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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.help.HelpSetException;
  36 import javax.swing.JColorChooser;
  37 import javax.swing.JFileChooser;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.ListSelectionModel;
  41 import javax.swing.RowFilter;
  42 import javax.swing.RowSorter;
  43 import javax.swing.SortOrder;
  44 import javax.swing.event.DocumentEvent;
  45 import javax.swing.event.DocumentListener;
  46 import javax.swing.event.ListSelectionEvent;
  47 import javax.swing.event.ListSelectionListener;
  48 import javax.swing.table.TableCellRenderer;
  49 import javax.swing.table.TableColumn;
  50 import javax.swing.table.TableModel;
  51 import javax.swing.table.TableRowSorter;
  52
  53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  54 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  55 import jalview.bin.Cache;
  56 import jalview.gui.Help.HelpId;
  57 import jalview.gui.StructureViewer.ViewerType;
  58 import jalview.io.BackupFiles;
  59 import jalview.io.BackupFilesPresetEntry;
  60 import jalview.io.FileFormatI;
  61 import jalview.io.JalviewFileChooser;
  62 import jalview.io.JalviewFileView;
  63 import jalview.jbgui.GPreferences;
  64 import jalview.jbgui.GSequenceLink;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.ColourSchemes;
  67 import jalview.schemes.ResidueColourScheme;
  68 import jalview.urls.UrlLinkTableModel;
  69 import jalview.urls.api.UrlProviderFactoryI;
  70 import jalview.urls.api.UrlProviderI;
  71 import jalview.urls.desktop.DesktopUrlProviderFactory;
  72 import jalview.util.MessageManager;
  73 import jalview.util.Platform;
  74 import jalview.util.UrlConstants;
  75 import jalview.ws.sifts.SiftsSettings;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   private String previousProxyType;
 126
 127   /**
 128    * Holds name and link separated with | character. Sequence ID must be
 129    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 130    */
 131   public static UrlProviderI sequenceUrlLinks;
 132
 133   public static UrlLinkTableModel dataModel;
 134
 135   /**
 136    * Holds name and link separated with | character. Sequence IDS and Sequences
 137    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 138    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 139    * for first and second token specified after a pipe character at end |,|.
 140    * (TODO: proper escape for using | to separate ids or sequences
 141    */
 142
 143   public static List<String> groupURLLinks;
 144   static
 145   {
 146     // get links selected to be in the menu (SEQUENCE_LINKS)
 147     // and links entered by the user but not selected (STORED_LINKS)
 148     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 149     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 150     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 151             UrlConstants.DEFAULT_LABEL);
 152
 153     // if both links lists are empty, add the DEFAULT_URL link
 154     // otherwise we assume the default link is in one of the lists
 155     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 156     {
 157       inMenuString = UrlConstants.DEFAULT_STRING;
 158     }
 159     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 160             inMenuString, notInMenuString);
 161     sequenceUrlLinks = factory.createUrlProvider();
 162     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 163
 164     /**
 165      * TODO: reformulate groupURL encoding so two or more can be stored in the
 166      * .properties file as '|' separated strings
 167      */
 168
 169     groupURLLinks = new ArrayList<>();
 170   }
 171
 172   JInternalFrame frame;
 173
 174   private WsPreferences wsPrefs;
 175
 176   private OptionsParam promptEachTimeOpt = new OptionsParam(
 177           MessageManager.getString("label.prompt_each_time"),
 178           "Prompt each time");
 179
 180   private OptionsParam lineArtOpt = new OptionsParam(
 181           MessageManager.getString("label.lineart"), "Lineart");
 182
 183   private OptionsParam textOpt = new OptionsParam(
 184           MessageManager.getString("action.text"), "Text");
 185
 186   /**
 187    * Creates a new Preferences object.
 188    */
 189   public Preferences()
 190   {
 191     super();
 192     frame = new JInternalFrame();
 193     frame.setContentPane(this);
 194     wsPrefs = new WsPreferences();
 195     wsTab.add(wsPrefs, BorderLayout.CENTER);
 196     int width = 500, height = 450;
 197     new jalview.util.Platform();
 198     if (Platform.isAMac())
 199     {
 200       width = 570;
 201       height = 480;
 202     }
 203
 204     Desktop.addInternalFrame(frame,
 205             MessageManager.getString("label.preferences"), width, height);
 206     frame.setMinimumSize(new Dimension(width, height));
 207
 208     /*
 209      * Set Visual tab defaults
 210      */
 211     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 212     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 213     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 214     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 215
 216     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 217     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 218     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 219     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 220     showUnconserved
 221             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 222     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 223     showGroupConsensus
 224             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 225     showGroupConservation.setSelected(
 226             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 227     showConsensHistogram.setSelected(
 228             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 229     showConsensLogo
 230             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 231     showNpTooltip
 232             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 233     showDbRefTooltip
 234             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 235
 236     String[] fonts = java.awt.GraphicsEnvironment
 237             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 238     for (int i = 0; i < fonts.length; i++)
 239     {
 240       fontNameCB.addItem(fonts[i]);
 241     }
 242
 243     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 244     {
 245       fontSizeCB.addItem(i + "");
 246     }
 247
 248     fontStyleCB.addItem("plain");
 249     fontStyleCB.addItem("bold");
 250     fontStyleCB.addItem("italic");
 251
 252     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 253     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 254     fontStyleCB.setSelectedItem(
 255             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 256
 257     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 258     scaleProteinToCdna
 259             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 260
 261     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 262
 263     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 264
 265     gapSymbolCB.addItem("-");
 266     gapSymbolCB.addItem(".");
 267
 268     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 269
 270     sortby.addItem("No sort");
 271     sortby.addItem("Id");
 272     sortby.addItem("Pairwise Identity");
 273     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 274
 275     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 278     sortAnnBy
 279             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 280     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 281             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 282                     SequenceAnnotationOrder.NONE.name()));
 283     sortAnnBy.setSelectedItem(savedSort.toString());
 284
 285     sortAutocalc.addItem("Autocalculated first");
 286     sortAutocalc.addItem("Autocalculated last");
 287     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 288     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 289             : sortAutocalc.getItemAt(1));
 290     startupCheckbox
 291             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 292     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 293             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 294                     + "/examples/exampleFile_2_3.jar"));
 295
 296     /*
 297      * Set Colours tab defaults
 298      */
 299     protColour.addItem(ResidueColourScheme.NONE);
 300     nucColour.addItem(ResidueColourScheme.NONE);
 301     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 302     {
 303       String name = cs.getSchemeName();
 304       protColour.addItem(name);
 305       nucColour.addItem(name);
 306     }
 307     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 308             ResidueColourScheme.NONE);
 309     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 310     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 312     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 313     minColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 315     maxColour.setBackground(
 316             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 317
 318     /*
 319      * Set overview panel defaults
 320      */
 321     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 322             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 323     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 324             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 325     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 326     gapLabel.setEnabled(!useLegacyGap.isSelected());
 327     gapColour.setEnabled(!useLegacyGap.isSelected());
 328     showHiddenAtStart
 329             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 330
 331     /*
 332      * Set Structure tab defaults.
 333      */
 334     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 335     structFromPdb.setSelected(structSelected);
 336     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 337     useRnaView.setEnabled(structSelected);
 338     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 339     addSecondaryStructure.setEnabled(structSelected);
 340     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 341     addTempFactor.setEnabled(structSelected);
 342     structViewer.setSelectedItem(
 343             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 344     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 345     chimeraPath.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         validateChimeraPath();
 351       }
 352     });
 353
 354     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 355     {
 356       siftsMapping.setSelected(true);
 357     }
 358     else
 359     {
 360       nwMapping.setSelected(true);
 361     }
 362
 363     SiftsSettings
 364             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 365
 366     /*
 367      * Set Connections tab defaults
 368      */
 369
 370     // set up sorting
 371     linkUrlTable.setModel(dataModel);
 372     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 373             linkUrlTable.getModel());
 374     linkUrlTable.setRowSorter(sorter);
 375     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 376
 377     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 378     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(
 383             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 384
 385     sorter.setSortKeys(sortKeys);
 386     sorter.sort();
 387
 388     // set up filtering
 389     ActionListener onReset;
 390     onReset = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         filterTB.setText("");
 396         sorter.setRowFilter(RowFilter.regexFilter(""));
 397       }
 398
 399     };
 400     doReset.addActionListener(onReset);
 401
 402     // filter to display only custom urls
 403     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 404     {
 405       @Override
 406       public boolean include(
 407               Entry<? extends TableModel, ? extends Object> entry)
 408       {
 409         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 410       }
 411     };
 412
 413     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 414             linkUrlTable.getModel());
 415     customSorter.setRowFilter(customUrlFilter);
 416
 417     ActionListener onCustomOnly;
 418     onCustomOnly = new ActionListener()
 419     {
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         filterTB.setText("");
 424         sorter.setRowFilter(customUrlFilter);
 425       }
 426     };
 427     userOnly.addActionListener(onCustomOnly);
 428
 429     filterTB.getDocument().addDocumentListener(new DocumentListener()
 430     {
 431       String caseInsensitiveFlag = "(?i)";
 432
 433       @Override
 434       public void changedUpdate(DocumentEvent e)
 435       {
 436         sorter.setRowFilter(RowFilter
 437                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 438       }
 439
 440       @Override
 441       public void removeUpdate(DocumentEvent e)
 442       {
 443         sorter.setRowFilter(RowFilter
 444                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 445       }
 446
 447       @Override
 448       public void insertUpdate(DocumentEvent e)
 449       {
 450         sorter.setRowFilter(RowFilter
 451                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 452       }
 453     });
 454
 455     // set up list selection functionality
 456     linkUrlTable.getSelectionModel()
 457             .addListSelectionListener(new UrlListSelectionHandler());
 458
 459     // set up radio buttons
 460     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 461             .getPrimaryColumn();
 462     String onClickName = linkUrlTable.getColumnName(onClickCol);
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellRenderer(new RadioButtonRenderer());
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellEditor(new RadioButtonEditor());
 467
 468     // get boolean columns and resize those to min possible
 469     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 470     {
 471       if (linkUrlTable.getModel().getColumnClass(column)
 472               .equals(Boolean.class))
 473       {
 474         TableColumn tableColumn = linkUrlTable.getColumnModel()
 475                 .getColumn(column);
 476         int preferredWidth = tableColumn.getMinWidth();
 477
 478         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 479                 column);
 480         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 481         int cwidth = c.getPreferredSize().width
 482                 + linkUrlTable.getIntercellSpacing().width;
 483         preferredWidth = Math.max(preferredWidth, cwidth);
 484
 485         tableColumn.setPreferredWidth(preferredWidth);
 486       }
 487     }
 488
 489     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 490     previousProxyType = proxyTypeString;
 491     switch (proxyTypeString)
 492     {
 493     case Cache.PROXYTYPE_NONE:
 494       proxyType.setSelected(noProxy.getModel(), true);
 495       break;
 496     case Cache.PROXYTYPE_SYSTEM:
 497       proxyType.setSelected(systemProxy.getModel(), true);
 498       break;
 499     case Cache.PROXYTYPE_CUSTOM:
 500       proxyType.setSelected(customProxy.getModel(), true);
 501       break;
 502     default:
 503       String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 504               + proxyTypeString;
 505       Cache.log.warn(message);
 506     }
 507     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 508     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 509     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 510     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 511     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 512     proxyAuthUsernameTB
 513             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 514     proxyAuthPasswordTB
 515             .setText(Cache.getDefault("PROXY_AUTH_PASSWORD", ""));
 516     setCustomProxyEnabled();
 517
 518     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 519
 520     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 521     // note antisense here: default is true
 522     questionnaire
 523             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 524     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 525
 526     /*
 527      * Set Output tab defaults
 528      */
 529     epsRendering.addItem(promptEachTimeOpt);
 530     epsRendering.addItem(lineArtOpt);
 531     epsRendering.addItem(textOpt);
 532     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 533             "Prompt each time");
 534     if (defaultEPS.equalsIgnoreCase("Text"))
 535     {
 536       epsRendering.setSelectedItem(textOpt);
 537     }
 538     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 539     {
 540       epsRendering.setSelectedItem(lineArtOpt);
 541     }
 542     else
 543     {
 544       epsRendering.setSelectedItem(promptEachTimeOpt);
 545     }
 546     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 547     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 548     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 549     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 550     userIdWidth.setText(wi == null ? "" : wi.toString());
 551     // TODO: refactor to use common enum via FormatAdapter and allow extension
 552     // for new flat file formats
 553     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 554     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 555     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 556     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 557     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 558     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 559     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 560     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 561     embbedBioJSON
 562             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 563
 564     /*
 565      * Set Editing tab defaults
 566      */
 567     autoCalculateConsCheck
 568             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 569     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 570     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 571
 572     annotations_actionPerformed(null); // update the display of the annotation
 573                                        // settings
 574
 575     /*
 576      * Set Backups tab defaults
 577      */
 578     loadLastSavedBackupsOptions();
 579   }
 580
 581   /**
 582    * Save user selections on the Preferences tabs to the Cache and write out to
 583    * file.
 584    *
 585    * @param e
 586    */
 587   @Override
 588   public void ok_actionPerformed(ActionEvent e)
 589   {
 590     if (!validateSettings())
 591     {
 592       return;
 593     }
 594
 595     /*
 596      * Save Visual settings
 597      */
 598     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 599             Boolean.toString(seqLimit.isSelected()));
 600     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 601             Boolean.toString(rightAlign.isSelected()));
 602     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 603             Boolean.toString(fullScreen.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 605             Boolean.toString(openoverv.isSelected()));
 606     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 607             Boolean.toString(annotations.isSelected()));
 608     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 609             Boolean.toString(conservation.isSelected()));
 610     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 611             Boolean.toString(quality.isSelected()));
 612     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 613             Boolean.toString(identity.isSelected()));
 614
 615     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 616             gapSymbolCB.getSelectedItem().toString());
 617
 618     Cache.applicationProperties.setProperty("FONT_NAME",
 619             fontNameCB.getSelectedItem().toString());
 620     Cache.applicationProperties.setProperty("FONT_STYLE",
 621             fontStyleCB.getSelectedItem().toString());
 622     Cache.applicationProperties.setProperty("FONT_SIZE",
 623             fontSizeCB.getSelectedItem().toString());
 624
 625     Cache.applicationProperties.setProperty("ID_ITALICS",
 626             Boolean.toString(idItalics.isSelected()));
 627     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 628             Boolean.toString(showUnconserved.isSelected()));
 629     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 630             Boolean.toString(showOccupancy.isSelected()));
 631     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 632             Boolean.toString(showGroupConsensus.isSelected()));
 633     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 634             Boolean.toString(showGroupConservation.isSelected()));
 635     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 636             Boolean.toString(showConsensHistogram.isSelected()));
 637     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 638             Boolean.toString(showConsensLogo.isSelected()));
 639     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 640             Boolean.toString(smoothFont.isSelected()));
 641     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 642             Boolean.toString(scaleProteinToCdna.isSelected()));
 643     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 644             Boolean.toString(showNpTooltip.isSelected()));
 645     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 646             Boolean.toString(showDbRefTooltip.isSelected()));
 647
 648     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 649             Boolean.toString(wrap.isSelected()));
 650
 651     Cache.applicationProperties.setProperty("STARTUP_FILE",
 652             startupFileTextfield.getText());
 653     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 654             Boolean.toString(startupCheckbox.isSelected()));
 655
 656     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 657             sortby.getSelectedItem().toString());
 658
 659     // convert description of sort order to enum name for save
 660     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 661             .forDescription(sortAnnBy.getSelectedItem().toString());
 662     if (annSortOrder != null)
 663     {
 664       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 665               annSortOrder.name());
 666     }
 667
 668     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 669     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 670             Boolean.valueOf(showAutocalcFirst).toString());
 671
 672     /*
 673      * Save Colours settings
 674      */
 675     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 676             protColour.getSelectedItem().toString());
 677     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 678             nucColour.getSelectedItem().toString());
 679     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 680             minColour.getBackground());
 681     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 682             maxColour.getBackground());
 683
 684     /*
 685      * Save Overview settings
 686      */
 687     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 688     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 689     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 690             Boolean.toString(useLegacyGap.isSelected()));
 691     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 692             Boolean.toString(showHiddenAtStart.isSelected()));
 693
 694     /*
 695      * Save Structure settings
 696      */
 697     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 698             Boolean.toString(addTempFactor.isSelected()));
 699     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 700             Boolean.toString(addSecondaryStructure.isSelected()));
 701     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 702             Boolean.toString(useRnaView.isSelected()));
 703     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 704             Boolean.toString(structFromPdb.isSelected()));
 705     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 706             structViewer.getSelectedItem().toString());
 707     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 708     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 709             Boolean.toString(siftsMapping.isSelected()));
 710     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 711
 712     /*
 713      * Save Output settings
 714      */
 715     Cache.applicationProperties.setProperty("EPS_RENDERING",
 716             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 717
 718     /*
 719      * Save Connections settings
 720      */
 721     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 722
 723     jalview.util.BrowserLauncher.resetBrowser();
 724
 725     // save user-defined and selected links
 726     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 727     if (menuLinks.isEmpty())
 728     {
 729       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 730     }
 731     else
 732     {
 733       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 734               menuLinks.toString());
 735     }
 736
 737     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 738     if (nonMenuLinks.isEmpty())
 739     {
 740       Cache.applicationProperties.remove("STORED_LINKS");
 741     }
 742     else
 743     {
 744       Cache.applicationProperties.setProperty("STORED_LINKS",
 745               nonMenuLinks.toString());
 746     }
 747
 748     Cache.applicationProperties.setProperty("DEFAULT_URL",
 749             sequenceUrlLinks.getPrimaryUrlId());
 750
 751     // Proxy settings
 752     Cache.applicationProperties.setProperty("USE_PROXY",
 753             customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 754                     : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 755                             : Cache.PROXYTYPE_SYSTEM);
 756     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 757     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 758     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 759     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 760     Cache.setOrRemove("PROXY_AUTH",
 761             Boolean.toString(proxyAuth.isSelected()));
 762     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
 763     Cache.setOrRemove("PROXY_AUTH_PASSWORD", proxyAuthPasswordTB.getText());
 764     setProxyFromSettings();
 765
 766     Cache.setProperty("VERSION_CHECK",
 767             Boolean.toString(versioncheck.isSelected()));
 768     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 769     {
 770       // default is false - we only set this if the user has actively agreed
 771       Cache.setProperty("USAGESTATS",
 772               Boolean.toString(usagestats.isSelected()));
 773     }
 774     if (!questionnaire.isSelected())
 775     {
 776       Cache.setProperty("NOQUESTIONNAIRES", "true");
 777     }
 778     else
 779     {
 780       // special - made easy to edit a property file to disable questionnaires
 781       // by just adding the given line
 782       Cache.removeProperty("NOQUESTIONNAIRES");
 783     }
 784
 785     /*
 786      * Save Output settings
 787      */
 788     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 789             Boolean.toString(blcjv.isSelected()));
 790     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 791             Boolean.toString(clustaljv.isSelected()));
 792     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 793             Boolean.toString(fastajv.isSelected()));
 794     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 795             Boolean.toString(msfjv.isSelected()));
 796     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 797             Boolean.toString(pfamjv.isSelected()));
 798     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 799             Boolean.toString(pileupjv.isSelected()));
 800     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 801             Boolean.toString(pirjv.isSelected()));
 802     Cache.applicationProperties.setProperty("PIR_MODELLER",
 803             Boolean.toString(modellerOutput.isSelected()));
 804     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 805             Boolean.toString(embbedBioJSON.isSelected()));
 806     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 807
 808     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 809             Boolean.toString(autoIdWidth.isSelected()));
 810     userIdWidth_actionPerformed();
 811     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 812             userIdWidth.getText());
 813
 814     /*
 815      * Save Editing settings
 816      */
 817     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 818             Boolean.toString(autoCalculateConsCheck.isSelected()));
 819     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 820             Boolean.toString(sortByTree.isSelected()));
 821     Cache.applicationProperties.setProperty("PAD_GAPS",
 822             Boolean.toString(padGaps.isSelected()));
 823
 824     wsPrefs.updateAndRefreshWsMenuConfig(false);
 825
 826     /*
 827      * Save Backups settings
 828      */
 829     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 830             Boolean.toString(enableBackupFiles.isSelected()));
 831     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 832     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 833             Integer.toString(preset));
 834
 835     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 836     {
 837       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 838       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 839               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 840       Cache.applicationProperties.setProperty(
 841               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 842     }
 843
 844     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 845             .get(preset);
 846     Cache.applicationProperties.setProperty(
 847             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 848
 849     Cache.saveProperties();
 850     Desktop.instance.doConfigureStructurePrefs();
 851     try
 852     {
 853       frame.setClosed(true);
 854     } catch (Exception ex)
 855     {
 856     }
 857   }
 858
 859   public void setProxyFromSettings()
 860   {
 861     String proxyType = Cache.getDefault("USE_PROXY",
 862             Cache.PROXYTYPE_SYSTEM);
 863     if (proxyType.equals(Cache.PROXYTYPE_NONE))
 864     {
 865       if (!previousProxyType.equals(proxyType))
 866         Cache.log.info("Setting no proxy settings");
 867       Cache.setProxyProperties(null, null, null, null, null, null, null,
 868               null);
 869     }
 870     else if (proxyType.equals(Cache.PROXYTYPE_CUSTOM))
 871     {
 872       if (!previousProxyType.equals(proxyType))
 873         Cache.log.info("Setting custom proxy settings");
 874       boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
 875       Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
 876               Cache.getDefault("PROXY_PORT", null),
 877               Cache.getDefault("PROXY_SERVER_HTTPS", null),
 878               Cache.getDefault("PROXY_PORT_HTTPS", null),
 879               proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
 880                       : null,
 881               proxyAuthSet ? Cache.getDefault("PROXY_AUTH_PASSWORD", "")
 882                       : null);
 883     }
 884     else // systemProxy should be selected and is sensible default anyway
 885     {
 886       if (!previousProxyType.equals(proxyType))
 887         Cache.log.info("Setting system proxy settings");
 888       Cache.resetProxyProperties();
 889     }
 890   }
 891
 892   /**
 893    * Do any necessary validation before saving settings. Return focus to the
 894    * first tab which fails validation.
 895    *
 896    * @return
 897    */
 898   private boolean validateSettings()
 899   {
 900     if (!validateStructure())
 901     {
 902       structureTab.requestFocusInWindow();
 903       return false;
 904     }
 905     return true;
 906   }
 907
 908   @Override
 909   protected boolean validateStructure()
 910   {
 911     return validateChimeraPath();
 912
 913   }
 914
 915   /**
 916    * DOCUMENT ME!
 917    */
 918   @Override
 919   public void startupFileTextfield_mouseClicked()
 920   {
 921     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 922     JalviewFileChooser chooser = JalviewFileChooser
 923             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 924     chooser.setFileView(new JalviewFileView());
 925     chooser.setDialogTitle(
 926             MessageManager.getString("label.select_startup_file"));
 927
 928     int value = chooser.showOpenDialog(this);
 929
 930     if (value == JalviewFileChooser.APPROVE_OPTION)
 931     {
 932       FileFormatI format = chooser.getSelectedFormat();
 933       if (format != null)
 934       {
 935         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 936                 format.getName());
 937       }
 938       startupFileTextfield
 939               .setText(chooser.getSelectedFile().getAbsolutePath());
 940     }
 941   }
 942
 943   /**
 944    * DOCUMENT ME!
 945    *
 946    * @param e
 947    *          DOCUMENT ME!
 948    */
 949   @Override
 950   public void cancel_actionPerformed(ActionEvent e)
 951   {
 952     try
 953     {
 954       wsPrefs.updateWsMenuConfig(true);
 955       wsPrefs.refreshWs_actionPerformed(e);
 956       frame.setClosed(true);
 957     } catch (Exception ex)
 958     {
 959     }
 960   }
 961
 962   /**
 963    * DOCUMENT ME!
 964    *
 965    * @param e
 966    *          DOCUMENT ME!
 967    */
 968   @Override
 969   public void annotations_actionPerformed(ActionEvent e)
 970   {
 971     conservation.setEnabled(annotations.isSelected());
 972     quality.setEnabled(annotations.isSelected());
 973     identity.setEnabled(annotations.isSelected());
 974     showOccupancy.setEnabled(annotations.isSelected());
 975     showGroupConsensus.setEnabled(annotations.isSelected());
 976     showGroupConservation.setEnabled(annotations.isSelected());
 977     showConsensHistogram.setEnabled(annotations.isSelected()
 978             && (identity.isSelected() || showGroupConsensus.isSelected()));
 979     showConsensLogo.setEnabled(annotations.isSelected()
 980             && (identity.isSelected() || showGroupConsensus.isSelected()));
 981   }
 982
 983   @Override
 984   public void newLink_actionPerformed(ActionEvent e)
 985   {
 986     GSequenceLink link = new GSequenceLink();
 987     boolean valid = false;
 988     while (!valid)
 989     {
 990       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 991               MessageManager.getString("label.new_sequence_url_link"),
 992               JvOptionPane.OK_CANCEL_OPTION, -1,
 993               null) == JvOptionPane.OK_OPTION)
 994       {
 995         if (link.checkValid())
 996         {
 997           if (((UrlLinkTableModel) linkUrlTable.getModel())
 998                   .isUniqueName(link.getName()))
 999           {
1000             ((UrlLinkTableModel) linkUrlTable.getModel())
1001                     .insertRow(link.getName(), link.getURL());
1002             valid = true;
1003           }
1004           else
1005           {
1006             link.notifyDuplicate();
1007             continue;
1008           }
1009         }
1010       }
1011       else
1012       {
1013         break;
1014       }
1015     }
1016   }
1017
1018   @Override
1019   public void editLink_actionPerformed(ActionEvent e)
1020   {
1021     GSequenceLink link = new GSequenceLink();
1022
1023     int index = linkUrlTable.getSelectedRow();
1024     if (index == -1)
1025     {
1026       // button no longer enabled if row is not selected
1027       Cache.log.debug("Edit with no row selected in linkUrlTable");
1028       return;
1029     }
1030
1031     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1032             .getNameColumn();
1033     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1034             .getUrlColumn();
1035     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1036     link.setName(oldName);
1037     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1038
1039     boolean valid = false;
1040     while (!valid)
1041     {
1042       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1043               MessageManager.getString("label.edit_sequence_url_link"),
1044               JvOptionPane.OK_CANCEL_OPTION, -1,
1045               null) == JvOptionPane.OK_OPTION)
1046       {
1047         if (link.checkValid())
1048         {
1049           if ((oldName.equals(link.getName()))
1050                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1051                           .isUniqueName(link.getName())))
1052           {
1053             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1054             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1055             valid = true;
1056           }
1057           else
1058           {
1059             link.notifyDuplicate();
1060             continue;
1061           }
1062         }
1063       }
1064       else
1065       {
1066         break;
1067       }
1068     }
1069   }
1070
1071   @Override
1072   public void deleteLink_actionPerformed(ActionEvent e)
1073   {
1074     int index = linkUrlTable.getSelectedRow();
1075     int modelIndex = -1;
1076     if (index == -1)
1077     {
1078       // button no longer enabled if row is not selected
1079       Cache.log.debug("Delete with no row selected in linkUrlTable");
1080       return;
1081     }
1082     else
1083     {
1084       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1085     }
1086
1087     // make sure we use the model index to delete, and not the table index
1088     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1089   }
1090
1091   @Override
1092   public void defaultBrowser_mouseClicked(MouseEvent e)
1093   {
1094     JFileChooser chooser = new JFileChooser(".");
1095     chooser.setDialogTitle(
1096             MessageManager.getString("label.select_default_browser"));
1097
1098     int value = chooser.showOpenDialog(this);
1099
1100     if (value == JFileChooser.APPROVE_OPTION)
1101     {
1102       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1103     }
1104
1105   }
1106
1107   /*
1108    * (non-Javadoc)
1109    *
1110    * @see
1111    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1112    * .ActionEvent)
1113    */
1114   @Override
1115   protected void showunconserved_actionPerformed(ActionEvent e)
1116   {
1117     // TODO Auto-generated method stub
1118     super.showunconserved_actionPerformed(e);
1119   }
1120
1121   public static List<String> getGroupURLLinks()
1122   {
1123     return groupURLLinks;
1124   }
1125
1126   @Override
1127   public void minColour_actionPerformed(JPanel panel)
1128   {
1129     Color col = JColorChooser.showDialog(this,
1130             MessageManager.getString("label.select_colour_minimum_value"),
1131             minColour.getBackground());
1132     if (col != null)
1133     {
1134       panel.setBackground(col);
1135     }
1136     panel.repaint();
1137   }
1138
1139   @Override
1140   public void maxColour_actionPerformed(JPanel panel)
1141   {
1142     Color col = JColorChooser.showDialog(this,
1143             MessageManager.getString("label.select_colour_maximum_value"),
1144             maxColour.getBackground());
1145     if (col != null)
1146     {
1147       panel.setBackground(col);
1148     }
1149     panel.repaint();
1150   }
1151
1152   @Override
1153   public void gapColour_actionPerformed(JPanel gap)
1154   {
1155     if (!useLegacyGap.isSelected())
1156     {
1157       Color col = JColorChooser.showDialog(this,
1158               MessageManager.getString("label.select_gap_colour"),
1159               gapColour.getBackground());
1160       if (col != null)
1161       {
1162         gap.setBackground(col);
1163       }
1164       gap.repaint();
1165     }
1166   }
1167
1168   @Override
1169   public void hiddenColour_actionPerformed(JPanel hidden)
1170   {
1171     Color col = JColorChooser.showDialog(this,
1172             MessageManager.getString("label.select_hidden_colour"),
1173             hiddenColour.getBackground());
1174     if (col != null)
1175     {
1176       hidden.setBackground(col);
1177     }
1178     hidden.repaint();
1179   }
1180
1181   @Override
1182   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1183   {
1184     boolean enabled = useLegacyGap.isSelected();
1185     if (enabled)
1186     {
1187       gapColour.setBackground(
1188               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1189     }
1190     else
1191     {
1192       gapColour.setBackground(
1193               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1194     }
1195     gapColour.setEnabled(!enabled);
1196     gapLabel.setEnabled(!enabled);
1197   }
1198
1199   @Override
1200   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1201   {
1202     useLegacyGap.setSelected(false);
1203     useLegacyGaps_actionPerformed(null);
1204     showHiddenAtStart.setSelected(false);
1205     hiddenColour.setBackground(
1206             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1207   }
1208
1209   @Override
1210   protected void userIdWidth_actionPerformed()
1211   {
1212     try
1213     {
1214       String val = userIdWidth.getText().trim();
1215       if (val.length() > 0)
1216       {
1217         Integer iw = Integer.parseInt(val);
1218         if (iw.intValue() < 12)
1219         {
1220           throw new NumberFormatException();
1221         }
1222         userIdWidth.setText(iw.toString());
1223       }
1224     } catch (NumberFormatException x)
1225     {
1226       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1227               MessageManager
1228                       .getString("warn.user_defined_width_requirements"),
1229               MessageManager.getString("label.invalid_id_column_width"),
1230               JvOptionPane.WARNING_MESSAGE);
1231       userIdWidth.setText("");
1232     }
1233   }
1234
1235   @Override
1236   protected void autoIdWidth_actionPerformed()
1237   {
1238     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1239     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1240   }
1241
1242   /**
1243    * Returns true if chimera path is to a valid executable, else show an error
1244    * dialog.
1245    */
1246   private boolean validateChimeraPath()
1247   {
1248     if (chimeraPath.getText().trim().length() > 0)
1249     {
1250       File f = new File(chimeraPath.getText());
1251       if (!f.canExecute())
1252       {
1253         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1254                 MessageManager.getString("label.invalid_chimera_path"),
1255                 MessageManager.getString("label.invalid_name"),
1256                 JvOptionPane.ERROR_MESSAGE);
1257         return false;
1258       }
1259     }
1260     return true;
1261   }
1262
1263   /**
1264    * If Chimera is selected, check it can be found on default or user-specified
1265    * path, if not show a warning/help dialog.
1266    */
1267   @Override
1268   protected void structureViewer_actionPerformed(String selectedItem)
1269   {
1270     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1271     {
1272       return;
1273     }
1274     boolean found = false;
1275
1276     /*
1277      * Try user-specified and standard paths for Chimera executable.
1278      */
1279     List<String> paths = StructureManager.getChimeraPaths();
1280     paths.add(0, chimeraPath.getText());
1281     for (String path : paths)
1282     {
1283       if (new File(path.trim()).canExecute())
1284       {
1285         found = true;
1286         break;
1287       }
1288     }
1289     if (!found)
1290     {
1291       String[] options = { "OK", "Help" };
1292       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1293               JvSwingUtils.wrapTooltip(true,
1294                       MessageManager.getString("label.chimera_missing")),
1295               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1296               null, options, options[0]);
1297       if (showHelp == JvOptionPane.NO_OPTION)
1298       {
1299         try
1300         {
1301           Help.showHelpWindow(HelpId.StructureViewer);
1302         } catch (HelpSetException e)
1303         {
1304           e.printStackTrace();
1305         }
1306       }
1307     }
1308   }
1309
1310   public class OptionsParam
1311   {
1312     private String name;
1313
1314     private String code;
1315
1316     public OptionsParam(String name, String code)
1317     {
1318       this.name = name;
1319       this.code = code;
1320     }
1321
1322     public String getName()
1323     {
1324       return name;
1325     }
1326
1327     public void setName(String name)
1328     {
1329       this.name = name;
1330     }
1331
1332     public String getCode()
1333     {
1334       return code;
1335     }
1336
1337     public void setCode(String code)
1338     {
1339       this.code = code;
1340     }
1341
1342     @Override
1343     public String toString()
1344     {
1345       return name;
1346     }
1347
1348     @Override
1349     public boolean equals(Object that)
1350     {
1351       if (!(that instanceof OptionsParam))
1352       {
1353         return false;
1354       }
1355       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1356     }
1357
1358     @Override
1359     public int hashCode()
1360     {
1361       return name.hashCode() + code.hashCode();
1362     }
1363   }
1364
1365   private class UrlListSelectionHandler implements ListSelectionListener
1366   {
1367
1368     @Override
1369     public void valueChanged(ListSelectionEvent e)
1370     {
1371       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1372
1373       int index = lsm.getMinSelectionIndex();
1374       if (index == -1)
1375       {
1376         // no selection, so disable delete/edit buttons
1377         editLink.setEnabled(false);
1378         deleteLink.setEnabled(false);
1379         return;
1380       }
1381       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1382
1383       // enable/disable edit and delete link buttons
1384       if (((UrlLinkTableModel) linkUrlTable.getModel())
1385               .isRowDeletable(modelIndex))
1386       {
1387         deleteLink.setEnabled(true);
1388       }
1389       else
1390       {
1391         deleteLink.setEnabled(false);
1392       }
1393
1394       if (((UrlLinkTableModel) linkUrlTable.getModel())
1395               .isRowEditable(modelIndex))
1396       {
1397         editLink.setEnabled(true);
1398       }
1399       else
1400       {
1401         editLink.setEnabled(false);
1402       }
1403     }
1404   }
1405
1406 }