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.ext.pymol.PymolManager;
  57 import jalview.gui.Help.HelpId;
  58 import jalview.gui.StructureViewer.ViewerType;
  59 import jalview.io.BackupFiles;
  60 import jalview.io.BackupFilesPresetEntry;
  61 import jalview.io.FileFormatI;
  62 import jalview.io.JalviewFileChooser;
  63 import jalview.io.JalviewFileView;
  64 import jalview.jbgui.GPreferences;
  65 import jalview.jbgui.GSequenceLink;
  66 import jalview.schemes.ColourSchemeI;
  67 import jalview.schemes.ColourSchemes;
  68 import jalview.schemes.ResidueColourScheme;
  69 import jalview.urls.UrlLinkTableModel;
  70 import jalview.urls.api.UrlProviderFactoryI;
  71 import jalview.urls.api.UrlProviderI;
  72 import jalview.urls.desktop.DesktopUrlProviderFactory;
  73 import jalview.util.MessageManager;
  74 import jalview.util.Platform;
  75 import jalview.util.UrlConstants;
  76 import jalview.ws.sifts.SiftsSettings;
  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 PYMOL_PATH = "PYMOL_PATH";
 111
 112   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 113
 114   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 115
 116   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 117
 118   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 119
 120   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 121
 122   public static final String GAP_COLOUR = "GAP_COLOUR";
 123
 124   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 125
 126   private static final int MIN_FONT_SIZE = 1;
 127
 128   private static final int MAX_FONT_SIZE = 30;
 129
 130   /**
 131    * Holds name and link separated with | character. Sequence ID must be
 132    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 133    */
 134   public static UrlProviderI sequenceUrlLinks;
 135
 136   public static UrlLinkTableModel dataModel;
 137
 138   /**
 139    * Holds name and link separated with | character. Sequence IDS and Sequences
 140    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 141    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 142    * for first and second token specified after a pipe character at end |,|.
 143    * (TODO: proper escape for using | to separate ids or sequences
 144    */
 145
 146   public static List<String> groupURLLinks;
 147   static
 148   {
 149     // get links selected to be in the menu (SEQUENCE_LINKS)
 150     // and links entered by the user but not selected (STORED_LINKS)
 151     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 152     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 153     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 154             UrlConstants.DEFAULT_LABEL);
 155
 156     // if both links lists are empty, add the DEFAULT_URL link
 157     // otherwise we assume the default link is in one of the lists
 158     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 159     {
 160       inMenuString = UrlConstants.DEFAULT_STRING;
 161     }
 162     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 163             inMenuString, notInMenuString);
 164     sequenceUrlLinks = factory.createUrlProvider();
 165     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 166
 167     /**
 168      * TODO: reformulate groupURL encoding so two or more can be stored in the
 169      * .properties file as '|' separated strings
 170      */
 171
 172     groupURLLinks = new ArrayList<>();
 173   }
 174
 175   JInternalFrame frame;
 176
 177   private WsPreferences wsPrefs;
 178
 179   private OptionsParam promptEachTimeOpt = new OptionsParam(
 180           MessageManager.getString("label.prompt_each_time"),
 181           "Prompt each time");
 182
 183   private OptionsParam lineArtOpt = new OptionsParam(
 184           MessageManager.getString("label.lineart"), "Lineart");
 185
 186   private OptionsParam textOpt = new OptionsParam(
 187           MessageManager.getString("action.text"), "Text");
 188
 189   /**
 190    * Creates a new Preferences object.
 191    */
 192   public Preferences()
 193   {
 194     super();
 195     frame = new JInternalFrame();
 196     frame.setContentPane(this);
 197     wsPrefs = new WsPreferences();
 198     wsTab.add(wsPrefs, BorderLayout.CENTER);
 199     int width = 500, height = 450;
 200     new jalview.util.Platform();
 201     if (Platform.isAMac())
 202     {
 203       width = 570;
 204       height = 480;
 205     }
 206
 207     Desktop.addInternalFrame(frame,
 208             MessageManager.getString("label.preferences"), width, height);
 209     frame.setMinimumSize(new Dimension(width, height));
 210
 211     /*
 212      * Set Visual tab defaults
 213      */
 214     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 215     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 216     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 217     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 218
 219     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 220     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 221     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 222     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 223     showUnconserved
 224             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 225     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 226     showGroupConsensus
 227             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 228     showGroupConservation.setSelected(
 229             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 230     showConsensHistogram.setSelected(
 231             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 232     showConsensLogo
 233             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 234     showNpTooltip
 235             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 236     showDbRefTooltip
 237             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 238
 239     String[] fonts = java.awt.GraphicsEnvironment
 240             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 241     for (int i = 0; i < fonts.length; i++)
 242     {
 243       fontNameCB.addItem(fonts[i]);
 244     }
 245
 246     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 247     {
 248       fontSizeCB.addItem(i + "");
 249     }
 250
 251     fontStyleCB.addItem("plain");
 252     fontStyleCB.addItem("bold");
 253     fontStyleCB.addItem("italic");
 254
 255     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 256     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 257     fontStyleCB.setSelectedItem(
 258             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 259
 260     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 261     scaleProteinToCdna
 262             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 263
 264     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 265
 266     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 267
 268     gapSymbolCB.addItem("-");
 269     gapSymbolCB.addItem(".");
 270
 271     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 272
 273     sortby.addItem("No sort");
 274     sortby.addItem("Id");
 275     sortby.addItem("Pairwise Identity");
 276     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 277
 278     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 279     sortAnnBy
 280             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 281     sortAnnBy
 282             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 283     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 284             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 285                     SequenceAnnotationOrder.NONE.name()));
 286     sortAnnBy.setSelectedItem(savedSort.toString());
 287
 288     sortAutocalc.addItem("Autocalculated first");
 289     sortAutocalc.addItem("Autocalculated last");
 290     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 291     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 292             : sortAutocalc.getItemAt(1));
 293     startupCheckbox
 294             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 295     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 296             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 297                     + "/examples/exampleFile_2_3.jar"));
 298
 299     /*
 300      * Set Colours tab defaults
 301      */
 302     protColour.addItem(ResidueColourScheme.NONE);
 303     nucColour.addItem(ResidueColourScheme.NONE);
 304     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 305     {
 306       String name = cs.getSchemeName();
 307       protColour.addItem(name);
 308       nucColour.addItem(name);
 309     }
 310     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 311             ResidueColourScheme.NONE);
 312     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 313     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 314     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 315     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 316     minColour.setBackground(
 317             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 318     maxColour.setBackground(
 319             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 320
 321     /*
 322      * Set overview panel defaults
 323      */
 324     gapColour.setBackground(
 325             Cache.getDefaultColour(GAP_COLOUR,
 326                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 327     hiddenColour.setBackground(
 328             Cache.getDefaultColour(HIDDEN_COLOUR,
 329                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 330     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 331     gapLabel.setEnabled(!useLegacyGap.isSelected());
 332     gapColour.setEnabled(!useLegacyGap.isSelected());
 333     showHiddenAtStart
 334             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 335
 336     /*
 337      * Set Structure tab defaults
 338      */
 339     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 340     structFromPdb.setSelected(structSelected);
 341     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 342     useRnaView.setEnabled(structSelected);
 343     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 344     addSecondaryStructure.setEnabled(structSelected);
 345     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 346     addTempFactor.setEnabled(structSelected);
 347
 348     /*
 349      * set choice of structure viewer, and path if saved as a preference;
 350      * default to Jmol (first choice) if an unexpected value is found
 351      */
 352     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
 353     structViewer.setSelectedItem(viewerType);
 354     String viewerPath = "";
 355     ViewerType type = null;
 356     try
 357     {
 358       type = ViewerType.valueOf(viewerType);
 359       switch (type)
 360       {
 361       case JMOL:
 362         break;
 363       case CHIMERA:
 364         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 365         break;
 366       case CHIMERAX:
 367         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 368         break;
 369       case PYMOL:
 370         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 371         break;
 372       }
 373     } catch (IllegalArgumentException e)
 374     {
 375       Cache.log.error("Unknown structure viewer type: " + viewerType
 376               + ", defaulting to Jmol");
 377       type = ViewerType.JMOL;
 378     }
 379     structureViewerPath.setText(viewerPath);
 380
 381     structureViewerPath.addActionListener(new ActionListener()
 382     {
 383       @Override
 384       public void actionPerformed(ActionEvent e)
 385       {
 386         if (validateViewerPath())
 387         {
 388           Cache.setProperty(structViewer.getSelectedItem()
 389                   .equals(ViewerType.CHIMERAX.name())
 390                   ? CHIMERAX_PATH
 391                   : CHIMERA_PATH, structureViewerPath.getText());
 392         }
 393       }
 394     });
 395
 396     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 397     {
 398       siftsMapping.setSelected(true);
 399     }
 400     else
 401     {
 402       nwMapping.setSelected(true);
 403     }
 404
 405     SiftsSettings
 406             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 407
 408     /*
 409      * Set Connections tab defaults
 410      */
 411
 412     // set up sorting
 413     linkUrlTable.setModel(dataModel);
 414     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 415             linkUrlTable.getModel());
 416     linkUrlTable.setRowSorter(sorter);
 417     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 418
 419     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 420     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 421             SortOrder.DESCENDING));
 422     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 423             SortOrder.DESCENDING));
 424     sortKeys.add(
 425             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 426
 427     sorter.setSortKeys(sortKeys);
 428     sorter.sort();
 429
 430     // set up filtering
 431     ActionListener onReset;
 432     onReset = new ActionListener()
 433     {
 434       @Override
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         filterTB.setText("");
 438         sorter.setRowFilter(RowFilter.regexFilter(""));
 439       }
 440
 441     };
 442     doReset.addActionListener(onReset);
 443
 444     // filter to display only custom urls
 445     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 446     {
 447       @Override
 448       public boolean include(
 449               Entry<? extends TableModel, ? extends Object> entry)
 450       {
 451         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 452       }
 453     };
 454
 455     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 456             linkUrlTable.getModel());
 457     customSorter.setRowFilter(customUrlFilter);
 458
 459     ActionListener onCustomOnly;
 460     onCustomOnly = new ActionListener()
 461     {
 462       @Override
 463       public void actionPerformed(ActionEvent e)
 464       {
 465         filterTB.setText("");
 466         sorter.setRowFilter(customUrlFilter);
 467       }
 468     };
 469     userOnly.addActionListener(onCustomOnly);
 470
 471     filterTB.getDocument().addDocumentListener(new DocumentListener()
 472     {
 473       String caseInsensitiveFlag = "(?i)";
 474
 475       @Override
 476       public void changedUpdate(DocumentEvent e)
 477       {
 478         sorter.setRowFilter(RowFilter
 479                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 480       }
 481
 482       @Override
 483       public void removeUpdate(DocumentEvent e)
 484       {
 485         sorter.setRowFilter(RowFilter
 486                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 487       }
 488
 489       @Override
 490       public void insertUpdate(DocumentEvent e)
 491       {
 492         sorter.setRowFilter(RowFilter
 493                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 494       }
 495     });
 496
 497     // set up list selection functionality
 498     linkUrlTable.getSelectionModel()
 499             .addListSelectionListener(new UrlListSelectionHandler());
 500
 501     // set up radio buttons
 502     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 503             .getPrimaryColumn();
 504     String onClickName = linkUrlTable.getColumnName(onClickCol);
 505     linkUrlTable.getColumn(onClickName)
 506             .setCellRenderer(new RadioButtonRenderer());
 507     linkUrlTable.getColumn(onClickName)
 508             .setCellEditor(new RadioButtonEditor());
 509
 510     // get boolean columns and resize those to min possible
 511     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 512     {
 513       if (linkUrlTable.getModel().getColumnClass(column)
 514               .equals(Boolean.class))
 515       {
 516         TableColumn tableColumn = linkUrlTable.getColumnModel()
 517                 .getColumn(column);
 518         int preferredWidth = tableColumn.getMinWidth();
 519
 520         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 521                 column);
 522         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 523         int cwidth = c.getPreferredSize().width
 524                 + linkUrlTable.getIntercellSpacing().width;
 525         preferredWidth = Math.max(preferredWidth, cwidth);
 526
 527         tableColumn.setPreferredWidth(preferredWidth);
 528       }
 529     }
 530
 531     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 532     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 533     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 534     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 535
 536     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 537
 538     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 539     // note antisense here: default is true
 540     questionnaire
 541             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 542     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 543
 544     /*
 545      * Set Output tab defaults
 546      */
 547     epsRendering.addItem(promptEachTimeOpt);
 548     epsRendering.addItem(lineArtOpt);
 549     epsRendering.addItem(textOpt);
 550     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 551             "Prompt each time");
 552     if (defaultEPS.equalsIgnoreCase("Text"))
 553     {
 554       epsRendering.setSelectedItem(textOpt);
 555     }
 556     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 557     {
 558       epsRendering.setSelectedItem(lineArtOpt);
 559     }
 560     else
 561     {
 562       epsRendering.setSelectedItem(promptEachTimeOpt);
 563     }
 564     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 565     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 566     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 567     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 568     userIdWidth.setText(wi == null ? "" : wi.toString());
 569     // TODO: refactor to use common enum via FormatAdapter and allow extension
 570     // for new flat file formats
 571     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 572     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 573     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 574     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 575     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 576     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 577     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 578     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 579     embbedBioJSON
 580             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 581
 582     /*
 583      * Set Editing tab defaults
 584      */
 585     autoCalculateConsCheck
 586             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 587     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 588     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 589
 590     annotations_actionPerformed(null); // update the display of the annotation
 591                                        // settings
 592
 593
 594     /*
 595      * Set Backups tab defaults
 596      */
 597     loadLastSavedBackupsOptions();
 598   }
 599
 600   /**
 601    * Save user selections on the Preferences tabs to the Cache and write out to
 602    * file.
 603    *
 604    * @param e
 605    */
 606   @Override
 607   public void ok_actionPerformed(ActionEvent e)
 608   {
 609     if (!validateSettings())
 610     {
 611       return;
 612     }
 613
 614     /*
 615      * Save Visual settings
 616      */
 617     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 618             Boolean.toString(seqLimit.isSelected()));
 619     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 620             Boolean.toString(rightAlign.isSelected()));
 621     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 622             Boolean.toString(fullScreen.isSelected()));
 623     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 624             Boolean.toString(openoverv.isSelected()));
 625     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 626             Boolean.toString(annotations.isSelected()));
 627     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 628             Boolean.toString(conservation.isSelected()));
 629     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 630             Boolean.toString(quality.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 632             Boolean.toString(identity.isSelected()));
 633
 634     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 635             gapSymbolCB.getSelectedItem().toString());
 636
 637     Cache.applicationProperties.setProperty("FONT_NAME",
 638             fontNameCB.getSelectedItem().toString());
 639     Cache.applicationProperties.setProperty("FONT_STYLE",
 640             fontStyleCB.getSelectedItem().toString());
 641     Cache.applicationProperties.setProperty("FONT_SIZE",
 642             fontSizeCB.getSelectedItem().toString());
 643
 644     Cache.applicationProperties.setProperty("ID_ITALICS",
 645             Boolean.toString(idItalics.isSelected()));
 646     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 647             Boolean.toString(showUnconserved.isSelected()));
 648     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 649             Boolean.toString(showOccupancy.isSelected()));
 650     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 651             Boolean.toString(showGroupConsensus.isSelected()));
 652     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 653             Boolean.toString(showGroupConservation.isSelected()));
 654     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 655             Boolean.toString(showConsensHistogram.isSelected()));
 656     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 657             Boolean.toString(showConsensLogo.isSelected()));
 658     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 659             Boolean.toString(smoothFont.isSelected()));
 660     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 661             Boolean.toString(scaleProteinToCdna.isSelected()));
 662     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 663             Boolean.toString(showNpTooltip.isSelected()));
 664     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 665             Boolean.toString(showDbRefTooltip.isSelected()));
 666
 667     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 668             Boolean.toString(wrap.isSelected()));
 669
 670     Cache.applicationProperties.setProperty("STARTUP_FILE",
 671             startupFileTextfield.getText());
 672     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 673             Boolean.toString(startupCheckbox.isSelected()));
 674
 675     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 676             sortby.getSelectedItem().toString());
 677
 678     // convert description of sort order to enum name for save
 679     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 680             .forDescription(sortAnnBy.getSelectedItem().toString());
 681     if (annSortOrder != null)
 682     {
 683       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 684               annSortOrder.name());
 685     }
 686
 687     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 688     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 689             Boolean.valueOf(showAutocalcFirst).toString());
 690
 691     /*
 692      * Save Colours settings
 693      */
 694     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 695             protColour.getSelectedItem().toString());
 696     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 697             nucColour.getSelectedItem().toString());
 698     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 699             minColour.getBackground());
 700     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 701             maxColour.getBackground());
 702
 703     /*
 704      * Save Overview settings
 705      */
 706     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 707     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 708     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 709             Boolean.toString(useLegacyGap.isSelected()));
 710     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 711             Boolean.toString(showHiddenAtStart.isSelected()));
 712
 713     /*
 714      * Save Structure settings
 715      */
 716     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 717             Boolean.toString(addTempFactor.isSelected()));
 718     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 719             Boolean.toString(addSecondaryStructure.isSelected()));
 720     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 721             Boolean.toString(useRnaView.isSelected()));
 722     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 723             Boolean.toString(structFromPdb.isSelected()));
 724     String viewer = structViewer.getSelectedItem().toString();
 725     String viewerPath = structureViewerPath.getText();
 726     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 727             viewer);
 728     if (viewer.equals(ViewerType.CHIMERA.name()))
 729     {
 730       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 731     }
 732     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 733     {
 734       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 735     }
 736     else if (viewer.equals(ViewerType.PYMOL.name()))
 737     {
 738       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 739     }
 740     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 741             Boolean.toString(siftsMapping.isSelected()));
 742     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 743
 744     /*
 745      * Save Output settings
 746      */
 747     Cache.applicationProperties.setProperty("EPS_RENDERING",
 748             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 749
 750     /*
 751      * Save Connections settings
 752      */
 753     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 754
 755     jalview.util.BrowserLauncher.resetBrowser();
 756
 757     // save user-defined and selected links
 758     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 759     if (menuLinks.isEmpty())
 760     {
 761       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 762     }
 763     else
 764     {
 765       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 766               menuLinks.toString());
 767     }
 768
 769     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 770     if (nonMenuLinks.isEmpty())
 771     {
 772       Cache.applicationProperties.remove("STORED_LINKS");
 773     }
 774     else
 775     {
 776       Cache.applicationProperties.setProperty("STORED_LINKS",
 777               nonMenuLinks.toString());
 778     }
 779
 780     Cache.applicationProperties.setProperty("DEFAULT_URL",
 781             sequenceUrlLinks.getPrimaryUrlId());
 782
 783     Cache.applicationProperties.setProperty("USE_PROXY",
 784             Boolean.toString(useProxy.isSelected()));
 785
 786     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 787
 788     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 789
 790     if (useProxy.isSelected())
 791     {
 792       System.setProperty("http.proxyHost", proxyServerTB.getText());
 793       System.setProperty("http.proxyPort", proxyPortTB.getText());
 794     }
 795     else
 796     {
 797       System.setProperty("http.proxyHost", "");
 798       System.setProperty("http.proxyPort", "");
 799     }
 800     Cache.setProperty("VERSION_CHECK",
 801             Boolean.toString(versioncheck.isSelected()));
 802     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 803     {
 804       // default is false - we only set this if the user has actively agreed
 805       Cache.setProperty("USAGESTATS",
 806               Boolean.toString(usagestats.isSelected()));
 807     }
 808     if (!questionnaire.isSelected())
 809     {
 810       Cache.setProperty("NOQUESTIONNAIRES", "true");
 811     }
 812     else
 813     {
 814       // special - made easy to edit a property file to disable questionnaires
 815       // by just adding the given line
 816       Cache.removeProperty("NOQUESTIONNAIRES");
 817     }
 818
 819     /*
 820      * Save Output settings
 821      */
 822     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 823             Boolean.toString(blcjv.isSelected()));
 824     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 825             Boolean.toString(clustaljv.isSelected()));
 826     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 827             Boolean.toString(fastajv.isSelected()));
 828     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 829             Boolean.toString(msfjv.isSelected()));
 830     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 831             Boolean.toString(pfamjv.isSelected()));
 832     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 833             Boolean.toString(pileupjv.isSelected()));
 834     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 835             Boolean.toString(pirjv.isSelected()));
 836     Cache.applicationProperties.setProperty("PIR_MODELLER",
 837             Boolean.toString(modellerOutput.isSelected()));
 838     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 839             Boolean.toString(embbedBioJSON.isSelected()));
 840     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 841
 842     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 843             Boolean.toString(autoIdWidth.isSelected()));
 844     userIdWidth_actionPerformed();
 845     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 846             userIdWidth.getText());
 847
 848     /*
 849      * Save Editing settings
 850      */
 851     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 852             Boolean.toString(autoCalculateConsCheck.isSelected()));
 853     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 854             Boolean.toString(sortByTree.isSelected()));
 855     Cache.applicationProperties.setProperty("PAD_GAPS",
 856             Boolean.toString(padGaps.isSelected()));
 857
 858     wsPrefs.updateAndRefreshWsMenuConfig(false);
 859
 860     /*
 861      * Save Backups settings
 862      */
 863     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 864             Boolean.toString(enableBackupFiles.isSelected()));
 865     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 866     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 867
 868     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 869     {
 870       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 871       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 872               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 873       Cache.applicationProperties
 874               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 875                       customBFPE.toString());
 876     }
 877
 878     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 879             .get(preset);
 880     Cache.applicationProperties.setProperty(
 881             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 882
 883     Cache.saveProperties();
 884     Desktop.instance.doConfigureStructurePrefs();
 885     try
 886     {
 887       frame.setClosed(true);
 888     } catch (Exception ex)
 889     {
 890     }
 891   }
 892
 893   /**
 894    * Do any necessary validation before saving settings. Return focus to the
 895    * first tab which fails validation.
 896    *
 897    * @return
 898    */
 899   private boolean validateSettings()
 900   {
 901     if (!validateStructure())
 902     {
 903       structureTab.requestFocusInWindow();
 904       return false;
 905     }
 906     return true;
 907   }
 908
 909   @Override
 910   protected boolean validateStructure()
 911   {
 912     return validateViewerPath();
 913
 914   }
 915
 916   /**
 917    * DOCUMENT ME!
 918    */
 919   @Override
 920   public void startupFileTextfield_mouseClicked()
 921   {
 922     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 923     JalviewFileChooser chooser = JalviewFileChooser
 924             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 925     chooser.setFileView(new JalviewFileView());
 926     chooser.setDialogTitle(
 927             MessageManager.getString("label.select_startup_file"));
 928
 929     int value = chooser.showOpenDialog(this);
 930
 931     if (value == JalviewFileChooser.APPROVE_OPTION)
 932     {
 933       FileFormatI format = chooser.getSelectedFormat();
 934       if (format != null)
 935       {
 936         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 937                 format.getName());
 938       }
 939       startupFileTextfield
 940               .setText(chooser.getSelectedFile().getAbsolutePath());
 941     }
 942   }
 943
 944   /**
 945    * DOCUMENT ME!
 946    *
 947    * @param e
 948    *          DOCUMENT ME!
 949    */
 950   @Override
 951   public void cancel_actionPerformed(ActionEvent e)
 952   {
 953     try
 954     {
 955       wsPrefs.updateWsMenuConfig(true);
 956       wsPrefs.refreshWs_actionPerformed(e);
 957       frame.setClosed(true);
 958     } catch (Exception ex)
 959     {
 960     }
 961   }
 962
 963   /**
 964    * DOCUMENT ME!
 965    *
 966    * @param e
 967    *          DOCUMENT ME!
 968    */
 969   @Override
 970   public void annotations_actionPerformed(ActionEvent e)
 971   {
 972     conservation.setEnabled(annotations.isSelected());
 973     quality.setEnabled(annotations.isSelected());
 974     identity.setEnabled(annotations.isSelected());
 975     showOccupancy.setEnabled(annotations.isSelected());
 976     showGroupConsensus.setEnabled(annotations.isSelected());
 977     showGroupConservation.setEnabled(annotations.isSelected());
 978     showConsensHistogram.setEnabled(annotations.isSelected()
 979             && (identity.isSelected() || showGroupConsensus.isSelected()));
 980     showConsensLogo.setEnabled(annotations.isSelected()
 981             && (identity.isSelected() || showGroupConsensus.isSelected()));
 982   }
 983
 984   @Override
 985   public void newLink_actionPerformed(ActionEvent e)
 986   {
 987     GSequenceLink link = new GSequenceLink();
 988     boolean valid = false;
 989     while (!valid)
 990     {
 991       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 992               MessageManager.getString("label.new_sequence_url_link"),
 993               JvOptionPane.OK_CANCEL_OPTION, -1,
 994               null) == JvOptionPane.OK_OPTION)
 995       {
 996         if (link.checkValid())
 997         {
 998           if (((UrlLinkTableModel) linkUrlTable.getModel())
 999                   .isUniqueName(link.getName()))
1000           {
1001             ((UrlLinkTableModel) linkUrlTable.getModel())
1002                     .insertRow(link.getName(), link.getURL());
1003             valid = true;
1004           }
1005           else
1006           {
1007             link.notifyDuplicate();
1008             continue;
1009           }
1010         }
1011       }
1012       else
1013       {
1014         break;
1015       }
1016     }
1017   }
1018
1019   @Override
1020   public void editLink_actionPerformed(ActionEvent e)
1021   {
1022     GSequenceLink link = new GSequenceLink();
1023
1024     int index = linkUrlTable.getSelectedRow();
1025     if (index == -1)
1026     {
1027       // button no longer enabled if row is not selected
1028       Cache.log.debug("Edit with no row selected in linkUrlTable");
1029       return;
1030     }
1031
1032     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1033             .getNameColumn();
1034     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1035             .getUrlColumn();
1036     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1037     link.setName(oldName);
1038     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1039
1040     boolean valid = false;
1041     while (!valid)
1042     {
1043       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1044               MessageManager.getString("label.edit_sequence_url_link"),
1045               JvOptionPane.OK_CANCEL_OPTION, -1,
1046               null) == JvOptionPane.OK_OPTION)
1047       {
1048         if (link.checkValid())
1049         {
1050           if ((oldName.equals(link.getName()))
1051                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1052                           .isUniqueName(link.getName())))
1053           {
1054             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1055             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1056             valid = true;
1057           }
1058           else
1059           {
1060             link.notifyDuplicate();
1061             continue;
1062           }
1063         }
1064       }
1065       else
1066       {
1067         break;
1068       }
1069     }
1070   }
1071
1072   @Override
1073   public void deleteLink_actionPerformed(ActionEvent e)
1074   {
1075     int index = linkUrlTable.getSelectedRow();
1076     int modelIndex = -1;
1077     if (index == -1)
1078     {
1079       // button no longer enabled if row is not selected
1080       Cache.log.debug("Delete with no row selected in linkUrlTable");
1081       return;
1082     }
1083     else
1084     {
1085       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1086     }
1087
1088     // make sure we use the model index to delete, and not the table index
1089     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1090   }
1091
1092   @Override
1093   public void defaultBrowser_mouseClicked(MouseEvent e)
1094   {
1095     JFileChooser chooser = new JFileChooser(".");
1096     chooser.setDialogTitle(
1097             MessageManager.getString("label.select_default_browser"));
1098
1099     int value = chooser.showOpenDialog(this);
1100
1101     if (value == JFileChooser.APPROVE_OPTION)
1102     {
1103       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1104     }
1105
1106   }
1107
1108   /*
1109    * (non-Javadoc)
1110    *
1111    * @see
1112    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1113    * .ActionEvent)
1114    */
1115   @Override
1116   protected void showunconserved_actionPerformed(ActionEvent e)
1117   {
1118     // TODO Auto-generated method stub
1119     super.showunconserved_actionPerformed(e);
1120   }
1121
1122   public static List<String> getGroupURLLinks()
1123   {
1124     return groupURLLinks;
1125   }
1126
1127   @Override
1128   public void minColour_actionPerformed(JPanel panel)
1129   {
1130     Color col = JColorChooser.showDialog(this,
1131             MessageManager.getString("label.select_colour_minimum_value"),
1132             minColour.getBackground());
1133     if (col != null)
1134     {
1135       panel.setBackground(col);
1136     }
1137     panel.repaint();
1138   }
1139
1140   @Override
1141   public void maxColour_actionPerformed(JPanel panel)
1142   {
1143     Color col = JColorChooser.showDialog(this,
1144             MessageManager.getString("label.select_colour_maximum_value"),
1145             maxColour.getBackground());
1146     if (col != null)
1147     {
1148       panel.setBackground(col);
1149     }
1150     panel.repaint();
1151   }
1152
1153   @Override
1154   public void gapColour_actionPerformed(JPanel gap)
1155   {
1156     if (!useLegacyGap.isSelected())
1157     {
1158       Color col = JColorChooser.showDialog(this,
1159               MessageManager.getString("label.select_gap_colour"),
1160               gapColour.getBackground());
1161       if (col != null)
1162       {
1163         gap.setBackground(col);
1164       }
1165       gap.repaint();
1166     }
1167   }
1168
1169   @Override
1170   public void hiddenColour_actionPerformed(JPanel hidden)
1171   {
1172     Color col = JColorChooser.showDialog(this,
1173             MessageManager.getString("label.select_hidden_colour"),
1174             hiddenColour.getBackground());
1175     if (col != null)
1176     {
1177       hidden.setBackground(col);
1178     }
1179     hidden.repaint();
1180   }
1181
1182   @Override
1183   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1184   {
1185     boolean enabled = useLegacyGap.isSelected();
1186     if (enabled)
1187     {
1188       gapColour.setBackground(
1189               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1190     }
1191     else
1192     {
1193       gapColour.setBackground(
1194               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1195     }
1196     gapColour.setEnabled(!enabled);
1197     gapLabel.setEnabled(!enabled);
1198   }
1199
1200   @Override
1201   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1202   {
1203     useLegacyGap.setSelected(false);
1204     useLegacyGaps_actionPerformed(null);
1205     showHiddenAtStart.setSelected(false);
1206     hiddenColour.setBackground(
1207             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1208   }
1209
1210   @Override
1211   protected void userIdWidth_actionPerformed()
1212   {
1213     try
1214     {
1215       String val = userIdWidth.getText().trim();
1216       if (val.length() > 0)
1217       {
1218         Integer iw = Integer.parseInt(val);
1219         if (iw.intValue() < 12)
1220         {
1221           throw new NumberFormatException();
1222         }
1223         userIdWidth.setText(iw.toString());
1224       }
1225     } catch (NumberFormatException x)
1226     {
1227       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1228               MessageManager
1229                       .getString("warn.user_defined_width_requirements"),
1230               MessageManager.getString("label.invalid_id_column_width"),
1231               JvOptionPane.WARNING_MESSAGE);
1232       userIdWidth.setText("");
1233     }
1234   }
1235
1236   @Override
1237   protected void autoIdWidth_actionPerformed()
1238   {
1239     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1240     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1241   }
1242
1243   /**
1244    * Returns true if structure viewer path is to a valid executable, else shows
1245    * an error dialog. Does nothing if the path is empty, as is the case for Jmol
1246    * (built in to Jalview) or when Jalview is left to try default paths.
1247    */
1248   private boolean validateViewerPath()
1249   {
1250     if (structureViewerPath.getText().trim().length() > 0)
1251     {
1252       File f = new File(structureViewerPath.getText());
1253       if (!f.canExecute())
1254       {
1255         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1256                 MessageManager.getString("label.invalid_viewer_path"),
1257                 MessageManager.getString("label.invalid_viewer_path"),
1258                 JvOptionPane.ERROR_MESSAGE);
1259         return false;
1260       }
1261     }
1262     return true;
1263   }
1264
1265   /**
1266    * If Chimera or ChimeraX or Pymol is selected, check it can be found on
1267    * default or user-specified path, if not show a warning/help dialog
1268    */
1269   @Override
1270   protected void structureViewer_actionPerformed(String selectedItem)
1271   {
1272     if (selectedItem.equals(ViewerType.JMOL.name()))
1273     {
1274       structureViewerPath.setEnabled(false);
1275       structureViewerPathLabel.setEnabled(false);
1276       return;
1277     }
1278     boolean found = false;
1279     structureViewerPath.setEnabled(true);
1280     structureViewerPathLabel.setEnabled(true);
1281     structureViewerPathLabel.setText(MessageManager
1282             .formatMessage("label.viewer_path", selectedItem));
1283
1284     /*
1285      * Try user-specified and standard paths for structure viewer executable
1286      */
1287     String viewerPath = "";
1288     List<String> paths = null;
1289     try
1290     {
1291       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1292       switch (viewerType)
1293       {
1294       case JMOL:
1295         // dealt with above
1296         break;
1297       case CHIMERA:
1298         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1299         paths = StructureManager.getChimeraPaths(false);
1300         break;
1301       case CHIMERAX:
1302         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1303         paths = StructureManager.getChimeraPaths(true);
1304         break;
1305       case PYMOL:
1306         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1307         paths = PymolManager.getPymolPaths();
1308         break;
1309       }
1310     } catch (IllegalArgumentException e)
1311     {
1312       // only valid entries should be in the drop-down
1313     }
1314     structureViewerPath.setText(viewerPath);
1315
1316     paths.add(0, structureViewerPath.getText());
1317     for (String path : paths)
1318     {
1319       if (new File(path.trim()).canExecute())
1320       {
1321         found = true;
1322         break;
1323       }
1324     }
1325
1326     if (!found)
1327     {
1328       String[] options = { "OK", "Help" };
1329       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1330               JvSwingUtils.wrapTooltip(true,
1331                       MessageManager.getString("label.viewer_missing")),
1332               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1333               null, options, options[0]);
1334       if (showHelp == JvOptionPane.NO_OPTION)
1335       {
1336         try
1337         {
1338           Help.showHelpWindow(HelpId.StructureViewer);
1339         } catch (HelpSetException e)
1340         {
1341           e.printStackTrace();
1342         }
1343       }
1344     }
1345   }
1346
1347   public class OptionsParam
1348   {
1349     private String name;
1350
1351     private String code;
1352
1353     public OptionsParam(String name, String code)
1354     {
1355       this.name = name;
1356       this.code = code;
1357     }
1358
1359     public String getName()
1360     {
1361       return name;
1362     }
1363
1364     public void setName(String name)
1365     {
1366       this.name = name;
1367     }
1368
1369     public String getCode()
1370     {
1371       return code;
1372     }
1373
1374     public void setCode(String code)
1375     {
1376       this.code = code;
1377     }
1378
1379     @Override
1380     public String toString()
1381     {
1382       return name;
1383     }
1384
1385     @Override
1386     public boolean equals(Object that)
1387     {
1388       if (!(that instanceof OptionsParam))
1389       {
1390         return false;
1391       }
1392       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1393     }
1394
1395     @Override
1396     public int hashCode()
1397     {
1398       return name.hashCode() + code.hashCode();
1399     }
1400   }
1401
1402   private class UrlListSelectionHandler implements ListSelectionListener
1403   {
1404
1405     @Override
1406     public void valueChanged(ListSelectionEvent e)
1407     {
1408       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1409
1410       int index = lsm.getMinSelectionIndex();
1411       if (index == -1)
1412       {
1413         // no selection, so disable delete/edit buttons
1414         editLink.setEnabled(false);
1415         deleteLink.setEnabled(false);
1416         return;
1417       }
1418       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1419
1420       // enable/disable edit and delete link buttons
1421       if (((UrlLinkTableModel) linkUrlTable.getModel())
1422               .isRowDeletable(modelIndex))
1423       {
1424         deleteLink.setEnabled(true);
1425       }
1426       else
1427       {
1428         deleteLink.setEnabled(false);
1429       }
1430
1431       if (((UrlLinkTableModel) linkUrlTable.getModel())
1432               .isRowEditable(modelIndex))
1433       {
1434         editLink.setEnabled(true);
1435       }
1436       else
1437       {
1438         editLink.setEnabled(false);
1439       }
1440     }
1441   }
1442 }