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