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