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.JalviewColourScheme;
  38 import jalview.schemes.ResidueColourScheme;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.ws.sifts.SiftsSettings;
  42
  43 import java.awt.BorderLayout;
  44 import java.awt.Color;
  45 import java.awt.Dimension;
  46 import java.awt.Font;
  47 import java.awt.event.ActionEvent;
  48 import java.awt.event.ActionListener;
  49 import java.awt.event.MouseEvent;
  50 import java.io.File;
  51 import java.util.ArrayList;
  52 import java.util.List;
  53 import java.util.StringTokenizer;
  54 import java.util.Vector;
  55
  56 import javax.help.HelpSetException;
  57 import javax.swing.JColorChooser;
  58 import javax.swing.JFileChooser;
  59 import javax.swing.JInternalFrame;
  60 import javax.swing.JPanel;
  61
  62 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  63
  64 /**
  65  * DOCUMENT ME!
  66  *
  67  * @author $author$
  68  * @version $Revision$
  69  */
  70 public class Preferences extends GPreferences
  71 {
  72   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  73
  74   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  75
  76   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  77
  78   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  79
  80   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  81
  82   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  83
  84   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  85
  86   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  87
  88   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  89
  90   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  91
  92   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  93
  94   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  95
  96   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  97
  98   private static final int MIN_FONT_SIZE = 1;
  99
 100   private static final int MAX_FONT_SIZE = 30;
 101
 102   /**
 103    * Holds name and link separated with | character. Sequence ID must be
 104    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 105    */
 106   public static Vector<String> sequenceURLLinks;
 107
 108   /**
 109    * Holds name and link separated with | character. Sequence IDS and Sequences
 110    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 111    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 112    * for first and second token specified after a pipe character at end |,|.
 113    * (TODO: proper escape for using | to separate ids or sequences
 114    */
 115
 116   public static List<String> groupURLLinks;
 117   static
 118   {
 119     String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
 120     sequenceURLLinks = new Vector<String>();
 121
 122     try
 123     {
 124       StringTokenizer st = new StringTokenizer(string, "|");
 125       while (st.hasMoreElements())
 126       {
 127         String name = st.nextToken();
 128         String url = st.nextToken();
 129         // check for '|' within a regex
 130         int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
 131         if (rxstart == -1)
 132         {
 133           rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
 134         }
 135         while (rxstart == -1 && url.indexOf("/=$") == -1)
 136         {
 137           url = url + "|" + st.nextToken();
 138         }
 139         sequenceURLLinks.addElement(name + "|" + url);
 140       }
 141     } catch (Exception ex)
 142     {
 143       System.out.println(ex + "\nError parsing sequence links");
 144     }
 145     {
 146       // upgrade old SRS link
 147       int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
 148       if (srsPos > -1)
 149       {
 150         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
 151       }
 152     }
 153
 154     /**
 155      * TODO: reformulate groupURL encoding so two or more can be stored in the
 156      * .properties file as '|' separated strings
 157      */
 158
 159     groupURLLinks = new ArrayList<String>();
 160   }
 161
 162   Vector<String> nameLinks, urlLinks;
 163
 164   JInternalFrame frame;
 165
 166   DasSourceBrowser dasSource;
 167
 168   private WsPreferences wsPrefs;
 169
 170   private OptionsParam promptEachTimeOpt = new OptionsParam(
 171           MessageManager.getString("label.prompt_each_time"),
 172           "Prompt each time");
 173
 174   private OptionsParam lineArtOpt = new OptionsParam(
 175           MessageManager.getString("label.lineart"), "Lineart");
 176
 177   private OptionsParam textOpt = new OptionsParam(
 178           MessageManager.getString("action.text"), "Text");
 179
 180   /**
 181    * Creates a new Preferences object.
 182    */
 183   public Preferences()
 184   {
 185     super();
 186     frame = new JInternalFrame();
 187     frame.setContentPane(this);
 188     dasSource = new DasSourceBrowser();
 189     dasTab.add(dasSource, BorderLayout.CENTER);
 190     wsPrefs = new WsPreferences();
 191     wsTab.add(wsPrefs, BorderLayout.CENTER);
 192     int width = 500, height = 450;
 193     new jalview.util.Platform();
 194     if (Platform.isAMac())
 195     {
 196       width = 570;
 197       height = 480;
 198     }
 199
 200     Desktop.addInternalFrame(frame,
 201             MessageManager.getString("label.preferences"), width, height);
 202     frame.setMinimumSize(new Dimension(width, height));
 203
 204     /*
 205      * Set Visual tab defaults
 206      */
 207     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 208     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 209     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 210     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 211
 212     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 213     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 214     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 215     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 216     showUnconserved
 217             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 218     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 219             false));
 220     showGroupConservation.setSelected(Cache.getDefault(
 221             "SHOW_GROUP_CONSERVATION", false));
 222     showConsensHistogram.setSelected(Cache.getDefault(
 223             "SHOW_CONSENSUS_HISTOGRAM", true));
 224     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 225             false));
 226     showNpTooltip.setSelected(Cache
 227             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 228     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 229             true));
 230
 231     String[] fonts = java.awt.GraphicsEnvironment
 232             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 233     for (int i = 0; i < fonts.length; i++)
 234     {
 235       fontNameCB.addItem(fonts[i]);
 236     }
 237
 238     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 239     {
 240       fontSizeCB.addItem(i + "");
 241     }
 242
 243     fontStyleCB.addItem("plain");
 244     fontStyleCB.addItem("bold");
 245     fontStyleCB.addItem("italic");
 246
 247     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 248     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 249     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 250             + ""));
 251
 252     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 253     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 254             false));
 255
 256     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 257
 258     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 259
 260     gapSymbolCB.addItem("-");
 261     gapSymbolCB.addItem(".");
 262
 263     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 264
 265     sortby.addItem("No sort");
 266     sortby.addItem("Id");
 267     sortby.addItem("Pairwise Identity");
 268     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 269
 270     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 271     sortAnnBy
 272             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 273     sortAnnBy
 274             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 275     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 276             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 277                     SequenceAnnotationOrder.NONE.name()));
 278     sortAnnBy.setSelectedItem(savedSort.toString());
 279
 280     sortAutocalc.addItem("Autocalculated first");
 281     sortAutocalc.addItem("Autocalculated last");
 282     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 283     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 284             : sortAutocalc.getItemAt(1));
 285     startupCheckbox
 286             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 287     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 288             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 289                     + "/examples/exampleFile_2_3.jar"));
 290
 291     /*
 292      * Set Colours tab defaults
 293      */
 294     protColour.addItem(ResidueColourScheme.NONE);
 295     nucColour.addItem(ResidueColourScheme.NONE);
 296     for (JalviewColourScheme cs : JalviewColourScheme.values())
 297     {
 298       if (cs != JalviewColourScheme.UserDefined)
 299       {
 300         protColour.addItem(cs.toString());
 301         nucColour.addItem(cs.toString());
 302       }
 303     }
 304     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 305             ResidueColourScheme.NONE);
 306     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 307     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 308     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 309     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 310     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 311             Color.orange));
 312     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 313             Color.red));
 314
 315     /*
 316      * Set Structure tab defaults.
 317      */
 318     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 319     structFromPdb.setSelected(structSelected);
 320     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 321     useRnaView.setEnabled(structSelected);
 322     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 323     addSecondaryStructure.setEnabled(structSelected);
 324     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 325     addTempFactor.setEnabled(structSelected);
 326     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 327             ViewerType.JMOL.name()));
 328     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 329     chimeraPath.addActionListener(new ActionListener()
 330     {
 331       @Override
 332       public void actionPerformed(ActionEvent e)
 333       {
 334         validateChimeraPath();
 335       }
 336     });
 337
 338     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 339     {
 340       siftsMapping.setSelected(true);
 341     }
 342     else
 343     {
 344       nwMapping.setSelected(true);
 345     }
 346
 347     SiftsSettings
 348             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 349
 350     /*
 351      * Set Connections tab defaults
 352      */
 353     nameLinks = new Vector<String>();
 354     urlLinks = new Vector<String>();
 355     for (int i = 0; i < sequenceURLLinks.size(); i++)
 356     {
 357       String link = sequenceURLLinks.elementAt(i).toString();
 358       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 359       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 360     }
 361
 362     updateLinkData();
 363
 364     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 365     proxyServerTB.setEnabled(useProxy.isSelected());
 366     proxyPortTB.setEnabled(useProxy.isSelected());
 367     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 368     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 369
 370     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 371
 372     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 373     // note antisense here: default is true
 374     questionnaire
 375             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 376     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 377
 378     /*
 379      * Set Output tab defaults
 380      */
 381     epsRendering.addItem(promptEachTimeOpt);
 382     epsRendering.addItem(lineArtOpt);
 383     epsRendering.addItem(textOpt);
 384     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 385             "Prompt each time");
 386     if (defaultEPS.equalsIgnoreCase("Text"))
 387     {
 388       epsRendering.setSelectedItem(textOpt);
 389     }
 390     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 391     {
 392       epsRendering.setSelectedItem(lineArtOpt);
 393     }
 394     else
 395     {
 396       epsRendering.setSelectedItem(promptEachTimeOpt);
 397     }
 398     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 399     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 400     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 401     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 402     userIdWidth.setText(wi == null ? "" : wi.toString());
 403     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 404     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 405     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 406     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 407     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 408     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 409     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 410     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 411     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 412             true));
 413
 414     /*
 415      * Set Editing tab defaults
 416      */
 417     autoCalculateConsCheck.setSelected(Cache.getDefault(
 418             "AUTO_CALC_CONSENSUS", true));
 419     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 420     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 421
 422     annotations_actionPerformed(null); // update the display of the annotation
 423                                        // settings
 424   }
 425
 426   /**
 427    * Save user selections on the Preferences tabs to the Cache and write out to
 428    * file.
 429    *
 430    * @param e
 431    */
 432   @Override
 433   public void ok_actionPerformed(ActionEvent e)
 434   {
 435     if (!validateSettings())
 436     {
 437       return;
 438     }
 439
 440     /*
 441      * Save Visual settings
 442      */
 443     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 444             Boolean.toString(seqLimit.isSelected()));
 445     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 446             Boolean.toString(rightAlign.isSelected()));
 447     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 448             Boolean.toString(fullScreen.isSelected()));
 449     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 450             Boolean.toString(openoverv.isSelected()));
 451     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 452             Boolean.toString(annotations.isSelected()));
 453     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 454             Boolean.toString(conservation.isSelected()));
 455     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 456             Boolean.toString(quality.isSelected()));
 457     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 458             Boolean.toString(identity.isSelected()));
 459
 460     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 461             .getSelectedItem().toString());
 462
 463     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 464             .getSelectedItem().toString());
 465     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 466             .getSelectedItem().toString());
 467     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 468             .getSelectedItem().toString());
 469
 470     Cache.applicationProperties.setProperty("ID_ITALICS",
 471             Boolean.toString(idItalics.isSelected()));
 472     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 473             Boolean.toString(showUnconserved.isSelected()));
 474     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 475             Boolean.toString(showGroupConsensus.isSelected()));
 476     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 477             Boolean.toString(showGroupConservation.isSelected()));
 478     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 479             Boolean.toString(showConsensHistogram.isSelected()));
 480     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 481             Boolean.toString(showConsensLogo.isSelected()));
 482     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 483             Boolean.toString(smoothFont.isSelected()));
 484     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 485             Boolean.toString(scaleProteinToCdna.isSelected()));
 486     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 487             Boolean.toString(showNpTooltip.isSelected()));
 488     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 489             Boolean.toString(showDbRefTooltip.isSelected()));
 490
 491     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 492             Boolean.toString(wrap.isSelected()));
 493
 494     Cache.applicationProperties.setProperty("STARTUP_FILE",
 495             startupFileTextfield.getText());
 496     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 497             Boolean.toString(startupCheckbox.isSelected()));
 498
 499     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 500             .getSelectedItem().toString());
 501
 502     // convert description of sort order to enum name for save
 503     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 504             .forDescription(sortAnnBy.getSelectedItem().toString());
 505     if (annSortOrder != null)
 506     {
 507       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 508               annSortOrder.name());
 509     }
 510
 511     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 512     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 513             .valueOf(showAutocalcFirst).toString());
 514
 515     /*
 516      * Save Colours settings
 517      */
 518     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 519             .getSelectedItem().toString());
 520     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 521             .getSelectedItem().toString());
 522     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 523             minColour.getBackground());
 524     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 525             maxColour.getBackground());
 526
 527     /*
 528      * Save Structure settings
 529      */
 530     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 531             Boolean.toString(addTempFactor.isSelected()));
 532     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 533             Boolean.toString(addSecondaryStructure.isSelected()));
 534     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 535             Boolean.toString(useRnaView.isSelected()));
 536     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 537             Boolean.toString(structFromPdb.isSelected()));
 538     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 539             .getSelectedItem().toString());
 540     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 541     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 542             Boolean.toString(siftsMapping.isSelected()));
 543     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 544
 545     /*
 546      * Save Output settings
 547      */
 548     Cache.applicationProperties.setProperty("EPS_RENDERING",
 549             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 550
 551     /*
 552      * Save Connections settings
 553      */
 554     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 555
 556     jalview.util.BrowserLauncher.resetBrowser();
 557
 558     if (nameLinks.size() > 0)
 559     {
 560       StringBuffer links = new StringBuffer();
 561       sequenceURLLinks = new Vector<String>();
 562       for (int i = 0; i < nameLinks.size(); i++)
 563       {
 564         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 565                 + urlLinks.elementAt(i));
 566         links.append(sequenceURLLinks.elementAt(i).toString());
 567         links.append("|");
 568       }
 569       // remove last "|"
 570       links.setLength(links.length() - 1);
 571       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 572               links.toString());
 573     }
 574     else
 575     {
 576       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 577       sequenceURLLinks.clear();
 578     }
 579
 580     Cache.applicationProperties.setProperty("USE_PROXY",
 581             Boolean.toString(useProxy.isSelected()));
 582
 583     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 584
 585     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 586
 587     if (useProxy.isSelected())
 588     {
 589       System.setProperty("http.proxyHost", proxyServerTB.getText());
 590       System.setProperty("http.proxyPort", proxyPortTB.getText());
 591     }
 592     else
 593     {
 594       System.setProperty("http.proxyHost", "");
 595       System.setProperty("http.proxyPort", "");
 596     }
 597     Cache.setProperty("VERSION_CHECK",
 598             Boolean.toString(versioncheck.isSelected()));
 599     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 600     {
 601       // default is false - we only set this if the user has actively agreed
 602       Cache.setProperty("USAGESTATS",
 603               Boolean.toString(usagestats.isSelected()));
 604     }
 605     if (!questionnaire.isSelected())
 606     {
 607       Cache.setProperty("NOQUESTIONNAIRES", "true");
 608     }
 609     else
 610     {
 611       // special - made easy to edit a property file to disable questionnaires
 612       // by just adding the given line
 613       Cache.removeProperty("NOQUESTIONNAIRES");
 614     }
 615
 616     /*
 617      * Save Output settings
 618      */
 619     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 620             Boolean.toString(blcjv.isSelected()));
 621     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 622             Boolean.toString(clustaljv.isSelected()));
 623     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 624             Boolean.toString(fastajv.isSelected()));
 625     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 626             Boolean.toString(msfjv.isSelected()));
 627     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 628             Boolean.toString(pfamjv.isSelected()));
 629     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 630             Boolean.toString(pileupjv.isSelected()));
 631     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 632             Boolean.toString(pirjv.isSelected()));
 633     Cache.applicationProperties.setProperty("PIR_MODELLER",
 634             Boolean.toString(modellerOutput.isSelected()));
 635     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 636             Boolean.toString(embbedBioJSON.isSelected()));
 637     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 638
 639     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 640             Boolean.toString(autoIdWidth.isSelected()));
 641     userIdWidth_actionPerformed();
 642     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 643             userIdWidth.getText());
 644
 645     /*
 646      * Save Editing settings
 647      */
 648     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 649             Boolean.toString(autoCalculateConsCheck.isSelected()));
 650     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 651             Boolean.toString(sortByTree.isSelected()));
 652     Cache.applicationProperties.setProperty("PAD_GAPS",
 653             Boolean.toString(padGaps.isSelected()));
 654
 655     dasSource.saveProperties(Cache.applicationProperties);
 656     wsPrefs.updateAndRefreshWsMenuConfig(false);
 657     Cache.saveProperties();
 658     Desktop.instance.doConfigureStructurePrefs();
 659     try
 660     {
 661       frame.setClosed(true);
 662     } catch (Exception ex)
 663     {
 664     }
 665   }
 666
 667   /**
 668    * Do any necessary validation before saving settings. Return focus to the
 669    * first tab which fails validation.
 670    *
 671    * @return
 672    */
 673   private boolean validateSettings()
 674   {
 675     if (!validateStructure())
 676     {
 677       structureTab.requestFocusInWindow();
 678       return false;
 679     }
 680     return true;
 681   }
 682
 683   @Override
 684   protected boolean validateStructure()
 685   {
 686     return validateChimeraPath();
 687
 688   }
 689
 690   /**
 691    * DOCUMENT ME!
 692    */
 693   @Override
 694   public void startupFileTextfield_mouseClicked()
 695   {
 696     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 697     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 698             Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 699     chooser.setFileView(new JalviewFileView());
 700     chooser.setDialogTitle(MessageManager
 701             .getString("label.select_startup_file"));
 702
 703     int value = chooser.showOpenDialog(this);
 704
 705     if (value == JalviewFileChooser.APPROVE_OPTION)
 706     {
 707       FileFormatI format = chooser.getSelectedFormat();
 708       if (format != null)
 709       {
 710         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 711                 format.toString());
 712       }
 713       startupFileTextfield.setText(chooser.getSelectedFile()
 714               .getAbsolutePath());
 715     }
 716   }
 717
 718   /**
 719    * DOCUMENT ME!
 720    *
 721    * @param e
 722    *          DOCUMENT ME!
 723    */
 724   @Override
 725   public void cancel_actionPerformed(ActionEvent e)
 726   {
 727     try
 728     {
 729       wsPrefs.updateWsMenuConfig(true);
 730       wsPrefs.refreshWs_actionPerformed(e);
 731       frame.setClosed(true);
 732     } catch (Exception ex)
 733     {
 734     }
 735   }
 736
 737   /**
 738    * DOCUMENT ME!
 739    *
 740    * @param e
 741    *          DOCUMENT ME!
 742    */
 743   @Override
 744   public void annotations_actionPerformed(ActionEvent e)
 745   {
 746     conservation.setEnabled(annotations.isSelected());
 747     quality.setEnabled(annotations.isSelected());
 748     identity.setEnabled(annotations.isSelected());
 749     showGroupConsensus.setEnabled(annotations.isSelected());
 750     showGroupConservation.setEnabled(annotations.isSelected());
 751     showConsensHistogram.setEnabled(annotations.isSelected()
 752             && (identity.isSelected() || showGroupConsensus.isSelected()));
 753     showConsensLogo.setEnabled(annotations.isSelected()
 754             && (identity.isSelected() || showGroupConsensus.isSelected()));
 755   }
 756
 757   @Override
 758   public void newLink_actionPerformed(ActionEvent e)
 759   {
 760
 761     GSequenceLink link = new GSequenceLink();
 762     boolean valid = false;
 763     while (!valid)
 764     {
 765       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 766               MessageManager.getString("label.new_sequence_url_link"),
 767               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 768       {
 769         if (link.checkValid())
 770         {
 771           nameLinks.addElement(link.getName());
 772           urlLinks.addElement(link.getURL());
 773           updateLinkData();
 774           valid = true;
 775         }
 776       }
 777       else
 778       {
 779         break;
 780       }
 781     }
 782   }
 783
 784   @Override
 785   public void editLink_actionPerformed(ActionEvent e)
 786   {
 787     GSequenceLink link = new GSequenceLink();
 788
 789     int index = linkNameList.getSelectedIndex();
 790     if (index == -1)
 791     {
 792       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 793               MessageManager.getString("label.no_link_selected"),
 794               MessageManager.getString("label.no_link_selected"),
 795               JvOptionPane.WARNING_MESSAGE);
 796       return;
 797     }
 798
 799     link.setName(nameLinks.elementAt(index).toString());
 800     link.setURL(urlLinks.elementAt(index).toString());
 801
 802     boolean valid = false;
 803     while (!valid)
 804     {
 805
 806       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 807               MessageManager.getString("label.new_sequence_url_link"),
 808               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
 809       {
 810         if (link.checkValid())
 811         {
 812           nameLinks.setElementAt(link.getName(), index);
 813           urlLinks.setElementAt(link.getURL(), index);
 814           updateLinkData();
 815           valid = true;
 816         }
 817       }
 818
 819       else
 820       {
 821         break;
 822       }
 823     }
 824   }
 825
 826   @Override
 827   public void deleteLink_actionPerformed(ActionEvent e)
 828   {
 829     int index = linkNameList.getSelectedIndex();
 830     if (index == -1)
 831     {
 832       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 833               MessageManager.getString("label.no_link_selected"),
 834               MessageManager.getString("label.no_link_selected"),
 835               JvOptionPane.WARNING_MESSAGE);
 836       return;
 837     }
 838     nameLinks.removeElementAt(index);
 839     urlLinks.removeElementAt(index);
 840     updateLinkData();
 841   }
 842
 843   void updateLinkData()
 844   {
 845     linkNameList.setListData(nameLinks);
 846     linkURLList.setListData(urlLinks);
 847   }
 848
 849   @Override
 850   public void defaultBrowser_mouseClicked(MouseEvent e)
 851   {
 852     JFileChooser chooser = new JFileChooser(".");
 853     chooser.setDialogTitle(MessageManager
 854             .getString("label.select_default_browser"));
 855
 856     int value = chooser.showOpenDialog(this);
 857
 858     if (value == JFileChooser.APPROVE_OPTION)
 859     {
 860       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 861     }
 862
 863   }
 864
 865   /*
 866    * (non-Javadoc)
 867    *
 868    * @see
 869    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 870    * .ActionEvent)
 871    */
 872   @Override
 873   protected void showunconserved_actionPerformed(ActionEvent e)
 874   {
 875     // TODO Auto-generated method stub
 876     super.showunconserved_actionPerformed(e);
 877   }
 878
 879   public static List<String> getGroupURLLinks()
 880   {
 881     return groupURLLinks;
 882   }
 883
 884   @Override
 885   public void minColour_actionPerformed(JPanel panel)
 886   {
 887     Color col = JColorChooser.showDialog(this,
 888             MessageManager.getString("label.select_colour_minimum_value"),
 889             minColour.getBackground());
 890     if (col != null)
 891     {
 892       panel.setBackground(col);
 893     }
 894     panel.repaint();
 895   }
 896
 897   @Override
 898   public void maxColour_actionPerformed(JPanel panel)
 899   {
 900     Color col = JColorChooser.showDialog(this,
 901             MessageManager.getString("label.select_colour_maximum_value"),
 902             maxColour.getBackground());
 903     if (col != null)
 904     {
 905       panel.setBackground(col);
 906     }
 907     panel.repaint();
 908   }
 909
 910   @Override
 911   protected void userIdWidth_actionPerformed()
 912   {
 913     try
 914     {
 915       String val = userIdWidth.getText().trim();
 916       if (val.length() > 0)
 917       {
 918         Integer iw = Integer.parseInt(val);
 919         if (iw.intValue() < 12)
 920         {
 921           throw new NumberFormatException();
 922         }
 923         userIdWidth.setText(iw.toString());
 924       }
 925     } catch (NumberFormatException x)
 926     {
 927       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 928               .getString("warn.user_defined_width_requirements"),
 929               MessageManager.getString("label.invalid_id_column_width"),
 930               JvOptionPane.WARNING_MESSAGE);
 931       userIdWidth.setText("");
 932     }
 933   }
 934
 935   @Override
 936   protected void autoIdWidth_actionPerformed()
 937   {
 938     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 939     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 940   }
 941
 942   /**
 943    * Returns true if chimera path is to a valid executable, else show an error
 944    * dialog.
 945    */
 946   private boolean validateChimeraPath()
 947   {
 948     if (chimeraPath.getText().trim().length() > 0)
 949     {
 950       File f = new File(chimeraPath.getText());
 951       if (!f.canExecute())
 952       {
 953         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 954                 MessageManager.getString("label.invalid_chimera_path"),
 955                 MessageManager.getString("label.invalid_name"),
 956                 JvOptionPane.ERROR_MESSAGE);
 957         return false;
 958       }
 959     }
 960     return true;
 961   }
 962
 963   /**
 964    * If Chimera is selected, check it can be found on default or user-specified
 965    * path, if not show a warning/help dialog.
 966    */
 967   @Override
 968   protected void structureViewer_actionPerformed(String selectedItem)
 969   {
 970     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 971     {
 972       return;
 973     }
 974     boolean found = false;
 975
 976     /*
 977      * Try user-specified and standard paths for Chimera executable.
 978      */
 979     List<String> paths = StructureManager.getChimeraPaths();
 980     paths.add(0, chimeraPath.getText());
 981     for (String path : paths)
 982     {
 983       if (new File(path.trim()).canExecute())
 984       {
 985         found = true;
 986         break;
 987       }
 988     }
 989     if (!found)
 990     {
 991       String[] options = { "OK", "Help" };
 992       int showHelp = JvOptionPane.showInternalOptionDialog(
 993               Desktop.desktop,
 994               JvSwingUtils.wrapTooltip(true,
 995                       MessageManager.getString("label.chimera_missing")),
 996               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
 997               null, options, options[0]);
 998       if (showHelp == JvOptionPane.NO_OPTION)
 999       {
1000         try
1001         {
1002           Help.showHelpWindow(HelpId.StructureViewer);
1003         } catch (HelpSetException e)
1004         {
1005           e.printStackTrace();
1006         }
1007       }
1008     }
1009   }
1010
1011   public class OptionsParam
1012   {
1013     private String name;
1014
1015     private String code;
1016
1017     public OptionsParam(String name, String code)
1018     {
1019       this.name = name;
1020       this.code = code;
1021     }
1022
1023     public String getName()
1024     {
1025       return name;
1026     }
1027
1028     public void setName(String name)
1029     {
1030       this.name = name;
1031     }
1032
1033     public String getCode()
1034     {
1035       return code;
1036     }
1037
1038     public void setCode(String code)
1039     {
1040       this.code = code;
1041     }
1042
1043     @Override
1044     public String toString()
1045     {
1046       return name;
1047     }
1048
1049     @Override
1050     public boolean equals(Object that)
1051     {
1052       if (!(that instanceof OptionsParam))
1053       {
1054         return false;
1055       }
1056       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1057     }
1058
1059     @Override
1060     public int hashCode()
1061     {
1062       return name.hashCode() + code.hashCode();
1063     }
1064   }
1065 }