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 inMenuString = Cache.getDefault("SEQUENCE_LINKS",
 132             UrlConstants.DEFAULT_STRING);
 133     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 134     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 135             UrlConstants.DEFAULT_LABEL);
 136     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 137             inMenuString, notInMenuString);
 138     sequenceUrlLinks = factory.createUrlProvider();
 139     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 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 menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 642     if (menuLinks.isEmpty())
 643     {
 644       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 645     }
 646     else
 647     {
 648       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 649               menuLinks.toString());
 650     }
 651
 652     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 653     if (nonMenuLinks.isEmpty())
 654     {
 655       Cache.applicationProperties.remove("STORED_LINKS");
 656     }
 657     else
 658     {
 659       Cache.applicationProperties.setProperty("STORED_LINKS",
 660               nonMenuLinks.toString());
 661     }
 662
 663     Cache.applicationProperties.setProperty("DEFAULT_URL",
 664             sequenceUrlLinks.getDefaultUrlId());
 665
 666     Cache.applicationProperties.setProperty("USE_PROXY",
 667             Boolean.toString(useProxy.isSelected()));
 668
 669     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 670
 671     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 672
 673     if (useProxy.isSelected())
 674     {
 675       System.setProperty("http.proxyHost", proxyServerTB.getText());
 676       System.setProperty("http.proxyPort", proxyPortTB.getText());
 677     }
 678     else
 679     {
 680       System.setProperty("http.proxyHost", "");
 681       System.setProperty("http.proxyPort", "");
 682     }
 683     Cache.setProperty("VERSION_CHECK",
 684             Boolean.toString(versioncheck.isSelected()));
 685     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 686     {
 687       // default is false - we only set this if the user has actively agreed
 688       Cache.setProperty("USAGESTATS",
 689               Boolean.toString(usagestats.isSelected()));
 690     }
 691     if (!questionnaire.isSelected())
 692     {
 693       Cache.setProperty("NOQUESTIONNAIRES", "true");
 694     }
 695     else
 696     {
 697       // special - made easy to edit a property file to disable questionnaires
 698       // by just adding the given line
 699       Cache.removeProperty("NOQUESTIONNAIRES");
 700     }
 701
 702     /*
 703      * Save Output settings
 704      */
 705     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 706             Boolean.toString(blcjv.isSelected()));
 707     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 708             Boolean.toString(clustaljv.isSelected()));
 709     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 710             Boolean.toString(fastajv.isSelected()));
 711     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 712             Boolean.toString(msfjv.isSelected()));
 713     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 714             Boolean.toString(pfamjv.isSelected()));
 715     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 716             Boolean.toString(pileupjv.isSelected()));
 717     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 718             Boolean.toString(pirjv.isSelected()));
 719     Cache.applicationProperties.setProperty("PIR_MODELLER",
 720             Boolean.toString(modellerOutput.isSelected()));
 721     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 722             Boolean.toString(embbedBioJSON.isSelected()));
 723     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 724
 725     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 726             Boolean.toString(autoIdWidth.isSelected()));
 727     userIdWidth_actionPerformed();
 728     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 729             userIdWidth.getText());
 730
 731     /*
 732      * Save Editing settings
 733      */
 734     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 735             Boolean.toString(autoCalculateConsCheck.isSelected()));
 736     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 737             Boolean.toString(sortByTree.isSelected()));
 738     Cache.applicationProperties.setProperty("PAD_GAPS",
 739             Boolean.toString(padGaps.isSelected()));
 740
 741     dasSource.saveProperties(Cache.applicationProperties);
 742     wsPrefs.updateAndRefreshWsMenuConfig(false);
 743     Cache.saveProperties();
 744     Desktop.instance.doConfigureStructurePrefs();
 745     try
 746     {
 747       frame.setClosed(true);
 748     } catch (Exception ex)
 749     {
 750     }
 751   }
 752
 753   /**
 754    * Do any necessary validation before saving settings. Return focus to the
 755    * first tab which fails validation.
 756    *
 757    * @return
 758    */
 759   private boolean validateSettings()
 760   {
 761     if (!validateStructure())
 762     {
 763       structureTab.requestFocusInWindow();
 764       return false;
 765     }
 766     return true;
 767   }
 768
 769   @Override
 770   protected boolean validateStructure()
 771   {
 772     return validateChimeraPath();
 773
 774   }
 775
 776   /**
 777    * DOCUMENT ME!
 778    */
 779   @Override
 780   public void startupFileTextfield_mouseClicked()
 781   {
 782     JalviewFileChooser chooser = new JalviewFileChooser(
 783             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 784                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 785                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 786                 "PIR", "BLC", "Jalview" },
 787             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 788     chooser.setFileView(new JalviewFileView());
 789     chooser.setDialogTitle(MessageManager
 790             .getString("label.select_startup_file"));
 791
 792     int value = chooser.showOpenDialog(this);
 793
 794     if (value == JalviewFileChooser.APPROVE_OPTION)
 795     {
 796       jalview.bin.Cache.applicationProperties.setProperty(
 797               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 798       startupFileTextfield.setText(chooser.getSelectedFile()
 799               .getAbsolutePath());
 800     }
 801   }
 802
 803   /**
 804    * DOCUMENT ME!
 805    *
 806    * @param e
 807    *          DOCUMENT ME!
 808    */
 809   @Override
 810   public void cancel_actionPerformed(ActionEvent e)
 811   {
 812     try
 813     {
 814       wsPrefs.updateWsMenuConfig(true);
 815       wsPrefs.refreshWs_actionPerformed(e);
 816       frame.setClosed(true);
 817     } catch (Exception ex)
 818     {
 819     }
 820   }
 821
 822   /**
 823    * DOCUMENT ME!
 824    *
 825    * @param e
 826    *          DOCUMENT ME!
 827    */
 828   @Override
 829   public void annotations_actionPerformed(ActionEvent e)
 830   {
 831     conservation.setEnabled(annotations.isSelected());
 832     quality.setEnabled(annotations.isSelected());
 833     identity.setEnabled(annotations.isSelected());
 834     showGroupConsensus.setEnabled(annotations.isSelected());
 835     showGroupConservation.setEnabled(annotations.isSelected());
 836     showConsensHistogram.setEnabled(annotations.isSelected()
 837             && (identity.isSelected() || showGroupConsensus.isSelected()));
 838     showConsensLogo.setEnabled(annotations.isSelected()
 839             && (identity.isSelected() || showGroupConsensus.isSelected()));
 840   }
 841
 842   @Override
 843   public void newLink_actionPerformed(ActionEvent e)
 844   {
 845     GSequenceLink link = new GSequenceLink();
 846     boolean valid = false;
 847     while (!valid)
 848     {
 849       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 850               MessageManager.getString("label.new_sequence_url_link"),
 851               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 852       {
 853         if (link.checkValid())
 854         {
 855           ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 856                   link.getName(), link.getURL());
 857           valid = true;
 858         }
 859       }
 860       else
 861       {
 862         break;
 863       }
 864     }
 865   }
 866
 867   @Override
 868   public void editLink_actionPerformed(ActionEvent e)
 869   {
 870     GSequenceLink link = new GSequenceLink();
 871
 872     int index = linkUrlTable.getSelectedRow();
 873     if (index == -1)
 874     {
 875       // no row was selected
 876       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 877               MessageManager.getString("label.no_link_selected"),
 878               MessageManager.getString("label.no_link_selected"),
 879               JOptionPane.WARNING_MESSAGE);
 880       return;
 881     }
 882
 883     link.setName(linkUrlTable.getValueAt(index, 0).toString());
 884     link.setURL(linkUrlTable.getValueAt(index, 1).toString());
 885
 886     boolean valid = false;
 887     while (!valid)
 888     {
 889       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 890               MessageManager.getString("label.new_sequence_url_link"),
 891               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 892       {
 893         if (link.checkValid())
 894         {
 895           linkUrlTable.setValueAt(link.getName(), index, 0);
 896           linkUrlTable.setValueAt(link.getURL(), index, 1);
 897           valid = true;
 898         }
 899       }
 900       else
 901       {
 902         break;
 903       }
 904     }
 905   }
 906
 907   @Override
 908   public void deleteLink_actionPerformed(ActionEvent e)
 909   {
 910     int index = linkUrlTable.getSelectedRow();
 911     int modelIndex = -1;
 912     if (index == -1)
 913     {
 914       // no row is selected
 915       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 916               MessageManager.getString("label.no_link_selected"),
 917               MessageManager.getString("label.no_link_selected"),
 918               JOptionPane.WARNING_MESSAGE);
 919       return;
 920     }
 921     else
 922     {
 923       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 924     }
 925
 926     // make sure we use the model index to delete, and not the table index
 927     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 928   }
 929
 930
 931   @Override
 932   public void defaultBrowser_mouseClicked(MouseEvent e)
 933   {
 934     JFileChooser chooser = new JFileChooser(".");
 935     chooser.setDialogTitle(MessageManager
 936             .getString("label.select_default_browser"));
 937
 938     int value = chooser.showOpenDialog(this);
 939
 940     if (value == JFileChooser.APPROVE_OPTION)
 941     {
 942       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 943     }
 944
 945   }
 946
 947   /*
 948    * (non-Javadoc)
 949    *
 950    * @see
 951    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 952    * .ActionEvent)
 953    */
 954   @Override
 955   protected void showunconserved_actionPerformed(ActionEvent e)
 956   {
 957     // TODO Auto-generated method stub
 958     super.showunconserved_actionPerformed(e);
 959   }
 960
 961   public static List<String> getGroupURLLinks()
 962   {
 963     return groupURLLinks;
 964   }
 965
 966   @Override
 967   public void minColour_actionPerformed(JPanel panel)
 968   {
 969     Color col = JColorChooser.showDialog(this,
 970             MessageManager.getString("label.select_colour_minimum_value"),
 971             minColour.getBackground());
 972     if (col != null)
 973     {
 974       panel.setBackground(col);
 975     }
 976     panel.repaint();
 977   }
 978
 979   @Override
 980   public void maxColour_actionPerformed(JPanel panel)
 981   {
 982     Color col = JColorChooser.showDialog(this,
 983             MessageManager.getString("label.select_colour_maximum_value"),
 984             maxColour.getBackground());
 985     if (col != null)
 986     {
 987       panel.setBackground(col);
 988     }
 989     panel.repaint();
 990   }
 991
 992   @Override
 993   protected void userIdWidth_actionPerformed()
 994   {
 995     try
 996     {
 997       String val = userIdWidth.getText().trim();
 998       if (val.length() > 0)
 999       {
1000         Integer iw = Integer.parseInt(val);
1001         if (iw.intValue() < 12)
1002         {
1003           throw new NumberFormatException();
1004         }
1005         userIdWidth.setText(iw.toString());
1006       }
1007     } catch (NumberFormatException x)
1008     {
1009       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1010               .getString("warn.user_defined_width_requirements"),
1011               MessageManager.getString("label.invalid_id_column_width"),
1012               JOptionPane.WARNING_MESSAGE);
1013       userIdWidth.setText("");
1014     }
1015   }
1016
1017   @Override
1018   protected void autoIdWidth_actionPerformed()
1019   {
1020     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1021     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1022   }
1023
1024   /**
1025    * Returns true if chimera path is to a valid executable, else show an error
1026    * dialog.
1027    */
1028   private boolean validateChimeraPath()
1029   {
1030     if (chimeraPath.getText().trim().length() > 0)
1031     {
1032       File f = new File(chimeraPath.getText());
1033       if (!f.canExecute())
1034       {
1035         JOptionPane.showInternalMessageDialog(Desktop.desktop,
1036                 MessageManager.getString("label.invalid_chimera_path"),
1037                 MessageManager.getString("label.invalid_name"),
1038                 JOptionPane.ERROR_MESSAGE);
1039         return false;
1040       }
1041     }
1042     return true;
1043   }
1044
1045   /**
1046    * If Chimera is selected, check it can be found on default or user-specified
1047    * path, if not show a warning/help dialog.
1048    */
1049   @Override
1050   protected void structureViewer_actionPerformed(String selectedItem)
1051   {
1052     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1053     {
1054       return;
1055     }
1056     boolean found = false;
1057
1058     /*
1059      * Try user-specified and standard paths for Chimera executable.
1060      */
1061     List<String> paths = StructureManager.getChimeraPaths();
1062     paths.add(0, chimeraPath.getText());
1063     for (String path : paths)
1064     {
1065       if (new File(path.trim()).canExecute())
1066       {
1067         found = true;
1068         break;
1069       }
1070     }
1071     if (!found)
1072     {
1073       String[] options = { "OK", "Help" };
1074       int showHelp = JOptionPane.showInternalOptionDialog(
1075               Desktop.desktop,
1076               JvSwingUtils.wrapTooltip(true,
1077                       MessageManager.getString("label.chimera_missing")),
1078               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
1079               null, options, options[0]);
1080       if (showHelp == JOptionPane.NO_OPTION)
1081       {
1082         try
1083         {
1084           Help.showHelpWindow(HelpId.StructureViewer);
1085         } catch (HelpSetException e)
1086         {
1087           e.printStackTrace();
1088         }
1089       }
1090     }
1091   }
1092
1093   public class OptionsParam
1094   {
1095     private String name;
1096
1097     private String code;
1098
1099     public OptionsParam(String name, String code)
1100     {
1101       this.name = name;
1102       this.code = code;
1103     }
1104
1105     public String getName()
1106     {
1107       return name;
1108     }
1109
1110     public void setName(String name)
1111     {
1112       this.name = name;
1113     }
1114
1115     public String getCode()
1116     {
1117       return code;
1118     }
1119
1120     public void setCode(String code)
1121     {
1122       this.code = code;
1123     }
1124
1125     @Override
1126     public String toString()
1127     {
1128       return name;
1129     }
1130
1131     @Override
1132     public boolean equals(Object that)
1133     {
1134       if (!(that instanceof OptionsParam))
1135       {
1136         return false;
1137       }
1138       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1139     }
1140
1141     @Override
1142     public int hashCode()
1143     {
1144       return name.hashCode() + code.hashCode();
1145     }
1146   }
1147
1148   private class UrlListSelectionHandler implements ListSelectionListener
1149   {
1150
1151     @Override
1152     public void valueChanged(ListSelectionEvent e)
1153     {
1154       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1155
1156       int index = lsm.getMinSelectionIndex();
1157       if (index == -1)
1158       {
1159         // no selection, so disable delete/edit buttons
1160         editLink.setEnabled(false);
1161         deleteLink.setEnabled(false);
1162         return;
1163       }
1164       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1165
1166       // determine if the new selection is a custom url or not
1167       if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable
1168 .getModel()
1169               .getValueAt(modelIndex, 4))) // KM TODO do this better
1170       {
1171         // entry is not a user-defined url and so should not be edited
1172         // disable edit and delete buttons
1173         deleteLink.setEnabled(false);
1174         editLink.setEnabled(false);
1175       }
1176       else
1177       {
1178         deleteLink.setEnabled(true);
1179         editLink.setEnabled(true);
1180       }
1181
1182       // BUT it's the default url, don't allow deletion
1183       if ((boolean) linkUrlTable.getValueAt(index, 3))
1184       {
1185         deleteLink.setEnabled(false);
1186       }
1187     }
1188 }
1189 }