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