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