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