src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.FileFormatI;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeI;
  33 import jalview.schemes.ColourSchemes;
  34 import jalview.schemes.ResidueColourScheme;
  35 import jalview.urls.UrlLinkTableModel;
  36 import jalview.urls.api.UrlProviderFactoryI;
  37 import jalview.urls.api.UrlProviderI;
  38 import jalview.urls.desktop.DesktopUrlProviderFactory;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.util.UrlConstants;
  42 import jalview.ws.sifts.SiftsSettings;
  43
  44 import java.awt.BorderLayout;
  45 import java.awt.Color;
  46 import java.awt.Component;
  47 import java.awt.Dimension;
  48 import java.awt.Font;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseEvent;
  52 import java.io.File;
  53 import java.util.ArrayList;
  54 import java.util.List;
  55
  56 import javax.help.HelpSetException;
  57 import javax.swing.JColorChooser;
  58 import javax.swing.JFileChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JPanel;
  61 import javax.swing.ListSelectionModel;
  62 import javax.swing.RowFilter;
  63 import javax.swing.RowSorter;
  64 import javax.swing.SortOrder;
  65 import javax.swing.event.DocumentEvent;
  66 import javax.swing.event.DocumentListener;
  67 import javax.swing.event.ListSelectionEvent;
  68 import javax.swing.event.ListSelectionListener;
  69 import javax.swing.table.TableCellRenderer;
  70 import javax.swing.table.TableColumn;
  71 import javax.swing.table.TableModel;
  72 import javax.swing.table.TableRowSorter;
  73
  74 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  75
  76 /**
  77  * DOCUMENT ME!
  78  *
  79  * @author $author$
  80  * @version $Revision$
  81  */
  82 public class Preferences extends GPreferences
  83 {
  84   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  85
  86   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  87
  88   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  89
  90   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  91
  92   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  93
  94   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  95
  96   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  97
  98   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  99
 100   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 101
 102   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 103
 104   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 105
 106   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 107
 108   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 109
 110   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 111
 112   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 113
 114   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 115
 116   public static final String GAP_COLOUR = "GAP_COLOUR";
 117
 118   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 119
 120   private static final int MIN_FONT_SIZE = 1;
 121
 122   private static final int MAX_FONT_SIZE = 30;
 123
 124   /**
 125    * Holds name and link separated with | character. Sequence ID must be
 126    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 127    */
 128   public static UrlProviderI sequenceUrlLinks;
 129
 130   public static UrlLinkTableModel dataModel;
 131
 132   /**
 133    * Holds name and link separated with | character. Sequence IDS and Sequences
 134    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 135    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 136    * for first and second token specified after a pipe character at end |,|.
 137    * (TODO: proper escape for using | to separate ids or sequences
 138    */
 139
 140   public static List<String> groupURLLinks;
 141   static
 142   {
 143     // get links selected to be in the menu (SEQUENCE_LINKS)
 144     // and links entered by the user but not selected (STORED_LINKS)
 145     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 146     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 147     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 148             UrlConstants.DEFAULT_LABEL);
 149
 150     // if both links lists are empty, add the DEFAULT_URL link
 151     // otherwise we assume the default link is in one of the lists
 152     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 153     {
 154       inMenuString = UrlConstants.DEFAULT_STRING;
 155     }
 156     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 157             inMenuString, notInMenuString);
 158     sequenceUrlLinks = factory.createUrlProvider();
 159     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 160
 161     /**
 162      * TODO: reformulate groupURL encoding so two or more can be stored in the
 163      * .properties file as '|' separated strings
 164      */
 165
 166     groupURLLinks = new ArrayList<>();
 167   }
 168
 169   JInternalFrame frame;
 170
 171   DasSourceBrowser dasSource;
 172
 173   private WsPreferences wsPrefs;
 174
 175   private OptionsParam promptEachTimeOpt = new OptionsParam(
 176           MessageManager.getString("label.prompt_each_time"),
 177           "Prompt each time");
 178
 179   private OptionsParam lineArtOpt = new OptionsParam(
 180           MessageManager.getString("label.lineart"), "Lineart");
 181
 182   private OptionsParam textOpt = new OptionsParam(
 183           MessageManager.getString("action.text"), "Text");
 184
 185   /**
 186    * Creates a new Preferences object.
 187    */
 188   public Preferences()
 189   {
 190     super();
 191     frame = new JInternalFrame();
 192     frame.setContentPane(this);
 193     dasSource = new DasSourceBrowser();
 194     dasTab.add(dasSource, BorderLayout.CENTER);
 195     wsPrefs = new WsPreferences();
 196     wsTab.add(wsPrefs, BorderLayout.CENTER);
 197     int width = 500, height = 450;
 198     new jalview.util.Platform();
 199     if (Platform.isAMac())
 200     {
 201       width = 570;
 202       height = 480;
 203     }
 204
 205     Desktop.addInternalFrame(frame,
 206             MessageManager.getString("label.preferences"), width, height);
 207     frame.setMinimumSize(new Dimension(width, height));
 208
 209     /*
 210      * Set Visual tab defaults
 211      */
 212     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 213     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 214     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 215     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 216
 217     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 218     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 219     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 220     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 221     showUnconserved
 222             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 223     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 224     showGroupConsensus
 225             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 226     showGroupConservation.setSelected(
 227             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 228     showConsensHistogram.setSelected(
 229             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 230     showConsensLogo
 231             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 232     showNpTooltip
 233             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 234     showDbRefTooltip
 235             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 236
 237     String[] fonts = java.awt.GraphicsEnvironment
 238             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 239     for (int i = 0; i < fonts.length; i++)
 240     {
 241       fontNameCB.addItem(fonts[i]);
 242     }
 243
 244     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 245     {
 246       fontSizeCB.addItem(i + "");
 247     }
 248
 249     fontStyleCB.addItem("plain");
 250     fontStyleCB.addItem("bold");
 251     fontStyleCB.addItem("italic");
 252
 253     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 254     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 255     fontStyleCB.setSelectedItem(
 256             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 257
 258     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 259     scaleProteinToCdna
 260             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 261
 262     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 263
 264     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 265
 266     gapSymbolCB.addItem("-");
 267     gapSymbolCB.addItem(".");
 268
 269     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 270
 271     sortby.addItem("No sort");
 272     sortby.addItem("Id");
 273     sortby.addItem("Pairwise Identity");
 274     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 275
 276     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 277     sortAnnBy
 278             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 279     sortAnnBy
 280             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 281     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 282             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 283                     SequenceAnnotationOrder.NONE.name()));
 284     sortAnnBy.setSelectedItem(savedSort.toString());
 285
 286     sortAutocalc.addItem("Autocalculated first");
 287     sortAutocalc.addItem("Autocalculated last");
 288     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 289     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 290             : sortAutocalc.getItemAt(1));
 291     startupCheckbox
 292             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 293     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 294             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 295                     + "/examples/exampleFile_2_3.jar"));
 296
 297     /*
 298      * Set Colours tab defaults
 299      */
 300     protColour.addItem(ResidueColourScheme.NONE);
 301     nucColour.addItem(ResidueColourScheme.NONE);
 302     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 303     {
 304       String name = cs.getSchemeName();
 305       protColour.addItem(name);
 306       nucColour.addItem(name);
 307     }
 308     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 309             ResidueColourScheme.NONE);
 310     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 311     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 312     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 313     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 314     minColour.setBackground(
 315             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 316     maxColour.setBackground(
 317             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 318
 319     /*
 320      * Set overview panel defaults
 321      */
 322     gapColour.setBackground(
 323             Cache.getDefaultColour(GAP_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 325     hiddenColour.setBackground(
 326             Cache.getDefaultColour(HIDDEN_COLOUR,
 327                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 328     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 329     gapLabel.setEnabled(!useLegacyGap.isSelected());
 330     gapColour.setEnabled(!useLegacyGap.isSelected());
 331     showHiddenAtStart
 332             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 333
 334     /*
 335      * Set Structure tab defaults.
 336      */
 337     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 338     structFromPdb.setSelected(structSelected);
 339     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 340     useRnaView.setEnabled(structSelected);
 341     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 342     addSecondaryStructure.setEnabled(structSelected);
 343     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 344     addTempFactor.setEnabled(structSelected);
 345     structViewer.setSelectedItem(
 346             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 347     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 348     chimeraPath.addActionListener(new ActionListener()
 349     {
 350       @Override
 351       public void actionPerformed(ActionEvent e)
 352       {
 353         validateChimeraPath();
 354       }
 355     });
 356
 357     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 358     {
 359       siftsMapping.setSelected(true);
 360     }
 361     else
 362     {
 363       nwMapping.setSelected(true);
 364     }
 365
 366     SiftsSettings
 367             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 368
 369     /*
 370      * Set Connections tab defaults
 371      */
 372
 373     // set up sorting
 374     linkUrlTable.setModel(dataModel);
 375     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 376             linkUrlTable.getModel());
 377     linkUrlTable.setRowSorter(sorter);
 378     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 379
 380     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 381     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 382             SortOrder.DESCENDING));
 383     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 384             SortOrder.DESCENDING));
 385     sortKeys.add(
 386             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 387
 388     sorter.setSortKeys(sortKeys);
 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     epsRendering.addItem(promptEachTimeOpt);
 509     epsRendering.addItem(lineArtOpt);
 510     epsRendering.addItem(textOpt);
 511     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 512             "Prompt each time");
 513     if (defaultEPS.equalsIgnoreCase("Text"))
 514     {
 515       epsRendering.setSelectedItem(textOpt);
 516     }
 517     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 518     {
 519       epsRendering.setSelectedItem(lineArtOpt);
 520     }
 521     else
 522     {
 523       epsRendering.setSelectedItem(promptEachTimeOpt);
 524     }
 525     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 526     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 527     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 528     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 529     userIdWidth.setText(wi == null ? "" : wi.toString());
 530     // TODO: refactor to use common enum via FormatAdapter and allow extension
 531     // for new flat file formats
 532     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 533     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 534     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 535     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 536     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 537     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 538     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 539     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 540     embbedBioJSON
 541             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 542
 543     /*
 544      * Set Editing tab defaults
 545      */
 546     autoCalculateConsCheck
 547             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 548     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 549     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 550
 551     annotations_actionPerformed(null); // update the display of the annotation
 552                                        // settings
 553   }
 554
 555   /**
 556    * Save user selections on the Preferences tabs to the Cache and write out to
 557    * file.
 558    *
 559    * @param e
 560    */
 561   @Override
 562   public void ok_actionPerformed(ActionEvent e)
 563   {
 564     if (!validateSettings())
 565     {
 566       return;
 567     }
 568
 569     /*
 570      * Save Visual settings
 571      */
 572     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 573             Boolean.toString(seqLimit.isSelected()));
 574     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 575             Boolean.toString(rightAlign.isSelected()));
 576     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 577             Boolean.toString(fullScreen.isSelected()));
 578     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 579             Boolean.toString(openoverv.isSelected()));
 580     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 581             Boolean.toString(annotations.isSelected()));
 582     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 583             Boolean.toString(conservation.isSelected()));
 584     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 585             Boolean.toString(quality.isSelected()));
 586     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 587             Boolean.toString(identity.isSelected()));
 588
 589     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 590             gapSymbolCB.getSelectedItem().toString());
 591
 592     Cache.applicationProperties.setProperty("FONT_NAME",
 593             fontNameCB.getSelectedItem().toString());
 594     Cache.applicationProperties.setProperty("FONT_STYLE",
 595             fontStyleCB.getSelectedItem().toString());
 596     Cache.applicationProperties.setProperty("FONT_SIZE",
 597             fontSizeCB.getSelectedItem().toString());
 598
 599     Cache.applicationProperties.setProperty("ID_ITALICS",
 600             Boolean.toString(idItalics.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 602             Boolean.toString(showUnconserved.isSelected()));
 603     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 604             Boolean.toString(showOccupancy.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 606             Boolean.toString(showGroupConsensus.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 608             Boolean.toString(showGroupConservation.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 610             Boolean.toString(showConsensHistogram.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 612             Boolean.toString(showConsensLogo.isSelected()));
 613     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 614             Boolean.toString(smoothFont.isSelected()));
 615     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 616             Boolean.toString(scaleProteinToCdna.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 618             Boolean.toString(showNpTooltip.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 620             Boolean.toString(showDbRefTooltip.isSelected()));
 621
 622     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 623             Boolean.toString(wrap.isSelected()));
 624
 625     Cache.applicationProperties.setProperty("STARTUP_FILE",
 626             startupFileTextfield.getText());
 627     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 628             Boolean.toString(startupCheckbox.isSelected()));
 629
 630     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 631             sortby.getSelectedItem().toString());
 632
 633     // convert description of sort order to enum name for save
 634     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 635             .forDescription(sortAnnBy.getSelectedItem().toString());
 636     if (annSortOrder != null)
 637     {
 638       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 639               annSortOrder.name());
 640     }
 641
 642     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 643     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 644             Boolean.valueOf(showAutocalcFirst).toString());
 645
 646     /*
 647      * Save Colours settings
 648      */
 649     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 650             protColour.getSelectedItem().toString());
 651     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 652             nucColour.getSelectedItem().toString());
 653     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 654             minColour.getBackground());
 655     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 656             maxColour.getBackground());
 657
 658     /*
 659      * Save Overview settings
 660      */
 661     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 662     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 663     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 664             Boolean.toString(useLegacyGap.isSelected()));
 665     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 666             Boolean.toString(showHiddenAtStart.isSelected()));
 667
 668     /*
 669      * Save Structure settings
 670      */
 671     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 672             Boolean.toString(addTempFactor.isSelected()));
 673     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 674             Boolean.toString(addSecondaryStructure.isSelected()));
 675     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 676             Boolean.toString(useRnaView.isSelected()));
 677     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 678             Boolean.toString(structFromPdb.isSelected()));
 679     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 680             structViewer.getSelectedItem().toString());
 681     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 682     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 683             Boolean.toString(siftsMapping.isSelected()));
 684     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 685
 686     /*
 687      * Save Output settings
 688      */
 689     Cache.applicationProperties.setProperty("EPS_RENDERING",
 690             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 691
 692     /*
 693      * Save Connections settings
 694      */
 695     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 696
 697     jalview.util.BrowserLauncher.resetBrowser();
 698
 699     // save user-defined and selected links
 700     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 701     if (menuLinks.isEmpty())
 702     {
 703       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 704     }
 705     else
 706     {
 707       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 708               menuLinks.toString());
 709     }
 710
 711     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 712     if (nonMenuLinks.isEmpty())
 713     {
 714       Cache.applicationProperties.remove("STORED_LINKS");
 715     }
 716     else
 717     {
 718       Cache.applicationProperties.setProperty("STORED_LINKS",
 719               nonMenuLinks.toString());
 720     }
 721
 722     Cache.applicationProperties.setProperty("DEFAULT_URL",
 723             sequenceUrlLinks.getPrimaryUrlId());
 724
 725     Cache.applicationProperties.setProperty("USE_PROXY",
 726             Boolean.toString(useProxy.isSelected()));
 727
 728     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 729
 730     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 731
 732     if (useProxy.isSelected())
 733     {
 734       System.setProperty("http.proxyHost", proxyServerTB.getText());
 735       System.setProperty("http.proxyPort", proxyPortTB.getText());
 736     }
 737     else
 738     {
 739       System.setProperty("http.proxyHost", "");
 740       System.setProperty("http.proxyPort", "");
 741     }
 742     Cache.setProperty("VERSION_CHECK",
 743             Boolean.toString(versioncheck.isSelected()));
 744     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 745     {
 746       // default is false - we only set this if the user has actively agreed
 747       Cache.setProperty("USAGESTATS",
 748               Boolean.toString(usagestats.isSelected()));
 749     }
 750     if (!questionnaire.isSelected())
 751     {
 752       Cache.setProperty("NOQUESTIONNAIRES", "true");
 753     }
 754     else
 755     {
 756       // special - made easy to edit a property file to disable questionnaires
 757       // by just adding the given line
 758       Cache.removeProperty("NOQUESTIONNAIRES");
 759     }
 760
 761     /*
 762      * Save Output settings
 763      */
 764     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 765             Boolean.toString(blcjv.isSelected()));
 766     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 767             Boolean.toString(clustaljv.isSelected()));
 768     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 769             Boolean.toString(fastajv.isSelected()));
 770     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 771             Boolean.toString(msfjv.isSelected()));
 772     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 773             Boolean.toString(pfamjv.isSelected()));
 774     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 775             Boolean.toString(pileupjv.isSelected()));
 776     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 777             Boolean.toString(pirjv.isSelected()));
 778     Cache.applicationProperties.setProperty("PIR_MODELLER",
 779             Boolean.toString(modellerOutput.isSelected()));
 780     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 781             Boolean.toString(embbedBioJSON.isSelected()));
 782     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 783
 784     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 785             Boolean.toString(autoIdWidth.isSelected()));
 786     userIdWidth_actionPerformed();
 787     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 788             userIdWidth.getText());
 789
 790     /*
 791      * Save Editing settings
 792      */
 793     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 794             Boolean.toString(autoCalculateConsCheck.isSelected()));
 795     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 796             Boolean.toString(sortByTree.isSelected()));
 797     Cache.applicationProperties.setProperty("PAD_GAPS",
 798             Boolean.toString(padGaps.isSelected()));
 799
 800     dasSource.saveProperties(Cache.applicationProperties);
 801     wsPrefs.updateAndRefreshWsMenuConfig(false);
 802     Cache.saveProperties();
 803     Desktop.instance.doConfigureStructurePrefs();
 804     try
 805     {
 806       frame.setClosed(true);
 807     } catch (Exception ex)
 808     {
 809     }
 810   }
 811
 812   /**
 813    * Do any necessary validation before saving settings. Return focus to the
 814    * first tab which fails validation.
 815    *
 816    * @return
 817    */
 818   private boolean validateSettings()
 819   {
 820     if (!validateStructure())
 821     {
 822       structureTab.requestFocusInWindow();
 823       return false;
 824     }
 825     return true;
 826   }
 827
 828   @Override
 829   protected boolean validateStructure()
 830   {
 831     return validateChimeraPath();
 832
 833   }
 834
 835   /**
 836    * DOCUMENT ME!
 837    */
 838   @Override
 839   public void startupFileTextfield_mouseClicked()
 840   {
 841     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 842     JalviewFileChooser chooser = JalviewFileChooser
 843             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 844     chooser.setFileView(new JalviewFileView());
 845     chooser.setDialogTitle(
 846             MessageManager.getString("label.select_startup_file"));
 847
 848     int value = chooser.showOpenDialog(this);
 849
 850     if (value == JalviewFileChooser.APPROVE_OPTION)
 851     {
 852       FileFormatI format = chooser.getSelectedFormat();
 853       if (format != null)
 854       {
 855         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 856                 format.getName());
 857       }
 858       startupFileTextfield
 859               .setText(chooser.getSelectedFile().getAbsolutePath());
 860     }
 861   }
 862
 863   /**
 864    * DOCUMENT ME!
 865    *
 866    * @param e
 867    *          DOCUMENT ME!
 868    */
 869   @Override
 870   public void cancel_actionPerformed(ActionEvent e)
 871   {
 872     try
 873     {
 874       wsPrefs.updateWsMenuConfig(true);
 875       wsPrefs.refreshWs_actionPerformed(e);
 876       frame.setClosed(true);
 877     } catch (Exception ex)
 878     {
 879     }
 880   }
 881
 882   /**
 883    * DOCUMENT ME!
 884    *
 885    * @param e
 886    *          DOCUMENT ME!
 887    */
 888   @Override
 889   public void annotations_actionPerformed(ActionEvent e)
 890   {
 891     conservation.setEnabled(annotations.isSelected());
 892     quality.setEnabled(annotations.isSelected());
 893     identity.setEnabled(annotations.isSelected());
 894     showOccupancy.setEnabled(annotations.isSelected());
 895     showGroupConsensus.setEnabled(annotations.isSelected());
 896     showGroupConservation.setEnabled(annotations.isSelected());
 897     showConsensHistogram.setEnabled(annotations.isSelected()
 898             && (identity.isSelected() || showGroupConsensus.isSelected()));
 899     showConsensLogo.setEnabled(annotations.isSelected()
 900             && (identity.isSelected() || showGroupConsensus.isSelected()));
 901   }
 902
 903   @Override
 904   public void newLink_actionPerformed(ActionEvent e)
 905   {
 906     GSequenceLink link = new GSequenceLink();
 907     boolean valid = false;
 908     while (!valid)
 909     {
 910       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 911               MessageManager.getString("label.new_sequence_url_link"),
 912               JvOptionPane.OK_CANCEL_OPTION, -1,
 913               null) == JvOptionPane.OK_OPTION)
 914       {
 915         if (link.checkValid())
 916         {
 917           if (((UrlLinkTableModel) linkUrlTable.getModel())
 918                   .isUniqueName(link.getName()))
 919           {
 920             ((UrlLinkTableModel) linkUrlTable.getModel())
 921                     .insertRow(link.getName(), link.getURL());
 922             valid = true;
 923           }
 924           else
 925           {
 926             link.notifyDuplicate();
 927             continue;
 928           }
 929         }
 930       }
 931       else
 932       {
 933         break;
 934       }
 935     }
 936   }
 937
 938   @Override
 939   public void editLink_actionPerformed(ActionEvent e)
 940   {
 941     GSequenceLink link = new GSequenceLink();
 942
 943     int index = linkUrlTable.getSelectedRow();
 944     if (index == -1)
 945     {
 946       // button no longer enabled if row is not selected
 947       Cache.log.debug("Edit with no row selected in linkUrlTable");
 948       return;
 949     }
 950
 951     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 952             .getNameColumn();
 953     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 954             .getUrlColumn();
 955     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 956     link.setName(oldName);
 957     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 958
 959     boolean valid = false;
 960     while (!valid)
 961     {
 962       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 963               MessageManager.getString("label.edit_sequence_url_link"),
 964               JvOptionPane.OK_CANCEL_OPTION, -1,
 965               null) == JvOptionPane.OK_OPTION)
 966       {
 967         if (link.checkValid())
 968         {
 969           if ((oldName.equals(link.getName()))
 970                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 971                           .isUniqueName(link.getName())))
 972           {
 973             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 974             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 975             valid = true;
 976           }
 977           else
 978           {
 979             link.notifyDuplicate();
 980             continue;
 981           }
 982         }
 983       }
 984       else
 985       {
 986         break;
 987       }
 988     }
 989   }
 990
 991   @Override
 992   public void deleteLink_actionPerformed(ActionEvent e)
 993   {
 994     int index = linkUrlTable.getSelectedRow();
 995     int modelIndex = -1;
 996     if (index == -1)
 997     {
 998       // button no longer enabled if row is not selected
 999       Cache.log.debug("Delete with no row selected in linkUrlTable");
1000       return;
1001     }
1002     else
1003     {
1004       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1005     }
1006
1007     // make sure we use the model index to delete, and not the table index
1008     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1009   }
1010
1011   @Override
1012   public void defaultBrowser_mouseClicked(MouseEvent e)
1013   {
1014     JFileChooser chooser = new JFileChooser(".");
1015     chooser.setDialogTitle(
1016             MessageManager.getString("label.select_default_browser"));
1017
1018     int value = chooser.showOpenDialog(this);
1019
1020     if (value == JFileChooser.APPROVE_OPTION)
1021     {
1022       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1023     }
1024
1025   }
1026
1027   /*
1028    * (non-Javadoc)
1029    *
1030    * @see
1031    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1032    * .ActionEvent)
1033    */
1034   @Override
1035   protected void showunconserved_actionPerformed(ActionEvent e)
1036   {
1037     // TODO Auto-generated method stub
1038     super.showunconserved_actionPerformed(e);
1039   }
1040
1041   public static List<String> getGroupURLLinks()
1042   {
1043     return groupURLLinks;
1044   }
1045
1046   @Override
1047   public void minColour_actionPerformed(JPanel panel)
1048   {
1049     Color col = JColorChooser.showDialog(this,
1050             MessageManager.getString("label.select_colour_minimum_value"),
1051             minColour.getBackground());
1052     if (col != null)
1053     {
1054       panel.setBackground(col);
1055     }
1056     panel.repaint();
1057   }
1058
1059   @Override
1060   public void maxColour_actionPerformed(JPanel panel)
1061   {
1062     Color col = JColorChooser.showDialog(this,
1063             MessageManager.getString("label.select_colour_maximum_value"),
1064             maxColour.getBackground());
1065     if (col != null)
1066     {
1067       panel.setBackground(col);
1068     }
1069     panel.repaint();
1070   }
1071
1072   @Override
1073   public void gapColour_actionPerformed(JPanel gap)
1074   {
1075     if (!useLegacyGap.isSelected())
1076     {
1077       Color col = JColorChooser.showDialog(this,
1078               MessageManager.getString("label.select_gap_colour"),
1079               gapColour.getBackground());
1080       if (col != null)
1081       {
1082         gap.setBackground(col);
1083       }
1084       gap.repaint();
1085     }
1086   }
1087
1088   @Override
1089   public void hiddenColour_actionPerformed(JPanel hidden)
1090   {
1091     Color col = JColorChooser.showDialog(this,
1092             MessageManager.getString("label.select_hidden_colour"),
1093             hiddenColour.getBackground());
1094     if (col != null)
1095     {
1096       hidden.setBackground(col);
1097     }
1098     hidden.repaint();
1099   }
1100
1101   @Override
1102   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1103   {
1104     boolean enabled = useLegacyGap.isSelected();
1105     if (enabled)
1106     {
1107       gapColour.setBackground(
1108               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1109     }
1110     else
1111     {
1112       gapColour.setBackground(
1113               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1114     }
1115     gapColour.setEnabled(!enabled);
1116     gapLabel.setEnabled(!enabled);
1117   }
1118
1119   @Override
1120   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1121   {
1122     useLegacyGap.setSelected(false);
1123     useLegacyGaps_actionPerformed(null);
1124     showHiddenAtStart.setSelected(true);
1125     hiddenColour.setBackground(
1126             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1127   }
1128
1129   @Override
1130   protected void userIdWidth_actionPerformed()
1131   {
1132     try
1133     {
1134       String val = userIdWidth.getText().trim();
1135       if (val.length() > 0)
1136       {
1137         Integer iw = Integer.parseInt(val);
1138         if (iw.intValue() < 12)
1139         {
1140           throw new NumberFormatException();
1141         }
1142         userIdWidth.setText(iw.toString());
1143       }
1144     } catch (NumberFormatException x)
1145     {
1146       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1147               MessageManager
1148                       .getString("warn.user_defined_width_requirements"),
1149               MessageManager.getString("label.invalid_id_column_width"),
1150               JvOptionPane.WARNING_MESSAGE);
1151       userIdWidth.setText("");
1152     }
1153   }
1154
1155   @Override
1156   protected void autoIdWidth_actionPerformed()
1157   {
1158     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1159     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1160   }
1161
1162   /**
1163    * Returns true if chimera path is to a valid executable, else show an error
1164    * dialog.
1165    */
1166   private boolean validateChimeraPath()
1167   {
1168     if (chimeraPath.getText().trim().length() > 0)
1169     {
1170       File f = new File(chimeraPath.getText());
1171       if (!f.canExecute())
1172       {
1173         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1174                 MessageManager.getString("label.invalid_chimera_path"),
1175                 MessageManager.getString("label.invalid_name"),
1176                 JvOptionPane.ERROR_MESSAGE);
1177         return false;
1178       }
1179     }
1180     return true;
1181   }
1182
1183   /**
1184    * If Chimera is selected, check it can be found on default or user-specified
1185    * path, if not show a warning/help dialog.
1186    */
1187   @Override
1188   protected void structureViewer_actionPerformed(String selectedItem)
1189   {
1190     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1191     {
1192       return;
1193     }
1194     boolean found = false;
1195
1196     /*
1197      * Try user-specified and standard paths for Chimera executable.
1198      */
1199     List<String> paths = StructureManager.getChimeraPaths();
1200     paths.add(0, chimeraPath.getText());
1201     for (String path : paths)
1202     {
1203       if (new File(path.trim()).canExecute())
1204       {
1205         found = true;
1206         break;
1207       }
1208     }
1209     if (!found)
1210     {
1211       String[] options = { "OK", "Help" };
1212       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1213               JvSwingUtils.wrapTooltip(true,
1214                       MessageManager.getString("label.chimera_missing")),
1215               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1216               null, options, options[0]);
1217       if (showHelp == JvOptionPane.NO_OPTION)
1218       {
1219         try
1220         {
1221           Help.showHelpWindow(HelpId.StructureViewer);
1222         } catch (HelpSetException e)
1223         {
1224           e.printStackTrace();
1225         }
1226       }
1227     }
1228   }
1229
1230   public class OptionsParam
1231   {
1232     private String name;
1233
1234     private String code;
1235
1236     public OptionsParam(String name, String code)
1237     {
1238       this.name = name;
1239       this.code = code;
1240     }
1241
1242     public String getName()
1243     {
1244       return name;
1245     }
1246
1247     public void setName(String name)
1248     {
1249       this.name = name;
1250     }
1251
1252     public String getCode()
1253     {
1254       return code;
1255     }
1256
1257     public void setCode(String code)
1258     {
1259       this.code = code;
1260     }
1261
1262     @Override
1263     public String toString()
1264     {
1265       return name;
1266     }
1267
1268     @Override
1269     public boolean equals(Object that)
1270     {
1271       if (!(that instanceof OptionsParam))
1272       {
1273         return false;
1274       }
1275       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1276     }
1277
1278     @Override
1279     public int hashCode()
1280     {
1281       return name.hashCode() + code.hashCode();
1282     }
1283   }
1284
1285   private class UrlListSelectionHandler implements ListSelectionListener
1286   {
1287
1288     @Override
1289     public void valueChanged(ListSelectionEvent e)
1290     {
1291       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1292
1293       int index = lsm.getMinSelectionIndex();
1294       if (index == -1)
1295       {
1296         // no selection, so disable delete/edit buttons
1297         editLink.setEnabled(false);
1298         deleteLink.setEnabled(false);
1299         return;
1300       }
1301       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1302
1303       // enable/disable edit and delete link buttons
1304       if (((UrlLinkTableModel) linkUrlTable.getModel())
1305               .isRowDeletable(modelIndex))
1306       {
1307         deleteLink.setEnabled(true);
1308       }
1309       else
1310       {
1311         deleteLink.setEnabled(false);
1312       }
1313
1314       if (((UrlLinkTableModel) linkUrlTable.getModel())
1315               .isRowEditable(modelIndex))
1316       {
1317         editLink.setEnabled(true);
1318       }
1319       else
1320       {
1321         editLink.setEnabled(false);
1322       }
1323     }
1324   }
1325 }