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 SlivkaPreferences slivkaPrefs;
 196
 197   private OptionsParam promptEachTimeOpt = new OptionsParam(
 198           MessageManager.getString("label.prompt_each_time"),
 199           "Prompt each time");
 200
 201   private OptionsParam lineArtOpt = new OptionsParam(
 202           MessageManager.getString("label.lineart"), "Lineart");
 203
 204   private OptionsParam textOpt = new OptionsParam(
 205           MessageManager.getString("action.text"), "Text");
 206
 207   /**
 208    * Creates a new Preferences object.
 209    */
 210   public Preferences()
 211   {
 212     super();
 213     frame = new JInternalFrame();
 214     frame.setContentPane(this);
 215     if (!Platform.isJS())
 216     /**
 217      * Java only
 218      *
 219      * @j2sIgnore
 220      */
 221     {
 222       wsPrefs = new WsPreferences();
 223       wsTab.add(wsPrefs, BorderLayout.CENTER);
 224       slivkaPrefs = new SlivkaPreferences();
 225       slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
 226     }
 227     int width = 500, height = 450;
 228     if (Platform.isAMacAndNotJS())
 229     {
 230       width = 570;
 231       height = 480;
 232     }
 233
 234     Desktop.addInternalFrame(frame,
 235             MessageManager.getString("label.preferences"), width, height);
 236     frame.setMinimumSize(new Dimension(width, height));
 237
 238     /*
 239      * Set HMMER tab defaults
 240      */
 241     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 242     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 243     {
 244       hmmerBackgroundUniprot.setSelected(true);
 245     }
 246     else
 247     {
 248       hmmerBackgroundAlignment.setSelected(true);
 249     }
 250     hmmerSequenceCount
 251             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 252     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 253     hmmerPath.addActionListener(new ActionListener()
 254     {
 255       @Override
 256       public void actionPerformed(ActionEvent e)
 257       {
 258         validateHmmerPath();
 259       }
 260     });
 261     hmmerPath.addFocusListener(new FocusAdapter()
 262     {
 263       @Override
 264       public void focusLost(FocusEvent e)
 265       {
 266         validateHmmerPath();
 267       }
 268     });
 269     if (cygwinPath != null)
 270     {
 271       String path = Cache.getProperty(CYGWIN_PATH);
 272       if (path == null)
 273       {
 274         path = FileUtils.getPathTo("bash");
 275       }
 276       cygwinPath.setText(path);
 277       cygwinPath.addActionListener(new ActionListener()
 278       {
 279         @Override
 280         public void actionPerformed(ActionEvent e)
 281         {
 282           validateCygwinPath();
 283         }
 284       });
 285       cygwinPath.addFocusListener(new FocusAdapter()
 286       {
 287         @Override
 288         public void focusLost(FocusEvent e)
 289         {
 290           validateCygwinPath();
 291         }
 292       });
 293     }
 294
 295     /*
 296      * Set Visual tab defaults
 297      */
 298     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 299     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 300     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 301     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 302
 303     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 304     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 305     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 306     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 307     showUnconserved
 308             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 309     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 310     showGroupConsensus
 311             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 312     showGroupConservation.setSelected(
 313             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 314     showConsensHistogram.setSelected(
 315             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 316     showConsensLogo
 317             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 318     showInformationHistogram.setSelected(
 319             Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
 320     showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
 321     showNpTooltip
 322             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 323     showDbRefTooltip
 324             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 325
 326     String[] fonts = java.awt.GraphicsEnvironment
 327             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 328     for (int i = 0; i < fonts.length; i++)
 329     {
 330       fontNameCB.addItem(fonts[i]);
 331     }
 332
 333     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 334     {
 335       fontSizeCB.addItem(i + "");
 336     }
 337
 338     fontStyleCB.addItem("plain");
 339     fontStyleCB.addItem("bold");
 340     fontStyleCB.addItem("italic");
 341
 342     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 343     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 344     fontStyleCB.setSelectedItem(
 345             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 346
 347     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 348     scaleProteinToCdna
 349             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 350
 351     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 352
 353     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 354
 355     gapSymbolCB.addItem("-");
 356     gapSymbolCB.addItem(".");
 357
 358     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 359
 360     sortby.addItem("No sort");
 361     sortby.addItem("Id");
 362     sortby.addItem("Pairwise Identity");
 363     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 364
 365     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 366     sortAnnBy
 367             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 368     sortAnnBy
 369             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 370     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 371             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 372                     SequenceAnnotationOrder.NONE.name()));
 373     sortAnnBy.setSelectedItem(savedSort.toString());
 374
 375     sortAutocalc.addItem("Autocalculated first");
 376     sortAutocalc.addItem("Autocalculated last");
 377     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 378     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 379             : sortAutocalc.getItemAt(1));
 380     startupCheckbox
 381             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 382     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 383             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 384                     + "/examples/exampleFile_2_3.jar"));
 385
 386     /*
 387      * Set Colours tab defaults
 388      */
 389     protColour.addItem(ResidueColourScheme.NONE);
 390     nucColour.addItem(ResidueColourScheme.NONE);
 391     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 392     {
 393       String name = cs.getSchemeName();
 394       protColour.addItem(name);
 395       nucColour.addItem(name);
 396     }
 397     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 398             ResidueColourScheme.NONE);
 399     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 400     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 401     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 402     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 403     minColour.setBackground(
 404             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 405     maxColour.setBackground(
 406             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 407
 408     /*
 409      * Set overview panel defaults
 410      */
 411     gapColour.setBackground(
 412             Cache.getDefaultColour(GAP_COLOUR,
 413                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 414     hiddenColour.setBackground(
 415             Cache.getDefaultColour(HIDDEN_COLOUR,
 416                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 417     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 418     gapLabel.setEnabled(!useLegacyGap.isSelected());
 419     gapColour.setEnabled(!useLegacyGap.isSelected());
 420     showHiddenAtStart
 421             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 422
 423     /*
 424      * Set Structure tab defaults.
 425      */
 426     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 427     structFromPdb.setSelected(structSelected);
 428     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 429     useRnaView.setEnabled(structSelected);
 430     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 431     addSecondaryStructure.setEnabled(structSelected);
 432     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 433     addTempFactor.setEnabled(structSelected);
 434     structViewer.setSelectedItem(
 435             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 436     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 437     chimeraPath.addActionListener(new ActionListener()
 438     {
 439       @Override
 440       public void actionPerformed(ActionEvent e)
 441       {
 442         validateChimeraPath();
 443       }
 444     });
 445
 446     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 447     {
 448       siftsMapping.setSelected(true);
 449     }
 450     else
 451     {
 452       nwMapping.setSelected(true);
 453     }
 454
 455     SiftsSettings
 456             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 457
 458     /*
 459      * Set Connections tab defaults
 460      */
 461
 462     // set up sorting
 463     linkUrlTable.setModel(dataModel);
 464     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 465             linkUrlTable.getModel());
 466     linkUrlTable.setRowSorter(sorter);
 467     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 468
 469     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 470     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 471             SortOrder.DESCENDING));
 472     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 473             SortOrder.DESCENDING));
 474     sortKeys.add(
 475             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 476
 477     sorter.setSortKeys(sortKeys);
 478     // BH 2018 setSortKeys will do the sort
 479     // sorter.sort();
 480
 481     // set up filtering
 482     ActionListener onReset;
 483     onReset = new ActionListener()
 484     {
 485       @Override
 486       public void actionPerformed(ActionEvent e)
 487       {
 488         filterTB.setText("");
 489         sorter.setRowFilter(RowFilter.regexFilter(""));
 490       }
 491
 492     };
 493     doReset.addActionListener(onReset);
 494
 495     // filter to display only custom urls
 496     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
 497     {
 498       @Override
 499       public boolean include(
 500               Entry<? extends TableModel, ? extends Object> entry)
 501       {
 502         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 503       }
 504     };
 505
 506     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 507             linkUrlTable.getModel());
 508     customSorter.setRowFilter(customUrlFilter);
 509
 510     ActionListener onCustomOnly;
 511     onCustomOnly = new ActionListener()
 512     {
 513       @Override
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         filterTB.setText("");
 517         sorter.setRowFilter(customUrlFilter);
 518       }
 519     };
 520     userOnly.addActionListener(onCustomOnly);
 521
 522     filterTB.getDocument().addDocumentListener(new DocumentListener()
 523     {
 524       String caseInsensitiveFlag = "(?i)";
 525
 526       @Override
 527       public void changedUpdate(DocumentEvent e)
 528       {
 529         sorter.setRowFilter(RowFilter
 530                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 531       }
 532
 533       @Override
 534       public void removeUpdate(DocumentEvent e)
 535       {
 536         sorter.setRowFilter(RowFilter
 537                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 538       }
 539
 540       @Override
 541       public void insertUpdate(DocumentEvent e)
 542       {
 543         sorter.setRowFilter(RowFilter
 544                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 545       }
 546     });
 547
 548     // set up list selection functionality
 549     linkUrlTable.getSelectionModel()
 550             .addListSelectionListener(new UrlListSelectionHandler());
 551
 552     // set up radio buttons
 553     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 554             .getPrimaryColumn();
 555     String onClickName = linkUrlTable.getColumnName(onClickCol);
 556     linkUrlTable.getColumn(onClickName)
 557             .setCellRenderer(new RadioButtonRenderer());
 558     linkUrlTable.getColumn(onClickName)
 559             .setCellEditor(new RadioButtonEditor());
 560
 561     // get boolean columns and resize those to min possible
 562     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 563     {
 564       if (linkUrlTable.getModel().getColumnClass(column)
 565               .equals(Boolean.class))
 566       {
 567         TableColumn tableColumn = linkUrlTable.getColumnModel()
 568                 .getColumn(column);
 569         int preferredWidth = tableColumn.getMinWidth();
 570
 571         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 572                 column);
 573         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 574         int cwidth = c.getPreferredSize().width
 575                 + linkUrlTable.getIntercellSpacing().width;
 576         preferredWidth = Math.max(preferredWidth, cwidth);
 577
 578         tableColumn.setPreferredWidth(preferredWidth);
 579       }
 580     }
 581
 582     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 583     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 584     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 585     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 586
 587     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 588
 589     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 590     // note antisense here: default is true
 591     questionnaire
 592             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 593     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 594
 595     /*
 596      * Set Output tab defaults
 597      */
 598     setupOutputCombo(epsRendering, "EPS_RENDERING");
 599     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 600     setupOutputCombo(svgRendering, "SVG_RENDERING");
 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      * Set Backups tab defaults
 633      */
 634     loadLastSavedBackupsOptions();
 635   }
 636
 637   /**
 638    * A helper method that sets the items and initial selection in a character
 639    * rendering option list (Prompt each time/Lineart/Text)
 640    *
 641    * @param comboBox
 642    * @param propertyKey
 643    */
 644   protected void setupOutputCombo(JComboBox<Object> comboBox,
 645           String propertyKey)
 646   {
 647     comboBox.addItem(promptEachTimeOpt);
 648     comboBox.addItem(lineArtOpt);
 649     comboBox.addItem(textOpt);
 650
 651     /*
 652      * JalviewJS doesn't support Lineart so force it to Text
 653      */
 654     String defaultOption = Platform.isJS() ? "Text"
 655             : Cache.getDefault(propertyKey, "Prompt each time");
 656     if (defaultOption.equalsIgnoreCase("Text"))
 657     {
 658       comboBox.setSelectedItem(textOpt);
 659     }
 660     else if (defaultOption.equalsIgnoreCase("Lineart"))
 661     {
 662       comboBox.setSelectedItem(lineArtOpt);
 663     }
 664     else
 665     {
 666       comboBox.setSelectedItem(promptEachTimeOpt);
 667     }
 668   }
 669
 670   /**
 671    * Save user selections on the Preferences tabs to the Cache and write out to
 672    * file.
 673    *
 674    * @param e
 675    */
 676   @Override
 677   public void ok_actionPerformed(ActionEvent e)
 678   {
 679     if (!validateSettings())
 680     {
 681       return;
 682     }
 683
 684     /*
 685      * Save Visual settings
 686      */
 687     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 688             Boolean.toString(seqLimit.isSelected()));
 689     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 690             Boolean.toString(rightAlign.isSelected()));
 691     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 692             Boolean.toString(fullScreen.isSelected()));
 693     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 694             Boolean.toString(openoverv.isSelected()));
 695     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 696             Boolean.toString(annotations.isSelected()));
 697     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 698             Boolean.toString(conservation.isSelected()));
 699     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 700             Boolean.toString(quality.isSelected()));
 701     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 702             Boolean.toString(identity.isSelected()));
 703
 704     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 705             gapSymbolCB.getSelectedItem().toString());
 706
 707     Cache.applicationProperties.setProperty("FONT_NAME",
 708             fontNameCB.getSelectedItem().toString());
 709     Cache.applicationProperties.setProperty("FONT_STYLE",
 710             fontStyleCB.getSelectedItem().toString());
 711     Cache.applicationProperties.setProperty("FONT_SIZE",
 712             fontSizeCB.getSelectedItem().toString());
 713
 714     Cache.applicationProperties.setProperty("ID_ITALICS",
 715             Boolean.toString(idItalics.isSelected()));
 716     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 717             Boolean.toString(showUnconserved.isSelected()));
 718     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 719             Boolean.toString(showOccupancy.isSelected()));
 720     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 721             Boolean.toString(showGroupConsensus.isSelected()));
 722     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 723             Boolean.toString(showGroupConservation.isSelected()));
 724     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 725             Boolean.toString(showConsensHistogram.isSelected()));
 726     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 727             Boolean.toString(showConsensLogo.isSelected()));
 728     Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
 729             Boolean.toString(showConsensHistogram.isSelected()));
 730     Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
 731             Boolean.toString(showHMMLogo.isSelected()));
 732     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 733             Boolean.toString(smoothFont.isSelected()));
 734     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 735             Boolean.toString(scaleProteinToCdna.isSelected()));
 736     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 737             Boolean.toString(showNpTooltip.isSelected()));
 738     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 739             Boolean.toString(showDbRefTooltip.isSelected()));
 740
 741     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 742             Boolean.toString(wrap.isSelected()));
 743
 744     Cache.applicationProperties.setProperty("STARTUP_FILE",
 745             startupFileTextfield.getText());
 746     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 747             Boolean.toString(startupCheckbox.isSelected()));
 748
 749     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 750             sortby.getSelectedItem().toString());
 751
 752     // convert description of sort order to enum name for save
 753     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 754             .forDescription(sortAnnBy.getSelectedItem().toString());
 755     if (annSortOrder != null)
 756     {
 757       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 758               annSortOrder.name());
 759     }
 760
 761     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 762     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 763             Boolean.valueOf(showAutocalcFirst).toString());
 764
 765     /*
 766      * Save Colours settings
 767      */
 768     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 769             protColour.getSelectedItem().toString());
 770     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 771             nucColour.getSelectedItem().toString());
 772     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 773             minColour.getBackground());
 774     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 775             maxColour.getBackground());
 776
 777     /*
 778      * Save HMMER settings
 779      */
 780     Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
 781             Boolean.toString(hmmrTrimTermini.isSelected()));
 782     Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
 783             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
 784     Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
 785             hmmerSequenceCount.getText());
 786     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
 787     if (cygwinPath != null)
 788     {
 789       Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
 790     }
 791     AlignFrame[] frames = Desktop.getAlignFrames();
 792     if (frames != null && frames.length > 0)
 793     {
 794       for (AlignFrame f : frames)
 795       {
 796         f.updateHMMERStatus();
 797       }
 798     }
 799
 800     hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
 801     if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
 802     {
 803       hmmerBackgroundUniprot.setSelected(true);
 804     }
 805     else
 806     {
 807       hmmerBackgroundAlignment.setSelected(true);
 808     }
 809     hmmerSequenceCount
 810             .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
 811     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 812
 813     /*
 814      * Save Overview settings
 815      */
 816     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 817     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 818     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 819             Boolean.toString(useLegacyGap.isSelected()));
 820     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 821             Boolean.toString(showHiddenAtStart.isSelected()));
 822
 823     /*
 824      * Save Structure settings
 825      */
 826     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 827             Boolean.toString(addTempFactor.isSelected()));
 828     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 829             Boolean.toString(addSecondaryStructure.isSelected()));
 830     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 831             Boolean.toString(useRnaView.isSelected()));
 832     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 833             Boolean.toString(structFromPdb.isSelected()));
 834     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 835             structViewer.getSelectedItem().toString());
 836     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 837     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 838             Boolean.toString(siftsMapping.isSelected()));
 839     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 840
 841     /*
 842      * Save Output settings
 843      */
 844     Cache.applicationProperties.setProperty("EPS_RENDERING",
 845             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 846     Cache.applicationProperties.setProperty("HTML_RENDERING",
 847             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 848     Cache.applicationProperties.setProperty("SVG_RENDERING",
 849             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 850
 851     /*
 852      * Save Connections settings
 853      */
 854     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 855
 856     jalview.util.BrowserLauncher.resetBrowser();
 857
 858     // save user-defined and selected links
 859     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 860     if (menuLinks.isEmpty())
 861     {
 862       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 863     }
 864     else
 865     {
 866       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 867               menuLinks.toString());
 868     }
 869
 870     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 871     if (nonMenuLinks.isEmpty())
 872     {
 873       Cache.applicationProperties.remove("STORED_LINKS");
 874     }
 875     else
 876     {
 877       Cache.applicationProperties.setProperty("STORED_LINKS",
 878               nonMenuLinks.toString());
 879     }
 880
 881     Cache.applicationProperties.setProperty("DEFAULT_URL",
 882             sequenceUrlLinks.getPrimaryUrlId());
 883
 884     Cache.applicationProperties.setProperty("USE_PROXY",
 885             Boolean.toString(useProxy.isSelected()));
 886
 887     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 888
 889     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 890
 891     if (useProxy.isSelected())
 892     {
 893       System.setProperty("http.proxyHost", proxyServerTB.getText());
 894       System.setProperty("http.proxyPort", proxyPortTB.getText());
 895     }
 896     else
 897     {
 898       System.setProperty("http.proxyHost", "");
 899       System.setProperty("http.proxyPort", "");
 900     }
 901     Cache.setProperty("VERSION_CHECK",
 902             Boolean.toString(versioncheck.isSelected()));
 903     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 904     {
 905       // default is false - we only set this if the user has actively agreed
 906       Cache.setProperty("USAGESTATS",
 907               Boolean.toString(usagestats.isSelected()));
 908     }
 909     if (!questionnaire.isSelected())
 910     {
 911       Cache.setProperty("NOQUESTIONNAIRES", "true");
 912     }
 913     else
 914     {
 915       // special - made easy to edit a property file to disable questionnaires
 916       // by just adding the given line
 917       Cache.removeProperty("NOQUESTIONNAIRES");
 918     }
 919
 920     /*
 921      * Save Output settings
 922      */
 923     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 924             Boolean.toString(blcjv.isSelected()));
 925     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 926             Boolean.toString(clustaljv.isSelected()));
 927     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 928             Boolean.toString(fastajv.isSelected()));
 929     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 930             Boolean.toString(msfjv.isSelected()));
 931     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 932             Boolean.toString(pfamjv.isSelected()));
 933     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 934             Boolean.toString(pileupjv.isSelected()));
 935     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 936             Boolean.toString(pirjv.isSelected()));
 937     Cache.applicationProperties.setProperty("PIR_MODELLER",
 938             Boolean.toString(modellerOutput.isSelected()));
 939     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 940             Boolean.toString(embbedBioJSON.isSelected()));
 941     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 942
 943     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 944             Boolean.toString(autoIdWidth.isSelected()));
 945     userIdWidth_actionPerformed();
 946     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 947             userIdWidth.getText());
 948
 949     /*
 950      * Save Editing settings
 951      */
 952     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 953             Boolean.toString(autoCalculateConsCheck.isSelected()));
 954     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 955             Boolean.toString(sortByTree.isSelected()));
 956     Cache.applicationProperties.setProperty("PAD_GAPS",
 957             Boolean.toString(padGaps.isSelected()));
 958
 959     if (!Platform.isJS())
 960     {
 961       wsPrefs.updateAndRefreshWsMenuConfig(false);
 962     }
 963
 964     /*
 965      * Save Backups settings
 966      */
 967     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 968             Boolean.toString(enableBackupFiles.isSelected()));
 969     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 970     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
 971
 972     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 973     {
 974       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 975       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 976               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 977       Cache.applicationProperties
 978               .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
 979                       customBFPE.toString());
 980     }
 981
 982     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 983             .get(preset);
 984     Cache.applicationProperties.setProperty(
 985             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 986
 987     Cache.saveProperties();
 988     Desktop.instance.doConfigureStructurePrefs();
 989     try
 990     {
 991       frame.setClosed(true);
 992     } catch (Exception ex)
 993     {
 994     }
 995   }
 996
 997   /**
 998    * Do any necessary validation before saving settings. Return focus to the
 999    * first tab which fails validation.
1000    *
1001    * @return
1002    */
1003   private boolean validateSettings()
1004   {
1005     if (!validateStructure())
1006     {
1007       structureTab.requestFocusInWindow();
1008       return false;
1009     }
1010     return true;
1011   }
1012
1013   @Override
1014   protected boolean validateStructure()
1015   {
1016     return validateChimeraPath();
1017
1018   }
1019
1020   /**
1021    * DOCUMENT ME!
1022    */
1023   @Override
1024   public void startupFileTextfield_mouseClicked()
1025   {
1026     // TODO: JAL-3048 not needed for Jalview-JS
1027     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1028     JalviewFileChooser chooser = JalviewFileChooser
1029             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1030     chooser.setFileView(new JalviewFileView());
1031     chooser.setDialogTitle(
1032             MessageManager.getString("label.select_startup_file"));
1033
1034     int value = chooser.showOpenDialog(this);
1035
1036     if (value == JalviewFileChooser.APPROVE_OPTION)
1037     {
1038       FileFormatI format = chooser.getSelectedFormat();
1039       if (format != null)
1040       {
1041         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1042                 format.getName());
1043       }
1044       startupFileTextfield
1045               .setText(chooser.getSelectedFile().getAbsolutePath());
1046     }
1047   }
1048
1049   /**
1050    * DOCUMENT ME!
1051    *
1052    * @param e
1053    *          DOCUMENT ME!
1054    */
1055   @Override
1056   public void cancel_actionPerformed(ActionEvent e)
1057   {
1058     try
1059     {
1060       if (!Platform.isJS())
1061       {
1062         wsPrefs.updateWsMenuConfig(true);
1063         wsPrefs.refreshWs_actionPerformed(e);
1064       }
1065       frame.setClosed(true);
1066     } catch (Exception ex)
1067     {
1068     }
1069   }
1070
1071   /**
1072    * DOCUMENT ME!
1073    *
1074    * @param e
1075    *          DOCUMENT ME!
1076    */
1077   @Override
1078   public void annotations_actionPerformed(ActionEvent e)
1079   {
1080     conservation.setEnabled(annotations.isSelected());
1081     quality.setEnabled(annotations.isSelected());
1082     identity.setEnabled(annotations.isSelected());
1083     showOccupancy.setEnabled(annotations.isSelected());
1084     showGroupConsensus.setEnabled(annotations.isSelected());
1085     showGroupConservation.setEnabled(annotations.isSelected());
1086     showConsensHistogram.setEnabled(annotations.isSelected()
1087             && (identity.isSelected() || showGroupConsensus.isSelected()));
1088     showConsensLogo.setEnabled(annotations.isSelected()
1089             && (identity.isSelected() || showGroupConsensus.isSelected()));
1090     showInformationHistogram.setEnabled(annotations.isSelected());
1091     showHMMLogo.setEnabled(annotations.isSelected());
1092   }
1093
1094   @Override
1095   public void newLink_actionPerformed(ActionEvent e)
1096   {
1097     GSequenceLink link = new GSequenceLink();
1098     boolean valid = false;
1099     while (!valid)
1100     {
1101       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1102               MessageManager.getString("label.new_sequence_url_link"),
1103               JvOptionPane.OK_CANCEL_OPTION, -1,
1104               null) == JvOptionPane.OK_OPTION)
1105       {
1106         if (link.checkValid())
1107         {
1108           if (((UrlLinkTableModel) linkUrlTable.getModel())
1109                   .isUniqueName(link.getName()))
1110           {
1111             ((UrlLinkTableModel) linkUrlTable.getModel())
1112                     .insertRow(link.getName(), link.getURL());
1113             valid = true;
1114           }
1115           else
1116           {
1117             link.notifyDuplicate();
1118             continue;
1119           }
1120         }
1121       }
1122       else
1123       {
1124         break;
1125       }
1126     }
1127   }
1128
1129   @Override
1130   public void editLink_actionPerformed(ActionEvent e)
1131   {
1132     GSequenceLink link = new GSequenceLink();
1133
1134     int index = linkUrlTable.getSelectedRow();
1135     if (index == -1)
1136     {
1137       // button no longer enabled if row is not selected
1138       Cache.log.debug("Edit with no row selected in linkUrlTable");
1139       return;
1140     }
1141
1142     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1143             .getNameColumn();
1144     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1145             .getUrlColumn();
1146     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1147     link.setName(oldName);
1148     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1149
1150     boolean valid = false;
1151     while (!valid)
1152     {
1153       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1154               MessageManager.getString("label.edit_sequence_url_link"),
1155               JvOptionPane.OK_CANCEL_OPTION, -1,
1156               null) == JvOptionPane.OK_OPTION)
1157       {
1158         if (link.checkValid())
1159         {
1160           if ((oldName.equals(link.getName()))
1161                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1162                           .isUniqueName(link.getName())))
1163           {
1164             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1165             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1166             valid = true;
1167           }
1168           else
1169           {
1170             link.notifyDuplicate();
1171             continue;
1172           }
1173         }
1174       }
1175       else
1176       {
1177         break;
1178       }
1179     }
1180   }
1181
1182   @Override
1183   public void deleteLink_actionPerformed(ActionEvent e)
1184   {
1185     int index = linkUrlTable.getSelectedRow();
1186     int modelIndex = -1;
1187     if (index == -1)
1188     {
1189       // button no longer enabled if row is not selected
1190       Cache.log.debug("Delete with no row selected in linkUrlTable");
1191       return;
1192     }
1193     else
1194     {
1195       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1196     }
1197
1198     // make sure we use the model index to delete, and not the table index
1199     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1200   }
1201
1202   @Override
1203   public void defaultBrowser_mouseClicked(MouseEvent e)
1204   {
1205     // TODO: JAL-3048 not needed for j2s
1206     if (!Platform.isJS()) // BH 2019
1207     /**
1208      * Java only
1209      *
1210      * @j2sIgnore
1211      */
1212     {
1213       JFileChooser chooser = new JFileChooser(".");
1214       chooser.setDialogTitle(
1215               MessageManager.getString("label.select_default_browser"));
1216
1217       int value = chooser.showOpenDialog(this);
1218
1219       if (value == JFileChooser.APPROVE_OPTION)
1220       {
1221         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1222       }
1223     }
1224   }
1225
1226   /*
1227    * (non-Javadoc)
1228    *
1229    * @see
1230    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1231    * .ActionEvent)
1232    */
1233   @Override
1234   protected void showunconserved_actionPerformed(ActionEvent e)
1235   {
1236     // TODO Auto-generated method stub
1237     super.showunconserved_actionPerformed(e);
1238   }
1239
1240   public static List<String> getGroupURLLinks()
1241   {
1242     return groupURLLinks;
1243   }
1244
1245   @Override
1246   public void minColour_actionPerformed(JPanel panel)
1247   {
1248     JalviewColourChooser.showColourChooser(this,
1249             MessageManager.getString("label.select_colour_minimum_value"),
1250             panel);
1251   }
1252
1253   @Override
1254   public void maxColour_actionPerformed(JPanel panel)
1255   {
1256     JalviewColourChooser.showColourChooser(this,
1257             MessageManager.getString("label.select_colour_maximum_value"),
1258             panel);
1259   }
1260
1261   @Override
1262   public void gapColour_actionPerformed(JPanel gap)
1263   {
1264     if (!useLegacyGap.isSelected())
1265     {
1266       JalviewColourChooser.showColourChooser(this,
1267               MessageManager.getString("label.select_gap_colour"),
1268               gap);
1269     }
1270   }
1271
1272   @Override
1273   public void hiddenColour_actionPerformed(JPanel hidden)
1274   {
1275     JalviewColourChooser.showColourChooser(this,
1276             MessageManager.getString("label.select_hidden_colour"),
1277             hidden);
1278   }
1279
1280   @Override
1281   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1282   {
1283     boolean enabled = useLegacyGap.isSelected();
1284     if (enabled)
1285     {
1286       gapColour.setBackground(
1287               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1288     }
1289     else
1290     {
1291       gapColour.setBackground(
1292               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1293     }
1294     gapColour.setEnabled(!enabled);
1295     gapLabel.setEnabled(!enabled);
1296   }
1297
1298   @Override
1299   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1300   {
1301     useLegacyGap.setSelected(false);
1302     useLegacyGaps_actionPerformed(null);
1303     showHiddenAtStart.setSelected(false);
1304     hiddenColour.setBackground(
1305             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1306   }
1307
1308   @Override
1309   protected void userIdWidth_actionPerformed()
1310   {
1311     try
1312     {
1313       String val = userIdWidth.getText().trim();
1314       if (val.length() > 0)
1315       {
1316         Integer iw = Integer.parseInt(val);
1317         if (iw.intValue() < 12)
1318         {
1319           throw new NumberFormatException();
1320         }
1321         userIdWidth.setText(iw.toString());
1322       }
1323     } catch (NumberFormatException x)
1324     {
1325       userIdWidth.setText("");
1326       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1327               MessageManager
1328                       .getString("warn.user_defined_width_requirements"),
1329               MessageManager.getString("label.invalid_id_column_width"),
1330               JvOptionPane.WARNING_MESSAGE);
1331     }
1332   }
1333
1334   @Override
1335   protected void autoIdWidth_actionPerformed()
1336   {
1337     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1338     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1339   }
1340
1341   /**
1342    * Returns true if chimera path is to a valid executable, else show an error
1343    * dialog.
1344    */
1345   private boolean validateChimeraPath()
1346   {
1347     if (chimeraPath.getText().trim().length() > 0)
1348     {
1349       File f = new File(chimeraPath.getText());
1350       if (!f.canExecute())
1351       {
1352         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1353                 MessageManager.getString("label.invalid_chimera_path"),
1354                 MessageManager.getString("label.invalid_name"),
1355                 JvOptionPane.ERROR_MESSAGE);
1356         return false;
1357       }
1358     }
1359     return true;
1360   }
1361
1362   /**
1363    * Returns true if the given text field contains a path to a folder that
1364    * contains an executable with the given name, else false (after showing a
1365    * warning dialog). The executable name will be tried with .exe appended if not
1366    * found.
1367    *
1368    * @param textField
1369    * @param executable
1370    */
1371   protected boolean validateExecutablePath(JTextField textField, String executable)
1372   {
1373     String folder = textField.getText().trim();
1374
1375     if (FileUtils.getExecutable(executable, folder) != null)
1376     {
1377       return true;
1378     }
1379     if (folder.length() > 0)
1380     {
1381       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1382               MessageManager.formatMessage("label.executable_not_found",
1383                       executable),
1384               MessageManager.getString("label.invalid_folder"),
1385               JvOptionPane.ERROR_MESSAGE);
1386     }
1387     return false;
1388   }
1389
1390   /**
1391    * Checks if a file can be executed
1392    *
1393    * @param path
1394    *          the path to the file
1395    * @return
1396    */
1397   public boolean canExecute(String path)
1398   {
1399     File file = new File(path);
1400     if (!file.canExecute())
1401     {
1402       file = new File(path + ".exe");
1403       {
1404         if (!file.canExecute())
1405         {
1406           return false;
1407         }
1408       }
1409     }
1410     return true;
1411   }
1412
1413   /**
1414    * If Chimera is selected, check it can be found on default or user-specified
1415    * path, if not show a warning/help dialog.
1416    */
1417   @Override
1418   protected void structureViewer_actionPerformed(String selectedItem)
1419   {
1420     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1421     {
1422       return;
1423     }
1424     boolean found = false;
1425
1426     /*
1427      * Try user-specified and standard paths for Chimera executable.
1428      */
1429     List<String> paths = StructureManager.getChimeraPaths();
1430     paths.add(0, chimeraPath.getText());
1431     for (String path : paths)
1432     {
1433       if (new File(path.trim()).canExecute())
1434       {
1435         found = true;
1436         break;
1437       }
1438     }
1439     if (!found)
1440     {
1441       String[] options = { "OK", "Help" };
1442       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1443               JvSwingUtils.wrapTooltip(true,
1444                       MessageManager.getString("label.chimera_missing")),
1445               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1446               null, options, options[0]);
1447       if (showHelp == JvOptionPane.NO_OPTION)
1448       {
1449         try
1450         {
1451           Help.showHelpWindow(HelpId.StructureViewer);
1452         } catch (HelpSetException e)
1453         {
1454           e.printStackTrace();
1455         }
1456       }
1457     }
1458   }
1459
1460   @Override
1461   protected void validateHmmerPath()
1462   {
1463     validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
1464   }
1465
1466   @Override
1467   protected void validateCygwinPath()
1468   {
1469     validateExecutablePath(cygwinPath, "run");
1470   }
1471
1472   public class OptionsParam
1473   {
1474     private String name;
1475
1476     private String code;
1477
1478     public OptionsParam(String name, String code)
1479     {
1480       this.name = name;
1481       this.code = code;
1482     }
1483
1484     public String getName()
1485     {
1486       return name;
1487     }
1488
1489     public void setName(String name)
1490     {
1491       this.name = name;
1492     }
1493
1494     public String getCode()
1495     {
1496       return code;
1497     }
1498
1499     public void setCode(String code)
1500     {
1501       this.code = code;
1502     }
1503
1504     @Override
1505     public String toString()
1506     {
1507       return name;
1508     }
1509
1510     @Override
1511     public boolean equals(Object that)
1512     {
1513       if (!(that instanceof OptionsParam))
1514       {
1515         return false;
1516       }
1517       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1518     }
1519
1520     @Override
1521     public int hashCode()
1522     {
1523       return name.hashCode() + code.hashCode();
1524     }
1525   }
1526
1527   private class UrlListSelectionHandler implements ListSelectionListener
1528   {
1529
1530     @Override
1531     public void valueChanged(ListSelectionEvent e)
1532     {
1533       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1534
1535       int index = lsm.getMinSelectionIndex();
1536       if (index == -1)
1537       {
1538         // no selection, so disable delete/edit buttons
1539         editLink.setEnabled(false);
1540         deleteLink.setEnabled(false);
1541         return;
1542       }
1543       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1544
1545       // enable/disable edit and delete link buttons
1546       if (((UrlLinkTableModel) linkUrlTable.getModel())
1547               .isRowDeletable(modelIndex))
1548       {
1549         deleteLink.setEnabled(true);
1550       }
1551       else
1552       {
1553         deleteLink.setEnabled(false);
1554       }
1555
1556       if (((UrlLinkTableModel) linkUrlTable.getModel())
1557               .isRowEditable(modelIndex))
1558       {
1559         editLink.setEnabled(true);
1560       }
1561       else
1562       {
1563         editLink.setEnabled(false);
1564       }
1565     }
1566   }
1567 }