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