src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.hmmer.HmmerCommand;
  28 import jalview.io.BackupFiles;
  29 import jalview.io.BackupFilesPresetEntry;
  30 import jalview.io.FileFormatI;
  31 import jalview.io.JalviewFileChooser;
  32 import jalview.io.JalviewFileView;
  33 import jalview.jbgui.GPreferences;
  34 import jalview.jbgui.GSequenceLink;
  35 import jalview.schemes.ColourSchemeI;
  36 import jalview.schemes.ColourSchemes;
  37 import jalview.schemes.ResidueColourScheme;
  38 import jalview.urls.UrlLinkTableModel;
  39 import jalview.urls.api.UrlProviderFactoryI;
  40 import jalview.urls.api.UrlProviderI;
  41 import jalview.urls.desktop.DesktopUrlProviderFactory;
  42 import jalview.util.FileUtils;
  43 import jalview.util.MessageManager;
  44 import jalview.util.Platform;
  45 import jalview.util.UrlConstants;
  46 import jalview.ws.sifts.SiftsSettings;
  47
  48 import java.awt.BorderLayout;
  49 import java.awt.Color;
  50 import java.awt.Component;
  51 import java.awt.Dimension;
  52 import java.awt.Font;
  53 import java.awt.event.ActionEvent;
  54 import java.awt.event.ActionListener;
  55 import java.awt.event.FocusAdapter;
  56 import java.awt.event.FocusEvent;
  57 import java.awt.event.MouseEvent;
  58 import java.io.File;
  59 import java.util.ArrayList;
  60 import java.util.List;
  61
  62 import javax.help.HelpSetException;
  63 import javax.swing.JComboBox;
  64 import javax.swing.JFileChooser;
  65 import javax.swing.JInternalFrame;
  66 import javax.swing.JPanel;
  67 import javax.swing.JTextField;
  68 import javax.swing.ListSelectionModel;
  69 import javax.swing.RowFilter;
  70 import javax.swing.RowSorter;
  71 import javax.swing.SortOrder;
  72 import javax.swing.event.DocumentEvent;
  73 import javax.swing.event.DocumentListener;
  74 import javax.swing.event.ListSelectionEvent;
  75 import javax.swing.event.ListSelectionListener;
  76 import javax.swing.table.TableCellRenderer;
  77 import javax.swing.table.TableColumn;
  78 import javax.swing.table.TableModel;
  79 import javax.swing.table.TableRowSorter;
  80
  81 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  82
  83 /**
  84  * DOCUMENT ME!
  85  *
  86  * @author $author$
  87  * @version $Revision$
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   // suggested list delimiter character
  92   public static final String COMMA = ",";
  93
  94   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
  95
  96   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
  97
  98   public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
  99
 100   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 101
 102   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
 103
 104   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 105
 106   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 107
 108   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 109
 110   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 111
 112   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 113
 114   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 115
 116   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 117
 118   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 119
 120   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 121
 122   public static final String HMMER_PATH = "HMMER_PATH";
 123
 124   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 125
 126   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 127
 128   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 129
 130   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 131
 132   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 133
 134   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 135
 136   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 137
 138   public static final String GAP_COLOUR = "GAP_COLOUR";
 139
 140   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 141
 142   private static final int MIN_FONT_SIZE = 1;
 143
 144   private static final int MAX_FONT_SIZE = 30;
 145
 146   /**
 147    * Holds name and link separated with | character. Sequence ID must be
 148    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 149    */
 150   public static UrlProviderI sequenceUrlLinks;
 151
 152   public static UrlLinkTableModel dataModel;
 153
 154   /**
 155    * Holds name and link separated with | character. Sequence IDS and Sequences
 156    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 157    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 158    * for first and second token specified after a pipe character at end |,|.
 159    * (TODO: proper escape for using | to separate ids or sequences
 160    */
 161
 162   public static List<String> groupURLLinks;
 163   static
 164   {
 165     // get links selected to be in the menu (SEQUENCE_LINKS)
 166     // and links entered by the user but not selected (STORED_LINKS)
 167     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 168     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 169     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 170             UrlConstants.DEFAULT_LABEL);
 171
 172     // if both links lists are empty, add the DEFAULT_URL link
 173     // otherwise we assume the default link is in one of the lists
 174     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 175     {
 176       inMenuString = UrlConstants.DEFAULT_STRING;
 177     }
 178     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 179             inMenuString, notInMenuString);
 180     sequenceUrlLinks = factory.createUrlProvider();
 181     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 182
 183     /**
 184      * TODO: reformulate groupURL encoding so two or more can be stored in the
 185      * .properties file as '|' separated strings
 186      */
 187
 188     groupURLLinks = new ArrayList<>();
 189   }
 190
 191   JInternalFrame frame;
 192
 193   private WsPreferences wsPrefs;
 194
 195   private OptionsParam promptEachTimeOpt = new OptionsParam(
 196           MessageManager.getString("label.prompt_each_time"),
 197           "Prompt each time");
 198
 199   private OptionsParam lineArtOpt = new OptionsParam(
 200           MessageManager.getString("label.lineart"), "Lineart");
 201
 202   private OptionsParam textOpt = new OptionsParam(
 203           MessageManager.getString("action.text"), "Text");
 204
 205   /**
 206    * Creates a new Preferences object.
 207    */
 208   public Preferences()
 209   {
 210     super();
 211     frame = new JInternalFrame();
 212     frame.setContentPane(this);
 213     if (!Platform.isJS())
 214     /**
 215      * Java only
 216      *
 217      * @j2sIgnore
 218      */
 219     {
 220       wsPrefs = new WsPreferences();
 221       wsTab.add(wsPrefs, BorderLayout.CENTER);
 222     }
 223     int width = 500, height = 450;
 224     if (Platform.isAMacAndNotJS())
 225     {
 226       width = 570;
 227       height = 480;
 228     }
 229
 230     Desktop.addInternalFrame(frame,
 231             MessageManager.getString("label.preferences"), width, height);
 232     frame.setMinimumSize(new Dimension(width, height));
 233
 234     /*
 235      * Set HMMER tab defaults
 236      */
 237     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 238     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 239     {
 240       hmmerBackgroundUniprot.setSelected(true);
 241     }
 242     else
 243     {
 244       hmmerBackgroundAlignment.setSelected(true);
 245     }
 246     hmmerSequenceCount
 247             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 248     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 249     hmmerPath.addActionListener(new ActionListener()
 250     {
 251       @Override
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         validateHmmerPath();
 255       }
 256     });
 257     hmmerPath.addFocusListener(new FocusAdapter()
 258     {
 259       @Override
 260       public void focusLost(FocusEvent e)
 261       {
 262         validateHmmerPath();
 263       }
 264     });
 265     if (cygwinPath != null)
 266     {
 267       String path = Cache.getProperty(CYGWIN_PATH);
 268       if (path == null)
 269       {
 270         path = FileUtils.getPathTo("bash");
 271       }
 272       cygwinPath.setText(path);
 273       cygwinPath.addActionListener(new ActionListener()
 274       {
 275         @Override
 276         public void actionPerformed(ActionEvent e)
 277         {
 278           validateCygwinPath();
 279         }
 280       });
 281       cygwinPath.addFocusListener(new FocusAdapter()
 282       {
 283         @Override
 284         public void focusLost(FocusEvent e)
 285         {
 286           validateCygwinPath();
 287         }
 288       });
 289     }
 290
 291     /*
 292      * Set Visual tab defaults
 293      */
 294     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 295     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 296     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 297     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 298
 299     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 300     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 301     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 302     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 303     showUnconserved
 304             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 305     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 306     showGroupConsensus
 307             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 308     showGroupConservation.setSelected(
 309             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 310     showConsensHistogram.setSelected(
 311             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 312     showConsensLogo
 313             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 314     showInformationHistogram.setSelected(
 315             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 316     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 317     showNpTooltip
 318             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 319     showDbRefTooltip
 320             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 321
 322     String[] fonts = java.awt.GraphicsEnvironment
 323             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 324     for (int i = 0; i < fonts.length; i++)
 325     {
 326       fontNameCB.addItem(fonts[i]);
 327     }
 328
 329     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 330     {
 331       fontSizeCB.addItem(i + "");
 332     }
 333
 334     fontStyleCB.addItem("plain");
 335     fontStyleCB.addItem("bold");
 336     fontStyleCB.addItem("italic");
 337
 338     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 339     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 340     fontStyleCB.setSelectedItem(
 341             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 342
 343     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 344     scaleProteinToCdna
 345             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 346
 347     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 348
 349     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 350
 351     gapSymbolCB.addItem("-");
 352     gapSymbolCB.addItem(".");
 353
 354     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 355
 356     sortby.addItem("No sort");
 357     sortby.addItem("Id");
 358     sortby.addItem("Pairwise Identity");
 359     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 360
 361     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 362     sortAnnBy
 363             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 364     sortAnnBy
 365             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 366     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 367             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 368                     SequenceAnnotationOrder.NONE.name()));
 369     sortAnnBy.setSelectedItem(savedSort.toString());
 370
 371     sortAutocalc.addItem("Autocalculated first");
 372     sortAutocalc.addItem("Autocalculated last");
 373     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 374     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 375             : sortAutocalc.getItemAt(1));
 376     startupCheckbox
 377             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 378     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 379             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 380                     + "/examples/exampleFile_2_3.jar"));
 381
 382     /*
 383      * Set Colours tab defaults
 384      */
 385     protColour.addItem(ResidueColourScheme.NONE);
 386     nucColour.addItem(ResidueColourScheme.NONE);
 387     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 388     {
 389       String name = cs.getSchemeName();
 390       protColour.addItem(name);
 391       nucColour.addItem(name);
 392     }
 393     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 394             ResidueColourScheme.NONE);
 395     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 396     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 397     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 398     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 399     minColour.setBackground(
 400             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 401     maxColour.setBackground(
 402             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 403
 404     /*
 405      * Set overview panel defaults
 406      */
 407     gapColour.setBackground(
 408             Cache.getDefaultColour(GAP_COLOUR,
 409                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 410     hiddenColour.setBackground(
 411             Cache.getDefaultColour(HIDDEN_COLOUR,
 412                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 413     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 414     gapLabel.setEnabled(!useLegacyGap.isSelected());
 415     gapColour.setEnabled(!useLegacyGap.isSelected());
 416     showHiddenAtStart
 417             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 418
 419     /*
 420      * Set Structure tab defaults.
 421      */
 422     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 423     structFromPdb.setSelected(structSelected);
 424     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 425     useRnaView.setEnabled(structSelected);
 426     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 427     addSecondaryStructure.setEnabled(structSelected);
 428     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 429     addTempFactor.setEnabled(structSelected);
 430     structViewer.setSelectedItem(
 431             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 432     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 433     chimeraPath.addActionListener(new ActionListener()
 434     {
 435       @Override
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         validateChimeraPath();
 439       }
 440     });
 441
 442     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 443     {
 444       siftsMapping.setSelected(true);
 445     }
 446     else
 447     {
 448       nwMapping.setSelected(true);
 449     }
 450
 451     SiftsSettings
 452             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 453
 454     /*
 455      * Set Connections tab defaults
 456      */
 457
 458     // set up sorting
 459     linkUrlTable.setModel(dataModel);
 460     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 461             linkUrlTable.getModel());
 462     linkUrlTable.setRowSorter(sorter);
 463     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 464
 465     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 466     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 467             SortOrder.DESCENDING));
 468     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 469             SortOrder.DESCENDING));
 470     sortKeys.add(
 471             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 472
 473     sorter.setSortKeys(sortKeys);
 474     // BH 2018 setSortKeys will do the sort
 475     // sorter.sort();
 476
 477     // set up filtering
 478     ActionListener onReset;
 479     onReset = new ActionListener()
 480     {
 481       @Override
 482       public void actionPerformed(ActionEvent e)
 483       {
 484         filterTB.setText("");
 485         sorter.setRowFilter(RowFilter.regexFilter(""));
 486       }
 487
 488     };
 489     doReset.addActionListener(onReset);
 490
 491     // filter to display only custom urls
 492     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 493     {
 494       @Override
 495       public boolean include(
 496               Entry<? extends TableModel, ? extends Object> entry)
 497       {
 498         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 499       }
 500     };
 501
 502     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 503             linkUrlTable.getModel());
 504     customSorter.setRowFilter(customUrlFilter);
 505
 506     ActionListener onCustomOnly;
 507     onCustomOnly = new ActionListener()
 508     {
 509       @Override
 510       public void actionPerformed(ActionEvent e)
 511       {
 512         filterTB.setText("");
 513         sorter.setRowFilter(customUrlFilter);
 514       }
 515     };
 516     userOnly.addActionListener(onCustomOnly);
 517
 518     filterTB.getDocument().addDocumentListener(new DocumentListener()
 519     {
 520       String caseInsensitiveFlag = "(?i)";
 521
 522       @Override
 523       public void changedUpdate(DocumentEvent e)
 524       {
 525         sorter.setRowFilter(RowFilter
 526                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 527       }
 528
 529       @Override
 530       public void removeUpdate(DocumentEvent e)
 531       {
 532         sorter.setRowFilter(RowFilter
 533                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 534       }
 535
 536       @Override
 537       public void insertUpdate(DocumentEvent e)
 538       {
 539         sorter.setRowFilter(RowFilter
 540                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 541       }
 542     });
 543
 544     // set up list selection functionality
 545     linkUrlTable.getSelectionModel()
 546             .addListSelectionListener(new UrlListSelectionHandler());
 547
 548     // set up radio buttons
 549     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 550             .getPrimaryColumn();
 551     String onClickName = linkUrlTable.getColumnName(onClickCol);
 552     linkUrlTable.getColumn(onClickName)
 553             .setCellRenderer(new RadioButtonRenderer());
 554     linkUrlTable.getColumn(onClickName)
 555             .setCellEditor(new RadioButtonEditor());
 556
 557     // get boolean columns and resize those to min possible
 558     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 559     {
 560       if (linkUrlTable.getModel().getColumnClass(column)
 561               .equals(Boolean.class))
 562       {
 563         TableColumn tableColumn = linkUrlTable.getColumnModel()
 564                 .getColumn(column);
 565         int preferredWidth = tableColumn.getMinWidth();
 566
 567         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 568                 column);
 569         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 570         int cwidth = c.getPreferredSize().width
 571                 + linkUrlTable.getIntercellSpacing().width;
 572         preferredWidth = Math.max(preferredWidth, cwidth);
 573
 574         tableColumn.setPreferredWidth(preferredWidth);
 575       }
 576     }
 577
 578     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 579     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 580     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 581     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 582
 583     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 584
 585     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 586     // note antisense here: default is true
 587     questionnaire
 588             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 589     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 590
 591     /*
 592      * Set Output tab defaults
 593      */
 594     setupOutputCombo(epsRendering, "EPS_RENDERING");
 595     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 596     setupOutputCombo(svgRendering, "SVG_RENDERING");
 597     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 598     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 599     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 600     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 601     userIdWidth.setText(wi == null ? "" : wi.toString());
 602     // TODO: refactor to use common enum via FormatAdapter and allow extension
 603     // for new flat file formats
 604     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 605     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 606     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 607     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 608     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 609     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 610     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 611     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 612     embbedBioJSON
 613             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 614
 615     /*
 616      * Set Editing tab defaults
 617      */
 618     autoCalculateConsCheck
 619             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 620     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 621     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 622
 623     annotations_actionPerformed(null); // update the display of the annotation
 624                                        // settings
 625
 626
 627     /*
 628      * Set Backups tab defaults
 629      */
 630     loadLastSavedBackupsOptions();
 631   }
 632
 633   /**
 634    * A helper method that sets the items and initial selection in a character
 635    * rendering option list (Prompt each time/Lineart/Text)
 636    *
 637    * @param comboBox
 638    * @param propertyKey
 639    */
 640   protected void setupOutputCombo(JComboBox<Object> comboBox,
 641           String propertyKey)
 642   {
 643     comboBox.addItem(promptEachTimeOpt);
 644     comboBox.addItem(lineArtOpt);
 645     comboBox.addItem(textOpt);
 646
 647     /*
 648      * JalviewJS doesn't support Lineart so force it to Text
 649      */
 650     String defaultOption = Platform.isJS() ? "Text"
 651             : Cache.getDefault(propertyKey, "Prompt each time");
 652     if (defaultOption.equalsIgnoreCase("Text"))
 653     {
 654       comboBox.setSelectedItem(textOpt);
 655     }
 656     else if (defaultOption.equalsIgnoreCase("Lineart"))
 657     {
 658       comboBox.setSelectedItem(lineArtOpt);
 659     }
 660     else
 661     {
 662       comboBox.setSelectedItem(promptEachTimeOpt);
 663     }
 664   }
 665
 666   /**
 667    * Save user selections on the Preferences tabs to the Cache and write out to
 668    * file.
 669    *
 670    * @param e
 671    */
 672   @Override
 673   public void ok_actionPerformed(ActionEvent e)
 674   {
 675     if (!validateSettings())
 676     {
 677       return;
 678     }
 679
 680     /*
 681      * Save Visual settings
 682      */
 683     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 684             Boolean.toString(seqLimit.isSelected()));
 685     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 686             Boolean.toString(rightAlign.isSelected()));
 687     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 688             Boolean.toString(fullScreen.isSelected()));
 689     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 690             Boolean.toString(openoverv.isSelected()));
 691     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 692             Boolean.toString(annotations.isSelected()));
 693     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 694             Boolean.toString(conservation.isSelected()));
 695     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 696             Boolean.toString(quality.isSelected()));
 697     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 698             Boolean.toString(identity.isSelected()));
 699
 700     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 701             gapSymbolCB.getSelectedItem().toString());
 702
 703     Cache.applicationProperties.setProperty("FONT_NAME",
 704             fontNameCB.getSelectedItem().toString());
 705     Cache.applicationProperties.setProperty("FONT_STYLE",
 706             fontStyleCB.getSelectedItem().toString());
 707     Cache.applicationProperties.setProperty("FONT_SIZE",
 708             fontSizeCB.getSelectedItem().toString());
 709
 710     Cache.applicationProperties.setProperty("ID_ITALICS",
 711             Boolean.toString(idItalics.isSelected()));
 712     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 713             Boolean.toString(showUnconserved.isSelected()));
 714     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 715             Boolean.toString(showOccupancy.isSelected()));
 716     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 717             Boolean.toString(showGroupConsensus.isSelected()));
 718     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 719             Boolean.toString(showGroupConservation.isSelected()));
 720     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 721             Boolean.toString(showConsensHistogram.isSelected()));
 722     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 723             Boolean.toString(showConsensLogo.isSelected()));
 724     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 725             Boolean.toString(showConsensHistogram.isSelected()));
 726     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 727             Boolean.toString(showHMMLogo.isSelected()));
 728     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 729             Boolean.toString(smoothFont.isSelected()));
 730     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 731             Boolean.toString(scaleProteinToCdna.isSelected()));
 732     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 733             Boolean.toString(showNpTooltip.isSelected()));
 734     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 735             Boolean.toString(showDbRefTooltip.isSelected()));
 736
 737     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 738             Boolean.toString(wrap.isSelected()));
 739
 740     Cache.applicationProperties.setProperty("STARTUP_FILE",
 741             startupFileTextfield.getText());
 742     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 743             Boolean.toString(startupCheckbox.isSelected()));
 744
 745     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 746             sortby.getSelectedItem().toString());
 747
 748     // convert description of sort order to enum name for save
 749     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 750             .forDescription(sortAnnBy.getSelectedItem().toString());
 751     if (annSortOrder != null)
 752     {
 753       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 754               annSortOrder.name());
 755     }
 756
 757     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 758     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 759             Boolean.valueOf(showAutocalcFirst).toString());
 760
 761     /*
 762      * Save Colours settings
 763      */
 764     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 765             protColour.getSelectedItem().toString());
 766     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 767             nucColour.getSelectedItem().toString());
 768     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 769             minColour.getBackground());
 770     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 771             maxColour.getBackground());
 772
 773     /*
 774      * Save HMMER settings
 775      */
 776     Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
 777             Boolean.toString(hmmrTrimTermini.isSelected()));
 778     Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
 779             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 780     Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
 781             hmmerSequenceCount.getText());
 782     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
 783     if (cygwinPath != null)
 784     {
 785       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
 786     }
 787     AlignFrame[] frames = Desktop.getAlignFrames();
 788     if (frames != null && frames.length > 0)
 789     {
 790       for (AlignFrame f : frames)
 791       {
 792         f.updateHMMERStatus();
 793       }
 794     }
 795
 796     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 797     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 798     {
 799       hmmerBackgroundUniprot.setSelected(true);
 800     }
 801     else
 802     {
 803       hmmerBackgroundAlignment.setSelected(true);
 804     }
 805     hmmerSequenceCount
 806             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 807     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 808
 809     /*
 810      * Save Overview settings
 811      */
 812     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 813     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 814     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 815             Boolean.toString(useLegacyGap.isSelected()));
 816     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 817             Boolean.toString(showHiddenAtStart.isSelected()));
 818
 819     /*
 820      * Save Structure settings
 821      */
 822     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 823             Boolean.toString(addTempFactor.isSelected()));
 824     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 825             Boolean.toString(addSecondaryStructure.isSelected()));
 826     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 827             Boolean.toString(useRnaView.isSelected()));
 828     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 829             Boolean.toString(structFromPdb.isSelected()));
 830     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 831             structViewer.getSelectedItem().toString());
 832     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 833     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 834             Boolean.toString(siftsMapping.isSelected()));
 835     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 836
 837     /*
 838      * Save Output settings
 839      */
 840     Cache.applicationProperties.setProperty("EPS_RENDERING",
 841             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 842     Cache.applicationProperties.setProperty("HTML_RENDERING",
 843             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 844     Cache.applicationProperties.setProperty("SVG_RENDERING",
 845             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 846
 847     /*
 848      * Save Connections settings
 849      */
 850     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 851
 852     jalview.util.BrowserLauncher.resetBrowser();
 853
 854     // save user-defined and selected links
 855     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 856     if (menuLinks.isEmpty())
 857     {
 858       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 859     }
 860     else
 861     {
 862       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 863               menuLinks.toString());
 864     }
 865
 866     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 867     if (nonMenuLinks.isEmpty())
 868     {
 869       Cache.applicationProperties.remove("STORED_LINKS");
 870     }
 871     else
 872     {
 873       Cache.applicationProperties.setProperty("STORED_LINKS",
 874               nonMenuLinks.toString());
 875     }
 876
 877     Cache.applicationProperties.setProperty("DEFAULT_URL",
 878             sequenceUrlLinks.getPrimaryUrlId());
 879
 880     Cache.applicationProperties.setProperty("USE_PROXY",
 881             Boolean.toString(useProxy.isSelected()));
 882
 883     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 884
 885     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 886
 887     if (useProxy.isSelected())
 888     {
 889       System.setProperty("http.proxyHost", proxyServerTB.getText());
 890       System.setProperty("http.proxyPort", proxyPortTB.getText());
 891     }
 892     else
 893     {
 894       System.setProperty("http.proxyHost", "");
 895       System.setProperty("http.proxyPort", "");
 896     }
 897     Cache.setProperty("VERSION_CHECK",
 898             Boolean.toString(versioncheck.isSelected()));
 899     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 900     {
 901       // default is false - we only set this if the user has actively agreed
 902       Cache.setProperty("USAGESTATS",
 903               Boolean.toString(usagestats.isSelected()));
 904     }
 905     if (!questionnaire.isSelected())
 906     {
 907       Cache.setProperty("NOQUESTIONNAIRES", "true");
 908     }
 909     else
 910     {
 911       // special - made easy to edit a property file to disable questionnaires
 912       // by just adding the given line
 913       Cache.removeProperty("NOQUESTIONNAIRES");
 914     }
 915
 916     /*
 917      * Save Output settings
 918      */
 919     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 920             Boolean.toString(blcjv.isSelected()));
 921     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 922             Boolean.toString(clustaljv.isSelected()));
 923     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 924             Boolean.toString(fastajv.isSelected()));
 925     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 926             Boolean.toString(msfjv.isSelected()));
 927     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 928             Boolean.toString(pfamjv.isSelected()));
 929     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 930             Boolean.toString(pileupjv.isSelected()));
 931     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 932             Boolean.toString(pirjv.isSelected()));
 933     Cache.applicationProperties.setProperty("PIR_MODELLER",
 934             Boolean.toString(modellerOutput.isSelected()));
 935     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 936             Boolean.toString(embbedBioJSON.isSelected()));
 937     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 938
 939     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 940             Boolean.toString(autoIdWidth.isSelected()));
 941     userIdWidth_actionPerformed();
 942     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 943             userIdWidth.getText());
 944
 945     /*
 946      * Save Editing settings
 947      */
 948     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 949             Boolean.toString(autoCalculateConsCheck.isSelected()));
 950     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 951             Boolean.toString(sortByTree.isSelected()));
 952     Cache.applicationProperties.setProperty("PAD_GAPS",
 953             Boolean.toString(padGaps.isSelected()));
 954
 955     if (!Platform.isJS())
 956     {
 957       wsPrefs.updateAndRefreshWsMenuConfig(false);
 958     }
 959
 960     /*
 961      * Save Backups settings
 962      */
 963     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 964             Boolean.toString(enableBackupFiles.isSelected()));
 965     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 966     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 967
 968     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 969     {
 970       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 971       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 972               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 973       Cache.applicationProperties
 974               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 975                       customBFPE.toString());
 976     }
 977
 978     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 979             .get(preset);
 980     Cache.applicationProperties.setProperty(
 981             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 982
 983     Cache.saveProperties();
 984     Desktop.instance.doConfigureStructurePrefs();
 985     try
 986     {
 987       frame.setClosed(true);
 988     } catch (Exception ex)
 989     {
 990     }
 991   }
 992
 993   /**
 994    * Do any necessary validation before saving settings. Return focus to the
 995    * first tab which fails validation.
 996    *
 997    * @return
 998    */
 999   private boolean validateSettings()
1000   {
1001     if (!validateStructure())
1002     {
1003       structureTab.requestFocusInWindow();
1004       return false;
1005     }
1006     return true;
1007   }
1008
1009   @Override
1010   protected boolean validateStructure()
1011   {
1012     return validateChimeraPath();
1013
1014   }
1015
1016   /**
1017    * DOCUMENT ME!
1018    */
1019   @Override
1020   public void startupFileTextfield_mouseClicked()
1021   {
1022     // TODO: JAL-3048 not needed for Jalview-JS
1023     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1024     JalviewFileChooser chooser = JalviewFileChooser
1025             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1026     chooser.setFileView(new JalviewFileView());
1027     chooser.setDialogTitle(
1028             MessageManager.getString("label.select_startup_file"));
1029
1030     int value = chooser.showOpenDialog(this);
1031
1032     if (value == JalviewFileChooser.APPROVE_OPTION)
1033     {
1034       FileFormatI format = chooser.getSelectedFormat();
1035       if (format != null)
1036       {
1037         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1038                 format.getName());
1039       }
1040       startupFileTextfield
1041               .setText(chooser.getSelectedFile().getAbsolutePath());
1042     }
1043   }
1044
1045   /**
1046    * DOCUMENT ME!
1047    *
1048    * @param e
1049    *          DOCUMENT ME!
1050    */
1051   @Override
1052   public void cancel_actionPerformed(ActionEvent e)
1053   {
1054     try
1055     {
1056       if (!Platform.isJS())
1057       {
1058         wsPrefs.updateWsMenuConfig(true);
1059         wsPrefs.refreshWs_actionPerformed(e);
1060       }
1061       frame.setClosed(true);
1062     } catch (Exception ex)
1063     {
1064     }
1065   }
1066
1067   /**
1068    * DOCUMENT ME!
1069    *
1070    * @param e
1071    *          DOCUMENT ME!
1072    */
1073   @Override
1074   public void annotations_actionPerformed(ActionEvent e)
1075   {
1076     conservation.setEnabled(annotations.isSelected());
1077     quality.setEnabled(annotations.isSelected());
1078     identity.setEnabled(annotations.isSelected());
1079     showOccupancy.setEnabled(annotations.isSelected());
1080     showGroupConsensus.setEnabled(annotations.isSelected());
1081     showGroupConservation.setEnabled(annotations.isSelected());
1082     showConsensHistogram.setEnabled(annotations.isSelected()
1083             && (identity.isSelected() || showGroupConsensus.isSelected()));
1084     showConsensLogo.setEnabled(annotations.isSelected()
1085             && (identity.isSelected() || showGroupConsensus.isSelected()));
1086     showInformationHistogram.setEnabled(annotations.isSelected());
1087     showHMMLogo.setEnabled(annotations.isSelected());
1088   }
1089
1090   @Override
1091   public void newLink_actionPerformed(ActionEvent e)
1092   {
1093     GSequenceLink link = new GSequenceLink();
1094     boolean valid = false;
1095     while (!valid)
1096     {
1097       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1098               MessageManager.getString("label.new_sequence_url_link"),
1099               JvOptionPane.OK_CANCEL_OPTION, -1,
1100               null) == JvOptionPane.OK_OPTION)
1101       {
1102         if (link.checkValid())
1103         {
1104           if (((UrlLinkTableModel) linkUrlTable.getModel())
1105                   .isUniqueName(link.getName()))
1106           {
1107             ((UrlLinkTableModel) linkUrlTable.getModel())
1108                     .insertRow(link.getName(), link.getURL());
1109             valid = true;
1110           }
1111           else
1112           {
1113             link.notifyDuplicate();
1114             continue;
1115           }
1116         }
1117       }
1118       else
1119       {
1120         break;
1121       }
1122     }
1123   }
1124
1125   @Override
1126   public void editLink_actionPerformed(ActionEvent e)
1127   {
1128     GSequenceLink link = new GSequenceLink();
1129
1130     int index = linkUrlTable.getSelectedRow();
1131     if (index == -1)
1132     {
1133       // button no longer enabled if row is not selected
1134       Cache.log.debug("Edit with no row selected in linkUrlTable");
1135       return;
1136     }
1137
1138     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1139             .getNameColumn();
1140     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1141             .getUrlColumn();
1142     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1143     link.setName(oldName);
1144     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1145
1146     boolean valid = false;
1147     while (!valid)
1148     {
1149       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1150               MessageManager.getString("label.edit_sequence_url_link"),
1151               JvOptionPane.OK_CANCEL_OPTION, -1,
1152               null) == JvOptionPane.OK_OPTION)
1153       {
1154         if (link.checkValid())
1155         {
1156           if ((oldName.equals(link.getName()))
1157                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1158                           .isUniqueName(link.getName())))
1159           {
1160             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1161             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1162             valid = true;
1163           }
1164           else
1165           {
1166             link.notifyDuplicate();
1167             continue;
1168           }
1169         }
1170       }
1171       else
1172       {
1173         break;
1174       }
1175     }
1176   }
1177
1178   @Override
1179   public void deleteLink_actionPerformed(ActionEvent e)
1180   {
1181     int index = linkUrlTable.getSelectedRow();
1182     int modelIndex = -1;
1183     if (index == -1)
1184     {
1185       // button no longer enabled if row is not selected
1186       Cache.log.debug("Delete with no row selected in linkUrlTable");
1187       return;
1188     }
1189     else
1190     {
1191       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1192     }
1193
1194     // make sure we use the model index to delete, and not the table index
1195     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1196   }
1197
1198   @Override
1199   public void defaultBrowser_mouseClicked(MouseEvent e)
1200   {
1201     // TODO: JAL-3048 not needed for j2s
1202     if (!Platform.isJS()) // BH 2019
1203     /**
1204      * Java only
1205      *
1206      * @j2sIgnore
1207      */
1208     {
1209       JFileChooser chooser = new JFileChooser(".");
1210       chooser.setDialogTitle(
1211               MessageManager.getString("label.select_default_browser"));
1212
1213       int value = chooser.showOpenDialog(this);
1214
1215       if (value == JFileChooser.APPROVE_OPTION)
1216       {
1217         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1218       }
1219     }
1220   }
1221
1222   /*
1223    * (non-Javadoc)
1224    *
1225    * @see
1226    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1227    * .ActionEvent)
1228    */
1229   @Override
1230   protected void showunconserved_actionPerformed(ActionEvent e)
1231   {
1232     // TODO Auto-generated method stub
1233     super.showunconserved_actionPerformed(e);
1234   }
1235
1236   public static List<String> getGroupURLLinks()
1237   {
1238     return groupURLLinks;
1239   }
1240
1241   @Override
1242   public void minColour_actionPerformed(JPanel panel)
1243   {
1244     JalviewColourChooser.showColourChooser(this,
1245             MessageManager.getString("label.select_colour_minimum_value"),
1246             panel);
1247   }
1248
1249   @Override
1250   public void maxColour_actionPerformed(JPanel panel)
1251   {
1252     JalviewColourChooser.showColourChooser(this,
1253             MessageManager.getString("label.select_colour_maximum_value"),
1254             panel);
1255   }
1256
1257   @Override
1258   public void gapColour_actionPerformed(JPanel gap)
1259   {
1260     if (!useLegacyGap.isSelected())
1261     {
1262       JalviewColourChooser.showColourChooser(this,
1263               MessageManager.getString("label.select_gap_colour"),
1264               gap);
1265     }
1266   }
1267
1268   @Override
1269   public void hiddenColour_actionPerformed(JPanel hidden)
1270   {
1271     JalviewColourChooser.showColourChooser(this,
1272             MessageManager.getString("label.select_hidden_colour"),
1273             hidden);
1274   }
1275
1276   @Override
1277   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1278   {
1279     boolean enabled = useLegacyGap.isSelected();
1280     if (enabled)
1281     {
1282       gapColour.setBackground(
1283               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1284     }
1285     else
1286     {
1287       gapColour.setBackground(
1288               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1289     }
1290     gapColour.setEnabled(!enabled);
1291     gapLabel.setEnabled(!enabled);
1292   }
1293
1294   @Override
1295   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1296   {
1297     useLegacyGap.setSelected(false);
1298     useLegacyGaps_actionPerformed(null);
1299     showHiddenAtStart.setSelected(false);
1300     hiddenColour.setBackground(
1301             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1302   }
1303
1304   @Override
1305   protected void userIdWidth_actionPerformed()
1306   {
1307     try
1308     {
1309       String val = userIdWidth.getText().trim();
1310       if (val.length() > 0)
1311       {
1312         Integer iw = Integer.parseInt(val);
1313         if (iw.intValue() < 12)
1314         {
1315           throw new NumberFormatException();
1316         }
1317         userIdWidth.setText(iw.toString());
1318       }
1319     } catch (NumberFormatException x)
1320     {
1321       userIdWidth.setText("");
1322       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1323               MessageManager
1324                       .getString("warn.user_defined_width_requirements"),
1325               MessageManager.getString("label.invalid_id_column_width"),
1326               JvOptionPane.WARNING_MESSAGE);
1327     }
1328   }
1329
1330   @Override
1331   protected void autoIdWidth_actionPerformed()
1332   {
1333     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1334     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1335   }
1336
1337   /**
1338    * Returns true if chimera path is to a valid executable, else show an error
1339    * dialog.
1340    */
1341   private boolean validateChimeraPath()
1342   {
1343     if (chimeraPath.getText().trim().length() > 0)
1344     {
1345       File f = new File(chimeraPath.getText());
1346       if (!f.canExecute())
1347       {
1348         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1349                 MessageManager.getString("label.invalid_chimera_path"),
1350                 MessageManager.getString("label.invalid_name"),
1351                 JvOptionPane.ERROR_MESSAGE);
1352         return false;
1353       }
1354     }
1355     return true;
1356   }
1357
1358   /**
1359    * Returns true if the given text field contains a path to a folder that
1360    * contains an executable with the given name, else false (after showing a
1361    * warning dialog). The executable name will be tried with .exe appended if not
1362    * found.
1363    *
1364    * @param textField
1365    * @param executable
1366    */
1367   protected boolean validateExecutablePath(JTextField textField, String executable)
1368   {
1369     String folder = textField.getText().trim();
1370
1371     if (FileUtils.getExecutable(executable, folder) != null)
1372     {
1373       return true;
1374     }
1375     if (folder.length() > 0)
1376     {
1377       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1378               MessageManager.formatMessage("label.executable_not_found",
1379                       executable),
1380               MessageManager.getString("label.invalid_folder"),
1381               JvOptionPane.ERROR_MESSAGE);
1382     }
1383     return false;
1384   }
1385
1386   /**
1387    * Checks if a file can be executed
1388    *
1389    * @param path
1390    *          the path to the file
1391    * @return
1392    */
1393   public boolean canExecute(String path)
1394   {
1395     File file = new File(path);
1396     if (!file.canExecute())
1397     {
1398       file = new File(path + ".exe");
1399       {
1400         if (!file.canExecute())
1401         {
1402           return false;
1403         }
1404       }
1405     }
1406     return true;
1407   }
1408
1409   /**
1410    * If Chimera is selected, check it can be found on default or user-specified
1411    * path, if not show a warning/help dialog.
1412    */
1413   @Override
1414   protected void structureViewer_actionPerformed(String selectedItem)
1415   {
1416     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1417     {
1418       return;
1419     }
1420     boolean found = false;
1421
1422     /*
1423      * Try user-specified and standard paths for Chimera executable.
1424      */
1425     List<String> paths = StructureManager.getChimeraPaths();
1426     paths.add(0, chimeraPath.getText());
1427     for (String path : paths)
1428     {
1429       if (new File(path.trim()).canExecute())
1430       {
1431         found = true;
1432         break;
1433       }
1434     }
1435     if (!found)
1436     {
1437       String[] options = { "OK", "Help" };
1438       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1439               JvSwingUtils.wrapTooltip(true,
1440                       MessageManager.getString("label.chimera_missing")),
1441               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1442               null, options, options[0]);
1443       if (showHelp == JvOptionPane.NO_OPTION)
1444       {
1445         try
1446         {
1447           Help.showHelpWindow(HelpId.StructureViewer);
1448         } catch (HelpSetException e)
1449         {
1450           e.printStackTrace();
1451         }
1452       }
1453     }
1454   }
1455
1456   @Override
1457   protected void validateHmmerPath()
1458   {
1459     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1460   }
1461
1462   @Override
1463   protected void validateCygwinPath()
1464   {
1465     validateExecutablePath(cygwinPath, "run");
1466   }
1467
1468   public class OptionsParam
1469   {
1470     private String name;
1471
1472     private String code;
1473
1474     public OptionsParam(String name, String code)
1475     {
1476       this.name = name;
1477       this.code = code;
1478     }
1479
1480     public String getName()
1481     {
1482       return name;
1483     }
1484
1485     public void setName(String name)
1486     {
1487       this.name = name;
1488     }
1489
1490     public String getCode()
1491     {
1492       return code;
1493     }
1494
1495     public void setCode(String code)
1496     {
1497       this.code = code;
1498     }
1499
1500     @Override
1501     public String toString()
1502     {
1503       return name;
1504     }
1505
1506     @Override
1507     public boolean equals(Object that)
1508     {
1509       if (!(that instanceof OptionsParam))
1510       {
1511         return false;
1512       }
1513       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1514     }
1515
1516     @Override
1517     public int hashCode()
1518     {
1519       return name.hashCode() + code.hashCode();
1520     }
1521   }
1522
1523   private class UrlListSelectionHandler implements ListSelectionListener
1524   {
1525
1526     @Override
1527     public void valueChanged(ListSelectionEvent e)
1528     {
1529       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1530
1531       int index = lsm.getMinSelectionIndex();
1532       if (index == -1)
1533       {
1534         // no selection, so disable delete/edit buttons
1535         editLink.setEnabled(false);
1536         deleteLink.setEnabled(false);
1537         return;
1538       }
1539       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1540
1541       // enable/disable edit and delete link buttons
1542       if (((UrlLinkTableModel) linkUrlTable.getModel())
1543               .isRowDeletable(modelIndex))
1544       {
1545         deleteLink.setEnabled(true);
1546       }
1547       else
1548       {
1549         deleteLink.setEnabled(false);
1550       }
1551
1552       if (((UrlLinkTableModel) linkUrlTable.getModel())
1553               .isRowEditable(modelIndex))
1554       {
1555         editLink.setEnabled(true);
1556       }
1557       else
1558       {
1559         editLink.setEnabled(false);
1560       }
1561     }
1562   }
1563 }