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.ColourSchemeI;
  33 import jalview.schemes.ColourSchemes;
  34 import jalview.schemes.ResidueColourScheme;
  35 import jalview.urls.UrlLinkTableModel;
  36 import jalview.urls.api.UrlProviderFactoryI;
  37 import jalview.urls.api.UrlProviderI;
  38 import jalview.urls.desktop.DesktopUrlProviderFactory;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.util.UrlConstants;
  42 import jalview.ws.sifts.SiftsSettings;
  43
  44 import java.awt.BorderLayout;
  45 import java.awt.Color;
  46 import java.awt.Component;
  47 import java.awt.Dimension;
  48 import java.awt.Font;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseEvent;
  52 import java.io.File;
  53 import java.util.ArrayList;
  54 import java.util.List;
  55
  56 import javax.help.HelpSetException;
  57 import javax.swing.JColorChooser;
  58 import javax.swing.JFileChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JPanel;
  61 import javax.swing.ListSelectionModel;
  62 import javax.swing.RowFilter;
  63 import javax.swing.RowSorter;
  64 import javax.swing.SortOrder;
  65 import javax.swing.event.DocumentEvent;
  66 import javax.swing.event.DocumentListener;
  67 import javax.swing.event.ListSelectionEvent;
  68 import javax.swing.event.ListSelectionListener;
  69 import javax.swing.table.TableCellRenderer;
  70 import javax.swing.table.TableColumn;
  71 import javax.swing.table.TableModel;
  72 import javax.swing.table.TableRowSorter;
  73
  74 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  75
  76 /**
  77  * DOCUMENT ME!
  78  *
  79  * @author $author$
  80  * @version $Revision$
  81  */
  82 public class Preferences extends GPreferences
  83 {
  84   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  85
  86   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  87
  88   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  89
  90   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  91
  92   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  93
  94   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  95
  96   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  97
  98   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  99
 100   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 101
 102   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 103
 104   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 105
 106   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 107
 108   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 109
 110   private static final int MIN_FONT_SIZE = 1;
 111
 112   private static final int MAX_FONT_SIZE = 30;
 113
 114   /**
 115    * Holds name and link separated with | character. Sequence ID must be
 116    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 117    */
 118   public static UrlProviderI sequenceUrlLinks;
 119
 120   public static UrlLinkTableModel dataModel;
 121
 122   /**
 123    * Holds name and link separated with | character. Sequence IDS and Sequences
 124    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 125    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 126    * for first and second token specified after a pipe character at end |,|.
 127    * (TODO: proper escape for using | to separate ids or sequences
 128    */
 129
 130   public static List<String> groupURLLinks;
 131   static
 132   {
 133     // get links selected to be in the menu (SEQUENCE_LINKS)
 134     // and links entered by the user but not selected (STORED_LINKS)
 135     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 136     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 137     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 138             UrlConstants.DEFAULT_LABEL);
 139
 140     // if both links lists are empty, add the DEFAULT_URL link
 141     // otherwise we assume the default link is in one of the lists
 142     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 143     {
 144       inMenuString = UrlConstants.DEFAULT_STRING;
 145     }
 146     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 147             inMenuString, notInMenuString);
 148     sequenceUrlLinks = factory.createUrlProvider();
 149     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 150
 151     /**
 152      * TODO: reformulate groupURL encoding so two or more can be stored in the
 153      * .properties file as '|' separated strings
 154      */
 155
 156     groupURLLinks = new ArrayList<String>();
 157   }
 158
 159   JInternalFrame frame;
 160
 161   DasSourceBrowser dasSource;
 162
 163   private WsPreferences wsPrefs;
 164
 165   private OptionsParam promptEachTimeOpt = new OptionsParam(
 166           MessageManager.getString("label.prompt_each_time"),
 167           "Prompt each time");
 168
 169   private OptionsParam lineArtOpt = new OptionsParam(
 170           MessageManager.getString("label.lineart"), "Lineart");
 171
 172   private OptionsParam textOpt = new OptionsParam(
 173           MessageManager.getString("action.text"), "Text");
 174
 175   /**
 176    * Creates a new Preferences object.
 177    */
 178   public Preferences()
 179   {
 180     super();
 181     frame = new JInternalFrame();
 182     frame.setContentPane(this);
 183     dasSource = new DasSourceBrowser();
 184     dasTab.add(dasSource, BorderLayout.CENTER);
 185     wsPrefs = new WsPreferences();
 186     wsTab.add(wsPrefs, BorderLayout.CENTER);
 187     int width = 500, height = 450;
 188     new jalview.util.Platform();
 189     if (Platform.isAMac())
 190     {
 191       width = 570;
 192       height = 480;
 193     }
 194
 195     Desktop.addInternalFrame(frame,
 196             MessageManager.getString("label.preferences"), width, height);
 197     frame.setMinimumSize(new Dimension(width, height));
 198
 199     /*
 200      * Set Visual tab defaults
 201      */
 202     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 203     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 204     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 205     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 206
 207     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 208     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 209     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 210     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 211     showUnconserved
 212             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 213     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 214             false));
 215     showGroupConservation.setSelected(Cache.getDefault(
 216             "SHOW_GROUP_CONSERVATION", false));
 217     showConsensHistogram.setSelected(Cache.getDefault(
 218             "SHOW_CONSENSUS_HISTOGRAM", true));
 219     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 220             false));
 221     showNpTooltip.setSelected(Cache
 222             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 223     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 224             true));
 225
 226     String[] fonts = java.awt.GraphicsEnvironment
 227             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 228     for (int i = 0; i < fonts.length; i++)
 229     {
 230       fontNameCB.addItem(fonts[i]);
 231     }
 232
 233     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 234     {
 235       fontSizeCB.addItem(i + "");
 236     }
 237
 238     fontStyleCB.addItem("plain");
 239     fontStyleCB.addItem("bold");
 240     fontStyleCB.addItem("italic");
 241
 242     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 243     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 244     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 245             + ""));
 246
 247     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 248     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 249             false));
 250
 251     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 252
 253     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 254
 255     gapSymbolCB.addItem("-");
 256     gapSymbolCB.addItem(".");
 257
 258     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 259
 260     sortby.addItem("No sort");
 261     sortby.addItem("Id");
 262     sortby.addItem("Pairwise Identity");
 263     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 264
 265     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 266     sortAnnBy
 267             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 268     sortAnnBy
 269             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 270     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 271             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 272                     SequenceAnnotationOrder.NONE.name()));
 273     sortAnnBy.setSelectedItem(savedSort.toString());
 274
 275     sortAutocalc.addItem("Autocalculated first");
 276     sortAutocalc.addItem("Autocalculated last");
 277     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 278     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 279             : sortAutocalc.getItemAt(1));
 280     startupCheckbox
 281             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 282     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 283             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 284                     + "/examples/exampleFile_2_3.jar"));
 285
 286     /*
 287      * Set Colours tab defaults
 288      */
 289     protColour.addItem(ResidueColourScheme.NONE);
 290     nucColour.addItem(ResidueColourScheme.NONE);
 291     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 292     {
 293       String name = cs.getSchemeName();
 294       protColour.addItem(name);
 295       nucColour.addItem(name);
 296     }
 297     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 298             ResidueColourScheme.NONE);
 299     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 300     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 301     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 302     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 303     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 304             Color.orange));
 305     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 306             Color.red));
 307
 308     /*
 309      * Set Structure tab defaults.
 310      */
 311     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 312     structFromPdb.setSelected(structSelected);
 313     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 314     useRnaView.setEnabled(structSelected);
 315     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 316     addSecondaryStructure.setEnabled(structSelected);
 317     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 318     addTempFactor.setEnabled(structSelected);
 319     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 320             ViewerType.JMOL.name()));
 321     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 322     chimeraPath.addActionListener(new ActionListener()
 323     {
 324       @Override
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         validateChimeraPath();
 328       }
 329     });
 330
 331     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 332     {
 333       siftsMapping.setSelected(true);
 334     }
 335     else
 336     {
 337       nwMapping.setSelected(true);
 338     }
 339
 340     SiftsSettings
 341             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 342
 343     /*
 344      * Set Connections tab defaults
 345      */
 346
 347     // set up sorting
 348     linkUrlTable.setModel(dataModel);
 349     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 350             linkUrlTable.getModel());
 351     linkUrlTable.setRowSorter(sorter);
 352     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 353
 354     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 355     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 356             SortOrder.DESCENDING));
 357     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 358             SortOrder.DESCENDING));
 359     sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
 360             SortOrder.ASCENDING));
 361
 362     sorter.setSortKeys(sortKeys);
 363     sorter.sort();
 364
 365     // set up filtering
 366     ActionListener onReset;
 367     onReset = new ActionListener()
 368     {
 369       @Override
 370       public void actionPerformed(ActionEvent e)
 371       {
 372         filterTB.setText("");
 373         sorter.setRowFilter(RowFilter.regexFilter(""));
 374       }
 375
 376     };
 377     doReset.addActionListener(onReset);
 378
 379     // filter to display only custom urls
 380     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 381     {
 382       @Override
 383       public boolean include(
 384               Entry<? extends TableModel, ? extends Object> entry)
 385       {
 386         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 387       }
 388     };
 389
 390     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 391             linkUrlTable.getModel());
 392     customSorter.setRowFilter(customUrlFilter);
 393
 394     ActionListener onCustomOnly;
 395     onCustomOnly = new ActionListener()
 396     {
 397       @Override
 398       public void actionPerformed(ActionEvent e)
 399       {
 400         filterTB.setText("");
 401         sorter.setRowFilter(customUrlFilter);
 402       }
 403     };
 404     userOnly.addActionListener(onCustomOnly);
 405
 406     filterTB.getDocument().addDocumentListener(new DocumentListener()
 407     {
 408       String caseInsensitiveFlag = "(?i)";
 409
 410       @Override
 411       public void changedUpdate(DocumentEvent e)
 412       {
 413         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 414                 + filterTB.getText()));
 415       }
 416
 417       @Override
 418       public void removeUpdate(DocumentEvent e)
 419       {
 420         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 421                 + filterTB.getText()));
 422       }
 423
 424       @Override
 425       public void insertUpdate(DocumentEvent e)
 426       {
 427         sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
 428                 + filterTB.getText()));
 429       }
 430     });
 431
 432     // set up list selection functionality
 433     linkUrlTable.getSelectionModel().addListSelectionListener(
 434             new UrlListSelectionHandler());
 435
 436     // set up radio buttons
 437     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 438             .getPrimaryColumn();
 439     String onClickName = linkUrlTable.getColumnName(onClickCol);
 440     linkUrlTable.getColumn(onClickName).setCellRenderer(
 441                new RadioButtonRenderer());
 442     linkUrlTable.getColumn(onClickName)
 443             .setCellEditor(new RadioButtonEditor());
 444
 445     // get boolean columns and resize those to min possible
 446     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 447     {
 448       if (linkUrlTable.getModel().getColumnClass(column)
 449               .equals(Boolean.class))
 450       {
 451         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 452                 column);
 453         int preferredWidth = tableColumn.getMinWidth();
 454
 455         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 456                 column);
 457         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 458         int cwidth = c.getPreferredSize().width
 459                 + linkUrlTable.getIntercellSpacing().width;
 460         preferredWidth = Math.max(preferredWidth, cwidth);
 461
 462         tableColumn.setPreferredWidth(preferredWidth);
 463       }
 464     }
 465
 466     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 467     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 468     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 469     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 470
 471     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 472
 473     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 474     // note antisense here: default is true
 475     questionnaire
 476             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 477     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 478
 479     /*
 480      * Set Output tab defaults
 481      */
 482     epsRendering.addItem(promptEachTimeOpt);
 483     epsRendering.addItem(lineArtOpt);
 484     epsRendering.addItem(textOpt);
 485     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 486             "Prompt each time");
 487     if (defaultEPS.equalsIgnoreCase("Text"))
 488     {
 489       epsRendering.setSelectedItem(textOpt);
 490     }
 491     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 492     {
 493       epsRendering.setSelectedItem(lineArtOpt);
 494     }
 495     else
 496     {
 497       epsRendering.setSelectedItem(promptEachTimeOpt);
 498     }
 499     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 500     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 501     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 502     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 503     userIdWidth.setText(wi == null ? "" : wi.toString());
 504     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 505     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 506     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 507     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 508     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 509     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 510     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 511     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 512     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 513             true));
 514
 515     /*
 516      * Set Editing tab defaults
 517      */
 518     autoCalculateConsCheck.setSelected(Cache.getDefault(
 519             "AUTO_CALC_CONSENSUS", true));
 520     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 521     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 522
 523     annotations_actionPerformed(null); // update the display of the annotation
 524                                        // settings
 525   }
 526
 527   /**
 528    * Save user selections on the Preferences tabs to the Cache and write out to
 529    * file.
 530    *
 531    * @param e
 532    */
 533   @Override
 534   public void ok_actionPerformed(ActionEvent e)
 535   {
 536     if (!validateSettings())
 537     {
 538       return;
 539     }
 540
 541     /*
 542      * Save Visual settings
 543      */
 544     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 545             Boolean.toString(seqLimit.isSelected()));
 546     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 547             Boolean.toString(rightAlign.isSelected()));
 548     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 549             Boolean.toString(fullScreen.isSelected()));
 550     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 551             Boolean.toString(openoverv.isSelected()));
 552     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 553             Boolean.toString(annotations.isSelected()));
 554     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 555             Boolean.toString(conservation.isSelected()));
 556     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 557             Boolean.toString(quality.isSelected()));
 558     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 559             Boolean.toString(identity.isSelected()));
 560
 561     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 562             .getSelectedItem().toString());
 563
 564     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 565             .getSelectedItem().toString());
 566     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 567             .getSelectedItem().toString());
 568     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 569             .getSelectedItem().toString());
 570
 571     Cache.applicationProperties.setProperty("ID_ITALICS",
 572             Boolean.toString(idItalics.isSelected()));
 573     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 574             Boolean.toString(showUnconserved.isSelected()));
 575     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 576             Boolean.toString(showGroupConsensus.isSelected()));
 577     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 578             Boolean.toString(showGroupConservation.isSelected()));
 579     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 580             Boolean.toString(showConsensHistogram.isSelected()));
 581     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 582             Boolean.toString(showConsensLogo.isSelected()));
 583     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 584             Boolean.toString(smoothFont.isSelected()));
 585     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 586             Boolean.toString(scaleProteinToCdna.isSelected()));
 587     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 588             Boolean.toString(showNpTooltip.isSelected()));
 589     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 590             Boolean.toString(showDbRefTooltip.isSelected()));
 591
 592     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 593             Boolean.toString(wrap.isSelected()));
 594
 595     Cache.applicationProperties.setProperty("STARTUP_FILE",
 596             startupFileTextfield.getText());
 597     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 598             Boolean.toString(startupCheckbox.isSelected()));
 599
 600     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 601             .getSelectedItem().toString());
 602
 603     // convert description of sort order to enum name for save
 604     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 605             .forDescription(sortAnnBy.getSelectedItem().toString());
 606     if (annSortOrder != null)
 607     {
 608       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 609               annSortOrder.name());
 610     }
 611
 612     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 613     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 614             .valueOf(showAutocalcFirst).toString());
 615
 616     /*
 617      * Save Colours settings
 618      */
 619     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 620             .getSelectedItem().toString());
 621     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 622             .getSelectedItem().toString());
 623     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 624             minColour.getBackground());
 625     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 626             maxColour.getBackground());
 627
 628     /*
 629      * Save Structure settings
 630      */
 631     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 632             Boolean.toString(addTempFactor.isSelected()));
 633     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 634             Boolean.toString(addSecondaryStructure.isSelected()));
 635     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 636             Boolean.toString(useRnaView.isSelected()));
 637     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 638             Boolean.toString(structFromPdb.isSelected()));
 639     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 640             .getSelectedItem().toString());
 641     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 642     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 643             Boolean.toString(siftsMapping.isSelected()));
 644     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 645
 646     /*
 647      * Save Output settings
 648      */
 649     Cache.applicationProperties.setProperty("EPS_RENDERING",
 650             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 651
 652     /*
 653      * Save Connections settings
 654      */
 655     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 656
 657     jalview.util.BrowserLauncher.resetBrowser();
 658
 659     // save user-defined and selected links
 660     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 661     if (menuLinks.isEmpty())
 662     {
 663       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 664     }
 665     else
 666     {
 667       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 668               menuLinks.toString());
 669     }
 670
 671     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 672     if (nonMenuLinks.isEmpty())
 673     {
 674       Cache.applicationProperties.remove("STORED_LINKS");
 675     }
 676     else
 677     {
 678       Cache.applicationProperties.setProperty("STORED_LINKS",
 679               nonMenuLinks.toString());
 680     }
 681
 682     Cache.applicationProperties.setProperty("DEFAULT_URL",
 683             sequenceUrlLinks.getPrimaryUrlId());
 684
 685     Cache.applicationProperties.setProperty("USE_PROXY",
 686             Boolean.toString(useProxy.isSelected()));
 687
 688     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 689
 690     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 691
 692     if (useProxy.isSelected())
 693     {
 694       System.setProperty("http.proxyHost", proxyServerTB.getText());
 695       System.setProperty("http.proxyPort", proxyPortTB.getText());
 696     }
 697     else
 698     {
 699       System.setProperty("http.proxyHost", "");
 700       System.setProperty("http.proxyPort", "");
 701     }
 702     Cache.setProperty("VERSION_CHECK",
 703             Boolean.toString(versioncheck.isSelected()));
 704     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 705     {
 706       // default is false - we only set this if the user has actively agreed
 707       Cache.setProperty("USAGESTATS",
 708               Boolean.toString(usagestats.isSelected()));
 709     }
 710     if (!questionnaire.isSelected())
 711     {
 712       Cache.setProperty("NOQUESTIONNAIRES", "true");
 713     }
 714     else
 715     {
 716       // special - made easy to edit a property file to disable questionnaires
 717       // by just adding the given line
 718       Cache.removeProperty("NOQUESTIONNAIRES");
 719     }
 720
 721     /*
 722      * Save Output settings
 723      */
 724     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 725             Boolean.toString(blcjv.isSelected()));
 726     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 727             Boolean.toString(clustaljv.isSelected()));
 728     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 729             Boolean.toString(fastajv.isSelected()));
 730     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 731             Boolean.toString(msfjv.isSelected()));
 732     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 733             Boolean.toString(pfamjv.isSelected()));
 734     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 735             Boolean.toString(pileupjv.isSelected()));
 736     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 737             Boolean.toString(pirjv.isSelected()));
 738     Cache.applicationProperties.setProperty("PIR_MODELLER",
 739             Boolean.toString(modellerOutput.isSelected()));
 740     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 741             Boolean.toString(embbedBioJSON.isSelected()));
 742     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 743
 744     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 745             Boolean.toString(autoIdWidth.isSelected()));
 746     userIdWidth_actionPerformed();
 747     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 748             userIdWidth.getText());
 749
 750     /*
 751      * Save Editing settings
 752      */
 753     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 754             Boolean.toString(autoCalculateConsCheck.isSelected()));
 755     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 756             Boolean.toString(sortByTree.isSelected()));
 757     Cache.applicationProperties.setProperty("PAD_GAPS",
 758             Boolean.toString(padGaps.isSelected()));
 759
 760     dasSource.saveProperties(Cache.applicationProperties);
 761     wsPrefs.updateAndRefreshWsMenuConfig(false);
 762     Cache.saveProperties();
 763     Desktop.instance.doConfigureStructurePrefs();
 764     try
 765     {
 766       frame.setClosed(true);
 767     } catch (Exception ex)
 768     {
 769     }
 770   }
 771
 772   /**
 773    * Do any necessary validation before saving settings. Return focus to the
 774    * first tab which fails validation.
 775    *
 776    * @return
 777    */
 778   private boolean validateSettings()
 779   {
 780     if (!validateStructure())
 781     {
 782       structureTab.requestFocusInWindow();
 783       return false;
 784     }
 785     return true;
 786   }
 787
 788   @Override
 789   protected boolean validateStructure()
 790   {
 791     return validateChimeraPath();
 792
 793   }
 794
 795   /**
 796    * DOCUMENT ME!
 797    */
 798   @Override
 799   public void startupFileTextfield_mouseClicked()
 800   {
 801     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 802     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 803             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 804     chooser.setFileView(new JalviewFileView());
 805     chooser.setDialogTitle(MessageManager
 806             .getString("label.select_startup_file"));
 807
 808     int value = chooser.showOpenDialog(this);
 809
 810     if (value == JalviewFileChooser.APPROVE_OPTION)
 811     {
 812       FileFormatI format = chooser.getSelectedFormat();
 813       if (format != null)
 814       {
 815         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 816                 format.getName());
 817       }
 818       startupFileTextfield.setText(chooser.getSelectedFile()
 819               .getAbsolutePath());
 820     }
 821   }
 822
 823   /**
 824    * DOCUMENT ME!
 825    *
 826    * @param e
 827    *          DOCUMENT ME!
 828    */
 829   @Override
 830   public void cancel_actionPerformed(ActionEvent e)
 831   {
 832     try
 833     {
 834       wsPrefs.updateWsMenuConfig(true);
 835       wsPrefs.refreshWs_actionPerformed(e);
 836       frame.setClosed(true);
 837     } catch (Exception ex)
 838     {
 839     }
 840   }
 841
 842   /**
 843    * DOCUMENT ME!
 844    *
 845    * @param e
 846    *          DOCUMENT ME!
 847    */
 848   @Override
 849   public void annotations_actionPerformed(ActionEvent e)
 850   {
 851     conservation.setEnabled(annotations.isSelected());
 852     quality.setEnabled(annotations.isSelected());
 853     identity.setEnabled(annotations.isSelected());
 854     showGroupConsensus.setEnabled(annotations.isSelected());
 855     showGroupConservation.setEnabled(annotations.isSelected());
 856     showConsensHistogram.setEnabled(annotations.isSelected()
 857             && (identity.isSelected() || showGroupConsensus.isSelected()));
 858     showConsensLogo.setEnabled(annotations.isSelected()
 859             && (identity.isSelected() || showGroupConsensus.isSelected()));
 860   }
 861
 862   @Override
 863   public void newLink_actionPerformed(ActionEvent e)
 864   {
 865     GSequenceLink link = new GSequenceLink();
 866     boolean valid = false;
 867     while (!valid)
 868     {
 869       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 870               MessageManager.getString("label.new_sequence_url_link"),
 871               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 872       {
 873         if (link.checkValid())
 874         {
 875           if (((UrlLinkTableModel) linkUrlTable.getModel())
 876                   .isUniqueName(link.getName()))
 877           {
 878             ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 879                     link.getName(), link.getURL());
 880             valid = true;
 881           }
 882           else
 883           {
 884             link.notifyDuplicate();
 885             continue;
 886           }
 887         }
 888       }
 889       else
 890       {
 891         break;
 892       }
 893     }
 894   }
 895
 896   @Override
 897   public void editLink_actionPerformed(ActionEvent e)
 898   {
 899     GSequenceLink link = new GSequenceLink();
 900
 901     int index = linkUrlTable.getSelectedRow();
 902     if (index == -1)
 903     {
 904       // button no longer enabled if row is not selected
 905       Cache.log.debug("Edit with no row selected in linkUrlTable");
 906       return;
 907     }
 908
 909     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 910             .getNameColumn();
 911     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 912             .getUrlColumn();
 913     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 914     link.setName(oldName);
 915     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 916
 917     boolean valid = false;
 918     while (!valid)
 919     {
 920       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 921               MessageManager.getString("label.edit_sequence_url_link"),
 922               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 923       {
 924         if (link.checkValid())
 925         {
 926           if ((oldName.equals(link.getName()))
 927                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 928                           .isUniqueName(link.getName())))
 929           {
 930             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 931             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 932             valid = true;
 933           }
 934           else
 935           {
 936             link.notifyDuplicate();
 937             continue;
 938           }
 939         }
 940       }
 941       else
 942       {
 943         break;
 944       }
 945     }
 946   }
 947
 948   @Override
 949   public void deleteLink_actionPerformed(ActionEvent e)
 950   {
 951     int index = linkUrlTable.getSelectedRow();
 952     int modelIndex = -1;
 953     if (index == -1)
 954     {
 955       // button no longer enabled if row is not selected
 956       Cache.log.debug("Delete with no row selected in linkUrlTable");
 957       return;
 958     }
 959     else
 960     {
 961       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 962     }
 963
 964     // make sure we use the model index to delete, and not the table index
 965     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 966   }
 967
 968
 969   @Override
 970   public void defaultBrowser_mouseClicked(MouseEvent e)
 971   {
 972     JFileChooser chooser = new JFileChooser(".");
 973     chooser.setDialogTitle(MessageManager
 974             .getString("label.select_default_browser"));
 975
 976     int value = chooser.showOpenDialog(this);
 977
 978     if (value == JFileChooser.APPROVE_OPTION)
 979     {
 980       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 981     }
 982
 983   }
 984
 985   /*
 986    * (non-Javadoc)
 987    *
 988    * @see
 989    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 990    * .ActionEvent)
 991    */
 992   @Override
 993   protected void showunconserved_actionPerformed(ActionEvent e)
 994   {
 995     // TODO Auto-generated method stub
 996     super.showunconserved_actionPerformed(e);
 997   }
 998
 999   public static List<String> getGroupURLLinks()
1000   {
1001     return groupURLLinks;
1002   }
1003
1004   @Override
1005   public void minColour_actionPerformed(JPanel panel)
1006   {
1007     Color col = JColorChooser.showDialog(this,
1008             MessageManager.getString("label.select_colour_minimum_value"),
1009             minColour.getBackground());
1010     if (col != null)
1011     {
1012       panel.setBackground(col);
1013     }
1014     panel.repaint();
1015   }
1016
1017   @Override
1018   public void maxColour_actionPerformed(JPanel panel)
1019   {
1020     Color col = JColorChooser.showDialog(this,
1021             MessageManager.getString("label.select_colour_maximum_value"),
1022             maxColour.getBackground());
1023     if (col != null)
1024     {
1025       panel.setBackground(col);
1026     }
1027     panel.repaint();
1028   }
1029
1030   @Override
1031   protected void userIdWidth_actionPerformed()
1032   {
1033     try
1034     {
1035       String val = userIdWidth.getText().trim();
1036       if (val.length() > 0)
1037       {
1038         Integer iw = Integer.parseInt(val);
1039         if (iw.intValue() < 12)
1040         {
1041           throw new NumberFormatException();
1042         }
1043         userIdWidth.setText(iw.toString());
1044       }
1045     } catch (NumberFormatException x)
1046     {
1047       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1048               .getString("warn.user_defined_width_requirements"),
1049               MessageManager.getString("label.invalid_id_column_width"),
1050               JvOptionPane.WARNING_MESSAGE);
1051       userIdWidth.setText("");
1052     }
1053   }
1054
1055   @Override
1056   protected void autoIdWidth_actionPerformed()
1057   {
1058     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1059     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1060   }
1061
1062   /**
1063    * Returns true if chimera path is to a valid executable, else show an error
1064    * dialog.
1065    */
1066   private boolean validateChimeraPath()
1067   {
1068     if (chimeraPath.getText().trim().length() > 0)
1069     {
1070       File f = new File(chimeraPath.getText());
1071       if (!f.canExecute())
1072       {
1073         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1074                 MessageManager.getString("label.invalid_chimera_path"),
1075                 MessageManager.getString("label.invalid_name"),
1076                 JvOptionPane.ERROR_MESSAGE);
1077         return false;
1078       }
1079     }
1080     return true;
1081   }
1082
1083   /**
1084    * If Chimera is selected, check it can be found on default or user-specified
1085    * path, if not show a warning/help dialog.
1086    */
1087   @Override
1088   protected void structureViewer_actionPerformed(String selectedItem)
1089   {
1090     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1091     {
1092       return;
1093     }
1094     boolean found = false;
1095
1096     /*
1097      * Try user-specified and standard paths for Chimera executable.
1098      */
1099     List<String> paths = StructureManager.getChimeraPaths();
1100     paths.add(0, chimeraPath.getText());
1101     for (String path : paths)
1102     {
1103       if (new File(path.trim()).canExecute())
1104       {
1105         found = true;
1106         break;
1107       }
1108     }
1109     if (!found)
1110     {
1111       String[] options = { "OK", "Help" };
1112       int showHelp = JvOptionPane.showInternalOptionDialog(
1113               Desktop.desktop,
1114               JvSwingUtils.wrapTooltip(true,
1115                       MessageManager.getString("label.chimera_missing")),
1116               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1117               null, options, options[0]);
1118       if (showHelp == JvOptionPane.NO_OPTION)
1119       {
1120         try
1121         {
1122           Help.showHelpWindow(HelpId.StructureViewer);
1123         } catch (HelpSetException e)
1124         {
1125           e.printStackTrace();
1126         }
1127       }
1128     }
1129   }
1130
1131   public class OptionsParam
1132   {
1133     private String name;
1134
1135     private String code;
1136
1137     public OptionsParam(String name, String code)
1138     {
1139       this.name = name;
1140       this.code = code;
1141     }
1142
1143     public String getName()
1144     {
1145       return name;
1146     }
1147
1148     public void setName(String name)
1149     {
1150       this.name = name;
1151     }
1152
1153     public String getCode()
1154     {
1155       return code;
1156     }
1157
1158     public void setCode(String code)
1159     {
1160       this.code = code;
1161     }
1162
1163     @Override
1164     public String toString()
1165     {
1166       return name;
1167     }
1168
1169     @Override
1170     public boolean equals(Object that)
1171     {
1172       if (!(that instanceof OptionsParam))
1173       {
1174         return false;
1175       }
1176       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1177     }
1178
1179     @Override
1180     public int hashCode()
1181     {
1182       return name.hashCode() + code.hashCode();
1183     }
1184   }
1185
1186   private class UrlListSelectionHandler implements ListSelectionListener
1187   {
1188
1189     @Override
1190     public void valueChanged(ListSelectionEvent e)
1191     {
1192       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1193
1194       int index = lsm.getMinSelectionIndex();
1195       if (index == -1)
1196       {
1197         // no selection, so disable delete/edit buttons
1198         editLink.setEnabled(false);
1199         deleteLink.setEnabled(false);
1200         return;
1201       }
1202       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1203
1204       // enable/disable edit and delete link buttons
1205       if (((UrlLinkTableModel) linkUrlTable.getModel())
1206               .isRowDeletable(modelIndex))
1207       {
1208         deleteLink.setEnabled(true);
1209       }
1210       else
1211       {
1212         deleteLink.setEnabled(false);
1213       }
1214
1215       if (((UrlLinkTableModel) linkUrlTable.getModel())
1216               .isRowEditable(modelIndex))
1217       {
1218         editLink.setEnabled(true);
1219       }
1220       else
1221       {
1222         editLink.setEnabled(false);
1223       }
1224     }
1225 }
1226 }