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.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.jbgui.GPreferences;
  30 import jalview.jbgui.GSequenceLink;
  31 import jalview.schemes.ColourSchemeProperty;
  32 import jalview.util.MessageManager;
  33 import jalview.ws.sifts.SiftsSettings;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.Dimension;
  38 import java.awt.Font;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.MouseEvent;
  42 import java.io.File;
  43 import java.util.Collection;
  44 import java.util.List;
  45 import java.util.StringTokenizer;
  46 import java.util.Vector;
  47
  48 import javax.help.HelpSetException;
  49 import javax.swing.JColorChooser;
  50 import javax.swing.JFileChooser;
  51 import javax.swing.JInternalFrame;
  52 import javax.swing.JOptionPane;
  53 import javax.swing.JPanel;
  54
  55 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class Preferences extends GPreferences
  64 {
  65   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  66
  67   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  68
  69   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  70
  71   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  72
  73   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  74
  75   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  76
  77   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  78
  79   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  80
  81   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  82
  83   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  84
  85   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  86
  87   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  88
  89   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  90
  91   public static final String HIDE_INTRONS = "HIDE_INTRONS";
  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 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 Vector 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();
 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 Vector();
 158   }
 159
 160   Vector nameLinks, urlLinks;
 161
 162   JInternalFrame frame;
 163
 164   DasSourceBrowser dasSource;
 165
 166   private WsPreferences wsPrefs;
 167
 168   /**
 169    * Creates a new Preferences object.
 170    */
 171   public Preferences()
 172   {
 173     super();
 174     frame = new JInternalFrame();
 175     frame.setContentPane(this);
 176     dasSource = new DasSourceBrowser();
 177     dasTab.add(dasSource, BorderLayout.CENTER);
 178     wsPrefs = new WsPreferences();
 179     wsTab.add(wsPrefs, BorderLayout.CENTER);
 180     int width = 500, height = 470;
 181     if (new jalview.util.Platform().isAMac())
 182     {
 183       width = 570;
 184       height = 500;
 185     }
 186
 187     Desktop.addInternalFrame(frame,
 188             MessageManager.getString("label.preferences"), width, height);
 189     frame.setMinimumSize(new Dimension(width, height));
 190
 191     /*
 192      * Set Visual tab defaults
 193      */
 194     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 195     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 196     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 197     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 198
 199     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 200     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 201     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 202     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 203     showUnconserved
 204             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 205     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 206             false));
 207     showGroupConservation.setSelected(Cache.getDefault(
 208             "SHOW_GROUP_CONSERVATION", false));
 209     showConsensHistogram.setSelected(Cache.getDefault(
 210             "SHOW_CONSENSUS_HISTOGRAM", true));
 211     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 212             false));
 213     showNpTooltip.setSelected(Cache
 214             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 215     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 216             true));
 217
 218     String[] fonts = java.awt.GraphicsEnvironment
 219             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 220     for (int i = 0; i < fonts.length; i++)
 221     {
 222       fontNameCB.addItem(fonts[i]);
 223     }
 224
 225     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 226     {
 227       fontSizeCB.addItem(i + "");
 228     }
 229
 230     fontStyleCB.addItem("plain");
 231     fontStyleCB.addItem("bold");
 232     fontStyleCB.addItem("italic");
 233
 234     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 235     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 236     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 237             + ""));
 238
 239     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 240     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 241             false));
 242
 243     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 244
 245     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 246     hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
 247
 248     gapSymbolCB.addItem("-");
 249     gapSymbolCB.addItem(".");
 250
 251     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 252
 253     sortby.addItem("No sort");
 254     sortby.addItem("Id");
 255     sortby.addItem("Pairwise Identity");
 256     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 257
 258     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 259     sortAnnBy
 260             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 261     sortAnnBy
 262             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 263     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 264             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 265                     SequenceAnnotationOrder.NONE.name()));
 266     sortAnnBy.setSelectedItem(savedSort.toString());
 267
 268     sortAutocalc.addItem("Autocalculated first");
 269     sortAutocalc.addItem("Autocalculated last");
 270     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 271     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 272             : sortAutocalc.getItemAt(1));
 273     startupCheckbox
 274             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 275     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 276             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 277                     + "/examples/exampleFile_2_3.jar"));
 278
 279     /*
 280      * Set Colours tab defaults
 281      */
 282     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 283     {
 284       protColour.addItem(ColourSchemeProperty.getColourName(i));
 285       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 286     }
 287     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 288     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 289     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 290     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 291     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 292     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 293             Color.orange));
 294     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 295             Color.red));
 296
 297     /*
 298      * Set Structure tab defaults.
 299      */
 300     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 301     structFromPdb.setSelected(structSelected);
 302     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 303     useRnaView.setEnabled(structSelected);
 304     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 305     addSecondaryStructure.setEnabled(structSelected);
 306     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 307     addTempFactor.setEnabled(structSelected);
 308     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 309             ViewerType.JMOL.name()));
 310     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 311     chimeraPath.addActionListener(new ActionListener()
 312     {
 313       @Override
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         validateChimeraPath();
 317       }
 318     });
 319
 320     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 321     {
 322       siftsMapping.setSelected(true);
 323     }
 324     else
 325     {
 326       nwMapping.setSelected(true);
 327     }
 328
 329     SiftsSettings
 330             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 331
 332     /*
 333      * Set Connections tab defaults
 334      */
 335     nameLinks = new Vector();
 336     urlLinks = new Vector();
 337     for (int i = 0; i < sequenceURLLinks.size(); i++)
 338     {
 339       String link = sequenceURLLinks.elementAt(i).toString();
 340       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 341       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 342     }
 343
 344     updateLinkData();
 345
 346     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 347     proxyServerTB.setEnabled(useProxy.isSelected());
 348     proxyPortTB.setEnabled(useProxy.isSelected());
 349     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 350     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 351
 352     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 353
 354     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 355     // note antisense here: default is true
 356     questionnaire
 357             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 358     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 359
 360     /*
 361      * Set Output tab defaults
 362      */
 363     epsRendering
 364             .addItem(MessageManager.getString("label.prompt_each_time"));
 365     epsRendering.addItem(MessageManager.getString("label.lineart"));
 366     epsRendering.addItem(MessageManager.getString("action.text"));
 367     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 368             "Prompt each time"));
 369     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 370     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 371     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 372     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 373     userIdWidth.setText(wi == null ? "" : wi.toString());
 374     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 375     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 376     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 377     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 378     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 379     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 380     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 381     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 382     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 383             true));
 384
 385     /*
 386      * Set Editing tab defaults
 387      */
 388     autoCalculateConsCheck.setSelected(Cache.getDefault(
 389             "AUTO_CALC_CONSENSUS", true));
 390     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 391     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 392
 393     annotations_actionPerformed(null); // update the display of the annotation
 394                                        // settings
 395   }
 396
 397   /**
 398    * Save user selections on the Preferences tabs to the Cache and write out to
 399    * file.
 400    *
 401    * @param e
 402    */
 403   @Override
 404   public void ok_actionPerformed(ActionEvent e)
 405   {
 406     if (!validateSettings())
 407     {
 408       return;
 409     }
 410
 411     /*
 412      * Save Visual settings
 413      */
 414     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 415             Boolean.toString(seqLimit.isSelected()));
 416     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 417             Boolean.toString(rightAlign.isSelected()));
 418     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 419             Boolean.toString(fullScreen.isSelected()));
 420     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 421             Boolean.toString(openoverv.isSelected()));
 422     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 423             Boolean.toString(annotations.isSelected()));
 424     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 425             Boolean.toString(conservation.isSelected()));
 426     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 427             Boolean.toString(quality.isSelected()));
 428     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 429             Boolean.toString(identity.isSelected()));
 430
 431     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 432             .getSelectedItem().toString());
 433
 434     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 435             .getSelectedItem().toString());
 436     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 437             .getSelectedItem().toString());
 438     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 439             .getSelectedItem().toString());
 440
 441     Cache.applicationProperties.setProperty("ID_ITALICS",
 442             Boolean.toString(idItalics.isSelected()));
 443     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 444             Boolean.toString(showUnconserved.isSelected()));
 445     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 446             Boolean.toString(showGroupConsensus.isSelected()));
 447     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 448             Boolean.toString(showGroupConservation.isSelected()));
 449     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 450             Boolean.toString(showConsensHistogram.isSelected()));
 451     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 452             Boolean.toString(showConsensLogo.isSelected()));
 453     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 454             Boolean.toString(smoothFont.isSelected()));
 455     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 456             Boolean.toString(scaleProteinToCdna.isSelected()));
 457     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 458             Boolean.toString(showNpTooltip.isSelected()));
 459     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 460             Boolean.toString(showDbRefTooltip.isSelected()));
 461
 462     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 463             Boolean.toString(wrap.isSelected()));
 464     Cache.applicationProperties.setProperty(HIDE_INTRONS,
 465             Boolean.toString(hideIntrons.isSelected()));
 466
 467     Cache.applicationProperties.setProperty("STARTUP_FILE",
 468             startupFileTextfield.getText());
 469     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 470             Boolean.toString(startupCheckbox.isSelected()));
 471
 472     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 473             .getSelectedItem().toString());
 474
 475     // convert description of sort order to enum name for save
 476     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 477             .forDescription(sortAnnBy.getSelectedItem().toString());
 478     if (annSortOrder != null)
 479     {
 480       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 481               annSortOrder.name());
 482     }
 483
 484     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 485     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 486             .valueOf(showAutocalcFirst).toString());
 487
 488     /*
 489      * Save Colours settings
 490      */
 491     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 492             .getSelectedItem().toString());
 493     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 494             .getSelectedItem().toString());
 495     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 496             minColour.getBackground());
 497     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 498             maxColour.getBackground());
 499
 500     /*
 501      * Save Structure settings
 502      */
 503     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 504             Boolean.toString(addTempFactor.isSelected()));
 505     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 506             Boolean.toString(addSecondaryStructure.isSelected()));
 507     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 508             Boolean.toString(useRnaView.isSelected()));
 509     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 510             Boolean.toString(structFromPdb.isSelected()));
 511     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 512             .getSelectedItem().toString());
 513     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 514     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 515             Boolean.toString(siftsMapping.isSelected()));
 516     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 517
 518     /*
 519      * Save Output settings
 520      */
 521     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 522     {
 523       Cache.applicationProperties.remove("EPS_RENDERING");
 524     }
 525     else
 526     {
 527       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 528               .getSelectedItem().toString());
 529     }
 530
 531     /*
 532      * Save Connections settings
 533      */
 534     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 535
 536     jalview.util.BrowserLauncher.resetBrowser();
 537
 538     if (nameLinks.size() > 0)
 539     {
 540       StringBuffer links = new StringBuffer();
 541       sequenceURLLinks = new Vector();
 542       for (int i = 0; i < nameLinks.size(); i++)
 543       {
 544         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 545                 + urlLinks.elementAt(i));
 546         links.append(sequenceURLLinks.elementAt(i).toString());
 547         links.append("|");
 548       }
 549       // remove last "|"
 550       links.setLength(links.length() - 1);
 551       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 552               links.toString());
 553     }
 554     else
 555     {
 556       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 557     }
 558
 559     Cache.applicationProperties.setProperty("USE_PROXY",
 560             Boolean.toString(useProxy.isSelected()));
 561
 562     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 563
 564     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 565
 566     if (useProxy.isSelected())
 567     {
 568       System.setProperty("http.proxyHost", proxyServerTB.getText());
 569       System.setProperty("http.proxyPort", proxyPortTB.getText());
 570     }
 571     else
 572     {
 573       System.setProperty("http.proxyHost", "");
 574       System.setProperty("http.proxyPort", "");
 575     }
 576     Cache.setProperty("VERSION_CHECK",
 577             Boolean.toString(versioncheck.isSelected()));
 578     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 579     {
 580       // default is false - we only set this if the user has actively agreed
 581       Cache.setProperty("USAGESTATS",
 582               Boolean.toString(usagestats.isSelected()));
 583     }
 584     if (!questionnaire.isSelected())
 585     {
 586       Cache.setProperty("NOQUESTIONNAIRES", "true");
 587     }
 588     else
 589     {
 590       // special - made easy to edit a property file to disable questionnaires
 591       // by just adding the given line
 592       Cache.removeProperty("NOQUESTIONNAIRES");
 593     }
 594
 595     /*
 596      * Save Output settings
 597      */
 598     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 599             Boolean.toString(blcjv.isSelected()));
 600     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 601             Boolean.toString(clustaljv.isSelected()));
 602     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 603             Boolean.toString(fastajv.isSelected()));
 604     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 605             Boolean.toString(msfjv.isSelected()));
 606     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 607             Boolean.toString(pfamjv.isSelected()));
 608     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 609             Boolean.toString(pileupjv.isSelected()));
 610     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 611             Boolean.toString(pirjv.isSelected()));
 612     Cache.applicationProperties.setProperty("PIR_MODELLER",
 613             Boolean.toString(modellerOutput.isSelected()));
 614     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 615             Boolean.toString(embbedBioJSON.isSelected()));
 616     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 617
 618     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 619             Boolean.toString(autoIdWidth.isSelected()));
 620     userIdWidth_actionPerformed();
 621     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 622             userIdWidth.getText());
 623
 624     /*
 625      * Save Editing settings
 626      */
 627     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 628             Boolean.toString(autoCalculateConsCheck.isSelected()));
 629     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 630             Boolean.toString(sortByTree.isSelected()));
 631     Cache.applicationProperties.setProperty("PAD_GAPS",
 632             Boolean.toString(padGaps.isSelected()));
 633
 634     dasSource.saveProperties(Cache.applicationProperties);
 635     wsPrefs.updateAndRefreshWsMenuConfig(false);
 636     Cache.saveProperties();
 637     Desktop.instance.doConfigureStructurePrefs();
 638     try
 639     {
 640       frame.setClosed(true);
 641     } catch (Exception ex)
 642     {
 643     }
 644   }
 645
 646   /**
 647    * Do any necessary validation before saving settings. Return focus to the
 648    * first tab which fails validation.
 649    *
 650    * @return
 651    */
 652   private boolean validateSettings()
 653   {
 654     if (!validateStructure())
 655     {
 656       structureTab.requestFocusInWindow();
 657       return false;
 658     }
 659     return true;
 660   }
 661
 662   @Override
 663   protected boolean validateStructure()
 664   {
 665     return validateChimeraPath();
 666
 667   }
 668
 669   /**
 670    * DOCUMENT ME!
 671    */
 672   @Override
 673   public void startupFileTextfield_mouseClicked()
 674   {
 675     JalviewFileChooser chooser = new JalviewFileChooser(
 676             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 677                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 678                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 679                 "PIR", "BLC", "Jalview" },
 680             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 681     chooser.setFileView(new JalviewFileView());
 682     chooser.setDialogTitle(MessageManager
 683             .getString("label.select_startup_file"));
 684
 685     int value = chooser.showOpenDialog(this);
 686
 687     if (value == JalviewFileChooser.APPROVE_OPTION)
 688     {
 689       jalview.bin.Cache.applicationProperties.setProperty(
 690               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 691       startupFileTextfield.setText(chooser.getSelectedFile()
 692               .getAbsolutePath());
 693     }
 694   }
 695
 696   /**
 697    * DOCUMENT ME!
 698    *
 699    * @param e
 700    *          DOCUMENT ME!
 701    */
 702   @Override
 703   public void cancel_actionPerformed(ActionEvent e)
 704   {
 705     try
 706     {
 707       wsPrefs.updateWsMenuConfig(true);
 708       wsPrefs.refreshWs_actionPerformed(e);
 709       frame.setClosed(true);
 710     } catch (Exception ex)
 711     {
 712     }
 713   }
 714
 715   /**
 716    * DOCUMENT ME!
 717    *
 718    * @param e
 719    *          DOCUMENT ME!
 720    */
 721   @Override
 722   public void annotations_actionPerformed(ActionEvent e)
 723   {
 724     conservation.setEnabled(annotations.isSelected());
 725     quality.setEnabled(annotations.isSelected());
 726     identity.setEnabled(annotations.isSelected());
 727     showGroupConsensus.setEnabled(annotations.isSelected());
 728     showGroupConservation.setEnabled(annotations.isSelected());
 729     showConsensHistogram.setEnabled(annotations.isSelected()
 730             && (identity.isSelected() || showGroupConsensus.isSelected()));
 731     showConsensLogo.setEnabled(annotations.isSelected()
 732             && (identity.isSelected() || showGroupConsensus.isSelected()));
 733   }
 734
 735   @Override
 736   public void newLink_actionPerformed(ActionEvent e)
 737   {
 738
 739     GSequenceLink link = new GSequenceLink();
 740     boolean valid = false;
 741     while (!valid)
 742     {
 743       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 744               MessageManager.getString("label.new_sequence_url_link"),
 745               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 746       {
 747         if (link.checkValid())
 748         {
 749           nameLinks.addElement(link.getName());
 750           urlLinks.addElement(link.getURL());
 751           updateLinkData();
 752           valid = true;
 753         }
 754       }
 755       else
 756       {
 757         break;
 758       }
 759     }
 760   }
 761
 762   @Override
 763   public void editLink_actionPerformed(ActionEvent e)
 764   {
 765     GSequenceLink link = new GSequenceLink();
 766
 767     int index = linkNameList.getSelectedIndex();
 768     if (index == -1)
 769     {
 770       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 771               MessageManager.getString("label.no_link_selected"),
 772               MessageManager.getString("label.no_link_selected"),
 773               JOptionPane.WARNING_MESSAGE);
 774       return;
 775     }
 776
 777     link.setName(nameLinks.elementAt(index).toString());
 778     link.setURL(urlLinks.elementAt(index).toString());
 779
 780     boolean valid = false;
 781     while (!valid)
 782     {
 783
 784       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 785               MessageManager.getString("label.new_sequence_url_link"),
 786               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 787       {
 788         if (link.checkValid())
 789         {
 790           nameLinks.setElementAt(link.getName(), index);
 791           urlLinks.setElementAt(link.getURL(), index);
 792           updateLinkData();
 793           valid = true;
 794         }
 795       }
 796
 797       else
 798       {
 799         break;
 800       }
 801     }
 802   }
 803
 804   @Override
 805   public void deleteLink_actionPerformed(ActionEvent e)
 806   {
 807     int index = linkNameList.getSelectedIndex();
 808     if (index == -1)
 809     {
 810       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 811               MessageManager.getString("label.no_link_selected"),
 812               MessageManager.getString("label.no_link_selected"),
 813               JOptionPane.WARNING_MESSAGE);
 814       return;
 815     }
 816     nameLinks.removeElementAt(index);
 817     urlLinks.removeElementAt(index);
 818     updateLinkData();
 819   }
 820
 821   void updateLinkData()
 822   {
 823     linkNameList.setListData(nameLinks);
 824     linkURLList.setListData(urlLinks);
 825   }
 826
 827   @Override
 828   public void defaultBrowser_mouseClicked(MouseEvent e)
 829   {
 830     JFileChooser chooser = new JFileChooser(".");
 831     chooser.setDialogTitle(MessageManager
 832             .getString("label.select_default_browser"));
 833
 834     int value = chooser.showOpenDialog(this);
 835
 836     if (value == JFileChooser.APPROVE_OPTION)
 837     {
 838       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 839     }
 840
 841   }
 842
 843   /*
 844    * (non-Javadoc)
 845    *
 846    * @see
 847    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 848    * .ActionEvent)
 849    */
 850   @Override
 851   protected void showunconserved_actionPerformed(ActionEvent e)
 852   {
 853     // TODO Auto-generated method stub
 854     super.showunconserved_actionPerformed(e);
 855   }
 856
 857   public static Collection getGroupURLLinks()
 858   {
 859     return groupURLLinks;
 860   }
 861
 862   @Override
 863   public void minColour_actionPerformed(JPanel panel)
 864   {
 865     Color col = JColorChooser.showDialog(this,
 866             MessageManager.getString("label.select_colour_minimum_value"),
 867             minColour.getBackground());
 868     if (col != null)
 869     {
 870       panel.setBackground(col);
 871     }
 872     panel.repaint();
 873   }
 874
 875   @Override
 876   public void maxColour_actionPerformed(JPanel panel)
 877   {
 878     Color col = JColorChooser.showDialog(this,
 879             MessageManager.getString("label.select_colour_maximum_value"),
 880             maxColour.getBackground());
 881     if (col != null)
 882     {
 883       panel.setBackground(col);
 884     }
 885     panel.repaint();
 886   }
 887
 888   @Override
 889   protected void userIdWidth_actionPerformed()
 890   {
 891     try
 892     {
 893       String val = userIdWidth.getText().trim();
 894       if (val.length() > 0)
 895       {
 896         Integer iw = Integer.parseInt(val);
 897         if (iw.intValue() < 12)
 898         {
 899           throw new NumberFormatException();
 900         }
 901         userIdWidth.setText(iw.toString());
 902       }
 903     } catch (NumberFormatException x)
 904     {
 905       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 906               .getString("warn.user_defined_width_requirements"),
 907               MessageManager.getString("label.invalid_id_column_width"),
 908               JOptionPane.WARNING_MESSAGE);
 909       userIdWidth.setText("");
 910     }
 911   }
 912
 913   @Override
 914   protected void autoIdWidth_actionPerformed()
 915   {
 916     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 917     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 918   }
 919
 920   /**
 921    * Returns true if chimera path is to a valid executable, else show an error
 922    * dialog.
 923    */
 924   private boolean validateChimeraPath()
 925   {
 926     if (chimeraPath.getText().trim().length() > 0)
 927     {
 928       File f = new File(chimeraPath.getText());
 929       if (!f.canExecute())
 930       {
 931         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 932                 MessageManager.getString("label.invalid_chimera_path"),
 933                 MessageManager.getString("label.invalid_name"),
 934                 JOptionPane.ERROR_MESSAGE);
 935         return false;
 936       }
 937     }
 938     return true;
 939   }
 940
 941   /**
 942    * If Chimera is selected, check it can be found on default or user-specified
 943    * path, if not show a warning/help dialog.
 944    */
 945   @Override
 946   protected void structureViewer_actionPerformed(String selectedItem)
 947   {
 948     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 949     {
 950       return;
 951     }
 952     boolean found = false;
 953
 954     /*
 955      * Try user-specified and standard paths for Chimera executable.
 956      */
 957     List<String> paths = StructureManager.getChimeraPaths();
 958     paths.add(0, chimeraPath.getText());
 959     for (String path : paths)
 960     {
 961       if (new File(path.trim()).canExecute())
 962       {
 963         found = true;
 964         break;
 965       }
 966     }
 967     if (!found)
 968     {
 969       String[] options = { "OK", "Help" };
 970       int showHelp = JOptionPane.showInternalOptionDialog(
 971               Desktop.desktop,
 972               JvSwingUtils.wrapTooltip(true,
 973                       MessageManager.getString("label.chimera_missing")),
 974               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 975               null, options, options[0]);
 976       if (showHelp == JOptionPane.NO_OPTION)
 977       {
 978         try
 979         {
 980           Help.showHelpWindow(HelpId.StructureViewer);
 981         } catch (HelpSetException e)
 982         {
 983           e.printStackTrace();
 984         }
 985       }
 986     }
 987   }
 988
 989 }