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