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   private String previousProxyType;
 126
 127   /**
 128    * Holds name and link separated with | character. Sequence ID must be
 129    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 130    */
 131   public static UrlProviderI sequenceUrlLinks;
 132
 133   public static UrlLinkTableModel dataModel;
 134
 135   /**
 136    * Holds name and link separated with | character. Sequence IDS and Sequences
 137    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 138    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 139    * for first and second token specified after a pipe character at end |,|.
 140    * (TODO: proper escape for using | to separate ids or sequences
 141    */
 142
 143   public static List<String> groupURLLinks;
 144   static
 145   {
 146     // get links selected to be in the menu (SEQUENCE_LINKS)
 147     // and links entered by the user but not selected (STORED_LINKS)
 148     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 149     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 150     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 151             UrlConstants.DEFAULT_LABEL);
 152
 153     // if both links lists are empty, add the DEFAULT_URL link
 154     // otherwise we assume the default link is in one of the lists
 155     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 156     {
 157       inMenuString = UrlConstants.DEFAULT_STRING;
 158     }
 159     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 160             inMenuString, notInMenuString);
 161     sequenceUrlLinks = factory.createUrlProvider();
 162     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 163
 164     /**
 165      * TODO: reformulate groupURL encoding so two or more can be stored in the
 166      * .properties file as '|' separated strings
 167      */
 168
 169     groupURLLinks = new ArrayList<>();
 170   }
 171
 172   JInternalFrame frame;
 173
 174   private WsPreferences wsPrefs;
 175
 176   private OptionsParam promptEachTimeOpt = new OptionsParam(
 177           MessageManager.getString("label.prompt_each_time"),
 178           "Prompt each time");
 179
 180   private OptionsParam lineArtOpt = new OptionsParam(
 181           MessageManager.getString("label.lineart"), "Lineart");
 182
 183   private OptionsParam textOpt = new OptionsParam(
 184           MessageManager.getString("action.text"), "Text");
 185
 186   /**
 187    * Creates a new Preferences object.
 188    */
 189   public Preferences()
 190   {
 191     new Preferences(0);
 192   }
 193
 194   public Preferences(int selectTab)
 195   {
 196     new Preferences(selectTab, null);
 197   }
 198
 199   public Preferences(int selectTab, String message)
 200   {
 201     super(selectTab, message);
 202     frame = new JInternalFrame();
 203     frame.setContentPane(this);
 204     wsPrefs = new WsPreferences();
 205     wsTab.add(wsPrefs, BorderLayout.CENTER);
 206     int width = 500, height = 450;
 207     new jalview.util.Platform();
 208     if (Platform.isAMac())
 209     {
 210       width = 570;
 211       height = 480;
 212     }
 213
 214     Desktop.addInternalFrame(frame,
 215             MessageManager.getString("label.preferences"), width, height);
 216     frame.setMinimumSize(new Dimension(width, height));
 217
 218     /*
 219      * Set Visual tab defaults
 220      */
 221     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 222     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 223     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 224     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 225
 226     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 227     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 228     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 229     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 230     showUnconserved
 231             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 232     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 233     showGroupConsensus
 234             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 235     showGroupConservation.setSelected(
 236             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 237     showConsensHistogram.setSelected(
 238             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 239     showConsensLogo
 240             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 241     showNpTooltip
 242             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 243     showDbRefTooltip
 244             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 245
 246     String[] fonts = java.awt.GraphicsEnvironment
 247             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 248     for (int i = 0; i < fonts.length; i++)
 249     {
 250       fontNameCB.addItem(fonts[i]);
 251     }
 252
 253     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 254     {
 255       fontSizeCB.addItem(i + "");
 256     }
 257
 258     fontStyleCB.addItem("plain");
 259     fontStyleCB.addItem("bold");
 260     fontStyleCB.addItem("italic");
 261
 262     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 263     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 264     fontStyleCB.setSelectedItem(
 265             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 266
 267     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 268     scaleProteinToCdna
 269             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 270
 271     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 272
 273     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 274
 275     gapSymbolCB.addItem("-");
 276     gapSymbolCB.addItem(".");
 277
 278     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 279
 280     sortby.addItem("No sort");
 281     sortby.addItem("Id");
 282     sortby.addItem("Pairwise Identity");
 283     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 284
 285     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 286     sortAnnBy
 287             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 288     sortAnnBy
 289             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 290     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 291             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 292                     SequenceAnnotationOrder.NONE.name()));
 293     sortAnnBy.setSelectedItem(savedSort.toString());
 294
 295     sortAutocalc.addItem("Autocalculated first");
 296     sortAutocalc.addItem("Autocalculated last");
 297     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 298     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 299             : sortAutocalc.getItemAt(1));
 300     startupCheckbox
 301             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 302     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 303             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 304                     + "/examples/exampleFile_2_3.jar"));
 305
 306     /*
 307      * Set Colours tab defaults
 308      */
 309     protColour.addItem(ResidueColourScheme.NONE);
 310     nucColour.addItem(ResidueColourScheme.NONE);
 311     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 312     {
 313       String name = cs.getSchemeName();
 314       protColour.addItem(name);
 315       nucColour.addItem(name);
 316     }
 317     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 318             ResidueColourScheme.NONE);
 319     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 320     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 321     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 322     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 323     minColour.setBackground(
 324             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 325     maxColour.setBackground(
 326             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 327
 328     /*
 329      * Set overview panel defaults
 330      */
 331     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 332             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 333     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 334             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 335     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 336     gapLabel.setEnabled(!useLegacyGap.isSelected());
 337     gapColour.setEnabled(!useLegacyGap.isSelected());
 338     showHiddenAtStart
 339             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 340
 341     /*
 342      * Set Structure tab defaults.
 343      */
 344     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 345     structFromPdb.setSelected(structSelected);
 346     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 347     useRnaView.setEnabled(structSelected);
 348     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 349     addSecondaryStructure.setEnabled(structSelected);
 350     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 351     addTempFactor.setEnabled(structSelected);
 352     structViewer.setSelectedItem(
 353             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 354     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 355     chimeraPath.addActionListener(new ActionListener()
 356     {
 357       @Override
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         validateChimeraPath();
 361       }
 362     });
 363
 364     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 365     {
 366       siftsMapping.setSelected(true);
 367     }
 368     else
 369     {
 370       nwMapping.setSelected(true);
 371     }
 372
 373     SiftsSettings
 374             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 375
 376     /*
 377      * Set Connections tab defaults
 378      */
 379
 380     // set up sorting
 381     linkUrlTable.setModel(dataModel);
 382     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 383             linkUrlTable.getModel());
 384     linkUrlTable.setRowSorter(sorter);
 385     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 386
 387     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 388     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 389             SortOrder.DESCENDING));
 390     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 391             SortOrder.DESCENDING));
 392     sortKeys.add(
 393             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 394
 395     sorter.setSortKeys(sortKeys);
 396     sorter.sort();
 397
 398     // set up filtering
 399     ActionListener onReset;
 400     onReset = new ActionListener()
 401     {
 402       @Override
 403       public void actionPerformed(ActionEvent e)
 404       {
 405         filterTB.setText("");
 406         sorter.setRowFilter(RowFilter.regexFilter(""));
 407       }
 408
 409     };
 410     doReset.addActionListener(onReset);
 411
 412     // filter to display only custom urls
 413     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 414     {
 415       @Override
 416       public boolean include(
 417               Entry<? extends TableModel, ? extends Object> entry)
 418       {
 419         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 420       }
 421     };
 422
 423     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 424             linkUrlTable.getModel());
 425     customSorter.setRowFilter(customUrlFilter);
 426
 427     ActionListener onCustomOnly;
 428     onCustomOnly = new ActionListener()
 429     {
 430       @Override
 431       public void actionPerformed(ActionEvent e)
 432       {
 433         filterTB.setText("");
 434         sorter.setRowFilter(customUrlFilter);
 435       }
 436     };
 437     userOnly.addActionListener(onCustomOnly);
 438
 439     filterTB.getDocument().addDocumentListener(new DocumentListener()
 440     {
 441       String caseInsensitiveFlag = "(?i)";
 442
 443       @Override
 444       public void changedUpdate(DocumentEvent e)
 445       {
 446         sorter.setRowFilter(RowFilter
 447                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 448       }
 449
 450       @Override
 451       public void removeUpdate(DocumentEvent e)
 452       {
 453         sorter.setRowFilter(RowFilter
 454                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 455       }
 456
 457       @Override
 458       public void insertUpdate(DocumentEvent e)
 459       {
 460         sorter.setRowFilter(RowFilter
 461                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 462       }
 463     });
 464
 465     // set up list selection functionality
 466     linkUrlTable.getSelectionModel()
 467             .addListSelectionListener(new UrlListSelectionHandler());
 468
 469     // set up radio buttons
 470     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 471             .getPrimaryColumn();
 472     String onClickName = linkUrlTable.getColumnName(onClickCol);
 473     linkUrlTable.getColumn(onClickName)
 474             .setCellRenderer(new RadioButtonRenderer());
 475     linkUrlTable.getColumn(onClickName)
 476             .setCellEditor(new RadioButtonEditor());
 477
 478     // get boolean columns and resize those to min possible
 479     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 480     {
 481       if (linkUrlTable.getModel().getColumnClass(column)
 482               .equals(Boolean.class))
 483       {
 484         TableColumn tableColumn = linkUrlTable.getColumnModel()
 485                 .getColumn(column);
 486         int preferredWidth = tableColumn.getMinWidth();
 487
 488         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 489                 column);
 490         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 491         int cwidth = c.getPreferredSize().width
 492                 + linkUrlTable.getIntercellSpacing().width;
 493         preferredWidth = Math.max(preferredWidth, cwidth);
 494
 495         tableColumn.setPreferredWidth(preferredWidth);
 496       }
 497     }
 498
 499     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 500     previousProxyType = proxyTypeString;
 501     switch (proxyTypeString)
 502     {
 503     case Cache.PROXYTYPE_NONE:
 504       proxyType.setSelected(noProxy.getModel(), true);
 505       break;
 506     case Cache.PROXYTYPE_SYSTEM:
 507       proxyType.setSelected(systemProxy.getModel(), true);
 508       break;
 509     case Cache.PROXYTYPE_CUSTOM:
 510       proxyType.setSelected(customProxy.getModel(), true);
 511       break;
 512     default:
 513       Cache.log.warn(
 514               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 515                       + proxyTypeString);
 516     }
 517     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 518     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 519     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 520     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 521     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 522     proxyAuthUsernameTB
 523             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 524     // we are not storing or retrieving proxy password from .jalview_properties
 525     proxyAuthPasswordTB.setText(Cache.proxyAuthPassword == null ? ""
 526             : new String(Cache.proxyAuthPassword));
 527     setCustomProxyEnabled();
 528
 529     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 530
 531     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 532     // note antisense here: default is true
 533     questionnaire
 534             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 535     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 536
 537     /*
 538      * Set Output tab defaults
 539      */
 540     epsRendering.addItem(promptEachTimeOpt);
 541     epsRendering.addItem(lineArtOpt);
 542     epsRendering.addItem(textOpt);
 543     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 544             "Prompt each time");
 545     if (defaultEPS.equalsIgnoreCase("Text"))
 546     {
 547       epsRendering.setSelectedItem(textOpt);
 548     }
 549     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 550     {
 551       epsRendering.setSelectedItem(lineArtOpt);
 552     }
 553     else
 554     {
 555       epsRendering.setSelectedItem(promptEachTimeOpt);
 556     }
 557     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 558     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 559     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 560     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 561     userIdWidth.setText(wi == null ? "" : wi.toString());
 562     // TODO: refactor to use common enum via FormatAdapter and allow extension
 563     // for new flat file formats
 564     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 565     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 566     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 567     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 568     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 569     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 570     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 571     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 572     embbedBioJSON
 573             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 574
 575     /*
 576      * Set Editing tab defaults
 577      */
 578     autoCalculateConsCheck
 579             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 580     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 581     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 582
 583     annotations_actionPerformed(null); // update the display of the annotation
 584                                        // settings
 585
 586     /*
 587      * Set Backups tab defaults
 588      */
 589     loadLastSavedBackupsOptions();
 590   }
 591
 592   /**
 593    * Save user selections on the Preferences tabs to the Cache and write out to
 594    * file.
 595    *
 596    * @param e
 597    */
 598   @Override
 599   public void ok_actionPerformed(ActionEvent e)
 600   {
 601     if (!validateSettings())
 602     {
 603       return;
 604     }
 605
 606     /*
 607      * Save Visual settings
 608      */
 609     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 610             Boolean.toString(seqLimit.isSelected()));
 611     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 612             Boolean.toString(rightAlign.isSelected()));
 613     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 614             Boolean.toString(fullScreen.isSelected()));
 615     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 616             Boolean.toString(openoverv.isSelected()));
 617     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 618             Boolean.toString(annotations.isSelected()));
 619     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 620             Boolean.toString(conservation.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 622             Boolean.toString(quality.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 624             Boolean.toString(identity.isSelected()));
 625
 626     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 627             gapSymbolCB.getSelectedItem().toString());
 628
 629     Cache.applicationProperties.setProperty("FONT_NAME",
 630             fontNameCB.getSelectedItem().toString());
 631     Cache.applicationProperties.setProperty("FONT_STYLE",
 632             fontStyleCB.getSelectedItem().toString());
 633     Cache.applicationProperties.setProperty("FONT_SIZE",
 634             fontSizeCB.getSelectedItem().toString());
 635
 636     Cache.applicationProperties.setProperty("ID_ITALICS",
 637             Boolean.toString(idItalics.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 639             Boolean.toString(showUnconserved.isSelected()));
 640     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 641             Boolean.toString(showOccupancy.isSelected()));
 642     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 643             Boolean.toString(showGroupConsensus.isSelected()));
 644     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 645             Boolean.toString(showGroupConservation.isSelected()));
 646     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 647             Boolean.toString(showConsensHistogram.isSelected()));
 648     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 649             Boolean.toString(showConsensLogo.isSelected()));
 650     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 651             Boolean.toString(smoothFont.isSelected()));
 652     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 653             Boolean.toString(scaleProteinToCdna.isSelected()));
 654     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 655             Boolean.toString(showNpTooltip.isSelected()));
 656     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 657             Boolean.toString(showDbRefTooltip.isSelected()));
 658
 659     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 660             Boolean.toString(wrap.isSelected()));
 661
 662     Cache.applicationProperties.setProperty("STARTUP_FILE",
 663             startupFileTextfield.getText());
 664     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 665             Boolean.toString(startupCheckbox.isSelected()));
 666
 667     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 668             sortby.getSelectedItem().toString());
 669
 670     // convert description of sort order to enum name for save
 671     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 672             .forDescription(sortAnnBy.getSelectedItem().toString());
 673     if (annSortOrder != null)
 674     {
 675       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 676               annSortOrder.name());
 677     }
 678
 679     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 680     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 681             Boolean.valueOf(showAutocalcFirst).toString());
 682
 683     /*
 684      * Save Colours settings
 685      */
 686     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 687             protColour.getSelectedItem().toString());
 688     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 689             nucColour.getSelectedItem().toString());
 690     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 691             minColour.getBackground());
 692     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 693             maxColour.getBackground());
 694
 695     /*
 696      * Save Overview settings
 697      */
 698     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 699     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 700     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 701             Boolean.toString(useLegacyGap.isSelected()));
 702     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 703             Boolean.toString(showHiddenAtStart.isSelected()));
 704
 705     /*
 706      * Save Structure settings
 707      */
 708     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 709             Boolean.toString(addTempFactor.isSelected()));
 710     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 711             Boolean.toString(addSecondaryStructure.isSelected()));
 712     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 713             Boolean.toString(useRnaView.isSelected()));
 714     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 715             Boolean.toString(structFromPdb.isSelected()));
 716     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 717             structViewer.getSelectedItem().toString());
 718     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 719     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 720             Boolean.toString(siftsMapping.isSelected()));
 721     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 722
 723     /*
 724      * Save Output settings
 725      */
 726     Cache.applicationProperties.setProperty("EPS_RENDERING",
 727             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 728
 729     /*
 730      * Save Connections settings
 731      */
 732     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 733
 734     jalview.util.BrowserLauncher.resetBrowser();
 735
 736     // save user-defined and selected links
 737     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 738     if (menuLinks.isEmpty())
 739     {
 740       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 741     }
 742     else
 743     {
 744       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 745               menuLinks.toString());
 746     }
 747
 748     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 749     if (nonMenuLinks.isEmpty())
 750     {
 751       Cache.applicationProperties.remove("STORED_LINKS");
 752     }
 753     else
 754     {
 755       Cache.applicationProperties.setProperty("STORED_LINKS",
 756               nonMenuLinks.toString());
 757     }
 758
 759     Cache.applicationProperties.setProperty("DEFAULT_URL",
 760             sequenceUrlLinks.getPrimaryUrlId());
 761
 762     // Proxy settings
 763     saveProxySettings();
 764
 765     Cache.setProperty("VERSION_CHECK",
 766             Boolean.toString(versioncheck.isSelected()));
 767     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 768     {
 769       // default is false - we only set this if the user has actively agreed
 770       Cache.setProperty("USAGESTATS",
 771               Boolean.toString(usagestats.isSelected()));
 772     }
 773     if (!questionnaire.isSelected())
 774     {
 775       Cache.setProperty("NOQUESTIONNAIRES", "true");
 776     }
 777     else
 778     {
 779       // special - made easy to edit a property file to disable questionnaires
 780       // by just adding the given line
 781       Cache.removeProperty("NOQUESTIONNAIRES");
 782     }
 783
 784     /*
 785      * Save Output settings
 786      */
 787     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 788             Boolean.toString(blcjv.isSelected()));
 789     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 790             Boolean.toString(clustaljv.isSelected()));
 791     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 792             Boolean.toString(fastajv.isSelected()));
 793     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 794             Boolean.toString(msfjv.isSelected()));
 795     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 796             Boolean.toString(pfamjv.isSelected()));
 797     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 798             Boolean.toString(pileupjv.isSelected()));
 799     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 800             Boolean.toString(pirjv.isSelected()));
 801     Cache.applicationProperties.setProperty("PIR_MODELLER",
 802             Boolean.toString(modellerOutput.isSelected()));
 803     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 804             Boolean.toString(embbedBioJSON.isSelected()));
 805     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 806
 807     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 808             Boolean.toString(autoIdWidth.isSelected()));
 809     userIdWidth_actionPerformed();
 810     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 811             userIdWidth.getText());
 812
 813     /*
 814      * Save Editing settings
 815      */
 816     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 817             Boolean.toString(autoCalculateConsCheck.isSelected()));
 818     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 819             Boolean.toString(sortByTree.isSelected()));
 820     Cache.applicationProperties.setProperty("PAD_GAPS",
 821             Boolean.toString(padGaps.isSelected()));
 822
 823     wsPrefs.updateAndRefreshWsMenuConfig(false);
 824
 825     /*
 826      * Save Backups settings
 827      */
 828     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 829             Boolean.toString(enableBackupFiles.isSelected()));
 830     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 831     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 832             Integer.toString(preset));
 833
 834     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 835     {
 836       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 837       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 838               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 839       Cache.applicationProperties.setProperty(
 840               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 841     }
 842
 843     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 844             .get(preset);
 845     Cache.applicationProperties.setProperty(
 846             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 847
 848     Cache.saveProperties();
 849     Desktop.instance.doConfigureStructurePrefs();
 850     try
 851     {
 852       frame.setClosed(true);
 853     } catch (Exception ex)
 854     {
 855     }
 856   }
 857
 858   public void saveProxySettings()
 859   {
 860     Cache.applicationProperties.setProperty("USE_PROXY",
 861             customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 862                     : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 863                             : Cache.PROXYTYPE_SYSTEM);
 864     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 865     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 866     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 867     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 868     Cache.setOrRemove("PROXY_AUTH",
 869             Boolean.toString(proxyAuth.isSelected()));
 870     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
 871     Cache.proxyAuthPassword = proxyAuthPasswordTB.getPassword();
 872     Cache.setProxyPropertiesFromPreferences(previousProxyType);
 873   }
 874
 875   /**
 876    * Do any necessary validation before saving settings. Return focus to the
 877    * first tab which fails validation.
 878    *
 879    * @return
 880    */
 881   private boolean validateSettings()
 882   {
 883     if (!validateStructure())
 884     {
 885       structureTab.requestFocusInWindow();
 886       return false;
 887     }
 888     return true;
 889   }
 890
 891   @Override
 892   protected boolean validateStructure()
 893   {
 894     return validateChimeraPath();
 895
 896   }
 897
 898   /**
 899    * DOCUMENT ME!
 900    */
 901   @Override
 902   public void startupFileTextfield_mouseClicked()
 903   {
 904     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 905     JalviewFileChooser chooser = JalviewFileChooser
 906             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 907     chooser.setFileView(new JalviewFileView());
 908     chooser.setDialogTitle(
 909             MessageManager.getString("label.select_startup_file"));
 910
 911     int value = chooser.showOpenDialog(this);
 912
 913     if (value == JalviewFileChooser.APPROVE_OPTION)
 914     {
 915       FileFormatI format = chooser.getSelectedFormat();
 916       if (format != null)
 917       {
 918         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 919                 format.getName());
 920       }
 921       startupFileTextfield
 922               .setText(chooser.getSelectedFile().getAbsolutePath());
 923     }
 924   }
 925
 926   /**
 927    * DOCUMENT ME!
 928    *
 929    * @param e
 930    *          DOCUMENT ME!
 931    */
 932   @Override
 933   public void cancel_actionPerformed(ActionEvent e)
 934   {
 935     try
 936     {
 937       wsPrefs.updateWsMenuConfig(true);
 938       wsPrefs.refreshWs_actionPerformed(e);
 939       frame.setClosed(true);
 940     } catch (Exception ex)
 941     {
 942     }
 943   }
 944
 945   /**
 946    * DOCUMENT ME!
 947    *
 948    * @param e
 949    *          DOCUMENT ME!
 950    */
 951   @Override
 952   public void annotations_actionPerformed(ActionEvent e)
 953   {
 954     conservation.setEnabled(annotations.isSelected());
 955     quality.setEnabled(annotations.isSelected());
 956     identity.setEnabled(annotations.isSelected());
 957     showOccupancy.setEnabled(annotations.isSelected());
 958     showGroupConsensus.setEnabled(annotations.isSelected());
 959     showGroupConservation.setEnabled(annotations.isSelected());
 960     showConsensHistogram.setEnabled(annotations.isSelected()
 961             && (identity.isSelected() || showGroupConsensus.isSelected()));
 962     showConsensLogo.setEnabled(annotations.isSelected()
 963             && (identity.isSelected() || showGroupConsensus.isSelected()));
 964   }
 965
 966   @Override
 967   public void newLink_actionPerformed(ActionEvent e)
 968   {
 969     GSequenceLink link = new GSequenceLink();
 970     boolean valid = false;
 971     while (!valid)
 972     {
 973       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 974               MessageManager.getString("label.new_sequence_url_link"),
 975               JvOptionPane.OK_CANCEL_OPTION, -1,
 976               null) == JvOptionPane.OK_OPTION)
 977       {
 978         if (link.checkValid())
 979         {
 980           if (((UrlLinkTableModel) linkUrlTable.getModel())
 981                   .isUniqueName(link.getName()))
 982           {
 983             ((UrlLinkTableModel) linkUrlTable.getModel())
 984                     .insertRow(link.getName(), link.getURL());
 985             valid = true;
 986           }
 987           else
 988           {
 989             link.notifyDuplicate();
 990             continue;
 991           }
 992         }
 993       }
 994       else
 995       {
 996         break;
 997       }
 998     }
 999   }
1000
1001   @Override
1002   public void editLink_actionPerformed(ActionEvent e)
1003   {
1004     GSequenceLink link = new GSequenceLink();
1005
1006     int index = linkUrlTable.getSelectedRow();
1007     if (index == -1)
1008     {
1009       // button no longer enabled if row is not selected
1010       Cache.log.debug("Edit with no row selected in linkUrlTable");
1011       return;
1012     }
1013
1014     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1015             .getNameColumn();
1016     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1017             .getUrlColumn();
1018     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1019     link.setName(oldName);
1020     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1021
1022     boolean valid = false;
1023     while (!valid)
1024     {
1025       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1026               MessageManager.getString("label.edit_sequence_url_link"),
1027               JvOptionPane.OK_CANCEL_OPTION, -1,
1028               null) == JvOptionPane.OK_OPTION)
1029       {
1030         if (link.checkValid())
1031         {
1032           if ((oldName.equals(link.getName()))
1033                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1034                           .isUniqueName(link.getName())))
1035           {
1036             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1037             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1038             valid = true;
1039           }
1040           else
1041           {
1042             link.notifyDuplicate();
1043             continue;
1044           }
1045         }
1046       }
1047       else
1048       {
1049         break;
1050       }
1051     }
1052   }
1053
1054   @Override
1055   public void deleteLink_actionPerformed(ActionEvent e)
1056   {
1057     int index = linkUrlTable.getSelectedRow();
1058     int modelIndex = -1;
1059     if (index == -1)
1060     {
1061       // button no longer enabled if row is not selected
1062       Cache.log.debug("Delete with no row selected in linkUrlTable");
1063       return;
1064     }
1065     else
1066     {
1067       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1068     }
1069
1070     // make sure we use the model index to delete, and not the table index
1071     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1072   }
1073
1074   @Override
1075   public void defaultBrowser_mouseClicked(MouseEvent e)
1076   {
1077     JFileChooser chooser = new JFileChooser(".");
1078     chooser.setDialogTitle(
1079             MessageManager.getString("label.select_default_browser"));
1080
1081     int value = chooser.showOpenDialog(this);
1082
1083     if (value == JFileChooser.APPROVE_OPTION)
1084     {
1085       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1086     }
1087
1088   }
1089
1090   /*
1091    * (non-Javadoc)
1092    *
1093    * @see
1094    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1095    * .ActionEvent)
1096    */
1097   @Override
1098   protected void showunconserved_actionPerformed(ActionEvent e)
1099   {
1100     // TODO Auto-generated method stub
1101     super.showunconserved_actionPerformed(e);
1102   }
1103
1104   public static List<String> getGroupURLLinks()
1105   {
1106     return groupURLLinks;
1107   }
1108
1109   @Override
1110   public void minColour_actionPerformed(JPanel panel)
1111   {
1112     Color col = JColorChooser.showDialog(this,
1113             MessageManager.getString("label.select_colour_minimum_value"),
1114             minColour.getBackground());
1115     if (col != null)
1116     {
1117       panel.setBackground(col);
1118     }
1119     panel.repaint();
1120   }
1121
1122   @Override
1123   public void maxColour_actionPerformed(JPanel panel)
1124   {
1125     Color col = JColorChooser.showDialog(this,
1126             MessageManager.getString("label.select_colour_maximum_value"),
1127             maxColour.getBackground());
1128     if (col != null)
1129     {
1130       panel.setBackground(col);
1131     }
1132     panel.repaint();
1133   }
1134
1135   @Override
1136   public void gapColour_actionPerformed(JPanel gap)
1137   {
1138     if (!useLegacyGap.isSelected())
1139     {
1140       Color col = JColorChooser.showDialog(this,
1141               MessageManager.getString("label.select_gap_colour"),
1142               gapColour.getBackground());
1143       if (col != null)
1144       {
1145         gap.setBackground(col);
1146       }
1147       gap.repaint();
1148     }
1149   }
1150
1151   @Override
1152   public void hiddenColour_actionPerformed(JPanel hidden)
1153   {
1154     Color col = JColorChooser.showDialog(this,
1155             MessageManager.getString("label.select_hidden_colour"),
1156             hiddenColour.getBackground());
1157     if (col != null)
1158     {
1159       hidden.setBackground(col);
1160     }
1161     hidden.repaint();
1162   }
1163
1164   @Override
1165   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1166   {
1167     boolean enabled = useLegacyGap.isSelected();
1168     if (enabled)
1169     {
1170       gapColour.setBackground(
1171               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1172     }
1173     else
1174     {
1175       gapColour.setBackground(
1176               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1177     }
1178     gapColour.setEnabled(!enabled);
1179     gapLabel.setEnabled(!enabled);
1180   }
1181
1182   @Override
1183   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1184   {
1185     useLegacyGap.setSelected(false);
1186     useLegacyGaps_actionPerformed(null);
1187     showHiddenAtStart.setSelected(false);
1188     hiddenColour.setBackground(
1189             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1190   }
1191
1192   @Override
1193   protected void userIdWidth_actionPerformed()
1194   {
1195     try
1196     {
1197       String val = userIdWidth.getText().trim();
1198       if (val.length() > 0)
1199       {
1200         Integer iw = Integer.parseInt(val);
1201         if (iw.intValue() < 12)
1202         {
1203           throw new NumberFormatException();
1204         }
1205         userIdWidth.setText(iw.toString());
1206       }
1207     } catch (NumberFormatException x)
1208     {
1209       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1210               MessageManager
1211                       .getString("warn.user_defined_width_requirements"),
1212               MessageManager.getString("label.invalid_id_column_width"),
1213               JvOptionPane.WARNING_MESSAGE);
1214       userIdWidth.setText("");
1215     }
1216   }
1217
1218   @Override
1219   protected void autoIdWidth_actionPerformed()
1220   {
1221     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1222     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1223   }
1224
1225   /**
1226    * Returns true if chimera path is to a valid executable, else show an error
1227    * dialog.
1228    */
1229   private boolean validateChimeraPath()
1230   {
1231     if (chimeraPath.getText().trim().length() > 0)
1232     {
1233       File f = new File(chimeraPath.getText());
1234       if (!f.canExecute())
1235       {
1236         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1237                 MessageManager.getString("label.invalid_chimera_path"),
1238                 MessageManager.getString("label.invalid_name"),
1239                 JvOptionPane.ERROR_MESSAGE);
1240         return false;
1241       }
1242     }
1243     return true;
1244   }
1245
1246   /**
1247    * If Chimera is selected, check it can be found on default or user-specified
1248    * path, if not show a warning/help dialog.
1249    */
1250   @Override
1251   protected void structureViewer_actionPerformed(String selectedItem)
1252   {
1253     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1254     {
1255       return;
1256     }
1257     boolean found = false;
1258
1259     /*
1260      * Try user-specified and standard paths for Chimera executable.
1261      */
1262     List<String> paths = StructureManager.getChimeraPaths();
1263     paths.add(0, chimeraPath.getText());
1264     for (String path : paths)
1265     {
1266       if (new File(path.trim()).canExecute())
1267       {
1268         found = true;
1269         break;
1270       }
1271     }
1272     if (!found)
1273     {
1274       String[] options = { "OK", "Help" };
1275       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1276               JvSwingUtils.wrapTooltip(true,
1277                       MessageManager.getString("label.chimera_missing")),
1278               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1279               null, options, options[0]);
1280       if (showHelp == JvOptionPane.NO_OPTION)
1281       {
1282         try
1283         {
1284           Help.showHelpWindow(HelpId.StructureViewer);
1285         } catch (HelpSetException e)
1286         {
1287           e.printStackTrace();
1288         }
1289       }
1290     }
1291   }
1292
1293   public class OptionsParam
1294   {
1295     private String name;
1296
1297     private String code;
1298
1299     public OptionsParam(String name, String code)
1300     {
1301       this.name = name;
1302       this.code = code;
1303     }
1304
1305     public String getName()
1306     {
1307       return name;
1308     }
1309
1310     public void setName(String name)
1311     {
1312       this.name = name;
1313     }
1314
1315     public String getCode()
1316     {
1317       return code;
1318     }
1319
1320     public void setCode(String code)
1321     {
1322       this.code = code;
1323     }
1324
1325     @Override
1326     public String toString()
1327     {
1328       return name;
1329     }
1330
1331     @Override
1332     public boolean equals(Object that)
1333     {
1334       if (!(that instanceof OptionsParam))
1335       {
1336         return false;
1337       }
1338       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1339     }
1340
1341     @Override
1342     public int hashCode()
1343     {
1344       return name.hashCode() + code.hashCode();
1345     }
1346   }
1347
1348   private class UrlListSelectionHandler implements ListSelectionListener
1349   {
1350
1351     @Override
1352     public void valueChanged(ListSelectionEvent e)
1353     {
1354       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1355
1356       int index = lsm.getMinSelectionIndex();
1357       if (index == -1)
1358       {
1359         // no selection, so disable delete/edit buttons
1360         editLink.setEnabled(false);
1361         deleteLink.setEnabled(false);
1362         return;
1363       }
1364       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1365
1366       // enable/disable edit and delete link buttons
1367       if (((UrlLinkTableModel) linkUrlTable.getModel())
1368               .isRowDeletable(modelIndex))
1369       {
1370         deleteLink.setEnabled(true);
1371       }
1372       else
1373       {
1374         deleteLink.setEnabled(false);
1375       }
1376
1377       if (((UrlLinkTableModel) linkUrlTable.getModel())
1378               .isRowEditable(modelIndex))
1379       {
1380         editLink.setEnabled(true);
1381       }
1382       else
1383       {
1384         editLink.setEnabled(false);
1385       }
1386     }
1387   }
1388
1389 }