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.JalviewFileChooser;
  33 import jalview.io.JalviewFileView;
  34 import jalview.jbgui.GPreferences;
  35 import jalview.jbgui.GSequenceLink;
  36 import jalview.schemes.ColourSchemeProperty;
  37 import jalview.util.MessageManager;
  38 import jalview.util.Platform;
  39 import jalview.ws.sifts.SiftsSettings;
  40
  41 import java.awt.BorderLayout;
  42 import java.awt.Color;
  43 import java.awt.Dimension;
  44 import java.awt.Font;
  45 import java.awt.event.ActionEvent;
  46 import java.awt.event.ActionListener;
  47 import java.awt.event.MouseEvent;
  48 import java.io.File;
  49 import java.util.ArrayList;
  50 import java.util.List;
  51 import java.util.StringTokenizer;
  52 import java.util.Vector;
  53
  54 import javax.help.HelpSetException;
  55 import javax.swing.JColorChooser;
  56 import javax.swing.JFileChooser;
  57 import javax.swing.JInternalFrame;
  58 import javax.swing.JOptionPane;
  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     JalviewFileChooser chooser = new JalviewFileChooser(
 690             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 691                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 692                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 693                 "PIR", "BLC", "Jalview" },
 694             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 695     chooser.setFileView(new JalviewFileView());
 696     chooser.setDialogTitle(MessageManager
 697             .getString("label.select_startup_file"));
 698
 699     int value = chooser.showOpenDialog(this);
 700
 701     if (value == JalviewFileChooser.APPROVE_OPTION)
 702     {
 703       jalview.bin.Cache.applicationProperties.setProperty(
 704               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 705       startupFileTextfield.setText(chooser.getSelectedFile()
 706               .getAbsolutePath());
 707     }
 708   }
 709
 710   /**
 711    * DOCUMENT ME!
 712    *
 713    * @param e
 714    *          DOCUMENT ME!
 715    */
 716   @Override
 717   public void cancel_actionPerformed(ActionEvent e)
 718   {
 719     try
 720     {
 721       wsPrefs.updateWsMenuConfig(true);
 722       wsPrefs.refreshWs_actionPerformed(e);
 723       frame.setClosed(true);
 724     } catch (Exception ex)
 725     {
 726     }
 727   }
 728
 729   /**
 730    * DOCUMENT ME!
 731    *
 732    * @param e
 733    *          DOCUMENT ME!
 734    */
 735   @Override
 736   public void annotations_actionPerformed(ActionEvent e)
 737   {
 738     conservation.setEnabled(annotations.isSelected());
 739     quality.setEnabled(annotations.isSelected());
 740     identity.setEnabled(annotations.isSelected());
 741     showGroupConsensus.setEnabled(annotations.isSelected());
 742     showGroupConservation.setEnabled(annotations.isSelected());
 743     showConsensHistogram.setEnabled(annotations.isSelected()
 744             && (identity.isSelected() || showGroupConsensus.isSelected()));
 745     showConsensLogo.setEnabled(annotations.isSelected()
 746             && (identity.isSelected() || showGroupConsensus.isSelected()));
 747   }
 748
 749   @Override
 750   public void newLink_actionPerformed(ActionEvent e)
 751   {
 752
 753     GSequenceLink link = new GSequenceLink();
 754     boolean valid = false;
 755     while (!valid)
 756     {
 757       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 758               MessageManager.getString("label.new_sequence_url_link"),
 759               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 760       {
 761         if (link.checkValid())
 762         {
 763           nameLinks.addElement(link.getName());
 764           urlLinks.addElement(link.getURL());
 765           updateLinkData();
 766           valid = true;
 767         }
 768       }
 769       else
 770       {
 771         break;
 772       }
 773     }
 774   }
 775
 776   @Override
 777   public void editLink_actionPerformed(ActionEvent e)
 778   {
 779     GSequenceLink link = new GSequenceLink();
 780
 781     int index = linkNameList.getSelectedIndex();
 782     if (index == -1)
 783     {
 784       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 785               MessageManager.getString("label.no_link_selected"),
 786               MessageManager.getString("label.no_link_selected"),
 787               JOptionPane.WARNING_MESSAGE);
 788       return;
 789     }
 790
 791     link.setName(nameLinks.elementAt(index).toString());
 792     link.setURL(urlLinks.elementAt(index).toString());
 793
 794     boolean valid = false;
 795     while (!valid)
 796     {
 797
 798       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 799               MessageManager.getString("label.new_sequence_url_link"),
 800               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 801       {
 802         if (link.checkValid())
 803         {
 804           nameLinks.setElementAt(link.getName(), index);
 805           urlLinks.setElementAt(link.getURL(), index);
 806           updateLinkData();
 807           valid = true;
 808         }
 809       }
 810
 811       else
 812       {
 813         break;
 814       }
 815     }
 816   }
 817
 818   @Override
 819   public void deleteLink_actionPerformed(ActionEvent e)
 820   {
 821     int index = linkNameList.getSelectedIndex();
 822     if (index == -1)
 823     {
 824       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 825               MessageManager.getString("label.no_link_selected"),
 826               MessageManager.getString("label.no_link_selected"),
 827               JOptionPane.WARNING_MESSAGE);
 828       return;
 829     }
 830     nameLinks.removeElementAt(index);
 831     urlLinks.removeElementAt(index);
 832     updateLinkData();
 833   }
 834
 835   void updateLinkData()
 836   {
 837     linkNameList.setListData(nameLinks);
 838     linkURLList.setListData(urlLinks);
 839   }
 840
 841   @Override
 842   public void defaultBrowser_mouseClicked(MouseEvent e)
 843   {
 844     JFileChooser chooser = new JFileChooser(".");
 845     chooser.setDialogTitle(MessageManager
 846             .getString("label.select_default_browser"));
 847
 848     int value = chooser.showOpenDialog(this);
 849
 850     if (value == JFileChooser.APPROVE_OPTION)
 851     {
 852       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 853     }
 854
 855   }
 856
 857   /*
 858    * (non-Javadoc)
 859    *
 860    * @see
 861    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 862    * .ActionEvent)
 863    */
 864   @Override
 865   protected void showunconserved_actionPerformed(ActionEvent e)
 866   {
 867     // TODO Auto-generated method stub
 868     super.showunconserved_actionPerformed(e);
 869   }
 870
 871   public static List<String> getGroupURLLinks()
 872   {
 873     return groupURLLinks;
 874   }
 875
 876   @Override
 877   public void minColour_actionPerformed(JPanel panel)
 878   {
 879     Color col = JColorChooser.showDialog(this,
 880             MessageManager.getString("label.select_colour_minimum_value"),
 881             minColour.getBackground());
 882     if (col != null)
 883     {
 884       panel.setBackground(col);
 885     }
 886     panel.repaint();
 887   }
 888
 889   @Override
 890   public void maxColour_actionPerformed(JPanel panel)
 891   {
 892     Color col = JColorChooser.showDialog(this,
 893             MessageManager.getString("label.select_colour_maximum_value"),
 894             maxColour.getBackground());
 895     if (col != null)
 896     {
 897       panel.setBackground(col);
 898     }
 899     panel.repaint();
 900   }
 901
 902   @Override
 903   protected void userIdWidth_actionPerformed()
 904   {
 905     try
 906     {
 907       String val = userIdWidth.getText().trim();
 908       if (val.length() > 0)
 909       {
 910         Integer iw = Integer.parseInt(val);
 911         if (iw.intValue() < 12)
 912         {
 913           throw new NumberFormatException();
 914         }
 915         userIdWidth.setText(iw.toString());
 916       }
 917     } catch (NumberFormatException x)
 918     {
 919       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 920               .getString("warn.user_defined_width_requirements"),
 921               MessageManager.getString("label.invalid_id_column_width"),
 922               JOptionPane.WARNING_MESSAGE);
 923       userIdWidth.setText("");
 924     }
 925   }
 926
 927   @Override
 928   protected void autoIdWidth_actionPerformed()
 929   {
 930     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 931     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 932   }
 933
 934   /**
 935    * Returns true if chimera path is to a valid executable, else show an error
 936    * dialog.
 937    */
 938   private boolean validateChimeraPath()
 939   {
 940     if (chimeraPath.getText().trim().length() > 0)
 941     {
 942       File f = new File(chimeraPath.getText());
 943       if (!f.canExecute())
 944       {
 945         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 946                 MessageManager.getString("label.invalid_chimera_path"),
 947                 MessageManager.getString("label.invalid_name"),
 948                 JOptionPane.ERROR_MESSAGE);
 949         return false;
 950       }
 951     }
 952     return true;
 953   }
 954
 955   /**
 956    * If Chimera is selected, check it can be found on default or user-specified
 957    * path, if not show a warning/help dialog.
 958    */
 959   @Override
 960   protected void structureViewer_actionPerformed(String selectedItem)
 961   {
 962     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 963     {
 964       return;
 965     }
 966     boolean found = false;
 967
 968     /*
 969      * Try user-specified and standard paths for Chimera executable.
 970      */
 971     List<String> paths = StructureManager.getChimeraPaths();
 972     paths.add(0, chimeraPath.getText());
 973     for (String path : paths)
 974     {
 975       if (new File(path.trim()).canExecute())
 976       {
 977         found = true;
 978         break;
 979       }
 980     }
 981     if (!found)
 982     {
 983       String[] options = { "OK", "Help" };
 984       int showHelp = JOptionPane.showInternalOptionDialog(
 985               Desktop.desktop,
 986               JvSwingUtils.wrapTooltip(true,
 987                       MessageManager.getString("label.chimera_missing")),
 988               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 989               null, options, options[0]);
 990       if (showHelp == JOptionPane.NO_OPTION)
 991       {
 992         try
 993         {
 994           Help.showHelpWindow(HelpId.StructureViewer);
 995         } catch (HelpSetException e)
 996         {
 997           e.printStackTrace();
 998         }
 999       }
1000     }
1001   }
1002
1003   public class OptionsParam
1004   {
1005     private String name;
1006
1007     private String code;
1008
1009     public OptionsParam(String name, String code)
1010     {
1011       this.name = name;
1012       this.code = code;
1013     }
1014
1015     public String getName()
1016     {
1017       return name;
1018     }
1019
1020     public void setName(String name)
1021     {
1022       this.name = name;
1023     }
1024
1025     public String getCode()
1026     {
1027       return code;
1028     }
1029
1030     public void setCode(String code)
1031     {
1032       this.code = code;
1033     }
1034
1035     @Override
1036     public String toString()
1037     {
1038       return name;
1039     }
1040
1041     @Override
1042     public boolean equals(Object that)
1043     {
1044       if (!(that instanceof OptionsParam))
1045       {
1046         return false;
1047       }
1048       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1049     }
1050
1051     @Override
1052     public int hashCode()
1053     {
1054       return name.hashCode() + code.hashCode();
1055     }
1056   }
1057 }