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