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