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