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 import java.util.concurrent.CompletableFuture;
  35
  36 import javax.help.HelpSetException;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JFileChooser;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JPanel;
  41 import javax.swing.ListSelectionModel;
  42 import javax.swing.RowFilter;
  43 import javax.swing.RowSorter;
  44 import javax.swing.SortOrder;
  45 import javax.swing.event.DocumentEvent;
  46 import javax.swing.event.DocumentListener;
  47 import javax.swing.event.ListSelectionEvent;
  48 import javax.swing.event.ListSelectionListener;
  49 import javax.swing.table.TableCellRenderer;
  50 import javax.swing.table.TableColumn;
  51 import javax.swing.table.TableModel;
  52 import javax.swing.table.TableRowSorter;
  53
  54 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  55 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  56 import jalview.bin.Cache;
  57 import jalview.ext.pymol.PymolManager;
  58 import jalview.gui.Help.HelpId;
  59 import jalview.gui.StructureViewer.ViewerType;
  60 import jalview.io.BackupFiles;
  61 import jalview.io.BackupFilesPresetEntry;
  62 import jalview.io.FileFormatI;
  63 import jalview.io.JalviewFileChooser;
  64 import jalview.io.JalviewFileView;
  65 import jalview.jbgui.GPreferences;
  66 import jalview.jbgui.GSequenceLink;
  67 import jalview.schemes.ColourSchemeI;
  68 import jalview.schemes.ColourSchemes;
  69 import jalview.schemes.ResidueColourScheme;
  70 import jalview.urls.UrlLinkTableModel;
  71 import jalview.urls.api.UrlProviderFactoryI;
  72 import jalview.urls.api.UrlProviderI;
  73 import jalview.urls.desktop.DesktopUrlProviderFactory;
  74 import jalview.util.MessageManager;
  75 import jalview.util.Platform;
  76 import jalview.util.UrlConstants;
  77 import jalview.ws.sifts.SiftsSettings;
  78
  79 /**
  80  * DOCUMENT ME!
  81  *
  82  * @author $author$
  83  * @version $Revision$
  84  */
  85 /*
  86  * for merge with Jalview-JS
  87  public class Preferences extends GPreferences implements ApplicationSingletonI
  88  */
  89 public class Preferences extends GPreferences
  90 {
  91   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  92
  93   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  94
  95   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  96
  97   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  98
  99   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 100
 101   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 102
 103   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 104
 105   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 106
 107   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 108
 109   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 110
 111   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 112
 113   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 114
 115   public static final String PYMOL_PATH = "PYMOL_PATH";
 116
 117   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 118
 119   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 120
 121   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 122
 123   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 124
 125   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 126
 127   public static final String GAP_COLOUR = "GAP_COLOUR";
 128
 129   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 130
 131   private static final int MIN_FONT_SIZE = 1;
 132
 133   private static final int MAX_FONT_SIZE = 30;
 134
 135   private String previousProxyType;
 136
 137   private static Preferences INSTANCE = null; // add "final"
 138
 139   /**
 140    * Holds name and link separated with | character. Sequence ID must be
 141    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 142    */
 143   public static UrlProviderI sequenceUrlLinks;
 144
 145   public static UrlLinkTableModel dataModel;
 146
 147   /**
 148    * Holds name and link separated with | character. Sequence IDS and Sequences
 149    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
 150    * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
 151    * second token specified after a pipe character at end |,|. (TODO: proper
 152    * escape for using | to separate ids or sequences
 153    */
 154
 155   public static List<String> groupURLLinks;
 156   static
 157   {
 158     // get links selected to be in the menu (SEQUENCE_LINKS)
 159     // and links entered by the user but not selected (STORED_LINKS)
 160     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 161     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 162     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 163             UrlConstants.DEFAULT_LABEL);
 164
 165     // if both links lists are empty, add the DEFAULT_URL link
 166     // otherwise we assume the default link is in one of the lists
 167     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 168     {
 169       inMenuString = UrlConstants.DEFAULT_STRING;
 170     }
 171     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 172             inMenuString, notInMenuString);
 173     sequenceUrlLinks = factory.createUrlProvider();
 174     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 175
 176     /**
 177      * TODO: reformulate groupURL encoding so two or more can be stored in the
 178      * .properties file as '|' separated strings
 179      */
 180
 181     groupURLLinks = new ArrayList<>();
 182   }
 183
 184   JInternalFrame frame;
 185
 186   private WsPreferences wsPrefs;
 187
 188   private OptionsParam promptEachTimeOpt = new OptionsParam(
 189           MessageManager.getString("label.prompt_each_time"),
 190           "Prompt each time");
 191
 192   private OptionsParam lineArtOpt = new OptionsParam(
 193           MessageManager.getString("label.lineart"), "Lineart");
 194
 195   private OptionsParam textOpt = new OptionsParam(
 196           MessageManager.getString("action.text"), "Text");
 197
 198   // get singleton Preferences instance
 199   public static Preferences getInstance()
 200   {
 201     if (INSTANCE == null || INSTANCE.frame == null
 202             || INSTANCE.frame.isClosed())
 203     {
 204       INSTANCE = new Preferences();
 205     }
 206     return INSTANCE;
 207
 208     /*
 209      * Replace code with the following for Jalvew-JS
 210     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 211     if (INSTANCE == null || INSTANCE.frame == null
 212             || INSTANCE.frame.isClosed())
 213     {
 214       ApplicationSingletonProvider.remove(Preferences.class);
 215       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 216     }
 217     return INSTANCE;
 218     */
 219   }
 220
 221   public static void openPreferences()
 222   {
 223     openPreferences(null, null);
 224   }
 225
 226   public static void openPreferences(TabRef selectTab, String message)
 227   {
 228     Preferences p = getInstance();
 229     if (selectTab != null)
 230       p.selectTab(selectTab, message);
 231     p.frame.show();
 232     p.frame.moveToFront();
 233     p.frame.grabFocus();
 234   }
 235
 236   public void selectTab(TabRef selectTab, String message)
 237   {
 238     this.selectTab(selectTab);
 239     if (message != null)
 240       this.setMessage(message);
 241     this.frame.show();
 242   }
 243
 244   /**
 245    * Creates a new Preferences object.
 246    */
 247   private Preferences()
 248   {
 249     super();
 250     frame = new JInternalFrame();
 251     frame.setContentPane(this);
 252     if (!Platform.isJS())
 253     /**
 254      * Java only
 255      *
 256      * @j2sIgnore
 257      */
 258     {
 259       wsPrefs = new WsPreferences();
 260       wsTab.add(wsPrefs, BorderLayout.CENTER);
 261     }
 262     int width = 500, height = 450;
 263     if (Platform.isAMacAndNotJS())
 264     {
 265       width = 570;
 266       height = 480;
 267     }
 268
 269     Desktop.addInternalFrame(frame,
 270             MessageManager.getString("label.preferences"), width, height);
 271     frame.setMinimumSize(new Dimension(width, height));
 272
 273     /*
 274      * Set Visual tab defaults
 275      */
 276     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 277     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 278     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 279     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 280
 281     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 282     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 283     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 284     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 285     showUnconserved
 286             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 287     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 288     showGroupConsensus
 289             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 290     showGroupConservation.setSelected(
 291             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 292     showConsensHistogram.setSelected(
 293             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 294     showConsensLogo
 295             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 296     showNpTooltip
 297             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 298     showDbRefTooltip
 299             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 300
 301     String[] fonts = java.awt.GraphicsEnvironment
 302             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 303     for (int i = 0; i < fonts.length; i++)
 304     {
 305       fontNameCB.addItem(fonts[i]);
 306     }
 307
 308     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 309     {
 310       fontSizeCB.addItem(i + "");
 311     }
 312
 313     fontStyleCB.addItem("plain");
 314     fontStyleCB.addItem("bold");
 315     fontStyleCB.addItem("italic");
 316
 317     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 318     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 319     fontStyleCB.setSelectedItem(
 320             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 321
 322     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 323     scaleProteinToCdna
 324             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 325
 326     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 327
 328     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 329
 330     gapSymbolCB.addItem("-");
 331     gapSymbolCB.addItem(".");
 332
 333     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 334
 335     sortby.addItem("No sort");
 336     sortby.addItem("Id");
 337     sortby.addItem("Pairwise Identity");
 338     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 339
 340     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 341     sortAnnBy
 342             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 343     sortAnnBy
 344             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 345     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 346             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 347                     SequenceAnnotationOrder.NONE.name()));
 348     sortAnnBy.setSelectedItem(savedSort.toString());
 349
 350     sortAutocalc.addItem("Autocalculated first");
 351     sortAutocalc.addItem("Autocalculated last");
 352     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 353     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 354             : sortAutocalc.getItemAt(1));
 355     startupCheckbox
 356             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 357     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 358             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 359                     + "/examples/exampleFile_2_7.jvp"));
 360
 361     /*
 362      * Set Colours tab defaults
 363      */
 364     protColour.addItem(ResidueColourScheme.NONE);
 365     nucColour.addItem(ResidueColourScheme.NONE);
 366     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 367     {
 368       String name = cs.getSchemeName();
 369       protColour.addItem(name);
 370       nucColour.addItem(name);
 371     }
 372     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 373             ResidueColourScheme.NONE);
 374     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 375     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 376     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 377     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 378     minColour.setBackground(
 379             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 380     maxColour.setBackground(
 381             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 382
 383     /*
 384      * Set overview panel defaults
 385      */
 386     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 387             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 388     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 389             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 390     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 391     gapLabel.setEnabled(!useLegacyGap.isSelected());
 392     gapColour.setEnabled(!useLegacyGap.isSelected());
 393     showHiddenAtStart
 394             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 395
 396     /*
 397      * Set Structure tab defaults
 398      */
 399     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
 400     structFromPdb.setSelected(structSelected);
 401     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
 402     addSecondaryStructure.setEnabled(structSelected);
 403     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
 404     addTempFactor.setEnabled(structSelected);
 405
 406     /*
 407      * set choice of structure viewer, and path if saved as a preference;
 408      * default to Jmol (first choice) if an unexpected value is found
 409      */
 410     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 411             ViewerType.JMOL.name());
 412     structViewer.setSelectedItem(viewerType);
 413     String viewerPath = "";
 414     ViewerType type = null;
 415     try
 416     {
 417       type = ViewerType.valueOf(viewerType);
 418       switch (type)
 419       {
 420       case JMOL:
 421         break;
 422       case CHIMERA:
 423         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 424         break;
 425       case CHIMERAX:
 426         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 427         break;
 428       case PYMOL:
 429         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 430         break;
 431       }
 432     } catch (IllegalArgumentException e)
 433     {
 434       Cache.log.error("Unknown structure viewer type: " + viewerType
 435               + ", defaulting to Jmol");
 436       type = ViewerType.JMOL;
 437     }
 438     structureViewerPath.setText(viewerPath);
 439
 440     structureViewerPath.addActionListener(new ActionListener()
 441     {
 442       @Override
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         if (validateViewerPath())
 446         {
 447           String path = structureViewerPath.getText();
 448           try {
 449           ViewerType type = ViewerType.valueOf(viewerType);
 450           switch (type)
 451           {
 452           case JMOL:
 453             break;
 454           case CHIMERA:
 455             Cache.setProperty(CHIMERA_PATH, path);
 456             break;
 457           case CHIMERAX:
 458             Cache.setProperty(CHIMERAX_PATH, path);
 459             break;
 460           case PYMOL:
 461             Cache.setProperty(PYMOL_PATH, path);
 462             break;
 463           }
 464         } catch (IllegalArgumentException x)
 465         {
 466           Cache.log.error("Failed to set path - unknown viewer type",x);
 467         }
 468         }
 469       }
 470     });
 471
 472     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 473     {
 474       siftsMapping.setSelected(true);
 475     }
 476     else
 477     {
 478       nwMapping.setSelected(true);
 479     }
 480
 481     SiftsSettings
 482             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 483
 484     /*
 485      * Set Connections tab defaults
 486      */
 487
 488     // set up sorting
 489     linkUrlTable.setModel(dataModel);
 490     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 491             linkUrlTable.getModel());
 492     linkUrlTable.setRowSorter(sorter);
 493     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 494
 495     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 496     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 497             SortOrder.DESCENDING));
 498     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 499             SortOrder.DESCENDING));
 500     sortKeys.add(
 501             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 502
 503     sorter.setSortKeys(sortKeys);
 504     // BH 2018 setSortKeys will do the sort
 505     // sorter.sort();
 506
 507     // set up filtering
 508     ActionListener onReset;
 509     onReset = new ActionListener()
 510     {
 511       @Override
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         filterTB.setText("");
 515         sorter.setRowFilter(RowFilter.regexFilter(""));
 516       }
 517
 518     };
 519     doReset.addActionListener(onReset);
 520
 521     // filter to display only custom urls
 522     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 523     {
 524       @Override
 525       public boolean include(
 526               Entry<? extends TableModel, ? extends Object> entry)
 527       {
 528         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 529       }
 530     };
 531
 532     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 533             linkUrlTable.getModel());
 534     customSorter.setRowFilter(customUrlFilter);
 535
 536     ActionListener onCustomOnly;
 537     onCustomOnly = new ActionListener()
 538     {
 539       @Override
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         filterTB.setText("");
 543         sorter.setRowFilter(customUrlFilter);
 544       }
 545     };
 546     userOnly.addActionListener(onCustomOnly);
 547
 548     filterTB.getDocument().addDocumentListener(new DocumentListener()
 549     {
 550       String caseInsensitiveFlag = "(?i)";
 551
 552       @Override
 553       public void changedUpdate(DocumentEvent e)
 554       {
 555         sorter.setRowFilter(RowFilter
 556                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 557       }
 558
 559       @Override
 560       public void removeUpdate(DocumentEvent e)
 561       {
 562         sorter.setRowFilter(RowFilter
 563                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 564       }
 565
 566       @Override
 567       public void insertUpdate(DocumentEvent e)
 568       {
 569         sorter.setRowFilter(RowFilter
 570                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 571       }
 572     });
 573
 574     // set up list selection functionality
 575     linkUrlTable.getSelectionModel()
 576             .addListSelectionListener(new UrlListSelectionHandler());
 577
 578     // set up radio buttons
 579     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 580             .getPrimaryColumn();
 581     String onClickName = linkUrlTable.getColumnName(onClickCol);
 582     linkUrlTable.getColumn(onClickName)
 583             .setCellRenderer(new RadioButtonRenderer());
 584     linkUrlTable.getColumn(onClickName)
 585             .setCellEditor(new RadioButtonEditor());
 586
 587     // get boolean columns and resize those to min possible
 588     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 589     {
 590       if (linkUrlTable.getModel().getColumnClass(column)
 591               .equals(Boolean.class))
 592       {
 593         TableColumn tableColumn = linkUrlTable.getColumnModel()
 594                 .getColumn(column);
 595         int preferredWidth = tableColumn.getMinWidth();
 596
 597         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 598                 column);
 599         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 600         int cwidth = c.getPreferredSize().width
 601                 + linkUrlTable.getIntercellSpacing().width;
 602         preferredWidth = Math.max(preferredWidth, cwidth);
 603
 604         tableColumn.setPreferredWidth(preferredWidth);
 605       }
 606     }
 607
 608     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 609     previousProxyType = proxyTypeString;
 610     switch (proxyTypeString)
 611     {
 612     case Cache.PROXYTYPE_NONE:
 613       proxyType.setSelected(noProxy.getModel(), true);
 614       break;
 615     case Cache.PROXYTYPE_SYSTEM:
 616       proxyType.setSelected(systemProxy.getModel(), true);
 617       break;
 618     case Cache.PROXYTYPE_CUSTOM:
 619       proxyType.setSelected(customProxy.getModel(), true);
 620       break;
 621     default:
 622       Cache.log.warn(
 623               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 624                       + proxyTypeString);
 625     }
 626     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 627     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 628     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 629     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 630     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 631     proxyAuthUsernameTB
 632             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 633     // we are not storing or retrieving proxy password from .jalview_properties
 634     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 635             : new String(Cache.proxyAuthPassword));
 636     setCustomProxyEnabled();
 637     applyProxyButtonEnabled(false);
 638
 639     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 640
 641     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 642     // note antisense here: default is true
 643     questionnaire
 644             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 645     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 646
 647     /*
 648      * Set Output tab defaults
 649      */
 650     setupOutputCombo(epsRendering, "EPS_RENDERING");
 651     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 652     setupOutputCombo(svgRendering, "SVG_RENDERING");
 653     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 654     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 655     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 656     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 657     userIdWidth.setText(wi == null ? "" : wi.toString());
 658     // TODO: refactor to use common enum via FormatAdapter and allow extension
 659     // for new flat file formats
 660     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 661     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 662     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 663     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 664     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 665     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 666     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 667     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 668     embbedBioJSON
 669             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 670
 671     /*
 672      * Set Editing tab defaults
 673      */
 674     autoCalculateConsCheck
 675             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 676     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 677     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 678
 679     annotations_actionPerformed(null); // update the display of the annotation
 680                                        // settings
 681
 682     /*
 683      * Set Backups tab defaults
 684      */
 685     loadLastSavedBackupsOptions();
 686   }
 687
 688   /**
 689    * A helper method that sets the items and initial selection in a character
 690    * rendering option list (Prompt each time/Lineart/Text)
 691    *
 692    * @param comboBox
 693    * @param propertyKey
 694    */
 695   protected void setupOutputCombo(JComboBox<Object> comboBox,
 696           String propertyKey)
 697   {
 698     comboBox.addItem(promptEachTimeOpt);
 699     comboBox.addItem(lineArtOpt);
 700     comboBox.addItem(textOpt);
 701
 702     /*
 703      * JalviewJS doesn't support Lineart so force it to Text
 704      */
 705     String defaultOption = Platform.isJS() ? "Text"
 706             : Cache.getDefault(propertyKey, "Prompt each time");
 707     if (defaultOption.equalsIgnoreCase("Text"))
 708     {
 709       comboBox.setSelectedItem(textOpt);
 710     }
 711     else if (defaultOption.equalsIgnoreCase("Lineart"))
 712     {
 713       comboBox.setSelectedItem(lineArtOpt);
 714     }
 715     else
 716     {
 717       comboBox.setSelectedItem(promptEachTimeOpt);
 718     }
 719   }
 720
 721   /**
 722    * Save user selections on the Preferences tabs to the Cache and write out to
 723    * file.
 724    *
 725    * @param e
 726    */
 727   @Override
 728   public void ok_actionPerformed(ActionEvent e)
 729   {
 730     if (!validateSettings())
 731     {
 732       return;
 733     }
 734
 735     /*
 736      * Set proxy settings first (to be before web services refresh)
 737      */
 738     saveProxySettings();
 739
 740     /*
 741      * Save Visual settings
 742      */
 743     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 744             Boolean.toString(seqLimit.isSelected()));
 745     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 746             Boolean.toString(rightAlign.isSelected()));
 747     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 748             Boolean.toString(fullScreen.isSelected()));
 749     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 750             Boolean.toString(openoverv.isSelected()));
 751     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 752             Boolean.toString(annotations.isSelected()));
 753     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 754             Boolean.toString(conservation.isSelected()));
 755     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 756             Boolean.toString(quality.isSelected()));
 757     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 758             Boolean.toString(identity.isSelected()));
 759
 760     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 761             gapSymbolCB.getSelectedItem().toString());
 762
 763     Cache.applicationProperties.setProperty("FONT_NAME",
 764             fontNameCB.getSelectedItem().toString());
 765     Cache.applicationProperties.setProperty("FONT_STYLE",
 766             fontStyleCB.getSelectedItem().toString());
 767     Cache.applicationProperties.setProperty("FONT_SIZE",
 768             fontSizeCB.getSelectedItem().toString());
 769
 770     Cache.applicationProperties.setProperty("ID_ITALICS",
 771             Boolean.toString(idItalics.isSelected()));
 772     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 773             Boolean.toString(showUnconserved.isSelected()));
 774     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 775             Boolean.toString(showOccupancy.isSelected()));
 776     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 777             Boolean.toString(showGroupConsensus.isSelected()));
 778     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 779             Boolean.toString(showGroupConservation.isSelected()));
 780     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 781             Boolean.toString(showConsensHistogram.isSelected()));
 782     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 783             Boolean.toString(showConsensLogo.isSelected()));
 784     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 785             Boolean.toString(smoothFont.isSelected()));
 786     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 787             Boolean.toString(scaleProteinToCdna.isSelected()));
 788     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 789             Boolean.toString(showNpTooltip.isSelected()));
 790     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 791             Boolean.toString(showDbRefTooltip.isSelected()));
 792
 793     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 794             Boolean.toString(wrap.isSelected()));
 795
 796     Cache.applicationProperties.setProperty("STARTUP_FILE",
 797             startupFileTextfield.getText());
 798     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 799             Boolean.toString(startupCheckbox.isSelected()));
 800
 801     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 802             sortby.getSelectedItem().toString());
 803
 804     // convert description of sort order to enum name for save
 805     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 806             .forDescription(sortAnnBy.getSelectedItem().toString());
 807     if (annSortOrder != null)
 808     {
 809       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 810               annSortOrder.name());
 811     }
 812
 813     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 814     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 815             Boolean.valueOf(showAutocalcFirst).toString());
 816
 817     /*
 818      * Save Colours settings
 819      */
 820     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 821             protColour.getSelectedItem().toString());
 822     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 823             nucColour.getSelectedItem().toString());
 824     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 825             minColour.getBackground());
 826     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 827             maxColour.getBackground());
 828
 829     /*
 830      * Save Overview settings
 831      */
 832     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 833     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 834     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 835             Boolean.toString(useLegacyGap.isSelected()));
 836     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 837             Boolean.toString(showHiddenAtStart.isSelected()));
 838
 839     /*
 840      * Save Structure settings
 841      */
 842     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 843             Boolean.toString(addTempFactor.isSelected()));
 844     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 845             Boolean.toString(addSecondaryStructure.isSelected()));
 846     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 847             Boolean.toString(structFromPdb.isSelected()));
 848     String viewer = structViewer.getSelectedItem().toString();
 849     String viewerPath = structureViewerPath.getText();
 850     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 851     if (viewer.equals(ViewerType.CHIMERA.name()))
 852     {
 853       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 854     }
 855     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 856     {
 857       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 858     }
 859     else if (viewer.equals(ViewerType.PYMOL.name()))
 860     {
 861       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 862     }
 863     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 864             Boolean.toString(siftsMapping.isSelected()));
 865     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 866
 867     /*
 868      * Save Output settings
 869      */
 870     Cache.applicationProperties.setProperty("EPS_RENDERING",
 871             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 872     Cache.applicationProperties.setProperty("HTML_RENDERING",
 873             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 874     Cache.applicationProperties.setProperty("SVG_RENDERING",
 875             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 876
 877     /*
 878      * Save Connections settings
 879      */
 880     // Proxy settings set first (to catch web services)
 881
 882     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 883
 884     jalview.util.BrowserLauncher.resetBrowser();
 885
 886     // save user-defined and selected links
 887     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 888     if (menuLinks.isEmpty())
 889     {
 890       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 891     }
 892     else
 893     {
 894       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 895               menuLinks.toString());
 896     }
 897
 898     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 899     if (nonMenuLinks.isEmpty())
 900     {
 901       Cache.applicationProperties.remove("STORED_LINKS");
 902     }
 903     else
 904     {
 905       Cache.applicationProperties.setProperty("STORED_LINKS",
 906               nonMenuLinks.toString());
 907     }
 908
 909     Cache.applicationProperties.setProperty("DEFAULT_URL",
 910             sequenceUrlLinks.getPrimaryUrlId());
 911
 912     Cache.setProperty("VERSION_CHECK",
 913             Boolean.toString(versioncheck.isSelected()));
 914     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 915     {
 916       // default is false - we only set this if the user has actively agreed
 917       Cache.setProperty("USAGESTATS",
 918               Boolean.toString(usagestats.isSelected()));
 919     }
 920     if (!questionnaire.isSelected())
 921     {
 922       Cache.setProperty("NOQUESTIONNAIRES", "true");
 923     }
 924     else
 925     {
 926       // special - made easy to edit a property file to disable questionnaires
 927       // by just adding the given line
 928       Cache.removeProperty("NOQUESTIONNAIRES");
 929     }
 930
 931     /*
 932      * Save Output settings
 933      */
 934     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 935             Boolean.toString(blcjv.isSelected()));
 936     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 937             Boolean.toString(clustaljv.isSelected()));
 938     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 939             Boolean.toString(fastajv.isSelected()));
 940     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 941             Boolean.toString(msfjv.isSelected()));
 942     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 943             Boolean.toString(pfamjv.isSelected()));
 944     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 945             Boolean.toString(pileupjv.isSelected()));
 946     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 947             Boolean.toString(pirjv.isSelected()));
 948     Cache.applicationProperties.setProperty("PIR_MODELLER",
 949             Boolean.toString(modellerOutput.isSelected()));
 950     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 951             Boolean.toString(embbedBioJSON.isSelected()));
 952     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 953
 954     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 955             Boolean.toString(autoIdWidth.isSelected()));
 956     userIdWidth_actionPerformed();
 957     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 958             userIdWidth.getText());
 959
 960     /*
 961      * Save Editing settings
 962      */
 963     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 964             Boolean.toString(autoCalculateConsCheck.isSelected()));
 965     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 966             Boolean.toString(sortByTree.isSelected()));
 967     Cache.applicationProperties.setProperty("PAD_GAPS",
 968             Boolean.toString(padGaps.isSelected()));
 969
 970     if (!Platform.isJS())
 971     {
 972       wsPrefs.updateAndRefreshWsMenuConfig(false);
 973     }
 974
 975     /*
 976      * Save Backups settings
 977      */
 978     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 979             Boolean.toString(enableBackupFiles.isSelected()));
 980     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 981     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 982             Integer.toString(preset));
 983
 984     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 985     {
 986       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 987       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 988               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 989       Cache.applicationProperties.setProperty(
 990               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 991     }
 992
 993     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 994             .get(preset);
 995     Cache.applicationProperties.setProperty(
 996             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 997
 998     Cache.saveProperties();
 999     Desktop.instance.doConfigureStructurePrefs();
1000     try
1001     {
1002       frame.setClosed(true);
1003     } catch (Exception ex)
1004     {
1005     }
1006   }
1007
1008   public void saveProxySettings()
1009   {
1010     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1011             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1012                     : Cache.PROXYTYPE_SYSTEM;
1013     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1014     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1015     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1016     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1017     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1018     Cache.setOrRemove("PROXY_AUTH",
1019             Boolean.toString(proxyAuth.isSelected()));
1020     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1021     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1022     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1023     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1024             || !newProxyType.equals(previousProxyType))
1025     {
1026       // force a re-lookup of ws if proxytype is custom or has changed
1027       wsPrefs.update++;
1028     }
1029     previousProxyType = newProxyType;
1030   }
1031
1032   /**
1033    * Do any necessary validation before saving settings. Return focus to the first
1034    * tab which fails validation.
1035    *
1036    * @return
1037    */
1038   private boolean validateSettings()
1039   {
1040     if (!validateStructure())
1041     {
1042       structureTab.requestFocusInWindow();
1043       return false;
1044     }
1045     return true;
1046   }
1047
1048   @Override
1049   protected boolean validateStructure()
1050   {
1051     return validateViewerPath();
1052
1053   }
1054
1055   /**
1056    * DOCUMENT ME!
1057    */
1058   @Override
1059   public void startupFileTextfield_mouseClicked()
1060   {
1061     // TODO: JAL-3048 not needed for Jalview-JS
1062     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1063     JalviewFileChooser chooser = JalviewFileChooser
1064             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1065     chooser.setFileView(new JalviewFileView());
1066     chooser.setDialogTitle(
1067             MessageManager.getString("label.select_startup_file"));
1068
1069     int value = chooser.showOpenDialog(this);
1070
1071     if (value == JalviewFileChooser.APPROVE_OPTION)
1072     {
1073       FileFormatI format = chooser.getSelectedFormat();
1074       if (format != null)
1075       {
1076         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1077                 format.getName());
1078       }
1079       startupFileTextfield
1080               .setText(chooser.getSelectedFile().getAbsolutePath());
1081     }
1082   }
1083
1084   /**
1085    * DOCUMENT ME!
1086    *
1087    * @param e
1088    *            DOCUMENT ME!
1089    */
1090   @Override
1091   public void cancel_actionPerformed(ActionEvent e)
1092   {
1093     try
1094     {
1095       if (!Platform.isJS())
1096       {
1097         wsPrefs.updateWsMenuConfig(true);
1098         wsPrefs.refreshWs_actionPerformed(e);
1099       }
1100       frame.setClosed(true);
1101     } catch (Exception ex)
1102     {
1103     }
1104   }
1105
1106   /**
1107    * DOCUMENT ME!
1108    *
1109    * @param e
1110    *            DOCUMENT ME!
1111    */
1112   @Override
1113   public void annotations_actionPerformed(ActionEvent e)
1114   {
1115     conservation.setEnabled(annotations.isSelected());
1116     quality.setEnabled(annotations.isSelected());
1117     identity.setEnabled(annotations.isSelected());
1118     showOccupancy.setEnabled(annotations.isSelected());
1119     showGroupConsensus.setEnabled(annotations.isSelected());
1120     showGroupConservation.setEnabled(annotations.isSelected());
1121     showConsensHistogram.setEnabled(annotations.isSelected()
1122             && (identity.isSelected() || showGroupConsensus.isSelected()));
1123     showConsensLogo.setEnabled(annotations.isSelected()
1124             && (identity.isSelected() || showGroupConsensus.isSelected()));
1125   }
1126
1127   @Override
1128   public void newLink_actionPerformed(ActionEvent e)
1129   {
1130     GSequenceLink link = new GSequenceLink();
1131     boolean valid = false;
1132     while (!valid)
1133     {
1134       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1135               MessageManager.getString("label.new_sequence_url_link"),
1136               JvOptionPane.OK_CANCEL_OPTION, -1,
1137               null) == JvOptionPane.OK_OPTION)
1138       {
1139         if (link.checkValid())
1140         {
1141           if (((UrlLinkTableModel) linkUrlTable.getModel())
1142                   .isUniqueName(link.getName()))
1143           {
1144             ((UrlLinkTableModel) linkUrlTable.getModel())
1145                     .insertRow(link.getName(), link.getURL());
1146             valid = true;
1147           }
1148           else
1149           {
1150             link.notifyDuplicate();
1151             continue;
1152           }
1153         }
1154       }
1155       else
1156       {
1157         break;
1158       }
1159     }
1160   }
1161
1162   @Override
1163   public void editLink_actionPerformed(ActionEvent e)
1164   {
1165     GSequenceLink link = new GSequenceLink();
1166
1167     int index = linkUrlTable.getSelectedRow();
1168     if (index == -1)
1169     {
1170       // button no longer enabled if row is not selected
1171       Cache.log.debug("Edit with no row selected in linkUrlTable");
1172       return;
1173     }
1174
1175     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1176             .getNameColumn();
1177     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1178             .getUrlColumn();
1179     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1180     link.setName(oldName);
1181     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1182
1183     boolean valid = false;
1184     while (!valid)
1185     {
1186       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1187               MessageManager.getString("label.edit_sequence_url_link"),
1188               JvOptionPane.OK_CANCEL_OPTION, -1,
1189               null) == JvOptionPane.OK_OPTION)
1190       {
1191         if (link.checkValid())
1192         {
1193           if ((oldName.equals(link.getName()))
1194                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1195                           .isUniqueName(link.getName())))
1196           {
1197             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1198             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1199             valid = true;
1200           }
1201           else
1202           {
1203             link.notifyDuplicate();
1204             continue;
1205           }
1206         }
1207       }
1208       else
1209       {
1210         break;
1211       }
1212     }
1213   }
1214
1215   @Override
1216   public void deleteLink_actionPerformed(ActionEvent e)
1217   {
1218     int index = linkUrlTable.getSelectedRow();
1219     int modelIndex = -1;
1220     if (index == -1)
1221     {
1222       // button no longer enabled if row is not selected
1223       Cache.log.debug("Delete with no row selected in linkUrlTable");
1224       return;
1225     }
1226     else
1227     {
1228       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1229     }
1230
1231     // make sure we use the model index to delete, and not the table index
1232     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1233   }
1234
1235   @Override
1236   public void defaultBrowser_mouseClicked(MouseEvent e)
1237   {
1238     // TODO: JAL-3048 not needed for j2s
1239     if (!Platform.isJS()) // BH 2019
1240     /**
1241      * Java only
1242      *
1243      * @j2sIgnore
1244      */
1245     {
1246       JFileChooser chooser = new JFileChooser(".");
1247       chooser.setDialogTitle(
1248               MessageManager.getString("label.select_default_browser"));
1249
1250       int value = chooser.showOpenDialog(this);
1251
1252       if (value == JFileChooser.APPROVE_OPTION)
1253       {
1254         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1255       }
1256     }
1257   }
1258
1259   /*
1260    * (non-Javadoc)
1261    *
1262    * @see
1263    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1264    * .ActionEvent)
1265    */
1266   @Override
1267   protected void showunconserved_actionPerformed(ActionEvent e)
1268   {
1269     // TODO Auto-generated method stub
1270     super.showunconserved_actionPerformed(e);
1271   }
1272
1273   public static List<String> getGroupURLLinks()
1274   {
1275     return groupURLLinks;
1276   }
1277
1278   @Override
1279   public void minColour_actionPerformed(JPanel panel)
1280   {
1281     JalviewColourChooser.showColourChooser(this,
1282             MessageManager.getString("label.select_colour_minimum_value"),
1283             panel);
1284   }
1285
1286   @Override
1287   public void maxColour_actionPerformed(JPanel panel)
1288   {
1289     JalviewColourChooser.showColourChooser(this,
1290             MessageManager.getString("label.select_colour_maximum_value"),
1291             panel);
1292   }
1293
1294   @Override
1295   public void gapColour_actionPerformed(JPanel gap)
1296   {
1297     if (!useLegacyGap.isSelected())
1298     {
1299       JalviewColourChooser.showColourChooser(this,
1300               MessageManager.getString("label.select_gap_colour"), gap);
1301     }
1302   }
1303
1304   @Override
1305   public void hiddenColour_actionPerformed(JPanel hidden)
1306   {
1307     JalviewColourChooser.showColourChooser(this,
1308             MessageManager.getString("label.select_hidden_colour"), hidden);
1309   }
1310
1311   @Override
1312   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1313   {
1314     boolean enabled = useLegacyGap.isSelected();
1315     if (enabled)
1316     {
1317       gapColour.setBackground(
1318               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1319     }
1320     else
1321     {
1322       gapColour.setBackground(
1323               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1324     }
1325     gapColour.setEnabled(!enabled);
1326     gapLabel.setEnabled(!enabled);
1327   }
1328
1329   @Override
1330   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1331   {
1332     useLegacyGap.setSelected(false);
1333     useLegacyGaps_actionPerformed(null);
1334     showHiddenAtStart.setSelected(false);
1335     hiddenColour.setBackground(
1336             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1337   }
1338
1339   @Override
1340   protected void userIdWidth_actionPerformed()
1341   {
1342     try
1343     {
1344       String val = userIdWidth.getText().trim();
1345       if (val.length() > 0)
1346       {
1347         Integer iw = Integer.parseInt(val);
1348         if (iw.intValue() < 12)
1349         {
1350           throw new NumberFormatException();
1351         }
1352         userIdWidth.setText(iw.toString());
1353       }
1354     } catch (NumberFormatException x)
1355     {
1356       userIdWidth.setText("");
1357       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1358               MessageManager
1359                       .getString("warn.user_defined_width_requirements"),
1360               MessageManager.getString("label.invalid_id_column_width"),
1361               JvOptionPane.WARNING_MESSAGE);
1362     }
1363   }
1364
1365   @Override
1366   protected void autoIdWidth_actionPerformed()
1367   {
1368     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1369     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1370   }
1371
1372   /**
1373    * Returns true if structure viewer path is to a valid executable, else shows an
1374    * error dialog. Does nothing if the path is empty, as is the case for Jmol
1375    * (built in to Jalview) or when Jalview is left to try default paths.
1376    */
1377   private boolean validateViewerPath()
1378   {
1379     if (structureViewerPath.getText().trim().length() > 0)
1380     {
1381       File f = new File(structureViewerPath.getText());
1382       if (!f.canExecute())
1383       {
1384         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1385                 MessageManager.getString("label.invalid_viewer_path"),
1386                 MessageManager.getString("label.invalid_viewer_path"),
1387                 JvOptionPane.ERROR_MESSAGE);
1388         return false;
1389       }
1390     }
1391     return true;
1392   }
1393
1394   /**
1395    * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
1396    * or user-specified path, if not show a warning/help dialog
1397    */
1398   @Override
1399   protected void structureViewer_actionPerformed(String selectedItem)
1400   {
1401     if (selectedItem.equals(ViewerType.JMOL.name()))
1402     {
1403       structureViewerPath.setEnabled(false);
1404       structureViewerPathLabel.setEnabled(false);
1405       return;
1406     }
1407     boolean found = false;
1408     structureViewerPath.setEnabled(true);
1409     structureViewerPathLabel.setEnabled(true);
1410     structureViewerPathLabel.setText(MessageManager
1411             .formatMessage("label.viewer_path", selectedItem));
1412
1413     /*
1414      * Try user-specified and standard paths for structure viewer executable
1415      */
1416     String viewerPath = "";
1417     List<String> paths = null;
1418     try
1419     {
1420       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1421       switch (viewerType)
1422       {
1423       case JMOL:
1424         // dealt with above
1425         break;
1426       case CHIMERA:
1427         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1428         paths = StructureManager.getChimeraPaths(false);
1429         break;
1430       case CHIMERAX:
1431         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1432         paths = StructureManager.getChimeraPaths(true);
1433         break;
1434       case PYMOL:
1435         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1436         paths = PymolManager.getPymolPaths();
1437         break;
1438       }
1439     } catch (IllegalArgumentException e)
1440     {
1441       // only valid entries should be in the drop-down
1442     }
1443     structureViewerPath.setText(viewerPath);
1444
1445     paths.add(0, structureViewerPath.getText());
1446     for (String path : paths)
1447     {
1448       if (new File(path.trim()).canExecute())
1449       {
1450         found = true;
1451         break;
1452       }
1453     }
1454
1455     if (!found)
1456     {
1457       String[] options = { "OK", "Help" };
1458       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1459               JvSwingUtils.wrapTooltip(true,
1460                       MessageManager.getString("label.viewer_missing")),
1461               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1462               null, options, options[0]);
1463
1464       if (showHelp == JvOptionPane.NO_OPTION)
1465       {
1466         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1467         try
1468         {
1469           Help.showHelpWindow(HelpId.StructureViewer);
1470         } catch (HelpSetException e)
1471         {
1472           e.printStackTrace();
1473         }
1474       }
1475       else if (showHelp == JvOptionPane.OK_OPTION)
1476       {
1477         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1478         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1479           try
1480           {
1481             for (int i = 0; i < 3; i++)
1482             {
1483               structureViewerPath.setBackground(Color.PINK);
1484               Thread.sleep(500);
1485               structureViewerPath.setBackground(Color.WHITE);
1486               Thread.sleep(500);
1487             }
1488           } catch (InterruptedException e)
1489           {
1490           }
1491         });
1492       }
1493     }
1494   }
1495
1496   public class OptionsParam
1497   {
1498     private String name;
1499
1500     private String code;
1501
1502     public OptionsParam(String name, String code)
1503     {
1504       this.name = name;
1505       this.code = code;
1506     }
1507
1508     public String getName()
1509     {
1510       return name;
1511     }
1512
1513     public void setName(String name)
1514     {
1515       this.name = name;
1516     }
1517
1518     public String getCode()
1519     {
1520       return code;
1521     }
1522
1523     public void setCode(String code)
1524     {
1525       this.code = code;
1526     }
1527
1528     @Override
1529     public String toString()
1530     {
1531       return name;
1532     }
1533
1534     @Override
1535     public boolean equals(Object that)
1536     {
1537       if (!(that instanceof OptionsParam))
1538       {
1539         return false;
1540       }
1541       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1542     }
1543
1544     @Override
1545     public int hashCode()
1546     {
1547       return name.hashCode() + code.hashCode();
1548     }
1549   }
1550
1551   private class UrlListSelectionHandler implements ListSelectionListener
1552   {
1553
1554     @Override
1555     public void valueChanged(ListSelectionEvent e)
1556     {
1557       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1558
1559       int index = lsm.getMinSelectionIndex();
1560       if (index == -1)
1561       {
1562         // no selection, so disable delete/edit buttons
1563         editLink.setEnabled(false);
1564         deleteLink.setEnabled(false);
1565         return;
1566       }
1567       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1568
1569       // enable/disable edit and delete link buttons
1570       if (((UrlLinkTableModel) linkUrlTable.getModel())
1571               .isRowDeletable(modelIndex))
1572       {
1573         deleteLink.setEnabled(true);
1574       }
1575       else
1576       {
1577         deleteLink.setEnabled(false);
1578       }
1579
1580       if (((UrlLinkTableModel) linkUrlTable.getModel())
1581               .isRowEditable(modelIndex))
1582       {
1583         editLink.setEnabled(true);
1584       }
1585       else
1586       {
1587         editLink.setEnabled(false);
1588       }
1589     }
1590   }
1591 }