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