src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  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.viewmodel.AlignmentViewport.AutoAnnotation;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JColorChooser;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 109
 110   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 111
 112   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 113
 114   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 115
 116   public static final String GAP_COLOUR = "GAP_COLOUR";
 117
 118   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 119
 120   private static final int MIN_FONT_SIZE = 1;
 121
 122   private static final int MAX_FONT_SIZE = 30;
 123
 124   /**
 125    * Holds name and link separated with | character. Sequence ID must be
 126    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 127    */
 128   public static UrlProviderI sequenceUrlLinks;
 129
 130   public static UrlLinkTableModel dataModel;
 131
 132   /**
 133    * Holds name and link separated with | character. Sequence IDS and Sequences
 134    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 135    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 136    * for first and second token specified after a pipe character at end |,|.
 137    * (TODO: proper escape for using | to separate ids or sequences
 138    */
 139
 140   public static List<String> groupURLLinks;
 141   static
 142   {
 143     // get links selected to be in the menu (SEQUENCE_LINKS)
 144     // and links entered by the user but not selected (STORED_LINKS)
 145     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 146     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 147     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 148             UrlConstants.DEFAULT_LABEL);
 149
 150     // if both links lists are empty, add the DEFAULT_URL link
 151     // otherwise we assume the default link is in one of the lists
 152     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 153     {
 154       inMenuString = UrlConstants.DEFAULT_STRING;
 155     }
 156     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 157             inMenuString, notInMenuString);
 158     sequenceUrlLinks = factory.createUrlProvider();
 159     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 160
 161     /**
 162      * TODO: reformulate groupURL encoding so two or more can be stored in the
 163      * .properties file as '|' separated strings
 164      */
 165
 166     groupURLLinks = new ArrayList<>();
 167   }
 168
 169   JInternalFrame frame;
 170
 171   private WsPreferences wsPrefs;
 172
 173   private OptionsParam promptEachTimeOpt = new OptionsParam(
 174           MessageManager.getString("label.prompt_each_time"),
 175           "Prompt each time");
 176
 177   private OptionsParam lineArtOpt = new OptionsParam(
 178           MessageManager.getString("label.lineart"), "Lineart");
 179
 180   private OptionsParam textOpt = new OptionsParam(
 181           MessageManager.getString("action.text"), "Text");
 182
 183   /**
 184    * Creates a new Preferences object.
 185    */
 186   public Preferences()
 187   {
 188     super();
 189     frame = new JInternalFrame();
 190     frame.setContentPane(this);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set Visual tab defaults
 207      */
 208     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 209     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 210     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 211     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 212
 213     conservation.setSelected(Cache
 214             .getDefault(AutoAnnotation.CONSERVATION.preferenceKey, true));
 215     quality.setSelected(
 216             Cache.getDefault(AutoAnnotation.QUALITY.preferenceKey, true));
 217     identity.setSelected(
 218             Cache.getDefault(AutoAnnotation.CONSENSUS.preferenceKey, true));
 219     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 220     showUnconserved
 221             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 222     showOccupancy.setSelected(Cache
 223             .getDefault(AutoAnnotation.OCCUPANCY.preferenceKey, false));
 224     showGroupConsensus
 225             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 226     showGroupConservation.setSelected(
 227             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 228     showConsensHistogram.setSelected(
 229             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 230     showConsensLogo
 231             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 232     showNpTooltip
 233             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 234     showDbRefTooltip
 235             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 236
 237     String[] fonts = java.awt.GraphicsEnvironment
 238             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 239     for (int i = 0; i < fonts.length; i++)
 240     {
 241       fontNameCB.addItem(fonts[i]);
 242     }
 243
 244     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 245     {
 246       fontSizeCB.addItem(i + "");
 247     }
 248
 249     fontStyleCB.addItem("plain");
 250     fontStyleCB.addItem("bold");
 251     fontStyleCB.addItem("italic");
 252
 253     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 254     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 255     fontStyleCB.setSelectedItem(
 256             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 257
 258     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 259     scaleProteinToCdna
 260             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 261
 262     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 263
 264     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 265
 266     gapSymbolCB.addItem("-");
 267     gapSymbolCB.addItem(".");
 268
 269     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 270
 271     sortby.addItem("No sort");
 272     sortby.addItem("Id");
 273     sortby.addItem("Pairwise Identity");
 274     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 275
 276     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 277     sortAnnBy
 278             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 279     sortAnnBy
 280             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 281     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 282             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 283                     SequenceAnnotationOrder.NONE.name()));
 284     sortAnnBy.setSelectedItem(savedSort.toString());
 285
 286     sortAutocalc.addItem("Autocalculated first");
 287     sortAutocalc.addItem("Autocalculated last");
 288     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 289     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 290             : sortAutocalc.getItemAt(1));
 291     startupCheckbox
 292             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 293     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 294             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 295                     + "/examples/exampleFile_2_3.jar"));
 296
 297     /*
 298      * Set Colours tab defaults
 299      */
 300     protColour.addItem(ResidueColourScheme.NONE);
 301     nucColour.addItem(ResidueColourScheme.NONE);
 302     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 303     {
 304       String name = cs.getSchemeName();
 305       protColour.addItem(name);
 306       nucColour.addItem(name);
 307     }
 308     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 309             ResidueColourScheme.NONE);
 310     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 311     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 312     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 313     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 314     minColour.setBackground(
 315             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 316     maxColour.setBackground(
 317             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 318
 319     /*
 320      * Set overview panel defaults
 321      */
 322     gapColour.setBackground(
 323             Cache.getDefaultColour(GAP_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 325     hiddenColour.setBackground(
 326             Cache.getDefaultColour(HIDDEN_COLOUR,
 327                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 328     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 329     gapLabel.setEnabled(!useLegacyGap.isSelected());
 330     gapColour.setEnabled(!useLegacyGap.isSelected());
 331     showHiddenAtStart
 332             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 333
 334     /*
 335      * Set Structure tab defaults.
 336      */
 337     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 338     structFromPdb.setSelected(structSelected);
 339     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 340     useRnaView.setEnabled(structSelected);
 341     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 342     addSecondaryStructure.setEnabled(structSelected);
 343     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 344     addTempFactor.setEnabled(structSelected);
 345     structViewer.setSelectedItem(
 346             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 347     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 348     chimeraPath.addActionListener(new ActionListener()
 349     {
 350       @Override
 351       public void actionPerformed(ActionEvent e)
 352       {
 353         validateChimeraPath();
 354       }
 355     });
 356
 357     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 358     {
 359       siftsMapping.setSelected(true);
 360     }
 361     else
 362     {
 363       nwMapping.setSelected(true);
 364     }
 365
 366     SiftsSettings
 367             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 368
 369     /*
 370      * Set Connections tab defaults
 371      */
 372
 373     // set up sorting
 374     linkUrlTable.setModel(dataModel);
 375     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 376             linkUrlTable.getModel());
 377     linkUrlTable.setRowSorter(sorter);
 378     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 379
 380     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 381     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 382             SortOrder.DESCENDING));
 383     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 384             SortOrder.DESCENDING));
 385     sortKeys.add(
 386             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 387
 388     sorter.setSortKeys(sortKeys);
 389     sorter.sort();
 390
 391     // set up filtering
 392     ActionListener onReset;
 393     onReset = new ActionListener()
 394     {
 395       @Override
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         filterTB.setText("");
 399         sorter.setRowFilter(RowFilter.regexFilter(""));
 400       }
 401
 402     };
 403     doReset.addActionListener(onReset);
 404
 405     // filter to display only custom urls
 406     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 407     {
 408       @Override
 409       public boolean include(
 410               Entry<? extends TableModel, ? extends Object> entry)
 411       {
 412         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 413       }
 414     };
 415
 416     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 417             linkUrlTable.getModel());
 418     customSorter.setRowFilter(customUrlFilter);
 419
 420     ActionListener onCustomOnly;
 421     onCustomOnly = new ActionListener()
 422     {
 423       @Override
 424       public void actionPerformed(ActionEvent e)
 425       {
 426         filterTB.setText("");
 427         sorter.setRowFilter(customUrlFilter);
 428       }
 429     };
 430     userOnly.addActionListener(onCustomOnly);
 431
 432     filterTB.getDocument().addDocumentListener(new DocumentListener()
 433     {
 434       String caseInsensitiveFlag = "(?i)";
 435
 436       @Override
 437       public void changedUpdate(DocumentEvent e)
 438       {
 439         sorter.setRowFilter(RowFilter
 440                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 441       }
 442
 443       @Override
 444       public void removeUpdate(DocumentEvent e)
 445       {
 446         sorter.setRowFilter(RowFilter
 447                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 448       }
 449
 450       @Override
 451       public void insertUpdate(DocumentEvent e)
 452       {
 453         sorter.setRowFilter(RowFilter
 454                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 455       }
 456     });
 457
 458     // set up list selection functionality
 459     linkUrlTable.getSelectionModel()
 460             .addListSelectionListener(new UrlListSelectionHandler());
 461
 462     // set up radio buttons
 463     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 464             .getPrimaryColumn();
 465     String onClickName = linkUrlTable.getColumnName(onClickCol);
 466     linkUrlTable.getColumn(onClickName)
 467             .setCellRenderer(new RadioButtonRenderer());
 468     linkUrlTable.getColumn(onClickName)
 469             .setCellEditor(new RadioButtonEditor());
 470
 471     // get boolean columns and resize those to min possible
 472     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 473     {
 474       if (linkUrlTable.getModel().getColumnClass(column)
 475               .equals(Boolean.class))
 476       {
 477         TableColumn tableColumn = linkUrlTable.getColumnModel()
 478                 .getColumn(column);
 479         int preferredWidth = tableColumn.getMinWidth();
 480
 481         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 482                 column);
 483         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 484         int cwidth = c.getPreferredSize().width
 485                 + linkUrlTable.getIntercellSpacing().width;
 486         preferredWidth = Math.max(preferredWidth, cwidth);
 487
 488         tableColumn.setPreferredWidth(preferredWidth);
 489       }
 490     }
 491
 492     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 493     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 494     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 495     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 496
 497     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 498
 499     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 500     // note antisense here: default is true
 501     questionnaire
 502             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 503     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 504
 505     /*
 506      * Set Output tab defaults
 507      */
 508     epsRendering.addItem(promptEachTimeOpt);
 509     epsRendering.addItem(lineArtOpt);
 510     epsRendering.addItem(textOpt);
 511     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 512             "Prompt each time");
 513     if (defaultEPS.equalsIgnoreCase("Text"))
 514     {
 515       epsRendering.setSelectedItem(textOpt);
 516     }
 517     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 518     {
 519       epsRendering.setSelectedItem(lineArtOpt);
 520     }
 521     else
 522     {
 523       epsRendering.setSelectedItem(promptEachTimeOpt);
 524     }
 525     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 526     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 527     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 528     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 529     userIdWidth.setText(wi == null ? "" : wi.toString());
 530     // TODO: refactor to use common enum via FormatAdapter and allow extension
 531     // for new flat file formats
 532     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 533     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 534     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 535     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 536     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 537     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 538     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 539     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 540     embbedBioJSON
 541             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 542
 543     /*
 544      * Set Editing tab defaults
 545      */
 546     autoCalculateConsCheck
 547             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 548     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 549     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 550
 551     annotations_actionPerformed(null); // update the display of the annotation
 552                                        // settings
 553
 554
 555     /*
 556      * Set Backups tab defaults
 557      */
 558     loadLastSavedBackupsOptions();
 559   }
 560
 561   /**
 562    * Save user selections on the Preferences tabs to the Cache and write out to
 563    * file.
 564    *
 565    * @param e
 566    */
 567   @Override
 568   public void ok_actionPerformed(ActionEvent e)
 569   {
 570     if (!validateSettings())
 571     {
 572       return;
 573     }
 574
 575     /*
 576      * Save Visual settings
 577      */
 578     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 579             Boolean.toString(seqLimit.isSelected()));
 580     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 581             Boolean.toString(rightAlign.isSelected()));
 582     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 583             Boolean.toString(fullScreen.isSelected()));
 584     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 585             Boolean.toString(openoverv.isSelected()));
 586     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 587             Boolean.toString(annotations.isSelected()));
 588     Cache.applicationProperties.setProperty(
 589             AutoAnnotation.CONSERVATION.preferenceKey,
 590             Boolean.toString(conservation.isSelected()));
 591     Cache.applicationProperties.setProperty(
 592             AutoAnnotation.QUALITY.preferenceKey,
 593             Boolean.toString(quality.isSelected()));
 594     Cache.applicationProperties.setProperty(
 595             AutoAnnotation.CONSENSUS.preferenceKey,
 596             Boolean.toString(identity.isSelected()));
 597     Cache.applicationProperties.setProperty(
 598             AutoAnnotation.OCCUPANCY.preferenceKey,
 599             Boolean.toString(showOccupancy.isSelected()));
 600
 601     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 602             gapSymbolCB.getSelectedItem().toString());
 603
 604     Cache.applicationProperties.setProperty("FONT_NAME",
 605             fontNameCB.getSelectedItem().toString());
 606     Cache.applicationProperties.setProperty("FONT_STYLE",
 607             fontStyleCB.getSelectedItem().toString());
 608     Cache.applicationProperties.setProperty("FONT_SIZE",
 609             fontSizeCB.getSelectedItem().toString());
 610
 611     Cache.applicationProperties.setProperty("ID_ITALICS",
 612             Boolean.toString(idItalics.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 614             Boolean.toString(showUnconserved.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 616             Boolean.toString(showGroupConsensus.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 618             Boolean.toString(showGroupConservation.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 620             Boolean.toString(showConsensHistogram.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 622             Boolean.toString(showConsensLogo.isSelected()));
 623     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 624             Boolean.toString(smoothFont.isSelected()));
 625     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 626             Boolean.toString(scaleProteinToCdna.isSelected()));
 627     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 628             Boolean.toString(showNpTooltip.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 630             Boolean.toString(showDbRefTooltip.isSelected()));
 631
 632     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 633             Boolean.toString(wrap.isSelected()));
 634
 635     Cache.applicationProperties.setProperty("STARTUP_FILE",
 636             startupFileTextfield.getText());
 637     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 638             Boolean.toString(startupCheckbox.isSelected()));
 639
 640     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 641             sortby.getSelectedItem().toString());
 642
 643     // convert description of sort order to enum name for save
 644     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 645             .forDescription(sortAnnBy.getSelectedItem().toString());
 646     if (annSortOrder != null)
 647     {
 648       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 649               annSortOrder.name());
 650     }
 651
 652     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 653     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 654             Boolean.valueOf(showAutocalcFirst).toString());
 655
 656     /*
 657      * Save Colours settings
 658      */
 659     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 660             protColour.getSelectedItem().toString());
 661     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 662             nucColour.getSelectedItem().toString());
 663     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 664             minColour.getBackground());
 665     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 666             maxColour.getBackground());
 667
 668     /*
 669      * Save Overview settings
 670      */
 671     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 672     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 673     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 674             Boolean.toString(useLegacyGap.isSelected()));
 675     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 676             Boolean.toString(showHiddenAtStart.isSelected()));
 677
 678     /*
 679      * Save Structure settings
 680      */
 681     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 682             Boolean.toString(addTempFactor.isSelected()));
 683     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 684             Boolean.toString(addSecondaryStructure.isSelected()));
 685     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 686             Boolean.toString(useRnaView.isSelected()));
 687     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 688             Boolean.toString(structFromPdb.isSelected()));
 689     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 690             structViewer.getSelectedItem().toString());
 691     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 692     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 693             Boolean.toString(siftsMapping.isSelected()));
 694     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 695
 696     /*
 697      * Save Output settings
 698      */
 699     Cache.applicationProperties.setProperty("EPS_RENDERING",
 700             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 701
 702     /*
 703      * Save Connections settings
 704      */
 705     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 706
 707     jalview.util.BrowserLauncher.resetBrowser();
 708
 709     // save user-defined and selected links
 710     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 711     if (menuLinks.isEmpty())
 712     {
 713       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 714     }
 715     else
 716     {
 717       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 718               menuLinks.toString());
 719     }
 720
 721     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 722     if (nonMenuLinks.isEmpty())
 723     {
 724       Cache.applicationProperties.remove("STORED_LINKS");
 725     }
 726     else
 727     {
 728       Cache.applicationProperties.setProperty("STORED_LINKS",
 729               nonMenuLinks.toString());
 730     }
 731
 732     Cache.applicationProperties.setProperty("DEFAULT_URL",
 733             sequenceUrlLinks.getPrimaryUrlId());
 734
 735     Cache.applicationProperties.setProperty("USE_PROXY",
 736             Boolean.toString(useProxy.isSelected()));
 737
 738     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 739
 740     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 741
 742     if (useProxy.isSelected())
 743     {
 744       System.setProperty("http.proxyHost", proxyServerTB.getText());
 745       System.setProperty("http.proxyPort", proxyPortTB.getText());
 746     }
 747     else
 748     {
 749       System.setProperty("http.proxyHost", "");
 750       System.setProperty("http.proxyPort", "");
 751     }
 752     Cache.setProperty("VERSION_CHECK",
 753             Boolean.toString(versioncheck.isSelected()));
 754     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 755     {
 756       // default is false - we only set this if the user has actively agreed
 757       Cache.setProperty("USAGESTATS",
 758               Boolean.toString(usagestats.isSelected()));
 759     }
 760     if (!questionnaire.isSelected())
 761     {
 762       Cache.setProperty("NOQUESTIONNAIRES", "true");
 763     }
 764     else
 765     {
 766       // special - made easy to edit a property file to disable questionnaires
 767       // by just adding the given line
 768       Cache.removeProperty("NOQUESTIONNAIRES");
 769     }
 770
 771     /*
 772      * Save Output settings
 773      */
 774     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 775             Boolean.toString(blcjv.isSelected()));
 776     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 777             Boolean.toString(clustaljv.isSelected()));
 778     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 779             Boolean.toString(fastajv.isSelected()));
 780     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 781             Boolean.toString(msfjv.isSelected()));
 782     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 783             Boolean.toString(pfamjv.isSelected()));
 784     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 785             Boolean.toString(pileupjv.isSelected()));
 786     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 787             Boolean.toString(pirjv.isSelected()));
 788     Cache.applicationProperties.setProperty("PIR_MODELLER",
 789             Boolean.toString(modellerOutput.isSelected()));
 790     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 791             Boolean.toString(embbedBioJSON.isSelected()));
 792     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 793
 794     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 795             Boolean.toString(autoIdWidth.isSelected()));
 796     userIdWidth_actionPerformed();
 797     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 798             userIdWidth.getText());
 799
 800     /*
 801      * Save Editing settings
 802      */
 803     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 804             Boolean.toString(autoCalculateConsCheck.isSelected()));
 805     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 806             Boolean.toString(sortByTree.isSelected()));
 807     Cache.applicationProperties.setProperty("PAD_GAPS",
 808             Boolean.toString(padGaps.isSelected()));
 809
 810     wsPrefs.updateAndRefreshWsMenuConfig(false);
 811
 812     /*
 813      * Save Backups settings
 814      */
 815     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 816             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 817     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 818             Boolean.toString(enableBackupFiles.isSelected()));
 819     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 820             Boolean.toString(backupfilesKeepAll.isSelected()));
 821     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 822             Boolean.toString(suffixReverse.isSelected()));
 823     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 824             suffixTemplate.getText());
 825     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 826             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 827     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 828             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 829     Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
 830             Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
 831
 832     Cache.saveProperties();
 833     Desktop.instance.doConfigureStructurePrefs();
 834     try
 835     {
 836       frame.setClosed(true);
 837     } catch (Exception ex)
 838     {
 839     }
 840   }
 841
 842   /**
 843    * Do any necessary validation before saving settings. Return focus to the
 844    * first tab which fails validation.
 845    *
 846    * @return
 847    */
 848   private boolean validateSettings()
 849   {
 850     if (!validateStructure())
 851     {
 852       structureTab.requestFocusInWindow();
 853       return false;
 854     }
 855     return true;
 856   }
 857
 858   @Override
 859   protected boolean validateStructure()
 860   {
 861     return validateChimeraPath();
 862
 863   }
 864
 865   /**
 866    * DOCUMENT ME!
 867    */
 868   @Override
 869   public void startupFileTextfield_mouseClicked()
 870   {
 871     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 872     JalviewFileChooser chooser = JalviewFileChooser
 873             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 874     chooser.setFileView(new JalviewFileView());
 875     chooser.setDialogTitle(
 876             MessageManager.getString("label.select_startup_file"));
 877
 878     int value = chooser.showOpenDialog(this);
 879
 880     if (value == JalviewFileChooser.APPROVE_OPTION)
 881     {
 882       FileFormatI format = chooser.getSelectedFormat();
 883       if (format != null)
 884       {
 885         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 886                 format.getName());
 887       }
 888       startupFileTextfield
 889               .setText(chooser.getSelectedFile().getAbsolutePath());
 890     }
 891   }
 892
 893   /**
 894    * DOCUMENT ME!
 895    *
 896    * @param e
 897    *          DOCUMENT ME!
 898    */
 899   @Override
 900   public void cancel_actionPerformed(ActionEvent e)
 901   {
 902     try
 903     {
 904       wsPrefs.updateWsMenuConfig(true);
 905       wsPrefs.refreshWs_actionPerformed(e);
 906       frame.setClosed(true);
 907     } catch (Exception ex)
 908     {
 909     }
 910   }
 911
 912   /**
 913    * DOCUMENT ME!
 914    *
 915    * @param e
 916    *          DOCUMENT ME!
 917    */
 918   @Override
 919   public void annotations_actionPerformed(ActionEvent e)
 920   {
 921     conservation.setEnabled(annotations.isSelected());
 922     quality.setEnabled(annotations.isSelected());
 923     identity.setEnabled(annotations.isSelected());
 924     showOccupancy.setEnabled(annotations.isSelected());
 925     showGroupConsensus.setEnabled(annotations.isSelected());
 926     showGroupConservation.setEnabled(annotations.isSelected());
 927     showConsensHistogram.setEnabled(annotations.isSelected()
 928             && (identity.isSelected() || showGroupConsensus.isSelected()));
 929     showConsensLogo.setEnabled(annotations.isSelected()
 930             && (identity.isSelected() || showGroupConsensus.isSelected()));
 931   }
 932
 933   @Override
 934   public void newLink_actionPerformed(ActionEvent e)
 935   {
 936     GSequenceLink link = new GSequenceLink();
 937     boolean valid = false;
 938     while (!valid)
 939     {
 940       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 941               MessageManager.getString("label.new_sequence_url_link"),
 942               JvOptionPane.OK_CANCEL_OPTION, -1,
 943               null) == JvOptionPane.OK_OPTION)
 944       {
 945         if (link.checkValid())
 946         {
 947           if (((UrlLinkTableModel) linkUrlTable.getModel())
 948                   .isUniqueName(link.getName()))
 949           {
 950             ((UrlLinkTableModel) linkUrlTable.getModel())
 951                     .insertRow(link.getName(), link.getURL());
 952             valid = true;
 953           }
 954           else
 955           {
 956             link.notifyDuplicate();
 957             continue;
 958           }
 959         }
 960       }
 961       else
 962       {
 963         break;
 964       }
 965     }
 966   }
 967
 968   @Override
 969   public void editLink_actionPerformed(ActionEvent e)
 970   {
 971     GSequenceLink link = new GSequenceLink();
 972
 973     int index = linkUrlTable.getSelectedRow();
 974     if (index == -1)
 975     {
 976       // button no longer enabled if row is not selected
 977       Cache.log.debug("Edit with no row selected in linkUrlTable");
 978       return;
 979     }
 980
 981     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 982             .getNameColumn();
 983     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 984             .getUrlColumn();
 985     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 986     link.setName(oldName);
 987     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 988
 989     boolean valid = false;
 990     while (!valid)
 991     {
 992       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 993               MessageManager.getString("label.edit_sequence_url_link"),
 994               JvOptionPane.OK_CANCEL_OPTION, -1,
 995               null) == JvOptionPane.OK_OPTION)
 996       {
 997         if (link.checkValid())
 998         {
 999           if ((oldName.equals(link.getName()))
1000                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1001                           .isUniqueName(link.getName())))
1002           {
1003             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1004             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1005             valid = true;
1006           }
1007           else
1008           {
1009             link.notifyDuplicate();
1010             continue;
1011           }
1012         }
1013       }
1014       else
1015       {
1016         break;
1017       }
1018     }
1019   }
1020
1021   @Override
1022   public void deleteLink_actionPerformed(ActionEvent e)
1023   {
1024     int index = linkUrlTable.getSelectedRow();
1025     int modelIndex = -1;
1026     if (index == -1)
1027     {
1028       // button no longer enabled if row is not selected
1029       Cache.log.debug("Delete with no row selected in linkUrlTable");
1030       return;
1031     }
1032     else
1033     {
1034       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1035     }
1036
1037     // make sure we use the model index to delete, and not the table index
1038     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1039   }
1040
1041   @Override
1042   public void defaultBrowser_mouseClicked(MouseEvent e)
1043   {
1044     JFileChooser chooser = new JFileChooser(".");
1045     chooser.setDialogTitle(
1046             MessageManager.getString("label.select_default_browser"));
1047
1048     int value = chooser.showOpenDialog(this);
1049
1050     if (value == JFileChooser.APPROVE_OPTION)
1051     {
1052       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1053     }
1054
1055   }
1056
1057   /*
1058    * (non-Javadoc)
1059    *
1060    * @see
1061    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1062    * .ActionEvent)
1063    */
1064   @Override
1065   protected void showunconserved_actionPerformed(ActionEvent e)
1066   {
1067     // TODO Auto-generated method stub
1068     super.showunconserved_actionPerformed(e);
1069   }
1070
1071   public static List<String> getGroupURLLinks()
1072   {
1073     return groupURLLinks;
1074   }
1075
1076   @Override
1077   public void minColour_actionPerformed(JPanel panel)
1078   {
1079     Color col = JColorChooser.showDialog(this,
1080             MessageManager.getString("label.select_colour_minimum_value"),
1081             minColour.getBackground());
1082     if (col != null)
1083     {
1084       panel.setBackground(col);
1085     }
1086     panel.repaint();
1087   }
1088
1089   @Override
1090   public void maxColour_actionPerformed(JPanel panel)
1091   {
1092     Color col = JColorChooser.showDialog(this,
1093             MessageManager.getString("label.select_colour_maximum_value"),
1094             maxColour.getBackground());
1095     if (col != null)
1096     {
1097       panel.setBackground(col);
1098     }
1099     panel.repaint();
1100   }
1101
1102   @Override
1103   public void gapColour_actionPerformed(JPanel gap)
1104   {
1105     if (!useLegacyGap.isSelected())
1106     {
1107       Color col = JColorChooser.showDialog(this,
1108               MessageManager.getString("label.select_gap_colour"),
1109               gapColour.getBackground());
1110       if (col != null)
1111       {
1112         gap.setBackground(col);
1113       }
1114       gap.repaint();
1115     }
1116   }
1117
1118   @Override
1119   public void hiddenColour_actionPerformed(JPanel hidden)
1120   {
1121     Color col = JColorChooser.showDialog(this,
1122             MessageManager.getString("label.select_hidden_colour"),
1123             hiddenColour.getBackground());
1124     if (col != null)
1125     {
1126       hidden.setBackground(col);
1127     }
1128     hidden.repaint();
1129   }
1130
1131   @Override
1132   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1133   {
1134     boolean enabled = useLegacyGap.isSelected();
1135     if (enabled)
1136     {
1137       gapColour.setBackground(
1138               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1139     }
1140     else
1141     {
1142       gapColour.setBackground(
1143               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1144     }
1145     gapColour.setEnabled(!enabled);
1146     gapLabel.setEnabled(!enabled);
1147   }
1148
1149   @Override
1150   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1151   {
1152     useLegacyGap.setSelected(false);
1153     useLegacyGaps_actionPerformed(null);
1154     showHiddenAtStart.setSelected(false);
1155     hiddenColour.setBackground(
1156             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1157   }
1158
1159   @Override
1160   protected void userIdWidth_actionPerformed()
1161   {
1162     try
1163     {
1164       String val = userIdWidth.getText().trim();
1165       if (val.length() > 0)
1166       {
1167         Integer iw = Integer.parseInt(val);
1168         if (iw.intValue() < 12)
1169         {
1170           throw new NumberFormatException();
1171         }
1172         userIdWidth.setText(iw.toString());
1173       }
1174     } catch (NumberFormatException x)
1175     {
1176       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1177               MessageManager
1178                       .getString("warn.user_defined_width_requirements"),
1179               MessageManager.getString("label.invalid_id_column_width"),
1180               JvOptionPane.WARNING_MESSAGE);
1181       userIdWidth.setText("");
1182     }
1183   }
1184
1185   @Override
1186   protected void autoIdWidth_actionPerformed()
1187   {
1188     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1189     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1190   }
1191
1192   /**
1193    * Returns true if chimera path is to a valid executable, else show an error
1194    * dialog.
1195    */
1196   private boolean validateChimeraPath()
1197   {
1198     if (chimeraPath.getText().trim().length() > 0)
1199     {
1200       File f = new File(chimeraPath.getText());
1201       if (!f.canExecute())
1202       {
1203         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1204                 MessageManager.getString("label.invalid_chimera_path"),
1205                 MessageManager.getString("label.invalid_name"),
1206                 JvOptionPane.ERROR_MESSAGE);
1207         return false;
1208       }
1209     }
1210     return true;
1211   }
1212
1213   /**
1214    * If Chimera is selected, check it can be found on default or user-specified
1215    * path, if not show a warning/help dialog.
1216    */
1217   @Override
1218   protected void structureViewer_actionPerformed(String selectedItem)
1219   {
1220     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1221     {
1222       return;
1223     }
1224     boolean found = false;
1225
1226     /*
1227      * Try user-specified and standard paths for Chimera executable.
1228      */
1229     List<String> paths = StructureManager.getChimeraPaths();
1230     paths.add(0, chimeraPath.getText());
1231     for (String path : paths)
1232     {
1233       if (new File(path.trim()).canExecute())
1234       {
1235         found = true;
1236         break;
1237       }
1238     }
1239     if (!found)
1240     {
1241       String[] options = { "OK", "Help" };
1242       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1243               JvSwingUtils.wrapTooltip(true,
1244                       MessageManager.getString("label.chimera_missing")),
1245               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1246               null, options, options[0]);
1247       if (showHelp == JvOptionPane.NO_OPTION)
1248       {
1249         try
1250         {
1251           Help.showHelpWindow(HelpId.StructureViewer);
1252         } catch (HelpSetException e)
1253         {
1254           e.printStackTrace();
1255         }
1256       }
1257     }
1258   }
1259
1260   public class OptionsParam
1261   {
1262     private String name;
1263
1264     private String code;
1265
1266     public OptionsParam(String name, String code)
1267     {
1268       this.name = name;
1269       this.code = code;
1270     }
1271
1272     public String getName()
1273     {
1274       return name;
1275     }
1276
1277     public void setName(String name)
1278     {
1279       this.name = name;
1280     }
1281
1282     public String getCode()
1283     {
1284       return code;
1285     }
1286
1287     public void setCode(String code)
1288     {
1289       this.code = code;
1290     }
1291
1292     @Override
1293     public String toString()
1294     {
1295       return name;
1296     }
1297
1298     @Override
1299     public boolean equals(Object that)
1300     {
1301       if (!(that instanceof OptionsParam))
1302       {
1303         return false;
1304       }
1305       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1306     }
1307
1308     @Override
1309     public int hashCode()
1310     {
1311       return name.hashCode() + code.hashCode();
1312     }
1313   }
1314
1315   private class UrlListSelectionHandler implements ListSelectionListener
1316   {
1317
1318     @Override
1319     public void valueChanged(ListSelectionEvent e)
1320     {
1321       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1322
1323       int index = lsm.getMinSelectionIndex();
1324       if (index == -1)
1325       {
1326         // no selection, so disable delete/edit buttons
1327         editLink.setEnabled(false);
1328         deleteLink.setEnabled(false);
1329         return;
1330       }
1331       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1332
1333       // enable/disable edit and delete link buttons
1334       if (((UrlLinkTableModel) linkUrlTable.getModel())
1335               .isRowDeletable(modelIndex))
1336       {
1337         deleteLink.setEnabled(true);
1338       }
1339       else
1340       {
1341         deleteLink.setEnabled(false);
1342       }
1343
1344       if (((UrlLinkTableModel) linkUrlTable.getModel())
1345               .isRowEditable(modelIndex))
1346       {
1347         editLink.setEnabled(true);
1348       }
1349       else
1350       {
1351         editLink.setEnabled(false);
1352       }
1353     }
1354   }
1355 }