src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.jbgui.GPreferences;
  30 import jalview.jbgui.GSequenceLink;
  31 import jalview.schemes.ColourSchemeProperty;
  32 import jalview.urls.UrlLinkTableModel;
  33 import jalview.urls.UrlProvider;
  34 import jalview.urls.UrlProviderI;
  35 import jalview.util.MessageManager;
  36 import jalview.util.Platform;
  37 import jalview.util.UrlConstants;
  38 import jalview.ws.sifts.SiftsSettings;
  39
  40 import java.awt.BorderLayout;
  41 import java.awt.Color;
  42 import java.awt.Component;
  43 import java.awt.Dimension;
  44 import java.awt.Font;
  45 import java.awt.event.ActionEvent;
  46 import java.awt.event.ActionListener;
  47 import java.awt.event.MouseEvent;
  48 import java.io.File;
  49 import java.util.ArrayList;
  50 import java.util.List;
  51
  52 import javax.help.HelpSetException;
  53 import javax.swing.JColorChooser;
  54 import javax.swing.JFileChooser;
  55 import javax.swing.JInternalFrame;
  56 import javax.swing.JOptionPane;
  57 import javax.swing.JPanel;
  58 import javax.swing.ListSelectionModel;
  59 import javax.swing.RowFilter;
  60 import javax.swing.RowSorter;
  61 import javax.swing.SortOrder;
  62 import javax.swing.event.DocumentEvent;
  63 import javax.swing.event.DocumentListener;
  64 import javax.swing.event.ListSelectionEvent;
  65 import javax.swing.event.ListSelectionListener;
  66 import javax.swing.table.TableCellRenderer;
  67 import javax.swing.table.TableColumn;
  68 import javax.swing.table.TableModel;
  69 import javax.swing.table.TableRowSorter;
  70
  71 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  72
  73 /**
  74  * DOCUMENT ME!
  75  *
  76  * @author $author$
  77  * @version $Revision$
  78  */
  79 public class Preferences extends GPreferences
  80 {
  81   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  82
  83   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  84
  85   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  86
  87   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  88
  89   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  90
  91   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  92
  93   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  94
  95   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  96
  97   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  98
  99   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 100
 101   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 102
 103   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 104
 105   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 106
 107   private static final int MIN_FONT_SIZE = 1;
 108
 109   private static final int MAX_FONT_SIZE = 30;
 110
 111   /**
 112    * Holds name and link separated with | character. Sequence ID must be
 113    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 114    */
 115   public static UrlProviderI sequenceUrlLinks;
 116
 117   public static UrlLinkTableModel dataModel;
 118
 119   /**
 120    * Holds name and link separated with | character. Sequence IDS and Sequences
 121    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 122    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 123    * for first and second token specified after a pipe character at end |,|.
 124    * (TODO: proper escape for using | to separate ids or sequences
 125    */
 126
 127   public static List<String> groupURLLinks;
 128   static
 129   {
 130     String string = Cache.getDefault("SEQUENCE_LINKS",
 131             UrlConstants.DEFAULT_STRING);
 132     sequenceUrlLinks = new UrlProvider(UrlConstants.DEFAULT_LABEL, string);
 133     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 134
 135     /**
 136      * TODO: reformulate groupURL encoding so two or more can be stored in the
 137      * .properties file as '|' separated strings
 138      */
 139
 140     groupURLLinks = new ArrayList<String>();
 141   }
 142
 143   JInternalFrame frame;
 144
 145   DasSourceBrowser dasSource;
 146
 147   private WsPreferences wsPrefs;
 148
 149   private OptionsParam promptEachTimeOpt = new OptionsParam(
 150           MessageManager.getString("label.prompt_each_time"),
 151           "Prompt each time");
 152
 153   private OptionsParam lineArtOpt = new OptionsParam(
 154           MessageManager.getString("label.lineart"), "Lineart");
 155
 156   private OptionsParam textOpt = new OptionsParam(
 157           MessageManager.getString("action.text"), "Text");
 158
 159   /**
 160    * Creates a new Preferences object.
 161    */
 162   public Preferences()
 163   {
 164     super();
 165     frame = new JInternalFrame();
 166     frame.setContentPane(this);
 167     dasSource = new DasSourceBrowser();
 168     dasTab.add(dasSource, BorderLayout.CENTER);
 169     wsPrefs = new WsPreferences();
 170     wsTab.add(wsPrefs, BorderLayout.CENTER);
 171     int width = 500, height = 450;
 172     new jalview.util.Platform();
 173     if (Platform.isAMac())
 174     {
 175       width = 570;
 176       height = 480;
 177     }
 178
 179     Desktop.addInternalFrame(frame,
 180             MessageManager.getString("label.preferences"), width, height);
 181     frame.setMinimumSize(new Dimension(width, height));
 182
 183     /*
 184      * Set Visual tab defaults
 185      */
 186     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 187     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 188     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 189     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 190
 191     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 192     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 193     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 194     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 195     showUnconserved
 196             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 197     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 198             false));
 199     showGroupConservation.setSelected(Cache.getDefault(
 200             "SHOW_GROUP_CONSERVATION", false));
 201     showConsensHistogram.setSelected(Cache.getDefault(
 202             "SHOW_CONSENSUS_HISTOGRAM", true));
 203     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 204             false));
 205     showNpTooltip.setSelected(Cache
 206             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 207     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 208             true));
 209
 210     String[] fonts = java.awt.GraphicsEnvironment
 211             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 212     for (int i = 0; i < fonts.length; i++)
 213     {
 214       fontNameCB.addItem(fonts[i]);
 215     }
 216
 217     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 218     {
 219       fontSizeCB.addItem(i + "");
 220     }
 221
 222     fontStyleCB.addItem("plain");
 223     fontStyleCB.addItem("bold");
 224     fontStyleCB.addItem("italic");
 225
 226     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 227     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 228     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 229             + ""));
 230
 231     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 232     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 233             false));
 234
 235     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 236
 237     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 238
 239     gapSymbolCB.addItem("-");
 240     gapSymbolCB.addItem(".");
 241
 242     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 243
 244     sortby.addItem("No sort");
 245     sortby.addItem("Id");
 246     sortby.addItem("Pairwise Identity");
 247     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 248
 249     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 250     sortAnnBy
 251             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 252     sortAnnBy
 253             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 254     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 255             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 256                     SequenceAnnotationOrder.NONE.name()));
 257     sortAnnBy.setSelectedItem(savedSort.toString());
 258
 259     sortAutocalc.addItem("Autocalculated first");
 260     sortAutocalc.addItem("Autocalculated last");
 261     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 262     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 263             : sortAutocalc.getItemAt(1));
 264     startupCheckbox
 265             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 266     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 267             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 268                     + "/examples/exampleFile_2_3.jar"));
 269
 270     /*
 271      * Set Colours tab defaults
 272      */
 273     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 274     {
 275       protColour.addItem(ColourSchemeProperty.getColourName(i));
 276       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 277     }
 278     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 279     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 280     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 281     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 282     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 283     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 284             Color.orange));
 285     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 286             Color.red));
 287
 288     /*
 289      * Set Structure tab defaults.
 290      */
 291     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 292     structFromPdb.setSelected(structSelected);
 293     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 294     useRnaView.setEnabled(structSelected);
 295     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 296     addSecondaryStructure.setEnabled(structSelected);
 297     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 298     addTempFactor.setEnabled(structSelected);
 299     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 300             ViewerType.JMOL.name()));
 301     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 302     chimeraPath.addActionListener(new ActionListener()
 303     {
 304       @Override
 305       public void actionPerformed(ActionEvent e)
 306       {
 307         validateChimeraPath();
 308       }
 309     });
 310
 311     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 312     {
 313       siftsMapping.setSelected(true);
 314     }
 315     else
 316     {
 317       nwMapping.setSelected(true);
 318     }
 319
 320     SiftsSettings
 321             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 322
 323     /*
 324      * Set Connections tab defaults
 325      */
 326
 327     // set up sorting
 328     linkUrlTable.setModel(dataModel);
 329     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 330             linkUrlTable.getModel());
 331     linkUrlTable.setRowSorter(sorter);
 332     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 333
 334     sortKeys.add(new RowSorter.SortKey(3,
 335             SortOrder.DESCENDING));
 336     sortKeys.add(new RowSorter.SortKey(2, SortOrder.DESCENDING));
 337     sortKeys.add(new RowSorter.SortKey(0, SortOrder.ASCENDING));
 338
 339     sorter.setSortKeys(sortKeys);
 340     sorter.sort();
 341
 342     // set up filtering
 343     ActionListener onReset;
 344     onReset = new ActionListener()
 345     {
 346       @Override
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         filterTB.setText("");
 350         sorter.setRowFilter(RowFilter.regexFilter(""));
 351       }
 352
 353     };
 354     doReset.addActionListener(onReset);
 355
 356     // filter to display only custom urls
 357     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 358     {
 359       @Override
 360       public boolean include(
 361               Entry<? extends TableModel, ? extends Object> entry)
 362       {
 363         String id = entry.getStringValue(4);
 364         return sequenceUrlLinks.isUserEntry(id);
 365       }
 366     };
 367
 368     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 369             linkUrlTable.getModel());
 370     customSorter.setRowFilter(customUrlFilter);
 371
 372     ActionListener onCustomOnly;
 373     onCustomOnly = new ActionListener()
 374     {
 375       @Override
 376       public void actionPerformed(ActionEvent e)
 377       {
 378         filterTB.setText("");
 379         sorter.setRowFilter(customUrlFilter);
 380       }
 381     };
 382     userOnly.addActionListener(onCustomOnly);
 383
 384     filterTB.getDocument().addDocumentListener(new DocumentListener()
 385     {
 386       @Override
 387       public void changedUpdate(DocumentEvent e)
 388       {
 389         sorter.setRowFilter(RowFilter.regexFilter("(?i)"
 390                 + filterTB.getText()));
 391       }
 392
 393       @Override
 394       public void removeUpdate(DocumentEvent e)
 395       {
 396         sorter.setRowFilter(RowFilter.regexFilter("(?i)"
 397                 + filterTB.getText()));
 398       }
 399
 400       @Override
 401       public void insertUpdate(DocumentEvent e)
 402       {
 403         sorter.setRowFilter(RowFilter.regexFilter("(?i)"
 404                 + filterTB.getText()));
 405       }
 406     });
 407
 408     // set up list selection functionality
 409     linkUrlTable.getSelectionModel().addListSelectionListener(
 410             new UrlListSelectionHandler());
 411
 412     // set up radio buttons
 413     linkUrlTable.getColumn("Default").setCellRenderer(
 414             new RadioButtonRenderer());
 415     linkUrlTable.getColumn("Default")
 416             .setCellEditor(new RadioButtonEditor());
 417
 418     // get boolean columns and resize those to min possible
 419     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 420     {
 421       if (linkUrlTable.getModel().getColumnClass(column)
 422               .equals(Boolean.class))
 423       {
 424         TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
 425                 column);
 426         int preferredWidth = tableColumn.getMinWidth();
 427
 428         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 429                 column);
 430         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 431         int cwidth = c.getPreferredSize().width
 432                 + linkUrlTable.getIntercellSpacing().width;
 433         preferredWidth = Math.max(preferredWidth, cwidth);
 434
 435         tableColumn.setPreferredWidth(preferredWidth);
 436       }
 437     }
 438
 439     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 440     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 441     proxyServerTB.setEnabled(useProxy.isSelected());
 442     proxyPortTB.setEnabled(useProxy.isSelected());
 443     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 444     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 445
 446     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 447
 448     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 449     // note antisense here: default is true
 450     questionnaire
 451             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 452     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 453
 454     /*
 455      * Set Output tab defaults
 456      */
 457     epsRendering.addItem(promptEachTimeOpt);
 458     epsRendering.addItem(lineArtOpt);
 459     epsRendering.addItem(textOpt);
 460     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 461             "Prompt each time");
 462     if (defaultEPS.equalsIgnoreCase("Text"))
 463     {
 464       epsRendering.setSelectedItem(textOpt);
 465     }
 466     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 467     {
 468       epsRendering.setSelectedItem(lineArtOpt);
 469     }
 470     else
 471     {
 472       epsRendering.setSelectedItem(promptEachTimeOpt);
 473     }
 474     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 475     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 476     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 477     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 478     userIdWidth.setText(wi == null ? "" : wi.toString());
 479     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 480     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 481     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 482     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 483     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 484     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 485     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 486     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 487     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 488             true));
 489
 490     /*
 491      * Set Editing tab defaults
 492      */
 493     autoCalculateConsCheck.setSelected(Cache.getDefault(
 494             "AUTO_CALC_CONSENSUS", true));
 495     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 496     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 497
 498     annotations_actionPerformed(null); // update the display of the annotation
 499                                        // settings
 500   }
 501
 502   /**
 503    * Save user selections on the Preferences tabs to the Cache and write out to
 504    * file.
 505    *
 506    * @param e
 507    */
 508   @Override
 509   public void ok_actionPerformed(ActionEvent e)
 510   {
 511     if (!validateSettings())
 512     {
 513       return;
 514     }
 515
 516     /*
 517      * Save Visual settings
 518      */
 519     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 520             Boolean.toString(seqLimit.isSelected()));
 521     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 522             Boolean.toString(rightAlign.isSelected()));
 523     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 524             Boolean.toString(fullScreen.isSelected()));
 525     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 526             Boolean.toString(openoverv.isSelected()));
 527     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 528             Boolean.toString(annotations.isSelected()));
 529     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 530             Boolean.toString(conservation.isSelected()));
 531     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 532             Boolean.toString(quality.isSelected()));
 533     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 534             Boolean.toString(identity.isSelected()));
 535
 536     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 537             .getSelectedItem().toString());
 538
 539     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 540             .getSelectedItem().toString());
 541     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 542             .getSelectedItem().toString());
 543     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 544             .getSelectedItem().toString());
 545
 546     Cache.applicationProperties.setProperty("ID_ITALICS",
 547             Boolean.toString(idItalics.isSelected()));
 548     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 549             Boolean.toString(showUnconserved.isSelected()));
 550     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 551             Boolean.toString(showGroupConsensus.isSelected()));
 552     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 553             Boolean.toString(showGroupConservation.isSelected()));
 554     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 555             Boolean.toString(showConsensHistogram.isSelected()));
 556     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 557             Boolean.toString(showConsensLogo.isSelected()));
 558     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 559             Boolean.toString(smoothFont.isSelected()));
 560     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 561             Boolean.toString(scaleProteinToCdna.isSelected()));
 562     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 563             Boolean.toString(showNpTooltip.isSelected()));
 564     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 565             Boolean.toString(showDbRefTooltip.isSelected()));
 566
 567     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 568             Boolean.toString(wrap.isSelected()));
 569
 570     Cache.applicationProperties.setProperty("STARTUP_FILE",
 571             startupFileTextfield.getText());
 572     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 573             Boolean.toString(startupCheckbox.isSelected()));
 574
 575     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 576             .getSelectedItem().toString());
 577
 578     // convert description of sort order to enum name for save
 579     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 580             .forDescription(sortAnnBy.getSelectedItem().toString());
 581     if (annSortOrder != null)
 582     {
 583       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 584               annSortOrder.name());
 585     }
 586
 587     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 588     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 589             .valueOf(showAutocalcFirst).toString());
 590
 591     /*
 592      * Save Colours settings
 593      */
 594     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 595             .getSelectedItem().toString());
 596     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 597             .getSelectedItem().toString());
 598     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 599             minColour.getBackground());
 600     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 601             maxColour.getBackground());
 602
 603     /*
 604      * Save Structure settings
 605      */
 606     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 607             Boolean.toString(addTempFactor.isSelected()));
 608     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 609             Boolean.toString(addSecondaryStructure.isSelected()));
 610     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 611             Boolean.toString(useRnaView.isSelected()));
 612     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 613             Boolean.toString(structFromPdb.isSelected()));
 614     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 615             .getSelectedItem().toString());
 616     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 617     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 618             Boolean.toString(siftsMapping.isSelected()));
 619     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 620
 621     /*
 622      * Save Output settings
 623      */
 624     Cache.applicationProperties.setProperty("EPS_RENDERING",
 625             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 626
 627     /*
 628      * Save Connections settings
 629      */
 630     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 631
 632     jalview.util.BrowserLauncher.resetBrowser();
 633
 634     // save user-defined and selected links
 635     String links = linkUrlTable.getModel().toString();
 636     if (links.isEmpty())
 637     {
 638       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 639     }
 640     else
 641     {
 642       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 643               links.toString());
 644     }
 645
 646     Cache.applicationProperties.setProperty("USE_PROXY",
 647             Boolean.toString(useProxy.isSelected()));
 648
 649     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 650
 651     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 652
 653     if (useProxy.isSelected())
 654     {
 655       System.setProperty("http.proxyHost", proxyServerTB.getText());
 656       System.setProperty("http.proxyPort", proxyPortTB.getText());
 657     }
 658     else
 659     {
 660       System.setProperty("http.proxyHost", "");
 661       System.setProperty("http.proxyPort", "");
 662     }
 663     Cache.setProperty("VERSION_CHECK",
 664             Boolean.toString(versioncheck.isSelected()));
 665     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 666     {
 667       // default is false - we only set this if the user has actively agreed
 668       Cache.setProperty("USAGESTATS",
 669               Boolean.toString(usagestats.isSelected()));
 670     }
 671     if (!questionnaire.isSelected())
 672     {
 673       Cache.setProperty("NOQUESTIONNAIRES", "true");
 674     }
 675     else
 676     {
 677       // special - made easy to edit a property file to disable questionnaires
 678       // by just adding the given line
 679       Cache.removeProperty("NOQUESTIONNAIRES");
 680     }
 681
 682     /*
 683      * Save Output settings
 684      */
 685     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 686             Boolean.toString(blcjv.isSelected()));
 687     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 688             Boolean.toString(clustaljv.isSelected()));
 689     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 690             Boolean.toString(fastajv.isSelected()));
 691     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 692             Boolean.toString(msfjv.isSelected()));
 693     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 694             Boolean.toString(pfamjv.isSelected()));
 695     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 696             Boolean.toString(pileupjv.isSelected()));
 697     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 698             Boolean.toString(pirjv.isSelected()));
 699     Cache.applicationProperties.setProperty("PIR_MODELLER",
 700             Boolean.toString(modellerOutput.isSelected()));
 701     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 702             Boolean.toString(embbedBioJSON.isSelected()));
 703     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 704
 705     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 706             Boolean.toString(autoIdWidth.isSelected()));
 707     userIdWidth_actionPerformed();
 708     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 709             userIdWidth.getText());
 710
 711     /*
 712      * Save Editing settings
 713      */
 714     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 715             Boolean.toString(autoCalculateConsCheck.isSelected()));
 716     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 717             Boolean.toString(sortByTree.isSelected()));
 718     Cache.applicationProperties.setProperty("PAD_GAPS",
 719             Boolean.toString(padGaps.isSelected()));
 720
 721     dasSource.saveProperties(Cache.applicationProperties);
 722     wsPrefs.updateAndRefreshWsMenuConfig(false);
 723     Cache.saveProperties();
 724     Desktop.instance.doConfigureStructurePrefs();
 725     try
 726     {
 727       frame.setClosed(true);
 728     } catch (Exception ex)
 729     {
 730     }
 731   }
 732
 733   /**
 734    * Do any necessary validation before saving settings. Return focus to the
 735    * first tab which fails validation.
 736    *
 737    * @return
 738    */
 739   private boolean validateSettings()
 740   {
 741     if (!validateStructure())
 742     {
 743       structureTab.requestFocusInWindow();
 744       return false;
 745     }
 746     return true;
 747   }
 748
 749   @Override
 750   protected boolean validateStructure()
 751   {
 752     return validateChimeraPath();
 753
 754   }
 755
 756   /**
 757    * DOCUMENT ME!
 758    */
 759   @Override
 760   public void startupFileTextfield_mouseClicked()
 761   {
 762     JalviewFileChooser chooser = new JalviewFileChooser(
 763             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 764                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 765                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 766                 "PIR", "BLC", "Jalview" },
 767             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 768     chooser.setFileView(new JalviewFileView());
 769     chooser.setDialogTitle(MessageManager
 770             .getString("label.select_startup_file"));
 771
 772     int value = chooser.showOpenDialog(this);
 773
 774     if (value == JalviewFileChooser.APPROVE_OPTION)
 775     {
 776       jalview.bin.Cache.applicationProperties.setProperty(
 777               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 778       startupFileTextfield.setText(chooser.getSelectedFile()
 779               .getAbsolutePath());
 780     }
 781   }
 782
 783   /**
 784    * DOCUMENT ME!
 785    *
 786    * @param e
 787    *          DOCUMENT ME!
 788    */
 789   @Override
 790   public void cancel_actionPerformed(ActionEvent e)
 791   {
 792     try
 793     {
 794       wsPrefs.updateWsMenuConfig(true);
 795       wsPrefs.refreshWs_actionPerformed(e);
 796       frame.setClosed(true);
 797     } catch (Exception ex)
 798     {
 799     }
 800   }
 801
 802   /**
 803    * DOCUMENT ME!
 804    *
 805    * @param e
 806    *          DOCUMENT ME!
 807    */
 808   @Override
 809   public void annotations_actionPerformed(ActionEvent e)
 810   {
 811     conservation.setEnabled(annotations.isSelected());
 812     quality.setEnabled(annotations.isSelected());
 813     identity.setEnabled(annotations.isSelected());
 814     showGroupConsensus.setEnabled(annotations.isSelected());
 815     showGroupConservation.setEnabled(annotations.isSelected());
 816     showConsensHistogram.setEnabled(annotations.isSelected()
 817             && (identity.isSelected() || showGroupConsensus.isSelected()));
 818     showConsensLogo.setEnabled(annotations.isSelected()
 819             && (identity.isSelected() || showGroupConsensus.isSelected()));
 820   }
 821
 822   @Override
 823   public void newLink_actionPerformed(ActionEvent e)
 824   {
 825     GSequenceLink link = new GSequenceLink();
 826     boolean valid = false;
 827     while (!valid)
 828     {
 829       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 830               MessageManager.getString("label.new_sequence_url_link"),
 831               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 832       {
 833         if (link.checkValid())
 834         {
 835           ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
 836                   link.getName(), link.getURL());
 837           valid = true;
 838         }
 839       }
 840       else
 841       {
 842         break;
 843       }
 844     }
 845   }
 846
 847   @Override
 848   public void editLink_actionPerformed(ActionEvent e)
 849   {
 850     GSequenceLink link = new GSequenceLink();
 851
 852     int index = linkUrlTable.getSelectedRow();
 853     if (index == -1)
 854     {
 855       // no row was selected
 856       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 857               MessageManager.getString("label.no_link_selected"),
 858               MessageManager.getString("label.no_link_selected"),
 859               JOptionPane.WARNING_MESSAGE);
 860       return;
 861     }
 862
 863     link.setName(linkUrlTable.getValueAt(index, 0).toString());
 864     link.setURL(linkUrlTable.getValueAt(index, 1).toString());
 865
 866     boolean valid = false;
 867     while (!valid)
 868     {
 869       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 870               MessageManager.getString("label.new_sequence_url_link"),
 871               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 872       {
 873         if (link.checkValid())
 874         {
 875           linkUrlTable.setValueAt(link.getName(), index, 0);
 876           linkUrlTable.setValueAt(link.getURL(), index, 1);
 877           valid = true;
 878         }
 879       }
 880       else
 881       {
 882         break;
 883       }
 884     }
 885   }
 886
 887   @Override
 888   public void deleteLink_actionPerformed(ActionEvent e)
 889   {
 890     int index = linkUrlTable.getSelectedRow();
 891     int modelIndex = -1;
 892     if (index == -1)
 893     {
 894       // no row is selected
 895       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 896               MessageManager.getString("label.no_link_selected"),
 897               MessageManager.getString("label.no_link_selected"),
 898               JOptionPane.WARNING_MESSAGE);
 899       return;
 900     }
 901     else
 902     {
 903       modelIndex = linkUrlTable.convertRowIndexToModel(index);
 904     }
 905
 906     // make sure we use the model index to delete, and not the table index
 907     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
 908   }
 909
 910
 911   @Override
 912   public void defaultBrowser_mouseClicked(MouseEvent e)
 913   {
 914     JFileChooser chooser = new JFileChooser(".");
 915     chooser.setDialogTitle(MessageManager
 916             .getString("label.select_default_browser"));
 917
 918     int value = chooser.showOpenDialog(this);
 919
 920     if (value == JFileChooser.APPROVE_OPTION)
 921     {
 922       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 923     }
 924
 925   }
 926
 927   /*
 928    * (non-Javadoc)
 929    *
 930    * @see
 931    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 932    * .ActionEvent)
 933    */
 934   @Override
 935   protected void showunconserved_actionPerformed(ActionEvent e)
 936   {
 937     // TODO Auto-generated method stub
 938     super.showunconserved_actionPerformed(e);
 939   }
 940
 941   public static List<String> getGroupURLLinks()
 942   {
 943     return groupURLLinks;
 944   }
 945
 946   @Override
 947   public void minColour_actionPerformed(JPanel panel)
 948   {
 949     Color col = JColorChooser.showDialog(this,
 950             MessageManager.getString("label.select_colour_minimum_value"),
 951             minColour.getBackground());
 952     if (col != null)
 953     {
 954       panel.setBackground(col);
 955     }
 956     panel.repaint();
 957   }
 958
 959   @Override
 960   public void maxColour_actionPerformed(JPanel panel)
 961   {
 962     Color col = JColorChooser.showDialog(this,
 963             MessageManager.getString("label.select_colour_maximum_value"),
 964             maxColour.getBackground());
 965     if (col != null)
 966     {
 967       panel.setBackground(col);
 968     }
 969     panel.repaint();
 970   }
 971
 972   @Override
 973   protected void userIdWidth_actionPerformed()
 974   {
 975     try
 976     {
 977       String val = userIdWidth.getText().trim();
 978       if (val.length() > 0)
 979       {
 980         Integer iw = Integer.parseInt(val);
 981         if (iw.intValue() < 12)
 982         {
 983           throw new NumberFormatException();
 984         }
 985         userIdWidth.setText(iw.toString());
 986       }
 987     } catch (NumberFormatException x)
 988     {
 989       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 990               .getString("warn.user_defined_width_requirements"),
 991               MessageManager.getString("label.invalid_id_column_width"),
 992               JOptionPane.WARNING_MESSAGE);
 993       userIdWidth.setText("");
 994     }
 995   }
 996
 997   @Override
 998   protected void autoIdWidth_actionPerformed()
 999   {
1000     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1001     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1002   }
1003
1004   /**
1005    * Returns true if chimera path is to a valid executable, else show an error
1006    * dialog.
1007    */
1008   private boolean validateChimeraPath()
1009   {
1010     if (chimeraPath.getText().trim().length() > 0)
1011     {
1012       File f = new File(chimeraPath.getText());
1013       if (!f.canExecute())
1014       {
1015         JOptionPane.showInternalMessageDialog(Desktop.desktop,
1016                 MessageManager.getString("label.invalid_chimera_path"),
1017                 MessageManager.getString("label.invalid_name"),
1018                 JOptionPane.ERROR_MESSAGE);
1019         return false;
1020       }
1021     }
1022     return true;
1023   }
1024
1025   /**
1026    * If Chimera is selected, check it can be found on default or user-specified
1027    * path, if not show a warning/help dialog.
1028    */
1029   @Override
1030   protected void structureViewer_actionPerformed(String selectedItem)
1031   {
1032     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1033     {
1034       return;
1035     }
1036     boolean found = false;
1037
1038     /*
1039      * Try user-specified and standard paths for Chimera executable.
1040      */
1041     List<String> paths = StructureManager.getChimeraPaths();
1042     paths.add(0, chimeraPath.getText());
1043     for (String path : paths)
1044     {
1045       if (new File(path.trim()).canExecute())
1046       {
1047         found = true;
1048         break;
1049       }
1050     }
1051     if (!found)
1052     {
1053       String[] options = { "OK", "Help" };
1054       int showHelp = JOptionPane.showInternalOptionDialog(
1055               Desktop.desktop,
1056               JvSwingUtils.wrapTooltip(true,
1057                       MessageManager.getString("label.chimera_missing")),
1058               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
1059               null, options, options[0]);
1060       if (showHelp == JOptionPane.NO_OPTION)
1061       {
1062         try
1063         {
1064           Help.showHelpWindow(HelpId.StructureViewer);
1065         } catch (HelpSetException e)
1066         {
1067           e.printStackTrace();
1068         }
1069       }
1070     }
1071   }
1072
1073   public class OptionsParam
1074   {
1075     private String name;
1076
1077     private String code;
1078
1079     public OptionsParam(String name, String code)
1080     {
1081       this.name = name;
1082       this.code = code;
1083     }
1084
1085     public String getName()
1086     {
1087       return name;
1088     }
1089
1090     public void setName(String name)
1091     {
1092       this.name = name;
1093     }
1094
1095     public String getCode()
1096     {
1097       return code;
1098     }
1099
1100     public void setCode(String code)
1101     {
1102       this.code = code;
1103     }
1104
1105     @Override
1106     public String toString()
1107     {
1108       return name;
1109     }
1110
1111     @Override
1112     public boolean equals(Object that)
1113     {
1114       if (!(that instanceof OptionsParam))
1115       {
1116         return false;
1117       }
1118       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1119     }
1120
1121     @Override
1122     public int hashCode()
1123     {
1124       return name.hashCode() + code.hashCode();
1125     }
1126   }
1127
1128   private class UrlListSelectionHandler implements ListSelectionListener
1129   {
1130
1131     @Override
1132     public void valueChanged(ListSelectionEvent e)
1133     {
1134       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1135
1136       int index = lsm.getMinSelectionIndex();
1137       if (index == -1)
1138       {
1139         // no selection, so disable delete/edit buttons
1140         editLink.setEnabled(false);
1141         deleteLink.setEnabled(false);
1142         return;
1143       }
1144       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1145
1146       // determine if the new selection is a custom url or not
1147       if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable
1148 .getModel()
1149               .getValueAt(modelIndex, 4))) // KM TODO do this better
1150       {
1151         // entry is not a user-defined url and so should not be edited
1152         // disable edit and delete buttons
1153         deleteLink.setEnabled(false);
1154         editLink.setEnabled(false);
1155       }
1156       else
1157       {
1158         deleteLink.setEnabled(true);
1159         editLink.setEnabled(true);
1160       }
1161
1162       // BUT it's the default url, don't allow deletion
1163       if ((boolean) linkUrlTable.getValueAt(index, 3))
1164       {
1165         deleteLink.setEnabled(false);
1166       }
1167     }
1168 }
1169 }