src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.jbgui.GPreferences;
  30 import jalview.jbgui.GSequenceLink;
  31 import jalview.schemes.ColourSchemeProperty;
  32 import jalview.urls.UrlLinkTableModel;
  33 import jalview.urls.api.UrlProviderFactoryI;
  34 import jalview.urls.api.UrlProviderI;
  35 import jalview.urls.desktop.DesktopUrlProviderFactory;
  36 import jalview.util.MessageManager;
  37 import jalview.util.Platform;
  38 import jalview.util.UrlConstants;
  39 import jalview.ws.sifts.SiftsSettings;
  40
  41 import java.awt.BorderLayout;
  42 import java.awt.Color;
  43 import java.awt.Component;
  44 import java.awt.Dimension;
  45 import java.awt.Font;
  46 import java.awt.event.ActionEvent;
  47 import java.awt.event.ActionListener;
  48 import java.awt.event.MouseEvent;
  49 import java.io.File;
  50 import java.util.ArrayList;
  51 import java.util.List;
  52
  53 import javax.help.HelpSetException;
  54 import javax.swing.JColorChooser;
  55 import javax.swing.JFileChooser;
  56 import javax.swing.JInternalFrame;
  57 import javax.swing.JOptionPane;
  58 import javax.swing.JPanel;
  59 import javax.swing.ListSelectionModel;
  60 import javax.swing.RowFilter;
  61 import javax.swing.RowSorter;
  62 import javax.swing.SortOrder;
  63 import javax.swing.event.DocumentEvent;
  64 import javax.swing.event.DocumentListener;
  65 import javax.swing.event.ListSelectionEvent;
  66 import javax.swing.event.ListSelectionListener;
  67 import javax.swing.table.TableCellRenderer;
  68 import javax.swing.table.TableColumn;
  69 import javax.swing.table.TableModel;
  70 import javax.swing.table.TableRowSorter;
  71
  72 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  73
  74 /**
  75  * DOCUMENT ME!
  76  *
  77  * @author $author$
  78  * @version $Revision$
  79  */
  80 public class Preferences extends GPreferences
  81 {
  82   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  83
  84   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  85
  86   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  87
  88   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  89
  90   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  91
  92   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  93
  94   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  95
  96   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  97
  98   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  99
 100   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 101
 102   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 103
 104   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 105
 106   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 107
 108   private static final int MIN_FONT_SIZE = 1;
 109
 110   private static final int MAX_FONT_SIZE = 30;
 111
 112   /**
 113    * Holds name and link separated with | character. Sequence ID must be
 114    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 115    */
 116   public static UrlProviderI sequenceUrlLinks;
 117
 118   public static UrlLinkTableModel dataModel;
 119
 120   /**
 121    * Holds name and link separated with | character. Sequence IDS and Sequences
 122    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 123    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 124    * for first and second token specified after a pipe character at end |,|.
 125    * (TODO: proper escape for using | to separate ids or sequences
 126    */
 127
 128   public static List<String> groupURLLinks;
 129   static
 130   {
 131     // get links selected to be in the menu (SEQUENCE_LINKS)
 132     // and links entered by the user but not selected (STORED_LINKS)
 133     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 134     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 135     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 136             UrlConstants.DEFAULT_LABEL);
 137
 138     // if both links lists are empty, add the DEFAULT_URL link
 139     // otherwise we assume the default link is in one of the lists
 140     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 141     {
 142       inMenuString = UrlConstants.DEFAULT_STRING;
 143     }
 144     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 145             inMenuString, notInMenuString);
 146     sequenceUrlLinks = factory.createUrlProvider();
 147     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 148
 149     /**
 150      * TODO: reformulate groupURL encoding so two or more can be stored in the
 151      * .properties file as '|' separated strings
 152      */
 153
 154     groupURLLinks = new ArrayList<String>();
 155   }
 156
 157   JInternalFrame frame;
 158
 159   DasSourceBrowser dasSource;
 160
 161   private WsPreferences wsPrefs;
 162
 163   private OptionsParam promptEachTimeOpt = new OptionsParam(
 164           MessageManager.getString("label.prompt_each_time"),
 165           "Prompt each time");
 166
 167   private OptionsParam lineArtOpt = new OptionsParam(
 168           MessageManager.getString("label.lineart"), "Lineart");
 169
 170   private OptionsParam textOpt = new OptionsParam(
 171           MessageManager.getString("action.text"), "Text");
 172
 173   /**
 174    * Creates a new Preferences object.
 175    */
 176   public Preferences()
 177   {
 178     super();
 179     frame = new JInternalFrame();
 180     frame.setContentPane(this);
 181     dasSource = new DasSourceBrowser();
 182     dasTab.add(dasSource, BorderLayout.CENTER);
 183     wsPrefs = new WsPreferences();
 184     wsTab.add(wsPrefs, BorderLayout.CENTER);
 185     int width = 500, height = 450;
 186     new jalview.util.Platform();
 187     if (Platform.isAMac())
 188     {
 189       width = 570;
 190       height = 480;
 191     }
 192
 193     Desktop.addInternalFrame(frame,
 194             MessageManager.getString("label.preferences"), width, height);
 195     frame.setMinimumSize(new Dimension(width, height));
 196
 197     /*
 198      * Set Visual tab defaults
 199      */
 200     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 201     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 202     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 203     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 204
 205     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 206     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 207     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 208     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 209     showUnconserved
 210             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 211     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 212             false));
 213     showGroupConservation.setSelected(Cache.getDefault(
 214             "SHOW_GROUP_CONSERVATION", false));
 215     showConsensHistogram.setSelected(Cache.getDefault(
 216             "SHOW_CONSENSUS_HISTOGRAM", true));
 217     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 218             false));
 219     showNpTooltip.setSelected(Cache
 220             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 221     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 222             true));
 223
 224     String[] fonts = java.awt.GraphicsEnvironment
 225             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 226     for (int i = 0; i < fonts.length; i++)
 227     {
 228       fontNameCB.addItem(fonts[i]);
 229     }
 230
 231     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 232     {
 233       fontSizeCB.addItem(i + "");
 234     }
 235
 236     fontStyleCB.addItem("plain");
 237     fontStyleCB.addItem("bold");
 238     fontStyleCB.addItem("italic");
 239
 240     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 241     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 242     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 243             + ""));
 244
 245     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 246     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 247             false));
 248
 249     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 250
 251     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 252
 253     gapSymbolCB.addItem("-");
 254     gapSymbolCB.addItem(".");
 255
 256     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 257
 258     sortby.addItem("No sort");
 259     sortby.addItem("Id");
 260     sortby.addItem("Pairwise Identity");
 261     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 262
 263     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 264     sortAnnBy
 265             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 266     sortAnnBy
 267             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 268     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 269             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 270                     SequenceAnnotationOrder.NONE.name()));
 271     sortAnnBy.setSelectedItem(savedSort.toString());
 272
 273     sortAutocalc.addItem("Autocalculated first");
 274     sortAutocalc.addItem("Autocalculated last");
 275     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 276     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 277             : sortAutocalc.getItemAt(1));
 278     startupCheckbox
 279             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 280     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 281             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 282                     + "/examples/exampleFile_2_3.jar"));
 283
 284     /*
 285      * Set Colours tab defaults
 286      */
 287     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 288     {
 289       protColour.addItem(ColourSchemeProperty.getColourName(i));
 290       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 291     }
 292     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 293     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 294     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 295     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 296     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 297     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 298             Color.orange));
 299     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 300             Color.red));
 301
 302     /*
 303      * Set Structure tab defaults.
 304      */
 305     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 306     structFromPdb.setSelected(structSelected);
 307     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 308     useRnaView.setEnabled(structSelected);
 309     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 310     addSecondaryStructure.setEnabled(structSelected);
 311     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 312     addTempFactor.setEnabled(structSelected);
 313     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 314             ViewerType.JMOL.name()));
 315     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 316     chimeraPath.addActionListener(new ActionListener()
 317     {
 318       @Override
 319       public void actionPerformed(ActionEvent e)
 320       {
 321         validateChimeraPath();
 322       }
 323     });
 324
 325     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 326     {
 327       siftsMapping.setSelected(true);
 328     }
 329     else
 330     {
 331       nwMapping.setSelected(true);
 332     }
 333
 334     SiftsSettings
 335             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 336
 337     /*
 338      * Set Connections tab defaults
 339      */
 340
 341     // set up sorting
 342     linkUrlTable.setModel(dataModel);
 343     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 344             linkUrlTable.getModel());
 345     linkUrlTable.setRowSorter(sorter);
 346     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 347
 348     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 349     sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(),
 350             SortOrder.DESCENDING));
 351     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 352             SortOrder.DESCENDING));
 353     sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
 354             SortOrder.ASCENDING));
 355
 356     sorter.setSortKeys(sortKeys);
 357     sorter.sort();
 358
 359     // set up filtering
 360     ActionListener onReset;
 361     onReset = new ActionListener()
 362     {
 363       @Override
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         filterTB.setText("");
 367         sorter.setRowFilter(RowFilter.regexFilter(""));
 368       }
 369
 370     };
 371     doReset.addActionListener(onReset);
 372
 373     // filter to display only custom urls
 374     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 375     {
 376       @Override
 377       public boolean include(
 378               Entry<? extends TableModel, ? extends Object> entry)
 379       {
 380         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 381       }
 382     };
 383
 384     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 385             linkUrlTable.getModel());
 386     customSorter.setRowFilter(customUrlFilter);
 387
 388     ActionListener onCustomOnly;
 389     onCustomOnly = new ActionListener()
 390     {
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         filterTB.setText("");
 395         sorter.setRowFilter(customUrlFilter);
 396       }
 397     };
 398     userOnly.addActionListener(onCustomOnly);
 399
 400     filterTB.getDocument().addDocumentListener(new DocumentListener()
 401     {
 402       String caseInsensitiveFlag = "(?i)";
 403
 404       @Override
 405       public void changedUpdate(DocumentEvent e)
 406       {
 407         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 408                 + filterTB.getText()));
 409       }
 410
 411       @Override
 412       public void removeUpdate(DocumentEvent e)
 413       {
 414         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 415                 + filterTB.getText()));
 416       }
 417
 418       @Override
 419       public void insertUpdate(DocumentEvent e)
 420       {
 421         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 422                 + filterTB.getText()));
 423       }
 424     });
 425
 426     // set up list selection functionality
 427     linkUrlTable.getSelectionModel().addListSelectionListener(
 428             new UrlListSelectionHandler());
 429
 430     // set up radio buttons
 431     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 432             .getDefaultColumn();
 433     String onClickName = linkUrlTable.getColumnName(onClickCol);
 434     linkUrlTable.getColumn(onClickName).setCellRenderer(
 435                new RadioButtonRenderer());
 436     linkUrlTable.getColumn(onClickName)
 437             .setCellEditor(new RadioButtonEditor());
 438
 439     // get boolean columns and resize those to min possible
 440     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 441     {
 442       if (linkUrlTable.getModel().getColumnClass(column)
 443               .equals(Boolean.class))
 444       {
 445         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 446                 column);
 447         int preferredWidth = tableColumn.getMinWidth();
 448
 449         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 450                 column);
 451         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 452         int cwidth = c.getPreferredSize().width
 453                 + linkUrlTable.getIntercellSpacing().width;
 454         preferredWidth = Math.max(preferredWidth, cwidth);
 455
 456         tableColumn.setPreferredWidth(preferredWidth);
 457       }
 458     }
 459
 460     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 461     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 462     proxyServerTB.setEnabled(useProxy.isSelected());
 463     proxyPortTB.setEnabled(useProxy.isSelected());
 464     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 465     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 466
 467     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 468
 469     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 470     // note antisense here: default is true
 471     questionnaire
 472             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 473     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 474
 475     /*
 476      * Set Output tab defaults
 477      */
 478     epsRendering.addItem(promptEachTimeOpt);
 479     epsRendering.addItem(lineArtOpt);
 480     epsRendering.addItem(textOpt);
 481     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 482             "Prompt each time");
 483     if (defaultEPS.equalsIgnoreCase("Text"))
 484     {
 485       epsRendering.setSelectedItem(textOpt);
 486     }
 487     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 488     {
 489       epsRendering.setSelectedItem(lineArtOpt);
 490     }
 491     else
 492     {
 493       epsRendering.setSelectedItem(promptEachTimeOpt);
 494     }
 495     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 496     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 497     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 498     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 499     userIdWidth.setText(wi == null ? "" : wi.toString());
 500     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 501     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 502     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 503     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 504     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 505     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 506     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 507     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 508     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 509             true));
 510
 511     /*
 512      * Set Editing tab defaults
 513      */
 514     autoCalculateConsCheck.setSelected(Cache.getDefault(
 515             "AUTO_CALC_CONSENSUS", true));
 516     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 517     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 518
 519     annotations_actionPerformed(null); // update the display of the annotation
 520                                        // settings
 521   }
 522
 523   /**
 524    * Save user selections on the Preferences tabs to the Cache and write out to
 525    * file.
 526    *
 527    * @param e
 528    */
 529   @Override
 530   public void ok_actionPerformed(ActionEvent e)
 531   {
 532     if (!validateSettings())
 533     {
 534       return;
 535     }
 536
 537     /*
 538      * Save Visual settings
 539      */
 540     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 541             Boolean.toString(seqLimit.isSelected()));
 542     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 543             Boolean.toString(rightAlign.isSelected()));
 544     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 545             Boolean.toString(fullScreen.isSelected()));
 546     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 547             Boolean.toString(openoverv.isSelected()));
 548     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 549             Boolean.toString(annotations.isSelected()));
 550     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 551             Boolean.toString(conservation.isSelected()));
 552     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 553             Boolean.toString(quality.isSelected()));
 554     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 555             Boolean.toString(identity.isSelected()));
 556
 557     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 558             .getSelectedItem().toString());
 559
 560     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 561             .getSelectedItem().toString());
 562     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 563             .getSelectedItem().toString());
 564     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 565             .getSelectedItem().toString());
 566
 567     Cache.applicationProperties.setProperty("ID_ITALICS",
 568             Boolean.toString(idItalics.isSelected()));
 569     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 570             Boolean.toString(showUnconserved.isSelected()));
 571     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 572             Boolean.toString(showGroupConsensus.isSelected()));
 573     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 574             Boolean.toString(showGroupConservation.isSelected()));
 575     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 576             Boolean.toString(showConsensHistogram.isSelected()));
 577     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 578             Boolean.toString(showConsensLogo.isSelected()));
 579     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 580             Boolean.toString(smoothFont.isSelected()));
 581     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 582             Boolean.toString(scaleProteinToCdna.isSelected()));
 583     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 584             Boolean.toString(showNpTooltip.isSelected()));
 585     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 586             Boolean.toString(showDbRefTooltip.isSelected()));
 587
 588     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 589             Boolean.toString(wrap.isSelected()));
 590
 591     Cache.applicationProperties.setProperty("STARTUP_FILE",
 592             startupFileTextfield.getText());
 593     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 594             Boolean.toString(startupCheckbox.isSelected()));
 595
 596     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 597             .getSelectedItem().toString());
 598
 599     // convert description of sort order to enum name for save
 600     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 601             .forDescription(sortAnnBy.getSelectedItem().toString());
 602     if (annSortOrder != null)
 603     {
 604       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 605               annSortOrder.name());
 606     }
 607
 608     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 609     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 610             .valueOf(showAutocalcFirst).toString());
 611
 612     /*
 613      * Save Colours settings
 614      */
 615     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 616             .getSelectedItem().toString());
 617     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 618             .getSelectedItem().toString());
 619     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 620             minColour.getBackground());
 621     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 622             maxColour.getBackground());
 623
 624     /*
 625      * Save Structure settings
 626      */
 627     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 628             Boolean.toString(addTempFactor.isSelected()));
 629     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 630             Boolean.toString(addSecondaryStructure.isSelected()));
 631     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 632             Boolean.toString(useRnaView.isSelected()));
 633     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 634             Boolean.toString(structFromPdb.isSelected()));
 635     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 636             .getSelectedItem().toString());
 637     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 638     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 639             Boolean.toString(siftsMapping.isSelected()));
 640     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 641
 642     /*
 643      * Save Output settings
 644      */
 645     Cache.applicationProperties.setProperty("EPS_RENDERING",
 646             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 647
 648     /*
 649      * Save Connections settings
 650      */
 651     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 652
 653     jalview.util.BrowserLauncher.resetBrowser();
 654
 655     // save user-defined and selected links
 656     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 657     if (menuLinks.isEmpty())
 658     {
 659       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 660     }
 661     else
 662     {
 663       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 664               menuLinks.toString());
 665     }
 666
 667     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 668     if (nonMenuLinks.isEmpty())
 669     {
 670       Cache.applicationProperties.remove("STORED_LINKS");
 671     }
 672     else
 673     {
 674       Cache.applicationProperties.setProperty("STORED_LINKS",
 675               nonMenuLinks.toString());
 676     }
 677
 678     Cache.applicationProperties.setProperty("DEFAULT_URL",
 679             sequenceUrlLinks.getDefaultUrlId());
 680
 681     Cache.applicationProperties.setProperty("USE_PROXY",
 682             Boolean.toString(useProxy.isSelected()));
 683
 684     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 685
 686     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 687
 688     if (useProxy.isSelected())
 689     {
 690       System.setProperty("http.proxyHost", proxyServerTB.getText());
 691       System.setProperty("http.proxyPort", proxyPortTB.getText());
 692     }
 693     else
 694     {
 695       System.setProperty("http.proxyHost", "");
 696       System.setProperty("http.proxyPort", "");
 697     }
 698     Cache.setProperty("VERSION_CHECK",
 699             Boolean.toString(versioncheck.isSelected()));
 700     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 701     {
 702       // default is false - we only set this if the user has actively agreed
 703       Cache.setProperty("USAGESTATS",
 704               Boolean.toString(usagestats.isSelected()));
 705     }
 706     if (!questionnaire.isSelected())
 707     {
 708       Cache.setProperty("NOQUESTIONNAIRES", "true");
 709     }
 710     else
 711     {
 712       // special - made easy to edit a property file to disable questionnaires
 713       // by just adding the given line
 714       Cache.removeProperty("NOQUESTIONNAIRES");
 715     }
 716
 717     /*
 718      * Save Output settings
 719      */
 720     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 721             Boolean.toString(blcjv.isSelected()));
 722     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 723             Boolean.toString(clustaljv.isSelected()));
 724     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 725             Boolean.toString(fastajv.isSelected()));
 726     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 727             Boolean.toString(msfjv.isSelected()));
 728     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 729             Boolean.toString(pfamjv.isSelected()));
 730     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 731             Boolean.toString(pileupjv.isSelected()));
 732     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 733             Boolean.toString(pirjv.isSelected()));
 734     Cache.applicationProperties.setProperty("PIR_MODELLER",
 735             Boolean.toString(modellerOutput.isSelected()));
 736     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 737             Boolean.toString(embbedBioJSON.isSelected()));
 738     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 739
 740     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 741             Boolean.toString(autoIdWidth.isSelected()));
 742     userIdWidth_actionPerformed();
 743     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 744             userIdWidth.getText());
 745
 746     /*
 747      * Save Editing settings
 748      */
 749     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 750             Boolean.toString(autoCalculateConsCheck.isSelected()));
 751     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 752             Boolean.toString(sortByTree.isSelected()));
 753     Cache.applicationProperties.setProperty("PAD_GAPS",
 754             Boolean.toString(padGaps.isSelected()));
 755
 756     dasSource.saveProperties(Cache.applicationProperties);
 757     wsPrefs.updateAndRefreshWsMenuConfig(false);
 758     Cache.saveProperties();
 759     Desktop.instance.doConfigureStructurePrefs();
 760     try
 761     {
 762       frame.setClosed(true);
 763     } catch (Exception ex)
 764     {
 765     }
 766   }
 767
 768   /**
 769    * Do any necessary validation before saving settings. Return focus to the
 770    * first tab which fails validation.
 771    *
 772    * @return
 773    */
 774   private boolean validateSettings()
 775   {
 776     if (!validateStructure())
 777     {
 778       structureTab.requestFocusInWindow();
 779       return false;
 780     }
 781     return true;
 782   }
 783
 784   @Override
 785   protected boolean validateStructure()
 786   {
 787     return validateChimeraPath();
 788
 789   }
 790
 791   /**
 792    * DOCUMENT ME!
 793    */
 794   @Override
 795   public void startupFileTextfield_mouseClicked()
 796   {
 797     JalviewFileChooser chooser = new JalviewFileChooser(
 798             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 799                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 800                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 801                 "PIR", "BLC", "Jalview" },
 802             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 803     chooser.setFileView(new JalviewFileView());
 804     chooser.setDialogTitle(MessageManager
 805             .getString("label.select_startup_file"));
 806
 807     int value = chooser.showOpenDialog(this);
 808
 809     if (value == JalviewFileChooser.APPROVE_OPTION)
 810     {
 811       jalview.bin.Cache.applicationProperties.setProperty(
 812               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 813       startupFileTextfield.setText(chooser.getSelectedFile()
 814               .getAbsolutePath());
 815     }
 816   }
 817
 818   /**
 819    * DOCUMENT ME!
 820    *
 821    * @param e
 822    *          DOCUMENT ME!
 823    */
 824   @Override
 825   public void cancel_actionPerformed(ActionEvent e)
 826   {
 827     try
 828     {
 829       wsPrefs.updateWsMenuConfig(true);
 830       wsPrefs.refreshWs_actionPerformed(e);
 831       frame.setClosed(true);
 832     } catch (Exception ex)
 833     {
 834     }
 835   }
 836
 837   /**
 838    * DOCUMENT ME!
 839    *
 840    * @param e
 841    *          DOCUMENT ME!
 842    */
 843   @Override
 844   public void annotations_actionPerformed(ActionEvent e)
 845   {
 846     conservation.setEnabled(annotations.isSelected());
 847     quality.setEnabled(annotations.isSelected());
 848     identity.setEnabled(annotations.isSelected());
 849     showGroupConsensus.setEnabled(annotations.isSelected());
 850     showGroupConservation.setEnabled(annotations.isSelected());
 851     showConsensHistogram.setEnabled(annotations.isSelected()
 852             && (identity.isSelected() || showGroupConsensus.isSelected()));
 853     showConsensLogo.setEnabled(annotations.isSelected()
 854             && (identity.isSelected() || showGroupConsensus.isSelected()));
 855   }
 856
 857   @Override
 858   public void newLink_actionPerformed(ActionEvent e)
 859   {
 860     GSequenceLink link = new GSequenceLink();
 861     boolean valid = false;
 862     while (!valid)
 863     {
 864       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 865               MessageManager.getString("label.new_sequence_url_link"),
 866               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 867       {
 868         if (link.checkValid())
 869         {
 870           if (((UrlLinkTableModel) linkUrlTable.getModel())
 871                   .isUniqueName(link.getName()))
 872           {
 873             ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 874                     link.getName(), link.getURL());
 875             valid = true;
 876           }
 877           else
 878           {
 879             link.notifyDuplicate();
 880             continue;
 881           }
 882         }
 883       }
 884       else
 885       {
 886         break;
 887       }
 888     }
 889   }
 890
 891   @Override
 892   public void editLink_actionPerformed(ActionEvent e)
 893   {
 894     GSequenceLink link = new GSequenceLink();
 895
 896     int index = linkUrlTable.getSelectedRow();
 897     if (index == -1)
 898     {
 899       // button no longer enabled if row is not selected
 900       Cache.log.debug("Edit with no row selected in linkUrlTable");
 901       return;
 902     }
 903
 904     link.setName(linkUrlTable.getValueAt(index, 0).toString());
 905     link.setURL(linkUrlTable.getValueAt(index, 1).toString());
 906
 907     boolean valid = false;
 908     while (!valid)
 909     {
 910       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 911               MessageManager.getString("label.edit_sequence_url_link"),
 912               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 913       {
 914         if (link.checkValid())
 915         {
 916           if (((UrlLinkTableModel) linkUrlTable.getModel())
 917                   .isUniqueName(link.getName()))
 918           {
 919             linkUrlTable.setValueAt(link.getName(), index, 0);
 920             linkUrlTable.setValueAt(link.getURL(), index, 1);
 921             valid = true;
 922           }
 923           else
 924           {
 925             link.notifyDuplicate();
 926             continue;
 927           }
 928         }
 929       }
 930       else
 931       {
 932         break;
 933       }
 934     }
 935   }
 936
 937   @Override
 938   public void deleteLink_actionPerformed(ActionEvent e)
 939   {
 940     int index = linkUrlTable.getSelectedRow();
 941     int modelIndex = -1;
 942     if (index == -1)
 943     {
 944       // button no longer enabled if row is not selected
 945       Cache.log.debug("Delete with no row selected in linkUrlTable");
 946       return;
 947     }
 948     else
 949     {
 950       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 951     }
 952
 953     // make sure we use the model index to delete, and not the table index
 954     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 955   }
 956
 957
 958   @Override
 959   public void defaultBrowser_mouseClicked(MouseEvent e)
 960   {
 961     JFileChooser chooser = new JFileChooser(".");
 962     chooser.setDialogTitle(MessageManager
 963             .getString("label.select_default_browser"));
 964
 965     int value = chooser.showOpenDialog(this);
 966
 967     if (value == JFileChooser.APPROVE_OPTION)
 968     {
 969       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 970     }
 971
 972   }
 973
 974   /*
 975    * (non-Javadoc)
 976    *
 977    * @see
 978    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 979    * .ActionEvent)
 980    */
 981   @Override
 982   protected void showunconserved_actionPerformed(ActionEvent e)
 983   {
 984     // TODO Auto-generated method stub
 985     super.showunconserved_actionPerformed(e);
 986   }
 987
 988   public static List<String> getGroupURLLinks()
 989   {
 990     return groupURLLinks;
 991   }
 992
 993   @Override
 994   public void minColour_actionPerformed(JPanel panel)
 995   {
 996     Color col = JColorChooser.showDialog(this,
 997             MessageManager.getString("label.select_colour_minimum_value"),
 998             minColour.getBackground());
 999     if (col != null)
1000     {
1001       panel.setBackground(col);
1002     }
1003     panel.repaint();
1004   }
1005
1006   @Override
1007   public void maxColour_actionPerformed(JPanel panel)
1008   {
1009     Color col = JColorChooser.showDialog(this,
1010             MessageManager.getString("label.select_colour_maximum_value"),
1011             maxColour.getBackground());
1012     if (col != null)
1013     {
1014       panel.setBackground(col);
1015     }
1016     panel.repaint();
1017   }
1018
1019   @Override
1020   protected void userIdWidth_actionPerformed()
1021   {
1022     try
1023     {
1024       String val = userIdWidth.getText().trim();
1025       if (val.length() > 0)
1026       {
1027         Integer iw = Integer.parseInt(val);
1028         if (iw.intValue() < 12)
1029         {
1030           throw new NumberFormatException();
1031         }
1032         userIdWidth.setText(iw.toString());
1033       }
1034     } catch (NumberFormatException x)
1035     {
1036       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1037               .getString("warn.user_defined_width_requirements"),
1038               MessageManager.getString("label.invalid_id_column_width"),
1039               JOptionPane.WARNING_MESSAGE);
1040       userIdWidth.setText("");
1041     }
1042   }
1043
1044   @Override
1045   protected void autoIdWidth_actionPerformed()
1046   {
1047     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1048     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1049   }
1050
1051   /**
1052    * Returns true if chimera path is to a valid executable, else show an error
1053    * dialog.
1054    */
1055   private boolean validateChimeraPath()
1056   {
1057     if (chimeraPath.getText().trim().length() > 0)
1058     {
1059       File f = new File(chimeraPath.getText());
1060       if (!f.canExecute())
1061       {
1062         JOptionPane.showInternalMessageDialog(Desktop.desktop,
1063                 MessageManager.getString("label.invalid_chimera_path"),
1064                 MessageManager.getString("label.invalid_name"),
1065                 JOptionPane.ERROR_MESSAGE);
1066         return false;
1067       }
1068     }
1069     return true;
1070   }
1071
1072   /**
1073    * If Chimera is selected, check it can be found on default or user-specified
1074    * path, if not show a warning/help dialog.
1075    */
1076   @Override
1077   protected void structureViewer_actionPerformed(String selectedItem)
1078   {
1079     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1080     {
1081       return;
1082     }
1083     boolean found = false;
1084
1085     /*
1086      * Try user-specified and standard paths for Chimera executable.
1087      */
1088     List<String> paths = StructureManager.getChimeraPaths();
1089     paths.add(0, chimeraPath.getText());
1090     for (String path : paths)
1091     {
1092       if (new File(path.trim()).canExecute())
1093       {
1094         found = true;
1095         break;
1096       }
1097     }
1098     if (!found)
1099     {
1100       String[] options = { "OK", "Help" };
1101       int showHelp = JOptionPane.showInternalOptionDialog(
1102               Desktop.desktop,
1103               JvSwingUtils.wrapTooltip(true,
1104                       MessageManager.getString("label.chimera_missing")),
1105               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
1106               null, options, options[0]);
1107       if (showHelp == JOptionPane.NO_OPTION)
1108       {
1109         try
1110         {
1111           Help.showHelpWindow(HelpId.StructureViewer);
1112         } catch (HelpSetException e)
1113         {
1114           e.printStackTrace();
1115         }
1116       }
1117     }
1118   }
1119
1120   public class OptionsParam
1121   {
1122     private String name;
1123
1124     private String code;
1125
1126     public OptionsParam(String name, String code)
1127     {
1128       this.name = name;
1129       this.code = code;
1130     }
1131
1132     public String getName()
1133     {
1134       return name;
1135     }
1136
1137     public void setName(String name)
1138     {
1139       this.name = name;
1140     }
1141
1142     public String getCode()
1143     {
1144       return code;
1145     }
1146
1147     public void setCode(String code)
1148     {
1149       this.code = code;
1150     }
1151
1152     @Override
1153     public String toString()
1154     {
1155       return name;
1156     }
1157
1158     @Override
1159     public boolean equals(Object that)
1160     {
1161       if (!(that instanceof OptionsParam))
1162       {
1163         return false;
1164       }
1165       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1166     }
1167
1168     @Override
1169     public int hashCode()
1170     {
1171       return name.hashCode() + code.hashCode();
1172     }
1173   }
1174
1175   private class UrlListSelectionHandler implements ListSelectionListener
1176   {
1177
1178     @Override
1179     public void valueChanged(ListSelectionEvent e)
1180     {
1181       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1182
1183       int index = lsm.getMinSelectionIndex();
1184       if (index == -1)
1185       {
1186         // no selection, so disable delete/edit buttons
1187         editLink.setEnabled(false);
1188         deleteLink.setEnabled(false);
1189         return;
1190       }
1191       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1192
1193       // enable/disable edit and delete link buttons
1194       if (((UrlLinkTableModel) linkUrlTable.getModel())
1195               .isRowDeletable(modelIndex))
1196       {
1197         deleteLink.setEnabled(true);
1198       }
1199       else
1200       {
1201         deleteLink.setEnabled(false);
1202       }
1203
1204       if (((UrlLinkTableModel) linkUrlTable.getModel())
1205               .isRowEditable(modelIndex))
1206       {
1207         editLink.setEnabled(true);
1208       }
1209       else
1210       {
1211         editLink.setEnabled(false);
1212       }
1213     }
1214 }
1215 }