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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.FileFormatI;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.jbgui.GPreferences;
  31 import jalview.jbgui.GSequenceLink;
  32 import jalview.schemes.ColourSchemeProperty;
  33 import jalview.util.MessageManager;
  34 import jalview.util.Platform;
  35 import jalview.ws.sifts.SiftsSettings;
  36
  37 import java.awt.BorderLayout;
  38 import java.awt.Color;
  39 import java.awt.Dimension;
  40 import java.awt.Font;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.MouseEvent;
  44 import java.io.File;
  45 import java.util.ArrayList;
  46 import java.util.List;
  47 import java.util.StringTokenizer;
  48 import java.util.Vector;
  49
  50 import javax.help.HelpSetException;
  51 import javax.swing.JColorChooser;
  52 import javax.swing.JFileChooser;
  53 import javax.swing.JInternalFrame;
  54 import javax.swing.JOptionPane;
  55 import javax.swing.JPanel;
  56
  57 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  58
  59 /**
  60  * DOCUMENT ME!
  61  *
  62  * @author $author$
  63  * @version $Revision$
  64  */
  65 public class Preferences extends GPreferences
  66 {
  67   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  68
  69   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  70
  71   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  72
  73   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  74
  75   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  76
  77   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  78
  79   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  80
  81   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  82
  83   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  84
  85   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  86
  87   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  88
  89   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  90
  91   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  92
  93   private static final int MIN_FONT_SIZE = 1;
  94
  95   private static final int MAX_FONT_SIZE = 30;
  96
  97   /**
  98    * Holds name and link separated with | character. Sequence ID must be
  99    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 100    */
 101   public static Vector<String> sequenceURLLinks;
 102
 103   /**
 104    * Holds name and link separated with | character. Sequence IDS and Sequences
 105    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 106    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 107    * for first and second token specified after a pipe character at end |,|.
 108    * (TODO: proper escape for using | to separate ids or sequences
 109    */
 110
 111   public static List<String> groupURLLinks;
 112   static
 113   {
 114     String string = Cache
 115             .getDefault(
 116                     "SEQUENCE_LINKS",
 117                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 118     sequenceURLLinks = new Vector<String>();
 119
 120     try
 121     {
 122       StringTokenizer st = new StringTokenizer(string, "|");
 123       while (st.hasMoreElements())
 124       {
 125         String name = st.nextToken();
 126         String url = st.nextToken();
 127         // check for '|' within a regex
 128         int rxstart = url.indexOf("$SEQUENCE_ID$");
 129         while (rxstart == -1 && url.indexOf("/=$") == -1)
 130         {
 131           url = url + "|" + st.nextToken();
 132         }
 133         sequenceURLLinks.addElement(name + "|" + url);
 134       }
 135     } catch (Exception ex)
 136     {
 137       System.out.println(ex + "\nError parsing sequence links");
 138     }
 139     {
 140       // upgrade old SRS link
 141       int srsPos = sequenceURLLinks
 142               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 143       if (srsPos > -1)
 144       {
 145         sequenceURLLinks
 146                 .setElementAt(
 147                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 148                         srsPos);
 149       }
 150     }
 151
 152     /**
 153      * TODO: reformulate groupURL encoding so two or more can be stored in the
 154      * .properties file as '|' separated strings
 155      */
 156
 157     groupURLLinks = new ArrayList<String>();
 158   }
 159
 160   Vector<String> nameLinks, urlLinks;
 161
 162   JInternalFrame frame;
 163
 164   DasSourceBrowser dasSource;
 165
 166   private WsPreferences wsPrefs;
 167
 168   private OptionsParam promptEachTimeOpt = new OptionsParam(
 169           MessageManager.getString("label.prompt_each_time"),
 170           "Prompt each time");
 171
 172   private OptionsParam lineArtOpt = new OptionsParam(
 173           MessageManager.getString("label.lineart"), "Lineart");
 174
 175   private OptionsParam textOpt = new OptionsParam(
 176           MessageManager.getString("action.text"), "Text");
 177
 178   /**
 179    * Creates a new Preferences object.
 180    */
 181   public Preferences()
 182   {
 183     super();
 184     frame = new JInternalFrame();
 185     frame.setContentPane(this);
 186     dasSource = new DasSourceBrowser();
 187     dasTab.add(dasSource, BorderLayout.CENTER);
 188     wsPrefs = new WsPreferences();
 189     wsTab.add(wsPrefs, BorderLayout.CENTER);
 190     int width = 500, height = 450;
 191     new jalview.util.Platform();
 192     if (Platform.isAMac())
 193     {
 194       width = 570;
 195       height = 480;
 196     }
 197
 198     Desktop.addInternalFrame(frame,
 199             MessageManager.getString("label.preferences"), width, height);
 200     frame.setMinimumSize(new Dimension(width, height));
 201
 202     /*
 203      * Set Visual tab defaults
 204      */
 205     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 206     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 207     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 208     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 209
 210     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 211     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 212     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 213     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 214     showUnconserved
 215             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 216     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 217             false));
 218     showGroupConservation.setSelected(Cache.getDefault(
 219             "SHOW_GROUP_CONSERVATION", false));
 220     showConsensHistogram.setSelected(Cache.getDefault(
 221             "SHOW_CONSENSUS_HISTOGRAM", true));
 222     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 223             false));
 224     showNpTooltip.setSelected(Cache
 225             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 226     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 227             true));
 228
 229     String[] fonts = java.awt.GraphicsEnvironment
 230             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 231     for (int i = 0; i < fonts.length; i++)
 232     {
 233       fontNameCB.addItem(fonts[i]);
 234     }
 235
 236     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 237     {
 238       fontSizeCB.addItem(i + "");
 239     }
 240
 241     fontStyleCB.addItem("plain");
 242     fontStyleCB.addItem("bold");
 243     fontStyleCB.addItem("italic");
 244
 245     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 246     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 247     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 248             + ""));
 249
 250     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 251     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 252             false));
 253
 254     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 255
 256     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 257
 258     gapSymbolCB.addItem("-");
 259     gapSymbolCB.addItem(".");
 260
 261     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 262
 263     sortby.addItem("No sort");
 264     sortby.addItem("Id");
 265     sortby.addItem("Pairwise Identity");
 266     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 267
 268     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 269     sortAnnBy
 270             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 271     sortAnnBy
 272             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 273     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 274             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 275                     SequenceAnnotationOrder.NONE.name()));
 276     sortAnnBy.setSelectedItem(savedSort.toString());
 277
 278     sortAutocalc.addItem("Autocalculated first");
 279     sortAutocalc.addItem("Autocalculated last");
 280     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 281     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 282             : sortAutocalc.getItemAt(1));
 283     startupCheckbox
 284             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 285     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 286             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 287                     + "/examples/exampleFile_2_3.jar"));
 288
 289     /*
 290      * Set Colours tab defaults
 291      */
 292     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 293     {
 294       protColour.addItem(ColourSchemeProperty.getColourName(i));
 295       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 296     }
 297     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 298     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 299     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 300     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 301     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 302     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 303             Color.orange));
 304     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 305             Color.red));
 306
 307     /*
 308      * Set Structure tab defaults.
 309      */
 310     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 311     structFromPdb.setSelected(structSelected);
 312     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 313     useRnaView.setEnabled(structSelected);
 314     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 315     addSecondaryStructure.setEnabled(structSelected);
 316     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 317     addTempFactor.setEnabled(structSelected);
 318     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 319             ViewerType.JMOL.name()));
 320     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 321     chimeraPath.addActionListener(new ActionListener()
 322     {
 323       @Override
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         validateChimeraPath();
 327       }
 328     });
 329
 330     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 331     {
 332       siftsMapping.setSelected(true);
 333     }
 334     else
 335     {
 336       nwMapping.setSelected(true);
 337     }
 338
 339     SiftsSettings
 340             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 341
 342     /*
 343      * Set Connections tab defaults
 344      */
 345     nameLinks = new Vector<String>();
 346     urlLinks = new Vector<String>();
 347     for (int i = 0; i < sequenceURLLinks.size(); i++)
 348     {
 349       String link = sequenceURLLinks.elementAt(i).toString();
 350       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 351       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 352     }
 353
 354     updateLinkData();
 355
 356     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 357     proxyServerTB.setEnabled(useProxy.isSelected());
 358     proxyPortTB.setEnabled(useProxy.isSelected());
 359     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 360     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 361
 362     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 363
 364     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 365     // note antisense here: default is true
 366     questionnaire
 367             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 368     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 369
 370     /*
 371      * Set Output tab defaults
 372      */
 373     epsRendering.addItem(promptEachTimeOpt);
 374     epsRendering.addItem(lineArtOpt);
 375     epsRendering.addItem(textOpt);
 376     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 377             "Prompt each time");
 378     if (defaultEPS.equalsIgnoreCase("Text"))
 379     {
 380       epsRendering.setSelectedItem(textOpt);
 381     }
 382     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 383     {
 384       epsRendering.setSelectedItem(lineArtOpt);
 385     }
 386     else
 387     {
 388       epsRendering.setSelectedItem(promptEachTimeOpt);
 389     }
 390     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 391     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 392     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 393     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 394     userIdWidth.setText(wi == null ? "" : wi.toString());
 395     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 396     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 397     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 398     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 399     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 400     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 401     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 402     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 403     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 404             true));
 405
 406     /*
 407      * Set Editing tab defaults
 408      */
 409     autoCalculateConsCheck.setSelected(Cache.getDefault(
 410             "AUTO_CALC_CONSENSUS", true));
 411     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 412     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 413
 414     annotations_actionPerformed(null); // update the display of the annotation
 415                                        // settings
 416   }
 417
 418   /**
 419    * Save user selections on the Preferences tabs to the Cache and write out to
 420    * file.
 421    *
 422    * @param e
 423    */
 424   @Override
 425   public void ok_actionPerformed(ActionEvent e)
 426   {
 427     if (!validateSettings())
 428     {
 429       return;
 430     }
 431
 432     /*
 433      * Save Visual settings
 434      */
 435     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 436             Boolean.toString(seqLimit.isSelected()));
 437     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 438             Boolean.toString(rightAlign.isSelected()));
 439     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 440             Boolean.toString(fullScreen.isSelected()));
 441     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 442             Boolean.toString(openoverv.isSelected()));
 443     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 444             Boolean.toString(annotations.isSelected()));
 445     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 446             Boolean.toString(conservation.isSelected()));
 447     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 448             Boolean.toString(quality.isSelected()));
 449     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 450             Boolean.toString(identity.isSelected()));
 451
 452     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 453             .getSelectedItem().toString());
 454
 455     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 456             .getSelectedItem().toString());
 457     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 458             .getSelectedItem().toString());
 459     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 460             .getSelectedItem().toString());
 461
 462     Cache.applicationProperties.setProperty("ID_ITALICS",
 463             Boolean.toString(idItalics.isSelected()));
 464     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 465             Boolean.toString(showUnconserved.isSelected()));
 466     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 467             Boolean.toString(showGroupConsensus.isSelected()));
 468     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 469             Boolean.toString(showGroupConservation.isSelected()));
 470     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 471             Boolean.toString(showConsensHistogram.isSelected()));
 472     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 473             Boolean.toString(showConsensLogo.isSelected()));
 474     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 475             Boolean.toString(smoothFont.isSelected()));
 476     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 477             Boolean.toString(scaleProteinToCdna.isSelected()));
 478     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 479             Boolean.toString(showNpTooltip.isSelected()));
 480     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 481             Boolean.toString(showDbRefTooltip.isSelected()));
 482
 483     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 484             Boolean.toString(wrap.isSelected()));
 485
 486     Cache.applicationProperties.setProperty("STARTUP_FILE",
 487             startupFileTextfield.getText());
 488     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 489             Boolean.toString(startupCheckbox.isSelected()));
 490
 491     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 492             .getSelectedItem().toString());
 493
 494     // convert description of sort order to enum name for save
 495     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 496             .forDescription(sortAnnBy.getSelectedItem().toString());
 497     if (annSortOrder != null)
 498     {
 499       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 500               annSortOrder.name());
 501     }
 502
 503     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 504     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 505             .valueOf(showAutocalcFirst).toString());
 506
 507     /*
 508      * Save Colours settings
 509      */
 510     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 511             .getSelectedItem().toString());
 512     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 513             .getSelectedItem().toString());
 514     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 515             minColour.getBackground());
 516     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 517             maxColour.getBackground());
 518
 519     /*
 520      * Save Structure settings
 521      */
 522     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 523             Boolean.toString(addTempFactor.isSelected()));
 524     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 525             Boolean.toString(addSecondaryStructure.isSelected()));
 526     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 527             Boolean.toString(useRnaView.isSelected()));
 528     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 529             Boolean.toString(structFromPdb.isSelected()));
 530     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 531             .getSelectedItem().toString());
 532     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 533     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 534             Boolean.toString(siftsMapping.isSelected()));
 535     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 536
 537     /*
 538      * Save Output settings
 539      */
 540       Cache.applicationProperties.setProperty("EPS_RENDERING",
 541               ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 542
 543     /*
 544      * Save Connections settings
 545      */
 546     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 547
 548     jalview.util.BrowserLauncher.resetBrowser();
 549
 550     if (nameLinks.size() > 0)
 551     {
 552       StringBuffer links = new StringBuffer();
 553       sequenceURLLinks = new Vector<String>();
 554       for (int i = 0; i < nameLinks.size(); i++)
 555       {
 556         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 557                 + urlLinks.elementAt(i));
 558         links.append(sequenceURLLinks.elementAt(i).toString());
 559         links.append("|");
 560       }
 561       // remove last "|"
 562       links.setLength(links.length() - 1);
 563       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 564               links.toString());
 565     }
 566     else
 567     {
 568       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 569     }
 570
 571     Cache.applicationProperties.setProperty("USE_PROXY",
 572             Boolean.toString(useProxy.isSelected()));
 573
 574     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 575
 576     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 577
 578     if (useProxy.isSelected())
 579     {
 580       System.setProperty("http.proxyHost", proxyServerTB.getText());
 581       System.setProperty("http.proxyPort", proxyPortTB.getText());
 582     }
 583     else
 584     {
 585       System.setProperty("http.proxyHost", "");
 586       System.setProperty("http.proxyPort", "");
 587     }
 588     Cache.setProperty("VERSION_CHECK",
 589             Boolean.toString(versioncheck.isSelected()));
 590     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 591     {
 592       // default is false - we only set this if the user has actively agreed
 593       Cache.setProperty("USAGESTATS",
 594               Boolean.toString(usagestats.isSelected()));
 595     }
 596     if (!questionnaire.isSelected())
 597     {
 598       Cache.setProperty("NOQUESTIONNAIRES", "true");
 599     }
 600     else
 601     {
 602       // special - made easy to edit a property file to disable questionnaires
 603       // by just adding the given line
 604       Cache.removeProperty("NOQUESTIONNAIRES");
 605     }
 606
 607     /*
 608      * Save Output settings
 609      */
 610     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 611             Boolean.toString(blcjv.isSelected()));
 612     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 613             Boolean.toString(clustaljv.isSelected()));
 614     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 615             Boolean.toString(fastajv.isSelected()));
 616     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 617             Boolean.toString(msfjv.isSelected()));
 618     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 619             Boolean.toString(pfamjv.isSelected()));
 620     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 621             Boolean.toString(pileupjv.isSelected()));
 622     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 623             Boolean.toString(pirjv.isSelected()));
 624     Cache.applicationProperties.setProperty("PIR_MODELLER",
 625             Boolean.toString(modellerOutput.isSelected()));
 626     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 627             Boolean.toString(embbedBioJSON.isSelected()));
 628     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 629
 630     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 631             Boolean.toString(autoIdWidth.isSelected()));
 632     userIdWidth_actionPerformed();
 633     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 634             userIdWidth.getText());
 635
 636     /*
 637      * Save Editing settings
 638      */
 639     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 640             Boolean.toString(autoCalculateConsCheck.isSelected()));
 641     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 642             Boolean.toString(sortByTree.isSelected()));
 643     Cache.applicationProperties.setProperty("PAD_GAPS",
 644             Boolean.toString(padGaps.isSelected()));
 645
 646     dasSource.saveProperties(Cache.applicationProperties);
 647     wsPrefs.updateAndRefreshWsMenuConfig(false);
 648     Cache.saveProperties();
 649     Desktop.instance.doConfigureStructurePrefs();
 650     try
 651     {
 652       frame.setClosed(true);
 653     } catch (Exception ex)
 654     {
 655     }
 656   }
 657
 658   /**
 659    * Do any necessary validation before saving settings. Return focus to the
 660    * first tab which fails validation.
 661    *
 662    * @return
 663    */
 664   private boolean validateSettings()
 665   {
 666     if (!validateStructure())
 667     {
 668       structureTab.requestFocusInWindow();
 669       return false;
 670     }
 671     return true;
 672   }
 673
 674   @Override
 675   protected boolean validateStructure()
 676   {
 677     return validateChimeraPath();
 678
 679   }
 680
 681   /**
 682    * DOCUMENT ME!
 683    */
 684   @Override
 685   public void startupFileTextfield_mouseClicked()
 686   {
 687     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 688     JalviewFileChooser chooser = JalviewFileChooser.forRead(
 689             Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
 690     // new String[] {
 691     // "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 692     // "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 693     // "PIR", "BLC", "Jalview" },
 694     // fileFormat);
 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       FileFormatI format = chooser.getSelectedFormat();
 704       if (format != null)
 705       {
 706         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 707                 format.toString());
 708       }
 709       startupFileTextfield.setText(chooser.getSelectedFile()
 710               .getAbsolutePath());
 711     }
 712   }
 713
 714   /**
 715    * DOCUMENT ME!
 716    *
 717    * @param e
 718    *          DOCUMENT ME!
 719    */
 720   @Override
 721   public void cancel_actionPerformed(ActionEvent e)
 722   {
 723     try
 724     {
 725       wsPrefs.updateWsMenuConfig(true);
 726       wsPrefs.refreshWs_actionPerformed(e);
 727       frame.setClosed(true);
 728     } catch (Exception ex)
 729     {
 730     }
 731   }
 732
 733   /**
 734    * DOCUMENT ME!
 735    *
 736    * @param e
 737    *          DOCUMENT ME!
 738    */
 739   @Override
 740   public void annotations_actionPerformed(ActionEvent e)
 741   {
 742     conservation.setEnabled(annotations.isSelected());
 743     quality.setEnabled(annotations.isSelected());
 744     identity.setEnabled(annotations.isSelected());
 745     showGroupConsensus.setEnabled(annotations.isSelected());
 746     showGroupConservation.setEnabled(annotations.isSelected());
 747     showConsensHistogram.setEnabled(annotations.isSelected()
 748             && (identity.isSelected() || showGroupConsensus.isSelected()));
 749     showConsensLogo.setEnabled(annotations.isSelected()
 750             && (identity.isSelected() || showGroupConsensus.isSelected()));
 751   }
 752
 753   @Override
 754   public void newLink_actionPerformed(ActionEvent e)
 755   {
 756
 757     GSequenceLink link = new GSequenceLink();
 758     boolean valid = false;
 759     while (!valid)
 760     {
 761       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 762               MessageManager.getString("label.new_sequence_url_link"),
 763               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 764       {
 765         if (link.checkValid())
 766         {
 767           nameLinks.addElement(link.getName());
 768           urlLinks.addElement(link.getURL());
 769           updateLinkData();
 770           valid = true;
 771         }
 772       }
 773       else
 774       {
 775         break;
 776       }
 777     }
 778   }
 779
 780   @Override
 781   public void editLink_actionPerformed(ActionEvent e)
 782   {
 783     GSequenceLink link = new GSequenceLink();
 784
 785     int index = linkNameList.getSelectedIndex();
 786     if (index == -1)
 787     {
 788       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 789               MessageManager.getString("label.no_link_selected"),
 790               MessageManager.getString("label.no_link_selected"),
 791               JOptionPane.WARNING_MESSAGE);
 792       return;
 793     }
 794
 795     link.setName(nameLinks.elementAt(index).toString());
 796     link.setURL(urlLinks.elementAt(index).toString());
 797
 798     boolean valid = false;
 799     while (!valid)
 800     {
 801
 802       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 803               MessageManager.getString("label.new_sequence_url_link"),
 804               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 805       {
 806         if (link.checkValid())
 807         {
 808           nameLinks.setElementAt(link.getName(), index);
 809           urlLinks.setElementAt(link.getURL(), index);
 810           updateLinkData();
 811           valid = true;
 812         }
 813       }
 814
 815       else
 816       {
 817         break;
 818       }
 819     }
 820   }
 821
 822   @Override
 823   public void deleteLink_actionPerformed(ActionEvent e)
 824   {
 825     int index = linkNameList.getSelectedIndex();
 826     if (index == -1)
 827     {
 828       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 829               MessageManager.getString("label.no_link_selected"),
 830               MessageManager.getString("label.no_link_selected"),
 831               JOptionPane.WARNING_MESSAGE);
 832       return;
 833     }
 834     nameLinks.removeElementAt(index);
 835     urlLinks.removeElementAt(index);
 836     updateLinkData();
 837   }
 838
 839   void updateLinkData()
 840   {
 841     linkNameList.setListData(nameLinks);
 842     linkURLList.setListData(urlLinks);
 843   }
 844
 845   @Override
 846   public void defaultBrowser_mouseClicked(MouseEvent e)
 847   {
 848     JFileChooser chooser = new JFileChooser(".");
 849     chooser.setDialogTitle(MessageManager
 850             .getString("label.select_default_browser"));
 851
 852     int value = chooser.showOpenDialog(this);
 853
 854     if (value == JFileChooser.APPROVE_OPTION)
 855     {
 856       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 857     }
 858
 859   }
 860
 861   /*
 862    * (non-Javadoc)
 863    *
 864    * @see
 865    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 866    * .ActionEvent)
 867    */
 868   @Override
 869   protected void showunconserved_actionPerformed(ActionEvent e)
 870   {
 871     // TODO Auto-generated method stub
 872     super.showunconserved_actionPerformed(e);
 873   }
 874
 875   public static List<String> getGroupURLLinks()
 876   {
 877     return groupURLLinks;
 878   }
 879
 880   @Override
 881   public void minColour_actionPerformed(JPanel panel)
 882   {
 883     Color col = JColorChooser.showDialog(this,
 884             MessageManager.getString("label.select_colour_minimum_value"),
 885             minColour.getBackground());
 886     if (col != null)
 887     {
 888       panel.setBackground(col);
 889     }
 890     panel.repaint();
 891   }
 892
 893   @Override
 894   public void maxColour_actionPerformed(JPanel panel)
 895   {
 896     Color col = JColorChooser.showDialog(this,
 897             MessageManager.getString("label.select_colour_maximum_value"),
 898             maxColour.getBackground());
 899     if (col != null)
 900     {
 901       panel.setBackground(col);
 902     }
 903     panel.repaint();
 904   }
 905
 906   @Override
 907   protected void userIdWidth_actionPerformed()
 908   {
 909     try
 910     {
 911       String val = userIdWidth.getText().trim();
 912       if (val.length() > 0)
 913       {
 914         Integer iw = Integer.parseInt(val);
 915         if (iw.intValue() < 12)
 916         {
 917           throw new NumberFormatException();
 918         }
 919         userIdWidth.setText(iw.toString());
 920       }
 921     } catch (NumberFormatException x)
 922     {
 923       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 924               .getString("warn.user_defined_width_requirements"),
 925               MessageManager.getString("label.invalid_id_column_width"),
 926               JOptionPane.WARNING_MESSAGE);
 927       userIdWidth.setText("");
 928     }
 929   }
 930
 931   @Override
 932   protected void autoIdWidth_actionPerformed()
 933   {
 934     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 935     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 936   }
 937
 938   /**
 939    * Returns true if chimera path is to a valid executable, else show an error
 940    * dialog.
 941    */
 942   private boolean validateChimeraPath()
 943   {
 944     if (chimeraPath.getText().trim().length() > 0)
 945     {
 946       File f = new File(chimeraPath.getText());
 947       if (!f.canExecute())
 948       {
 949         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 950                 MessageManager.getString("label.invalid_chimera_path"),
 951                 MessageManager.getString("label.invalid_name"),
 952                 JOptionPane.ERROR_MESSAGE);
 953         return false;
 954       }
 955     }
 956     return true;
 957   }
 958
 959   /**
 960    * If Chimera is selected, check it can be found on default or user-specified
 961    * path, if not show a warning/help dialog.
 962    */
 963   @Override
 964   protected void structureViewer_actionPerformed(String selectedItem)
 965   {
 966     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 967     {
 968       return;
 969     }
 970     boolean found = false;
 971
 972     /*
 973      * Try user-specified and standard paths for Chimera executable.
 974      */
 975     List<String> paths = StructureManager.getChimeraPaths();
 976     paths.add(0, chimeraPath.getText());
 977     for (String path : paths)
 978     {
 979       if (new File(path.trim()).canExecute())
 980       {
 981         found = true;
 982         break;
 983       }
 984     }
 985     if (!found)
 986     {
 987       String[] options = { "OK", "Help" };
 988       int showHelp = JOptionPane.showInternalOptionDialog(
 989               Desktop.desktop,
 990               JvSwingUtils.wrapTooltip(true,
 991                       MessageManager.getString("label.chimera_missing")),
 992               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 993               null, options, options[0]);
 994       if (showHelp == JOptionPane.NO_OPTION)
 995       {
 996         try
 997         {
 998           Help.showHelpWindow(HelpId.StructureViewer);
 999         } catch (HelpSetException e)
1000         {
1001           e.printStackTrace();
1002         }
1003       }
1004     }
1005   }
1006
1007   public class OptionsParam
1008   {
1009     private String name;
1010
1011     private String code;
1012
1013     public OptionsParam(String name, String code)
1014     {
1015       this.name = name;
1016       this.code = code;
1017     }
1018
1019     public String getName()
1020     {
1021       return name;
1022     }
1023
1024     public void setName(String name)
1025     {
1026       this.name = name;
1027     }
1028
1029     public String getCode()
1030     {
1031       return code;
1032     }
1033
1034     public void setCode(String code)
1035     {
1036       this.code = code;
1037     }
1038
1039     @Override
1040     public String toString()
1041     {
1042       return name;
1043     }
1044
1045     @Override
1046     public boolean equals(Object that)
1047     {
1048       if (!(that instanceof OptionsParam))
1049       {
1050         return false;
1051       }
1052       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1053     }
1054
1055     @Override
1056     public int hashCode(){
1057       return name.hashCode() + code.hashCode();
1058     }
1059   }
1060 }