src/jalview/gui/Preferences.java

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