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