src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.FileFormatI;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeProperty;
  33 import jalview.urls.UrlLinkTableModel;
  34 import jalview.urls.api.UrlProviderFactoryI;
  35 import jalview.urls.api.UrlProviderI;
  36 import jalview.urls.desktop.DesktopUrlProviderFactory;
  37 import jalview.util.MessageManager;
  38 import jalview.util.Platform;
  39 import jalview.util.UrlConstants;
  40 import jalview.ws.sifts.SiftsSettings;
  41
  42 import java.awt.BorderLayout;
  43 import java.awt.Color;
  44 import java.awt.Component;
  45 import java.awt.Dimension;
  46 import java.awt.Font;
  47 import java.awt.event.ActionEvent;
  48 import java.awt.event.ActionListener;
  49 import java.awt.event.MouseEvent;
  50 import java.io.File;
  51 import java.util.ArrayList;
  52 import java.util.List;
  53
  54 import javax.help.HelpSetException;
  55 import javax.swing.JColorChooser;
  56 import javax.swing.JFileChooser;
  57 import javax.swing.JInternalFrame;
  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.getPrimaryColumn(),
 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         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 381       }
 382     };
 383
 384     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 385             linkUrlTable.getModel());
 386     customSorter.setRowFilter(customUrlFilter);
 387
 388     ActionListener onCustomOnly;
 389     onCustomOnly = new ActionListener()
 390     {
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         filterTB.setText("");
 395         sorter.setRowFilter(customUrlFilter);
 396       }
 397     };
 398     userOnly.addActionListener(onCustomOnly);
 399
 400     filterTB.getDocument().addDocumentListener(new DocumentListener()
 401     {
 402       String caseInsensitiveFlag = "(?i)";
 403
 404       @Override
 405       public void changedUpdate(DocumentEvent e)
 406       {
 407         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 408                 + filterTB.getText()));
 409       }
 410
 411       @Override
 412       public void removeUpdate(DocumentEvent e)
 413       {
 414         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 415                 + filterTB.getText()));
 416       }
 417
 418       @Override
 419       public void insertUpdate(DocumentEvent e)
 420       {
 421         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 422                 + filterTB.getText()));
 423       }
 424     });
 425
 426     // set up list selection functionality
 427     linkUrlTable.getSelectionModel().addListSelectionListener(
 428             new UrlListSelectionHandler());
 429
 430     // set up radio buttons
 431     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 432             .getPrimaryColumn();
 433     String onClickName = linkUrlTable.getColumnName(onClickCol);
 434     linkUrlTable.getColumn(onClickName).setCellRenderer(
 435                new RadioButtonRenderer());
 436     linkUrlTable.getColumn(onClickName)
 437             .setCellEditor(new RadioButtonEditor());
 438
 439     // get boolean columns and resize those to min possible
 440     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 441     {
 442       if (linkUrlTable.getModel().getColumnClass(column)
 443               .equals(Boolean.class))
 444       {
 445         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 446                 column);
 447         int preferredWidth = tableColumn.getMinWidth();
 448
 449         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 450                 column);
 451         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 452         int cwidth = c.getPreferredSize().width
 453                 + linkUrlTable.getIntercellSpacing().width;
 454         preferredWidth = Math.max(preferredWidth, cwidth);
 455
 456         tableColumn.setPreferredWidth(preferredWidth);
 457       }
 458     }
 459
 460     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 461     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 462     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 463     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 464
 465     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 466
 467     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 468     // note antisense here: default is true
 469     questionnaire
 470             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 471     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 472
 473     /*
 474      * Set Output tab defaults
 475      */
 476     epsRendering.addItem(promptEachTimeOpt);
 477     epsRendering.addItem(lineArtOpt);
 478     epsRendering.addItem(textOpt);
 479     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 480             "Prompt each time");
 481     if (defaultEPS.equalsIgnoreCase("Text"))
 482     {
 483       epsRendering.setSelectedItem(textOpt);
 484     }
 485     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 486     {
 487       epsRendering.setSelectedItem(lineArtOpt);
 488     }
 489     else
 490     {
 491       epsRendering.setSelectedItem(promptEachTimeOpt);
 492     }
 493     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 494     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 495     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 496     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 497     userIdWidth.setText(wi == null ? "" : wi.toString());
 498     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 499     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 500     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 501     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 502     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 503     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 504     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 505     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 506     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 507             true));
 508
 509     /*
 510      * Set Editing tab defaults
 511      */
 512     autoCalculateConsCheck.setSelected(Cache.getDefault(
 513             "AUTO_CALC_CONSENSUS", true));
 514     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 515     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 516
 517     annotations_actionPerformed(null); // update the display of the annotation
 518                                        // settings
 519   }
 520
 521   /**
 522    * Save user selections on the Preferences tabs to the Cache and write out to
 523    * file.
 524    *
 525    * @param e
 526    */
 527   @Override
 528   public void ok_actionPerformed(ActionEvent e)
 529   {
 530     if (!validateSettings())
 531     {
 532       return;
 533     }
 534
 535     /*
 536      * Save Visual settings
 537      */
 538     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 539             Boolean.toString(seqLimit.isSelected()));
 540     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 541             Boolean.toString(rightAlign.isSelected()));
 542     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 543             Boolean.toString(fullScreen.isSelected()));
 544     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 545             Boolean.toString(openoverv.isSelected()));
 546     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 547             Boolean.toString(annotations.isSelected()));
 548     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 549             Boolean.toString(conservation.isSelected()));
 550     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 551             Boolean.toString(quality.isSelected()));
 552     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 553             Boolean.toString(identity.isSelected()));
 554
 555     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 556             .getSelectedItem().toString());
 557
 558     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 559             .getSelectedItem().toString());
 560     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 561             .getSelectedItem().toString());
 562     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 563             .getSelectedItem().toString());
 564
 565     Cache.applicationProperties.setProperty("ID_ITALICS",
 566             Boolean.toString(idItalics.isSelected()));
 567     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 568             Boolean.toString(showUnconserved.isSelected()));
 569     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 570             Boolean.toString(showGroupConsensus.isSelected()));
 571     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 572             Boolean.toString(showGroupConservation.isSelected()));
 573     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 574             Boolean.toString(showConsensHistogram.isSelected()));
 575     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 576             Boolean.toString(showConsensLogo.isSelected()));
 577     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 578             Boolean.toString(smoothFont.isSelected()));
 579     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 580             Boolean.toString(scaleProteinToCdna.isSelected()));
 581     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 582             Boolean.toString(showNpTooltip.isSelected()));
 583     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 584             Boolean.toString(showDbRefTooltip.isSelected()));
 585
 586     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 587             Boolean.toString(wrap.isSelected()));
 588
 589     Cache.applicationProperties.setProperty("STARTUP_FILE",
 590             startupFileTextfield.getText());
 591     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 592             Boolean.toString(startupCheckbox.isSelected()));
 593
 594     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 595             .getSelectedItem().toString());
 596
 597     // convert description of sort order to enum name for save
 598     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 599             .forDescription(sortAnnBy.getSelectedItem().toString());
 600     if (annSortOrder != null)
 601     {
 602       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 603               annSortOrder.name());
 604     }
 605
 606     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 607     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 608             .valueOf(showAutocalcFirst).toString());
 609
 610     /*
 611      * Save Colours settings
 612      */
 613     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 614             .getSelectedItem().toString());
 615     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 616             .getSelectedItem().toString());
 617     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 618             minColour.getBackground());
 619     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 620             maxColour.getBackground());
 621
 622     /*
 623      * Save Structure settings
 624      */
 625     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 626             Boolean.toString(addTempFactor.isSelected()));
 627     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 628             Boolean.toString(addSecondaryStructure.isSelected()));
 629     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 630             Boolean.toString(useRnaView.isSelected()));
 631     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 632             Boolean.toString(structFromPdb.isSelected()));
 633     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 634             .getSelectedItem().toString());
 635     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 636     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 637             Boolean.toString(siftsMapping.isSelected()));
 638     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 639
 640     /*
 641      * Save Output settings
 642      */
 643     Cache.applicationProperties.setProperty("EPS_RENDERING",
 644             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 645
 646     /*
 647      * Save Connections settings
 648      */
 649     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 650
 651     jalview.util.BrowserLauncher.resetBrowser();
 652
 653     // save user-defined and selected links
 654     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 655     if (menuLinks.isEmpty())
 656     {
 657       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 658     }
 659     else
 660     {
 661       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 662               menuLinks.toString());
 663     }
 664
 665     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 666     if (nonMenuLinks.isEmpty())
 667     {
 668       Cache.applicationProperties.remove("STORED_LINKS");
 669     }
 670     else
 671     {
 672       Cache.applicationProperties.setProperty("STORED_LINKS",
 673               nonMenuLinks.toString());
 674     }
 675
 676     Cache.applicationProperties.setProperty("DEFAULT_URL",
 677             sequenceUrlLinks.getPrimaryUrlId());
 678
 679     Cache.applicationProperties.setProperty("USE_PROXY",
 680             Boolean.toString(useProxy.isSelected()));
 681
 682     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 683
 684     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 685
 686     if (useProxy.isSelected())
 687     {
 688       System.setProperty("http.proxyHost", proxyServerTB.getText());
 689       System.setProperty("http.proxyPort", proxyPortTB.getText());
 690     }
 691     else
 692     {
 693       System.setProperty("http.proxyHost", "");
 694       System.setProperty("http.proxyPort", "");
 695     }
 696     Cache.setProperty("VERSION_CHECK",
 697             Boolean.toString(versioncheck.isSelected()));
 698     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 699     {
 700       // default is false - we only set this if the user has actively agreed
 701       Cache.setProperty("USAGESTATS",
 702               Boolean.toString(usagestats.isSelected()));
 703     }
 704     if (!questionnaire.isSelected())
 705     {
 706       Cache.setProperty("NOQUESTIONNAIRES", "true");
 707     }
 708     else
 709     {
 710       // special - made easy to edit a property file to disable questionnaires
 711       // by just adding the given line
 712       Cache.removeProperty("NOQUESTIONNAIRES");
 713     }
 714
 715     /*
 716      * Save Output settings
 717      */
 718     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 719             Boolean.toString(blcjv.isSelected()));
 720     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 721             Boolean.toString(clustaljv.isSelected()));
 722     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 723             Boolean.toString(fastajv.isSelected()));
 724     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 725             Boolean.toString(msfjv.isSelected()));
 726     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 727             Boolean.toString(pfamjv.isSelected()));
 728     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 729             Boolean.toString(pileupjv.isSelected()));
 730     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 731             Boolean.toString(pirjv.isSelected()));
 732     Cache.applicationProperties.setProperty("PIR_MODELLER",
 733             Boolean.toString(modellerOutput.isSelected()));
 734     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 735             Boolean.toString(embbedBioJSON.isSelected()));
 736     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 737
 738     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 739             Boolean.toString(autoIdWidth.isSelected()));
 740     userIdWidth_actionPerformed();
 741     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 742             userIdWidth.getText());
 743
 744     /*
 745      * Save Editing settings
 746      */
 747     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 748             Boolean.toString(autoCalculateConsCheck.isSelected()));
 749     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 750             Boolean.toString(sortByTree.isSelected()));
 751     Cache.applicationProperties.setProperty("PAD_GAPS",
 752             Boolean.toString(padGaps.isSelected()));
 753
 754     dasSource.saveProperties(Cache.applicationProperties);
 755     wsPrefs.updateAndRefreshWsMenuConfig(false);
 756     Cache.saveProperties();
 757     Desktop.instance.doConfigureStructurePrefs();
 758     try
 759     {
 760       frame.setClosed(true);
 761     } catch (Exception ex)
 762     {
 763     }
 764   }
 765
 766   /**
 767    * Do any necessary validation before saving settings. Return focus to the
 768    * first tab which fails validation.
 769    *
 770    * @return
 771    */
 772   private boolean validateSettings()
 773   {
 774     if (!validateStructure())
 775     {
 776       structureTab.requestFocusInWindow();
 777       return false;
 778     }
 779     return true;
 780   }
 781
 782   @Override
 783   protected boolean validateStructure()
 784   {
 785     return validateChimeraPath();
 786
 787   }
 788
 789   /**
 790    * DOCUMENT ME!
 791    */
 792   @Override
 793   public void startupFileTextfield_mouseClicked()
 794   {
 795     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 796     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 797             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 798     chooser.setFileView(new JalviewFileView());
 799     chooser.setDialogTitle(MessageManager
 800             .getString("label.select_startup_file"));
 801
 802     int value = chooser.showOpenDialog(this);
 803
 804     if (value == JalviewFileChooser.APPROVE_OPTION)
 805     {
 806       FileFormatI format = chooser.getSelectedFormat();
 807       if (format != null)
 808       {
 809         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 810                 format.getName());
 811       }
 812       startupFileTextfield.setText(chooser.getSelectedFile()
 813               .getAbsolutePath());
 814     }
 815   }
 816
 817   /**
 818    * DOCUMENT ME!
 819    *
 820    * @param e
 821    *          DOCUMENT ME!
 822    */
 823   @Override
 824   public void cancel_actionPerformed(ActionEvent e)
 825   {
 826     try
 827     {
 828       wsPrefs.updateWsMenuConfig(true);
 829       wsPrefs.refreshWs_actionPerformed(e);
 830       frame.setClosed(true);
 831     } catch (Exception ex)
 832     {
 833     }
 834   }
 835
 836   /**
 837    * DOCUMENT ME!
 838    *
 839    * @param e
 840    *          DOCUMENT ME!
 841    */
 842   @Override
 843   public void annotations_actionPerformed(ActionEvent e)
 844   {
 845     conservation.setEnabled(annotations.isSelected());
 846     quality.setEnabled(annotations.isSelected());
 847     identity.setEnabled(annotations.isSelected());
 848     showGroupConsensus.setEnabled(annotations.isSelected());
 849     showGroupConservation.setEnabled(annotations.isSelected());
 850     showConsensHistogram.setEnabled(annotations.isSelected()
 851             && (identity.isSelected() || showGroupConsensus.isSelected()));
 852     showConsensLogo.setEnabled(annotations.isSelected()
 853             && (identity.isSelected() || showGroupConsensus.isSelected()));
 854   }
 855
 856   @Override
 857   public void newLink_actionPerformed(ActionEvent e)
 858   {
 859     GSequenceLink link = new GSequenceLink();
 860     boolean valid = false;
 861     while (!valid)
 862     {
 863       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 864               MessageManager.getString("label.new_sequence_url_link"),
 865               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 866       {
 867         if (link.checkValid())
 868         {
 869           if (((UrlLinkTableModel) linkUrlTable.getModel())
 870                   .isUniqueName(link.getName()))
 871           {
 872             ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 873                     link.getName(), link.getURL());
 874             valid = true;
 875           }
 876           else
 877           {
 878             link.notifyDuplicate();
 879             continue;
 880           }
 881         }
 882       }
 883       else
 884       {
 885         break;
 886       }
 887     }
 888   }
 889
 890   @Override
 891   public void editLink_actionPerformed(ActionEvent e)
 892   {
 893     GSequenceLink link = new GSequenceLink();
 894
 895     int index = linkUrlTable.getSelectedRow();
 896     if (index == -1)
 897     {
 898       // button no longer enabled if row is not selected
 899       Cache.log.debug("Edit with no row selected in linkUrlTable");
 900       return;
 901     }
 902
 903     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 904             .getNameColumn();
 905     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 906             .getUrlColumn();
 907     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 908     link.setName(oldName);
 909     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 910
 911     boolean valid = false;
 912     while (!valid)
 913     {
 914       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 915               MessageManager.getString("label.edit_sequence_url_link"),
 916               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 917       {
 918         if (link.checkValid())
 919         {
 920           if ((oldName.equals(link.getName()))
 921                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 922                           .isUniqueName(link.getName())))
 923           {
 924             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 925             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 926             valid = true;
 927           }
 928           else
 929           {
 930             link.notifyDuplicate();
 931             continue;
 932           }
 933         }
 934       }
 935       else
 936       {
 937         break;
 938       }
 939     }
 940   }
 941
 942   @Override
 943   public void deleteLink_actionPerformed(ActionEvent e)
 944   {
 945     int index = linkUrlTable.getSelectedRow();
 946     int modelIndex = -1;
 947     if (index == -1)
 948     {
 949       // button no longer enabled if row is not selected
 950       Cache.log.debug("Delete with no row selected in linkUrlTable");
 951       return;
 952     }
 953     else
 954     {
 955       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 956     }
 957
 958     // make sure we use the model index to delete, and not the table index
 959     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 960   }
 961
 962
 963   @Override
 964   public void defaultBrowser_mouseClicked(MouseEvent e)
 965   {
 966     JFileChooser chooser = new JFileChooser(".");
 967     chooser.setDialogTitle(MessageManager
 968             .getString("label.select_default_browser"));
 969
 970     int value = chooser.showOpenDialog(this);
 971
 972     if (value == JFileChooser.APPROVE_OPTION)
 973     {
 974       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 975     }
 976
 977   }
 978
 979   /*
 980    * (non-Javadoc)
 981    *
 982    * @see
 983    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 984    * .ActionEvent)
 985    */
 986   @Override
 987   protected void showunconserved_actionPerformed(ActionEvent e)
 988   {
 989     // TODO Auto-generated method stub
 990     super.showunconserved_actionPerformed(e);
 991   }
 992
 993   public static List<String> getGroupURLLinks()
 994   {
 995     return groupURLLinks;
 996   }
 997
 998   @Override
 999   public void minColour_actionPerformed(JPanel panel)
1000   {
1001     Color col = JColorChooser.showDialog(this,
1002             MessageManager.getString("label.select_colour_minimum_value"),
1003             minColour.getBackground());
1004     if (col != null)
1005     {
1006       panel.setBackground(col);
1007     }
1008     panel.repaint();
1009   }
1010
1011   @Override
1012   public void maxColour_actionPerformed(JPanel panel)
1013   {
1014     Color col = JColorChooser.showDialog(this,
1015             MessageManager.getString("label.select_colour_maximum_value"),
1016             maxColour.getBackground());
1017     if (col != null)
1018     {
1019       panel.setBackground(col);
1020     }
1021     panel.repaint();
1022   }
1023
1024   @Override
1025   protected void userIdWidth_actionPerformed()
1026   {
1027     try
1028     {
1029       String val = userIdWidth.getText().trim();
1030       if (val.length() > 0)
1031       {
1032         Integer iw = Integer.parseInt(val);
1033         if (iw.intValue() < 12)
1034         {
1035           throw new NumberFormatException();
1036         }
1037         userIdWidth.setText(iw.toString());
1038       }
1039     } catch (NumberFormatException x)
1040     {
1041       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1042               .getString("warn.user_defined_width_requirements"),
1043               MessageManager.getString("label.invalid_id_column_width"),
1044               JvOptionPane.WARNING_MESSAGE);
1045       userIdWidth.setText("");
1046     }
1047   }
1048
1049   @Override
1050   protected void autoIdWidth_actionPerformed()
1051   {
1052     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1053     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1054   }
1055
1056   /**
1057    * Returns true if chimera path is to a valid executable, else show an error
1058    * dialog.
1059    */
1060   private boolean validateChimeraPath()
1061   {
1062     if (chimeraPath.getText().trim().length() > 0)
1063     {
1064       File f = new File(chimeraPath.getText());
1065       if (!f.canExecute())
1066       {
1067         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1068                 MessageManager.getString("label.invalid_chimera_path"),
1069                 MessageManager.getString("label.invalid_name"),
1070                 JvOptionPane.ERROR_MESSAGE);
1071         return false;
1072       }
1073     }
1074     return true;
1075   }
1076
1077   /**
1078    * If Chimera is selected, check it can be found on default or user-specified
1079    * path, if not show a warning/help dialog.
1080    */
1081   @Override
1082   protected void structureViewer_actionPerformed(String selectedItem)
1083   {
1084     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1085     {
1086       return;
1087     }
1088     boolean found = false;
1089
1090     /*
1091      * Try user-specified and standard paths for Chimera executable.
1092      */
1093     List<String> paths = StructureManager.getChimeraPaths();
1094     paths.add(0, chimeraPath.getText());
1095     for (String path : paths)
1096     {
1097       if (new File(path.trim()).canExecute())
1098       {
1099         found = true;
1100         break;
1101       }
1102     }
1103     if (!found)
1104     {
1105       String[] options = { "OK", "Help" };
1106       int showHelp = JvOptionPane.showInternalOptionDialog(
1107               Desktop.desktop,
1108               JvSwingUtils.wrapTooltip(true,
1109                       MessageManager.getString("label.chimera_missing")),
1110               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1111               null, options, options[0]);
1112       if (showHelp == JvOptionPane.NO_OPTION)
1113       {
1114         try
1115         {
1116           Help.showHelpWindow(HelpId.StructureViewer);
1117         } catch (HelpSetException e)
1118         {
1119           e.printStackTrace();
1120         }
1121       }
1122     }
1123   }
1124
1125   public class OptionsParam
1126   {
1127     private String name;
1128
1129     private String code;
1130
1131     public OptionsParam(String name, String code)
1132     {
1133       this.name = name;
1134       this.code = code;
1135     }
1136
1137     public String getName()
1138     {
1139       return name;
1140     }
1141
1142     public void setName(String name)
1143     {
1144       this.name = name;
1145     }
1146
1147     public String getCode()
1148     {
1149       return code;
1150     }
1151
1152     public void setCode(String code)
1153     {
1154       this.code = code;
1155     }
1156
1157     @Override
1158     public String toString()
1159     {
1160       return name;
1161     }
1162
1163     @Override
1164     public boolean equals(Object that)
1165     {
1166       if (!(that instanceof OptionsParam))
1167       {
1168         return false;
1169       }
1170       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1171     }
1172
1173     @Override
1174     public int hashCode()
1175     {
1176       return name.hashCode() + code.hashCode();
1177     }
1178   }
1179
1180   private class UrlListSelectionHandler implements ListSelectionListener
1181   {
1182
1183     @Override
1184     public void valueChanged(ListSelectionEvent e)
1185     {
1186       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1187
1188       int index = lsm.getMinSelectionIndex();
1189       if (index == -1)
1190       {
1191         // no selection, so disable delete/edit buttons
1192         editLink.setEnabled(false);
1193         deleteLink.setEnabled(false);
1194         return;
1195       }
1196       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1197
1198       // enable/disable edit and delete link buttons
1199       if (((UrlLinkTableModel) linkUrlTable.getModel())
1200               .isRowDeletable(modelIndex))
1201       {
1202         deleteLink.setEnabled(true);
1203       }
1204       else
1205       {
1206         deleteLink.setEnabled(false);
1207       }
1208
1209       if (((UrlLinkTableModel) linkUrlTable.getModel())
1210               .isRowEditable(modelIndex))
1211       {
1212         editLink.setEnabled(true);
1213       }
1214       else
1215       {
1216         editLink.setEnabled(false);
1217       }
1218     }
1219 }
1220 }