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.hmmer.HmmerCommand;
  28 import jalview.io.BackupFiles;
  29 import jalview.io.BackupFilesPresetEntry;
  30 import jalview.io.FileFormatI;
  31 import jalview.io.JalviewFileChooser;
  32 import jalview.io.JalviewFileView;
  33 import jalview.jbgui.GPreferences;
  34 import jalview.jbgui.GSequenceLink;
  35 import jalview.schemes.ColourSchemeI;
  36 import jalview.schemes.ColourSchemes;
  37 import jalview.schemes.ResidueColourScheme;
  38 import jalview.urls.UrlLinkTableModel;
  39 import jalview.urls.api.UrlProviderFactoryI;
  40 import jalview.urls.api.UrlProviderI;
  41 import jalview.urls.desktop.DesktopUrlProviderFactory;
  42 import jalview.util.FileUtils;
  43 import jalview.util.MessageManager;
  44 import jalview.util.Platform;
  45 import jalview.util.UrlConstants;
  46 import jalview.ws.sifts.SiftsSettings;
  47
  48 import java.awt.BorderLayout;
  49 import java.awt.Color;
  50 import java.awt.Component;
  51 import java.awt.Dimension;
  52 import java.awt.Font;
  53 import java.awt.event.ActionEvent;
  54 import java.awt.event.ActionListener;
  55 import java.awt.event.FocusAdapter;
  56 import java.awt.event.FocusEvent;
  57 import java.awt.event.MouseEvent;
  58 import java.io.File;
  59 import java.util.ArrayList;
  60 import java.util.List;
  61
  62 import javax.help.HelpSetException;
  63 import javax.swing.JColorChooser;
  64 import javax.swing.JFileChooser;
  65 import javax.swing.JInternalFrame;
  66 import javax.swing.JPanel;
  67 import javax.swing.JTextField;
  68 import javax.swing.ListSelectionModel;
  69 import javax.swing.RowFilter;
  70 import javax.swing.RowSorter;
  71 import javax.swing.SortOrder;
  72 import javax.swing.event.DocumentEvent;
  73 import javax.swing.event.DocumentListener;
  74 import javax.swing.event.ListSelectionEvent;
  75 import javax.swing.event.ListSelectionListener;
  76 import javax.swing.table.TableCellRenderer;
  77 import javax.swing.table.TableColumn;
  78 import javax.swing.table.TableModel;
  79 import javax.swing.table.TableRowSorter;
  80
  81 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  82
  83 /**
  84  * DOCUMENT ME!
  85  *
  86  * @author $author$
  87  * @version $Revision$
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   // suggested list delimiter character
  92   public static final String COMMA = ",";
  93
  94   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
  95
  96   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
  97
  98   public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
  99
 100   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 101
 102   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 103
 104   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 105
 106   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 107
 108   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 109
 110   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 111
 112   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 113
 114   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 115
 116   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 117
 118   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 119
 120   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 121
 122   public static final String HMMER_PATH = "HMMER_PATH";
 123
 124   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 125
 126   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 127
 128   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 129
 130   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 131
 132   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 133
 134   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 135
 136   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 137
 138   public static final String GAP_COLOUR = "GAP_COLOUR";
 139
 140   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 141
 142   private static final int MIN_FONT_SIZE = 1;
 143
 144   private static final int MAX_FONT_SIZE = 30;
 145
 146   /**
 147    * Holds name and link separated with | character. Sequence ID must be
 148    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 149    */
 150   public static UrlProviderI sequenceUrlLinks;
 151
 152   public static UrlLinkTableModel dataModel;
 153
 154   /**
 155    * Holds name and link separated with | character. Sequence IDS and Sequences
 156    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 157    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 158    * for first and second token specified after a pipe character at end |,|.
 159    * (TODO: proper escape for using | to separate ids or sequences
 160    */
 161
 162   public static List<String> groupURLLinks;
 163   static
 164   {
 165     // get links selected to be in the menu (SEQUENCE_LINKS)
 166     // and links entered by the user but not selected (STORED_LINKS)
 167     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 168     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 169     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 170             UrlConstants.DEFAULT_LABEL);
 171
 172     // if both links lists are empty, add the DEFAULT_URL link
 173     // otherwise we assume the default link is in one of the lists
 174     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 175     {
 176       inMenuString = UrlConstants.DEFAULT_STRING;
 177     }
 178     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 179             inMenuString, notInMenuString);
 180     sequenceUrlLinks = factory.createUrlProvider();
 181     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 182
 183     /**
 184      * TODO: reformulate groupURL encoding so two or more can be stored in the
 185      * .properties file as '|' separated strings
 186      */
 187
 188     groupURLLinks = new ArrayList<>();
 189   }
 190
 191   JInternalFrame frame;
 192
 193   private WsPreferences wsPrefs;
 194
 195   private SlivkaPreferences slivkaPrefs;
 196
 197   private OptionsParam promptEachTimeOpt = new OptionsParam(
 198           MessageManager.getString("label.prompt_each_time"),
 199           "Prompt each time");
 200
 201   private OptionsParam lineArtOpt = new OptionsParam(
 202           MessageManager.getString("label.lineart"), "Lineart");
 203
 204   private OptionsParam textOpt = new OptionsParam(
 205           MessageManager.getString("action.text"), "Text");
 206
 207   /**
 208    * Creates a new Preferences object.
 209    */
 210   public Preferences()
 211   {
 212     super();
 213     frame = new JInternalFrame();
 214     frame.setContentPane(this);
 215     wsPrefs = new WsPreferences();
 216     wsTab.add(wsPrefs, BorderLayout.CENTER);
 217     slivkaTab.add(slivkaPrefs = new SlivkaPreferences(),
 218         BorderLayout.CENTER);
 219     int width = 500, height = 450;
 220     new jalview.util.Platform();
 221     if (Platform.isAMac())
 222     {
 223       width = 570;
 224       height = 480;
 225     }
 226
 227     Desktop.addInternalFrame(frame,
 228             MessageManager.getString("label.preferences"), width, height);
 229     frame.setMinimumSize(new Dimension(width, height));
 230
 231     /*
 232      * Set HMMER tab defaults
 233      */
 234     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 235     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 236     {
 237       hmmerBackgroundUniprot.setSelected(true);
 238     }
 239     else
 240     {
 241       hmmerBackgroundAlignment.setSelected(true);
 242     }
 243     hmmerSequenceCount
 244             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 245     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 246     hmmerPath.addActionListener(new ActionListener()
 247     {
 248       @Override
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         validateHmmerPath();
 252       }
 253     });
 254     hmmerPath.addFocusListener(new FocusAdapter()
 255     {
 256       @Override
 257       public void focusLost(FocusEvent e)
 258       {
 259         validateHmmerPath();
 260       }
 261     });
 262     if (cygwinPath != null)
 263     {
 264       String path = Cache.getProperty(CYGWIN_PATH);
 265       if (path == null)
 266       {
 267         path = FileUtils.getPathTo("bash");
 268       }
 269       cygwinPath.setText(path);
 270       cygwinPath.addActionListener(new ActionListener()
 271       {
 272         @Override
 273         public void actionPerformed(ActionEvent e)
 274         {
 275           validateCygwinPath();
 276         }
 277       });
 278       cygwinPath.addFocusListener(new FocusAdapter()
 279       {
 280         @Override
 281         public void focusLost(FocusEvent e)
 282         {
 283           validateCygwinPath();
 284         }
 285       });
 286     }
 287
 288     /*
 289      * Set Visual tab defaults
 290      */
 291     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 292     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 293     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 294     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 295
 296     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 297     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 298     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 299     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 300     showUnconserved
 301             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 302     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 303     showGroupConsensus
 304             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 305     showGroupConservation.setSelected(
 306             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 307     showConsensHistogram.setSelected(
 308             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 309     showConsensLogo
 310             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 311     showInformationHistogram.setSelected(
 312             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 313     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 314     showNpTooltip
 315             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 316     showDbRefTooltip
 317             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 318
 319     String[] fonts = java.awt.GraphicsEnvironment
 320             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 321     for (int i = 0; i < fonts.length; i++)
 322     {
 323       fontNameCB.addItem(fonts[i]);
 324     }
 325
 326     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 327     {
 328       fontSizeCB.addItem(i + "");
 329     }
 330
 331     fontStyleCB.addItem("plain");
 332     fontStyleCB.addItem("bold");
 333     fontStyleCB.addItem("italic");
 334
 335     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 336     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 337     fontStyleCB.setSelectedItem(
 338             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 339
 340     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 341     scaleProteinToCdna
 342             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 343
 344     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 345
 346     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 347
 348     gapSymbolCB.addItem("-");
 349     gapSymbolCB.addItem(".");
 350
 351     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 352
 353     sortby.addItem("No sort");
 354     sortby.addItem("Id");
 355     sortby.addItem("Pairwise Identity");
 356     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 357
 358     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 359     sortAnnBy
 360             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 361     sortAnnBy
 362             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 363     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 364             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 365                     SequenceAnnotationOrder.NONE.name()));
 366     sortAnnBy.setSelectedItem(savedSort.toString());
 367
 368     sortAutocalc.addItem("Autocalculated first");
 369     sortAutocalc.addItem("Autocalculated last");
 370     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 371     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 372             : sortAutocalc.getItemAt(1));
 373     startupCheckbox
 374             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 375     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 376             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 377                     + "/examples/exampleFile_2_3.jar"));
 378
 379     /*
 380      * Set Colours tab defaults
 381      */
 382     protColour.addItem(ResidueColourScheme.NONE);
 383     nucColour.addItem(ResidueColourScheme.NONE);
 384     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 385     {
 386       String name = cs.getSchemeName();
 387       protColour.addItem(name);
 388       nucColour.addItem(name);
 389     }
 390     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 391             ResidueColourScheme.NONE);
 392     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 393     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 394     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 395     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 396     minColour.setBackground(
 397             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 398     maxColour.setBackground(
 399             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 400
 401     /*
 402      * Set overview panel defaults
 403      */
 404     gapColour.setBackground(
 405             Cache.getDefaultColour(GAP_COLOUR,
 406                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 407     hiddenColour.setBackground(
 408             Cache.getDefaultColour(HIDDEN_COLOUR,
 409                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 410     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 411     gapLabel.setEnabled(!useLegacyGap.isSelected());
 412     gapColour.setEnabled(!useLegacyGap.isSelected());
 413     showHiddenAtStart
 414             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 415
 416     /*
 417      * Set Structure tab defaults.
 418      */
 419     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 420     structFromPdb.setSelected(structSelected);
 421     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 422     useRnaView.setEnabled(structSelected);
 423     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 424     addSecondaryStructure.setEnabled(structSelected);
 425     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 426     addTempFactor.setEnabled(structSelected);
 427     structViewer.setSelectedItem(
 428             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 429     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 430     chimeraPath.addActionListener(new ActionListener()
 431     {
 432       @Override
 433       public void actionPerformed(ActionEvent e)
 434       {
 435         validateChimeraPath();
 436       }
 437     });
 438
 439     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 440     {
 441       siftsMapping.setSelected(true);
 442     }
 443     else
 444     {
 445       nwMapping.setSelected(true);
 446     }
 447
 448     SiftsSettings
 449             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 450
 451     /*
 452      * Set Connections tab defaults
 453      */
 454
 455     // set up sorting
 456     linkUrlTable.setModel(dataModel);
 457     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 458             linkUrlTable.getModel());
 459     linkUrlTable.setRowSorter(sorter);
 460     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 461
 462     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 463     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 464             SortOrder.DESCENDING));
 465     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 466             SortOrder.DESCENDING));
 467     sortKeys.add(
 468             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 469
 470     sorter.setSortKeys(sortKeys);
 471     sorter.sort();
 472
 473     // set up filtering
 474     ActionListener onReset;
 475     onReset = new ActionListener()
 476     {
 477       @Override
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         filterTB.setText("");
 481         sorter.setRowFilter(RowFilter.regexFilter(""));
 482       }
 483
 484     };
 485     doReset.addActionListener(onReset);
 486
 487     // filter to display only custom urls
 488     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 489     {
 490       @Override
 491       public boolean include(
 492               Entry<? extends TableModel, ? extends Object> entry)
 493       {
 494         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 495       }
 496     };
 497
 498     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 499             linkUrlTable.getModel());
 500     customSorter.setRowFilter(customUrlFilter);
 501
 502     ActionListener onCustomOnly;
 503     onCustomOnly = new ActionListener()
 504     {
 505       @Override
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         filterTB.setText("");
 509         sorter.setRowFilter(customUrlFilter);
 510       }
 511     };
 512     userOnly.addActionListener(onCustomOnly);
 513
 514     filterTB.getDocument().addDocumentListener(new DocumentListener()
 515     {
 516       String caseInsensitiveFlag = "(?i)";
 517
 518       @Override
 519       public void changedUpdate(DocumentEvent e)
 520       {
 521         sorter.setRowFilter(RowFilter
 522                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 523       }
 524
 525       @Override
 526       public void removeUpdate(DocumentEvent e)
 527       {
 528         sorter.setRowFilter(RowFilter
 529                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 530       }
 531
 532       @Override
 533       public void insertUpdate(DocumentEvent e)
 534       {
 535         sorter.setRowFilter(RowFilter
 536                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 537       }
 538     });
 539
 540     // set up list selection functionality
 541     linkUrlTable.getSelectionModel()
 542             .addListSelectionListener(new UrlListSelectionHandler());
 543
 544     // set up radio buttons
 545     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 546             .getPrimaryColumn();
 547     String onClickName = linkUrlTable.getColumnName(onClickCol);
 548     linkUrlTable.getColumn(onClickName)
 549             .setCellRenderer(new RadioButtonRenderer());
 550     linkUrlTable.getColumn(onClickName)
 551             .setCellEditor(new RadioButtonEditor());
 552
 553     // get boolean columns and resize those to min possible
 554     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 555     {
 556       if (linkUrlTable.getModel().getColumnClass(column)
 557               .equals(Boolean.class))
 558       {
 559         TableColumn tableColumn = linkUrlTable.getColumnModel()
 560                 .getColumn(column);
 561         int preferredWidth = tableColumn.getMinWidth();
 562
 563         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 564                 column);
 565         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 566         int cwidth = c.getPreferredSize().width
 567                 + linkUrlTable.getIntercellSpacing().width;
 568         preferredWidth = Math.max(preferredWidth, cwidth);
 569
 570         tableColumn.setPreferredWidth(preferredWidth);
 571       }
 572     }
 573
 574     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 575     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 576     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 577     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 578
 579     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 580
 581     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 582     // note antisense here: default is true
 583     questionnaire
 584             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 585     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 586
 587     /*
 588      * Set Output tab defaults
 589      */
 590     epsRendering.addItem(promptEachTimeOpt);
 591     epsRendering.addItem(lineArtOpt);
 592     epsRendering.addItem(textOpt);
 593     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 594             "Prompt each time");
 595     if (defaultEPS.equalsIgnoreCase("Text"))
 596     {
 597       epsRendering.setSelectedItem(textOpt);
 598     }
 599     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 600     {
 601       epsRendering.setSelectedItem(lineArtOpt);
 602     }
 603     else
 604     {
 605       epsRendering.setSelectedItem(promptEachTimeOpt);
 606     }
 607     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 608     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 609     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 610     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 611     userIdWidth.setText(wi == null ? "" : wi.toString());
 612     // TODO: refactor to use common enum via FormatAdapter and allow extension
 613     // for new flat file formats
 614     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 615     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 616     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 617     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 618     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 619     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 620     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 621     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 622     embbedBioJSON
 623             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 624
 625     /*
 626      * Set Editing tab defaults
 627      */
 628     autoCalculateConsCheck
 629             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 630     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 631     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 632
 633     annotations_actionPerformed(null); // update the display of the annotation
 634                                        // settings
 635
 636
 637     /*
 638      * Set Backups tab defaults
 639      */
 640     loadLastSavedBackupsOptions();
 641   }
 642
 643   /**
 644    * Save user selections on the Preferences tabs to the Cache and write out to
 645    * file.
 646    *
 647    * @param e
 648    */
 649   @Override
 650   public void ok_actionPerformed(ActionEvent e)
 651   {
 652     if (!validateSettings())
 653     {
 654       return;
 655     }
 656
 657     /*
 658      * Save Visual settings
 659      */
 660     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 661             Boolean.toString(seqLimit.isSelected()));
 662     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 663             Boolean.toString(rightAlign.isSelected()));
 664     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 665             Boolean.toString(fullScreen.isSelected()));
 666     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 667             Boolean.toString(openoverv.isSelected()));
 668     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 669             Boolean.toString(annotations.isSelected()));
 670     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 671             Boolean.toString(conservation.isSelected()));
 672     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 673             Boolean.toString(quality.isSelected()));
 674     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 675             Boolean.toString(identity.isSelected()));
 676
 677     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 678             gapSymbolCB.getSelectedItem().toString());
 679
 680     Cache.applicationProperties.setProperty("FONT_NAME",
 681             fontNameCB.getSelectedItem().toString());
 682     Cache.applicationProperties.setProperty("FONT_STYLE",
 683             fontStyleCB.getSelectedItem().toString());
 684     Cache.applicationProperties.setProperty("FONT_SIZE",
 685             fontSizeCB.getSelectedItem().toString());
 686
 687     Cache.applicationProperties.setProperty("ID_ITALICS",
 688             Boolean.toString(idItalics.isSelected()));
 689     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 690             Boolean.toString(showUnconserved.isSelected()));
 691     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 692             Boolean.toString(showOccupancy.isSelected()));
 693     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 694             Boolean.toString(showGroupConsensus.isSelected()));
 695     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 696             Boolean.toString(showGroupConservation.isSelected()));
 697     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 698             Boolean.toString(showConsensHistogram.isSelected()));
 699     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 700             Boolean.toString(showConsensLogo.isSelected()));
 701     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 702             Boolean.toString(showConsensHistogram.isSelected()));
 703     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 704             Boolean.toString(showHMMLogo.isSelected()));
 705     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 706             Boolean.toString(smoothFont.isSelected()));
 707     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 708             Boolean.toString(scaleProteinToCdna.isSelected()));
 709     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 710             Boolean.toString(showNpTooltip.isSelected()));
 711     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 712             Boolean.toString(showDbRefTooltip.isSelected()));
 713
 714     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 715             Boolean.toString(wrap.isSelected()));
 716
 717     Cache.applicationProperties.setProperty("STARTUP_FILE",
 718             startupFileTextfield.getText());
 719     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 720             Boolean.toString(startupCheckbox.isSelected()));
 721
 722     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 723             sortby.getSelectedItem().toString());
 724
 725     // convert description of sort order to enum name for save
 726     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 727             .forDescription(sortAnnBy.getSelectedItem().toString());
 728     if (annSortOrder != null)
 729     {
 730       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 731               annSortOrder.name());
 732     }
 733
 734     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 735     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 736             Boolean.valueOf(showAutocalcFirst).toString());
 737
 738     /*
 739      * Save Colours settings
 740      */
 741     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 742             protColour.getSelectedItem().toString());
 743     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 744             nucColour.getSelectedItem().toString());
 745     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 746             minColour.getBackground());
 747     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 748             maxColour.getBackground());
 749
 750     /*
 751      * Save HMMER settings
 752      */
 753     Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
 754             Boolean.toString(hmmrTrimTermini.isSelected()));
 755     Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
 756             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 757     Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
 758             hmmerSequenceCount.getText());
 759     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
 760     if (cygwinPath != null)
 761     {
 762       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
 763     }
 764     AlignFrame[] frames = Desktop.getAlignFrames();
 765     if (frames != null && frames.length > 0)
 766     {
 767       for (AlignFrame f : frames)
 768       {
 769         f.updateHMMERStatus();
 770       }
 771     }
 772
 773     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 774     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 775     {
 776       hmmerBackgroundUniprot.setSelected(true);
 777     }
 778     else
 779     {
 780       hmmerBackgroundAlignment.setSelected(true);
 781     }
 782     hmmerSequenceCount
 783             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 784     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 785
 786     /*
 787      * Save Overview settings
 788      */
 789     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 790     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 791     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 792             Boolean.toString(useLegacyGap.isSelected()));
 793     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 794             Boolean.toString(showHiddenAtStart.isSelected()));
 795
 796     /*
 797      * Save Structure settings
 798      */
 799     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 800             Boolean.toString(addTempFactor.isSelected()));
 801     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 802             Boolean.toString(addSecondaryStructure.isSelected()));
 803     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 804             Boolean.toString(useRnaView.isSelected()));
 805     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 806             Boolean.toString(structFromPdb.isSelected()));
 807     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 808             structViewer.getSelectedItem().toString());
 809     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 810     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 811             Boolean.toString(siftsMapping.isSelected()));
 812     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 813
 814     /*
 815      * Save Output settings
 816      */
 817     Cache.applicationProperties.setProperty("EPS_RENDERING",
 818             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 819
 820     /*
 821      * Save Connections settings
 822      */
 823     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 824
 825     jalview.util.BrowserLauncher.resetBrowser();
 826
 827     // save user-defined and selected links
 828     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 829     if (menuLinks.isEmpty())
 830     {
 831       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 832     }
 833     else
 834     {
 835       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 836               menuLinks.toString());
 837     }
 838
 839     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 840     if (nonMenuLinks.isEmpty())
 841     {
 842       Cache.applicationProperties.remove("STORED_LINKS");
 843     }
 844     else
 845     {
 846       Cache.applicationProperties.setProperty("STORED_LINKS",
 847               nonMenuLinks.toString());
 848     }
 849
 850     Cache.applicationProperties.setProperty("DEFAULT_URL",
 851             sequenceUrlLinks.getPrimaryUrlId());
 852
 853     Cache.applicationProperties.setProperty("USE_PROXY",
 854             Boolean.toString(useProxy.isSelected()));
 855
 856     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 857
 858     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 859
 860     if (useProxy.isSelected())
 861     {
 862       System.setProperty("http.proxyHost", proxyServerTB.getText());
 863       System.setProperty("http.proxyPort", proxyPortTB.getText());
 864     }
 865     else
 866     {
 867       System.setProperty("http.proxyHost", "");
 868       System.setProperty("http.proxyPort", "");
 869     }
 870     Cache.setProperty("VERSION_CHECK",
 871             Boolean.toString(versioncheck.isSelected()));
 872     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 873     {
 874       // default is false - we only set this if the user has actively agreed
 875       Cache.setProperty("USAGESTATS",
 876               Boolean.toString(usagestats.isSelected()));
 877     }
 878     if (!questionnaire.isSelected())
 879     {
 880       Cache.setProperty("NOQUESTIONNAIRES", "true");
 881     }
 882     else
 883     {
 884       // special - made easy to edit a property file to disable questionnaires
 885       // by just adding the given line
 886       Cache.removeProperty("NOQUESTIONNAIRES");
 887     }
 888
 889     /*
 890      * Save Output settings
 891      */
 892     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 893             Boolean.toString(blcjv.isSelected()));
 894     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 895             Boolean.toString(clustaljv.isSelected()));
 896     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 897             Boolean.toString(fastajv.isSelected()));
 898     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 899             Boolean.toString(msfjv.isSelected()));
 900     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 901             Boolean.toString(pfamjv.isSelected()));
 902     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 903             Boolean.toString(pileupjv.isSelected()));
 904     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 905             Boolean.toString(pirjv.isSelected()));
 906     Cache.applicationProperties.setProperty("PIR_MODELLER",
 907             Boolean.toString(modellerOutput.isSelected()));
 908     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 909             Boolean.toString(embbedBioJSON.isSelected()));
 910     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 911
 912     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 913             Boolean.toString(autoIdWidth.isSelected()));
 914     userIdWidth_actionPerformed();
 915     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 916             userIdWidth.getText());
 917
 918     /*
 919      * Save Editing settings
 920      */
 921     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 922             Boolean.toString(autoCalculateConsCheck.isSelected()));
 923     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 924             Boolean.toString(sortByTree.isSelected()));
 925     Cache.applicationProperties.setProperty("PAD_GAPS",
 926             Boolean.toString(padGaps.isSelected()));
 927
 928     wsPrefs.updateAndRefreshWsMenuConfig(false);
 929
 930     /*
 931      * Save Backups settings
 932      */
 933     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 934             Boolean.toString(enableBackupFiles.isSelected()));
 935     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 936     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 937
 938     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 939     {
 940       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 941       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 942               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 943       Cache.applicationProperties
 944               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 945                       customBFPE.toString());
 946     }
 947
 948     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 949             .get(preset);
 950     Cache.applicationProperties.setProperty(
 951             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 952
 953     Cache.saveProperties();
 954     Desktop.instance.doConfigureStructurePrefs();
 955     try
 956     {
 957       frame.setClosed(true);
 958     } catch (Exception ex)
 959     {
 960     }
 961   }
 962
 963   /**
 964    * Do any necessary validation before saving settings. Return focus to the
 965    * first tab which fails validation.
 966    *
 967    * @return
 968    */
 969   private boolean validateSettings()
 970   {
 971     if (!validateStructure())
 972     {
 973       structureTab.requestFocusInWindow();
 974       return false;
 975     }
 976     return true;
 977   }
 978
 979   @Override
 980   protected boolean validateStructure()
 981   {
 982     return validateChimeraPath();
 983
 984   }
 985
 986   /**
 987    * DOCUMENT ME!
 988    */
 989   @Override
 990   public void startupFileTextfield_mouseClicked()
 991   {
 992     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 993     JalviewFileChooser chooser = JalviewFileChooser
 994             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 995     chooser.setFileView(new JalviewFileView());
 996     chooser.setDialogTitle(
 997             MessageManager.getString("label.select_startup_file"));
 998
 999     int value = chooser.showOpenDialog(this);
1000
1001     if (value == JalviewFileChooser.APPROVE_OPTION)
1002     {
1003       FileFormatI format = chooser.getSelectedFormat();
1004       if (format != null)
1005       {
1006         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1007                 format.getName());
1008       }
1009       startupFileTextfield
1010               .setText(chooser.getSelectedFile().getAbsolutePath());
1011     }
1012   }
1013
1014   /**
1015    * DOCUMENT ME!
1016    *
1017    * @param e
1018    *          DOCUMENT ME!
1019    */
1020   @Override
1021   public void cancel_actionPerformed(ActionEvent e)
1022   {
1023     try
1024     {
1025       wsPrefs.updateWsMenuConfig(true);
1026       wsPrefs.refreshWs_actionPerformed(e);
1027       frame.setClosed(true);
1028     } catch (Exception ex)
1029     {
1030     }
1031   }
1032
1033   /**
1034    * DOCUMENT ME!
1035    *
1036    * @param e
1037    *          DOCUMENT ME!
1038    */
1039   @Override
1040   public void annotations_actionPerformed(ActionEvent e)
1041   {
1042     conservation.setEnabled(annotations.isSelected());
1043     quality.setEnabled(annotations.isSelected());
1044     identity.setEnabled(annotations.isSelected());
1045     showOccupancy.setEnabled(annotations.isSelected());
1046     showGroupConsensus.setEnabled(annotations.isSelected());
1047     showGroupConservation.setEnabled(annotations.isSelected());
1048     showConsensHistogram.setEnabled(annotations.isSelected()
1049             && (identity.isSelected() || showGroupConsensus.isSelected()));
1050     showConsensLogo.setEnabled(annotations.isSelected()
1051             && (identity.isSelected() || showGroupConsensus.isSelected()));
1052     showInformationHistogram.setEnabled(annotations.isSelected());
1053     showHMMLogo.setEnabled(annotations.isSelected());
1054   }
1055
1056   @Override
1057   public void newLink_actionPerformed(ActionEvent e)
1058   {
1059     GSequenceLink link = new GSequenceLink();
1060     boolean valid = false;
1061     while (!valid)
1062     {
1063       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1064               MessageManager.getString("label.new_sequence_url_link"),
1065               JvOptionPane.OK_CANCEL_OPTION, -1,
1066               null) == JvOptionPane.OK_OPTION)
1067       {
1068         if (link.checkValid())
1069         {
1070           if (((UrlLinkTableModel) linkUrlTable.getModel())
1071                   .isUniqueName(link.getName()))
1072           {
1073             ((UrlLinkTableModel) linkUrlTable.getModel())
1074                     .insertRow(link.getName(), link.getURL());
1075             valid = true;
1076           }
1077           else
1078           {
1079             link.notifyDuplicate();
1080             continue;
1081           }
1082         }
1083       }
1084       else
1085       {
1086         break;
1087       }
1088     }
1089   }
1090
1091   @Override
1092   public void editLink_actionPerformed(ActionEvent e)
1093   {
1094     GSequenceLink link = new GSequenceLink();
1095
1096     int index = linkUrlTable.getSelectedRow();
1097     if (index == -1)
1098     {
1099       // button no longer enabled if row is not selected
1100       Cache.log.debug("Edit with no row selected in linkUrlTable");
1101       return;
1102     }
1103
1104     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1105             .getNameColumn();
1106     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1107             .getUrlColumn();
1108     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1109     link.setName(oldName);
1110     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1111
1112     boolean valid = false;
1113     while (!valid)
1114     {
1115       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1116               MessageManager.getString("label.edit_sequence_url_link"),
1117               JvOptionPane.OK_CANCEL_OPTION, -1,
1118               null) == JvOptionPane.OK_OPTION)
1119       {
1120         if (link.checkValid())
1121         {
1122           if ((oldName.equals(link.getName()))
1123                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1124                           .isUniqueName(link.getName())))
1125           {
1126             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1127             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1128             valid = true;
1129           }
1130           else
1131           {
1132             link.notifyDuplicate();
1133             continue;
1134           }
1135         }
1136       }
1137       else
1138       {
1139         break;
1140       }
1141     }
1142   }
1143
1144   @Override
1145   public void deleteLink_actionPerformed(ActionEvent e)
1146   {
1147     int index = linkUrlTable.getSelectedRow();
1148     int modelIndex = -1;
1149     if (index == -1)
1150     {
1151       // button no longer enabled if row is not selected
1152       Cache.log.debug("Delete with no row selected in linkUrlTable");
1153       return;
1154     }
1155     else
1156     {
1157       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1158     }
1159
1160     // make sure we use the model index to delete, and not the table index
1161     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1162   }
1163
1164   @Override
1165   public void defaultBrowser_mouseClicked(MouseEvent e)
1166   {
1167     JFileChooser chooser = new JFileChooser(".");
1168     chooser.setDialogTitle(
1169             MessageManager.getString("label.select_default_browser"));
1170
1171     int value = chooser.showOpenDialog(this);
1172
1173     if (value == JFileChooser.APPROVE_OPTION)
1174     {
1175       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1176     }
1177
1178   }
1179
1180   /*
1181    * (non-Javadoc)
1182    *
1183    * @see
1184    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1185    * .ActionEvent)
1186    */
1187   @Override
1188   protected void showunconserved_actionPerformed(ActionEvent e)
1189   {
1190     // TODO Auto-generated method stub
1191     super.showunconserved_actionPerformed(e);
1192   }
1193
1194   public static List<String> getGroupURLLinks()
1195   {
1196     return groupURLLinks;
1197   }
1198
1199   @Override
1200   public void minColour_actionPerformed(JPanel panel)
1201   {
1202     Color col = JColorChooser.showDialog(this,
1203             MessageManager.getString("label.select_colour_minimum_value"),
1204             minColour.getBackground());
1205     if (col != null)
1206     {
1207       panel.setBackground(col);
1208     }
1209     panel.repaint();
1210   }
1211
1212   @Override
1213   public void maxColour_actionPerformed(JPanel panel)
1214   {
1215     Color col = JColorChooser.showDialog(this,
1216             MessageManager.getString("label.select_colour_maximum_value"),
1217             maxColour.getBackground());
1218     if (col != null)
1219     {
1220       panel.setBackground(col);
1221     }
1222     panel.repaint();
1223   }
1224
1225   @Override
1226   public void gapColour_actionPerformed(JPanel gap)
1227   {
1228     if (!useLegacyGap.isSelected())
1229     {
1230       Color col = JColorChooser.showDialog(this,
1231               MessageManager.getString("label.select_gap_colour"),
1232               gapColour.getBackground());
1233       if (col != null)
1234       {
1235         gap.setBackground(col);
1236       }
1237       gap.repaint();
1238     }
1239   }
1240
1241   @Override
1242   public void hiddenColour_actionPerformed(JPanel hidden)
1243   {
1244     Color col = JColorChooser.showDialog(this,
1245             MessageManager.getString("label.select_hidden_colour"),
1246             hiddenColour.getBackground());
1247     if (col != null)
1248     {
1249       hidden.setBackground(col);
1250     }
1251     hidden.repaint();
1252   }
1253
1254   @Override
1255   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1256   {
1257     boolean enabled = useLegacyGap.isSelected();
1258     if (enabled)
1259     {
1260       gapColour.setBackground(
1261               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1262     }
1263     else
1264     {
1265       gapColour.setBackground(
1266               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1267     }
1268     gapColour.setEnabled(!enabled);
1269     gapLabel.setEnabled(!enabled);
1270   }
1271
1272   @Override
1273   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1274   {
1275     useLegacyGap.setSelected(false);
1276     useLegacyGaps_actionPerformed(null);
1277     showHiddenAtStart.setSelected(false);
1278     hiddenColour.setBackground(
1279             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1280   }
1281
1282   @Override
1283   protected void userIdWidth_actionPerformed()
1284   {
1285     try
1286     {
1287       String val = userIdWidth.getText().trim();
1288       if (val.length() > 0)
1289       {
1290         Integer iw = Integer.parseInt(val);
1291         if (iw.intValue() < 12)
1292         {
1293           throw new NumberFormatException();
1294         }
1295         userIdWidth.setText(iw.toString());
1296       }
1297     } catch (NumberFormatException x)
1298     {
1299       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1300               MessageManager
1301                       .getString("warn.user_defined_width_requirements"),
1302               MessageManager.getString("label.invalid_id_column_width"),
1303               JvOptionPane.WARNING_MESSAGE);
1304       userIdWidth.setText("");
1305     }
1306   }
1307
1308   @Override
1309   protected void autoIdWidth_actionPerformed()
1310   {
1311     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1312     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1313   }
1314
1315   /**
1316    * Returns true if chimera path is to a valid executable, else show an error
1317    * dialog.
1318    */
1319   private boolean validateChimeraPath()
1320   {
1321     if (chimeraPath.getText().trim().length() > 0)
1322     {
1323       File f = new File(chimeraPath.getText());
1324       if (!f.canExecute())
1325       {
1326         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1327                 MessageManager.getString("label.invalid_chimera_path"),
1328                 MessageManager.getString("label.invalid_name"),
1329                 JvOptionPane.ERROR_MESSAGE);
1330         return false;
1331       }
1332     }
1333     return true;
1334   }
1335
1336   /**
1337    * Returns true if the given text field contains a path to a folder that
1338    * contains an executable with the given name, else false (after showing a
1339    * warning dialog). The executable name will be tried with .exe appended if not
1340    * found.
1341    *
1342    * @param textField
1343    * @param executable
1344    */
1345   protected boolean validateExecutablePath(JTextField textField, String executable)
1346   {
1347     String folder = textField.getText().trim();
1348
1349     if (FileUtils.getExecutable(executable, folder) != null)
1350     {
1351       return true;
1352     }
1353     if (folder.length() > 0)
1354     {
1355       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1356               MessageManager.formatMessage("label.executable_not_found",
1357                       executable),
1358               MessageManager.getString("label.invalid_folder"),
1359               JvOptionPane.ERROR_MESSAGE);
1360     }
1361     return false;
1362   }
1363
1364   /**
1365    * Checks if a file can be executed
1366    *
1367    * @param path
1368    *          the path to the file
1369    * @return
1370    */
1371   public boolean canExecute(String path)
1372   {
1373     File file = new File(path);
1374     if (!file.canExecute())
1375     {
1376       file = new File(path + ".exe");
1377       {
1378         if (!file.canExecute())
1379         {
1380           return false;
1381         }
1382       }
1383     }
1384     return true;
1385   }
1386
1387   /**
1388    * If Chimera is selected, check it can be found on default or user-specified
1389    * path, if not show a warning/help dialog.
1390    */
1391   @Override
1392   protected void structureViewer_actionPerformed(String selectedItem)
1393   {
1394     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1395     {
1396       return;
1397     }
1398     boolean found = false;
1399
1400     /*
1401      * Try user-specified and standard paths for Chimera executable.
1402      */
1403     List<String> paths = StructureManager.getChimeraPaths();
1404     paths.add(0, chimeraPath.getText());
1405     for (String path : paths)
1406     {
1407       if (new File(path.trim()).canExecute())
1408       {
1409         found = true;
1410         break;
1411       }
1412     }
1413     if (!found)
1414     {
1415       String[] options = { "OK", "Help" };
1416       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1417               JvSwingUtils.wrapTooltip(true,
1418                       MessageManager.getString("label.chimera_missing")),
1419               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1420               null, options, options[0]);
1421       if (showHelp == JvOptionPane.NO_OPTION)
1422       {
1423         try
1424         {
1425           Help.showHelpWindow(HelpId.StructureViewer);
1426         } catch (HelpSetException e)
1427         {
1428           e.printStackTrace();
1429         }
1430       }
1431     }
1432   }
1433
1434   @Override
1435   protected void validateHmmerPath()
1436   {
1437     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1438   }
1439
1440   @Override
1441   protected void validateCygwinPath()
1442   {
1443     validateExecutablePath(cygwinPath, "run");
1444   }
1445
1446   public class OptionsParam
1447   {
1448     private String name;
1449
1450     private String code;
1451
1452     public OptionsParam(String name, String code)
1453     {
1454       this.name = name;
1455       this.code = code;
1456     }
1457
1458     public String getName()
1459     {
1460       return name;
1461     }
1462
1463     public void setName(String name)
1464     {
1465       this.name = name;
1466     }
1467
1468     public String getCode()
1469     {
1470       return code;
1471     }
1472
1473     public void setCode(String code)
1474     {
1475       this.code = code;
1476     }
1477
1478     @Override
1479     public String toString()
1480     {
1481       return name;
1482     }
1483
1484     @Override
1485     public boolean equals(Object that)
1486     {
1487       if (!(that instanceof OptionsParam))
1488       {
1489         return false;
1490       }
1491       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1492     }
1493
1494     @Override
1495     public int hashCode()
1496     {
1497       return name.hashCode() + code.hashCode();
1498     }
1499   }
1500
1501   private class UrlListSelectionHandler implements ListSelectionListener
1502   {
1503
1504     @Override
1505     public void valueChanged(ListSelectionEvent e)
1506     {
1507       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1508
1509       int index = lsm.getMinSelectionIndex();
1510       if (index == -1)
1511       {
1512         // no selection, so disable delete/edit buttons
1513         editLink.setEnabled(false);
1514         deleteLink.setEnabled(false);
1515         return;
1516       }
1517       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1518
1519       // enable/disable edit and delete link buttons
1520       if (((UrlLinkTableModel) linkUrlTable.getModel())
1521               .isRowDeletable(modelIndex))
1522       {
1523         deleteLink.setEnabled(true);
1524       }
1525       else
1526       {
1527         deleteLink.setEnabled(false);
1528       }
1529
1530       if (((UrlLinkTableModel) linkUrlTable.getModel())
1531               .isRowEditable(modelIndex))
1532       {
1533         editLink.setEnabled(true);
1534       }
1535       else
1536       {
1537         editLink.setEnabled(false);
1538       }
1539     }
1540   }
1541 }