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 /*
  84  * for merge with Jalview-JS
  85  public class Preferences extends GPreferences implements ApplicationSingletonI
  86  */
  87 public class Preferences extends GPreferences
  88 {
  89   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  90
  91   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  92
  93   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  94
  95   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  96
  97   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  98
  99   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 100
 101   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 102
 103   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 104
 105   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 106
 107   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 108
 109   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 110
 111   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 112
 113   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 114
 115   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 116
 117   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 118
 119   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 120
 121   public static final String GAP_COLOUR = "GAP_COLOUR";
 122
 123   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 124
 125   private static final int MIN_FONT_SIZE = 1;
 126
 127   private static final int MAX_FONT_SIZE = 30;
 128
 129   private String previousProxyType;
 130
 131   private static Preferences INSTANCE = null; // add "final"
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence ID must be
 135    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 136    */
 137   public static UrlProviderI sequenceUrlLinks;
 138
 139   public static UrlLinkTableModel dataModel;
 140
 141   /**
 142    * Holds name and link separated with | character. Sequence IDS and Sequences
 143    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 144    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 145    * for first and second token specified after a pipe character at end |,|.
 146    * (TODO: proper escape for using | to separate ids or sequences
 147    */
 148
 149   public static List<String> groupURLLinks;
 150   static
 151   {
 152     // get links selected to be in the menu (SEQUENCE_LINKS)
 153     // and links entered by the user but not selected (STORED_LINKS)
 154     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 155     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 156     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 157             UrlConstants.DEFAULT_LABEL);
 158
 159     // if both links lists are empty, add the DEFAULT_URL link
 160     // otherwise we assume the default link is in one of the lists
 161     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 162     {
 163       inMenuString = UrlConstants.DEFAULT_STRING;
 164     }
 165     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 166             inMenuString, notInMenuString);
 167     sequenceUrlLinks = factory.createUrlProvider();
 168     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 169
 170     /**
 171      * TODO: reformulate groupURL encoding so two or more can be stored in the
 172      * .properties file as '|' separated strings
 173      */
 174
 175     groupURLLinks = new ArrayList<>();
 176   }
 177
 178   JInternalFrame frame;
 179
 180   private WsPreferences wsPrefs;
 181
 182   private OptionsParam promptEachTimeOpt = new OptionsParam(
 183           MessageManager.getString("label.prompt_each_time"),
 184           "Prompt each time");
 185
 186   private OptionsParam lineArtOpt = new OptionsParam(
 187           MessageManager.getString("label.lineart"), "Lineart");
 188
 189   private OptionsParam textOpt = new OptionsParam(
 190           MessageManager.getString("action.text"), "Text");
 191
 192   // get singleton Preferences instance
 193   public static Preferences getInstance()
 194   {
 195     if (INSTANCE == null || INSTANCE.frame == null
 196             || INSTANCE.frame.isClosed())
 197     {
 198       INSTANCE = new Preferences();
 199     }
 200     return INSTANCE;
 201
 202     /*
 203      * Replace code with the following for Jalvew-JS
 204     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 205     if (INSTANCE == null || INSTANCE.frame == null
 206             || INSTANCE.frame.isClosed())
 207     {
 208       ApplicationSingletonProvider.remove(Preferences.class);
 209       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 210     }
 211     return INSTANCE;
 212     */
 213   }
 214
 215   public static void openPreferences()
 216   {
 217     openPreferences(0, null);
 218   }
 219
 220   public static void openPreferences(int selectTab, String message)
 221   {
 222     Preferences p = getInstance();
 223     p.selectTab(selectTab);
 224     p.setMessage(message);
 225     p.frame.show();
 226     p.frame.moveToFront();
 227     p.frame.grabFocus();
 228   }
 229
 230   /**
 231    * Creates a new Preferences object.
 232    */
 233   private Preferences()
 234   {
 235     super();
 236     frame = new JInternalFrame();
 237     frame.setContentPane(this);
 238     wsPrefs = new WsPreferences();
 239     wsTab.add(wsPrefs, BorderLayout.CENTER);
 240     int width = 500, height = 450;
 241     new jalview.util.Platform();
 242     if (Platform.isAMac())
 243     {
 244       width = 570;
 245       height = 480;
 246     }
 247
 248     Desktop.addInternalFrame(frame,
 249             MessageManager.getString("label.preferences"), width, height);
 250     frame.setMinimumSize(new Dimension(width, height));
 251
 252     /*
 253      * Set Visual tab defaults
 254      */
 255     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 256     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 257     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 258     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 259
 260     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 261     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 262     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 263     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 264     showUnconserved
 265             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 266     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 267     showGroupConsensus
 268             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 269     showGroupConservation.setSelected(
 270             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 271     showConsensHistogram.setSelected(
 272             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 273     showConsensLogo
 274             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 275     showNpTooltip
 276             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 277     showDbRefTooltip
 278             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 279
 280     String[] fonts = java.awt.GraphicsEnvironment
 281             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 282     for (int i = 0; i < fonts.length; i++)
 283     {
 284       fontNameCB.addItem(fonts[i]);
 285     }
 286
 287     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 288     {
 289       fontSizeCB.addItem(i + "");
 290     }
 291
 292     fontStyleCB.addItem("plain");
 293     fontStyleCB.addItem("bold");
 294     fontStyleCB.addItem("italic");
 295
 296     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 297     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 298     fontStyleCB.setSelectedItem(
 299             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 300
 301     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 302     scaleProteinToCdna
 303             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 304
 305     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 306
 307     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 308
 309     gapSymbolCB.addItem("-");
 310     gapSymbolCB.addItem(".");
 311
 312     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 313
 314     sortby.addItem("No sort");
 315     sortby.addItem("Id");
 316     sortby.addItem("Pairwise Identity");
 317     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 318
 319     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 320     sortAnnBy
 321             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 322     sortAnnBy
 323             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 324     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 325             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 326                     SequenceAnnotationOrder.NONE.name()));
 327     sortAnnBy.setSelectedItem(savedSort.toString());
 328
 329     sortAutocalc.addItem("Autocalculated first");
 330     sortAutocalc.addItem("Autocalculated last");
 331     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 332     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 333             : sortAutocalc.getItemAt(1));
 334     startupCheckbox
 335             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 336     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 337             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 338                     + "/examples/exampleFile_2_3.jar"));
 339
 340     /*
 341      * Set Colours tab defaults
 342      */
 343     protColour.addItem(ResidueColourScheme.NONE);
 344     nucColour.addItem(ResidueColourScheme.NONE);
 345     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 346     {
 347       String name = cs.getSchemeName();
 348       protColour.addItem(name);
 349       nucColour.addItem(name);
 350     }
 351     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 352             ResidueColourScheme.NONE);
 353     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 354     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 355     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 356     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 357     minColour.setBackground(
 358             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 359     maxColour.setBackground(
 360             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 361
 362     /*
 363      * Set overview panel defaults
 364      */
 365     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 366             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 367     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 368             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 369     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 370     gapLabel.setEnabled(!useLegacyGap.isSelected());
 371     gapColour.setEnabled(!useLegacyGap.isSelected());
 372     showHiddenAtStart
 373             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 374
 375     /*
 376      * Set Structure tab defaults.
 377      */
 378     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 379     structFromPdb.setSelected(structSelected);
 380     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 381     useRnaView.setEnabled(structSelected);
 382     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 383     addSecondaryStructure.setEnabled(structSelected);
 384     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 385     addTempFactor.setEnabled(structSelected);
 386     structViewer.setSelectedItem(
 387             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 388     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 389     chimeraPath.addActionListener(new ActionListener()
 390     {
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         validateChimeraPath();
 395       }
 396     });
 397
 398     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 399     {
 400       siftsMapping.setSelected(true);
 401     }
 402     else
 403     {
 404       nwMapping.setSelected(true);
 405     }
 406
 407     SiftsSettings
 408             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 409
 410     /*
 411      * Set Connections tab defaults
 412      */
 413
 414     // set up sorting
 415     linkUrlTable.setModel(dataModel);
 416     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 417             linkUrlTable.getModel());
 418     linkUrlTable.setRowSorter(sorter);
 419     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 420
 421     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 422     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 423             SortOrder.DESCENDING));
 424     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 425             SortOrder.DESCENDING));
 426     sortKeys.add(
 427             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 428
 429     sorter.setSortKeys(sortKeys);
 430     sorter.sort();
 431
 432     // set up filtering
 433     ActionListener onReset;
 434     onReset = new ActionListener()
 435     {
 436       @Override
 437       public void actionPerformed(ActionEvent e)
 438       {
 439         filterTB.setText("");
 440         sorter.setRowFilter(RowFilter.regexFilter(""));
 441       }
 442
 443     };
 444     doReset.addActionListener(onReset);
 445
 446     // filter to display only custom urls
 447     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 448     {
 449       @Override
 450       public boolean include(
 451               Entry<? extends TableModel, ? extends Object> entry)
 452       {
 453         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 454       }
 455     };
 456
 457     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 458             linkUrlTable.getModel());
 459     customSorter.setRowFilter(customUrlFilter);
 460
 461     ActionListener onCustomOnly;
 462     onCustomOnly = new ActionListener()
 463     {
 464       @Override
 465       public void actionPerformed(ActionEvent e)
 466       {
 467         filterTB.setText("");
 468         sorter.setRowFilter(customUrlFilter);
 469       }
 470     };
 471     userOnly.addActionListener(onCustomOnly);
 472
 473     filterTB.getDocument().addDocumentListener(new DocumentListener()
 474     {
 475       String caseInsensitiveFlag = "(?i)";
 476
 477       @Override
 478       public void changedUpdate(DocumentEvent e)
 479       {
 480         sorter.setRowFilter(RowFilter
 481                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 482       }
 483
 484       @Override
 485       public void removeUpdate(DocumentEvent e)
 486       {
 487         sorter.setRowFilter(RowFilter
 488                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 489       }
 490
 491       @Override
 492       public void insertUpdate(DocumentEvent e)
 493       {
 494         sorter.setRowFilter(RowFilter
 495                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 496       }
 497     });
 498
 499     // set up list selection functionality
 500     linkUrlTable.getSelectionModel()
 501             .addListSelectionListener(new UrlListSelectionHandler());
 502
 503     // set up radio buttons
 504     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 505             .getPrimaryColumn();
 506     String onClickName = linkUrlTable.getColumnName(onClickCol);
 507     linkUrlTable.getColumn(onClickName)
 508             .setCellRenderer(new RadioButtonRenderer());
 509     linkUrlTable.getColumn(onClickName)
 510             .setCellEditor(new RadioButtonEditor());
 511
 512     // get boolean columns and resize those to min possible
 513     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 514     {
 515       if (linkUrlTable.getModel().getColumnClass(column)
 516               .equals(Boolean.class))
 517       {
 518         TableColumn tableColumn = linkUrlTable.getColumnModel()
 519                 .getColumn(column);
 520         int preferredWidth = tableColumn.getMinWidth();
 521
 522         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 523                 column);
 524         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 525         int cwidth = c.getPreferredSize().width
 526                 + linkUrlTable.getIntercellSpacing().width;
 527         preferredWidth = Math.max(preferredWidth, cwidth);
 528
 529         tableColumn.setPreferredWidth(preferredWidth);
 530       }
 531     }
 532
 533     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 534     previousProxyType = proxyTypeString;
 535     switch (proxyTypeString)
 536     {
 537     case Cache.PROXYTYPE_NONE:
 538       proxyType.setSelected(noProxy.getModel(), true);
 539       break;
 540     case Cache.PROXYTYPE_SYSTEM:
 541       proxyType.setSelected(systemProxy.getModel(), true);
 542       break;
 543     case Cache.PROXYTYPE_CUSTOM:
 544       proxyType.setSelected(customProxy.getModel(), true);
 545       break;
 546     default:
 547       Cache.log.warn(
 548               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 549                       + proxyTypeString);
 550     }
 551     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 552     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 553     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 554     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 555     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 556     proxyAuthUsernameTB
 557             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 558     // we are not storing or retrieving proxy password from .jalview_properties
 559     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 560             : new String(Cache.proxyAuthPassword));
 561     setCustomProxyEnabled();
 562
 563     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 564
 565     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 566     // note antisense here: default is true
 567     questionnaire
 568             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 569     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 570
 571     /*
 572      * Set Output tab defaults
 573      */
 574     epsRendering.addItem(promptEachTimeOpt);
 575     epsRendering.addItem(lineArtOpt);
 576     epsRendering.addItem(textOpt);
 577     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 578             "Prompt each time");
 579     if (defaultEPS.equalsIgnoreCase("Text"))
 580     {
 581       epsRendering.setSelectedItem(textOpt);
 582     }
 583     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 584     {
 585       epsRendering.setSelectedItem(lineArtOpt);
 586     }
 587     else
 588     {
 589       epsRendering.setSelectedItem(promptEachTimeOpt);
 590     }
 591     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 592     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 593     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 594     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 595     userIdWidth.setText(wi == null ? "" : wi.toString());
 596     // TODO: refactor to use common enum via FormatAdapter and allow extension
 597     // for new flat file formats
 598     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 599     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 600     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 601     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 602     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 603     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 604     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 605     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 606     embbedBioJSON
 607             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 608
 609     /*
 610      * Set Editing tab defaults
 611      */
 612     autoCalculateConsCheck
 613             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 614     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 615     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 616
 617     annotations_actionPerformed(null); // update the display of the annotation
 618                                        // settings
 619
 620     /*
 621      * Set Backups tab defaults
 622      */
 623     loadLastSavedBackupsOptions();
 624   }
 625
 626   /**
 627    * Save user selections on the Preferences tabs to the Cache and write out to
 628    * file.
 629    *
 630    * @param e
 631    */
 632   @Override
 633   public void ok_actionPerformed(ActionEvent e)
 634   {
 635     if (!validateSettings())
 636     {
 637       return;
 638     }
 639
 640     /*
 641      * Set proxy settings first (to be before web services refresh)
 642      */
 643     saveProxySettings();
 644
 645     /*
 646      * Save Visual settings
 647      */
 648     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 649             Boolean.toString(seqLimit.isSelected()));
 650     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 651             Boolean.toString(rightAlign.isSelected()));
 652     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 653             Boolean.toString(fullScreen.isSelected()));
 654     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 655             Boolean.toString(openoverv.isSelected()));
 656     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 657             Boolean.toString(annotations.isSelected()));
 658     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 659             Boolean.toString(conservation.isSelected()));
 660     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 661             Boolean.toString(quality.isSelected()));
 662     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 663             Boolean.toString(identity.isSelected()));
 664
 665     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 666             gapSymbolCB.getSelectedItem().toString());
 667
 668     Cache.applicationProperties.setProperty("FONT_NAME",
 669             fontNameCB.getSelectedItem().toString());
 670     Cache.applicationProperties.setProperty("FONT_STYLE",
 671             fontStyleCB.getSelectedItem().toString());
 672     Cache.applicationProperties.setProperty("FONT_SIZE",
 673             fontSizeCB.getSelectedItem().toString());
 674
 675     Cache.applicationProperties.setProperty("ID_ITALICS",
 676             Boolean.toString(idItalics.isSelected()));
 677     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 678             Boolean.toString(showUnconserved.isSelected()));
 679     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 680             Boolean.toString(showOccupancy.isSelected()));
 681     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 682             Boolean.toString(showGroupConsensus.isSelected()));
 683     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 684             Boolean.toString(showGroupConservation.isSelected()));
 685     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 686             Boolean.toString(showConsensHistogram.isSelected()));
 687     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 688             Boolean.toString(showConsensLogo.isSelected()));
 689     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 690             Boolean.toString(smoothFont.isSelected()));
 691     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 692             Boolean.toString(scaleProteinToCdna.isSelected()));
 693     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 694             Boolean.toString(showNpTooltip.isSelected()));
 695     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 696             Boolean.toString(showDbRefTooltip.isSelected()));
 697
 698     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 699             Boolean.toString(wrap.isSelected()));
 700
 701     Cache.applicationProperties.setProperty("STARTUP_FILE",
 702             startupFileTextfield.getText());
 703     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 704             Boolean.toString(startupCheckbox.isSelected()));
 705
 706     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 707             sortby.getSelectedItem().toString());
 708
 709     // convert description of sort order to enum name for save
 710     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 711             .forDescription(sortAnnBy.getSelectedItem().toString());
 712     if (annSortOrder != null)
 713     {
 714       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 715               annSortOrder.name());
 716     }
 717
 718     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 719     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 720             Boolean.valueOf(showAutocalcFirst).toString());
 721
 722     /*
 723      * Save Colours settings
 724      */
 725     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 726             protColour.getSelectedItem().toString());
 727     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 728             nucColour.getSelectedItem().toString());
 729     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 730             minColour.getBackground());
 731     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 732             maxColour.getBackground());
 733
 734     /*
 735      * Save Overview settings
 736      */
 737     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 738     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 739     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 740             Boolean.toString(useLegacyGap.isSelected()));
 741     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 742             Boolean.toString(showHiddenAtStart.isSelected()));
 743
 744     /*
 745      * Save Structure settings
 746      */
 747     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 748             Boolean.toString(addTempFactor.isSelected()));
 749     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 750             Boolean.toString(addSecondaryStructure.isSelected()));
 751     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 752             Boolean.toString(useRnaView.isSelected()));
 753     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 754             Boolean.toString(structFromPdb.isSelected()));
 755     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 756             structViewer.getSelectedItem().toString());
 757     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 758     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 759             Boolean.toString(siftsMapping.isSelected()));
 760     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 761
 762     /*
 763      * Save Output settings
 764      */
 765     Cache.applicationProperties.setProperty("EPS_RENDERING",
 766             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 767
 768     /*
 769      * Save Connections settings
 770      */
 771     // Proxy settings set first (to catch web services)
 772
 773     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 774
 775     jalview.util.BrowserLauncher.resetBrowser();
 776
 777     // save user-defined and selected links
 778     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 779     if (menuLinks.isEmpty())
 780     {
 781       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 782     }
 783     else
 784     {
 785       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 786               menuLinks.toString());
 787     }
 788
 789     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 790     if (nonMenuLinks.isEmpty())
 791     {
 792       Cache.applicationProperties.remove("STORED_LINKS");
 793     }
 794     else
 795     {
 796       Cache.applicationProperties.setProperty("STORED_LINKS",
 797               nonMenuLinks.toString());
 798     }
 799
 800     Cache.applicationProperties.setProperty("DEFAULT_URL",
 801             sequenceUrlLinks.getPrimaryUrlId());
 802
 803     Cache.setProperty("VERSION_CHECK",
 804             Boolean.toString(versioncheck.isSelected()));
 805     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 806     {
 807       // default is false - we only set this if the user has actively agreed
 808       Cache.setProperty("USAGESTATS",
 809               Boolean.toString(usagestats.isSelected()));
 810     }
 811     if (!questionnaire.isSelected())
 812     {
 813       Cache.setProperty("NOQUESTIONNAIRES", "true");
 814     }
 815     else
 816     {
 817       // special - made easy to edit a property file to disable questionnaires
 818       // by just adding the given line
 819       Cache.removeProperty("NOQUESTIONNAIRES");
 820     }
 821
 822     /*
 823      * Save Output settings
 824      */
 825     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 826             Boolean.toString(blcjv.isSelected()));
 827     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 828             Boolean.toString(clustaljv.isSelected()));
 829     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 830             Boolean.toString(fastajv.isSelected()));
 831     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 832             Boolean.toString(msfjv.isSelected()));
 833     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 834             Boolean.toString(pfamjv.isSelected()));
 835     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 836             Boolean.toString(pileupjv.isSelected()));
 837     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 838             Boolean.toString(pirjv.isSelected()));
 839     Cache.applicationProperties.setProperty("PIR_MODELLER",
 840             Boolean.toString(modellerOutput.isSelected()));
 841     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 842             Boolean.toString(embbedBioJSON.isSelected()));
 843     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 844
 845     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 846             Boolean.toString(autoIdWidth.isSelected()));
 847     userIdWidth_actionPerformed();
 848     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 849             userIdWidth.getText());
 850
 851     /*
 852      * Save Editing settings
 853      */
 854     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 855             Boolean.toString(autoCalculateConsCheck.isSelected()));
 856     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 857             Boolean.toString(sortByTree.isSelected()));
 858     Cache.applicationProperties.setProperty("PAD_GAPS",
 859             Boolean.toString(padGaps.isSelected()));
 860
 861     wsPrefs.updateAndRefreshWsMenuConfig(false);
 862
 863     /*
 864      * Save Backups settings
 865      */
 866     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 867             Boolean.toString(enableBackupFiles.isSelected()));
 868     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 869     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 870             Integer.toString(preset));
 871
 872     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 873     {
 874       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 875       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 876               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 877       Cache.applicationProperties.setProperty(
 878               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 879     }
 880
 881     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
 882             .get(preset);
 883     Cache.applicationProperties.setProperty(
 884             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 885
 886     Cache.saveProperties();
 887     Desktop.instance.doConfigureStructurePrefs();
 888     try
 889     {
 890       frame.setClosed(true);
 891     } catch (Exception ex)
 892     {
 893     }
 894   }
 895
 896   public void saveProxySettings()
 897   {
 898     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
 899             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
 900                     : Cache.PROXYTYPE_SYSTEM;
 901     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
 902     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
 903     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
 904     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
 905     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
 906     Cache.setOrRemove("PROXY_AUTH",
 907             Boolean.toString(proxyAuth.isSelected()));
 908     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
 909     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
 910     Cache.setProxyPropertiesFromPreferences(previousProxyType);
 911     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
 912             || !newProxyType.equals(previousProxyType))
 913     {
 914       // force a re-lookup of ws if proxytype is custom or has changed
 915       wsPrefs.update++;
 916     }
 917     previousProxyType = newProxyType;
 918   }
 919
 920   /**
 921    * Do any necessary validation before saving settings. Return focus to the
 922    * first tab which fails validation.
 923    *
 924    * @return
 925    */
 926   private boolean validateSettings()
 927   {
 928     if (!validateStructure())
 929     {
 930       structureTab.requestFocusInWindow();
 931       return false;
 932     }
 933     return true;
 934   }
 935
 936   @Override
 937   protected boolean validateStructure()
 938   {
 939     return validateChimeraPath();
 940
 941   }
 942
 943   /**
 944    * DOCUMENT ME!
 945    */
 946   @Override
 947   public void startupFileTextfield_mouseClicked()
 948   {
 949     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 950     JalviewFileChooser chooser = JalviewFileChooser
 951             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 952     chooser.setFileView(new JalviewFileView());
 953     chooser.setDialogTitle(
 954             MessageManager.getString("label.select_startup_file"));
 955
 956     int value = chooser.showOpenDialog(this);
 957
 958     if (value == JalviewFileChooser.APPROVE_OPTION)
 959     {
 960       FileFormatI format = chooser.getSelectedFormat();
 961       if (format != null)
 962       {
 963         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 964                 format.getName());
 965       }
 966       startupFileTextfield
 967               .setText(chooser.getSelectedFile().getAbsolutePath());
 968     }
 969   }
 970
 971   /**
 972    * DOCUMENT ME!
 973    *
 974    * @param e
 975    *          DOCUMENT ME!
 976    */
 977   @Override
 978   public void cancel_actionPerformed(ActionEvent e)
 979   {
 980     try
 981     {
 982       wsPrefs.updateWsMenuConfig(true);
 983       wsPrefs.refreshWs_actionPerformed(e);
 984       frame.setClosed(true);
 985     } catch (Exception ex)
 986     {
 987     }
 988   }
 989
 990   /**
 991    * DOCUMENT ME!
 992    *
 993    * @param e
 994    *          DOCUMENT ME!
 995    */
 996   @Override
 997   public void annotations_actionPerformed(ActionEvent e)
 998   {
 999     conservation.setEnabled(annotations.isSelected());
1000     quality.setEnabled(annotations.isSelected());
1001     identity.setEnabled(annotations.isSelected());
1002     showOccupancy.setEnabled(annotations.isSelected());
1003     showGroupConsensus.setEnabled(annotations.isSelected());
1004     showGroupConservation.setEnabled(annotations.isSelected());
1005     showConsensHistogram.setEnabled(annotations.isSelected()
1006             && (identity.isSelected() || showGroupConsensus.isSelected()));
1007     showConsensLogo.setEnabled(annotations.isSelected()
1008             && (identity.isSelected() || showGroupConsensus.isSelected()));
1009   }
1010
1011   @Override
1012   public void newLink_actionPerformed(ActionEvent e)
1013   {
1014     GSequenceLink link = new GSequenceLink();
1015     boolean valid = false;
1016     while (!valid)
1017     {
1018       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1019               MessageManager.getString("label.new_sequence_url_link"),
1020               JvOptionPane.OK_CANCEL_OPTION, -1,
1021               null) == JvOptionPane.OK_OPTION)
1022       {
1023         if (link.checkValid())
1024         {
1025           if (((UrlLinkTableModel) linkUrlTable.getModel())
1026                   .isUniqueName(link.getName()))
1027           {
1028             ((UrlLinkTableModel) linkUrlTable.getModel())
1029                     .insertRow(link.getName(), link.getURL());
1030             valid = true;
1031           }
1032           else
1033           {
1034             link.notifyDuplicate();
1035             continue;
1036           }
1037         }
1038       }
1039       else
1040       {
1041         break;
1042       }
1043     }
1044   }
1045
1046   @Override
1047   public void editLink_actionPerformed(ActionEvent e)
1048   {
1049     GSequenceLink link = new GSequenceLink();
1050
1051     int index = linkUrlTable.getSelectedRow();
1052     if (index == -1)
1053     {
1054       // button no longer enabled if row is not selected
1055       Cache.log.debug("Edit with no row selected in linkUrlTable");
1056       return;
1057     }
1058
1059     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1060             .getNameColumn();
1061     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1062             .getUrlColumn();
1063     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1064     link.setName(oldName);
1065     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1066
1067     boolean valid = false;
1068     while (!valid)
1069     {
1070       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1071               MessageManager.getString("label.edit_sequence_url_link"),
1072               JvOptionPane.OK_CANCEL_OPTION, -1,
1073               null) == JvOptionPane.OK_OPTION)
1074       {
1075         if (link.checkValid())
1076         {
1077           if ((oldName.equals(link.getName()))
1078                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1079                           .isUniqueName(link.getName())))
1080           {
1081             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1082             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1083             valid = true;
1084           }
1085           else
1086           {
1087             link.notifyDuplicate();
1088             continue;
1089           }
1090         }
1091       }
1092       else
1093       {
1094         break;
1095       }
1096     }
1097   }
1098
1099   @Override
1100   public void deleteLink_actionPerformed(ActionEvent e)
1101   {
1102     int index = linkUrlTable.getSelectedRow();
1103     int modelIndex = -1;
1104     if (index == -1)
1105     {
1106       // button no longer enabled if row is not selected
1107       Cache.log.debug("Delete with no row selected in linkUrlTable");
1108       return;
1109     }
1110     else
1111     {
1112       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1113     }
1114
1115     // make sure we use the model index to delete, and not the table index
1116     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1117   }
1118
1119   @Override
1120   public void defaultBrowser_mouseClicked(MouseEvent e)
1121   {
1122     JFileChooser chooser = new JFileChooser(".");
1123     chooser.setDialogTitle(
1124             MessageManager.getString("label.select_default_browser"));
1125
1126     int value = chooser.showOpenDialog(this);
1127
1128     if (value == JFileChooser.APPROVE_OPTION)
1129     {
1130       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1131     }
1132
1133   }
1134
1135   /*
1136    * (non-Javadoc)
1137    *
1138    * @see
1139    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1140    * .ActionEvent)
1141    */
1142   @Override
1143   protected void showunconserved_actionPerformed(ActionEvent e)
1144   {
1145     // TODO Auto-generated method stub
1146     super.showunconserved_actionPerformed(e);
1147   }
1148
1149   public static List<String> getGroupURLLinks()
1150   {
1151     return groupURLLinks;
1152   }
1153
1154   @Override
1155   public void minColour_actionPerformed(JPanel panel)
1156   {
1157     Color col = JColorChooser.showDialog(this,
1158             MessageManager.getString("label.select_colour_minimum_value"),
1159             minColour.getBackground());
1160     if (col != null)
1161     {
1162       panel.setBackground(col);
1163     }
1164     panel.repaint();
1165   }
1166
1167   @Override
1168   public void maxColour_actionPerformed(JPanel panel)
1169   {
1170     Color col = JColorChooser.showDialog(this,
1171             MessageManager.getString("label.select_colour_maximum_value"),
1172             maxColour.getBackground());
1173     if (col != null)
1174     {
1175       panel.setBackground(col);
1176     }
1177     panel.repaint();
1178   }
1179
1180   @Override
1181   public void gapColour_actionPerformed(JPanel gap)
1182   {
1183     if (!useLegacyGap.isSelected())
1184     {
1185       Color col = JColorChooser.showDialog(this,
1186               MessageManager.getString("label.select_gap_colour"),
1187               gapColour.getBackground());
1188       if (col != null)
1189       {
1190         gap.setBackground(col);
1191       }
1192       gap.repaint();
1193     }
1194   }
1195
1196   @Override
1197   public void hiddenColour_actionPerformed(JPanel hidden)
1198   {
1199     Color col = JColorChooser.showDialog(this,
1200             MessageManager.getString("label.select_hidden_colour"),
1201             hiddenColour.getBackground());
1202     if (col != null)
1203     {
1204       hidden.setBackground(col);
1205     }
1206     hidden.repaint();
1207   }
1208
1209   @Override
1210   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1211   {
1212     boolean enabled = useLegacyGap.isSelected();
1213     if (enabled)
1214     {
1215       gapColour.setBackground(
1216               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1217     }
1218     else
1219     {
1220       gapColour.setBackground(
1221               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1222     }
1223     gapColour.setEnabled(!enabled);
1224     gapLabel.setEnabled(!enabled);
1225   }
1226
1227   @Override
1228   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1229   {
1230     useLegacyGap.setSelected(false);
1231     useLegacyGaps_actionPerformed(null);
1232     showHiddenAtStart.setSelected(false);
1233     hiddenColour.setBackground(
1234             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1235   }
1236
1237   @Override
1238   protected void userIdWidth_actionPerformed()
1239   {
1240     try
1241     {
1242       String val = userIdWidth.getText().trim();
1243       if (val.length() > 0)
1244       {
1245         Integer iw = Integer.parseInt(val);
1246         if (iw.intValue() < 12)
1247         {
1248           throw new NumberFormatException();
1249         }
1250         userIdWidth.setText(iw.toString());
1251       }
1252     } catch (NumberFormatException x)
1253     {
1254       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1255               MessageManager
1256                       .getString("warn.user_defined_width_requirements"),
1257               MessageManager.getString("label.invalid_id_column_width"),
1258               JvOptionPane.WARNING_MESSAGE);
1259       userIdWidth.setText("");
1260     }
1261   }
1262
1263   @Override
1264   protected void autoIdWidth_actionPerformed()
1265   {
1266     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1267     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1268   }
1269
1270   /**
1271    * Returns true if chimera path is to a valid executable, else show an error
1272    * dialog.
1273    */
1274   private boolean validateChimeraPath()
1275   {
1276     if (chimeraPath.getText().trim().length() > 0)
1277     {
1278       File f = new File(chimeraPath.getText());
1279       if (!f.canExecute())
1280       {
1281         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1282                 MessageManager.getString("label.invalid_chimera_path"),
1283                 MessageManager.getString("label.invalid_name"),
1284                 JvOptionPane.ERROR_MESSAGE);
1285         return false;
1286       }
1287     }
1288     return true;
1289   }
1290
1291   /**
1292    * If Chimera is selected, check it can be found on default or user-specified
1293    * path, if not show a warning/help dialog.
1294    */
1295   @Override
1296   protected void structureViewer_actionPerformed(String selectedItem)
1297   {
1298     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1299     {
1300       return;
1301     }
1302     boolean found = false;
1303
1304     /*
1305      * Try user-specified and standard paths for Chimera executable.
1306      */
1307     List<String> paths = StructureManager.getChimeraPaths();
1308     paths.add(0, chimeraPath.getText());
1309     for (String path : paths)
1310     {
1311       if (new File(path.trim()).canExecute())
1312       {
1313         found = true;
1314         break;
1315       }
1316     }
1317     if (!found)
1318     {
1319       String[] options = { "OK", "Help" };
1320       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1321               JvSwingUtils.wrapTooltip(true,
1322                       MessageManager.getString("label.chimera_missing")),
1323               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1324               null, options, options[0]);
1325       if (showHelp == JvOptionPane.NO_OPTION)
1326       {
1327         try
1328         {
1329           Help.showHelpWindow(HelpId.StructureViewer);
1330         } catch (HelpSetException e)
1331         {
1332           e.printStackTrace();
1333         }
1334       }
1335     }
1336   }
1337
1338   public class OptionsParam
1339   {
1340     private String name;
1341
1342     private String code;
1343
1344     public OptionsParam(String name, String code)
1345     {
1346       this.name = name;
1347       this.code = code;
1348     }
1349
1350     public String getName()
1351     {
1352       return name;
1353     }
1354
1355     public void setName(String name)
1356     {
1357       this.name = name;
1358     }
1359
1360     public String getCode()
1361     {
1362       return code;
1363     }
1364
1365     public void setCode(String code)
1366     {
1367       this.code = code;
1368     }
1369
1370     @Override
1371     public String toString()
1372     {
1373       return name;
1374     }
1375
1376     @Override
1377     public boolean equals(Object that)
1378     {
1379       if (!(that instanceof OptionsParam))
1380       {
1381         return false;
1382       }
1383       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1384     }
1385
1386     @Override
1387     public int hashCode()
1388     {
1389       return name.hashCode() + code.hashCode();
1390     }
1391   }
1392
1393   private class UrlListSelectionHandler implements ListSelectionListener
1394   {
1395
1396     @Override
1397     public void valueChanged(ListSelectionEvent e)
1398     {
1399       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1400
1401       int index = lsm.getMinSelectionIndex();
1402       if (index == -1)
1403       {
1404         // no selection, so disable delete/edit buttons
1405         editLink.setEnabled(false);
1406         deleteLink.setEnabled(false);
1407         return;
1408       }
1409       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1410
1411       // enable/disable edit and delete link buttons
1412       if (((UrlLinkTableModel) linkUrlTable.getModel())
1413               .isRowDeletable(modelIndex))
1414       {
1415         deleteLink.setEnabled(true);
1416       }
1417       else
1418       {
1419         deleteLink.setEnabled(false);
1420       }
1421
1422       if (((UrlLinkTableModel) linkUrlTable.getModel())
1423               .isRowEditable(modelIndex))
1424       {
1425         editLink.setEnabled(true);
1426       }
1427       else
1428       {
1429         editLink.setEnabled(false);
1430       }
1431     }
1432   }
1433
1434 }