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.JalviewColourChooser.ColourChooserListener;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.io.FileFormatI;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeI;
  34 import jalview.schemes.ColourSchemes;
  35 import jalview.schemes.ResidueColourScheme;
  36 import jalview.urls.UrlLinkTableModel;
  37 import jalview.urls.api.UrlProviderFactoryI;
  38 import jalview.urls.api.UrlProviderI;
  39 import jalview.urls.desktop.DesktopUrlProviderFactory;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.util.UrlConstants;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.BorderLayout;
  46 import java.awt.Color;
  47 import java.awt.Component;
  48 import java.awt.Dimension;
  49 import java.awt.Font;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.MouseEvent;
  53 import java.io.File;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56
  57 import javax.help.HelpSetException;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.RowFilter;
  64 import javax.swing.RowSorter;
  65 import javax.swing.SortOrder;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70 import javax.swing.table.TableCellRenderer;
  71 import javax.swing.table.TableColumn;
  72 import javax.swing.table.TableModel;
  73 import javax.swing.table.TableRowSorter;
  74
  75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence ID must be
 127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 128    */
 129   public static UrlProviderI sequenceUrlLinks;
 130
 131   public static UrlLinkTableModel dataModel;
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence IDS and Sequences
 135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 137    * for first and second token specified after a pipe character at end |,|.
 138    * (TODO: proper escape for using | to separate ids or sequences
 139    */
 140
 141   public static List<String> groupURLLinks;
 142   static
 143   {
 144     // get links selected to be in the menu (SEQUENCE_LINKS)
 145     // and links entered by the user but not selected (STORED_LINKS)
 146     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 147     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 148     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 149             UrlConstants.DEFAULT_LABEL);
 150
 151     // if both links lists are empty, add the DEFAULT_URL link
 152     // otherwise we assume the default link is in one of the lists
 153     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 154     {
 155       inMenuString = UrlConstants.DEFAULT_STRING;
 156     }
 157     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 158             inMenuString, notInMenuString);
 159     sequenceUrlLinks = factory.createUrlProvider();
 160     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 161
 162     /**
 163      * TODO: reformulate groupURL encoding so two or more can be stored in the
 164      * .properties file as '|' separated strings
 165      */
 166
 167     groupURLLinks = new ArrayList<>();
 168   }
 169
 170   JInternalFrame frame;
 171
 172   private WsPreferences wsPrefs;
 173
 174   private OptionsParam promptEachTimeOpt = new OptionsParam(
 175           MessageManager.getString("label.prompt_each_time"),
 176           "Prompt each time");
 177
 178   private OptionsParam lineArtOpt = new OptionsParam(
 179           MessageManager.getString("label.lineart"), "Lineart");
 180
 181   private OptionsParam textOpt = new OptionsParam(
 182           MessageManager.getString("action.text"), "Text");
 183
 184   /**
 185    * Creates a new Preferences object.
 186    */
 187   public Preferences()
 188   {
 189     super();
 190     frame = new JInternalFrame();
 191     frame.setContentPane(this);
 192     wsPrefs = new WsPreferences();
 193     wsTab.add(wsPrefs, BorderLayout.CENTER);
 194     int width = 500, height = 450;
 195     new jalview.util.Platform();
 196     if (Platform.isAMac())
 197     {
 198       width = 570;
 199       height = 480;
 200     }
 201
 202     Desktop.addInternalFrame(frame,
 203             MessageManager.getString("label.preferences"), width, height);
 204     frame.setMinimumSize(new Dimension(width, height));
 205
 206     /*
 207      * Set Visual tab defaults
 208      */
 209     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 210     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 211     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 212     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 213
 214     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 215     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 216     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 217     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 218     showUnconserved
 219             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 220     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 221     showGroupConsensus
 222             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 223     showGroupConservation.setSelected(
 224             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 225     showConsensHistogram.setSelected(
 226             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 227     showConsensLogo
 228             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 229     showNpTooltip
 230             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 231     showDbRefTooltip
 232             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 233
 234     String[] fonts = java.awt.GraphicsEnvironment
 235             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 236     for (int i = 0; i < fonts.length; i++)
 237     {
 238       fontNameCB.addItem(fonts[i]);
 239     }
 240
 241     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 242     {
 243       fontSizeCB.addItem(i + "");
 244     }
 245
 246     fontStyleCB.addItem("plain");
 247     fontStyleCB.addItem("bold");
 248     fontStyleCB.addItem("italic");
 249
 250     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 251     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 252     fontStyleCB.setSelectedItem(
 253             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 254
 255     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 256     scaleProteinToCdna
 257             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 258
 259     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 260
 261     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 262
 263     gapSymbolCB.addItem("-");
 264     gapSymbolCB.addItem(".");
 265
 266     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 267
 268     sortby.addItem("No sort");
 269     sortby.addItem("Id");
 270     sortby.addItem("Pairwise Identity");
 271     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 272
 273     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 278     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 279             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 280                     SequenceAnnotationOrder.NONE.name()));
 281     sortAnnBy.setSelectedItem(savedSort.toString());
 282
 283     sortAutocalc.addItem("Autocalculated first");
 284     sortAutocalc.addItem("Autocalculated last");
 285     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 286     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 287             : sortAutocalc.getItemAt(1));
 288     startupCheckbox
 289             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 290     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 291             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 292                     + "/examples/exampleFile_2_3.jar"));
 293
 294     /*
 295      * Set Colours tab defaults
 296      */
 297     protColour.addItem(ResidueColourScheme.NONE);
 298     nucColour.addItem(ResidueColourScheme.NONE);
 299     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 300     {
 301       String name = cs.getSchemeName();
 302       protColour.addItem(name);
 303       nucColour.addItem(name);
 304     }
 305     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 306             ResidueColourScheme.NONE);
 307     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 308     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 309     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 310     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     minColour.setBackground(
 312             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 313     maxColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 315
 316     /*
 317      * Set overview panel defaults
 318      */
 319     gapColour.setBackground(
 320             Cache.getDefaultColour(GAP_COLOUR,
 321                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 322     hiddenColour.setBackground(
 323             Cache.getDefaultColour(HIDDEN_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 325     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 326     gapLabel.setEnabled(!useLegacyGap.isSelected());
 327     gapColour.setEnabled(!useLegacyGap.isSelected());
 328     showHiddenAtStart
 329             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 330
 331     /*
 332      * Set Structure tab defaults.
 333      */
 334     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 335     structFromPdb.setSelected(structSelected);
 336     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 337     useRnaView.setEnabled(structSelected);
 338     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 339     addSecondaryStructure.setEnabled(structSelected);
 340     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 341     addTempFactor.setEnabled(structSelected);
 342     structViewer.setSelectedItem(
 343             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 344     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 345     chimeraPath.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         validateChimeraPath();
 351       }
 352     });
 353
 354     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 355     {
 356       siftsMapping.setSelected(true);
 357     }
 358     else
 359     {
 360       nwMapping.setSelected(true);
 361     }
 362
 363     SiftsSettings
 364             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 365
 366     /*
 367      * Set Connections tab defaults
 368      */
 369
 370     // set up sorting
 371     linkUrlTable.setModel(dataModel);
 372     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 373             linkUrlTable.getModel());
 374     linkUrlTable.setRowSorter(sorter);
 375     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 376
 377     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 378     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(
 383             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 384
 385     sorter.setSortKeys(sortKeys);
 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     epsRendering.addItem(promptEachTimeOpt);
 506     epsRendering.addItem(lineArtOpt);
 507     epsRendering.addItem(textOpt);
 508     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 509             "Prompt each time");
 510     if (defaultEPS.equalsIgnoreCase("Text"))
 511     {
 512       epsRendering.setSelectedItem(textOpt);
 513     }
 514     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 515     {
 516       epsRendering.setSelectedItem(lineArtOpt);
 517     }
 518     else
 519     {
 520       epsRendering.setSelectedItem(promptEachTimeOpt);
 521     }
 522     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 523     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 524     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 525     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 526     userIdWidth.setText(wi == null ? "" : wi.toString());
 527     // TODO: refactor to use common enum via FormatAdapter and allow extension
 528     // for new flat file formats
 529     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 530     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 531     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 532     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 533     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 534     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 535     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 536     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 537     embbedBioJSON
 538             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 539
 540     /*
 541      * Set Editing tab defaults
 542      */
 543     autoCalculateConsCheck
 544             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 545     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 546     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 547
 548     annotations_actionPerformed(null); // update the display of the annotation
 549                                        // settings
 550   }
 551
 552   /**
 553    * Save user selections on the Preferences tabs to the Cache and write out to
 554    * file.
 555    *
 556    * @param e
 557    */
 558   @Override
 559   public void ok_actionPerformed(ActionEvent e)
 560   {
 561     if (!validateSettings())
 562     {
 563       return;
 564     }
 565
 566     /*
 567      * Save Visual settings
 568      */
 569     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 570             Boolean.toString(seqLimit.isSelected()));
 571     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 572             Boolean.toString(rightAlign.isSelected()));
 573     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 574             Boolean.toString(fullScreen.isSelected()));
 575     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 576             Boolean.toString(openoverv.isSelected()));
 577     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 578             Boolean.toString(annotations.isSelected()));
 579     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 580             Boolean.toString(conservation.isSelected()));
 581     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 582             Boolean.toString(quality.isSelected()));
 583     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 584             Boolean.toString(identity.isSelected()));
 585
 586     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 587             gapSymbolCB.getSelectedItem().toString());
 588
 589     Cache.applicationProperties.setProperty("FONT_NAME",
 590             fontNameCB.getSelectedItem().toString());
 591     Cache.applicationProperties.setProperty("FONT_STYLE",
 592             fontStyleCB.getSelectedItem().toString());
 593     Cache.applicationProperties.setProperty("FONT_SIZE",
 594             fontSizeCB.getSelectedItem().toString());
 595
 596     Cache.applicationProperties.setProperty("ID_ITALICS",
 597             Boolean.toString(idItalics.isSelected()));
 598     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 599             Boolean.toString(showUnconserved.isSelected()));
 600     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 601             Boolean.toString(showOccupancy.isSelected()));
 602     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 603             Boolean.toString(showGroupConsensus.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 605             Boolean.toString(showGroupConservation.isSelected()));
 606     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 607             Boolean.toString(showConsensHistogram.isSelected()));
 608     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 609             Boolean.toString(showConsensLogo.isSelected()));
 610     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 611             Boolean.toString(smoothFont.isSelected()));
 612     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 613             Boolean.toString(scaleProteinToCdna.isSelected()));
 614     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 615             Boolean.toString(showNpTooltip.isSelected()));
 616     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 617             Boolean.toString(showDbRefTooltip.isSelected()));
 618
 619     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 620             Boolean.toString(wrap.isSelected()));
 621
 622     Cache.applicationProperties.setProperty("STARTUP_FILE",
 623             startupFileTextfield.getText());
 624     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 625             Boolean.toString(startupCheckbox.isSelected()));
 626
 627     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 628             sortby.getSelectedItem().toString());
 629
 630     // convert description of sort order to enum name for save
 631     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 632             .forDescription(sortAnnBy.getSelectedItem().toString());
 633     if (annSortOrder != null)
 634     {
 635       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 636               annSortOrder.name());
 637     }
 638
 639     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 640     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 641             Boolean.valueOf(showAutocalcFirst).toString());
 642
 643     /*
 644      * Save Colours settings
 645      */
 646     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 647             protColour.getSelectedItem().toString());
 648     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 649             nucColour.getSelectedItem().toString());
 650     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 651             minColour.getBackground());
 652     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 653             maxColour.getBackground());
 654
 655     /*
 656      * Save Overview settings
 657      */
 658     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 659     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 660     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 661             Boolean.toString(useLegacyGap.isSelected()));
 662     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 663             Boolean.toString(showHiddenAtStart.isSelected()));
 664
 665     /*
 666      * Save Structure settings
 667      */
 668     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 669             Boolean.toString(addTempFactor.isSelected()));
 670     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 671             Boolean.toString(addSecondaryStructure.isSelected()));
 672     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 673             Boolean.toString(useRnaView.isSelected()));
 674     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 675             Boolean.toString(structFromPdb.isSelected()));
 676     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 677             structViewer.getSelectedItem().toString());
 678     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 679     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 680             Boolean.toString(siftsMapping.isSelected()));
 681     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 682
 683     /*
 684      * Save Output settings
 685      */
 686     Cache.applicationProperties.setProperty("EPS_RENDERING",
 687             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 688
 689     /*
 690      * Save Connections settings
 691      */
 692     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 693
 694     jalview.util.BrowserLauncher.resetBrowser();
 695
 696     // save user-defined and selected links
 697     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 698     if (menuLinks.isEmpty())
 699     {
 700       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 701     }
 702     else
 703     {
 704       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 705               menuLinks.toString());
 706     }
 707
 708     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 709     if (nonMenuLinks.isEmpty())
 710     {
 711       Cache.applicationProperties.remove("STORED_LINKS");
 712     }
 713     else
 714     {
 715       Cache.applicationProperties.setProperty("STORED_LINKS",
 716               nonMenuLinks.toString());
 717     }
 718
 719     Cache.applicationProperties.setProperty("DEFAULT_URL",
 720             sequenceUrlLinks.getPrimaryUrlId());
 721
 722     Cache.applicationProperties.setProperty("USE_PROXY",
 723             Boolean.toString(useProxy.isSelected()));
 724
 725     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 726
 727     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 728
 729     if (useProxy.isSelected())
 730     {
 731       System.setProperty("http.proxyHost", proxyServerTB.getText());
 732       System.setProperty("http.proxyPort", proxyPortTB.getText());
 733     }
 734     else
 735     {
 736       System.setProperty("http.proxyHost", "");
 737       System.setProperty("http.proxyPort", "");
 738     }
 739     Cache.setProperty("VERSION_CHECK",
 740             Boolean.toString(versioncheck.isSelected()));
 741     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 742     {
 743       // default is false - we only set this if the user has actively agreed
 744       Cache.setProperty("USAGESTATS",
 745               Boolean.toString(usagestats.isSelected()));
 746     }
 747     if (!questionnaire.isSelected())
 748     {
 749       Cache.setProperty("NOQUESTIONNAIRES", "true");
 750     }
 751     else
 752     {
 753       // special - made easy to edit a property file to disable questionnaires
 754       // by just adding the given line
 755       Cache.removeProperty("NOQUESTIONNAIRES");
 756     }
 757
 758     /*
 759      * Save Output settings
 760      */
 761     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 762             Boolean.toString(blcjv.isSelected()));
 763     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 764             Boolean.toString(clustaljv.isSelected()));
 765     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 766             Boolean.toString(fastajv.isSelected()));
 767     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 768             Boolean.toString(msfjv.isSelected()));
 769     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 770             Boolean.toString(pfamjv.isSelected()));
 771     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 772             Boolean.toString(pileupjv.isSelected()));
 773     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 774             Boolean.toString(pirjv.isSelected()));
 775     Cache.applicationProperties.setProperty("PIR_MODELLER",
 776             Boolean.toString(modellerOutput.isSelected()));
 777     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 778             Boolean.toString(embbedBioJSON.isSelected()));
 779     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 780
 781     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 782             Boolean.toString(autoIdWidth.isSelected()));
 783     userIdWidth_actionPerformed();
 784     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 785             userIdWidth.getText());
 786
 787     /*
 788      * Save Editing settings
 789      */
 790     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 791             Boolean.toString(autoCalculateConsCheck.isSelected()));
 792     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 793             Boolean.toString(sortByTree.isSelected()));
 794     Cache.applicationProperties.setProperty("PAD_GAPS",
 795             Boolean.toString(padGaps.isSelected()));
 796
 797     wsPrefs.updateAndRefreshWsMenuConfig(false);
 798     Cache.saveProperties();
 799     Desktop.instance.doConfigureStructurePrefs();
 800     try
 801     {
 802       frame.setClosed(true);
 803     } catch (Exception ex)
 804     {
 805     }
 806   }
 807
 808   /**
 809    * Do any necessary validation before saving settings. Return focus to the
 810    * first tab which fails validation.
 811    *
 812    * @return
 813    */
 814   private boolean validateSettings()
 815   {
 816     if (!validateStructure())
 817     {
 818       structureTab.requestFocusInWindow();
 819       return false;
 820     }
 821     return true;
 822   }
 823
 824   @Override
 825   protected boolean validateStructure()
 826   {
 827     return validateChimeraPath();
 828
 829   }
 830
 831   /**
 832    * DOCUMENT ME!
 833    */
 834   @Override
 835   public void startupFileTextfield_mouseClicked()
 836   {
 837     // TODO: JAL-3048 not needed for Jalview-JS
 838     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 839     JalviewFileChooser chooser = JalviewFileChooser
 840             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 841     chooser.setFileView(new JalviewFileView());
 842     chooser.setDialogTitle(
 843             MessageManager.getString("label.select_startup_file"));
 844
 845     int value = chooser.showOpenDialog(this);
 846
 847     if (value == JalviewFileChooser.APPROVE_OPTION)
 848     {
 849       FileFormatI format = chooser.getSelectedFormat();
 850       if (format != null)
 851       {
 852         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 853                 format.getName());
 854       }
 855       startupFileTextfield
 856               .setText(chooser.getSelectedFile().getAbsolutePath());
 857     }
 858   }
 859
 860   /**
 861    * DOCUMENT ME!
 862    *
 863    * @param e
 864    *          DOCUMENT ME!
 865    */
 866   @Override
 867   public void cancel_actionPerformed(ActionEvent e)
 868   {
 869     try
 870     {
 871       wsPrefs.updateWsMenuConfig(true);
 872       wsPrefs.refreshWs_actionPerformed(e);
 873       frame.setClosed(true);
 874     } catch (Exception ex)
 875     {
 876     }
 877   }
 878
 879   /**
 880    * DOCUMENT ME!
 881    *
 882    * @param e
 883    *          DOCUMENT ME!
 884    */
 885   @Override
 886   public void annotations_actionPerformed(ActionEvent e)
 887   {
 888     conservation.setEnabled(annotations.isSelected());
 889     quality.setEnabled(annotations.isSelected());
 890     identity.setEnabled(annotations.isSelected());
 891     showOccupancy.setEnabled(annotations.isSelected());
 892     showGroupConsensus.setEnabled(annotations.isSelected());
 893     showGroupConservation.setEnabled(annotations.isSelected());
 894     showConsensHistogram.setEnabled(annotations.isSelected()
 895             && (identity.isSelected() || showGroupConsensus.isSelected()));
 896     showConsensLogo.setEnabled(annotations.isSelected()
 897             && (identity.isSelected() || showGroupConsensus.isSelected()));
 898   }
 899
 900   @Override
 901   public void newLink_actionPerformed(ActionEvent e)
 902   {
 903     GSequenceLink link = new GSequenceLink();
 904     boolean valid = false;
 905     while (!valid)
 906     {
 907       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 908               MessageManager.getString("label.new_sequence_url_link"),
 909               JvOptionPane.OK_CANCEL_OPTION, -1,
 910               null) == JvOptionPane.OK_OPTION)
 911       {
 912         if (link.checkValid())
 913         {
 914           if (((UrlLinkTableModel) linkUrlTable.getModel())
 915                   .isUniqueName(link.getName()))
 916           {
 917             ((UrlLinkTableModel) linkUrlTable.getModel())
 918                     .insertRow(link.getName(), link.getURL());
 919             valid = true;
 920           }
 921           else
 922           {
 923             link.notifyDuplicate();
 924             continue;
 925           }
 926         }
 927       }
 928       else
 929       {
 930         break;
 931       }
 932     }
 933   }
 934
 935   @Override
 936   public void editLink_actionPerformed(ActionEvent e)
 937   {
 938     GSequenceLink link = new GSequenceLink();
 939
 940     int index = linkUrlTable.getSelectedRow();
 941     if (index == -1)
 942     {
 943       // button no longer enabled if row is not selected
 944       Cache.log.debug("Edit with no row selected in linkUrlTable");
 945       return;
 946     }
 947
 948     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 949             .getNameColumn();
 950     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 951             .getUrlColumn();
 952     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 953     link.setName(oldName);
 954     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 955
 956     boolean valid = false;
 957     while (!valid)
 958     {
 959       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 960               MessageManager.getString("label.edit_sequence_url_link"),
 961               JvOptionPane.OK_CANCEL_OPTION, -1,
 962               null) == JvOptionPane.OK_OPTION)
 963       {
 964         if (link.checkValid())
 965         {
 966           if ((oldName.equals(link.getName()))
 967                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 968                           .isUniqueName(link.getName())))
 969           {
 970             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 971             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 972             valid = true;
 973           }
 974           else
 975           {
 976             link.notifyDuplicate();
 977             continue;
 978           }
 979         }
 980       }
 981       else
 982       {
 983         break;
 984       }
 985     }
 986   }
 987
 988   @Override
 989   public void deleteLink_actionPerformed(ActionEvent e)
 990   {
 991     int index = linkUrlTable.getSelectedRow();
 992     int modelIndex = -1;
 993     if (index == -1)
 994     {
 995       // button no longer enabled if row is not selected
 996       Cache.log.debug("Delete with no row selected in linkUrlTable");
 997       return;
 998     }
 999     else
1000     {
1001       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1002     }
1003
1004     // make sure we use the model index to delete, and not the table index
1005     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1006   }
1007
1008   @Override
1009   public void defaultBrowser_mouseClicked(MouseEvent e)
1010   {
1011     // TODO: JAL-3048 not needed for j2s
1012     /*
1013      * @j2sNative
1014      */
1015     {
1016       JFileChooser chooser = new JFileChooser(".");
1017       chooser.setDialogTitle(
1018               MessageManager.getString("label.select_default_browser"));
1019
1020       int value = chooser.showOpenDialog(this);
1021
1022       if (value == JFileChooser.APPROVE_OPTION)
1023       {
1024         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1025       }
1026     }
1027   }
1028
1029   /*
1030    * (non-Javadoc)
1031    *
1032    * @see
1033    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1034    * .ActionEvent)
1035    */
1036   @Override
1037   protected void showunconserved_actionPerformed(ActionEvent e)
1038   {
1039     // TODO Auto-generated method stub
1040     super.showunconserved_actionPerformed(e);
1041   }
1042
1043   public static List<String> getGroupURLLinks()
1044   {
1045     return groupURLLinks;
1046   }
1047
1048   @Override
1049   public void minColour_actionPerformed(JPanel panel)
1050   {
1051     JalviewColourChooser.showColourChooser(this,
1052             MessageManager.getString("label.select_colour_minimum_value"),
1053             panel);
1054   }
1055
1056   @Override
1057   public void maxColour_actionPerformed(JPanel panel)
1058   {
1059     JalviewColourChooser.showColourChooser(this,
1060             MessageManager.getString("label.select_colour_maximum_value"),
1061             panel);
1062   }
1063
1064   @Override
1065   public void gapColour_actionPerformed(JPanel gap)
1066   {
1067     if (!useLegacyGap.isSelected())
1068     {
1069       JalviewColourChooser.showColourChooser(this,
1070               MessageManager.getString("label.select_gap_colour"),
1071               gap);
1072     }
1073   }
1074
1075   @Override
1076   public void hiddenColour_actionPerformed(JPanel hidden)
1077   {
1078     JalviewColourChooser.showColourChooser(this,
1079             MessageManager.getString("label.select_hidden_colour"),
1080             hidden);
1081   }
1082
1083   @Override
1084   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1085   {
1086     boolean enabled = useLegacyGap.isSelected();
1087     if (enabled)
1088     {
1089       gapColour.setBackground(
1090               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1091     }
1092     else
1093     {
1094       gapColour.setBackground(
1095               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1096     }
1097     gapColour.setEnabled(!enabled);
1098     gapLabel.setEnabled(!enabled);
1099   }
1100
1101   @Override
1102   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1103   {
1104     useLegacyGap.setSelected(false);
1105     useLegacyGaps_actionPerformed(null);
1106     showHiddenAtStart.setSelected(true);
1107     hiddenColour.setBackground(
1108             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1109   }
1110
1111   @Override
1112   protected void userIdWidth_actionPerformed()
1113   {
1114     try
1115     {
1116       String val = userIdWidth.getText().trim();
1117       if (val.length() > 0)
1118       {
1119         Integer iw = Integer.parseInt(val);
1120         if (iw.intValue() < 12)
1121         {
1122           throw new NumberFormatException();
1123         }
1124         userIdWidth.setText(iw.toString());
1125       }
1126     } catch (NumberFormatException x)
1127     {
1128       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1129               MessageManager
1130                       .getString("warn.user_defined_width_requirements"),
1131               MessageManager.getString("label.invalid_id_column_width"),
1132               JvOptionPane.WARNING_MESSAGE);
1133       userIdWidth.setText("");
1134     }
1135   }
1136
1137   @Override
1138   protected void autoIdWidth_actionPerformed()
1139   {
1140     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1141     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1142   }
1143
1144   /**
1145    * Returns true if chimera path is to a valid executable, else show an error
1146    * dialog.
1147    */
1148   private boolean validateChimeraPath()
1149   {
1150     if (chimeraPath.getText().trim().length() > 0)
1151     {
1152       File f = new File(chimeraPath.getText());
1153       if (!f.canExecute())
1154       {
1155         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1156                 MessageManager.getString("label.invalid_chimera_path"),
1157                 MessageManager.getString("label.invalid_name"),
1158                 JvOptionPane.ERROR_MESSAGE);
1159         return false;
1160       }
1161     }
1162     return true;
1163   }
1164
1165   /**
1166    * If Chimera is selected, check it can be found on default or user-specified
1167    * path, if not show a warning/help dialog.
1168    */
1169   @Override
1170   protected void structureViewer_actionPerformed(String selectedItem)
1171   {
1172     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1173     {
1174       return;
1175     }
1176     boolean found = false;
1177
1178     /*
1179      * Try user-specified and standard paths for Chimera executable.
1180      */
1181     List<String> paths = StructureManager.getChimeraPaths();
1182     paths.add(0, chimeraPath.getText());
1183     for (String path : paths)
1184     {
1185       if (new File(path.trim()).canExecute())
1186       {
1187         found = true;
1188         break;
1189       }
1190     }
1191     if (!found)
1192     {
1193       String[] options = { "OK", "Help" };
1194       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1195               JvSwingUtils.wrapTooltip(true,
1196                       MessageManager.getString("label.chimera_missing")),
1197               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1198               null, options, options[0]);
1199       if (showHelp == JvOptionPane.NO_OPTION)
1200       {
1201         try
1202         {
1203           Help.showHelpWindow(HelpId.StructureViewer);
1204         } catch (HelpSetException e)
1205         {
1206           e.printStackTrace();
1207         }
1208       }
1209     }
1210   }
1211
1212   public class OptionsParam
1213   {
1214     private String name;
1215
1216     private String code;
1217
1218     public OptionsParam(String name, String code)
1219     {
1220       this.name = name;
1221       this.code = code;
1222     }
1223
1224     public String getName()
1225     {
1226       return name;
1227     }
1228
1229     public void setName(String name)
1230     {
1231       this.name = name;
1232     }
1233
1234     public String getCode()
1235     {
1236       return code;
1237     }
1238
1239     public void setCode(String code)
1240     {
1241       this.code = code;
1242     }
1243
1244     @Override
1245     public String toString()
1246     {
1247       return name;
1248     }
1249
1250     @Override
1251     public boolean equals(Object that)
1252     {
1253       if (!(that instanceof OptionsParam))
1254       {
1255         return false;
1256       }
1257       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1258     }
1259
1260     @Override
1261     public int hashCode()
1262     {
1263       return name.hashCode() + code.hashCode();
1264     }
1265   }
1266
1267   private class UrlListSelectionHandler implements ListSelectionListener
1268   {
1269
1270     @Override
1271     public void valueChanged(ListSelectionEvent e)
1272     {
1273       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1274
1275       int index = lsm.getMinSelectionIndex();
1276       if (index == -1)
1277       {
1278         // no selection, so disable delete/edit buttons
1279         editLink.setEnabled(false);
1280         deleteLink.setEnabled(false);
1281         return;
1282       }
1283       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1284
1285       // enable/disable edit and delete link buttons
1286       if (((UrlLinkTableModel) linkUrlTable.getModel())
1287               .isRowDeletable(modelIndex))
1288       {
1289         deleteLink.setEnabled(true);
1290       }
1291       else
1292       {
1293         deleteLink.setEnabled(false);
1294       }
1295
1296       if (((UrlLinkTableModel) linkUrlTable.getModel())
1297               .isRowEditable(modelIndex))
1298       {
1299         editLink.setEnabled(true);
1300       }
1301       else
1302       {
1303         editLink.setEnabled(false);
1304       }
1305     }
1306   }
1307 }