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