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