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.DB_ACCESSION;
  24 import static jalview.util.UrlConstants.EMBLEBI_STRING;
  25 import static jalview.util.UrlConstants.SEQUENCE_ID;
  26 import static jalview.util.UrlConstants.SRS_STRING;
  27
  28 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  29 import jalview.bin.Cache;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.StructureViewer.ViewerType;
  32 import jalview.io.FileFormatI;
  33 import jalview.io.JalviewFileChooser;
  34 import jalview.io.JalviewFileView;
  35 import jalview.jbgui.GPreferences;
  36 import jalview.jbgui.GSequenceLink;
  37 import jalview.schemes.ColourSchemeI;
  38 import jalview.schemes.ColourSchemes;
  39 import jalview.schemes.ResidueColourScheme;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.ws.sifts.SiftsSettings;
  43
  44 import java.awt.BorderLayout;
  45 import java.awt.Color;
  46 import java.awt.Dimension;
  47 import java.awt.Font;
  48 import java.awt.event.ActionEvent;
  49 import java.awt.event.ActionListener;
  50 import java.awt.event.MouseEvent;
  51 import java.io.File;
  52 import java.util.ArrayList;
  53 import java.util.List;
  54 import java.util.StringTokenizer;
  55 import java.util.Vector;
  56
  57 import javax.help.HelpSetException;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62
  63 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  64
  65 /**
  66  * DOCUMENT ME!
  67  *
  68  * @author $author$
  69  * @version $Revision$
  70  */
  71 public class Preferences extends GPreferences
  72 {
  73   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  74
  75   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  76
  77   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  78
  79   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  80
  81   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  82
  83   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  84
  85   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  86
  87   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  88
  89   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  90
  91   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  92
  93   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  94
  95   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  96
  97   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  98
  99   private static final int MIN_FONT_SIZE = 1;
 100
 101   private static final int MAX_FONT_SIZE = 30;
 102
 103   /**
 104    * Holds name and link separated with | character. Sequence ID must be
 105    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 106    */
 107   public static Vector<String> sequenceURLLinks;
 108
 109   /**
 110    * Holds name and link separated with | character. Sequence IDS and Sequences
 111    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 112    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 113    * for first and second token specified after a pipe character at end |,|.
 114    * (TODO: proper escape for using | to separate ids or sequences
 115    */
 116
 117   public static List<String> groupURLLinks;
 118   static
 119   {
 120     String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
 121     sequenceURLLinks = new Vector<String>();
 122
 123     try
 124     {
 125       StringTokenizer st = new StringTokenizer(string, "|");
 126       while (st.hasMoreElements())
 127       {
 128         String name = st.nextToken();
 129         String url = st.nextToken();
 130         // check for '|' within a regex
 131         int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
 132         if (rxstart == -1)
 133         {
 134           rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 135         }
 136         while (rxstart == -1 && url.indexOf("/=$") == -1)
 137         {
 138           url = url + "|" + st.nextToken();
 139         }
 140         sequenceURLLinks.addElement(name + "|" + url);
 141       }
 142     } catch (Exception ex)
 143     {
 144       System.out.println(ex + "\nError parsing sequence links");
 145     }
 146     {
 147       // upgrade old SRS link
 148       int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 149       if (srsPos > -1)
 150       {
 151         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 152       }
 153     }
 154
 155     /**
 156      * TODO: reformulate groupURL encoding so two or more can be stored in the
 157      * .properties file as '|' separated strings
 158      */
 159
 160     groupURLLinks = new ArrayList<String>();
 161   }
 162
 163   Vector<String> nameLinks, urlLinks;
 164
 165   JInternalFrame frame;
 166
 167   DasSourceBrowser dasSource;
 168
 169   private WsPreferences wsPrefs;
 170
 171   private OptionsParam promptEachTimeOpt = new OptionsParam(
 172           MessageManager.getString("label.prompt_each_time"),
 173           "Prompt each time");
 174
 175   private OptionsParam lineArtOpt = new OptionsParam(
 176           MessageManager.getString("label.lineart"), "Lineart");
 177
 178   private OptionsParam textOpt = new OptionsParam(
 179           MessageManager.getString("action.text"), "Text");
 180
 181   /**
 182    * Creates a new Preferences object.
 183    */
 184   public Preferences()
 185   {
 186     super();
 187     frame = new JInternalFrame();
 188     frame.setContentPane(this);
 189     dasSource = new DasSourceBrowser();
 190     dasTab.add(dasSource, BorderLayout.CENTER);
 191     wsPrefs = new WsPreferences();
 192     wsTab.add(wsPrefs, BorderLayout.CENTER);
 193     int width = 500, height = 450;
 194     new jalview.util.Platform();
 195     if (Platform.isAMac())
 196     {
 197       width = 570;
 198       height = 480;
 199     }
 200
 201     Desktop.addInternalFrame(frame,
 202             MessageManager.getString("label.preferences"), width, height);
 203     frame.setMinimumSize(new Dimension(width, height));
 204
 205     /*
 206      * Set Visual tab defaults
 207      */
 208     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 209     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 210     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 211     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 212
 213     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 214     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 215     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 216     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 217     showUnconserved
 218             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 219     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 220             false));
 221     showGroupConservation.setSelected(Cache.getDefault(
 222             "SHOW_GROUP_CONSERVATION", false));
 223     showConsensHistogram.setSelected(Cache.getDefault(
 224             "SHOW_CONSENSUS_HISTOGRAM", true));
 225     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 226             false));
 227     showNpTooltip.setSelected(Cache
 228             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 229     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 230             true));
 231
 232     String[] fonts = java.awt.GraphicsEnvironment
 233             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 234     for (int i = 0; i < fonts.length; i++)
 235     {
 236       fontNameCB.addItem(fonts[i]);
 237     }
 238
 239     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 240     {
 241       fontSizeCB.addItem(i + "");
 242     }
 243
 244     fontStyleCB.addItem("plain");
 245     fontStyleCB.addItem("bold");
 246     fontStyleCB.addItem("italic");
 247
 248     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 249     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 250     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 251             + ""));
 252
 253     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 254     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 255             false));
 256
 257     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 258
 259     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 260
 261     gapSymbolCB.addItem("-");
 262     gapSymbolCB.addItem(".");
 263
 264     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 265
 266     sortby.addItem("No sort");
 267     sortby.addItem("Id");
 268     sortby.addItem("Pairwise Identity");
 269     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 270
 271     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 272     sortAnnBy
 273             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 276     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 277             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 278                     SequenceAnnotationOrder.NONE.name()));
 279     sortAnnBy.setSelectedItem(savedSort.toString());
 280
 281     sortAutocalc.addItem("Autocalculated first");
 282     sortAutocalc.addItem("Autocalculated last");
 283     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 284     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 285             : sortAutocalc.getItemAt(1));
 286     startupCheckbox
 287             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 288     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 289             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 290                     + "/examples/exampleFile_2_3.jar"));
 291
 292     /*
 293      * Set Colours tab defaults
 294      */
 295     protColour.addItem(ResidueColourScheme.NONE);
 296     nucColour.addItem(ResidueColourScheme.NONE);
 297     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 298     {
 299       String name = cs.getSchemeName();
 300       protColour.addItem(name);
 301       nucColour.addItem(name);
 302     }
 303     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 304             ResidueColourScheme.NONE);
 305     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 306     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 307     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 308     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 309     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 310             Color.orange));
 311     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 312             Color.red));
 313
 314     /*
 315      * Set Structure tab defaults.
 316      */
 317     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 318     structFromPdb.setSelected(structSelected);
 319     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 320     useRnaView.setEnabled(structSelected);
 321     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 322     addSecondaryStructure.setEnabled(structSelected);
 323     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 324     addTempFactor.setEnabled(structSelected);
 325     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 326             ViewerType.JMOL.name()));
 327     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 328     chimeraPath.addActionListener(new ActionListener()
 329     {
 330       @Override
 331       public void actionPerformed(ActionEvent e)
 332       {
 333         validateChimeraPath();
 334       }
 335     });
 336
 337     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 338     {
 339       siftsMapping.setSelected(true);
 340     }
 341     else
 342     {
 343       nwMapping.setSelected(true);
 344     }
 345
 346     SiftsSettings
 347             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 348
 349     /*
 350      * Set Connections tab defaults
 351      */
 352     nameLinks = new Vector<String>();
 353     urlLinks = new Vector<String>();
 354     for (int i = 0; i < sequenceURLLinks.size(); i++)
 355     {
 356       String link = sequenceURLLinks.elementAt(i).toString();
 357       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 358       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 359     }
 360
 361     updateLinkData();
 362
 363     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 364     proxyServerTB.setEnabled(useProxy.isSelected());
 365     proxyPortTB.setEnabled(useProxy.isSelected());
 366     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 367     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 368
 369     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 370
 371     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 372     // note antisense here: default is true
 373     questionnaire
 374             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 375     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 376
 377     /*
 378      * Set Output tab defaults
 379      */
 380     epsRendering.addItem(promptEachTimeOpt);
 381     epsRendering.addItem(lineArtOpt);
 382     epsRendering.addItem(textOpt);
 383     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 384             "Prompt each time");
 385     if (defaultEPS.equalsIgnoreCase("Text"))
 386     {
 387       epsRendering.setSelectedItem(textOpt);
 388     }
 389     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 390     {
 391       epsRendering.setSelectedItem(lineArtOpt);
 392     }
 393     else
 394     {
 395       epsRendering.setSelectedItem(promptEachTimeOpt);
 396     }
 397     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 398     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 399     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 400     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 401     userIdWidth.setText(wi == null ? "" : wi.toString());
 402     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 403     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 404     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 405     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 406     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 407     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 408     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 409     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 410     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 411             true));
 412
 413     /*
 414      * Set Editing tab defaults
 415      */
 416     autoCalculateConsCheck.setSelected(Cache.getDefault(
 417             "AUTO_CALC_CONSENSUS", true));
 418     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 419     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 420
 421     annotations_actionPerformed(null); // update the display of the annotation
 422                                        // settings
 423   }
 424
 425   /**
 426    * Save user selections on the Preferences tabs to the Cache and write out to
 427    * file.
 428    *
 429    * @param e
 430    */
 431   @Override
 432   public void ok_actionPerformed(ActionEvent e)
 433   {
 434     if (!validateSettings())
 435     {
 436       return;
 437     }
 438
 439     /*
 440      * Save Visual settings
 441      */
 442     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 443             Boolean.toString(seqLimit.isSelected()));
 444     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 445             Boolean.toString(rightAlign.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 447             Boolean.toString(fullScreen.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 449             Boolean.toString(openoverv.isSelected()));
 450     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 451             Boolean.toString(annotations.isSelected()));
 452     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 453             Boolean.toString(conservation.isSelected()));
 454     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 455             Boolean.toString(quality.isSelected()));
 456     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 457             Boolean.toString(identity.isSelected()));
 458
 459     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 460             .getSelectedItem().toString());
 461
 462     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 463             .getSelectedItem().toString());
 464     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 465             .getSelectedItem().toString());
 466     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 467             .getSelectedItem().toString());
 468
 469     Cache.applicationProperties.setProperty("ID_ITALICS",
 470             Boolean.toString(idItalics.isSelected()));
 471     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 472             Boolean.toString(showUnconserved.isSelected()));
 473     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 474             Boolean.toString(showGroupConsensus.isSelected()));
 475     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 476             Boolean.toString(showGroupConservation.isSelected()));
 477     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 478             Boolean.toString(showConsensHistogram.isSelected()));
 479     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 480             Boolean.toString(showConsensLogo.isSelected()));
 481     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 482             Boolean.toString(smoothFont.isSelected()));
 483     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 484             Boolean.toString(scaleProteinToCdna.isSelected()));
 485     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 486             Boolean.toString(showNpTooltip.isSelected()));
 487     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 488             Boolean.toString(showDbRefTooltip.isSelected()));
 489
 490     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 491             Boolean.toString(wrap.isSelected()));
 492
 493     Cache.applicationProperties.setProperty("STARTUP_FILE",
 494             startupFileTextfield.getText());
 495     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 496             Boolean.toString(startupCheckbox.isSelected()));
 497
 498     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 499             .getSelectedItem().toString());
 500
 501     // convert description of sort order to enum name for save
 502     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 503             .forDescription(sortAnnBy.getSelectedItem().toString());
 504     if (annSortOrder != null)
 505     {
 506       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 507               annSortOrder.name());
 508     }
 509
 510     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 511     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 512             .valueOf(showAutocalcFirst).toString());
 513
 514     /*
 515      * Save Colours settings
 516      */
 517     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 518             .getSelectedItem().toString());
 519     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 520             .getSelectedItem().toString());
 521     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 522             minColour.getBackground());
 523     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 524             maxColour.getBackground());
 525
 526     /*
 527      * Save Structure settings
 528      */
 529     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 530             Boolean.toString(addTempFactor.isSelected()));
 531     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 532             Boolean.toString(addSecondaryStructure.isSelected()));
 533     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 534             Boolean.toString(useRnaView.isSelected()));
 535     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 536             Boolean.toString(structFromPdb.isSelected()));
 537     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 538             .getSelectedItem().toString());
 539     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 540     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 541             Boolean.toString(siftsMapping.isSelected()));
 542     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 543
 544     /*
 545      * Save Output settings
 546      */
 547     Cache.applicationProperties.setProperty("EPS_RENDERING",
 548             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 549
 550     /*
 551      * Save Connections settings
 552      */
 553     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 554
 555     jalview.util.BrowserLauncher.resetBrowser();
 556
 557     if (nameLinks.size() > 0)
 558     {
 559       StringBuffer links = new StringBuffer();
 560       sequenceURLLinks = new Vector<String>();
 561       for (int i = 0; i < nameLinks.size(); i++)
 562       {
 563         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 564                 + urlLinks.elementAt(i));
 565         links.append(sequenceURLLinks.elementAt(i).toString());
 566         links.append("|");
 567       }
 568       // remove last "|"
 569       links.setLength(links.length() - 1);
 570       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 571               links.toString());
 572     }
 573     else
 574     {
 575       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 576       sequenceURLLinks.clear();
 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     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 696     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 697             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 698     chooser.setFileView(new JalviewFileView());
 699     chooser.setDialogTitle(MessageManager
 700             .getString("label.select_startup_file"));
 701
 702     int value = chooser.showOpenDialog(this);
 703
 704     if (value == JalviewFileChooser.APPROVE_OPTION)
 705     {
 706       FileFormatI format = chooser.getSelectedFormat();
 707       if (format != null)
 708       {
 709         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 710                 format.getName());
 711       }
 712       startupFileTextfield.setText(chooser.getSelectedFile()
 713               .getAbsolutePath());
 714     }
 715   }
 716
 717   /**
 718    * DOCUMENT ME!
 719    *
 720    * @param e
 721    *          DOCUMENT ME!
 722    */
 723   @Override
 724   public void cancel_actionPerformed(ActionEvent e)
 725   {
 726     try
 727     {
 728       wsPrefs.updateWsMenuConfig(true);
 729       wsPrefs.refreshWs_actionPerformed(e);
 730       frame.setClosed(true);
 731     } catch (Exception ex)
 732     {
 733     }
 734   }
 735
 736   /**
 737    * DOCUMENT ME!
 738    *
 739    * @param e
 740    *          DOCUMENT ME!
 741    */
 742   @Override
 743   public void annotations_actionPerformed(ActionEvent e)
 744   {
 745     conservation.setEnabled(annotations.isSelected());
 746     quality.setEnabled(annotations.isSelected());
 747     identity.setEnabled(annotations.isSelected());
 748     showGroupConsensus.setEnabled(annotations.isSelected());
 749     showGroupConservation.setEnabled(annotations.isSelected());
 750     showConsensHistogram.setEnabled(annotations.isSelected()
 751             && (identity.isSelected() || showGroupConsensus.isSelected()));
 752     showConsensLogo.setEnabled(annotations.isSelected()
 753             && (identity.isSelected() || showGroupConsensus.isSelected()));
 754   }
 755
 756   @Override
 757   public void newLink_actionPerformed(ActionEvent e)
 758   {
 759
 760     GSequenceLink link = new GSequenceLink();
 761     boolean valid = false;
 762     while (!valid)
 763     {
 764       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 765               MessageManager.getString("label.new_sequence_url_link"),
 766               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 767       {
 768         if (link.checkValid())
 769         {
 770           nameLinks.addElement(link.getName());
 771           urlLinks.addElement(link.getURL());
 772           updateLinkData();
 773           valid = true;
 774         }
 775       }
 776       else
 777       {
 778         break;
 779       }
 780     }
 781   }
 782
 783   @Override
 784   public void editLink_actionPerformed(ActionEvent e)
 785   {
 786     GSequenceLink link = new GSequenceLink();
 787
 788     int index = linkNameList.getSelectedIndex();
 789     if (index == -1)
 790     {
 791       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 792               MessageManager.getString("label.no_link_selected"),
 793               MessageManager.getString("label.no_link_selected"),
 794               JvOptionPane.WARNING_MESSAGE);
 795       return;
 796     }
 797
 798     link.setName(nameLinks.elementAt(index).toString());
 799     link.setURL(urlLinks.elementAt(index).toString());
 800
 801     boolean valid = false;
 802     while (!valid)
 803     {
 804
 805       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 806               MessageManager.getString("label.new_sequence_url_link"),
 807               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 808       {
 809         if (link.checkValid())
 810         {
 811           nameLinks.setElementAt(link.getName(), index);
 812           urlLinks.setElementAt(link.getURL(), index);
 813           updateLinkData();
 814           valid = true;
 815         }
 816       }
 817
 818       else
 819       {
 820         break;
 821       }
 822     }
 823   }
 824
 825   @Override
 826   public void deleteLink_actionPerformed(ActionEvent e)
 827   {
 828     int index = linkNameList.getSelectedIndex();
 829     if (index == -1)
 830     {
 831       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 832               MessageManager.getString("label.no_link_selected"),
 833               MessageManager.getString("label.no_link_selected"),
 834               JvOptionPane.WARNING_MESSAGE);
 835       return;
 836     }
 837     nameLinks.removeElementAt(index);
 838     urlLinks.removeElementAt(index);
 839     updateLinkData();
 840   }
 841
 842   void updateLinkData()
 843   {
 844     linkNameList.setListData(nameLinks);
 845     linkURLList.setListData(urlLinks);
 846   }
 847
 848   @Override
 849   public void defaultBrowser_mouseClicked(MouseEvent e)
 850   {
 851     JFileChooser chooser = new JFileChooser(".");
 852     chooser.setDialogTitle(MessageManager
 853             .getString("label.select_default_browser"));
 854
 855     int value = chooser.showOpenDialog(this);
 856
 857     if (value == JFileChooser.APPROVE_OPTION)
 858     {
 859       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 860     }
 861
 862   }
 863
 864   /*
 865    * (non-Javadoc)
 866    *
 867    * @see
 868    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 869    * .ActionEvent)
 870    */
 871   @Override
 872   protected void showunconserved_actionPerformed(ActionEvent e)
 873   {
 874     // TODO Auto-generated method stub
 875     super.showunconserved_actionPerformed(e);
 876   }
 877
 878   public static List<String> getGroupURLLinks()
 879   {
 880     return groupURLLinks;
 881   }
 882
 883   @Override
 884   public void minColour_actionPerformed(JPanel panel)
 885   {
 886     Color col = JColorChooser.showDialog(this,
 887             MessageManager.getString("label.select_colour_minimum_value"),
 888             minColour.getBackground());
 889     if (col != null)
 890     {
 891       panel.setBackground(col);
 892     }
 893     panel.repaint();
 894   }
 895
 896   @Override
 897   public void maxColour_actionPerformed(JPanel panel)
 898   {
 899     Color col = JColorChooser.showDialog(this,
 900             MessageManager.getString("label.select_colour_maximum_value"),
 901             maxColour.getBackground());
 902     if (col != null)
 903     {
 904       panel.setBackground(col);
 905     }
 906     panel.repaint();
 907   }
 908
 909   @Override
 910   protected void userIdWidth_actionPerformed()
 911   {
 912     try
 913     {
 914       String val = userIdWidth.getText().trim();
 915       if (val.length() > 0)
 916       {
 917         Integer iw = Integer.parseInt(val);
 918         if (iw.intValue() < 12)
 919         {
 920           throw new NumberFormatException();
 921         }
 922         userIdWidth.setText(iw.toString());
 923       }
 924     } catch (NumberFormatException x)
 925     {
 926       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 927               .getString("warn.user_defined_width_requirements"),
 928               MessageManager.getString("label.invalid_id_column_width"),
 929               JvOptionPane.WARNING_MESSAGE);
 930       userIdWidth.setText("");
 931     }
 932   }
 933
 934   @Override
 935   protected void autoIdWidth_actionPerformed()
 936   {
 937     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 938     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 939   }
 940
 941   /**
 942    * Returns true if chimera path is to a valid executable, else show an error
 943    * dialog.
 944    */
 945   private boolean validateChimeraPath()
 946   {
 947     if (chimeraPath.getText().trim().length() > 0)
 948     {
 949       File f = new File(chimeraPath.getText());
 950       if (!f.canExecute())
 951       {
 952         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 953                 MessageManager.getString("label.invalid_chimera_path"),
 954                 MessageManager.getString("label.invalid_name"),
 955                 JvOptionPane.ERROR_MESSAGE);
 956         return false;
 957       }
 958     }
 959     return true;
 960   }
 961
 962   /**
 963    * If Chimera is selected, check it can be found on default or user-specified
 964    * path, if not show a warning/help dialog.
 965    */
 966   @Override
 967   protected void structureViewer_actionPerformed(String selectedItem)
 968   {
 969     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 970     {
 971       return;
 972     }
 973     boolean found = false;
 974
 975     /*
 976      * Try user-specified and standard paths for Chimera executable.
 977      */
 978     List<String> paths = StructureManager.getChimeraPaths();
 979     paths.add(0, chimeraPath.getText());
 980     for (String path : paths)
 981     {
 982       if (new File(path.trim()).canExecute())
 983       {
 984         found = true;
 985         break;
 986       }
 987     }
 988     if (!found)
 989     {
 990       String[] options = { "OK", "Help" };
 991       int showHelp = JvOptionPane.showInternalOptionDialog(
 992               Desktop.desktop,
 993               JvSwingUtils.wrapTooltip(true,
 994                       MessageManager.getString("label.chimera_missing")),
 995               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
 996               null, options, options[0]);
 997       if (showHelp == JvOptionPane.NO_OPTION)
 998       {
 999         try
1000         {
1001           Help.showHelpWindow(HelpId.StructureViewer);
1002         } catch (HelpSetException e)
1003         {
1004           e.printStackTrace();
1005         }
1006       }
1007     }
1008   }
1009
1010   public class OptionsParam
1011   {
1012     private String name;
1013
1014     private String code;
1015
1016     public OptionsParam(String name, String code)
1017     {
1018       this.name = name;
1019       this.code = code;
1020     }
1021
1022     public String getName()
1023     {
1024       return name;
1025     }
1026
1027     public void setName(String name)
1028     {
1029       this.name = name;
1030     }
1031
1032     public String getCode()
1033     {
1034       return code;
1035     }
1036
1037     public void setCode(String code)
1038     {
1039       this.code = code;
1040     }
1041
1042     @Override
1043     public String toString()
1044     {
1045       return name;
1046     }
1047
1048     @Override
1049     public boolean equals(Object that)
1050     {
1051       if (!(that instanceof OptionsParam))
1052       {
1053         return false;
1054       }
1055       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1056     }
1057
1058     @Override
1059     public int hashCode()
1060     {
1061       return name.hashCode() + code.hashCode();
1062     }
1063   }
1064 }