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,
 558             "-bak" + BackupFiles.NUM_PLACEHOLDER));
 559     suffixDigitsSpinner
 560             .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
 561     suffixReverse.setSelected(
 562             Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
 563     backupfilesKeepAll
 564             .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
 565     backupfilesRollMaxSpinner
 566             .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4));
 567     backupfilesConfirmDelete.setSelected(
 568             Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
 569     backupsOptionsSetEnabled(enableBackupFiles.isSelected());
 570     updateBackupFilesExampleLabel();
 571     /*
 572     suffixPanel.setPreferredSize(
 573             new Dimension(width, suffixPanel.getHeight()));
 574     keepfilesPanel.setPreferredSize(
 575             new Dimension(width, keepfilesPanel.getHeight()));
 576     exampleFilesPanel.setPreferredSize(
 577             new Dimension(width, exampleFilesPanel.getHeight()));
 578             */
 579
 580   }
 581
 582   /**
 583    * Save user selections on the Preferences tabs to the Cache and write out to
 584    * file.
 585    *
 586    * @param e
 587    */
 588   @Override
 589   public void ok_actionPerformed(ActionEvent e)
 590   {
 591     if (!validateSettings())
 592     {
 593       return;
 594     }
 595
 596     /*
 597      * Save Visual settings
 598      */
 599     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 600             Boolean.toString(seqLimit.isSelected()));
 601     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 602             Boolean.toString(rightAlign.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 604             Boolean.toString(fullScreen.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 606             Boolean.toString(openoverv.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 608             Boolean.toString(annotations.isSelected()));
 609     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 610             Boolean.toString(conservation.isSelected()));
 611     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 612             Boolean.toString(quality.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 614             Boolean.toString(identity.isSelected()));
 615
 616     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 617             gapSymbolCB.getSelectedItem().toString());
 618
 619     Cache.applicationProperties.setProperty("FONT_NAME",
 620             fontNameCB.getSelectedItem().toString());
 621     Cache.applicationProperties.setProperty("FONT_STYLE",
 622             fontStyleCB.getSelectedItem().toString());
 623     Cache.applicationProperties.setProperty("FONT_SIZE",
 624             fontSizeCB.getSelectedItem().toString());
 625
 626     Cache.applicationProperties.setProperty("ID_ITALICS",
 627             Boolean.toString(idItalics.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 629             Boolean.toString(showUnconserved.isSelected()));
 630     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 631             Boolean.toString(showOccupancy.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 633             Boolean.toString(showGroupConsensus.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 635             Boolean.toString(showGroupConservation.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 637             Boolean.toString(showConsensHistogram.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 639             Boolean.toString(showConsensLogo.isSelected()));
 640     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 641             Boolean.toString(smoothFont.isSelected()));
 642     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 643             Boolean.toString(scaleProteinToCdna.isSelected()));
 644     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 645             Boolean.toString(showNpTooltip.isSelected()));
 646     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 647             Boolean.toString(showDbRefTooltip.isSelected()));
 648
 649     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 650             Boolean.toString(wrap.isSelected()));
 651
 652     Cache.applicationProperties.setProperty("STARTUP_FILE",
 653             startupFileTextfield.getText());
 654     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 655             Boolean.toString(startupCheckbox.isSelected()));
 656
 657     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 658             sortby.getSelectedItem().toString());
 659
 660     // convert description of sort order to enum name for save
 661     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 662             .forDescription(sortAnnBy.getSelectedItem().toString());
 663     if (annSortOrder != null)
 664     {
 665       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 666               annSortOrder.name());
 667     }
 668
 669     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 670     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 671             Boolean.valueOf(showAutocalcFirst).toString());
 672
 673     /*
 674      * Save Colours settings
 675      */
 676     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 677             protColour.getSelectedItem().toString());
 678     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 679             nucColour.getSelectedItem().toString());
 680     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 681             minColour.getBackground());
 682     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 683             maxColour.getBackground());
 684
 685     /*
 686      * Save Overview settings
 687      */
 688     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 689     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 690     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 691             Boolean.toString(useLegacyGap.isSelected()));
 692     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 693             Boolean.toString(showHiddenAtStart.isSelected()));
 694
 695     /*
 696      * Save Structure settings
 697      */
 698     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 699             Boolean.toString(addTempFactor.isSelected()));
 700     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 701             Boolean.toString(addSecondaryStructure.isSelected()));
 702     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 703             Boolean.toString(useRnaView.isSelected()));
 704     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 705             Boolean.toString(structFromPdb.isSelected()));
 706     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 707             structViewer.getSelectedItem().toString());
 708     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 709     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 710             Boolean.toString(siftsMapping.isSelected()));
 711     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 712
 713     /*
 714      * Save Output settings
 715      */
 716     Cache.applicationProperties.setProperty("EPS_RENDERING",
 717             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 718
 719     /*
 720      * Save Connections settings
 721      */
 722     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 723
 724     jalview.util.BrowserLauncher.resetBrowser();
 725
 726     // save user-defined and selected links
 727     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 728     if (menuLinks.isEmpty())
 729     {
 730       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 731     }
 732     else
 733     {
 734       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 735               menuLinks.toString());
 736     }
 737
 738     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 739     if (nonMenuLinks.isEmpty())
 740     {
 741       Cache.applicationProperties.remove("STORED_LINKS");
 742     }
 743     else
 744     {
 745       Cache.applicationProperties.setProperty("STORED_LINKS",
 746               nonMenuLinks.toString());
 747     }
 748
 749     Cache.applicationProperties.setProperty("DEFAULT_URL",
 750             sequenceUrlLinks.getPrimaryUrlId());
 751
 752     Cache.applicationProperties.setProperty("USE_PROXY",
 753             Boolean.toString(useProxy.isSelected()));
 754
 755     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 756
 757     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 758
 759     if (useProxy.isSelected())
 760     {
 761       System.setProperty("http.proxyHost", proxyServerTB.getText());
 762       System.setProperty("http.proxyPort", proxyPortTB.getText());
 763     }
 764     else
 765     {
 766       System.setProperty("http.proxyHost", "");
 767       System.setProperty("http.proxyPort", "");
 768     }
 769     Cache.setProperty("VERSION_CHECK",
 770             Boolean.toString(versioncheck.isSelected()));
 771     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 772     {
 773       // default is false - we only set this if the user has actively agreed
 774       Cache.setProperty("USAGESTATS",
 775               Boolean.toString(usagestats.isSelected()));
 776     }
 777     if (!questionnaire.isSelected())
 778     {
 779       Cache.setProperty("NOQUESTIONNAIRES", "true");
 780     }
 781     else
 782     {
 783       // special - made easy to edit a property file to disable questionnaires
 784       // by just adding the given line
 785       Cache.removeProperty("NOQUESTIONNAIRES");
 786     }
 787
 788     /*
 789      * Save Output settings
 790      */
 791     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 792             Boolean.toString(blcjv.isSelected()));
 793     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 794             Boolean.toString(clustaljv.isSelected()));
 795     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 796             Boolean.toString(fastajv.isSelected()));
 797     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 798             Boolean.toString(msfjv.isSelected()));
 799     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 800             Boolean.toString(pfamjv.isSelected()));
 801     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 802             Boolean.toString(pileupjv.isSelected()));
 803     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 804             Boolean.toString(pirjv.isSelected()));
 805     Cache.applicationProperties.setProperty("PIR_MODELLER",
 806             Boolean.toString(modellerOutput.isSelected()));
 807     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 808             Boolean.toString(embbedBioJSON.isSelected()));
 809     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 810
 811     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 812             Boolean.toString(autoIdWidth.isSelected()));
 813     userIdWidth_actionPerformed();
 814     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 815             userIdWidth.getText());
 816
 817     /*
 818      * Save Editing settings
 819      */
 820     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 821             Boolean.toString(autoCalculateConsCheck.isSelected()));
 822     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 823             Boolean.toString(sortByTree.isSelected()));
 824     Cache.applicationProperties.setProperty("PAD_GAPS",
 825             Boolean.toString(padGaps.isSelected()));
 826
 827     wsPrefs.updateAndRefreshWsMenuConfig(false);
 828
 829     /*
 830      * Save Backups settings
 831      */
 832     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 833             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 834     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 835             Boolean.toString(enableBackupFiles.isSelected()));
 836     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 837             Boolean.toString(backupfilesKeepAll.isSelected()));
 838     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 839             Boolean.toString(suffixReverse.isSelected()));
 840     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 841             suffixTemplate.getText());
 842     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 843             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 844     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 845             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 846
 847     Cache.saveProperties();
 848     Desktop.instance.doConfigureStructurePrefs();
 849     try
 850     {
 851       frame.setClosed(true);
 852     } catch (Exception ex)
 853     {
 854     }
 855   }
 856
 857   /**
 858    * Do any necessary validation before saving settings. Return focus to the
 859    * first tab which fails validation.
 860    *
 861    * @return
 862    */
 863   private boolean validateSettings()
 864   {
 865     if (!validateStructure())
 866     {
 867       structureTab.requestFocusInWindow();
 868       return false;
 869     }
 870     return true;
 871   }
 872
 873   @Override
 874   protected boolean validateStructure()
 875   {
 876     return validateChimeraPath();
 877
 878   }
 879
 880   /**
 881    * DOCUMENT ME!
 882    */
 883   @Override
 884   public void startupFileTextfield_mouseClicked()
 885   {
 886     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 887     JalviewFileChooser chooser = JalviewFileChooser
 888             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 889     chooser.setFileView(new JalviewFileView());
 890     chooser.setDialogTitle(
 891             MessageManager.getString("label.select_startup_file"));
 892
 893     int value = chooser.showOpenDialog(this);
 894
 895     if (value == JalviewFileChooser.APPROVE_OPTION)
 896     {
 897       FileFormatI format = chooser.getSelectedFormat();
 898       if (format != null)
 899       {
 900         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 901                 format.getName());
 902       }
 903       startupFileTextfield
 904               .setText(chooser.getSelectedFile().getAbsolutePath());
 905     }
 906   }
 907
 908   /**
 909    * DOCUMENT ME!
 910    *
 911    * @param e
 912    *          DOCUMENT ME!
 913    */
 914   @Override
 915   public void cancel_actionPerformed(ActionEvent e)
 916   {
 917     try
 918     {
 919       wsPrefs.updateWsMenuConfig(true);
 920       wsPrefs.refreshWs_actionPerformed(e);
 921       frame.setClosed(true);
 922     } catch (Exception ex)
 923     {
 924     }
 925   }
 926
 927   /**
 928    * DOCUMENT ME!
 929    *
 930    * @param e
 931    *          DOCUMENT ME!
 932    */
 933   @Override
 934   public void annotations_actionPerformed(ActionEvent e)
 935   {
 936     conservation.setEnabled(annotations.isSelected());
 937     quality.setEnabled(annotations.isSelected());
 938     identity.setEnabled(annotations.isSelected());
 939     showOccupancy.setEnabled(annotations.isSelected());
 940     showGroupConsensus.setEnabled(annotations.isSelected());
 941     showGroupConservation.setEnabled(annotations.isSelected());
 942     showConsensHistogram.setEnabled(annotations.isSelected()
 943             && (identity.isSelected() || showGroupConsensus.isSelected()));
 944     showConsensLogo.setEnabled(annotations.isSelected()
 945             && (identity.isSelected() || showGroupConsensus.isSelected()));
 946   }
 947
 948   @Override
 949   public void newLink_actionPerformed(ActionEvent e)
 950   {
 951     GSequenceLink link = new GSequenceLink();
 952     boolean valid = false;
 953     while (!valid)
 954     {
 955       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 956               MessageManager.getString("label.new_sequence_url_link"),
 957               JvOptionPane.OK_CANCEL_OPTION, -1,
 958               null) == JvOptionPane.OK_OPTION)
 959       {
 960         if (link.checkValid())
 961         {
 962           if (((UrlLinkTableModel) linkUrlTable.getModel())
 963                   .isUniqueName(link.getName()))
 964           {
 965             ((UrlLinkTableModel) linkUrlTable.getModel())
 966                     .insertRow(link.getName(), link.getURL());
 967             valid = true;
 968           }
 969           else
 970           {
 971             link.notifyDuplicate();
 972             continue;
 973           }
 974         }
 975       }
 976       else
 977       {
 978         break;
 979       }
 980     }
 981   }
 982
 983   @Override
 984   public void editLink_actionPerformed(ActionEvent e)
 985   {
 986     GSequenceLink link = new GSequenceLink();
 987
 988     int index = linkUrlTable.getSelectedRow();
 989     if (index == -1)
 990     {
 991       // button no longer enabled if row is not selected
 992       Cache.log.debug("Edit with no row selected in linkUrlTable");
 993       return;
 994     }
 995
 996     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 997             .getNameColumn();
 998     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 999             .getUrlColumn();
1000     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1001     link.setName(oldName);
1002     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1003
1004     boolean valid = false;
1005     while (!valid)
1006     {
1007       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1008               MessageManager.getString("label.edit_sequence_url_link"),
1009               JvOptionPane.OK_CANCEL_OPTION, -1,
1010               null) == JvOptionPane.OK_OPTION)
1011       {
1012         if (link.checkValid())
1013         {
1014           if ((oldName.equals(link.getName()))
1015                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1016                           .isUniqueName(link.getName())))
1017           {
1018             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1019             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1020             valid = true;
1021           }
1022           else
1023           {
1024             link.notifyDuplicate();
1025             continue;
1026           }
1027         }
1028       }
1029       else
1030       {
1031         break;
1032       }
1033     }
1034   }
1035
1036   @Override
1037   public void deleteLink_actionPerformed(ActionEvent e)
1038   {
1039     int index = linkUrlTable.getSelectedRow();
1040     int modelIndex = -1;
1041     if (index == -1)
1042     {
1043       // button no longer enabled if row is not selected
1044       Cache.log.debug("Delete with no row selected in linkUrlTable");
1045       return;
1046     }
1047     else
1048     {
1049       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1050     }
1051
1052     // make sure we use the model index to delete, and not the table index
1053     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1054   }
1055
1056   @Override
1057   public void defaultBrowser_mouseClicked(MouseEvent e)
1058   {
1059     JFileChooser chooser = new JFileChooser(".");
1060     chooser.setDialogTitle(
1061             MessageManager.getString("label.select_default_browser"));
1062
1063     int value = chooser.showOpenDialog(this);
1064
1065     if (value == JFileChooser.APPROVE_OPTION)
1066     {
1067       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1068     }
1069
1070   }
1071
1072   /*
1073    * (non-Javadoc)
1074    *
1075    * @see
1076    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1077    * .ActionEvent)
1078    */
1079   @Override
1080   protected void showunconserved_actionPerformed(ActionEvent e)
1081   {
1082     // TODO Auto-generated method stub
1083     super.showunconserved_actionPerformed(e);
1084   }
1085
1086   public static List<String> getGroupURLLinks()
1087   {
1088     return groupURLLinks;
1089   }
1090
1091   @Override
1092   public void minColour_actionPerformed(JPanel panel)
1093   {
1094     Color col = JColorChooser.showDialog(this,
1095             MessageManager.getString("label.select_colour_minimum_value"),
1096             minColour.getBackground());
1097     if (col != null)
1098     {
1099       panel.setBackground(col);
1100     }
1101     panel.repaint();
1102   }
1103
1104   @Override
1105   public void maxColour_actionPerformed(JPanel panel)
1106   {
1107     Color col = JColorChooser.showDialog(this,
1108             MessageManager.getString("label.select_colour_maximum_value"),
1109             maxColour.getBackground());
1110     if (col != null)
1111     {
1112       panel.setBackground(col);
1113     }
1114     panel.repaint();
1115   }
1116
1117   @Override
1118   public void gapColour_actionPerformed(JPanel gap)
1119   {
1120     if (!useLegacyGap.isSelected())
1121     {
1122       Color col = JColorChooser.showDialog(this,
1123               MessageManager.getString("label.select_gap_colour"),
1124               gapColour.getBackground());
1125       if (col != null)
1126       {
1127         gap.setBackground(col);
1128       }
1129       gap.repaint();
1130     }
1131   }
1132
1133   @Override
1134   public void hiddenColour_actionPerformed(JPanel hidden)
1135   {
1136     Color col = JColorChooser.showDialog(this,
1137             MessageManager.getString("label.select_hidden_colour"),
1138             hiddenColour.getBackground());
1139     if (col != null)
1140     {
1141       hidden.setBackground(col);
1142     }
1143     hidden.repaint();
1144   }
1145
1146   @Override
1147   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1148   {
1149     boolean enabled = useLegacyGap.isSelected();
1150     if (enabled)
1151     {
1152       gapColour.setBackground(
1153               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1154     }
1155     else
1156     {
1157       gapColour.setBackground(
1158               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1159     }
1160     gapColour.setEnabled(!enabled);
1161     gapLabel.setEnabled(!enabled);
1162   }
1163
1164   @Override
1165   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1166   {
1167     useLegacyGap.setSelected(false);
1168     useLegacyGaps_actionPerformed(null);
1169     showHiddenAtStart.setSelected(true);
1170     hiddenColour.setBackground(
1171             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1172   }
1173
1174   @Override
1175   protected void userIdWidth_actionPerformed()
1176   {
1177     try
1178     {
1179       String val = userIdWidth.getText().trim();
1180       if (val.length() > 0)
1181       {
1182         Integer iw = Integer.parseInt(val);
1183         if (iw.intValue() < 12)
1184         {
1185           throw new NumberFormatException();
1186         }
1187         userIdWidth.setText(iw.toString());
1188       }
1189     } catch (NumberFormatException x)
1190     {
1191       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1192               MessageManager
1193                       .getString("warn.user_defined_width_requirements"),
1194               MessageManager.getString("label.invalid_id_column_width"),
1195               JvOptionPane.WARNING_MESSAGE);
1196       userIdWidth.setText("");
1197     }
1198   }
1199
1200   @Override
1201   protected void autoIdWidth_actionPerformed()
1202   {
1203     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1204     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1205   }
1206
1207   /**
1208    * Returns true if chimera path is to a valid executable, else show an error
1209    * dialog.
1210    */
1211   private boolean validateChimeraPath()
1212   {
1213     if (chimeraPath.getText().trim().length() > 0)
1214     {
1215       File f = new File(chimeraPath.getText());
1216       if (!f.canExecute())
1217       {
1218         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1219                 MessageManager.getString("label.invalid_chimera_path"),
1220                 MessageManager.getString("label.invalid_name"),
1221                 JvOptionPane.ERROR_MESSAGE);
1222         return false;
1223       }
1224     }
1225     return true;
1226   }
1227
1228   /**
1229    * If Chimera is selected, check it can be found on default or user-specified
1230    * path, if not show a warning/help dialog.
1231    */
1232   @Override
1233   protected void structureViewer_actionPerformed(String selectedItem)
1234   {
1235     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1236     {
1237       return;
1238     }
1239     boolean found = false;
1240
1241     /*
1242      * Try user-specified and standard paths for Chimera executable.
1243      */
1244     List<String> paths = StructureManager.getChimeraPaths();
1245     paths.add(0, chimeraPath.getText());
1246     for (String path : paths)
1247     {
1248       if (new File(path.trim()).canExecute())
1249       {
1250         found = true;
1251         break;
1252       }
1253     }
1254     if (!found)
1255     {
1256       String[] options = { "OK", "Help" };
1257       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1258               JvSwingUtils.wrapTooltip(true,
1259                       MessageManager.getString("label.chimera_missing")),
1260               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1261               null, options, options[0]);
1262       if (showHelp == JvOptionPane.NO_OPTION)
1263       {
1264         try
1265         {
1266           Help.showHelpWindow(HelpId.StructureViewer);
1267         } catch (HelpSetException e)
1268         {
1269           e.printStackTrace();
1270         }
1271       }
1272     }
1273   }
1274
1275   public class OptionsParam
1276   {
1277     private String name;
1278
1279     private String code;
1280
1281     public OptionsParam(String name, String code)
1282     {
1283       this.name = name;
1284       this.code = code;
1285     }
1286
1287     public String getName()
1288     {
1289       return name;
1290     }
1291
1292     public void setName(String name)
1293     {
1294       this.name = name;
1295     }
1296
1297     public String getCode()
1298     {
1299       return code;
1300     }
1301
1302     public void setCode(String code)
1303     {
1304       this.code = code;
1305     }
1306
1307     @Override
1308     public String toString()
1309     {
1310       return name;
1311     }
1312
1313     @Override
1314     public boolean equals(Object that)
1315     {
1316       if (!(that instanceof OptionsParam))
1317       {
1318         return false;
1319       }
1320       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1321     }
1322
1323     @Override
1324     public int hashCode()
1325     {
1326       return name.hashCode() + code.hashCode();
1327     }
1328   }
1329
1330   private class UrlListSelectionHandler implements ListSelectionListener
1331   {
1332
1333     @Override
1334     public void valueChanged(ListSelectionEvent e)
1335     {
1336       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1337
1338       int index = lsm.getMinSelectionIndex();
1339       if (index == -1)
1340       {
1341         // no selection, so disable delete/edit buttons
1342         editLink.setEnabled(false);
1343         deleteLink.setEnabled(false);
1344         return;
1345       }
1346       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1347
1348       // enable/disable edit and delete link buttons
1349       if (((UrlLinkTableModel) linkUrlTable.getModel())
1350               .isRowDeletable(modelIndex))
1351       {
1352         deleteLink.setEnabled(true);
1353       }
1354       else
1355       {
1356         deleteLink.setEnabled(false);
1357       }
1358
1359       if (((UrlLinkTableModel) linkUrlTable.getModel())
1360               .isRowEditable(modelIndex))
1361       {
1362         editLink.setEnabled(true);
1363       }
1364       else
1365       {
1366         editLink.setEnabled(false);
1367       }
1368     }
1369   }
1370 }