ((oldName.equals(link.getName()))
 995                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 996                           .isUniqueName(link.getName())))
 997           {
 998             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 999             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1000             valid = true;
1001           }
1002           else
1003           {
1004             link.notifyDuplicate();
1005             continue;
1006           }
1007         }
1008       }
1009       else
1010       {
1011         break;
1012       }
1013     }
1014   }
1015
1016   @Override
1017   public void deleteLink_actionPerformed(ActionEvent e)
1018   {
1019     int index = linkUrlTable.getSelectedRow();
1020     int modelIndex = -1;
1021     if (index == -1)
1022     {
1023       // button no longer enabled if row is not selected
1024       Cache.log.debug("Delete with no row selected in linkUrlTable");
1025       return;
1026     }
1027     else
1028     {
1029       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1030     }
1031
1032     // make sure we use the model index to delete, and not the table index
1033     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1034   }
1035
1036   @Override
1037   public void defaultBrowser_mouseClicked(MouseEvent e)
1038   {
1039     // TODO: JAL-3048 not needed for j2s
1040     /*
1041      * @j2sNative
1042      */
1043     {
1044       JFileChooser chooser = new JFileChooser(".");
1045       chooser.setDialogTitle(
1046               MessageManager.getString("label.select_default_browser"));
1047
1048       int value = chooser.showOpenDialog(this);
1049
1050       if (value == JFileChooser.APPROVE_OPTION)
1051       {
1052         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1053       }
1054     }
1055   }
1056
1057   /*
1058    * (non-Javadoc)
1059    *
1060    * @see
1061    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1062    * .ActionEvent)
1063    */
1064   @Override
1065   protected void showunconserved_actionPerformed(ActionEvent e)
1066   {
1067     // TODO Auto-generated method stub
1068     super.showunconserved_actionPerformed(e);
1069   }
1070
1071   public static List<String> getGroupURLLinks()
1072   {
1073     return groupURLLinks;
1074   }
1075
1076   @Override
1077   public void minColour_actionPerformed(JPanel panel)
1078   {
1079     JalviewColourChooser.showColourChooser(this,
1080             MessageManager.getString("label.select_colour_minimum_value"),
1081             panel);
1082   }
1083
1084   @Override
1085   public void maxColour_actionPerformed(JPanel panel)
1086   {
1087     JalviewColourChooser.showColourChooser(this,
1088             MessageManager.getString("label.select_colour_maximum_value"),
1089             panel);
1090   }
1091
1092   @Override
1093   public void gapColour_actionPerformed(JPanel gap)
1094   {
1095     if (!useLegacyGap.isSelected())
1096     {
1097       JalviewColourChooser.showColourChooser(this,
1098               MessageManager.getString("label.select_gap_colour"),
1099               gap);
1100     }
1101   }
1102
1103   @Override
1104   public void hiddenColour_actionPerformed(JPanel hidden)
1105   {
1106     JalviewColourChooser.showColourChooser(this,
1107             MessageManager.getString("label.select_hidden_colour"),
1108             hidden);
1109   }
1110
1111   @Override
1112   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1113   {
1114     boolean enabled = useLegacyGap.isSelected();
1115     if (enabled)
1116     {
1117       gapColour.setBackground(
1118               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1119     }
1120     else
1121     {
1122       gapColour.setBackground(
1123               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1124     }
1125     gapColour.setEnabled(!enabled);
1126     gapLabel.setEnabled(!enabled);
1127   }
1128
1129   @Override
1130   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1131   {
1132     useLegacyGap.setSelected(false);
1133     useLegacyGaps_actionPerformed(null);
1134     showHiddenAtStart.setSelected(true);
1135     hiddenColour.setBackground(
1136             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1137   }
1138
1139   @Override
1140   protected void userIdWidth_actionPerformed()
1141   {
1142     try
1143     {
1144       String val = userIdWidth.getText().trim();
1145       if (val.length() > 0)
1146       {
1147         Integer iw = Integer.parseInt(val);
1148         if (iw.intValue() < 12)
1149         {
1150           throw new NumberFormatException();
1151         }
1152         userIdWidth.setText(iw.toString());
1153       }
1154     } catch (NumberFormatException x)
1155     {
1156       userIdWidth.setText("");
1157       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1158               MessageManager
1159                       .getString("warn.user_defined_width_requirements"),
1160               MessageManager.getString("label.invalid_id_column_width"),
1161               JvOptionPane.WARNING_MESSAGE);
1162     }
1163   }
1164
1165   @Override
1166   protected void autoIdWidth_actionPerformed()
1167   {
1168     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1169     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1170   }
1171
1172   /**
1173    * Returns true if chimera path is to a valid executable, else show an error
1174    * dialog.
1175    */
1176   private boolean validateChimeraPath()
1177   {
1178     if (chimeraPath.getText().trim().length() > 0)
1179     {
1180       File f = new File(chimeraPath.getText());
1181       if (!f.canExecute())
1182       {
1183         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1184                 MessageManager.getString("label.invalid_chimera_path"),
1185                 MessageManager.getString("label.invalid_name"),
1186                 JvOptionPane.ERROR_MESSAGE);
1187         return false;
1188       }
1189     }
1190     return true;
1191   }
1192
1193   /**
1194    * If Chimera is selected, check it can be found on default or user-specified
1195    * path, if not show a warning/help dialog.
1196    */
1197   @Override
1198   protected void structureViewer_actionPerformed(String selectedItem)
1199   {
1200     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1201     {
1202       return;
1203     }
1204     boolean found = false;
1205
1206     /*
1207      * Try user-specified and standard paths for Chimera executable.
1208      */
1209     List<String> paths = StructureManager.getChimeraPaths();
1210     paths.add(0, chimeraPath.getText());
1211     for (String path : paths)
1212     {
1213       if (new File(path.trim()).canExecute())
1214       {
1215         found = true;
1216         break;
1217       }
1218     }
1219     if (!found)
1220     {
1221       String[] options = { "OK", "Help" };
1222       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1223               JvSwingUtils.wrapTooltip(true,
1224                       MessageManager.getString("label.chimera_missing")),
1225               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1226               null, options, options[0]);
1227       if (showHelp == JvOptionPane.NO_OPTION)
1228       {
1229         try
1230         {
1231           Help.showHelpWindow(HelpId.StructureViewer);
1232         } catch (HelpSetException e)
1233         {
1234           e.printStackTrace();
1235         }
1236       }
1237     }
1238   }
1239
1240   public class OptionsParam
1241   {
1242     private String name;
1243
1244     private String code;
1245
1246     public OptionsParam(String name, String code)
1247     {
1248       this.name = name;
1249       this.code = code;
1250     }
1251
1252     public String getName()
1253     {
1254       return name;
1255     }
1256
1257     public void setName(String name)
1258     {
1259       this.name = name;
1260     }
1261
1262     public String getCode()
1263     {
1264       return code;
1265     }
1266
1267     public void setCode(String code)
1268     {
1269       this.code = code;
1270     }
1271
1272     @Override
1273     public String toString()
1274     {
1275       return name;
1276     }
1277
1278     @Override
1279     public boolean equals(Object that)
1280     {
1281       if (!(that instanceof OptionsParam))
1282       {
1283         return false;
1284       }
1285       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1286     }
1287
1288     @Override
1289     public int hashCode()
1290     {
1291       return name.hashCode() + code.hashCode();
1292     }
1293   }
1294
1295   private class UrlListSelectionHandler implements ListSelectionListener
1296   {
1297
1298     @Override
1299     public void valueChanged(ListSelectionEvent e)
1300     {
1301       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1302
1303       int index = lsm.getMinSelectionIndex();
1304       if (index == -1)
1305       {
1306         // no selection, so disable delete/edit buttons
1307         editLink.setEnabled(false);
1308         deleteLink.setEnabled(false);
1309         return;
1310       }
1311       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1312
1313       // enable/disable edit and delete link buttons
1314       if (((UrlLinkTableModel) linkUrlTable.getModel())
1315               .isRowDeletable(modelIndex))
1316       {
1317         deleteLink.setEnabled(true);
1318       }
1319       else
1320       {
1321         deleteLink.setEnabled(false);
1322       }
1323
1324       if (((UrlLinkTableModel) linkUrlTable.getModel())
1325               .isRowEditable(modelIndex))
1326       {
1327         editLink.setEnabled(true);
1328       }
1329       else
1330       {
1331         editLink.setEnabled(false);
1332       }
1333     }
1334   }
1335 }