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.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.JPanel;
  60
  61 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  62
  63 /**
  64  * DOCUMENT ME!
  65  *
  66  * @author $author$
  67  * @version $Revision$
  68  */
  69 public class Preferences extends GPreferences
  70 {
  71   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  72
  73   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  74
  75   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  76
  77   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  78
  79   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  80
  81   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  82
  83   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  84
  85   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  86
  87   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  88
  89   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  90
  91   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  92
  93   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  94
  95   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  96
  97   private static final int MIN_FONT_SIZE = 1;
  98
  99   private static final int MAX_FONT_SIZE = 30;
 100
 101   /**
 102    * Holds name and link separated with | character. Sequence ID must be
 103    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 104    */
 105   public static Vector<String> sequenceURLLinks;
 106
 107   /**
 108    * Holds name and link separated with | character. Sequence IDS and Sequences
 109    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 110    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 111    * for first and second token specified after a pipe character at end |,|.
 112    * (TODO: proper escape for using | to separate ids or sequences
 113    */
 114
 115   public static List<String> groupURLLinks;
 116   static
 117   {
 118     String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
 119     sequenceURLLinks = new Vector<String>();
 120
 121     try
 122     {
 123       StringTokenizer st = new StringTokenizer(string, "|");
 124       while (st.hasMoreElements())
 125       {
 126         String name = st.nextToken();
 127         String url = st.nextToken();
 128         // check for '|' within a regex
 129         int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
 130         if (rxstart == -1)
 131         {
 132           rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 133         }
 134         while (rxstart == -1 && url.indexOf("/=$") == -1)
 135         {
 136           url = url + "|" + st.nextToken();
 137         }
 138         sequenceURLLinks.addElement(name + "|" + url);
 139       }
 140     } catch (Exception ex)
 141     {
 142       System.out.println(ex + "\nError parsing sequence links");
 143     }
 144     {
 145       // upgrade old SRS link
 146       int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 147       if (srsPos > -1)
 148       {
 149         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 150       }
 151     }
 152
 153     /**
 154      * TODO: reformulate groupURL encoding so two or more can be stored in the
 155      * .properties file as '|' separated strings
 156      */
 157
 158     groupURLLinks = new ArrayList<String>();
 159   }
 160
 161   Vector<String> nameLinks, urlLinks;
 162
 163   JInternalFrame frame;
 164
 165   DasSourceBrowser dasSource;
 166
 167   private WsPreferences wsPrefs;
 168
 169   private OptionsParam promptEachTimeOpt = new OptionsParam(
 170           MessageManager.getString("label.prompt_each_time"),
 171           "Prompt each time");
 172
 173   private OptionsParam lineArtOpt = new OptionsParam(
 174           MessageManager.getString("label.lineart"), "Lineart");
 175
 176   private OptionsParam textOpt = new OptionsParam(
 177           MessageManager.getString("action.text"), "Text");
 178
 179   /**
 180    * Creates a new Preferences object.
 181    */
 182   public Preferences()
 183   {
 184     super();
 185     frame = new JInternalFrame();
 186     frame.setContentPane(this);
 187     dasSource = new DasSourceBrowser();
 188     dasTab.add(dasSource, BorderLayout.CENTER);
 189     wsPrefs = new WsPreferences();
 190     wsTab.add(wsPrefs, BorderLayout.CENTER);
 191     int width = 500, height = 450;
 192     new jalview.util.Platform();
 193     if (Platform.isAMac())
 194     {
 195       width = 570;
 196       height = 480;
 197     }
 198
 199     Desktop.addInternalFrame(frame,
 200             MessageManager.getString("label.preferences"), width, height);
 201     frame.setMinimumSize(new Dimension(width, height));
 202
 203     /*
 204      * Set Visual tab defaults
 205      */
 206     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 207     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 208     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 209     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 210
 211     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 212     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 213     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 214     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 215     showUnconserved
 216             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 217     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 218             false));
 219     showGroupConservation.setSelected(Cache.getDefault(
 220             "SHOW_GROUP_CONSERVATION", false));
 221     showConsensHistogram.setSelected(Cache.getDefault(
 222             "SHOW_CONSENSUS_HISTOGRAM", true));
 223     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 224             false));
 225     showNpTooltip.setSelected(Cache
 226             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 227     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 228             true));
 229
 230     String[] fonts = java.awt.GraphicsEnvironment
 231             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 232     for (int i = 0; i < fonts.length; i++)
 233     {
 234       fontNameCB.addItem(fonts[i]);
 235     }
 236
 237     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 238     {
 239       fontSizeCB.addItem(i + "");
 240     }
 241
 242     fontStyleCB.addItem("plain");
 243     fontStyleCB.addItem("bold");
 244     fontStyleCB.addItem("italic");
 245
 246     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 247     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 248     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 249             + ""));
 250
 251     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 252     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 253             false));
 254
 255     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 256
 257     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 258
 259     gapSymbolCB.addItem("-");
 260     gapSymbolCB.addItem(".");
 261
 262     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 263
 264     sortby.addItem("No sort");
 265     sortby.addItem("Id");
 266     sortby.addItem("Pairwise Identity");
 267     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 268
 269     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 270     sortAnnBy
 271             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 272     sortAnnBy
 273             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 274     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 275             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 276                     SequenceAnnotationOrder.NONE.name()));
 277     sortAnnBy.setSelectedItem(savedSort.toString());
 278
 279     sortAutocalc.addItem("Autocalculated first");
 280     sortAutocalc.addItem("Autocalculated last");
 281     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 282     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 283             : sortAutocalc.getItemAt(1));
 284     startupCheckbox
 285             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 286     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 287             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 288                     + "/examples/exampleFile_2_3.jar"));
 289
 290     /*
 291      * Set Colours tab defaults
 292      */
 293     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 294     {
 295       protColour.addItem(ColourSchemeProperty.getColourName(i));
 296       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 297     }
 298     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 299     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 300     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 301     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 302     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 303     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 304             Color.orange));
 305     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 306             Color.red));
 307
 308     /*
 309      * Set Structure tab defaults.
 310      */
 311     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 312     structFromPdb.setSelected(structSelected);
 313     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 314     useRnaView.setEnabled(structSelected);
 315     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 316     addSecondaryStructure.setEnabled(structSelected);
 317     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 318     addTempFactor.setEnabled(structSelected);
 319     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 320             ViewerType.JMOL.name()));
 321     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 322     chimeraPath.addActionListener(new ActionListener()
 323     {
 324       @Override
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         validateChimeraPath();
 328       }
 329     });
 330
 331     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 332     {
 333       siftsMapping.setSelected(true);
 334     }
 335     else
 336     {
 337       nwMapping.setSelected(true);
 338     }
 339
 340     SiftsSettings
 341             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 342
 343     /*
 344      * Set Connections tab defaults
 345      */
 346     nameLinks = new Vector<String>();
 347     urlLinks = new Vector<String>();
 348     for (int i = 0; i < sequenceURLLinks.size(); i++)
 349     {
 350       String link = sequenceURLLinks.elementAt(i).toString();
 351       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 352       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 353     }
 354
 355     updateLinkData();
 356
 357     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 358     proxyServerTB.setEnabled(useProxy.isSelected());
 359     proxyPortTB.setEnabled(useProxy.isSelected());
 360     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 361     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 362
 363     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 364
 365     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 366     // note antisense here: default is true
 367     questionnaire
 368             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 369     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 370
 371     /*
 372      * Set Output tab defaults
 373      */
 374     epsRendering.addItem(promptEachTimeOpt);
 375     epsRendering.addItem(lineArtOpt);
 376     epsRendering.addItem(textOpt);
 377     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 378             "Prompt each time");
 379     if (defaultEPS.equalsIgnoreCase("Text"))
 380     {
 381       epsRendering.setSelectedItem(textOpt);
 382     }
 383     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 384     {
 385       epsRendering.setSelectedItem(lineArtOpt);
 386     }
 387     else
 388     {
 389       epsRendering.setSelectedItem(promptEachTimeOpt);
 390     }
 391     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 392     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 393     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 394     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 395     userIdWidth.setText(wi == null ? "" : wi.toString());
 396     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 397     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 398     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 399     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 400     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 401     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 402     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 403     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 404     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 405             true));
 406
 407     /*
 408      * Set Editing tab defaults
 409      */
 410     autoCalculateConsCheck.setSelected(Cache.getDefault(
 411             "AUTO_CALC_CONSENSUS", true));
 412     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 413     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 414
 415     annotations_actionPerformed(null); // update the display of the annotation
 416                                        // settings
 417   }
 418
 419   /**
 420    * Save user selections on the Preferences tabs to the Cache and write out to
 421    * file.
 422    *
 423    * @param e
 424    */
 425   @Override
 426   public void ok_actionPerformed(ActionEvent e)
 427   {
 428     if (!validateSettings())
 429     {
 430       return;
 431     }
 432
 433     /*
 434      * Save Visual settings
 435      */
 436     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 437             Boolean.toString(seqLimit.isSelected()));
 438     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 439             Boolean.toString(rightAlign.isSelected()));
 440     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 441             Boolean.toString(fullScreen.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 443             Boolean.toString(openoverv.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 445             Boolean.toString(annotations.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 447             Boolean.toString(conservation.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 449             Boolean.toString(quality.isSelected()));
 450     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 451             Boolean.toString(identity.isSelected()));
 452
 453     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 454             .getSelectedItem().toString());
 455
 456     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 457             .getSelectedItem().toString());
 458     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 459             .getSelectedItem().toString());
 460     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 461             .getSelectedItem().toString());
 462
 463     Cache.applicationProperties.setProperty("ID_ITALICS",
 464             Boolean.toString(idItalics.isSelected()));
 465     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 466             Boolean.toString(showUnconserved.isSelected()));
 467     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 468             Boolean.toString(showGroupConsensus.isSelected()));
 469     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 470             Boolean.toString(showGroupConservation.isSelected()));
 471     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 472             Boolean.toString(showConsensHistogram.isSelected()));
 473     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 474             Boolean.toString(showConsensLogo.isSelected()));
 475     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 476             Boolean.toString(smoothFont.isSelected()));
 477     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 478             Boolean.toString(scaleProteinToCdna.isSelected()));
 479     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 480             Boolean.toString(showNpTooltip.isSelected()));
 481     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 482             Boolean.toString(showDbRefTooltip.isSelected()));
 483
 484     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 485             Boolean.toString(wrap.isSelected()));
 486
 487     Cache.applicationProperties.setProperty("STARTUP_FILE",
 488             startupFileTextfield.getText());
 489     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 490             Boolean.toString(startupCheckbox.isSelected()));
 491
 492     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 493             .getSelectedItem().toString());
 494
 495     // convert description of sort order to enum name for save
 496     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 497             .forDescription(sortAnnBy.getSelectedItem().toString());
 498     if (annSortOrder != null)
 499     {
 500       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 501               annSortOrder.name());
 502     }
 503
 504     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 505     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 506             .valueOf(showAutocalcFirst).toString());
 507
 508     /*
 509      * Save Colours settings
 510      */
 511     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 512             .getSelectedItem().toString());
 513     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 514             .getSelectedItem().toString());
 515     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 516             minColour.getBackground());
 517     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 518             maxColour.getBackground());
 519
 520     /*
 521      * Save Structure settings
 522      */
 523     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 524             Boolean.toString(addTempFactor.isSelected()));
 525     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 526             Boolean.toString(addSecondaryStructure.isSelected()));
 527     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 528             Boolean.toString(useRnaView.isSelected()));
 529     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 530             Boolean.toString(structFromPdb.isSelected()));
 531     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 532             .getSelectedItem().toString());
 533     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 534     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 535             Boolean.toString(siftsMapping.isSelected()));
 536     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 537
 538     /*
 539      * Save Output settings
 540      */
 541     Cache.applicationProperties.setProperty("EPS_RENDERING",
 542             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 543
 544     /*
 545      * Save Connections settings
 546      */
 547     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 548
 549     jalview.util.BrowserLauncher.resetBrowser();
 550
 551     if (nameLinks.size() > 0)
 552     {
 553       StringBuffer links = new StringBuffer();
 554       sequenceURLLinks = new Vector<String>();
 555       for (int i = 0; i < nameLinks.size(); i++)
 556       {
 557         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 558                 + urlLinks.elementAt(i));
 559         links.append(sequenceURLLinks.elementAt(i).toString());
 560         links.append("|");
 561       }
 562       // remove last "|"
 563       links.setLength(links.length() - 1);
 564       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 565               links.toString());
 566     }
 567     else
 568     {
 569       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 570       sequenceURLLinks.clear();
 571     }
 572
 573     Cache.applicationProperties.setProperty("USE_PROXY",
 574             Boolean.toString(useProxy.isSelected()));
 575
 576     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 577
 578     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 579
 580     if (useProxy.isSelected())
 581     {
 582       System.setProperty("http.proxyHost", proxyServerTB.getText());
 583       System.setProperty("http.proxyPort", proxyPortTB.getText());
 584     }
 585     else
 586     {
 587       System.setProperty("http.proxyHost", "");
 588       System.setProperty("http.proxyPort", "");
 589     }
 590     Cache.setProperty("VERSION_CHECK",
 591             Boolean.toString(versioncheck.isSelected()));
 592     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 593     {
 594       // default is false - we only set this if the user has actively agreed
 595       Cache.setProperty("USAGESTATS",
 596               Boolean.toString(usagestats.isSelected()));
 597     }
 598     if (!questionnaire.isSelected())
 599     {
 600       Cache.setProperty("NOQUESTIONNAIRES", "true");
 601     }
 602     else
 603     {
 604       // special - made easy to edit a property file to disable questionnaires
 605       // by just adding the given line
 606       Cache.removeProperty("NOQUESTIONNAIRES");
 607     }
 608
 609     /*
 610      * Save Output settings
 611      */
 612     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 613             Boolean.toString(blcjv.isSelected()));
 614     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 615             Boolean.toString(clustaljv.isSelected()));
 616     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 617             Boolean.toString(fastajv.isSelected()));
 618     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 619             Boolean.toString(msfjv.isSelected()));
 620     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 621             Boolean.toString(pfamjv.isSelected()));
 622     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 623             Boolean.toString(pileupjv.isSelected()));
 624     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 625             Boolean.toString(pirjv.isSelected()));
 626     Cache.applicationProperties.setProperty("PIR_MODELLER",
 627             Boolean.toString(modellerOutput.isSelected()));
 628     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 629             Boolean.toString(embbedBioJSON.isSelected()));
 630     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 631
 632     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 633             Boolean.toString(autoIdWidth.isSelected()));
 634     userIdWidth_actionPerformed();
 635     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 636             userIdWidth.getText());
 637
 638     /*
 639      * Save Editing settings
 640      */
 641     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 642             Boolean.toString(autoCalculateConsCheck.isSelected()));
 643     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 644             Boolean.toString(sortByTree.isSelected()));
 645     Cache.applicationProperties.setProperty("PAD_GAPS",
 646             Boolean.toString(padGaps.isSelected()));
 647
 648     dasSource.saveProperties(Cache.applicationProperties);
 649     wsPrefs.updateAndRefreshWsMenuConfig(false);
 650     Cache.saveProperties();
 651     Desktop.instance.doConfigureStructurePrefs();
 652     try
 653     {
 654       frame.setClosed(true);
 655     } catch (Exception ex)
 656     {
 657     }
 658   }
 659
 660   /**
 661    * Do any necessary validation before saving settings. Return focus to the
 662    * first tab which fails validation.
 663    *
 664    * @return
 665    */
 666   private boolean validateSettings()
 667   {
 668     if (!validateStructure())
 669     {
 670       structureTab.requestFocusInWindow();
 671       return false;
 672     }
 673     return true;
 674   }
 675
 676   @Override
 677   protected boolean validateStructure()
 678   {
 679     return validateChimeraPath();
 680
 681   }
 682
 683   /**
 684    * DOCUMENT ME!
 685    */
 686   @Override
 687   public void startupFileTextfield_mouseClicked()
 688   {
 689     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 690     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 691             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 692     chooser.setFileView(new JalviewFileView());
 693     chooser.setDialogTitle(MessageManager
 694             .getString("label.select_startup_file"));
 695
 696     int value = chooser.showOpenDialog(this);
 697
 698     if (value == JalviewFileChooser.APPROVE_OPTION)
 699     {
 700       FileFormatI format = chooser.getSelectedFormat();
 701       if (format != null)
 702       {
 703         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 704                 format.getName());
 705       }
 706       startupFileTextfield.setText(chooser.getSelectedFile()
 707               .getAbsolutePath());
 708     }
 709   }
 710
 711   /**
 712    * DOCUMENT ME!
 713    *
 714    * @param e
 715    *          DOCUMENT ME!
 716    */
 717   @Override
 718   public void cancel_actionPerformed(ActionEvent e)
 719   {
 720     try
 721     {
 722       wsPrefs.updateWsMenuConfig(true);
 723       wsPrefs.refreshWs_actionPerformed(e);
 724       frame.setClosed(true);
 725     } catch (Exception ex)
 726     {
 727     }
 728   }
 729
 730   /**
 731    * DOCUMENT ME!
 732    *
 733    * @param e
 734    *          DOCUMENT ME!
 735    */
 736   @Override
 737   public void annotations_actionPerformed(ActionEvent e)
 738   {
 739     conservation.setEnabled(annotations.isSelected());
 740     quality.setEnabled(annotations.isSelected());
 741     identity.setEnabled(annotations.isSelected());
 742     showGroupConsensus.setEnabled(annotations.isSelected());
 743     showGroupConservation.setEnabled(annotations.isSelected());
 744     showConsensHistogram.setEnabled(annotations.isSelected()
 745             && (identity.isSelected() || showGroupConsensus.isSelected()));
 746     showConsensLogo.setEnabled(annotations.isSelected()
 747             && (identity.isSelected() || showGroupConsensus.isSelected()));
 748   }
 749
 750   @Override
 751   public void newLink_actionPerformed(ActionEvent e)
 752   {
 753
 754     GSequenceLink link = new GSequenceLink();
 755     boolean valid = false;
 756     while (!valid)
 757     {
 758       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 759               MessageManager.getString("label.new_sequence_url_link"),
 760               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 761       {
 762         if (link.checkValid())
 763         {
 764           nameLinks.addElement(link.getName());
 765           urlLinks.addElement(link.getURL());
 766           updateLinkData();
 767           valid = true;
 768         }
 769       }
 770       else
 771       {
 772         break;
 773       }
 774     }
 775   }
 776
 777   @Override
 778   public void editLink_actionPerformed(ActionEvent e)
 779   {
 780     GSequenceLink link = new GSequenceLink();
 781
 782     int index = linkNameList.getSelectedIndex();
 783     if (index == -1)
 784     {
 785       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 786               MessageManager.getString("label.no_link_selected"),
 787               MessageManager.getString("label.no_link_selected"),
 788               JvOptionPane.WARNING_MESSAGE);
 789       return;
 790     }
 791
 792     link.setName(nameLinks.elementAt(index).toString());
 793     link.setURL(urlLinks.elementAt(index).toString());
 794
 795     boolean valid = false;
 796     while (!valid)
 797     {
 798
 799       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 800               MessageManager.getString("label.new_sequence_url_link"),
 801               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 802       {
 803         if (link.checkValid())
 804         {
 805           nameLinks.setElementAt(link.getName(), index);
 806           urlLinks.setElementAt(link.getURL(), index);
 807           updateLinkData();
 808           valid = true;
 809         }
 810       }
 811
 812       else
 813       {
 814         break;
 815       }
 816     }
 817   }
 818
 819   @Override
 820   public void deleteLink_actionPerformed(ActionEvent e)
 821   {
 822     int index = linkNameList.getSelectedIndex();
 823     if (index == -1)
 824     {
 825       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 826               MessageManager.getString("label.no_link_selected"),
 827               MessageManager.getString("label.no_link_selected"),
 828               JvOptionPane.WARNING_MESSAGE);
 829       return;
 830     }
 831     nameLinks.removeElementAt(index);
 832     urlLinks.removeElementAt(index);
 833     updateLinkData();
 834   }
 835
 836   void updateLinkData()
 837   {
 838     linkNameList.setListData(nameLinks);
 839     linkURLList.setListData(urlLinks);
 840   }
 841
 842   @Override
 843   public void defaultBrowser_mouseClicked(MouseEvent e)
 844   {
 845     JFileChooser chooser = new JFileChooser(".");
 846     chooser.setDialogTitle(MessageManager
 847             .getString("label.select_default_browser"));
 848
 849     int value = chooser.showOpenDialog(this);
 850
 851     if (value == JFileChooser.APPROVE_OPTION)
 852     {
 853       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 854     }
 855
 856   }
 857
 858   /*
 859    * (non-Javadoc)
 860    *
 861    * @see
 862    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 863    * .ActionEvent)
 864    */
 865   @Override
 866   protected void showunconserved_actionPerformed(ActionEvent e)
 867   {
 868     // TODO Auto-generated method stub
 869     super.showunconserved_actionPerformed(e);
 870   }
 871
 872   public static List<String> getGroupURLLinks()
 873   {
 874     return groupURLLinks;
 875   }
 876
 877   @Override
 878   public void minColour_actionPerformed(JPanel panel)
 879   {
 880     Color col = JColorChooser.showDialog(this,
 881             MessageManager.getString("label.select_colour_minimum_value"),
 882             minColour.getBackground());
 883     if (col != null)
 884     {
 885       panel.setBackground(col);
 886     }
 887     panel.repaint();
 888   }
 889
 890   @Override
 891   public void maxColour_actionPerformed(JPanel panel)
 892   {
 893     Color col = JColorChooser.showDialog(this,
 894             MessageManager.getString("label.select_colour_maximum_value"),
 895             maxColour.getBackground());
 896     if (col != null)
 897     {
 898       panel.setBackground(col);
 899     }
 900     panel.repaint();
 901   }
 902
 903   @Override
 904   protected void userIdWidth_actionPerformed()
 905   {
 906     try
 907     {
 908       String val = userIdWidth.getText().trim();
 909       if (val.length() > 0)
 910       {
 911         Integer iw = Integer.parseInt(val);
 912         if (iw.intValue() < 12)
 913         {
 914           throw new NumberFormatException();
 915         }
 916         userIdWidth.setText(iw.toString());
 917       }
 918     } catch (NumberFormatException x)
 919     {
 920       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 921               .getString("warn.user_defined_width_requirements"),
 922               MessageManager.getString("label.invalid_id_column_width"),
 923               JvOptionPane.WARNING_MESSAGE);
 924       userIdWidth.setText("");
 925     }
 926   }
 927
 928   @Override
 929   protected void autoIdWidth_actionPerformed()
 930   {
 931     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 932     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 933   }
 934
 935   /**
 936    * Returns true if chimera path is to a valid executable, else show an error
 937    * dialog.
 938    */
 939   private boolean validateChimeraPath()
 940   {
 941     if (chimeraPath.getText().trim().length() > 0)
 942     {
 943       File f = new File(chimeraPath.getText());
 944       if (!f.canExecute())
 945       {
 946         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 947                 MessageManager.getString("label.invalid_chimera_path"),
 948                 MessageManager.getString("label.invalid_name"),
 949                 JvOptionPane.ERROR_MESSAGE);
 950         return false;
 951       }
 952     }
 953     return true;
 954   }
 955
 956   /**
 957    * If Chimera is selected, check it can be found on default or user-specified
 958    * path, if not show a warning/help dialog.
 959    */
 960   @Override
 961   protected void structureViewer_actionPerformed(String selectedItem)
 962   {
 963     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 964     {
 965       return;
 966     }
 967     boolean found = false;
 968
 969     /*
 970      * Try user-specified and standard paths for Chimera executable.
 971      */
 972     List<String> paths = StructureManager.getChimeraPaths();
 973     paths.add(0, chimeraPath.getText());
 974     for (String path : paths)
 975     {
 976       if (new File(path.trim()).canExecute())
 977       {
 978         found = true;
 979         break;
 980       }
 981     }
 982     if (!found)
 983     {
 984       String[] options = { "OK", "Help" };
 985       int showHelp = JvOptionPane.showInternalOptionDialog(
 986               Desktop.desktop,
 987               JvSwingUtils.wrapTooltip(true,
 988                       MessageManager.getString("label.chimera_missing")),
 989               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
 990               null, options, options[0]);
 991       if (showHelp == JvOptionPane.NO_OPTION)
 992       {
 993         try
 994         {
 995           Help.showHelpWindow(HelpId.StructureViewer);
 996         } catch (HelpSetException e)
 997         {
 998           e.printStackTrace();
 999         }
1000       }
1001     }
1002   }
1003
1004   public class OptionsParam
1005   {
1006     private String name;
1007
1008     private String code;
1009
1010     public OptionsParam(String name, String code)
1011     {
1012       this.name = name;
1013       this.code = code;
1014     }
1015
1016     public String getName()
1017     {
1018       return name;
1019     }
1020
1021     public void setName(String name)
1022     {
1023       this.name = name;
1024     }
1025
1026     public String getCode()
1027     {
1028       return code;
1029     }
1030
1031     public void setCode(String code)
1032     {
1033       this.code = code;
1034     }
1035
1036     @Override
1037     public String toString()
1038     {
1039       return name;
1040     }
1041
1042     @Override
1043     public boolean equals(Object that)
1044     {
1045       if (!(that instanceof OptionsParam))
1046       {
1047         return false;
1048       }
1049       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1050     }
1051
1052     @Override
1053     public int hashCode()
1054     {
1055       return name.hashCode() + code.hashCode();
1056     }
1057   }
1058 }