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.ws.sifts.SiftsSettings;
  44
  45 import java.awt.BorderLayout;
  46 import java.awt.Color;
  47 import java.awt.Component;
  48 import java.awt.Dimension;
  49 import java.awt.Font;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.MouseEvent;
  53 import java.io.File;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56
  57 import javax.help.HelpSetException;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.RowFilter;
  64 import javax.swing.RowSorter;
  65 import javax.swing.SortOrder;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70 import javax.swing.table.TableCellRenderer;
  71 import javax.swing.table.TableColumn;
  72 import javax.swing.table.TableModel;
  73 import javax.swing.table.TableRowSorter;
  74
  75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence ID must be
 127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 128    */
 129   public static UrlProviderI sequenceUrlLinks;
 130
 131   public static UrlLinkTableModel dataModel;
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence IDS and Sequences
 135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 137    * for first and second token specified after a pipe character at end |,|.
 138    * (TODO: proper escape for using | to separate ids or sequences
 139    */
 140
 141   public static List<String> groupURLLinks;
 142   static
 143   {
 144     // get links selected to be in the menu (SEQUENCE_LINKS)
 145     // and links entered by the user but not selected (STORED_LINKS)
 146     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 147     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 148     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 149             UrlConstants.DEFAULT_LABEL);
 150
 151     // if both links lists are empty, add the DEFAULT_URL link
 152     // otherwise we assume the default link is in one of the lists
 153     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 154     {
 155       inMenuString = UrlConstants.DEFAULT_STRING;
 156     }
 157     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 158             inMenuString, notInMenuString);
 159     sequenceUrlLinks = factory.createUrlProvider();
 160     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 161
 162     /**
 163      * TODO: reformulate groupURL encoding so two or more can be stored in the
 164      * .properties file as '|' separated strings
 165      */
 166
 167     groupURLLinks = new ArrayList<>();
 168   }
 169
 170   JInternalFrame frame;
 171
 172   private WsPreferences wsPrefs;
 173
 174   private OptionsParam promptEachTimeOpt = new OptionsParam(
 175           MessageManager.getString("label.prompt_each_time"),
 176           "Prompt each time");
 177
 178   private OptionsParam lineArtOpt = new OptionsParam(
 179           MessageManager.getString("label.lineart"), "Lineart");
 180
 181   private OptionsParam textOpt = new OptionsParam(
 182           MessageManager.getString("action.text"), "Text");
 183
 184   /**
 185    * Creates a new Preferences object.
 186    */
 187   public Preferences()
 188   {
 189     super();
 190     frame = new JInternalFrame();
 191     frame.setContentPane(this);
 192     wsPrefs = new WsPreferences();
 193     wsTab.add(wsPrefs, BorderLayout.CENTER);
 194     int width = 500, height = 450;
 195     new jalview.util.Platform();
 196     if (Platform.isAMac())
 197     {
 198       width = 570;
 199       height = 480;
 200     }
 201
 202     Desktop.addInternalFrame(frame,
 203             MessageManager.getString("label.preferences"), width, height);
 204     frame.setMinimumSize(new Dimension(width, height));
 205
 206     /*
 207      * Set Visual tab defaults
 208      */
 209     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 210     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 211     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 212     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 213
 214     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 215     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 216     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 217     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 218     showUnconserved
 219             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 220     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 221     showGroupConsensus
 222             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 223     showGroupConservation.setSelected(
 224             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 225     showConsensHistogram.setSelected(
 226             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 227     showConsensLogo
 228             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 229     showNpTooltip
 230             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 231     showDbRefTooltip
 232             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 233
 234     String[] fonts = java.awt.GraphicsEnvironment
 235             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 236     for (int i = 0; i < fonts.length; i++)
 237     {
 238       fontNameCB.addItem(fonts[i]);
 239     }
 240
 241     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 242     {
 243       fontSizeCB.addItem(i + "");
 244     }
 245
 246     fontStyleCB.addItem("plain");
 247     fontStyleCB.addItem("bold");
 248     fontStyleCB.addItem("italic");
 249
 250     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 251     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 252     fontStyleCB.setSelectedItem(
 253             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 254
 255     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 256     scaleProteinToCdna
 257             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 258
 259     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 260
 261     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 262
 263     gapSymbolCB.addItem("-");
 264     gapSymbolCB.addItem(".");
 265
 266     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 267
 268     sortby.addItem("No sort");
 269     sortby.addItem("Id");
 270     sortby.addItem("Pairwise Identity");
 271     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 272
 273     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 278     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 279             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 280                     SequenceAnnotationOrder.NONE.name()));
 281     sortAnnBy.setSelectedItem(savedSort.toString());
 282
 283     sortAutocalc.addItem("Autocalculated first");
 284     sortAutocalc.addItem("Autocalculated last");
 285     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 286     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 287             : sortAutocalc.getItemAt(1));
 288     startupCheckbox
 289             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 290     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 291             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 292                     + "/examples/exampleFile_2_3.jar"));
 293
 294     /*
 295      * Set Colours tab defaults
 296      */
 297     protColour.addItem(ResidueColourScheme.NONE);
 298     nucColour.addItem(ResidueColourScheme.NONE);
 299     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 300     {
 301       String name = cs.getSchemeName();
 302       protColour.addItem(name);
 303       nucColour.addItem(name);
 304     }
 305     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 306             ResidueColourScheme.NONE);
 307     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 308     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 309     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 310     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     minColour.setBackground(
 312             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 313     maxColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 315
 316     /*
 317      * Set overview panel defaults
 318      */
 319     gapColour.setBackground(
 320             Cache.getDefaultColour(GAP_COLOUR,
 321                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 322     hiddenColour.setBackground(
 323             Cache.getDefaultColour(HIDDEN_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 325     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 326     gapLabel.setEnabled(!useLegacyGap.isSelected());
 327     gapColour.setEnabled(!useLegacyGap.isSelected());
 328     showHiddenAtStart
 329             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 330
 331     /*
 332      * Set Structure tab defaults.
 333      */
 334     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 335     structFromPdb.setSelected(structSelected);
 336     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 337     useRnaView.setEnabled(structSelected);
 338     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 339     addSecondaryStructure.setEnabled(structSelected);
 340     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 341     addTempFactor.setEnabled(structSelected);
 342     structViewer.setSelectedItem(
 343             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 344     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 345     chimeraPath.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         validateChimeraPath();
 351       }
 352     });
 353
 354     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 355     {
 356       siftsMapping.setSelected(true);
 357     }
 358     else
 359     {
 360       nwMapping.setSelected(true);
 361     }
 362
 363     SiftsSettings
 364             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 365
 366     /*
 367      * Set Connections tab defaults
 368      */
 369
 370     // set up sorting
 371     linkUrlTable.setModel(dataModel);
 372     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 373             linkUrlTable.getModel());
 374     linkUrlTable.setRowSorter(sorter);
 375     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 376
 377     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 378     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(
 383             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 384
 385     sorter.setSortKeys(sortKeys);
 386     sorter.sort();
 387
 388     // set up filtering
 389     ActionListener onReset;
 390     onReset = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         filterTB.setText("");
 396         sorter.setRowFilter(RowFilter.regexFilter(""));
 397       }
 398
 399     };
 400     doReset.addActionListener(onReset);
 401
 402     // filter to display only custom urls
 403     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 404     {
 405       @Override
 406       public boolean include(
 407               Entry<? extends TableModel, ? extends Object> entry)
 408       {
 409         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 410       }
 411     };
 412
 413     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 414             linkUrlTable.getModel());
 415     customSorter.setRowFilter(customUrlFilter);
 416
 417     ActionListener onCustomOnly;
 418     onCustomOnly = new ActionListener()
 419     {
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         filterTB.setText("");
 424         sorter.setRowFilter(customUrlFilter);
 425       }
 426     };
 427     userOnly.addActionListener(onCustomOnly);
 428
 429     filterTB.getDocument().addDocumentListener(new DocumentListener()
 430     {
 431       String caseInsensitiveFlag = "(?i)";
 432
 433       @Override
 434       public void changedUpdate(DocumentEvent e)
 435       {
 436         sorter.setRowFilter(RowFilter
 437                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 438       }
 439
 440       @Override
 441       public void removeUpdate(DocumentEvent e)
 442       {
 443         sorter.setRowFilter(RowFilter
 444                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 445       }
 446
 447       @Override
 448       public void insertUpdate(DocumentEvent e)
 449       {
 450         sorter.setRowFilter(RowFilter
 451                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 452       }
 453     });
 454
 455     // set up list selection functionality
 456     linkUrlTable.getSelectionModel()
 457             .addListSelectionListener(new UrlListSelectionHandler());
 458
 459     // set up radio buttons
 460     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 461             .getPrimaryColumn();
 462     String onClickName = linkUrlTable.getColumnName(onClickCol);
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellRenderer(new RadioButtonRenderer());
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellEditor(new RadioButtonEditor());
 467
 468     // get boolean columns and resize those to min possible
 469     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 470     {
 471       if (linkUrlTable.getModel().getColumnClass(column)
 472               .equals(Boolean.class))
 473       {
 474         TableColumn tableColumn = linkUrlTable.getColumnModel()
 475                 .getColumn(column);
 476         int preferredWidth = tableColumn.getMinWidth();
 477
 478         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 479                 column);
 480         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 481         int cwidth = c.getPreferredSize().width
 482                 + linkUrlTable.getIntercellSpacing().width;
 483         preferredWidth = Math.max(preferredWidth, cwidth);
 484
 485         tableColumn.setPreferredWidth(preferredWidth);
 486       }
 487     }
 488
 489     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 490     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 491     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 492     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 493
 494     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 495
 496     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 497     // note antisense here: default is true
 498     questionnaire
 499             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 500     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 501
 502     /*
 503      * Set Output tab defaults
 504      */
 505     epsRendering.addItem(promptEachTimeOpt);
 506     epsRendering.addItem(lineArtOpt);
 507     epsRendering.addItem(textOpt);
 508     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 509             "Prompt each time");
 510     if (defaultEPS.equalsIgnoreCase("Text"))
 511     {
 512       epsRendering.setSelectedItem(textOpt);
 513     }
 514     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 515     {
 516       epsRendering.setSelectedItem(lineArtOpt);
 517     }
 518     else
 519     {
 520       epsRendering.setSelectedItem(promptEachTimeOpt);
 521     }
 522     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 523     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 524     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 525     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 526     userIdWidth.setText(wi == null ? "" : wi.toString());
 527     // TODO: refactor to use common enum via FormatAdapter and allow extension
 528     // for new flat file formats
 529     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 530     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 531     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 532     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 533     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 534     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 535     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 536     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 537     embbedBioJSON
 538             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 539
 540     /*
 541      * Set Editing tab defaults
 542      */
 543     autoCalculateConsCheck
 544             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 545     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 546     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 547
 548     annotations_actionPerformed(null); // update the display of the annotation
 549                                        // settings
 550
 551
 552     /*
 553      * Set Backups tab defaults
 554      */
 555     enableBackupFiles
 556             .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
 557     suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX, "-v"+BackupFiles.getNumPlaceHolder()));
 558     suffixDigitsSpinner.setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
 559     suffixReverse.setSelected(
 560             Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
 561     backupfilesKeepAll
 562             .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
 563     backupfilesRollMaxSpinner
 564             .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4));
 565     backupfilesConfirmDelete.setSelected(
 566             Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
 567     backupsOptionsSetEnabled(enableBackupFiles.isSelected());
 568     /*
 569     suffixPanel.setPreferredSize(
 570             new Dimension(width, suffixPanel.getHeight()));
 571     keepfilesPanel.setPreferredSize(
 572             new Dimension(width, keepfilesPanel.getHeight()));
 573     exampleFilesPanel.setPreferredSize(
 574             new Dimension(width, exampleFilesPanel.getHeight()));
 575             */
 576
 577   }
 578
 579   /**
 580    * Save user selections on the Preferences tabs to the Cache and write out to
 581    * file.
 582    *
 583    * @param e
 584    */
 585   @Override
 586   public void ok_actionPerformed(ActionEvent e)
 587   {
 588     if (!validateSettings())
 589     {
 590       return;
 591     }
 592
 593     /*
 594      * Save Visual settings
 595      */
 596     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 597             Boolean.toString(seqLimit.isSelected()));
 598     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 599             Boolean.toString(rightAlign.isSelected()));
 600     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 601             Boolean.toString(fullScreen.isSelected()));
 602     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 603             Boolean.toString(openoverv.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 605             Boolean.toString(annotations.isSelected()));
 606     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 607             Boolean.toString(conservation.isSelected()));
 608     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 609             Boolean.toString(quality.isSelected()));
 610     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 611             Boolean.toString(identity.isSelected()));
 612
 613     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 614             gapSymbolCB.getSelectedItem().toString());
 615
 616     Cache.applicationProperties.setProperty("FONT_NAME",
 617             fontNameCB.getSelectedItem().toString());
 618     Cache.applicationProperties.setProperty("FONT_STYLE",
 619             fontStyleCB.getSelectedItem().toString());
 620     Cache.applicationProperties.setProperty("FONT_SIZE",
 621             fontSizeCB.getSelectedItem().toString());
 622
 623     Cache.applicationProperties.setProperty("ID_ITALICS",
 624             Boolean.toString(idItalics.isSelected()));
 625     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 626             Boolean.toString(showUnconserved.isSelected()));
 627     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 628             Boolean.toString(showOccupancy.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 630             Boolean.toString(showGroupConsensus.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 632             Boolean.toString(showGroupConservation.isSelected()));
 633     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 634             Boolean.toString(showConsensHistogram.isSelected()));
 635     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 636             Boolean.toString(showConsensLogo.isSelected()));
 637     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 638             Boolean.toString(smoothFont.isSelected()));
 639     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 640             Boolean.toString(scaleProteinToCdna.isSelected()));
 641     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 642             Boolean.toString(showNpTooltip.isSelected()));
 643     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 644             Boolean.toString(showDbRefTooltip.isSelected()));
 645
 646     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 647             Boolean.toString(wrap.isSelected()));
 648
 649     Cache.applicationProperties.setProperty("STARTUP_FILE",
 650             startupFileTextfield.getText());
 651     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 652             Boolean.toString(startupCheckbox.isSelected()));
 653
 654     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 655             sortby.getSelectedItem().toString());
 656
 657     // convert description of sort order to enum name for save
 658     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 659             .forDescription(sortAnnBy.getSelectedItem().toString());
 660     if (annSortOrder != null)
 661     {
 662       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 663               annSortOrder.name());
 664     }
 665
 666     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 667     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 668             Boolean.valueOf(showAutocalcFirst).toString());
 669
 670     /*
 671      * Save Colours settings
 672      */
 673     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 674             protColour.getSelectedItem().toString());
 675     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 676             nucColour.getSelectedItem().toString());
 677     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 678             minColour.getBackground());
 679     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 680             maxColour.getBackground());
 681
 682     /*
 683      * Save Overview settings
 684      */
 685     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 686     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 687     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 688             Boolean.toString(useLegacyGap.isSelected()));
 689     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 690             Boolean.toString(showHiddenAtStart.isSelected()));
 691
 692     /*
 693      * Save Structure settings
 694      */
 695     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 696             Boolean.toString(addTempFactor.isSelected()));
 697     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 698             Boolean.toString(addSecondaryStructure.isSelected()));
 699     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 700             Boolean.toString(useRnaView.isSelected()));
 701     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 702             Boolean.toString(structFromPdb.isSelected()));
 703     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 704             structViewer.getSelectedItem().toString());
 705     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 706     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 707             Boolean.toString(siftsMapping.isSelected()));
 708     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 709
 710     /*
 711      * Save Output settings
 712      */
 713     Cache.applicationProperties.setProperty("EPS_RENDERING",
 714             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 715
 716     /*
 717      * Save Connections settings
 718      */
 719     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 720
 721     jalview.util.BrowserLauncher.resetBrowser();
 722
 723     // save user-defined and selected links
 724     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 725     if (menuLinks.isEmpty())
 726     {
 727       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 728     }
 729     else
 730     {
 731       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 732               menuLinks.toString());
 733     }
 734
 735     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 736     if (nonMenuLinks.isEmpty())
 737     {
 738       Cache.applicationProperties.remove("STORED_LINKS");
 739     }
 740     else
 741     {
 742       Cache.applicationProperties.setProperty("STORED_LINKS",
 743               nonMenuLinks.toString());
 744     }
 745
 746     Cache.applicationProperties.setProperty("DEFAULT_URL",
 747             sequenceUrlLinks.getPrimaryUrlId());
 748
 749     Cache.applicationProperties.setProperty("USE_PROXY",
 750             Boolean.toString(useProxy.isSelected()));
 751
 752     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 753
 754     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 755
 756     if (useProxy.isSelected())
 757     {
 758       System.setProperty("http.proxyHost", proxyServerTB.getText());
 759       System.setProperty("http.proxyPort", proxyPortTB.getText());
 760     }
 761     else
 762     {
 763       System.setProperty("http.proxyHost", "");
 764       System.setProperty("http.proxyPort", "");
 765     }
 766     Cache.setProperty("VERSION_CHECK",
 767             Boolean.toString(versioncheck.isSelected()));
 768     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 769     {
 770       // default is false - we only set this if the user has actively agreed
 771       Cache.setProperty("USAGESTATS",
 772               Boolean.toString(usagestats.isSelected()));
 773     }
 774     if (!questionnaire.isSelected())
 775     {
 776       Cache.setProperty("NOQUESTIONNAIRES", "true");
 777     }
 778     else
 779     {
 780       // special - made easy to edit a property file to disable questionnaires
 781       // by just adding the given line
 782       Cache.removeProperty("NOQUESTIONNAIRES");
 783     }
 784
 785     /*
 786      * Save Output settings
 787      */
 788     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 789             Boolean.toString(blcjv.isSelected()));
 790     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 791             Boolean.toString(clustaljv.isSelected()));
 792     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 793             Boolean.toString(fastajv.isSelected()));
 794     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 795             Boolean.toString(msfjv.isSelected()));
 796     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 797             Boolean.toString(pfamjv.isSelected()));
 798     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 799             Boolean.toString(pileupjv.isSelected()));
 800     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 801             Boolean.toString(pirjv.isSelected()));
 802     Cache.applicationProperties.setProperty("PIR_MODELLER",
 803             Boolean.toString(modellerOutput.isSelected()));
 804     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 805             Boolean.toString(embbedBioJSON.isSelected()));
 806     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 807
 808     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 809             Boolean.toString(autoIdWidth.isSelected()));
 810     userIdWidth_actionPerformed();
 811     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 812             userIdWidth.getText());
 813
 814     /*
 815      * Save Editing settings
 816      */
 817     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 818             Boolean.toString(autoCalculateConsCheck.isSelected()));
 819     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 820             Boolean.toString(sortByTree.isSelected()));
 821     Cache.applicationProperties.setProperty("PAD_GAPS",
 822             Boolean.toString(padGaps.isSelected()));
 823
 824     wsPrefs.updateAndRefreshWsMenuConfig(false);
 825
 826     /*
 827      * Save Backups settings
 828      */
 829     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 830             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 831     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 832             Boolean.toString(enableBackupFiles.isSelected()));
 833     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 834             Boolean.toString(backupfilesKeepAll.isSelected()));
 835     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 836             Boolean.toString(suffixReverse.isSelected()));
 837     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 838             suffixTemplate.getText());
 839     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 840             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 841     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 842             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 843
 844     Cache.saveProperties();
 845     Desktop.instance.doConfigureStructurePrefs();
 846     try
 847     {
 848       frame.setClosed(true);
 849     } catch (Exception ex)
 850     {
 851     }
 852   }
 853
 854   /**
 855    * Do any necessary validation before saving settings. Return focus to the
 856    * first tab which fails validation.
 857    *
 858    * @return
 859    */
 860   private boolean validateSettings()
 861   {
 862     if (!validateStructure())
 863     {
 864       structureTab.requestFocusInWindow();
 865       return false;
 866     }
 867     return true;
 868   }
 869
 870   @Override
 871   protected boolean validateStructure()
 872   {
 873     return validateChimeraPath();
 874
 875   }
 876
 877   /**
 878    * DOCUMENT ME!
 879    */
 880   @Override
 881   public void startupFileTextfield_mouseClicked()
 882   {
 883     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 884     JalviewFileChooser chooser = JalviewFileChooser
 885             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 886     chooser.setFileView(new JalviewFileView());
 887     chooser.setDialogTitle(
 888             MessageManager.getString("label.select_startup_file"));
 889
 890     int value = chooser.showOpenDialog(this);
 891
 892     if (value == JalviewFileChooser.APPROVE_OPTION)
 893     {
 894       FileFormatI format = chooser.getSelectedFormat();
 895       if (format != null)
 896       {
 897         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 898                 format.getName());
 899       }
 900       startupFileTextfield
 901               .setText(chooser.getSelectedFile().getAbsolutePath());
 902     }
 903   }
 904
 905   /**
 906    * DOCUMENT ME!
 907    *
 908    * @param e
 909    *          DOCUMENT ME!
 910    */
 911   @Override
 912   public void cancel_actionPerformed(ActionEvent e)
 913   {
 914     try
 915     {
 916       wsPrefs.updateWsMenuConfig(true);
 917       wsPrefs.refreshWs_actionPerformed(e);
 918       frame.setClosed(true);
 919     } catch (Exception ex)
 920     {
 921     }
 922   }
 923
 924   /**
 925    * DOCUMENT ME!
 926    *
 927    * @param e
 928    *          DOCUMENT ME!
 929    */
 930   @Override
 931   public void annotations_actionPerformed(ActionEvent e)
 932   {
 933     conservation.setEnabled(annotations.isSelected());
 934     quality.setEnabled(annotations.isSelected());
 935     identity.setEnabled(annotations.isSelected());
 936     showOccupancy.setEnabled(annotations.isSelected());
 937     showGroupConsensus.setEnabled(annotations.isSelected());
 938     showGroupConservation.setEnabled(annotations.isSelected());
 939     showConsensHistogram.setEnabled(annotations.isSelected()
 940             && (identity.isSelected() || showGroupConsensus.isSelected()));
 941     showConsensLogo.setEnabled(annotations.isSelected()
 942             && (identity.isSelected() || showGroupConsensus.isSelected()));
 943   }
 944
 945   @Override
 946   public void newLink_actionPerformed(ActionEvent e)
 947   {
 948     GSequenceLink link = new GSequenceLink();
 949     boolean valid = false;
 950     while (!valid)
 951     {
 952       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 953               MessageManager.getString("label.new_sequence_url_link"),
 954               JvOptionPane.OK_CANCEL_OPTION, -1,
 955               null) == JvOptionPane.OK_OPTION)
 956       {
 957         if (link.checkValid())
 958         {
 959           if (((UrlLinkTableModel) linkUrlTable.getModel())
 960                   .isUniqueName(link.getName()))
 961           {
 962             ((UrlLinkTableModel) linkUrlTable.getModel())
 963                     .insertRow(link.getName(), link.getURL());
 964             valid = true;
 965           }
 966           else
 967           {
 968             link.notifyDuplicate();
 969             continue;
 970           }
 971         }
 972       }
 973       else
 974       {
 975         break;
 976       }
 977     }
 978   }
 979
 980   @Override
 981   public void editLink_actionPerformed(ActionEvent e)
 982   {
 983     GSequenceLink link = new GSequenceLink();
 984
 985     int index = linkUrlTable.getSelectedRow();
 986     if (index == -1)
 987     {
 988       // button no longer enabled if row is not selected
 989       Cache.log.debug("Edit with no row selected in linkUrlTable");
 990       return;
 991     }
 992
 993     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 994             .getNameColumn();
 995     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 996             .getUrlColumn();
 997     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 998     link.setName(oldName);
 999     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1000
1001     boolean valid = false;
1002     while (!valid)
1003     {
1004       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1005               MessageManager.getString("label.edit_sequence_url_link"),
1006               JvOptionPane.OK_CANCEL_OPTION, -1,
1007               null) == JvOptionPane.OK_OPTION)
1008       {
1009         if (link.checkValid())
1010         {
1011           if ((oldName.equals(link.getName()))
1012                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1013                           .isUniqueName(link.getName())))
1014           {
1015             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1016             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1017             valid = true;
1018           }
1019           else
1020           {
1021             link.notifyDuplicate();
1022             continue;
1023           }
1024         }
1025       }
1026       else
1027       {
1028         break;
1029       }
1030     }
1031   }
1032
1033   @Override
1034   public void deleteLink_actionPerformed(ActionEvent e)
1035   {
1036     int index = linkUrlTable.getSelectedRow();
1037     int modelIndex = -1;
1038     if (index == -1)
1039     {
1040       // button no longer enabled if row is not selected
1041       Cache.log.debug("Delete with no row selected in linkUrlTable");
1042       return;
1043     }
1044     else
1045     {
1046       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1047     }
1048
1049     // make sure we use the model index to delete, and not the table index
1050     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1051   }
1052
1053   @Override
1054   public void defaultBrowser_mouseClicked(MouseEvent e)
1055   {
1056     JFileChooser chooser = new JFileChooser(".");
1057     chooser.setDialogTitle(
1058             MessageManager.getString("label.select_default_browser"));
1059
1060     int value = chooser.showOpenDialog(this);
1061
1062     if (value == JFileChooser.APPROVE_OPTION)
1063     {
1064       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1065     }
1066
1067   }
1068
1069   /*
1070    * (non-Javadoc)
1071    *
1072    * @see
1073    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1074    * .ActionEvent)
1075    */
1076   @Override
1077   protected void showunconserved_actionPerformed(ActionEvent e)
1078   {
1079     // TODO Auto-generated method stub
1080     super.showunconserved_actionPerformed(e);
1081   }
1082
1083   public static List<String> getGroupURLLinks()
1084   {
1085     return groupURLLinks;
1086   }
1087
1088   @Override
1089   public void minColour_actionPerformed(JPanel panel)
1090   {
1091     Color col = JColorChooser.showDialog(this,
1092             MessageManager.getString("label.select_colour_minimum_value"),
1093             minColour.getBackground());
1094     if (col != null)
1095     {
1096       panel.setBackground(col);
1097     }
1098     panel.repaint();
1099   }
1100
1101   @Override
1102   public void maxColour_actionPerformed(JPanel panel)
1103   {
1104     Color col = JColorChooser.showDialog(this,
1105             MessageManager.getString("label.select_colour_maximum_value"),
1106             maxColour.getBackground());
1107     if (col != null)
1108     {
1109       panel.setBackground(col);
1110     }
1111     panel.repaint();
1112   }
1113
1114   @Override
1115   public void gapColour_actionPerformed(JPanel gap)
1116   {
1117     if (!useLegacyGap.isSelected())
1118     {
1119       Color col = JColorChooser.showDialog(this,
1120               MessageManager.getString("label.select_gap_colour"),
1121               gapColour.getBackground());
1122       if (col != null)
1123       {
1124         gap.setBackground(col);
1125       }
1126       gap.repaint();
1127     }
1128   }
1129
1130   @Override
1131   public void hiddenColour_actionPerformed(JPanel hidden)
1132   {
1133     Color col = JColorChooser.showDialog(this,
1134             MessageManager.getString("label.select_hidden_colour"),
1135             hiddenColour.getBackground());
1136     if (col != null)
1137     {
1138       hidden.setBackground(col);
1139     }
1140     hidden.repaint();
1141   }
1142
1143   @Override
1144   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1145   {
1146     boolean enabled = useLegacyGap.isSelected();
1147     if (enabled)
1148     {
1149       gapColour.setBackground(
1150               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1151     }
1152     else
1153     {
1154       gapColour.setBackground(
1155               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1156     }
1157     gapColour.setEnabled(!enabled);
1158     gapLabel.setEnabled(!enabled);
1159   }
1160
1161   @Override
1162   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1163   {
1164     useLegacyGap.setSelected(false);
1165     useLegacyGaps_actionPerformed(null);
1166     showHiddenAtStart.setSelected(true);
1167     hiddenColour.setBackground(
1168             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1169   }
1170
1171   @Override
1172   protected void userIdWidth_actionPerformed()
1173   {
1174     try
1175     {
1176       String val = userIdWidth.getText().trim();
1177       if (val.length() > 0)
1178       {
1179         Integer iw = Integer.parseInt(val);
1180         if (iw.intValue() < 12)
1181         {
1182           throw new NumberFormatException();
1183         }
1184         userIdWidth.setText(iw.toString());
1185       }
1186     } catch (NumberFormatException x)
1187     {
1188       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1189               MessageManager
1190                       .getString("warn.user_defined_width_requirements"),
1191               MessageManager.getString("label.invalid_id_column_width"),
1192               JvOptionPane.WARNING_MESSAGE);
1193       userIdWidth.setText("");
1194     }
1195   }
1196
1197   @Override
1198   protected void autoIdWidth_actionPerformed()
1199   {
1200     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1201     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1202   }
1203
1204   /**
1205    * Returns true if chimera path is to a valid executable, else show an error
1206    * dialog.
1207    */
1208   private boolean validateChimeraPath()
1209   {
1210     if (chimeraPath.getText().trim().length() > 0)
1211     {
1212       File f = new File(chimeraPath.getText());
1213       if (!f.canExecute())
1214       {
1215         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1216                 MessageManager.getString("label.invalid_chimera_path"),
1217                 MessageManager.getString("label.invalid_name"),
1218                 JvOptionPane.ERROR_MESSAGE);
1219         return false;
1220       }
1221     }
1222     return true;
1223   }
1224
1225   /**
1226    * If Chimera is selected, check it can be found on default or user-specified
1227    * path, if not show a warning/help dialog.
1228    */
1229   @Override
1230   protected void structureViewer_actionPerformed(String selectedItem)
1231   {
1232     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1233     {
1234       return;
1235     }
1236     boolean found = false;
1237
1238     /*
1239      * Try user-specified and standard paths for Chimera executable.
1240      */
1241     List<String> paths = StructureManager.getChimeraPaths();
1242     paths.add(0, chimeraPath.getText());
1243     for (String path : paths)
1244     {
1245       if (new File(path.trim()).canExecute())
1246       {
1247         found = true;
1248         break;
1249       }
1250     }
1251     if (!found)
1252     {
1253       String[] options = { "OK", "Help" };
1254       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1255               JvSwingUtils.wrapTooltip(true,
1256                       MessageManager.getString("label.chimera_missing")),
1257               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1258               null, options, options[0]);
1259       if (showHelp == JvOptionPane.NO_OPTION)
1260       {
1261         try
1262         {
1263           Help.showHelpWindow(HelpId.StructureViewer);
1264         } catch (HelpSetException e)
1265         {
1266           e.printStackTrace();
1267         }
1268       }
1269     }
1270   }
1271
1272   public class OptionsParam
1273   {
1274     private String name;
1275
1276     private String code;
1277
1278     public OptionsParam(String name, String code)
1279     {
1280       this.name = name;
1281       this.code = code;
1282     }
1283
1284     public String getName()
1285     {
1286       return name;
1287     }
1288
1289     public void setName(String name)
1290     {
1291       this.name = name;
1292     }
1293
1294     public String getCode()
1295     {
1296       return code;
1297     }
1298
1299     public void setCode(String code)
1300     {
1301       this.code = code;
1302     }
1303
1304     @Override
1305     public String toString()
1306     {
1307       return name;
1308     }
1309
1310     @Override
1311     public boolean equals(Object that)
1312     {
1313       if (!(that instanceof OptionsParam))
1314       {
1315         return false;
1316       }
1317       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1318     }
1319
1320     @Override
1321     public int hashCode()
1322     {
1323       return name.hashCode() + code.hashCode();
1324     }
1325   }
1326
1327   private class UrlListSelectionHandler implements ListSelectionListener
1328   {
1329
1330     @Override
1331     public void valueChanged(ListSelectionEvent e)
1332     {
1333       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1334
1335       int index = lsm.getMinSelectionIndex();
1336       if (index == -1)
1337       {
1338         // no selection, so disable delete/edit buttons
1339         editLink.setEnabled(false);
1340         deleteLink.setEnabled(false);
1341         return;
1342       }
1343       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1344
1345       // enable/disable edit and delete link buttons
1346       if (((UrlLinkTableModel) linkUrlTable.getModel())
1347               .isRowDeletable(modelIndex))
1348       {
1349         deleteLink.setEnabled(true);
1350       }
1351       else
1352       {
1353         deleteLink.setEnabled(false);
1354       }
1355
1356       if (((UrlLinkTableModel) linkUrlTable.getModel())
1357               .isRowEditable(modelIndex))
1358       {
1359         editLink.setEnabled(true);
1360       }
1361       else
1362       {
1363         editLink.setEnabled(false);
1364       }
1365     }
1366   }
1367 }