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   private WsPreferences wsPrefs;
 172
 173   private OptionsParam promptEachTimeOpt = new OptionsParam(
 174           MessageManager.getString("label.prompt_each_time"),
 175           "Prompt each time");
 176
 177   private OptionsParam lineArtOpt = new OptionsParam(
 178           MessageManager.getString("label.lineart"), "Lineart");
 179
 180   private OptionsParam textOpt = new OptionsParam(
 181           MessageManager.getString("action.text"), "Text");
 182
 183   /**
 184    * Creates a new Preferences object.
 185    */
 186   public Preferences()
 187   {
 188     super();
 189     frame = new JInternalFrame();
 190     frame.setContentPane(this);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set Visual tab defaults
 207      */
 208     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 209     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 210     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 211     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 212
 213     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 214     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 215     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 216     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 217     showUnconserved
 218             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 219     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 220     showGroupConsensus
 221             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 222     showGroupConservation.setSelected(
 223             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 224     showConsensHistogram.setSelected(
 225             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 226     showConsensLogo
 227             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 228     showNpTooltip
 229             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 230     showDbRefTooltip
 231             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 232
 233     String[] fonts = java.awt.GraphicsEnvironment
 234             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 235     for (int i = 0; i < fonts.length; i++)
 236     {
 237       fontNameCB.addItem(fonts[i]);
 238     }
 239
 240     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 241     {
 242       fontSizeCB.addItem(i + "");
 243     }
 244
 245     fontStyleCB.addItem("plain");
 246     fontStyleCB.addItem("bold");
 247     fontStyleCB.addItem("italic");
 248
 249     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 250     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 251     fontStyleCB.setSelectedItem(
 252             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 253
 254     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 255     scaleProteinToCdna
 256             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 257
 258     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 259
 260     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 261
 262     gapSymbolCB.addItem("-");
 263     gapSymbolCB.addItem(".");
 264
 265     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 266
 267     sortby.addItem("No sort");
 268     sortby.addItem("Id");
 269     sortby.addItem("Pairwise Identity");
 270     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 271
 272     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 273     sortAnnBy
 274             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 275     sortAnnBy
 276             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 277     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 278             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 279                     SequenceAnnotationOrder.NONE.name()));
 280     sortAnnBy.setSelectedItem(savedSort.toString());
 281
 282     sortAutocalc.addItem("Autocalculated first");
 283     sortAutocalc.addItem("Autocalculated last");
 284     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 285     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 286             : sortAutocalc.getItemAt(1));
 287     startupCheckbox
 288             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 289     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 290             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 291                     + "/examples/exampleFile_2_3.jar"));
 292
 293     /*
 294      * Set Colours tab defaults
 295      */
 296     protColour.addItem(ResidueColourScheme.NONE);
 297     nucColour.addItem(ResidueColourScheme.NONE);
 298     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 299     {
 300       String name = cs.getSchemeName();
 301       protColour.addItem(name);
 302       nucColour.addItem(name);
 303     }
 304     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 305             ResidueColourScheme.NONE);
 306     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 307     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 308     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 309     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 310     minColour.setBackground(
 311             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 312     maxColour.setBackground(
 313             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 314
 315     /*
 316      * Set overview panel defaults
 317      */
 318     gapColour.setBackground(
 319             Cache.getDefaultColour(GAP_COLOUR,
 320                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 321     hiddenColour.setBackground(
 322             Cache.getDefaultColour(HIDDEN_COLOUR,
 323                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 324     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 325     gapLabel.setEnabled(!useLegacyGap.isSelected());
 326     gapColour.setEnabled(!useLegacyGap.isSelected());
 327     showHiddenAtStart
 328             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 329
 330     /*
 331      * Set Structure tab defaults.
 332      */
 333     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 334     structFromPdb.setSelected(structSelected);
 335     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 336     useRnaView.setEnabled(structSelected);
 337     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 338     addSecondaryStructure.setEnabled(structSelected);
 339     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 340     addTempFactor.setEnabled(structSelected);
 341     structViewer.setSelectedItem(
 342             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 343     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 344     chimeraPath.addActionListener(new ActionListener()
 345     {
 346       @Override
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         validateChimeraPath();
 350       }
 351     });
 352
 353     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 354     {
 355       siftsMapping.setSelected(true);
 356     }
 357     else
 358     {
 359       nwMapping.setSelected(true);
 360     }
 361
 362     SiftsSettings
 363             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 364
 365     /*
 366      * Set Connections tab defaults
 367      */
 368
 369     // set up sorting
 370     linkUrlTable.setModel(dataModel);
 371     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 372             linkUrlTable.getModel());
 373     linkUrlTable.setRowSorter(sorter);
 374     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 375
 376     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 377     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 378             SortOrder.DESCENDING));
 379     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 380             SortOrder.DESCENDING));
 381     sortKeys.add(
 382             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 383
 384     sorter.setSortKeys(sortKeys);
 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     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 837     JalviewFileChooser chooser = JalviewFileChooser
 838             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 839     chooser.setFileView(new JalviewFileView());
 840     chooser.setDialogTitle(
 841             MessageManager.getString("label.select_startup_file"));
 842
 843     int value = chooser.showOpenDialog(this);
 844
 845     if (value == JalviewFileChooser.APPROVE_OPTION)
 846     {
 847       FileFormatI format = chooser.getSelectedFormat();
 848       if (format != null)
 849       {
 850         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 851                 format.getName());
 852       }
 853       startupFileTextfield
 854               .setText(chooser.getSelectedFile().getAbsolutePath());
 855     }
 856   }
 857
 858   /**
 859    * DOCUMENT ME!
 860    *
 861    * @param e
 862    *          DOCUMENT ME!
 863    */
 864   @Override
 865   public void cancel_actionPerformed(ActionEvent e)
 866   {
 867     try
 868     {
 869       wsPrefs.updateWsMenuConfig(true);
 870       wsPrefs.refreshWs_actionPerformed(e);
 871       frame.setClosed(true);
 872     } catch (Exception ex)
 873     {
 874     }
 875   }
 876
 877   /**
 878    * DOCUMENT ME!
 879    *
 880    * @param e
 881    *          DOCUMENT ME!
 882    */
 883   @Override
 884   public void annotations_actionPerformed(ActionEvent e)
 885   {
 886     conservation.setEnabled(annotations.isSelected());
 887     quality.setEnabled(annotations.isSelected());
 888     identity.setEnabled(annotations.isSelected());
 889     showOccupancy.setEnabled(annotations.isSelected());
 890     showGroupConsensus.setEnabled(annotations.isSelected());
 891     showGroupConservation.setEnabled(annotations.isSelected());
 892     showConsensHistogram.setEnabled(annotations.isSelected()
 893             && (identity.isSelected() || showGroupConsensus.isSelected()));
 894     showConsensLogo.setEnabled(annotations.isSelected()
 895             && (identity.isSelected() || showGroupConsensus.isSelected()));
 896   }
 897
 898   @Override
 899   public void newLink_actionPerformed(ActionEvent e)
 900   {
 901     GSequenceLink link = new GSequenceLink();
 902     boolean valid = false;
 903     while (!valid)
 904     {
 905       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 906               MessageManager.getString("label.new_sequence_url_link"),
 907               JvOptionPane.OK_CANCEL_OPTION, -1,
 908               null) == JvOptionPane.OK_OPTION)
 909       {
 910         if (link.checkValid())
 911         {
 912           if (((UrlLinkTableModel) linkUrlTable.getModel())
 913                   .isUniqueName(link.getName()))
 914           {
 915             ((UrlLinkTableModel) linkUrlTable.getModel())
 916                     .insertRow(link.getName(), link.getURL());
 917             valid = true;
 918           }
 919           else
 920           {
 921             link.notifyDuplicate();
 922             continue;
 923           }
 924         }
 925       }
 926       else
 927       {
 928         break;
 929       }
 930     }
 931   }
 932
 933   @Override
 934   public void editLink_actionPerformed(ActionEvent e)
 935   {
 936     GSequenceLink link = new GSequenceLink();
 937
 938     int index = linkUrlTable.getSelectedRow();
 939     if (index == -1)
 940     {
 941       // button no longer enabled if row is not selected
 942       Cache.log.debug("Edit with no row selected in linkUrlTable");
 943       return;
 944     }
 945
 946     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 947             .getNameColumn();
 948     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 949             .getUrlColumn();
 950     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 951     link.setName(oldName);
 952     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 953
 954     boolean valid = false;
 955     while (!valid)
 956     {
 957       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 958               MessageManager.getString("label.edit_sequence_url_link"),
 959               JvOptionPane.OK_CANCEL_OPTION, -1,
 960               null) == JvOptionPane.OK_OPTION)
 961       {
 962         if (link.checkValid())
 963         {
 964           if ((oldName.equals(link.getName()))
 965                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 966                           .isUniqueName(link.getName())))
 967           {
 968             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 969             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 970             valid = true;
 971           }
 972           else
 973           {
 974             link.notifyDuplicate();
 975             continue;
 976           }
 977         }
 978       }
 979       else
 980       {
 981         break;
 982       }
 983     }
 984   }
 985
 986   @Override
 987   public void deleteLink_actionPerformed(ActionEvent e)
 988   {
 989     int index = linkUrlTable.getSelectedRow();
 990     int modelIndex = -1;
 991     if (index == -1)
 992     {
 993       // button no longer enabled if row is not selected
 994       Cache.log.debug("Delete with no row selected in linkUrlTable");
 995       return;
 996     }
 997     else
 998     {
 999       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1000     }
1001
1002     // make sure we use the model index to delete, and not the table index
1003     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1004   }
1005
1006   @Override
1007   public void defaultBrowser_mouseClicked(MouseEvent e)
1008   {
1009     JFileChooser chooser = new JFileChooser(".");
1010     chooser.setDialogTitle(
1011             MessageManager.getString("label.select_default_browser"));
1012
1013     int value = chooser.showOpenDialog(this);
1014
1015     if (value == JFileChooser.APPROVE_OPTION)
1016     {
1017       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1018     }
1019
1020   }
1021
1022   /*
1023    * (non-Javadoc)
1024    *
1025    * @see
1026    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1027    * .ActionEvent)
1028    */
1029   @Override
1030   protected void showunconserved_actionPerformed(ActionEvent e)
1031   {
1032     // TODO Auto-generated method stub
1033     super.showunconserved_actionPerformed(e);
1034   }
1035
1036   public static List<String> getGroupURLLinks()
1037   {
1038     return groupURLLinks;
1039   }
1040
1041   @Override
1042   public void minColour_actionPerformed(JPanel panel)
1043   {
1044     Color col = JColorChooser.showDialog(this,
1045             MessageManager.getString("label.select_colour_minimum_value"),
1046             minColour.getBackground());
1047     if (col != null)
1048     {
1049       panel.setBackground(col);
1050     }
1051     panel.repaint();
1052   }
1053
1054   @Override
1055   public void maxColour_actionPerformed(JPanel panel)
1056   {
1057     Color col = JColorChooser.showDialog(this,
1058             MessageManager.getString("label.select_colour_maximum_value"),
1059             maxColour.getBackground());
1060     if (col != null)
1061     {
1062       panel.setBackground(col);
1063     }
1064     panel.repaint();
1065   }
1066
1067   @Override
1068   public void gapColour_actionPerformed(JPanel gap)
1069   {
1070     if (!useLegacyGap.isSelected())
1071     {
1072       Color col = JColorChooser.showDialog(this,
1073               MessageManager.getString("label.select_gap_colour"),
1074               gapColour.getBackground());
1075       if (col != null)
1076       {
1077         gap.setBackground(col);
1078       }
1079       gap.repaint();
1080     }
1081   }
1082
1083   @Override
1084   public void hiddenColour_actionPerformed(JPanel hidden)
1085   {
1086     Color col = JColorChooser.showDialog(this,
1087             MessageManager.getString("label.select_hidden_colour"),
1088             hiddenColour.getBackground());
1089     if (col != null)
1090     {
1091       hidden.setBackground(col);
1092     }
1093     hidden.repaint();
1094   }
1095
1096   @Override
1097   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1098   {
1099     boolean enabled = useLegacyGap.isSelected();
1100     if (enabled)
1101     {
1102       gapColour.setBackground(
1103               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1104     }
1105     else
1106     {
1107       gapColour.setBackground(
1108               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1109     }
1110     gapColour.setEnabled(!enabled);
1111     gapLabel.setEnabled(!enabled);
1112   }
1113
1114   @Override
1115   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1116   {
1117     useLegacyGap.setSelected(false);
1118     useLegacyGaps_actionPerformed(null);
1119     showHiddenAtStart.setSelected(true);
1120     hiddenColour.setBackground(
1121             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1122   }
1123
1124   @Override
1125   protected void userIdWidth_actionPerformed()
1126   {
1127     try
1128     {
1129       String val = userIdWidth.getText().trim();
1130       if (val.length() > 0)
1131       {
1132         Integer iw = Integer.parseInt(val);
1133         if (iw.intValue() < 12)
1134         {
1135           throw new NumberFormatException();
1136         }
1137         userIdWidth.setText(iw.toString());
1138       }
1139     } catch (NumberFormatException x)
1140     {
1141       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1142               MessageManager
1143                       .getString("warn.user_defined_width_requirements"),
1144               MessageManager.getString("label.invalid_id_column_width"),
1145               JvOptionPane.WARNING_MESSAGE);
1146       userIdWidth.setText("");
1147     }
1148   }
1149
1150   @Override
1151   protected void autoIdWidth_actionPerformed()
1152   {
1153     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1154     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1155   }
1156
1157   /**
1158    * Returns true if chimera path is to a valid executable, else show an error
1159    * dialog.
1160    */
1161   private boolean validateChimeraPath()
1162   {
1163     if (chimeraPath.getText().trim().length() > 0)
1164     {
1165       File f = new File(chimeraPath.getText());
1166       if (!f.canExecute())
1167       {
1168         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1169                 MessageManager.getString("label.invalid_chimera_path"),
1170                 MessageManager.getString("label.invalid_name"),
1171                 JvOptionPane.ERROR_MESSAGE);
1172         return false;
1173       }
1174     }
1175     return true;
1176   }
1177
1178   /**
1179    * If Chimera is selected, check it can be found on default or user-specified
1180    * path, if not show a warning/help dialog.
1181    */
1182   @Override
1183   protected void structureViewer_actionPerformed(String selectedItem)
1184   {
1185     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1186     {
1187       return;
1188     }
1189     boolean found = false;
1190
1191     /*
1192      * Try user-specified and standard paths for Chimera executable.
1193      */
1194     List<String> paths = StructureManager.getChimeraPaths();
1195     paths.add(0, chimeraPath.getText());
1196     for (String path : paths)
1197     {
1198       if (new File(path.trim()).canExecute())
1199       {
1200         found = true;
1201         break;
1202       }
1203     }
1204     if (!found)
1205     {
1206       String[] options = { "OK", "Help" };
1207       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1208               JvSwingUtils.wrapTooltip(true,
1209                       MessageManager.getString("label.chimera_missing")),
1210               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1211               null, options, options[0]);
1212       if (showHelp == JvOptionPane.NO_OPTION)
1213       {
1214         try
1215         {
1216           Help.showHelpWindow(HelpId.StructureViewer);
1217         } catch (HelpSetException e)
1218         {
1219           e.printStackTrace();
1220         }
1221       }
1222     }
1223   }
1224
1225   public class OptionsParam
1226   {
1227     private String name;
1228
1229     private String code;
1230
1231     public OptionsParam(String name, String code)
1232     {
1233       this.name = name;
1234       this.code = code;
1235     }
1236
1237     public String getName()
1238     {
1239       return name;
1240     }
1241
1242     public void setName(String name)
1243     {
1244       this.name = name;
1245     }
1246
1247     public String getCode()
1248     {
1249       return code;
1250     }
1251
1252     public void setCode(String code)
1253     {
1254       this.code = code;
1255     }
1256
1257     @Override
1258     public String toString()
1259     {
1260       return name;
1261     }
1262
1263     @Override
1264     public boolean equals(Object that)
1265     {
1266       if (!(that instanceof OptionsParam))
1267       {
1268         return false;
1269       }
1270       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1271     }
1272
1273     @Override
1274     public int hashCode()
1275     {
1276       return name.hashCode() + code.hashCode();
1277     }
1278   }
1279
1280   private class UrlListSelectionHandler implements ListSelectionListener
1281   {
1282
1283     @Override
1284     public void valueChanged(ListSelectionEvent e)
1285     {
1286       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1287
1288       int index = lsm.getMinSelectionIndex();
1289       if (index == -1)
1290       {
1291         // no selection, so disable delete/edit buttons
1292         editLink.setEnabled(false);
1293         deleteLink.setEnabled(false);
1294         return;
1295       }
1296       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1297
1298       // enable/disable edit and delete link buttons
1299       if (((UrlLinkTableModel) linkUrlTable.getModel())
1300               .isRowDeletable(modelIndex))
1301       {
1302         deleteLink.setEnabled(true);
1303       }
1304       else
1305       {
1306         deleteLink.setEnabled(false);
1307       }
1308
1309       if (((UrlLinkTableModel) linkUrlTable.getModel())
1310               .isRowEditable(modelIndex))
1311       {
1312         editLink.setEnabled(true);
1313       }
1314       else
1315       {
1316         editLink.setEnabled(false);
1317       }
1318     }
1319   }
1320 }