src/jalview/gui/Preferences.java

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