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