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   private static final int MIN_FONT_SIZE = 1;
 117
 118   private static final int MAX_FONT_SIZE = 30;
 119
 120   private static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
 121
 122   private static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
 123
 124   private static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
 125           .darker();
 126
 127   /**
 128    * Holds name and link separated with | character. Sequence ID must be
 129    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 130    */
 131   public static UrlProviderI sequenceUrlLinks;
 132
 133   public static UrlLinkTableModel dataModel;
 134
 135   /**
 136    * Holds name and link separated with | character. Sequence IDS and Sequences
 137    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 138    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 139    * for first and second token specified after a pipe character at end |,|.
 140    * (TODO: proper escape for using | to separate ids or sequences
 141    */
 142
 143   public static List<String> groupURLLinks;
 144   static
 145   {
 146     // get links selected to be in the menu (SEQUENCE_LINKS)
 147     // and links entered by the user but not selected (STORED_LINKS)
 148     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 149     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 150     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 151             UrlConstants.DEFAULT_LABEL);
 152
 153     // if both links lists are empty, add the DEFAULT_URL link
 154     // otherwise we assume the default link is in one of the lists
 155     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 156     {
 157       inMenuString = UrlConstants.DEFAULT_STRING;
 158     }
 159     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 160             inMenuString, notInMenuString);
 161     sequenceUrlLinks = factory.createUrlProvider();
 162     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 163
 164     /**
 165      * TODO: reformulate groupURL encoding so two or more can be stored in the
 166      * .properties file as '|' separated strings
 167      */
 168
 169     groupURLLinks = new ArrayList<>();
 170   }
 171
 172   JInternalFrame frame;
 173
 174   DasSourceBrowser dasSource;
 175
 176   private WsPreferences wsPrefs;
 177
 178   private OptionsParam promptEachTimeOpt = new OptionsParam(
 179           MessageManager.getString("label.prompt_each_time"),
 180           "Prompt each time");
 181
 182   private OptionsParam lineArtOpt = new OptionsParam(
 183           MessageManager.getString("label.lineart"), "Lineart");
 184
 185   private OptionsParam textOpt = new OptionsParam(
 186           MessageManager.getString("action.text"), "Text");
 187
 188   /**
 189    * Creates a new Preferences object.
 190    */
 191   public Preferences()
 192   {
 193     super();
 194     frame = new JInternalFrame();
 195     frame.setContentPane(this);
 196     dasSource = new DasSourceBrowser();
 197     dasTab.add(dasSource, BorderLayout.CENTER);
 198     wsPrefs = new WsPreferences();
 199     wsTab.add(wsPrefs, BorderLayout.CENTER);
 200     int width = 500, height = 450;
 201     new jalview.util.Platform();
 202     if (Platform.isAMac())
 203     {
 204       width = 570;
 205       height = 480;
 206     }
 207
 208     Desktop.addInternalFrame(frame,
 209             MessageManager.getString("label.preferences"), width, height);
 210     frame.setMinimumSize(new Dimension(width, height));
 211
 212     /*
 213      * Set Visual tab defaults
 214      */
 215     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 216     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 217     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 218     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 219
 220     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 221     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 222     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 223     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 224     showUnconserved
 225             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 226     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 227     showGroupConsensus
 228             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 229     showGroupConservation.setSelected(
 230             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 231     showConsensHistogram.setSelected(
 232             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 233     showConsensLogo
 234             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 235     showNpTooltip
 236             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 237     showDbRefTooltip
 238             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 239
 240     String[] fonts = java.awt.GraphicsEnvironment
 241             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 242     for (int i = 0; i < fonts.length; i++)
 243     {
 244       fontNameCB.addItem(fonts[i]);
 245     }
 246
 247     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 248     {
 249       fontSizeCB.addItem(i + "");
 250     }
 251
 252     fontStyleCB.addItem("plain");
 253     fontStyleCB.addItem("bold");
 254     fontStyleCB.addItem("italic");
 255
 256     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 257     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 258     fontStyleCB.setSelectedItem(
 259             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 260
 261     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 262     scaleProteinToCdna
 263             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 264
 265     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 266
 267     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 268
 269     gapSymbolCB.addItem("-");
 270     gapSymbolCB.addItem(".");
 271
 272     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 273
 274     sortby.addItem("No sort");
 275     sortby.addItem("Id");
 276     sortby.addItem("Pairwise Identity");
 277     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 278
 279     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 280     sortAnnBy
 281             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 282     sortAnnBy
 283             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 284     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 285             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 286                     SequenceAnnotationOrder.NONE.name()));
 287     sortAnnBy.setSelectedItem(savedSort.toString());
 288
 289     sortAutocalc.addItem("Autocalculated first");
 290     sortAutocalc.addItem("Autocalculated last");
 291     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 292     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 293             : sortAutocalc.getItemAt(1));
 294     startupCheckbox
 295             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 296     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 297             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 298                     + "/examples/exampleFile_2_3.jar"));
 299
 300     /*
 301      * Set Colours tab defaults
 302      */
 303     protColour.addItem(ResidueColourScheme.NONE);
 304     nucColour.addItem(ResidueColourScheme.NONE);
 305     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 306     {
 307       String name = cs.getSchemeName();
 308       protColour.addItem(name);
 309       nucColour.addItem(name);
 310     }
 311     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 312             ResidueColourScheme.NONE);
 313     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 314     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 315     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 316     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 317     minColour.setBackground(
 318             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 319     maxColour.setBackground(
 320             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 321
 322     /*
 323      * Set overview panel defaults
 324      */
 325     gapColour.setBackground(
 326             Cache.getDefaultColour("GAP_COLOUR", OVERVIEW_DEFAULT_GAP));
 327     hiddenColour.setBackground(
 328             Cache.getDefaultColour("HIDDEN_COLOUR",
 329                     OVERVIEW_DEFAULT_HIDDEN));
 330     useLegacyGap.setSelected(Cache.getDefault("USE_LEGACY_GAP", false));
 331     gapLabel.setEnabled(!useLegacyGap.isSelected());
 332     gapColour.setEnabled(!useLegacyGap.isSelected());
 333     showHiddenAtStart
 334             .setSelected(Cache.getDefault("SHOW_OV_HIDDEN_AT_START", true));
 335
 336     /*
 337      * Set Structure tab defaults.
 338      */
 339     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 340     structFromPdb.setSelected(structSelected);
 341     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 342     useRnaView.setEnabled(structSelected);
 343     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 344     addSecondaryStructure.setEnabled(structSelected);
 345     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 346     addTempFactor.setEnabled(structSelected);
 347     structViewer.setSelectedItem(
 348             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 349     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 350     chimeraPath.addActionListener(new ActionListener()
 351     {
 352       @Override
 353       public void actionPerformed(ActionEvent e)
 354       {
 355         validateChimeraPath();
 356       }
 357     });
 358
 359     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 360     {
 361       siftsMapping.setSelected(true);
 362     }
 363     else
 364     {
 365       nwMapping.setSelected(true);
 366     }
 367
 368     SiftsSettings
 369             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 370
 371     /*
 372      * Set Connections tab defaults
 373      */
 374
 375     // set up sorting
 376     linkUrlTable.setModel(dataModel);
 377     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 378             linkUrlTable.getModel());
 379     linkUrlTable.setRowSorter(sorter);
 380     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 381
 382     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 383     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 384             SortOrder.DESCENDING));
 385     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 386             SortOrder.DESCENDING));
 387     sortKeys.add(
 388             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 389
 390     sorter.setSortKeys(sortKeys);
 391     sorter.sort();
 392
 393     // set up filtering
 394     ActionListener onReset;
 395     onReset = new ActionListener()
 396     {
 397       @Override
 398       public void actionPerformed(ActionEvent e)
 399       {
 400         filterTB.setText("");
 401         sorter.setRowFilter(RowFilter.regexFilter(""));
 402       }
 403
 404     };
 405     doReset.addActionListener(onReset);
 406
 407     // filter to display only custom urls
 408     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 409     {
 410       @Override
 411       public boolean include(
 412               Entry<? extends TableModel, ? extends Object> entry)
 413       {
 414         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 415       }
 416     };
 417
 418     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 419             linkUrlTable.getModel());
 420     customSorter.setRowFilter(customUrlFilter);
 421
 422     ActionListener onCustomOnly;
 423     onCustomOnly = new ActionListener()
 424     {
 425       @Override
 426       public void actionPerformed(ActionEvent e)
 427       {
 428         filterTB.setText("");
 429         sorter.setRowFilter(customUrlFilter);
 430       }
 431     };
 432     userOnly.addActionListener(onCustomOnly);
 433
 434     filterTB.getDocument().addDocumentListener(new DocumentListener()
 435     {
 436       String caseInsensitiveFlag = "(?i)";
 437
 438       @Override
 439       public void changedUpdate(DocumentEvent e)
 440       {
 441         sorter.setRowFilter(RowFilter
 442                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 443       }
 444
 445       @Override
 446       public void removeUpdate(DocumentEvent e)
 447       {
 448         sorter.setRowFilter(RowFilter
 449                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 450       }
 451
 452       @Override
 453       public void insertUpdate(DocumentEvent e)
 454       {
 455         sorter.setRowFilter(RowFilter
 456                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 457       }
 458     });
 459
 460     // set up list selection functionality
 461     linkUrlTable.getSelectionModel()
 462             .addListSelectionListener(new UrlListSelectionHandler());
 463
 464     // set up radio buttons
 465     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 466             .getPrimaryColumn();
 467     String onClickName = linkUrlTable.getColumnName(onClickCol);
 468     linkUrlTable.getColumn(onClickName)
 469             .setCellRenderer(new RadioButtonRenderer());
 470     linkUrlTable.getColumn(onClickName)
 471             .setCellEditor(new RadioButtonEditor());
 472
 473     // get boolean columns and resize those to min possible
 474     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 475     {
 476       if (linkUrlTable.getModel().getColumnClass(column)
 477               .equals(Boolean.class))
 478       {
 479         TableColumn tableColumn = linkUrlTable.getColumnModel()
 480                 .getColumn(column);
 481         int preferredWidth = tableColumn.getMinWidth();
 482
 483         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 484                 column);
 485         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 486         int cwidth = c.getPreferredSize().width
 487                 + linkUrlTable.getIntercellSpacing().width;
 488         preferredWidth = Math.max(preferredWidth, cwidth);
 489
 490         tableColumn.setPreferredWidth(preferredWidth);
 491       }
 492     }
 493
 494     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 495     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 496     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 497     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 498
 499     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 500
 501     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 502     // note antisense here: default is true
 503     questionnaire
 504             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 505     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 506
 507     /*
 508      * Set Output tab defaults
 509      */
 510     epsRendering.addItem(promptEachTimeOpt);
 511     epsRendering.addItem(lineArtOpt);
 512     epsRendering.addItem(textOpt);
 513     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 514             "Prompt each time");
 515     if (defaultEPS.equalsIgnoreCase("Text"))
 516     {
 517       epsRendering.setSelectedItem(textOpt);
 518     }
 519     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 520     {
 521       epsRendering.setSelectedItem(lineArtOpt);
 522     }
 523     else
 524     {
 525       epsRendering.setSelectedItem(promptEachTimeOpt);
 526     }
 527     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 528     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 529     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 530     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 531     userIdWidth.setText(wi == null ? "" : wi.toString());
 532     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 533     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 534     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 535     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 536     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 537     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 538     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 539     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 540     embbedBioJSON
 541             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 542
 543     /*
 544      * Set Editing tab defaults
 545      */
 546     autoCalculateConsCheck
 547             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 548     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 549     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 550
 551     annotations_actionPerformed(null); // update the display of the annotation
 552                                        // settings
 553   }
 554
 555   /**
 556    * Save user selections on the Preferences tabs to the Cache and write out to
 557    * file.
 558    *
 559    * @param e
 560    */
 561   @Override
 562   public void ok_actionPerformed(ActionEvent e)
 563   {
 564     if (!validateSettings())
 565     {
 566       return;
 567     }
 568
 569     /*
 570      * Save Visual settings
 571      */
 572     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 573             Boolean.toString(seqLimit.isSelected()));
 574     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 575             Boolean.toString(rightAlign.isSelected()));
 576     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 577             Boolean.toString(fullScreen.isSelected()));
 578     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 579             Boolean.toString(openoverv.isSelected()));
 580     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 581             Boolean.toString(annotations.isSelected()));
 582     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 583             Boolean.toString(conservation.isSelected()));
 584     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 585             Boolean.toString(quality.isSelected()));
 586     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 587             Boolean.toString(identity.isSelected()));
 588
 589     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 590             gapSymbolCB.getSelectedItem().toString());
 591
 592     Cache.applicationProperties.setProperty("FONT_NAME",
 593             fontNameCB.getSelectedItem().toString());
 594     Cache.applicationProperties.setProperty("FONT_STYLE",
 595             fontStyleCB.getSelectedItem().toString());
 596     Cache.applicationProperties.setProperty("FONT_SIZE",
 597             fontSizeCB.getSelectedItem().toString());
 598
 599     Cache.applicationProperties.setProperty("ID_ITALICS",
 600             Boolean.toString(idItalics.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 602             Boolean.toString(showUnconserved.isSelected()));
 603     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 604             Boolean.toString(showOccupancy.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 606             Boolean.toString(showGroupConsensus.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 608             Boolean.toString(showGroupConservation.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 610             Boolean.toString(showConsensHistogram.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 612             Boolean.toString(showConsensLogo.isSelected()));
 613     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 614             Boolean.toString(smoothFont.isSelected()));
 615     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 616             Boolean.toString(scaleProteinToCdna.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 618             Boolean.toString(showNpTooltip.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 620             Boolean.toString(showDbRefTooltip.isSelected()));
 621
 622     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 623             Boolean.toString(wrap.isSelected()));
 624
 625     Cache.applicationProperties.setProperty("STARTUP_FILE",
 626             startupFileTextfield.getText());
 627     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 628             Boolean.toString(startupCheckbox.isSelected()));
 629
 630     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 631             sortby.getSelectedItem().toString());
 632
 633     // convert description of sort order to enum name for save
 634     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 635             .forDescription(sortAnnBy.getSelectedItem().toString());
 636     if (annSortOrder != null)
 637     {
 638       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 639               annSortOrder.name());
 640     }
 641
 642     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 643     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 644             Boolean.valueOf(showAutocalcFirst).toString());
 645
 646     /*
 647      * Save Colours settings
 648      */
 649     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 650             protColour.getSelectedItem().toString());
 651     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 652             nucColour.getSelectedItem().toString());
 653     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 654             minColour.getBackground());
 655     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 656             maxColour.getBackground());
 657
 658     /*
 659      * Save Overview settings
 660      */
 661     Cache.setColourProperty("GAP_COLOUR", gapColour.getBackground());
 662     Cache.setColourProperty("HIDDEN_COLOUR", hiddenColour.getBackground());
 663     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 664             Boolean.toString(useLegacyGap.isSelected()));
 665     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 666             Boolean.toString(showHiddenAtStart.isSelected()));
 667
 668     /*
 669      * Save Structure settings
 670      */
 671     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 672             Boolean.toString(addTempFactor.isSelected()));
 673     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 674             Boolean.toString(addSecondaryStructure.isSelected()));
 675     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 676             Boolean.toString(useRnaView.isSelected()));
 677     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 678             Boolean.toString(structFromPdb.isSelected()));
 679     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 680             structViewer.getSelectedItem().toString());
 681     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 682     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 683             Boolean.toString(siftsMapping.isSelected()));
 684     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 685
 686     /*
 687      * Save Output settings
 688      */
 689     Cache.applicationProperties.setProperty("EPS_RENDERING",
 690             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 691
 692     /*
 693      * Save Connections settings
 694      */
 695     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 696
 697     jalview.util.BrowserLauncher.resetBrowser();
 698
 699     // save user-defined and selected links
 700     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 701     if (menuLinks.isEmpty())
 702     {
 703       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 704     }
 705     else
 706     {
 707       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 708               menuLinks.toString());
 709     }
 710
 711     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 712     if (nonMenuLinks.isEmpty())
 713     {
 714       Cache.applicationProperties.remove("STORED_LINKS");
 715     }
 716     else
 717     {
 718       Cache.applicationProperties.setProperty("STORED_LINKS",
 719               nonMenuLinks.toString());
 720     }
 721
 722     Cache.applicationProperties.setProperty("DEFAULT_URL",
 723             sequenceUrlLinks.getPrimaryUrlId());
 724
 725     Cache.applicationProperties.setProperty("USE_PROXY",
 726             Boolean.toString(useProxy.isSelected()));
 727
 728     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 729
 730     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 731
 732     if (useProxy.isSelected())
 733     {
 734       System.setProperty("http.proxyHost", proxyServerTB.getText());
 735       System.setProperty("http.proxyPort", proxyPortTB.getText());
 736     }
 737     else
 738     {
 739       System.setProperty("http.proxyHost", "");
 740       System.setProperty("http.proxyPort", "");
 741     }
 742     Cache.setProperty("VERSION_CHECK",
 743             Boolean.toString(versioncheck.isSelected()));
 744     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 745     {
 746       // default is false - we only set this if the user has actively agreed
 747       Cache.setProperty("USAGESTATS",
 748               Boolean.toString(usagestats.isSelected()));
 749     }
 750     if (!questionnaire.isSelected())
 751     {
 752       Cache.setProperty("NOQUESTIONNAIRES", "true");
 753     }
 754     else
 755     {
 756       // special - made easy to edit a property file to disable questionnaires
 757       // by just adding the given line
 758       Cache.removeProperty("NOQUESTIONNAIRES");
 759     }
 760
 761     /*
 762      * Save Output settings
 763      */
 764     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 765             Boolean.toString(blcjv.isSelected()));
 766     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 767             Boolean.toString(clustaljv.isSelected()));
 768     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 769             Boolean.toString(fastajv.isSelected()));
 770     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 771             Boolean.toString(msfjv.isSelected()));
 772     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 773             Boolean.toString(pfamjv.isSelected()));
 774     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 775             Boolean.toString(pileupjv.isSelected()));
 776     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 777             Boolean.toString(pirjv.isSelected()));
 778     Cache.applicationProperties.setProperty("PIR_MODELLER",
 779             Boolean.toString(modellerOutput.isSelected()));
 780     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 781             Boolean.toString(embbedBioJSON.isSelected()));
 782     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 783
 784     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 785             Boolean.toString(autoIdWidth.isSelected()));
 786     userIdWidth_actionPerformed();
 787     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 788             userIdWidth.getText());
 789
 790     /*
 791      * Save Editing settings
 792      */
 793     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 794             Boolean.toString(autoCalculateConsCheck.isSelected()));
 795     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 796             Boolean.toString(sortByTree.isSelected()));
 797     Cache.applicationProperties.setProperty("PAD_GAPS",
 798             Boolean.toString(padGaps.isSelected()));
 799
 800     dasSource.saveProperties(Cache.applicationProperties);
 801     wsPrefs.updateAndRefreshWsMenuConfig(false);
 802     Cache.saveProperties();
 803     Desktop.instance.doConfigureStructurePrefs();
 804     try
 805     {
 806       frame.setClosed(true);
 807     } catch (Exception ex)
 808     {
 809     }
 810   }
 811
 812   /**
 813    * Do any necessary validation before saving settings. Return focus to the
 814    * first tab which fails validation.
 815    *
 816    * @return
 817    */
 818   private boolean validateSettings()
 819   {
 820     if (!validateStructure())
 821     {
 822       structureTab.requestFocusInWindow();
 823       return false;
 824     }
 825     return true;
 826   }
 827
 828   @Override
 829   protected boolean validateStructure()
 830   {
 831     return validateChimeraPath();
 832
 833   }
 834
 835   /**
 836    * DOCUMENT ME!
 837    */
 838   @Override
 839   public void startupFileTextfield_mouseClicked()
 840   {
 841     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 842     JalviewFileChooser chooser = JalviewFileChooser
 843             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 844     chooser.setFileView(new JalviewFileView());
 845     chooser.setDialogTitle(
 846             MessageManager.getString("label.select_startup_file"));
 847
 848     int value = chooser.showOpenDialog(this);
 849
 850     if (value == JalviewFileChooser.APPROVE_OPTION)
 851     {
 852       FileFormatI format = chooser.getSelectedFormat();
 853       if (format != null)
 854       {
 855         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 856                 format.getName());
 857       }
 858       startupFileTextfield
 859               .setText(chooser.getSelectedFile().getAbsolutePath());
 860     }
 861   }
 862
 863   /**
 864    * DOCUMENT ME!
 865    *
 866    * @param e
 867    *          DOCUMENT ME!
 868    */
 869   @Override
 870   public void cancel_actionPerformed(ActionEvent e)
 871   {
 872     try
 873     {
 874       wsPrefs.updateWsMenuConfig(true);
 875       wsPrefs.refreshWs_actionPerformed(e);
 876       frame.setClosed(true);
 877     } catch (Exception ex)
 878     {
 879     }
 880   }
 881
 882   /**
 883    * DOCUMENT ME!
 884    *
 885    * @param e
 886    *          DOCUMENT ME!
 887    */
 888   @Override
 889   public void annotations_actionPerformed(ActionEvent e)
 890   {
 891     conservation.setEnabled(annotations.isSelected());
 892     quality.setEnabled(annotations.isSelected());
 893     identity.setEnabled(annotations.isSelected());
 894     showOccupancy.setEnabled(annotations.isSelected());
 895     showGroupConsensus.setEnabled(annotations.isSelected());
 896     showGroupConservation.setEnabled(annotations.isSelected());
 897     showConsensHistogram.setEnabled(annotations.isSelected()
 898             && (identity.isSelected() || showGroupConsensus.isSelected()));
 899     showConsensLogo.setEnabled(annotations.isSelected()
 900             && (identity.isSelected() || showGroupConsensus.isSelected()));
 901   }
 902
 903   @Override
 904   public void newLink_actionPerformed(ActionEvent e)
 905   {
 906     GSequenceLink link = new GSequenceLink();
 907     boolean valid = false;
 908     while (!valid)
 909     {
 910       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 911               MessageManager.getString("label.new_sequence_url_link"),
 912               JvOptionPane.OK_CANCEL_OPTION, -1,
 913               null) == JvOptionPane.OK_OPTION)
 914       {
 915         if (link.checkValid())
 916         {
 917           if (((UrlLinkTableModel) linkUrlTable.getModel())
 918                   .isUniqueName(link.getName()))
 919           {
 920             ((UrlLinkTableModel) linkUrlTable.getModel())
 921                     .insertRow(link.getName(), link.getURL());
 922             valid = true;
 923           }
 924           else
 925           {
 926             link.notifyDuplicate();
 927             continue;
 928           }
 929         }
 930       }
 931       else
 932       {
 933         break;
 934       }
 935     }
 936   }
 937
 938   @Override
 939   public void editLink_actionPerformed(ActionEvent e)
 940   {
 941     GSequenceLink link = new GSequenceLink();
 942
 943     int index = linkUrlTable.getSelectedRow();
 944     if (index == -1)
 945     {
 946       // button no longer enabled if row is not selected
 947       Cache.log.debug("Edit with no row selected in linkUrlTable");
 948       return;
 949     }
 950
 951     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 952             .getNameColumn();
 953     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 954             .getUrlColumn();
 955     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 956     link.setName(oldName);
 957     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 958
 959     boolean valid = false;
 960     while (!valid)
 961     {
 962       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 963               MessageManager.getString("label.edit_sequence_url_link"),
 964               JvOptionPane.OK_CANCEL_OPTION, -1,
 965               null) == JvOptionPane.OK_OPTION)
 966       {
 967         if (link.checkValid())
 968         {
 969           if ((oldName.equals(link.getName()))
 970                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 971                           .isUniqueName(link.getName())))
 972           {
 973             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 974             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 975             valid = true;
 976           }
 977           else
 978           {
 979             link.notifyDuplicate();
 980             continue;
 981           }
 982         }
 983       }
 984       else
 985       {
 986         break;
 987       }
 988     }
 989   }
 990
 991   @Override
 992   public void deleteLink_actionPerformed(ActionEvent e)
 993   {
 994     int index = linkUrlTable.getSelectedRow();
 995     int modelIndex = -1;
 996     if (index == -1)
 997     {
 998       // button no longer enabled if row is not selected
 999       Cache.log.debug("Delete with no row selected in linkUrlTable");
1000       return;
1001     }
1002     else
1003     {
1004       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1005     }
1006
1007     // make sure we use the model index to delete, and not the table index
1008     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1009   }
1010
1011   @Override
1012   public void defaultBrowser_mouseClicked(MouseEvent e)
1013   {
1014     JFileChooser chooser = new JFileChooser(".");
1015     chooser.setDialogTitle(
1016             MessageManager.getString("label.select_default_browser"));
1017
1018     int value = chooser.showOpenDialog(this);
1019
1020     if (value == JFileChooser.APPROVE_OPTION)
1021     {
1022       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1023     }
1024
1025   }
1026
1027   /*
1028    * (non-Javadoc)
1029    *
1030    * @see
1031    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1032    * .ActionEvent)
1033    */
1034   @Override
1035   protected void showunconserved_actionPerformed(ActionEvent e)
1036   {
1037     // TODO Auto-generated method stub
1038     super.showunconserved_actionPerformed(e);
1039   }
1040
1041   public static List<String> getGroupURLLinks()
1042   {
1043     return groupURLLinks;
1044   }
1045
1046   @Override
1047   public void minColour_actionPerformed(JPanel panel)
1048   {
1049     Color col = JColorChooser.showDialog(this,
1050             MessageManager.getString("label.select_colour_minimum_value"),
1051             minColour.getBackground());
1052     if (col != null)
1053     {
1054       panel.setBackground(col);
1055     }
1056     panel.repaint();
1057   }
1058
1059   @Override
1060   public void maxColour_actionPerformed(JPanel panel)
1061   {
1062     Color col = JColorChooser.showDialog(this,
1063             MessageManager.getString("label.select_colour_maximum_value"),
1064             maxColour.getBackground());
1065     if (col != null)
1066     {
1067       panel.setBackground(col);
1068     }
1069     panel.repaint();
1070   }
1071
1072   @Override
1073   public void gapColour_actionPerformed(JPanel gap)
1074   {
1075     if (!useLegacyGap.isSelected())
1076     {
1077       Color col = JColorChooser.showDialog(this,
1078               MessageManager.getString("label.select_gap_colour"),
1079               gapColour.getBackground());
1080       if (col != null)
1081       {
1082         gap.setBackground(col);
1083       }
1084       gap.repaint();
1085     }
1086   }
1087
1088   @Override
1089   public void hiddenColour_actionPerformed(JPanel hidden)
1090   {
1091     Color col = JColorChooser.showDialog(this,
1092             MessageManager.getString("label.select_hidden_colour"),
1093             hiddenColour.getBackground());
1094     if (col != null)
1095     {
1096       hidden.setBackground(col);
1097     }
1098     hidden.repaint();
1099   }
1100
1101   @Override
1102   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1103   {
1104     boolean enabled = useLegacyGap.isSelected();
1105     if (enabled)
1106     {
1107       gapColour.setBackground(OVERVIEW_DEFAULT_LEGACY_GAP);
1108     }
1109     else
1110     {
1111       gapColour.setBackground(OVERVIEW_DEFAULT_GAP);
1112     }
1113     gapColour.setEnabled(!enabled);
1114     gapLabel.setEnabled(!enabled);
1115   }
1116
1117   @Override
1118   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1119   {
1120     useLegacyGap.setSelected(false);
1121     useLegacyGaps_actionPerformed(null);
1122     showHiddenAtStart.setSelected(true);
1123     hiddenColour.setBackground(OVERVIEW_DEFAULT_HIDDEN);
1124   }
1125
1126   @Override
1127   protected void userIdWidth_actionPerformed()
1128   {
1129     try
1130     {
1131       String val = userIdWidth.getText().trim();
1132       if (val.length() > 0)
1133       {
1134         Integer iw = Integer.parseInt(val);
1135         if (iw.intValue() < 12)
1136         {
1137           throw new NumberFormatException();
1138         }
1139         userIdWidth.setText(iw.toString());
1140       }
1141     } catch (NumberFormatException x)
1142     {
1143       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1144               MessageManager
1145                       .getString("warn.user_defined_width_requirements"),
1146               MessageManager.getString("label.invalid_id_column_width"),
1147               JvOptionPane.WARNING_MESSAGE);
1148       userIdWidth.setText("");
1149     }
1150   }
1151
1152   @Override
1153   protected void autoIdWidth_actionPerformed()
1154   {
1155     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1156     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1157   }
1158
1159   /**
1160    * Returns true if chimera path is to a valid executable, else show an error
1161    * dialog.
1162    */
1163   private boolean validateChimeraPath()
1164   {
1165     if (chimeraPath.getText().trim().length() > 0)
1166     {
1167       File f = new File(chimeraPath.getText());
1168       if (!f.canExecute())
1169       {
1170         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1171                 MessageManager.getString("label.invalid_chimera_path"),
1172                 MessageManager.getString("label.invalid_name"),
1173                 JvOptionPane.ERROR_MESSAGE);
1174         return false;
1175       }
1176     }
1177     return true;
1178   }
1179
1180   /**
1181    * If Chimera is selected, check it can be found on default or user-specified
1182    * path, if not show a warning/help dialog.
1183    */
1184   @Override
1185   protected void structureViewer_actionPerformed(String selectedItem)
1186   {
1187     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1188     {
1189       return;
1190     }
1191     boolean found = false;
1192
1193     /*
1194      * Try user-specified and standard paths for Chimera executable.
1195      */
1196     List<String> paths = StructureManager.getChimeraPaths();
1197     paths.add(0, chimeraPath.getText());
1198     for (String path : paths)
1199     {
1200       if (new File(path.trim()).canExecute())
1201       {
1202         found = true;
1203         break;
1204       }
1205     }
1206     if (!found)
1207     {
1208       String[] options = { "OK", "Help" };
1209       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1210               JvSwingUtils.wrapTooltip(true,
1211                       MessageManager.getString("label.chimera_missing")),
1212               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1213               null, options, options[0]);
1214       if (showHelp == JvOptionPane.NO_OPTION)
1215       {
1216         try
1217         {
1218           Help.showHelpWindow(HelpId.StructureViewer);
1219         } catch (HelpSetException e)
1220         {
1221           e.printStackTrace();
1222         }
1223       }
1224     }
1225   }
1226
1227   public class OptionsParam
1228   {
1229     private String name;
1230
1231     private String code;
1232
1233     public OptionsParam(String name, String code)
1234     {
1235       this.name = name;
1236       this.code = code;
1237     }
1238
1239     public String getName()
1240     {
1241       return name;
1242     }
1243
1244     public void setName(String name)
1245     {
1246       this.name = name;
1247     }
1248
1249     public String getCode()
1250     {
1251       return code;
1252     }
1253
1254     public void setCode(String code)
1255     {
1256       this.code = code;
1257     }
1258
1259     @Override
1260     public String toString()
1261     {
1262       return name;
1263     }
1264
1265     @Override
1266     public boolean equals(Object that)
1267     {
1268       if (!(that instanceof OptionsParam))
1269       {
1270         return false;
1271       }
1272       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1273     }
1274
1275     @Override
1276     public int hashCode()
1277     {
1278       return name.hashCode() + code.hashCode();
1279     }
1280   }
1281
1282   private class UrlListSelectionHandler implements ListSelectionListener
1283   {
1284
1285     @Override
1286     public void valueChanged(ListSelectionEvent e)
1287     {
1288       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1289
1290       int index = lsm.getMinSelectionIndex();
1291       if (index == -1)
1292       {
1293         // no selection, so disable delete/edit buttons
1294         editLink.setEnabled(false);
1295         deleteLink.setEnabled(false);
1296         return;
1297       }
1298       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1299
1300       // enable/disable edit and delete link buttons
1301       if (((UrlLinkTableModel) linkUrlTable.getModel())
1302               .isRowDeletable(modelIndex))
1303       {
1304         deleteLink.setEnabled(true);
1305       }
1306       else
1307       {
1308         deleteLink.setEnabled(false);
1309       }
1310
1311       if (((UrlLinkTableModel) linkUrlTable.getModel())
1312               .isRowEditable(modelIndex))
1313       {
1314         editLink.setEnabled(true);
1315       }
1316       else
1317       {
1318         editLink.setEnabled(false);
1319       }
1320     }
1321   }
1322 }