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