src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  28 import jalview.io.BackupFilesPresetEntry;
  29 import jalview.io.FileFormatI;
  30 import jalview.io.JalviewFileChooser;
  31 import jalview.io.JalviewFileView;
  32 import jalview.jbgui.GPreferences;
  33 import jalview.jbgui.GSequenceLink;
  34 import jalview.schemes.ColourSchemeI;
  35 import jalview.schemes.ColourSchemes;
  36 import jalview.schemes.ResidueColourScheme;
  37 import jalview.urls.UrlLinkTableModel;
  38 import jalview.urls.api.UrlProviderFactoryI;
  39 import jalview.urls.api.UrlProviderI;
  40 import jalview.urls.desktop.DesktopUrlProviderFactory;
  41 import jalview.util.MessageManager;
  42 import jalview.util.Platform;
  43 import jalview.util.UrlConstants;
  44 import jalview.ws.sifts.SiftsSettings;
  45
  46 import java.awt.BorderLayout;
  47 import java.awt.Color;
  48 import java.awt.Component;
  49 import java.awt.Dimension;
  50 import java.awt.Font;
  51 import java.awt.event.ActionEvent;
  52 import java.awt.event.ActionListener;
  53 import java.awt.event.MouseEvent;
  54 import java.io.File;
  55 import java.util.ArrayList;
  56 import java.util.List;
  57
  58 import javax.help.HelpSetException;
  59 import javax.swing.JColorChooser;
  60 import javax.swing.JFileChooser;
  61 import javax.swing.JInternalFrame;
  62 import javax.swing.JPanel;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.RowFilter;
  65 import javax.swing.RowSorter;
  66 import javax.swing.SortOrder;
  67 import javax.swing.event.DocumentEvent;
  68 import javax.swing.event.DocumentListener;
  69 import javax.swing.event.ListSelectionEvent;
  70 import javax.swing.event.ListSelectionListener;
  71 import javax.swing.table.TableCellRenderer;
  72 import javax.swing.table.TableColumn;
  73 import javax.swing.table.TableModel;
  74 import javax.swing.table.TableRowSorter;
  75
  76 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  77
  78 /**
  79  * DOCUMENT ME!
  80  *
  81  * @author $author$
  82  * @version $Revision$
  83  */
  84 public class Preferences extends GPreferences
  85 {
  86   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  87
  88   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  89
  90   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  91
  92   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  93
  94   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  95
  96   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  97
  98   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  99
 100   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 101
 102   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 103
 104   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 105
 106   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 107
 108   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 109
 110   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 111
 112   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 113
 114   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 115
 116   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 117
 118   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 119
 120   public static final String GAP_COLOUR = "GAP_COLOUR";
 121
 122   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 123
 124   private static final int MIN_FONT_SIZE = 1;
 125
 126   private static final int MAX_FONT_SIZE = 30;
 127
 128   /**
 129    * Holds name and link separated with | character. Sequence ID must be
 130    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 131    */
 132   public static UrlProviderI sequenceUrlLinks;
 133
 134   public static UrlLinkTableModel dataModel;
 135
 136   /**
 137    * Holds name and link separated with | character. Sequence IDS and Sequences
 138    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 139    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 140    * for first and second token specified after a pipe character at end |,|.
 141    * (TODO: proper escape for using | to separate ids or sequences
 142    */
 143
 144   public static List<String> groupURLLinks;
 145   static
 146   {
 147     // get links selected to be in the menu (SEQUENCE_LINKS)
 148     // and links entered by the user but not selected (STORED_LINKS)
 149     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 150     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 151     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 152             UrlConstants.DEFAULT_LABEL);
 153
 154     // if both links lists are empty, add the DEFAULT_URL link
 155     // otherwise we assume the default link is in one of the lists
 156     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 157     {
 158       inMenuString = UrlConstants.DEFAULT_STRING;
 159     }
 160     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 161             inMenuString, notInMenuString);
 162     sequenceUrlLinks = factory.createUrlProvider();
 163     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 164
 165     /**
 166      * TODO: reformulate groupURL encoding so two or more can be stored in the
 167      * .properties file as '|' separated strings
 168      */
 169
 170     groupURLLinks = new ArrayList<>();
 171   }
 172
 173   JInternalFrame frame;
 174
 175   private WsPreferences wsPrefs;
 176
 177   private OptionsParam promptEachTimeOpt = new OptionsParam(
 178           MessageManager.getString("label.prompt_each_time"),
 179           "Prompt each time");
 180
 181   private OptionsParam lineArtOpt = new OptionsParam(
 182           MessageManager.getString("label.lineart"), "Lineart");
 183
 184   private OptionsParam textOpt = new OptionsParam(
 185           MessageManager.getString("action.text"), "Text");
 186
 187   /**
 188    * Creates a new Preferences object.
 189    */
 190   public Preferences()
 191   {
 192     super();
 193     frame = new JInternalFrame();
 194     frame.setContentPane(this);
 195     wsPrefs = new WsPreferences();
 196     wsTab.add(wsPrefs, BorderLayout.CENTER);
 197     int width = 500, height = 450;
 198     new jalview.util.Platform();
 199     if (Platform.isAMac())
 200     {
 201       width = 570;
 202       height = 480;
 203     }
 204
 205     Desktop.addInternalFrame(frame,
 206             MessageManager.getString("label.preferences"), width, height);
 207     frame.setMinimumSize(new Dimension(width, height));
 208
 209     /*
 210      * Set Visual tab defaults
 211      */
 212     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 213     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 214     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 215     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 216
 217     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 218     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 219     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 220     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 221     showUnconserved
 222             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 223     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 224     showGroupConsensus
 225             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 226     showGroupConservation.setSelected(
 227             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 228     showConsensHistogram.setSelected(
 229             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 230     showConsensLogo
 231             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 232     showNpTooltip
 233             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 234     showDbRefTooltip
 235             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 236
 237     String[] fonts = java.awt.GraphicsEnvironment
 238             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 239     for (int i = 0; i < fonts.length; i++)
 240     {
 241       fontNameCB.addItem(fonts[i]);
 242     }
 243
 244     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 245     {
 246       fontSizeCB.addItem(i + "");
 247     }
 248
 249     fontStyleCB.addItem("plain");
 250     fontStyleCB.addItem("bold");
 251     fontStyleCB.addItem("italic");
 252
 253     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 254     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 255     fontStyleCB.setSelectedItem(
 256             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 257
 258     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 259     scaleProteinToCdna
 260             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 261
 262     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 263
 264     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 265
 266     gapSymbolCB.addItem("-");
 267     gapSymbolCB.addItem(".");
 268
 269     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 270
 271     sortby.addItem("No sort");
 272     sortby.addItem("Id");
 273     sortby.addItem("Pairwise Identity");
 274     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 275
 276     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 277     sortAnnBy
 278             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 279     sortAnnBy
 280             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 281     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 282             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 283                     SequenceAnnotationOrder.NONE.name()));
 284     sortAnnBy.setSelectedItem(savedSort.toString());
 285
 286     sortAutocalc.addItem("Autocalculated first");
 287     sortAutocalc.addItem("Autocalculated last");
 288     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 289     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 290             : sortAutocalc.getItemAt(1));
 291     startupCheckbox
 292             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 293     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 294             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 295                     + "/examples/exampleFile_2_3.jar"));
 296
 297     /*
 298      * Set Colours tab defaults
 299      */
 300     protColour.addItem(ResidueColourScheme.NONE);
 301     nucColour.addItem(ResidueColourScheme.NONE);
 302     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 303     {
 304       String name = cs.getSchemeName();
 305       protColour.addItem(name);
 306       nucColour.addItem(name);
 307     }
 308     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 309             ResidueColourScheme.NONE);
 310     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 311     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 312     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 313     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 314     minColour.setBackground(
 315             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 316     maxColour.setBackground(
 317             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 318
 319     /*
 320      * Set overview panel defaults
 321      */
 322     gapColour.setBackground(
 323             Cache.getDefaultColour(GAP_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 325     hiddenColour.setBackground(
 326             Cache.getDefaultColour(HIDDEN_COLOUR,
 327                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 328     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 329     gapLabel.setEnabled(!useLegacyGap.isSelected());
 330     gapColour.setEnabled(!useLegacyGap.isSelected());
 331     showHiddenAtStart
 332             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 333
 334     /*
 335      * Set Structure tab defaults.
 336      */
 337     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 338     structFromPdb.setSelected(structSelected);
 339     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 340     useRnaView.setEnabled(structSelected);
 341     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 342     addSecondaryStructure.setEnabled(structSelected);
 343     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 344     addTempFactor.setEnabled(structSelected);
 345     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 346     structViewer.setSelectedItem(viewerType);
 347     boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name());
 348     if (viewerType.equals(ViewerType.JMOL.name()))
 349     {
 350       chimeraPath.setText("");
 351     }
 352     else
 353     {
 354       chimeraPath.setText(Cache
 355               .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
 356     }
 357     chimeraPath.addActionListener(new ActionListener()
 358     {
 359       @Override
 360       public void actionPerformed(ActionEvent e)
 361       {
 362         if (validateChimeraPath())
 363         {
 364           Cache.setProperty(structViewer.getSelectedItem()
 365                   .equals(ViewerType.CHIMERAX.name())
 366                   ? CHIMERAX_PATH
 367                   : CHIMERA_PATH, chimeraPath.getText());
 368         }
 369       }
 370     });
 371
 372     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 373     {
 374       siftsMapping.setSelected(true);
 375     }
 376     else
 377     {
 378       nwMapping.setSelected(true);
 379     }
 380
 381     SiftsSettings
 382             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 383
 384     /*
 385      * Set Connections tab defaults
 386      */
 387
 388     // set up sorting
 389     linkUrlTable.setModel(dataModel);
 390     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 391             linkUrlTable.getModel());
 392     linkUrlTable.setRowSorter(sorter);
 393     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 394
 395     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 396     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 397             SortOrder.DESCENDING));
 398     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 399             SortOrder.DESCENDING));
 400     sortKeys.add(
 401             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 402
 403     sorter.setSortKeys(sortKeys);
 404     sorter.sort();
 405
 406     // set up filtering
 407     ActionListener onReset;
 408     onReset = new ActionListener()
 409     {
 410       @Override
 411       public void actionPerformed(ActionEvent e)
 412       {
 413         filterTB.setText("");
 414         sorter.setRowFilter(RowFilter.regexFilter(""));
 415       }
 416
 417     };
 418     doReset.addActionListener(onReset);
 419
 420     // filter to display only custom urls
 421     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 422     {
 423       @Override
 424       public boolean include(
 425               Entry<? extends TableModel, ? extends Object> entry)
 426       {
 427         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 428       }
 429     };
 430
 431     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 432             linkUrlTable.getModel());
 433     customSorter.setRowFilter(customUrlFilter);
 434
 435     ActionListener onCustomOnly;
 436     onCustomOnly = new ActionListener()
 437     {
 438       @Override
 439       public void actionPerformed(ActionEvent e)
 440       {
 441         filterTB.setText("");
 442         sorter.setRowFilter(customUrlFilter);
 443       }
 444     };
 445     userOnly.addActionListener(onCustomOnly);
 446
 447     filterTB.getDocument().addDocumentListener(new DocumentListener()
 448     {
 449       String caseInsensitiveFlag = "(?i)";
 450
 451       @Override
 452       public void changedUpdate(DocumentEvent e)
 453       {
 454         sorter.setRowFilter(RowFilter
 455                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 456       }
 457
 458       @Override
 459       public void removeUpdate(DocumentEvent e)
 460       {
 461         sorter.setRowFilter(RowFilter
 462                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 463       }
 464
 465       @Override
 466       public void insertUpdate(DocumentEvent e)
 467       {
 468         sorter.setRowFilter(RowFilter
 469                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 470       }
 471     });
 472
 473     // set up list selection functionality
 474     linkUrlTable.getSelectionModel()
 475             .addListSelectionListener(new UrlListSelectionHandler());
 476
 477     // set up radio buttons
 478     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 479             .getPrimaryColumn();
 480     String onClickName = linkUrlTable.getColumnName(onClickCol);
 481     linkUrlTable.getColumn(onClickName)
 482             .setCellRenderer(new RadioButtonRenderer());
 483     linkUrlTable.getColumn(onClickName)
 484             .setCellEditor(new RadioButtonEditor());
 485
 486     // get boolean columns and resize those to min possible
 487     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 488     {
 489       if (linkUrlTable.getModel().getColumnClass(column)
 490               .equals(Boolean.class))
 491       {
 492         TableColumn tableColumn = linkUrlTable.getColumnModel()
 493                 .getColumn(column);
 494         int preferredWidth = tableColumn.getMinWidth();
 495
 496         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 497                 column);
 498         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 499         int cwidth = c.getPreferredSize().width
 500                 + linkUrlTable.getIntercellSpacing().width;
 501         preferredWidth = Math.max(preferredWidth, cwidth);
 502
 503         tableColumn.setPreferredWidth(preferredWidth);
 504       }
 505     }
 506
 507     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 508     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 509     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 510     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 511
 512     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 513
 514     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 515     // note antisense here: default is true
 516     questionnaire
 517             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 518     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 519
 520     /*
 521      * Set Output tab defaults
 522      */
 523     epsRendering.addItem(promptEachTimeOpt);
 524     epsRendering.addItem(lineArtOpt);
 525     epsRendering.addItem(textOpt);
 526     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 527             "Prompt each time");
 528     if (defaultEPS.equalsIgnoreCase("Text"))
 529     {
 530       epsRendering.setSelectedItem(textOpt);
 531     }
 532     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 533     {
 534       epsRendering.setSelectedItem(lineArtOpt);
 535     }
 536     else
 537     {
 538       epsRendering.setSelectedItem(promptEachTimeOpt);
 539     }
 540     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 541     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 542     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 543     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 544     userIdWidth.setText(wi == null ? "" : wi.toString());
 545     // TODO: refactor to use common enum via FormatAdapter and allow extension
 546     // for new flat file formats
 547     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 548     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 549     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 550     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 551     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 552     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 553     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 554     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 555     embbedBioJSON
 556             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 557
 558     /*
 559      * Set Editing tab defaults
 560      */
 561     autoCalculateConsCheck
 562             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 563     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 564     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 565
 566     annotations_actionPerformed(null); // update the display of the annotation
 567                                        // settings
 568
 569
 570     /*
 571      * Set Backups tab defaults
 572      */
 573     loadLastSavedBackupsOptions();
 574   }
 575
 576   /**
 577    * Save user selections on the Preferences tabs to the Cache and write out to
 578    * file.
 579    *
 580    * @param e
 581    */
 582   @Override
 583   public void ok_actionPerformed(ActionEvent e)
 584   {
 585     if (!validateSettings())
 586     {
 587       return;
 588     }
 589
 590     /*
 591      * Save Visual settings
 592      */
 593     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 594             Boolean.toString(seqLimit.isSelected()));
 595     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 596             Boolean.toString(rightAlign.isSelected()));
 597     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 598             Boolean.toString(fullScreen.isSelected()));
 599     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 600             Boolean.toString(openoverv.isSelected()));
 601     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 602             Boolean.toString(annotations.isSelected()));
 603     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 604             Boolean.toString(conservation.isSelected()));
 605     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 606             Boolean.toString(quality.isSelected()));
 607     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 608             Boolean.toString(identity.isSelected()));
 609
 610     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 611             gapSymbolCB.getSelectedItem().toString());
 612
 613     Cache.applicationProperties.setProperty("FONT_NAME",
 614             fontNameCB.getSelectedItem().toString());
 615     Cache.applicationProperties.setProperty("FONT_STYLE",
 616             fontStyleCB.getSelectedItem().toString());
 617     Cache.applicationProperties.setProperty("FONT_SIZE",
 618             fontSizeCB.getSelectedItem().toString());
 619
 620     Cache.applicationProperties.setProperty("ID_ITALICS",
 621             Boolean.toString(idItalics.isSelected()));
 622     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 623             Boolean.toString(showUnconserved.isSelected()));
 624     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 625             Boolean.toString(showOccupancy.isSelected()));
 626     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 627             Boolean.toString(showGroupConsensus.isSelected()));
 628     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 629             Boolean.toString(showGroupConservation.isSelected()));
 630     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 631             Boolean.toString(showConsensHistogram.isSelected()));
 632     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 633             Boolean.toString(showConsensLogo.isSelected()));
 634     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 635             Boolean.toString(smoothFont.isSelected()));
 636     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 637             Boolean.toString(scaleProteinToCdna.isSelected()));
 638     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 639             Boolean.toString(showNpTooltip.isSelected()));
 640     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 641             Boolean.toString(showDbRefTooltip.isSelected()));
 642
 643     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 644             Boolean.toString(wrap.isSelected()));
 645
 646     Cache.applicationProperties.setProperty("STARTUP_FILE",
 647             startupFileTextfield.getText());
 648     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 649             Boolean.toString(startupCheckbox.isSelected()));
 650
 651     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 652             sortby.getSelectedItem().toString());
 653
 654     // convert description of sort order to enum name for save
 655     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 656             .forDescription(sortAnnBy.getSelectedItem().toString());
 657     if (annSortOrder != null)
 658     {
 659       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 660               annSortOrder.name());
 661     }
 662
 663     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 664     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 665             Boolean.valueOf(showAutocalcFirst).toString());
 666
 667     /*
 668      * Save Colours settings
 669      */
 670     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 671             protColour.getSelectedItem().toString());
 672     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 673             nucColour.getSelectedItem().toString());
 674     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 675             minColour.getBackground());
 676     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 677             maxColour.getBackground());
 678
 679     /*
 680      * Save Overview settings
 681      */
 682     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 683     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 684     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 685             Boolean.toString(useLegacyGap.isSelected()));
 686     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 687             Boolean.toString(showHiddenAtStart.isSelected()));
 688
 689     /*
 690      * Save Structure settings
 691      */
 692     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 693             Boolean.toString(addTempFactor.isSelected()));
 694     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 695             Boolean.toString(addSecondaryStructure.isSelected()));
 696     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 697             Boolean.toString(useRnaView.isSelected()));
 698     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 699             Boolean.toString(structFromPdb.isSelected()));
 700     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 701             structViewer.getSelectedItem().toString());
 702     boolean isChimeraX = structViewer.getSelectedItem().toString()
 703             .equals(ViewerType.CHIMERAX.name());
 704     Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH,
 705             chimeraPath.getText());
 706     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 707             Boolean.toString(siftsMapping.isSelected()));
 708     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 709
 710     /*
 711      * Save Output settings
 712      */
 713     Cache.applicationProperties.setProperty("EPS_RENDERING",
 714             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 715
 716     /*
 717      * Save Connections settings
 718      */
 719     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 720
 721     jalview.util.BrowserLauncher.resetBrowser();
 722
 723     // save user-defined and selected links
 724     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 725     if (menuLinks.isEmpty())
 726     {
 727       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 728     }
 729     else
 730     {
 731       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 732               menuLinks.toString());
 733     }
 734
 735     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 736     if (nonMenuLinks.isEmpty())
 737     {
 738       Cache.applicationProperties.remove("STORED_LINKS");
 739     }
 740     else
 741     {
 742       Cache.applicationProperties.setProperty("STORED_LINKS",
 743               nonMenuLinks.toString());
 744     }
 745
 746     Cache.applicationProperties.setProperty("DEFAULT_URL",
 747             sequenceUrlLinks.getPrimaryUrlId());
 748
 749     Cache.applicationProperties.setProperty("USE_PROXY",
 750             Boolean.toString(useProxy.isSelected()));
 751
 752     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 753
 754     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 755
 756     if (useProxy.isSelected())
 757     {
 758       System.setProperty("http.proxyHost", proxyServerTB.getText());
 759       System.setProperty("http.proxyPort", proxyPortTB.getText());
 760     }
 761     else
 762     {
 763       System.setProperty("http.proxyHost", "");
 764       System.setProperty("http.proxyPort", "");
 765     }
 766     Cache.setProperty("VERSION_CHECK",
 767             Boolean.toString(versioncheck.isSelected()));
 768     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 769     {
 770       // default is false - we only set this if the user has actively agreed
 771       Cache.setProperty("USAGESTATS",
 772               Boolean.toString(usagestats.isSelected()));
 773     }
 774     if (!questionnaire.isSelected())
 775     {
 776       Cache.setProperty("NOQUESTIONNAIRES", "true");
 777     }
 778     else
 779     {
 780       // special - made easy to edit a property file to disable questionnaires
 781       // by just adding the given line
 782       Cache.removeProperty("NOQUESTIONNAIRES");
 783     }
 784
 785     /*
 786      * Save Output settings
 787      */
 788     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 789             Boolean.toString(blcjv.isSelected()));
 790     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 791             Boolean.toString(clustaljv.isSelected()));
 792     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 793             Boolean.toString(fastajv.isSelected()));
 794     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 795             Boolean.toString(msfjv.isSelected()));
 796     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 797             Boolean.toString(pfamjv.isSelected()));
 798     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 799             Boolean.toString(pileupjv.isSelected()));
 800     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 801             Boolean.toString(pirjv.isSelected()));
 802     Cache.applicationProperties.setProperty("PIR_MODELLER",
 803             Boolean.toString(modellerOutput.isSelected()));
 804     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 805             Boolean.toString(embbedBioJSON.isSelected()));
 806     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 807
 808     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 809             Boolean.toString(autoIdWidth.isSelected()));
 810     userIdWidth_actionPerformed();
 811     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 812             userIdWidth.getText());
 813
 814     /*
 815      * Save Editing settings
 816      */
 817     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 818             Boolean.toString(autoCalculateConsCheck.isSelected()));
 819     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 820             Boolean.toString(sortByTree.isSelected()));
 821     Cache.applicationProperties.setProperty("PAD_GAPS",
 822             Boolean.toString(padGaps.isSelected()));
 823
 824     wsPrefs.updateAndRefreshWsMenuConfig(false);
 825
 826     /*
 827      * Save Backups settings
 828      */
 829     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 830             Boolean.toString(enableBackupFiles.isSelected()));
 831     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 832     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", 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
 840               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 841                       customBFPE.toString());
 842     }
 843
 844     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 845             .get(preset);
 846     Cache.applicationProperties.setProperty(
 847             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 848
 849     Cache.saveProperties();
 850     Desktop.instance.doConfigureStructurePrefs();
 851     try
 852     {
 853       frame.setClosed(true);
 854     } catch (Exception ex)
 855     {
 856     }
 857   }
 858
 859   /**
 860    * Do any necessary validation before saving settings. Return focus to the
 861    * first tab which fails validation.
 862    *
 863    * @return
 864    */
 865   private boolean validateSettings()
 866   {
 867     if (!validateStructure())
 868     {
 869       structureTab.requestFocusInWindow();
 870       return false;
 871     }
 872     return true;
 873   }
 874
 875   @Override
 876   protected boolean validateStructure()
 877   {
 878     return validateChimeraPath();
 879
 880   }
 881
 882   /**
 883    * DOCUMENT ME!
 884    */
 885   @Override
 886   public void startupFileTextfield_mouseClicked()
 887   {
 888     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 889     JalviewFileChooser chooser = JalviewFileChooser
 890             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 891     chooser.setFileView(new JalviewFileView());
 892     chooser.setDialogTitle(
 893             MessageManager.getString("label.select_startup_file"));
 894
 895     int value = chooser.showOpenDialog(this);
 896
 897     if (value == JalviewFileChooser.APPROVE_OPTION)
 898     {
 899       FileFormatI format = chooser.getSelectedFormat();
 900       if (format != null)
 901       {
 902         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 903                 format.getName());
 904       }
 905       startupFileTextfield
 906               .setText(chooser.getSelectedFile().getAbsolutePath());
 907     }
 908   }
 909
 910   /**
 911    * DOCUMENT ME!
 912    *
 913    * @param e
 914    *          DOCUMENT ME!
 915    */
 916   @Override
 917   public void cancel_actionPerformed(ActionEvent e)
 918   {
 919     try
 920     {
 921       wsPrefs.updateWsMenuConfig(true);
 922       wsPrefs.refreshWs_actionPerformed(e);
 923       frame.setClosed(true);
 924     } catch (Exception ex)
 925     {
 926     }
 927   }
 928
 929   /**
 930    * DOCUMENT ME!
 931    *
 932    * @param e
 933    *          DOCUMENT ME!
 934    */
 935   @Override
 936   public void annotations_actionPerformed(ActionEvent e)
 937   {
 938     conservation.setEnabled(annotations.isSelected());
 939     quality.setEnabled(annotations.isSelected());
 940     identity.setEnabled(annotations.isSelected());
 941     showOccupancy.setEnabled(annotations.isSelected());
 942     showGroupConsensus.setEnabled(annotations.isSelected());
 943     showGroupConservation.setEnabled(annotations.isSelected());
 944     showConsensHistogram.setEnabled(annotations.isSelected()
 945             && (identity.isSelected() || showGroupConsensus.isSelected()));
 946     showConsensLogo.setEnabled(annotations.isSelected()
 947             && (identity.isSelected() || showGroupConsensus.isSelected()));
 948   }
 949
 950   @Override
 951   public void newLink_actionPerformed(ActionEvent e)
 952   {
 953     GSequenceLink link = new GSequenceLink();
 954     boolean valid = false;
 955     while (!valid)
 956     {
 957       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 958               MessageManager.getString("label.new_sequence_url_link"),
 959               JvOptionPane.OK_CANCEL_OPTION, -1,
 960               null) == JvOptionPane.OK_OPTION)
 961       {
 962         if (link.checkValid())
 963         {
 964           if (((UrlLinkTableModel) linkUrlTable.getModel())
 965                   .isUniqueName(link.getName()))
 966           {
 967             ((UrlLinkTableModel) linkUrlTable.getModel())
 968                     .insertRow(link.getName(), link.getURL());
 969             valid = true;
 970           }
 971           else
 972           {
 973             link.notifyDuplicate();
 974             continue;
 975           }
 976         }
 977       }
 978       else
 979       {
 980         break;
 981       }
 982     }
 983   }
 984
 985   @Override
 986   public void editLink_actionPerformed(ActionEvent e)
 987   {
 988     GSequenceLink link = new GSequenceLink();
 989
 990     int index = linkUrlTable.getSelectedRow();
 991     if (index == -1)
 992     {
 993       // button no longer enabled if row is not selected
 994       Cache.log.debug("Edit with no row selected in linkUrlTable");
 995       return;
 996     }
 997
 998     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 999             .getNameColumn();
1000     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1001             .getUrlColumn();
1002     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1003     link.setName(oldName);
1004     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1005
1006     boolean valid = false;
1007     while (!valid)
1008     {
1009       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1010               MessageManager.getString("label.edit_sequence_url_link"),
1011               JvOptionPane.OK_CANCEL_OPTION, -1,
1012               null) == JvOptionPane.OK_OPTION)
1013       {
1014         if (link.checkValid())
1015         {
1016           if ((oldName.equals(link.getName()))
1017                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1018                           .isUniqueName(link.getName())))
1019           {
1020             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1021             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1022             valid = true;
1023           }
1024           else
1025           {
1026             link.notifyDuplicate();
1027             continue;
1028           }
1029         }
1030       }
1031       else
1032       {
1033         break;
1034       }
1035     }
1036   }
1037
1038   @Override
1039   public void deleteLink_actionPerformed(ActionEvent e)
1040   {
1041     int index = linkUrlTable.getSelectedRow();
1042     int modelIndex = -1;
1043     if (index == -1)
1044     {
1045       // button no longer enabled if row is not selected
1046       Cache.log.debug("Delete with no row selected in linkUrlTable");
1047       return;
1048     }
1049     else
1050     {
1051       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1052     }
1053
1054     // make sure we use the model index to delete, and not the table index
1055     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1056   }
1057
1058   @Override
1059   public void defaultBrowser_mouseClicked(MouseEvent e)
1060   {
1061     JFileChooser chooser = new JFileChooser(".");
1062     chooser.setDialogTitle(
1063             MessageManager.getString("label.select_default_browser"));
1064
1065     int value = chooser.showOpenDialog(this);
1066
1067     if (value == JFileChooser.APPROVE_OPTION)
1068     {
1069       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1070     }
1071
1072   }
1073
1074   /*
1075    * (non-Javadoc)
1076    *
1077    * @see
1078    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1079    * .ActionEvent)
1080    */
1081   @Override
1082   protected void showunconserved_actionPerformed(ActionEvent e)
1083   {
1084     // TODO Auto-generated method stub
1085     super.showunconserved_actionPerformed(e);
1086   }
1087
1088   public static List<String> getGroupURLLinks()
1089   {
1090     return groupURLLinks;
1091   }
1092
1093   @Override
1094   public void minColour_actionPerformed(JPanel panel)
1095   {
1096     Color col = JColorChooser.showDialog(this,
1097             MessageManager.getString("label.select_colour_minimum_value"),
1098             minColour.getBackground());
1099     if (col != null)
1100     {
1101       panel.setBackground(col);
1102     }
1103     panel.repaint();
1104   }
1105
1106   @Override
1107   public void maxColour_actionPerformed(JPanel panel)
1108   {
1109     Color col = JColorChooser.showDialog(this,
1110             MessageManager.getString("label.select_colour_maximum_value"),
1111             maxColour.getBackground());
1112     if (col != null)
1113     {
1114       panel.setBackground(col);
1115     }
1116     panel.repaint();
1117   }
1118
1119   @Override
1120   public void gapColour_actionPerformed(JPanel gap)
1121   {
1122     if (!useLegacyGap.isSelected())
1123     {
1124       Color col = JColorChooser.showDialog(this,
1125               MessageManager.getString("label.select_gap_colour"),
1126               gapColour.getBackground());
1127       if (col != null)
1128       {
1129         gap.setBackground(col);
1130       }
1131       gap.repaint();
1132     }
1133   }
1134
1135   @Override
1136   public void hiddenColour_actionPerformed(JPanel hidden)
1137   {
1138     Color col = JColorChooser.showDialog(this,
1139             MessageManager.getString("label.select_hidden_colour"),
1140             hiddenColour.getBackground());
1141     if (col != null)
1142     {
1143       hidden.setBackground(col);
1144     }
1145     hidden.repaint();
1146   }
1147
1148   @Override
1149   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1150   {
1151     boolean enabled = useLegacyGap.isSelected();
1152     if (enabled)
1153     {
1154       gapColour.setBackground(
1155               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1156     }
1157     else
1158     {
1159       gapColour.setBackground(
1160               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1161     }
1162     gapColour.setEnabled(!enabled);
1163     gapLabel.setEnabled(!enabled);
1164   }
1165
1166   @Override
1167   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1168   {
1169     useLegacyGap.setSelected(false);
1170     useLegacyGaps_actionPerformed(null);
1171     showHiddenAtStart.setSelected(false);
1172     hiddenColour.setBackground(
1173             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1174   }
1175
1176   @Override
1177   protected void userIdWidth_actionPerformed()
1178   {
1179     try
1180     {
1181       String val = userIdWidth.getText().trim();
1182       if (val.length() > 0)
1183       {
1184         Integer iw = Integer.parseInt(val);
1185         if (iw.intValue() < 12)
1186         {
1187           throw new NumberFormatException();
1188         }
1189         userIdWidth.setText(iw.toString());
1190       }
1191     } catch (NumberFormatException x)
1192     {
1193       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1194               MessageManager
1195                       .getString("warn.user_defined_width_requirements"),
1196               MessageManager.getString("label.invalid_id_column_width"),
1197               JvOptionPane.WARNING_MESSAGE);
1198       userIdWidth.setText("");
1199     }
1200   }
1201
1202   @Override
1203   protected void autoIdWidth_actionPerformed()
1204   {
1205     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1206     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1207   }
1208
1209   /**
1210    * Returns true if chimera path is to a valid executable, else show an error
1211    * dialog.
1212    */
1213   private boolean validateChimeraPath()
1214   {
1215     if (chimeraPath.getText().trim().length() > 0)
1216     {
1217       File f = new File(chimeraPath.getText());
1218       if (!f.canExecute())
1219       {
1220         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1221                 MessageManager.getString("label.invalid_chimera_path"),
1222                 MessageManager.getString("label.invalid_name"),
1223                 JvOptionPane.ERROR_MESSAGE);
1224         return false;
1225       }
1226     }
1227     return true;
1228   }
1229
1230   /**
1231    * If Chimera or ChimeraX is selected, check it can be found on default or
1232    * user-specified path, if not show a warning/help dialog.
1233    */
1234   @Override
1235   protected void structureViewer_actionPerformed(String selectedItem)
1236   {
1237     if (selectedItem.equals(ViewerType.JMOL.name()))
1238     {
1239       chimeraPath.setEnabled(false);
1240       chimeraPathLabel.setEnabled(false);
1241       return;
1242     }
1243     boolean found = false;
1244     chimeraPath.setEnabled(true);
1245     chimeraPathLabel.setEnabled(true);
1246     chimeraPathLabel.setText(MessageManager
1247             .formatMessage("label.chimera_path", selectedItem));
1248
1249     /*
1250      * Try user-specified and standard paths for Chimera executable
1251      */
1252     boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name());
1253     chimeraPath.setText(Cache
1254             .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
1255
1256     List<String> paths = StructureManager.getChimeraPaths(isChimeraX);
1257     paths.add(0, chimeraPath.getText());
1258     for (String path : paths)
1259     {
1260       if (new File(path.trim()).canExecute())
1261       {
1262         found = true;
1263         break;
1264       }
1265     }
1266     if (!found)
1267     {
1268       String[] options = { "OK", "Help" };
1269       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1270               JvSwingUtils.wrapTooltip(true,
1271                       MessageManager.getString("label.chimera_missing")),
1272               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1273               null, options, options[0]);
1274       if (showHelp == JvOptionPane.NO_OPTION)
1275       {
1276         try
1277         {
1278           Help.showHelpWindow(HelpId.StructureViewer);
1279         } catch (HelpSetException e)
1280         {
1281           e.printStackTrace();
1282         }
1283       }
1284     }
1285   }
1286
1287   public class OptionsParam
1288   {
1289     private String name;
1290
1291     private String code;
1292
1293     public OptionsParam(String name, String code)
1294     {
1295       this.name = name;
1296       this.code = code;
1297     }
1298
1299     public String getName()
1300     {
1301       return name;
1302     }
1303
1304     public void setName(String name)
1305     {
1306       this.name = name;
1307     }
1308
1309     public String getCode()
1310     {
1311       return code;
1312     }
1313
1314     public void setCode(String code)
1315     {
1316       this.code = code;
1317     }
1318
1319     @Override
1320     public String toString()
1321     {
1322       return name;
1323     }
1324
1325     @Override
1326     public boolean equals(Object that)
1327     {
1328       if (!(that instanceof OptionsParam))
1329       {
1330         return false;
1331       }
1332       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1333     }
1334
1335     @Override
1336     public int hashCode()
1337     {
1338       return name.hashCode() + code.hashCode();
1339     }
1340   }
1341
1342   private class UrlListSelectionHandler implements ListSelectionListener
1343   {
1344
1345     @Override
1346     public void valueChanged(ListSelectionEvent e)
1347     {
1348       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1349
1350       int index = lsm.getMinSelectionIndex();
1351       if (index == -1)
1352       {
1353         // no selection, so disable delete/edit buttons
1354         editLink.setEnabled(false);
1355         deleteLink.setEnabled(false);
1356         return;
1357       }
1358       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1359
1360       // enable/disable edit and delete link buttons
1361       if (((UrlLinkTableModel) linkUrlTable.getModel())
1362               .isRowDeletable(modelIndex))
1363       {
1364         deleteLink.setEnabled(true);
1365       }
1366       else
1367       {
1368         deleteLink.setEnabled(false);
1369       }
1370
1371       if (((UrlLinkTableModel) linkUrlTable.getModel())
1372               .isRowEditable(modelIndex))
1373       {
1374         editLink.setEnabled(true);
1375       }
1376       else
1377       {
1378         editLink.setEnabled(false);
1379       }
1380     }
1381   }
1382 }