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.JComboBox;
  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     // BH 2018 setSortKeys will do the sort
 386     // sorter.sort();
 387
 388     // set up filtering
 389     ActionListener onReset;
 390     onReset = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         filterTB.setText("");
 396         sorter.setRowFilter(RowFilter.regexFilter(""));
 397       }
 398
 399     };
 400     doReset.addActionListener(onReset);
 401
 402     // filter to display only custom urls
 403     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 404     {
 405       @Override
 406       public boolean include(
 407               Entry<? extends TableModel, ? extends Object> entry)
 408       {
 409         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 410       }
 411     };
 412
 413     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 414             linkUrlTable.getModel());
 415     customSorter.setRowFilter(customUrlFilter);
 416
 417     ActionListener onCustomOnly;
 418     onCustomOnly = new ActionListener()
 419     {
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         filterTB.setText("");
 424         sorter.setRowFilter(customUrlFilter);
 425       }
 426     };
 427     userOnly.addActionListener(onCustomOnly);
 428
 429     filterTB.getDocument().addDocumentListener(new DocumentListener()
 430     {
 431       String caseInsensitiveFlag = "(?i)";
 432
 433       @Override
 434       public void changedUpdate(DocumentEvent e)
 435       {
 436         sorter.setRowFilter(RowFilter
 437                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 438       }
 439
 440       @Override
 441       public void removeUpdate(DocumentEvent e)
 442       {
 443         sorter.setRowFilter(RowFilter
 444                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 445       }
 446
 447       @Override
 448       public void insertUpdate(DocumentEvent e)
 449       {
 450         sorter.setRowFilter(RowFilter
 451                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 452       }
 453     });
 454
 455     // set up list selection functionality
 456     linkUrlTable.getSelectionModel()
 457             .addListSelectionListener(new UrlListSelectionHandler());
 458
 459     // set up radio buttons
 460     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 461             .getPrimaryColumn();
 462     String onClickName = linkUrlTable.getColumnName(onClickCol);
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellRenderer(new RadioButtonRenderer());
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellEditor(new RadioButtonEditor());
 467
 468     // get boolean columns and resize those to min possible
 469     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 470     {
 471       if (linkUrlTable.getModel().getColumnClass(column)
 472               .equals(Boolean.class))
 473       {
 474         TableColumn tableColumn = linkUrlTable.getColumnModel()
 475                 .getColumn(column);
 476         int preferredWidth = tableColumn.getMinWidth();
 477
 478         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 479                 column);
 480         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 481         int cwidth = c.getPreferredSize().width
 482                 + linkUrlTable.getIntercellSpacing().width;
 483         preferredWidth = Math.max(preferredWidth, cwidth);
 484
 485         tableColumn.setPreferredWidth(preferredWidth);
 486       }
 487     }
 488
 489     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 490     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 491     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 492     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 493
 494     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 495
 496     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 497     // note antisense here: default is true
 498     questionnaire
 499             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 500     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 501
 502     /*
 503      * Set Output tab defaults
 504      */
 505     setupOutputCombo(epsRendering, "EPS_RENDERING");
 506     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 507     setupOutputCombo(svgRendering, "SVG_RENDERING");
 508     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 509     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 510     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 511     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 512     userIdWidth.setText(wi == null ? "" : wi.toString());
 513     // TODO: refactor to use common enum via FormatAdapter and allow extension
 514     // for new flat file formats
 515     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 516     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 517     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 518     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 519     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 520     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 521     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 522     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 523     embbedBioJSON
 524             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 525
 526     /*
 527      * Set Editing tab defaults
 528      */
 529     autoCalculateConsCheck
 530             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 531     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 532     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 533
 534     annotations_actionPerformed(null); // update the display of the annotation
 535                                        // settings
 536   }
 537
 538   /**
 539    * A helper method that sets the items and initial selection in a character
 540    * rendering option list (Prompt each time/Lineart/Text)
 541    *
 542    * @param comboBox
 543    * @param propertyKey
 544    */
 545   protected void setupOutputCombo(JComboBox<Object> comboBox,
 546           String propertyKey)
 547   {
 548     comboBox.addItem(promptEachTimeOpt);
 549     comboBox.addItem(lineArtOpt);
 550     comboBox.addItem(textOpt);
 551     String defaultOption = Cache.getDefault(propertyKey,
 552             "Prompt each time");
 553     if (defaultOption.equalsIgnoreCase("Text"))
 554     {
 555       comboBox.setSelectedItem(textOpt);
 556     }
 557     else if (defaultOption.equalsIgnoreCase("Lineart"))
 558     {
 559       comboBox.setSelectedItem(lineArtOpt);
 560     }
 561     else
 562     {
 563       comboBox.setSelectedItem(promptEachTimeOpt);
 564     }
 565   }
 566
 567   /**
 568    * Save user selections on the Preferences tabs to the Cache and write out to
 569    * file.
 570    *
 571    * @param e
 572    */
 573   @Override
 574   public void ok_actionPerformed(ActionEvent e)
 575   {
 576     if (!validateSettings())
 577     {
 578       return;
 579     }
 580
 581     /*
 582      * Save Visual settings
 583      */
 584     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 585             Boolean.toString(seqLimit.isSelected()));
 586     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 587             Boolean.toString(rightAlign.isSelected()));
 588     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 589             Boolean.toString(fullScreen.isSelected()));
 590     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 591             Boolean.toString(openoverv.isSelected()));
 592     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 593             Boolean.toString(annotations.isSelected()));
 594     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 595             Boolean.toString(conservation.isSelected()));
 596     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 597             Boolean.toString(quality.isSelected()));
 598     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 599             Boolean.toString(identity.isSelected()));
 600
 601     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 602             gapSymbolCB.getSelectedItem().toString());
 603
 604     Cache.applicationProperties.setProperty("FONT_NAME",
 605             fontNameCB.getSelectedItem().toString());
 606     Cache.applicationProperties.setProperty("FONT_STYLE",
 607             fontStyleCB.getSelectedItem().toString());
 608     Cache.applicationProperties.setProperty("FONT_SIZE",
 609             fontSizeCB.getSelectedItem().toString());
 610
 611     Cache.applicationProperties.setProperty("ID_ITALICS",
 612             Boolean.toString(idItalics.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 614             Boolean.toString(showUnconserved.isSelected()));
 615     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 616             Boolean.toString(showOccupancy.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 618             Boolean.toString(showGroupConsensus.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 620             Boolean.toString(showGroupConservation.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 622             Boolean.toString(showConsensHistogram.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 624             Boolean.toString(showConsensLogo.isSelected()));
 625     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 626             Boolean.toString(smoothFont.isSelected()));
 627     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 628             Boolean.toString(scaleProteinToCdna.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 630             Boolean.toString(showNpTooltip.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 632             Boolean.toString(showDbRefTooltip.isSelected()));
 633
 634     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 635             Boolean.toString(wrap.isSelected()));
 636
 637     Cache.applicationProperties.setProperty("STARTUP_FILE",
 638             startupFileTextfield.getText());
 639     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 640             Boolean.toString(startupCheckbox.isSelected()));
 641
 642     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 643             sortby.getSelectedItem().toString());
 644
 645     // convert description of sort order to enum name for save
 646     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 647             .forDescription(sortAnnBy.getSelectedItem().toString());
 648     if (annSortOrder != null)
 649     {
 650       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 651               annSortOrder.name());
 652     }
 653
 654     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 655     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 656             Boolean.valueOf(showAutocalcFirst).toString());
 657
 658     /*
 659      * Save Colours settings
 660      */
 661     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 662             protColour.getSelectedItem().toString());
 663     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 664             nucColour.getSelectedItem().toString());
 665     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 666             minColour.getBackground());
 667     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 668             maxColour.getBackground());
 669
 670     /*
 671      * Save Overview settings
 672      */
 673     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 674     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 675     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 676             Boolean.toString(useLegacyGap.isSelected()));
 677     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 678             Boolean.toString(showHiddenAtStart.isSelected()));
 679
 680     /*
 681      * Save Structure settings
 682      */
 683     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 684             Boolean.toString(addTempFactor.isSelected()));
 685     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 686             Boolean.toString(addSecondaryStructure.isSelected()));
 687     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 688             Boolean.toString(useRnaView.isSelected()));
 689     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 690             Boolean.toString(structFromPdb.isSelected()));
 691     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 692             structViewer.getSelectedItem().toString());
 693     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 694     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 695             Boolean.toString(siftsMapping.isSelected()));
 696     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 697
 698     /*
 699      * Save Output settings
 700      */
 701     Cache.applicationProperties.setProperty("EPS_RENDERING",
 702             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 703     Cache.applicationProperties.setProperty("HTML_RENDERING",
 704             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 705     Cache.applicationProperties.setProperty("SVG_RENDERING",
 706             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 707
 708     /*
 709      * Save Connections settings
 710      */
 711     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 712
 713     jalview.util.BrowserLauncher.resetBrowser();
 714
 715     // save user-defined and selected links
 716     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 717     if (menuLinks.isEmpty())
 718     {
 719       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 720     }
 721     else
 722     {
 723       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 724               menuLinks.toString());
 725     }
 726
 727     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 728     if (nonMenuLinks.isEmpty())
 729     {
 730       Cache.applicationProperties.remove("STORED_LINKS");
 731     }
 732     else
 733     {
 734       Cache.applicationProperties.setProperty("STORED_LINKS",
 735               nonMenuLinks.toString());
 736     }
 737
 738     Cache.applicationProperties.setProperty("DEFAULT_URL",
 739             sequenceUrlLinks.getPrimaryUrlId());
 740
 741     Cache.applicationProperties.setProperty("USE_PROXY",
 742             Boolean.toString(useProxy.isSelected()));
 743
 744     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 745
 746     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 747
 748     if (useProxy.isSelected())
 749     {
 750       System.setProperty("http.proxyHost", proxyServerTB.getText());
 751       System.setProperty("http.proxyPort", proxyPortTB.getText());
 752     }
 753     else
 754     {
 755       System.setProperty("http.proxyHost", "");
 756       System.setProperty("http.proxyPort", "");
 757     }
 758     Cache.setProperty("VERSION_CHECK",
 759             Boolean.toString(versioncheck.isSelected()));
 760     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 761     {
 762       // default is false - we only set this if the user has actively agreed
 763       Cache.setProperty("USAGESTATS",
 764               Boolean.toString(usagestats.isSelected()));
 765     }
 766     if (!questionnaire.isSelected())
 767     {
 768       Cache.setProperty("NOQUESTIONNAIRES", "true");
 769     }
 770     else
 771     {
 772       // special - made easy to edit a property file to disable questionnaires
 773       // by just adding the given line
 774       Cache.removeProperty("NOQUESTIONNAIRES");
 775     }
 776
 777     /*
 778      * Save Output settings
 779      */
 780     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 781             Boolean.toString(blcjv.isSelected()));
 782     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 783             Boolean.toString(clustaljv.isSelected()));
 784     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 785             Boolean.toString(fastajv.isSelected()));
 786     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 787             Boolean.toString(msfjv.isSelected()));
 788     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 789             Boolean.toString(pfamjv.isSelected()));
 790     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 791             Boolean.toString(pileupjv.isSelected()));
 792     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 793             Boolean.toString(pirjv.isSelected()));
 794     Cache.applicationProperties.setProperty("PIR_MODELLER",
 795             Boolean.toString(modellerOutput.isSelected()));
 796     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 797             Boolean.toString(embbedBioJSON.isSelected()));
 798     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 799
 800     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 801             Boolean.toString(autoIdWidth.isSelected()));
 802     userIdWidth_actionPerformed();
 803     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 804             userIdWidth.getText());
 805
 806     /*
 807      * Save Editing settings
 808      */
 809     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 810             Boolean.toString(autoCalculateConsCheck.isSelected()));
 811     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 812             Boolean.toString(sortByTree.isSelected()));
 813     Cache.applicationProperties.setProperty("PAD_GAPS",
 814             Boolean.toString(padGaps.isSelected()));
 815
 816     wsPrefs.updateAndRefreshWsMenuConfig(false);
 817     Cache.saveProperties();
 818     Desktop.instance.doConfigureStructurePrefs();
 819     try
 820     {
 821       frame.setClosed(true);
 822     } catch (Exception ex)
 823     {
 824     }
 825   }
 826
 827   /**
 828    * Do any necessary validation before saving settings. Return focus to the
 829    * first tab which fails validation.
 830    *
 831    * @return
 832    */
 833   private boolean validateSettings()
 834   {
 835     if (!validateStructure())
 836     {
 837       structureTab.requestFocusInWindow();
 838       return false;
 839     }
 840     return true;
 841   }
 842
 843   @Override
 844   protected boolean validateStructure()
 845   {
 846     return validateChimeraPath();
 847
 848   }
 849
 850   /**
 851    * DOCUMENT ME!
 852    */
 853   @Override
 854   public void startupFileTextfield_mouseClicked()
 855   {
 856     // TODO: JAL-3048 not needed for Jalview-JS
 857     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 858     JalviewFileChooser chooser = JalviewFileChooser
 859             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 860     chooser.setFileView(new JalviewFileView());
 861     chooser.setDialogTitle(
 862             MessageManager.getString("label.select_startup_file"));
 863
 864     int value = chooser.showOpenDialog(this);
 865
 866     if (value == JalviewFileChooser.APPROVE_OPTION)
 867     {
 868       FileFormatI format = chooser.getSelectedFormat();
 869       if (format != null)
 870       {
 871         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 872                 format.getName());
 873       }
 874       startupFileTextfield
 875               .setText(chooser.getSelectedFile().getAbsolutePath());
 876     }
 877   }
 878
 879   /**
 880    * DOCUMENT ME!
 881    *
 882    * @param e
 883    *          DOCUMENT ME!
 884    */
 885   @Override
 886   public void cancel_actionPerformed(ActionEvent e)
 887   {
 888     try
 889     {
 890       wsPrefs.updateWsMenuConfig(true);
 891       wsPrefs.refreshWs_actionPerformed(e);
 892       frame.setClosed(true);
 893     } catch (Exception ex)
 894     {
 895     }
 896   }
 897
 898   /**
 899    * DOCUMENT ME!
 900    *
 901    * @param e
 902    *          DOCUMENT ME!
 903    */
 904   @Override
 905   public void annotations_actionPerformed(ActionEvent e)
 906   {
 907     conservation.setEnabled(annotations.isSelected());
 908     quality.setEnabled(annotations.isSelected());
 909     identity.setEnabled(annotations.isSelected());
 910     showOccupancy.setEnabled(annotations.isSelected());
 911     showGroupConsensus.setEnabled(annotations.isSelected());
 912     showGroupConservation.setEnabled(annotations.isSelected());
 913     showConsensHistogram.setEnabled(annotations.isSelected()
 914             && (identity.isSelected() || showGroupConsensus.isSelected()));
 915     showConsensLogo.setEnabled(annotations.isSelected()
 916             && (identity.isSelected() || showGroupConsensus.isSelected()));
 917   }
 918
 919   @Override
 920   public void newLink_actionPerformed(ActionEvent e)
 921   {
 922     GSequenceLink link = new GSequenceLink();
 923     boolean valid = false;
 924     while (!valid)
 925     {
 926       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 927               MessageManager.getString("label.new_sequence_url_link"),
 928               JvOptionPane.OK_CANCEL_OPTION, -1,
 929               null) == JvOptionPane.OK_OPTION)
 930       {
 931         if (link.checkValid())
 932         {
 933           if (((UrlLinkTableModel) linkUrlTable.getModel())
 934                   .isUniqueName(link.getName()))
 935           {
 936             ((UrlLinkTableModel) linkUrlTable.getModel())
 937                     .insertRow(link.getName(), link.getURL());
 938             valid = true;
 939           }
 940           else
 941           {
 942             link.notifyDuplicate();
 943             continue;
 944           }
 945         }
 946       }
 947       else
 948       {
 949         break;
 950       }
 951     }
 952   }
 953
 954   @Override
 955   public void editLink_actionPerformed(ActionEvent e)
 956   {
 957     GSequenceLink link = new GSequenceLink();
 958
 959     int index = linkUrlTable.getSelectedRow();
 960     if (index == -1)
 961     {
 962       // button no longer enabled if row is not selected
 963       Cache.log.debug("Edit with no row selected in linkUrlTable");
 964       return;
 965     }
 966
 967     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 968             .getNameColumn();
 969     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 970             .getUrlColumn();
 971     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 972     link.setName(oldName);
 973     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 974
 975     boolean valid = false;
 976     while (!valid)
 977     {
 978       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 979               MessageManager.getString("label.edit_sequence_url_link"),
 980               JvOptionPane.OK_CANCEL_OPTION, -1,
 981               null) == JvOptionPane.OK_OPTION)
 982       {
 983         if (link.checkValid())
 984         {
 985           if ((oldName.equals(link.getName()))
 986                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 987                           .isUniqueName(link.getName())))
 988           {
 989             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 990             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 991             valid = true;
 992           }
 993           else
 994           {
 995             link.notifyDuplicate();
 996             continue;
 997           }
 998         }
 999       }
1000       else
1001       {
1002         break;
1003       }
1004     }
1005   }
1006
1007   @Override
1008   public void deleteLink_actionPerformed(ActionEvent e)
1009   {
1010     int index = linkUrlTable.getSelectedRow();
1011     int modelIndex = -1;
1012     if (index == -1)
1013     {
1014       // button no longer enabled if row is not selected
1015       Cache.log.debug("Delete with no row selected in linkUrlTable");
1016       return;
1017     }
1018     else
1019     {
1020       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1021     }
1022
1023     // make sure we use the model index to delete, and not the table index
1024     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1025   }
1026
1027   @Override
1028   public void defaultBrowser_mouseClicked(MouseEvent e)
1029   {
1030     // TODO: JAL-3048 not needed for j2s
1031     /*
1032      * @j2sNative
1033      */
1034     {
1035       JFileChooser chooser = new JFileChooser(".");
1036       chooser.setDialogTitle(
1037               MessageManager.getString("label.select_default_browser"));
1038
1039       int value = chooser.showOpenDialog(this);
1040
1041       if (value == JFileChooser.APPROVE_OPTION)
1042       {
1043         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1044       }
1045     }
1046   }
1047
1048   /*
1049    * (non-Javadoc)
1050    *
1051    * @see
1052    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1053    * .ActionEvent)
1054    */
1055   @Override
1056   protected void showunconserved_actionPerformed(ActionEvent e)
1057   {
1058     // TODO Auto-generated method stub
1059     super.showunconserved_actionPerformed(e);
1060   }
1061
1062   public static List<String> getGroupURLLinks()
1063   {
1064     return groupURLLinks;
1065   }
1066
1067   @Override
1068   public void minColour_actionPerformed(JPanel panel)
1069   {
1070     JalviewColourChooser.showColourChooser(this,
1071             MessageManager.getString("label.select_colour_minimum_value"),
1072             panel);
1073   }
1074
1075   @Override
1076   public void maxColour_actionPerformed(JPanel panel)
1077   {
1078     JalviewColourChooser.showColourChooser(this,
1079             MessageManager.getString("label.select_colour_maximum_value"),
1080             panel);
1081   }
1082
1083   @Override
1084   public void gapColour_actionPerformed(JPanel gap)
1085   {
1086     if (!useLegacyGap.isSelected())
1087     {
1088       JalviewColourChooser.showColourChooser(this,
1089               MessageManager.getString("label.select_gap_colour"),
1090               gap);
1091     }
1092   }
1093
1094   @Override
1095   public void hiddenColour_actionPerformed(JPanel hidden)
1096   {
1097     JalviewColourChooser.showColourChooser(this,
1098             MessageManager.getString("label.select_hidden_colour"),
1099             hidden);
1100   }
1101
1102   @Override
1103   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1104   {
1105     boolean enabled = useLegacyGap.isSelected();
1106     if (enabled)
1107     {
1108       gapColour.setBackground(
1109               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1110     }
1111     else
1112     {
1113       gapColour.setBackground(
1114               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1115     }
1116     gapColour.setEnabled(!enabled);
1117     gapLabel.setEnabled(!enabled);
1118   }
1119
1120   @Override
1121   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1122   {
1123     useLegacyGap.setSelected(false);
1124     useLegacyGaps_actionPerformed(null);
1125     showHiddenAtStart.setSelected(true);
1126     hiddenColour.setBackground(
1127             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1128   }
1129
1130   @Override
1131   protected void userIdWidth_actionPerformed()
1132   {
1133     try
1134     {
1135       String val = userIdWidth.getText().trim();
1136       if (val.length() > 0)
1137       {
1138         Integer iw = Integer.parseInt(val);
1139         if (iw.intValue() < 12)
1140         {
1141           throw new NumberFormatException();
1142         }
1143         userIdWidth.setText(iw.toString());
1144       }
1145     } catch (NumberFormatException x)
1146     {
1147       userIdWidth.setText("");
1148       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1149               MessageManager
1150                       .getString("warn.user_defined_width_requirements"),
1151               MessageManager.getString("label.invalid_id_column_width"),
1152               JvOptionPane.WARNING_MESSAGE);
1153     }
1154   }
1155
1156   @Override
1157   protected void autoIdWidth_actionPerformed()
1158   {
1159     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1160     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1161   }
1162
1163   /**
1164    * Returns true if chimera path is to a valid executable, else show an error
1165    * dialog.
1166    */
1167   private boolean validateChimeraPath()
1168   {
1169     if (chimeraPath.getText().trim().length() > 0)
1170     {
1171       File f = new File(chimeraPath.getText());
1172       if (!f.canExecute())
1173       {
1174         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1175                 MessageManager.getString("label.invalid_chimera_path"),
1176                 MessageManager.getString("label.invalid_name"),
1177                 JvOptionPane.ERROR_MESSAGE);
1178         return false;
1179       }
1180     }
1181     return true;
1182   }
1183
1184   /**
1185    * If Chimera is selected, check it can be found on default or user-specified
1186    * path, if not show a warning/help dialog.
1187    */
1188   @Override
1189   protected void structureViewer_actionPerformed(String selectedItem)
1190   {
1191     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1192     {
1193       return;
1194     }
1195     boolean found = false;
1196
1197     /*
1198      * Try user-specified and standard paths for Chimera executable.
1199      */
1200     List<String> paths = StructureManager.getChimeraPaths();
1201     paths.add(0, chimeraPath.getText());
1202     for (String path : paths)
1203     {
1204       if (new File(path.trim()).canExecute())
1205       {
1206         found = true;
1207         break;
1208       }
1209     }
1210     if (!found)
1211     {
1212       String[] options = { "OK", "Help" };
1213       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1214               JvSwingUtils.wrapTooltip(true,
1215                       MessageManager.getString("label.chimera_missing")),
1216               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1217               null, options, options[0]);
1218       if (showHelp == JvOptionPane.NO_OPTION)
1219       {
1220         try
1221         {
1222           Help.showHelpWindow(HelpId.StructureViewer);
1223         } catch (HelpSetException e)
1224         {
1225           e.printStackTrace();
1226         }
1227       }
1228     }
1229   }
1230
1231   public class OptionsParam
1232   {
1233     private String name;
1234
1235     private String code;
1236
1237     public OptionsParam(String name, String code)
1238     {
1239       this.name = name;
1240       this.code = code;
1241     }
1242
1243     public String getName()
1244     {
1245       return name;
1246     }
1247
1248     public void setName(String name)
1249     {
1250       this.name = name;
1251     }
1252
1253     public String getCode()
1254     {
1255       return code;
1256     }
1257
1258     public void setCode(String code)
1259     {
1260       this.code = code;
1261     }
1262
1263     @Override
1264     public String toString()
1265     {
1266       return name;
1267     }
1268
1269     @Override
1270     public boolean equals(Object that)
1271     {
1272       if (!(that instanceof OptionsParam))
1273       {
1274         return false;
1275       }
1276       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1277     }
1278
1279     @Override
1280     public int hashCode()
1281     {
1282       return name.hashCode() + code.hashCode();
1283     }
1284   }
1285
1286   private class UrlListSelectionHandler implements ListSelectionListener
1287   {
1288
1289     @Override
1290     public void valueChanged(ListSelectionEvent e)
1291     {
1292       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1293
1294       int index = lsm.getMinSelectionIndex();
1295       if (index == -1)
1296       {
1297         // no selection, so disable delete/edit buttons
1298         editLink.setEnabled(false);
1299         deleteLink.setEnabled(false);
1300         return;
1301       }
1302       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1303
1304       // enable/disable edit and delete link buttons
1305       if (((UrlLinkTableModel) linkUrlTable.getModel())
1306               .isRowDeletable(modelIndex))
1307       {
1308         deleteLink.setEnabled(true);
1309       }
1310       else
1311       {
1312         deleteLink.setEnabled(false);
1313       }
1314
1315       if (((UrlLinkTableModel) linkUrlTable.getModel())
1316               .isRowEditable(modelIndex))
1317       {
1318         editLink.setEnabled(true);
1319       }
1320       else
1321       {
1322         editLink.setEnabled(false);
1323       }
1324     }
1325   }
1326 }