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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JColorChooser;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.gui.Help.HelpId;
  57 import jalview.gui.StructureViewer.ViewerType;
  58 import jalview.io.BackupFiles;
  59 import jalview.io.BackupFilesPresetEntry;
  60 import jalview.io.FileFormatI;
  61 import jalview.io.JalviewFileChooser;
  62 import jalview.io.JalviewFileView;
  63 import jalview.jbgui.GPreferences;
  64 import jalview.jbgui.GSequenceLink;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.ColourSchemes;
  67 import jalview.schemes.ResidueColourScheme;
  68 import jalview.urls.UrlLinkTableModel;
  69 import jalview.urls.api.UrlProviderFactoryI;
  70 import jalview.urls.api.UrlProviderI;
  71 import jalview.urls.desktop.DesktopUrlProviderFactory;
  72 import jalview.util.MessageManager;
  73 import jalview.util.Platform;
  74 import jalview.util.UrlConstants;
  75 import jalview.ws.sifts.SiftsSettings;
  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", true));
 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(Cache.getDefaultColour(GAP_COLOUR,
 320             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 321     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 322             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 323     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 324     gapLabel.setEnabled(!useLegacyGap.isSelected());
 325     gapColour.setEnabled(!useLegacyGap.isSelected());
 326     showHiddenAtStart
 327             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 328
 329     /*
 330      * Set Structure tab defaults.
 331      */
 332     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 333     structFromPdb.setSelected(structSelected);
 334     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 335     useRnaView.setEnabled(structSelected);
 336     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 337     addSecondaryStructure.setEnabled(structSelected);
 338     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 339     addTempFactor.setEnabled(structSelected);
 340     structViewer.setSelectedItem(
 341             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 342     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 343     chimeraPath.addActionListener(new ActionListener()
 344     {
 345       @Override
 346       public void actionPerformed(ActionEvent e)
 347       {
 348         validateChimeraPath();
 349       }
 350     });
 351
 352     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 353     {
 354       siftsMapping.setSelected(true);
 355     }
 356     else
 357     {
 358       nwMapping.setSelected(true);
 359     }
 360
 361     SiftsSettings
 362             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 363
 364     /*
 365      * Set Connections tab defaults
 366      */
 367
 368     // set up sorting
 369     linkUrlTable.setModel(dataModel);
 370     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 371             linkUrlTable.getModel());
 372     linkUrlTable.setRowSorter(sorter);
 373     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 374
 375     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 376     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 377             SortOrder.DESCENDING));
 378     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(
 381             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 382
 383     sorter.setSortKeys(sortKeys);
 384     sorter.sort();
 385
 386     // set up filtering
 387     ActionListener onReset;
 388     onReset = new ActionListener()
 389     {
 390       @Override
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         filterTB.setText("");
 394         sorter.setRowFilter(RowFilter.regexFilter(""));
 395       }
 396
 397     };
 398     doReset.addActionListener(onReset);
 399
 400     // filter to display only custom urls
 401     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 402     {
 403       @Override
 404       public boolean include(
 405               Entry<? extends TableModel, ? extends Object> entry)
 406       {
 407         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 408       }
 409     };
 410
 411     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 412             linkUrlTable.getModel());
 413     customSorter.setRowFilter(customUrlFilter);
 414
 415     ActionListener onCustomOnly;
 416     onCustomOnly = new ActionListener()
 417     {
 418       @Override
 419       public void actionPerformed(ActionEvent e)
 420       {
 421         filterTB.setText("");
 422         sorter.setRowFilter(customUrlFilter);
 423       }
 424     };
 425     userOnly.addActionListener(onCustomOnly);
 426
 427     filterTB.getDocument().addDocumentListener(new DocumentListener()
 428     {
 429       String caseInsensitiveFlag = "(?i)";
 430
 431       @Override
 432       public void changedUpdate(DocumentEvent e)
 433       {
 434         sorter.setRowFilter(RowFilter
 435                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 436       }
 437
 438       @Override
 439       public void removeUpdate(DocumentEvent e)
 440       {
 441         sorter.setRowFilter(RowFilter
 442                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 443       }
 444
 445       @Override
 446       public void insertUpdate(DocumentEvent e)
 447       {
 448         sorter.setRowFilter(RowFilter
 449                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 450       }
 451     });
 452
 453     // set up list selection functionality
 454     linkUrlTable.getSelectionModel()
 455             .addListSelectionListener(new UrlListSelectionHandler());
 456
 457     // set up radio buttons
 458     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 459             .getPrimaryColumn();
 460     String onClickName = linkUrlTable.getColumnName(onClickCol);
 461     linkUrlTable.getColumn(onClickName)
 462             .setCellRenderer(new RadioButtonRenderer());
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellEditor(new RadioButtonEditor());
 465
 466     // get boolean columns and resize those to min possible
 467     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 468     {
 469       if (linkUrlTable.getModel().getColumnClass(column)
 470               .equals(Boolean.class))
 471       {
 472         TableColumn tableColumn = linkUrlTable.getColumnModel()
 473                 .getColumn(column);
 474         int preferredWidth = tableColumn.getMinWidth();
 475
 476         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 477                 column);
 478         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 479         int cwidth = c.getPreferredSize().width
 480                 + linkUrlTable.getIntercellSpacing().width;
 481         preferredWidth = Math.max(preferredWidth, cwidth);
 482
 483         tableColumn.setPreferredWidth(preferredWidth);
 484       }
 485     }
 486
 487     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 488     switch (proxyTypeString)
 489     {
 490     case "none":
 491       proxyType.setSelected(noProxy.getModel(), true);
 492       break;
 493     case "false":
 494       proxyType.setSelected(systemProxy.getModel(), true);
 495       break;
 496     case "true":
 497       proxyType.setSelected(customProxy.getModel(), true);
 498       break;
 499     default:
 500       String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 501               + proxyTypeString;
 502       Cache.log.warn(message);
 503     }
 504     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 505     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 506     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 507     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 508
 509     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 510
 511     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 512     // note antisense here: default is true
 513     questionnaire
 514             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 515     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 516
 517     /*
 518      * Set Output tab defaults
 519      */
 520     epsRendering.addItem(promptEachTimeOpt);
 521     epsRendering.addItem(lineArtOpt);
 522     epsRendering.addItem(textOpt);
 523     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 524             "Prompt each time");
 525     if (defaultEPS.equalsIgnoreCase("Text"))
 526     {
 527       epsRendering.setSelectedItem(textOpt);
 528     }
 529     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 530     {
 531       epsRendering.setSelectedItem(lineArtOpt);
 532     }
 533     else
 534     {
 535       epsRendering.setSelectedItem(promptEachTimeOpt);
 536     }
 537     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 538     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 539     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 540     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 541     userIdWidth.setText(wi == null ? "" : wi.toString());
 542     // TODO: refactor to use common enum via FormatAdapter and allow extension
 543     // for new flat file formats
 544     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 545     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 546     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 547     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 548     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 549     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 550     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 551     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 552     embbedBioJSON
 553             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 554
 555     /*
 556      * Set Editing tab defaults
 557      */
 558     autoCalculateConsCheck
 559             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 560     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 561     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 562
 563     annotations_actionPerformed(null); // update the display of the annotation
 564                                        // settings
 565
 566     /*
 567      * Set Backups tab defaults
 568      */
 569     loadLastSavedBackupsOptions();
 570   }
 571
 572   /**
 573    * Save user selections on the Preferences tabs to the Cache and write out to
 574    * file.
 575    *
 576    * @param e
 577    */
 578   @Override
 579   public void ok_actionPerformed(ActionEvent e)
 580   {
 581     if (!validateSettings())
 582     {
 583       return;
 584     }
 585
 586     /*
 587      * Save Visual settings
 588      */
 589     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 590             Boolean.toString(seqLimit.isSelected()));
 591     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 592             Boolean.toString(rightAlign.isSelected()));
 593     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 594             Boolean.toString(fullScreen.isSelected()));
 595     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 596             Boolean.toString(openoverv.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 598             Boolean.toString(annotations.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 600             Boolean.toString(conservation.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 602             Boolean.toString(quality.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 604             Boolean.toString(identity.isSelected()));
 605
 606     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 607             gapSymbolCB.getSelectedItem().toString());
 608
 609     Cache.applicationProperties.setProperty("FONT_NAME",
 610             fontNameCB.getSelectedItem().toString());
 611     Cache.applicationProperties.setProperty("FONT_STYLE",
 612             fontStyleCB.getSelectedItem().toString());
 613     Cache.applicationProperties.setProperty("FONT_SIZE",
 614             fontSizeCB.getSelectedItem().toString());
 615
 616     Cache.applicationProperties.setProperty("ID_ITALICS",
 617             Boolean.toString(idItalics.isSelected()));
 618     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 619             Boolean.toString(showUnconserved.isSelected()));
 620     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 621             Boolean.toString(showOccupancy.isSelected()));
 622     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 623             Boolean.toString(showGroupConsensus.isSelected()));
 624     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 625             Boolean.toString(showGroupConservation.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 627             Boolean.toString(showConsensHistogram.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 629             Boolean.toString(showConsensLogo.isSelected()));
 630     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 631             Boolean.toString(smoothFont.isSelected()));
 632     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 633             Boolean.toString(scaleProteinToCdna.isSelected()));
 634     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 635             Boolean.toString(showNpTooltip.isSelected()));
 636     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 637             Boolean.toString(showDbRefTooltip.isSelected()));
 638
 639     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 640             Boolean.toString(wrap.isSelected()));
 641
 642     Cache.applicationProperties.setProperty("STARTUP_FILE",
 643             startupFileTextfield.getText());
 644     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 645             Boolean.toString(startupCheckbox.isSelected()));
 646
 647     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 648             sortby.getSelectedItem().toString());
 649
 650     // convert description of sort order to enum name for save
 651     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 652             .forDescription(sortAnnBy.getSelectedItem().toString());
 653     if (annSortOrder != null)
 654     {
 655       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 656               annSortOrder.name());
 657     }
 658
 659     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 660     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 661             Boolean.valueOf(showAutocalcFirst).toString());
 662
 663     /*
 664      * Save Colours settings
 665      */
 666     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 667             protColour.getSelectedItem().toString());
 668     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 669             nucColour.getSelectedItem().toString());
 670     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 671             minColour.getBackground());
 672     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 673             maxColour.getBackground());
 674
 675     /*
 676      * Save Overview settings
 677      */
 678     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 679     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 680     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 681             Boolean.toString(useLegacyGap.isSelected()));
 682     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 683             Boolean.toString(showHiddenAtStart.isSelected()));
 684
 685     /*
 686      * Save Structure settings
 687      */
 688     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 689             Boolean.toString(addTempFactor.isSelected()));
 690     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 691             Boolean.toString(addSecondaryStructure.isSelected()));
 692     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 693             Boolean.toString(useRnaView.isSelected()));
 694     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 695             Boolean.toString(structFromPdb.isSelected()));
 696     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 697             structViewer.getSelectedItem().toString());
 698     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 699     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 700             Boolean.toString(siftsMapping.isSelected()));
 701     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 702
 703     /*
 704      * Save Output settings
 705      */
 706     Cache.applicationProperties.setProperty("EPS_RENDERING",
 707             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 708
 709     /*
 710      * Save Connections settings
 711      */
 712     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 713
 714     jalview.util.BrowserLauncher.resetBrowser();
 715
 716     // save user-defined and selected links
 717     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 718     if (menuLinks.isEmpty())
 719     {
 720       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 721     }
 722     else
 723     {
 724       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 725               menuLinks.toString());
 726     }
 727
 728     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 729     if (nonMenuLinks.isEmpty())
 730     {
 731       Cache.applicationProperties.remove("STORED_LINKS");
 732     }
 733     else
 734     {
 735       Cache.applicationProperties.setProperty("STORED_LINKS",
 736               nonMenuLinks.toString());
 737     }
 738
 739     Cache.applicationProperties.setProperty("DEFAULT_URL",
 740             sequenceUrlLinks.getPrimaryUrlId());
 741
 742     Cache.applicationProperties.setProperty("USE_PROXY",
 743             customProxy.isSelected() ? "true"
 744                     : noProxy.isSelected() ? "none" : "false");
 745
 746     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 747
 748     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 749
 750     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 751
 752     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 753
 754     if (noProxy.isSelected())
 755     {
 756       Cache.log.warn("Setting no proxy settings");
 757       Cache.setProxyProperties(null, null, null, null);
 758     }
 759     else if (customProxy.isSelected())
 760     {
 761       Cache.log.warn("Setting custom proxy settings");
 762       Cache.setProxyProperties(proxyServerHttpTB.getText(),
 763               proxyPortHttpTB.getText(), proxyServerHttpsTB.getText(),
 764               proxyPortHttpsTB.getText());
 765     }
 766     else // systemProxy should be selected and is sensible default
 767     {
 768       Cache.log.warn("Setting system proxy settings");
 769       Cache.resetProxyProperties();
 770     }
 771
 772     Cache.setProperty("VERSION_CHECK",
 773             Boolean.toString(versioncheck.isSelected()));
 774     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 775     {
 776       // default is false - we only set this if the user has actively agreed
 777       Cache.setProperty("USAGESTATS",
 778               Boolean.toString(usagestats.isSelected()));
 779     }
 780     if (!questionnaire.isSelected())
 781     {
 782       Cache.setProperty("NOQUESTIONNAIRES", "true");
 783     }
 784     else
 785     {
 786       // special - made easy to edit a property file to disable questionnaires
 787       // by just adding the given line
 788       Cache.removeProperty("NOQUESTIONNAIRES");
 789     }
 790
 791     /*
 792      * Save Output settings
 793      */
 794     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 795             Boolean.toString(blcjv.isSelected()));
 796     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 797             Boolean.toString(clustaljv.isSelected()));
 798     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 799             Boolean.toString(fastajv.isSelected()));
 800     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 801             Boolean.toString(msfjv.isSelected()));
 802     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 803             Boolean.toString(pfamjv.isSelected()));
 804     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 805             Boolean.toString(pileupjv.isSelected()));
 806     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 807             Boolean.toString(pirjv.isSelected()));
 808     Cache.applicationProperties.setProperty("PIR_MODELLER",
 809             Boolean.toString(modellerOutput.isSelected()));
 810     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 811             Boolean.toString(embbedBioJSON.isSelected()));
 812     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 813
 814     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 815             Boolean.toString(autoIdWidth.isSelected()));
 816     userIdWidth_actionPerformed();
 817     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 818             userIdWidth.getText());
 819
 820     /*
 821      * Save Editing settings
 822      */
 823     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 824             Boolean.toString(autoCalculateConsCheck.isSelected()));
 825     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 826             Boolean.toString(sortByTree.isSelected()));
 827     Cache.applicationProperties.setProperty("PAD_GAPS",
 828             Boolean.toString(padGaps.isSelected()));
 829
 830     wsPrefs.updateAndRefreshWsMenuConfig(false);
 831
 832     /*
 833      * Save Backups settings
 834      */
 835     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 836             Boolean.toString(enableBackupFiles.isSelected()));
 837     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 838     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 839             Integer.toString(preset));
 840
 841     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 842     {
 843       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 844       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 845               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 846       Cache.applicationProperties.setProperty(
 847               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 848     }
 849
 850     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 851             .get(preset);
 852     Cache.applicationProperties.setProperty(
 853             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 854
 855     Cache.saveProperties();
 856     Desktop.instance.doConfigureStructurePrefs();
 857     try
 858     {
 859       frame.setClosed(true);
 860     } catch (Exception ex)
 861     {
 862     }
 863   }
 864
 865   /**
 866    * Do any necessary validation before saving settings. Return focus to the
 867    * first tab which fails validation.
 868    *
 869    * @return
 870    */
 871   private boolean validateSettings()
 872   {
 873     if (!validateStructure())
 874     {
 875       structureTab.requestFocusInWindow();
 876       return false;
 877     }
 878     return true;
 879   }
 880
 881   @Override
 882   protected boolean validateStructure()
 883   {
 884     return validateChimeraPath();
 885
 886   }
 887
 888   /**
 889    * DOCUMENT ME!
 890    */
 891   @Override
 892   public void startupFileTextfield_mouseClicked()
 893   {
 894     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 895     JalviewFileChooser chooser = JalviewFileChooser
 896             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 897     chooser.setFileView(new JalviewFileView());
 898     chooser.setDialogTitle(
 899             MessageManager.getString("label.select_startup_file"));
 900
 901     int value = chooser.showOpenDialog(this);
 902
 903     if (value == JalviewFileChooser.APPROVE_OPTION)
 904     {
 905       FileFormatI format = chooser.getSelectedFormat();
 906       if (format != null)
 907       {
 908         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 909                 format.getName());
 910       }
 911       startupFileTextfield
 912               .setText(chooser.getSelectedFile().getAbsolutePath());
 913     }
 914   }
 915
 916   /**
 917    * DOCUMENT ME!
 918    *
 919    * @param e
 920    *          DOCUMENT ME!
 921    */
 922   @Override
 923   public void cancel_actionPerformed(ActionEvent e)
 924   {
 925     try
 926     {
 927       wsPrefs.updateWsMenuConfig(true);
 928       wsPrefs.refreshWs_actionPerformed(e);
 929       frame.setClosed(true);
 930     } catch (Exception ex)
 931     {
 932     }
 933   }
 934
 935   /**
 936    * DOCUMENT ME!
 937    *
 938    * @param e
 939    *          DOCUMENT ME!
 940    */
 941   @Override
 942   public void annotations_actionPerformed(ActionEvent e)
 943   {
 944     conservation.setEnabled(annotations.isSelected());
 945     quality.setEnabled(annotations.isSelected());
 946     identity.setEnabled(annotations.isSelected());
 947     showOccupancy.setEnabled(annotations.isSelected());
 948     showGroupConsensus.setEnabled(annotations.isSelected());
 949     showGroupConservation.setEnabled(annotations.isSelected());
 950     showConsensHistogram.setEnabled(annotations.isSelected()
 951             && (identity.isSelected() || showGroupConsensus.isSelected()));
 952     showConsensLogo.setEnabled(annotations.isSelected()
 953             && (identity.isSelected() || showGroupConsensus.isSelected()));
 954   }
 955
 956   @Override
 957   public void newLink_actionPerformed(ActionEvent e)
 958   {
 959     GSequenceLink link = new GSequenceLink();
 960     boolean valid = false;
 961     while (!valid)
 962     {
 963       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 964               MessageManager.getString("label.new_sequence_url_link"),
 965               JvOptionPane.OK_CANCEL_OPTION, -1,
 966               null) == JvOptionPane.OK_OPTION)
 967       {
 968         if (link.checkValid())
 969         {
 970           if (((UrlLinkTableModel) linkUrlTable.getModel())
 971                   .isUniqueName(link.getName()))
 972           {
 973             ((UrlLinkTableModel) linkUrlTable.getModel())
 974                     .insertRow(link.getName(), link.getURL());
 975             valid = true;
 976           }
 977           else
 978           {
 979             link.notifyDuplicate();
 980             continue;
 981           }
 982         }
 983       }
 984       else
 985       {
 986         break;
 987       }
 988     }
 989   }
 990
 991   @Override
 992   public void editLink_actionPerformed(ActionEvent e)
 993   {
 994     GSequenceLink link = new GSequenceLink();
 995
 996     int index = linkUrlTable.getSelectedRow();
 997     if (index == -1)
 998     {
 999       // button no longer enabled if row is not selected
1000       Cache.log.debug("Edit with no row selected in linkUrlTable");
1001       return;
1002     }
1003
1004     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1005             .getNameColumn();
1006     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1007             .getUrlColumn();
1008     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1009     link.setName(oldName);
1010     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1011
1012     boolean valid = false;
1013     while (!valid)
1014     {
1015       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1016               MessageManager.getString("label.edit_sequence_url_link"),
1017               JvOptionPane.OK_CANCEL_OPTION, -1,
1018               null) == JvOptionPane.OK_OPTION)
1019       {
1020         if (link.checkValid())
1021         {
1022           if ((oldName.equals(link.getName()))
1023                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1024                           .isUniqueName(link.getName())))
1025           {
1026             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1027             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1028             valid = true;
1029           }
1030           else
1031           {
1032             link.notifyDuplicate();
1033             continue;
1034           }
1035         }
1036       }
1037       else
1038       {
1039         break;
1040       }
1041     }
1042   }
1043
1044   @Override
1045   public void deleteLink_actionPerformed(ActionEvent e)
1046   {
1047     int index = linkUrlTable.getSelectedRow();
1048     int modelIndex = -1;
1049     if (index == -1)
1050     {
1051       // button no longer enabled if row is not selected
1052       Cache.log.debug("Delete with no row selected in linkUrlTable");
1053       return;
1054     }
1055     else
1056     {
1057       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1058     }
1059
1060     // make sure we use the model index to delete, and not the table index
1061     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1062   }
1063
1064   @Override
1065   public void defaultBrowser_mouseClicked(MouseEvent e)
1066   {
1067     JFileChooser chooser = new JFileChooser(".");
1068     chooser.setDialogTitle(
1069             MessageManager.getString("label.select_default_browser"));
1070
1071     int value = chooser.showOpenDialog(this);
1072
1073     if (value == JFileChooser.APPROVE_OPTION)
1074     {
1075       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1076     }
1077
1078   }
1079
1080   /*
1081    * (non-Javadoc)
1082    *
1083    * @see
1084    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1085    * .ActionEvent)
1086    */
1087   @Override
1088   protected void showunconserved_actionPerformed(ActionEvent e)
1089   {
1090     // TODO Auto-generated method stub
1091     super.showunconserved_actionPerformed(e);
1092   }
1093
1094   public static List<String> getGroupURLLinks()
1095   {
1096     return groupURLLinks;
1097   }
1098
1099   @Override
1100   public void minColour_actionPerformed(JPanel panel)
1101   {
1102     Color col = JColorChooser.showDialog(this,
1103             MessageManager.getString("label.select_colour_minimum_value"),
1104             minColour.getBackground());
1105     if (col != null)
1106     {
1107       panel.setBackground(col);
1108     }
1109     panel.repaint();
1110   }
1111
1112   @Override
1113   public void maxColour_actionPerformed(JPanel panel)
1114   {
1115     Color col = JColorChooser.showDialog(this,
1116             MessageManager.getString("label.select_colour_maximum_value"),
1117             maxColour.getBackground());
1118     if (col != null)
1119     {
1120       panel.setBackground(col);
1121     }
1122     panel.repaint();
1123   }
1124
1125   @Override
1126   public void gapColour_actionPerformed(JPanel gap)
1127   {
1128     if (!useLegacyGap.isSelected())
1129     {
1130       Color col = JColorChooser.showDialog(this,
1131               MessageManager.getString("label.select_gap_colour"),
1132               gapColour.getBackground());
1133       if (col != null)
1134       {
1135         gap.setBackground(col);
1136       }
1137       gap.repaint();
1138     }
1139   }
1140
1141   @Override
1142   public void hiddenColour_actionPerformed(JPanel hidden)
1143   {
1144     Color col = JColorChooser.showDialog(this,
1145             MessageManager.getString("label.select_hidden_colour"),
1146             hiddenColour.getBackground());
1147     if (col != null)
1148     {
1149       hidden.setBackground(col);
1150     }
1151     hidden.repaint();
1152   }
1153
1154   @Override
1155   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1156   {
1157     boolean enabled = useLegacyGap.isSelected();
1158     if (enabled)
1159     {
1160       gapColour.setBackground(
1161               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1162     }
1163     else
1164     {
1165       gapColour.setBackground(
1166               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1167     }
1168     gapColour.setEnabled(!enabled);
1169     gapLabel.setEnabled(!enabled);
1170   }
1171
1172   @Override
1173   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1174   {
1175     useLegacyGap.setSelected(false);
1176     useLegacyGaps_actionPerformed(null);
1177     showHiddenAtStart.setSelected(false);
1178     hiddenColour.setBackground(
1179             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1180   }
1181
1182   @Override
1183   protected void userIdWidth_actionPerformed()
1184   {
1185     try
1186     {
1187       String val = userIdWidth.getText().trim();
1188       if (val.length() > 0)
1189       {
1190         Integer iw = Integer.parseInt(val);
1191         if (iw.intValue() < 12)
1192         {
1193           throw new NumberFormatException();
1194         }
1195         userIdWidth.setText(iw.toString());
1196       }
1197     } catch (NumberFormatException x)
1198     {
1199       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1200               MessageManager
1201                       .getString("warn.user_defined_width_requirements"),
1202               MessageManager.getString("label.invalid_id_column_width"),
1203               JvOptionPane.WARNING_MESSAGE);
1204       userIdWidth.setText("");
1205     }
1206   }
1207
1208   @Override
1209   protected void autoIdWidth_actionPerformed()
1210   {
1211     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1212     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1213   }
1214
1215   /**
1216    * Returns true if chimera path is to a valid executable, else show an error
1217    * dialog.
1218    */
1219   private boolean validateChimeraPath()
1220   {
1221     if (chimeraPath.getText().trim().length() > 0)
1222     {
1223       File f = new File(chimeraPath.getText());
1224       if (!f.canExecute())
1225       {
1226         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1227                 MessageManager.getString("label.invalid_chimera_path"),
1228                 MessageManager.getString("label.invalid_name"),
1229                 JvOptionPane.ERROR_MESSAGE);
1230         return false;
1231       }
1232     }
1233     return true;
1234   }
1235
1236   /**
1237    * If Chimera is selected, check it can be found on default or user-specified
1238    * path, if not show a warning/help dialog.
1239    */
1240   @Override
1241   protected void structureViewer_actionPerformed(String selectedItem)
1242   {
1243     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1244     {
1245       return;
1246     }
1247     boolean found = false;
1248
1249     /*
1250      * Try user-specified and standard paths for Chimera executable.
1251      */
1252     List<String> paths = StructureManager.getChimeraPaths();
1253     paths.add(0, chimeraPath.getText());
1254     for (String path : paths)
1255     {
1256       if (new File(path.trim()).canExecute())
1257       {
1258         found = true;
1259         break;
1260       }
1261     }
1262     if (!found)
1263     {
1264       String[] options = { "OK", "Help" };
1265       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1266               JvSwingUtils.wrapTooltip(true,
1267                       MessageManager.getString("label.chimera_missing")),
1268               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1269               null, options, options[0]);
1270       if (showHelp == JvOptionPane.NO_OPTION)
1271       {
1272         try
1273         {
1274           Help.showHelpWindow(HelpId.StructureViewer);
1275         } catch (HelpSetException e)
1276         {
1277           e.printStackTrace();
1278         }
1279       }
1280     }
1281   }
1282
1283   public class OptionsParam
1284   {
1285     private String name;
1286
1287     private String code;
1288
1289     public OptionsParam(String name, String code)
1290     {
1291       this.name = name;
1292       this.code = code;
1293     }
1294
1295     public String getName()
1296     {
1297       return name;
1298     }
1299
1300     public void setName(String name)
1301     {
1302       this.name = name;
1303     }
1304
1305     public String getCode()
1306     {
1307       return code;
1308     }
1309
1310     public void setCode(String code)
1311     {
1312       this.code = code;
1313     }
1314
1315     @Override
1316     public String toString()
1317     {
1318       return name;
1319     }
1320
1321     @Override
1322     public boolean equals(Object that)
1323     {
1324       if (!(that instanceof OptionsParam))
1325       {
1326         return false;
1327       }
1328       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1329     }
1330
1331     @Override
1332     public int hashCode()
1333     {
1334       return name.hashCode() + code.hashCode();
1335     }
1336   }
1337
1338   private class UrlListSelectionHandler implements ListSelectionListener
1339   {
1340
1341     @Override
1342     public void valueChanged(ListSelectionEvent e)
1343     {
1344       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1345
1346       int index = lsm.getMinSelectionIndex();
1347       if (index == -1)
1348       {
1349         // no selection, so disable delete/edit buttons
1350         editLink.setEnabled(false);
1351         deleteLink.setEnabled(false);
1352         return;
1353       }
1354       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1355
1356       // enable/disable edit and delete link buttons
1357       if (((UrlLinkTableModel) linkUrlTable.getModel())
1358               .isRowDeletable(modelIndex))
1359       {
1360         deleteLink.setEnabled(true);
1361       }
1362       else
1363       {
1364         deleteLink.setEnabled(false);
1365       }
1366
1367       if (((UrlLinkTableModel) linkUrlTable.getModel())
1368               .isRowEditable(modelIndex))
1369       {
1370         editLink.setEnabled(true);
1371       }
1372       else
1373       {
1374         editLink.setEnabled(false);
1375       }
1376     }
1377   }
1378
1379 }