src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.StructureViewer.Viewer;
  26 import jalview.io.JalviewFileChooser;
  27 import jalview.io.JalviewFileView;
  28 import jalview.jbgui.GPreferences;
  29 import jalview.jbgui.GSequenceLink;
  30 import jalview.schemes.ColourSchemeProperty;
  31 import jalview.util.MessageManager;
  32
  33 import java.awt.BorderLayout;
  34 import java.awt.Color;
  35 import java.awt.Dimension;
  36 import java.awt.Font;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.MouseEvent;
  40 import java.io.File;
  41 import java.util.Collection;
  42 import java.util.StringTokenizer;
  43 import java.util.Vector;
  44
  45 import javax.swing.JColorChooser;
  46 import javax.swing.JFileChooser;
  47 import javax.swing.JInternalFrame;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50
  51 /**
  52  * DOCUMENT ME!
  53  *
  54  * @author $author$
  55  * @version $Revision$
  56  */
  57 public class Preferences extends GPreferences
  58 {
  59
  60   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  61
  62   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  63
  64   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  65
  66   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  67
  68   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  69
  70   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  71
  72   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  73
  74   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  75
  76   private static final int MIN_FONT_SIZE = 1;
  77
  78   private static final int MAX_FONT_SIZE = 30;
  79
  80   /**
  81    * Holds name and link separated with | character. Sequence ID must be
  82    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  83    */
  84   public static Vector sequenceURLLinks;
  85
  86   /**
  87    * Holds name and link separated with | character. Sequence IDS and Sequences
  88    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  89    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  90    * for first and second token specified after a pipe character at end |,|.
  91    * (TODO: proper escape for using | to separate ids or sequences
  92    */
  93
  94   public static Vector groupURLLinks;
  95   static
  96   {
  97     String string = Cache
  98             .getDefault(
  99                     "SEQUENCE_LINKS",
 100                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 101     sequenceURLLinks = new Vector();
 102
 103     try
 104     {
 105       StringTokenizer st = new StringTokenizer(string, "|");
 106       while (st.hasMoreElements())
 107       {
 108         String name = st.nextToken();
 109         String url = st.nextToken();
 110         // check for '|' within a regex
 111         int rxstart = url.indexOf("$SEQUENCE_ID$");
 112         while (rxstart == -1 && url.indexOf("/=$") == -1)
 113         {
 114           url = url + "|" + st.nextToken();
 115         }
 116         sequenceURLLinks.addElement(name + "|" + url);
 117       }
 118     } catch (Exception ex)
 119     {
 120       System.out.println(ex + "\nError parsing sequence links");
 121     }
 122     {
 123       // upgrade old SRS link
 124       int srsPos = sequenceURLLinks
 125               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 126       if (srsPos > -1)
 127       {
 128         sequenceURLLinks
 129                 .setElementAt(
 130                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 131                         srsPos);
 132       }
 133     }
 134
 135     /**
 136      * TODO: reformulate groupURL encoding so two or more can be stored in the
 137      * .properties file as '|' separated strings
 138      */
 139
 140     groupURLLinks = new Vector();
 141   }
 142
 143   Vector nameLinks, urlLinks;
 144
 145   JInternalFrame frame;
 146
 147   DasSourceBrowser dasSource;
 148
 149   private WsPreferences wsPrefs;
 150
 151   /**
 152    * Creates a new Preferences object.
 153    */
 154   public Preferences()
 155   {
 156     super();
 157     frame = new JInternalFrame();
 158     frame.setContentPane(this);
 159     dasSource = new DasSourceBrowser();
 160     dasTab.add(dasSource, BorderLayout.CENTER);
 161     wsPrefs = new WsPreferences();
 162     wsTab.add(wsPrefs, BorderLayout.CENTER);
 163     int width = 500, height = 420;
 164     if (new jalview.util.Platform().isAMac())
 165     {
 166       width = 570;
 167       height = 460;
 168     }
 169
 170     Desktop.addInternalFrame(frame,
 171             MessageManager.getString("label.preferences"), width, height);
 172     frame.setMinimumSize(new Dimension(width, height));
 173
 174     /*
 175      * Set Visual tab defaults
 176      */
 177     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 178     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 179     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 180     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 181
 182     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 183     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 184     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 185     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 186     showUnconserved
 187             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 188     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 189             false));
 190     showGroupConservation.setSelected(Cache.getDefault(
 191             "SHOW_GROUP_CONSERVATION", false));
 192     showConsensHistogram.setSelected(Cache.getDefault(
 193             "SHOW_CONSENSUS_HISTOGRAM", true));
 194     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 195             false));
 196     showNpTooltip.setSelected(Cache
 197             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 198     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 199             true));
 200
 201     String[] fonts = java.awt.GraphicsEnvironment
 202             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 203     for (int i = 0; i < fonts.length; i++)
 204     {
 205       fontNameCB.addItem(fonts[i]);
 206     }
 207
 208     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 209     {
 210       fontSizeCB.addItem(i + "");
 211     }
 212
 213     fontStyleCB.addItem("plain");
 214     fontStyleCB.addItem("bold");
 215     fontStyleCB.addItem("italic");
 216
 217     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 218     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 219     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 220             + ""));
 221
 222     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 223
 224     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 225
 226     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 227
 228     gapSymbolCB.addItem("-");
 229     gapSymbolCB.addItem(".");
 230
 231     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 232
 233     sortby.addItem("No sort");
 234     sortby.addItem("Id");
 235     sortby.addItem("Pairwise Identity");
 236     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 237
 238     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 239     sortAnnBy
 240             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 241     sortAnnBy
 242             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 243     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 244             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 245                     SequenceAnnotationOrder.NONE.name()));
 246     sortAnnBy.setSelectedItem(savedSort.toString());
 247
 248     sortAutocalc.addItem("Autocalculated first");
 249     sortAutocalc.addItem("Autocalculated last");
 250     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
 251             true);
 252     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 253             : sortAutocalc.getItemAt(1));
 254     startupCheckbox
 255             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 256     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 257             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 258                     + "/examples/exampleFile_2_3.jar"));
 259
 260     /*
 261      * Set Colours tab defaults
 262      */
 263     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 264     {
 265       colour.addItem(ColourSchemeProperty.getColourName(i));
 266     }
 267     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 268     colour.setSelectedItem(string);
 269     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 270             Color.orange));
 271     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 272             Color.red));
 273
 274     /*
 275      * Set Structure tab defaults.
 276      */
 277     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 278     structFromPdb.setSelected(structSelected);
 279     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 280     useRnaView.setEnabled(structSelected);
 281     addSecondaryStructure
 282             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 283     addSecondaryStructure.setEnabled(structSelected);
 284     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 285     addTempFactor.setEnabled(structSelected);
 286     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 287             Viewer.JMOL.name()));
 288     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 289     chimeraPath.addActionListener(new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         if (chimeraPath.getText().trim().length() > 0)
 295         {
 296           File f = new File(chimeraPath.getText());
 297           if (!f.canExecute())
 298           {
 299             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 300                     MessageManager.getString("label.invalid_path"),
 301                     MessageManager.getString("label.invalid_name"),
 302                     JOptionPane.ERROR_MESSAGE);
 303           }
 304         }
 305       }
 306     });
 307
 308     /*
 309      * Set Connections tab defaults
 310      */
 311     nameLinks = new Vector();
 312     urlLinks = new Vector();
 313     for (int i = 0; i < sequenceURLLinks.size(); i++)
 314     {
 315       String link = sequenceURLLinks.elementAt(i).toString();
 316       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 317       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 318     }
 319
 320     updateLinkData();
 321
 322     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 323     proxyServerTB.setEnabled(useProxy.isSelected());
 324     proxyPortTB.setEnabled(useProxy.isSelected());
 325     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 326     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 327
 328     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 329
 330     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 331     // note antisense here: default is true
 332     questionnaire
 333             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 334     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 335
 336     /*
 337      * Set Output tab defaults
 338      */
 339     epsRendering
 340             .addItem(MessageManager.getString("label.prompt_each_time"));
 341     epsRendering.addItem(MessageManager.getString("label.lineart"));
 342     epsRendering.addItem(MessageManager.getString("action.text"));
 343     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 344             "Prompt each time"));
 345     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 346     userIdWidth.setEnabled(autoIdWidth.isSelected());
 347     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 348     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 349     userIdWidth.setText(wi == null ? "" : wi.toString());
 350     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 351     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 352     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 353     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 354     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 355     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 356     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 357     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 358
 359     /*
 360      * Set Editing tab defaults
 361      */
 362     autoCalculateConsCheck.setSelected(Cache.getDefault(
 363             "AUTO_CALC_CONSENSUS", true));
 364     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 365     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 366
 367     annotations_actionPerformed(null); // update the display of the annotation
 368                                        // settings
 369   }
 370
 371   /**
 372    * Save user selections on the Preferences tabs to the Cache and write out to
 373    * file.
 374    *
 375    * @param e
 376    */
 377   public void ok_actionPerformed(ActionEvent e)
 378   {
 379     /*
 380      * Save Visual settings
 381      */
 382     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 383             Boolean.toString(seqLimit.isSelected()));
 384     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 385             Boolean.toString(rightAlign.isSelected()));
 386     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 387             Boolean.toString(fullScreen.isSelected()));
 388     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 389             Boolean.toString(openoverv.isSelected()));
 390     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 391             Boolean.toString(annotations.isSelected()));
 392     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 393             Boolean.toString(conservation.isSelected()));
 394     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 395             Boolean.toString(quality.isSelected()));
 396     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 397             Boolean.toString(identity.isSelected()));
 398
 399     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 400             .getSelectedItem().toString());
 401
 402     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 403             .getSelectedItem().toString());
 404     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 405             .getSelectedItem().toString());
 406     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 407             .getSelectedItem().toString());
 408
 409     Cache.applicationProperties.setProperty("ID_ITALICS",
 410             Boolean.toString(idItalics.isSelected()));
 411     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 412             Boolean.toString(showUnconserved.isSelected()));
 413     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 414             Boolean.toString(showGroupConsensus.isSelected()));
 415     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 416             Boolean.toString(showGroupConservation.isSelected()));
 417     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 418             Boolean.toString(showConsensHistogram.isSelected()));
 419     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 420             Boolean.toString(showConsensLogo.isSelected()));
 421     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 422             Boolean.toString(smoothFont.isSelected()));
 423     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 424             Boolean.toString(showNpTooltip.isSelected()));
 425     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 426             Boolean.toString(showDbRefTooltip.isSelected()));
 427
 428     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 429             Boolean.toString(wrap.isSelected()));
 430
 431     Cache.applicationProperties.setProperty("STARTUP_FILE",
 432             startupFileTextfield.getText());
 433     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 434             Boolean.toString(startupCheckbox.isSelected()));
 435
 436     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 437             .getSelectedItem().toString());
 438
 439     // convert description of sort order to enum name for save
 440     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 441             .forDescription(sortAnnBy.getSelectedItem().toString());
 442     if (annSortOrder != null)
 443     {
 444       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 445               annSortOrder.name());
 446     }
 447
 448     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 449     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 450             Boolean.valueOf(showAutocalcFirst).toString());
 451
 452     /*
 453      * Save Colours settings
 454      */
 455     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 456             .getSelectedItem().toString());
 457     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 458             minColour.getBackground());
 459     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 460             maxColour.getBackground());
 461
 462     /*
 463      * Save Structure settings
 464      */
 465     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 466             Boolean.toString(addTempFactor.isSelected()));
 467     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 468             Boolean.toString(addSecondaryStructure.isSelected()));
 469     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 470             Boolean.toString(useRnaView.isSelected()));
 471     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 472             Boolean.toString(structFromPdb.isSelected()));
 473     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 474             .getSelectedItem().toString());
 475     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 476
 477     /*
 478      * Save Output settings
 479      */
 480     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 481     {
 482       Cache.applicationProperties.remove("EPS_RENDERING");
 483     }
 484     else
 485     {
 486       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 487               .getSelectedItem().toString());
 488     }
 489
 490     /*
 491      * Save Connections settings
 492      */
 493     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 494
 495     jalview.util.BrowserLauncher.resetBrowser();
 496
 497     if (nameLinks.size() > 0)
 498     {
 499       StringBuffer links = new StringBuffer();
 500       sequenceURLLinks = new Vector();
 501       for (int i = 0; i < nameLinks.size(); i++)
 502       {
 503         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 504                 + urlLinks.elementAt(i));
 505         links.append(sequenceURLLinks.elementAt(i).toString());
 506         links.append("|");
 507       }
 508       // remove last "|"
 509       links.setLength(links.length() - 1);
 510       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 511               links.toString());
 512     }
 513     else
 514     {
 515       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 516     }
 517
 518     Cache.applicationProperties.setProperty("USE_PROXY",
 519             Boolean.toString(useProxy.isSelected()));
 520
 521     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 522
 523     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 524
 525     if (useProxy.isSelected())
 526     {
 527       System.setProperty("http.proxyHost", proxyServerTB.getText());
 528       System.setProperty("http.proxyPort", proxyPortTB.getText());
 529     }
 530     else
 531     {
 532       System.setProperty("http.proxyHost", "");
 533       System.setProperty("http.proxyPort", "");
 534     }
 535     Cache.setProperty("VERSION_CHECK",
 536             Boolean.toString(versioncheck.isSelected()));
 537     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 538     {
 539       // default is false - we only set this if the user has actively agreed
 540       Cache.setProperty("USAGESTATS",
 541               Boolean.toString(usagestats.isSelected()));
 542     }
 543     if (!questionnaire.isSelected())
 544     {
 545       Cache.setProperty("NOQUESTIONNAIRES", "true");
 546     }
 547     else
 548     {
 549       // special - made easy to edit a property file to disable questionnaires
 550       // by just adding the given line
 551       Cache.removeProperty("NOQUESTIONNAIRES");
 552     }
 553
 554     /*
 555      * Save Output settings
 556      */
 557     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 558             Boolean.toString(blcjv.isSelected()));
 559     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 560             Boolean.toString(clustaljv.isSelected()));
 561     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 562             Boolean.toString(fastajv.isSelected()));
 563     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 564             Boolean.toString(msfjv.isSelected()));
 565     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 566             Boolean.toString(pfamjv.isSelected()));
 567     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 568             Boolean.toString(pileupjv.isSelected()));
 569     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 570             Boolean.toString(pirjv.isSelected()));
 571     Cache.applicationProperties.setProperty("PIR_MODELLER",
 572             Boolean.toString(modellerOutput.isSelected()));
 573     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 574
 575     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 576             Boolean.toString(autoIdWidth.isSelected()));
 577     userIdWidth_actionPerformed();
 578     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 579             userIdWidth.getText());
 580
 581     /*
 582      * Save Editing settings
 583      */
 584     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 585             Boolean.toString(autoCalculateConsCheck.isSelected()));
 586     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 587             Boolean.toString(sortByTree.isSelected()));
 588     Cache.applicationProperties.setProperty("PAD_GAPS",
 589             Boolean.toString(padGaps.isSelected()));
 590
 591     dasSource.saveProperties(Cache.applicationProperties);
 592     wsPrefs.updateAndRefreshWsMenuConfig(false);
 593     Cache.saveProperties();
 594     Desktop.instance.doConfigureStructurePrefs();
 595     try
 596     {
 597       frame.setClosed(true);
 598     } catch (Exception ex)
 599     {
 600     }
 601   }
 602
 603   /**
 604    * DOCUMENT ME!
 605    */
 606   public void startupFileTextfield_mouseClicked()
 607   {
 608     JalviewFileChooser chooser = new JalviewFileChooser(
 609             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 610             new String[]
 611             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 612             new String[]
 613             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 614             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 615     chooser.setFileView(new JalviewFileView());
 616     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 617
 618     int value = chooser.showOpenDialog(this);
 619
 620     if (value == JalviewFileChooser.APPROVE_OPTION)
 621     {
 622       jalview.bin.Cache.applicationProperties.setProperty(
 623               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 624       startupFileTextfield.setText(chooser.getSelectedFile()
 625               .getAbsolutePath());
 626     }
 627   }
 628
 629   /**
 630    * DOCUMENT ME!
 631    *
 632    * @param e
 633    *          DOCUMENT ME!
 634    */
 635   public void cancel_actionPerformed(ActionEvent e)
 636   {
 637     try
 638     {
 639       wsPrefs.updateWsMenuConfig(true);
 640       wsPrefs.refreshWs_actionPerformed(e);
 641       frame.setClosed(true);
 642     } catch (Exception ex)
 643     {
 644     }
 645   }
 646
 647   /**
 648    * DOCUMENT ME!
 649    *
 650    * @param e
 651    *          DOCUMENT ME!
 652    */
 653   public void annotations_actionPerformed(ActionEvent e)
 654   {
 655     conservation.setEnabled(annotations.isSelected());
 656     quality.setEnabled(annotations.isSelected());
 657     identity.setEnabled(annotations.isSelected());
 658     showGroupConsensus.setEnabled(annotations.isSelected());
 659     showGroupConservation.setEnabled(annotations.isSelected());
 660     showConsensHistogram.setEnabled(annotations.isSelected()
 661             && (identity.isSelected() || showGroupConsensus.isSelected()));
 662     showConsensLogo.setEnabled(annotations.isSelected()
 663             && (identity.isSelected() || showGroupConsensus.isSelected()));
 664   }
 665
 666   public void newLink_actionPerformed(ActionEvent e)
 667   {
 668
 669     GSequenceLink link = new GSequenceLink();
 670     boolean valid = false;
 671     while (!valid)
 672     {
 673       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 674               MessageManager.getString("label.new_sequence_url_link"),
 675               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 676       {
 677         if (link.checkValid())
 678         {
 679           nameLinks.addElement(link.getName());
 680           urlLinks.addElement(link.getURL());
 681           updateLinkData();
 682           valid = true;
 683         }
 684       }
 685       else
 686       {
 687         break;
 688       }
 689     }
 690   }
 691
 692   public void editLink_actionPerformed(ActionEvent e)
 693   {
 694     GSequenceLink link = new GSequenceLink();
 695
 696     int index = linkNameList.getSelectedIndex();
 697     if (index == -1)
 698     {
 699       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 700               MessageManager.getString("label.no_link_selected"),
 701               MessageManager.getString("label.no_link_selected"),
 702               JOptionPane.WARNING_MESSAGE);
 703       return;
 704     }
 705
 706     link.setName(nameLinks.elementAt(index).toString());
 707     link.setURL(urlLinks.elementAt(index).toString());
 708
 709     boolean valid = false;
 710     while (!valid)
 711     {
 712
 713       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 714               MessageManager.getString("label.new_sequence_url_link"),
 715               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 716       {
 717         if (link.checkValid())
 718         {
 719           nameLinks.setElementAt(link.getName(), index);
 720           urlLinks.setElementAt(link.getURL(), index);
 721           updateLinkData();
 722           valid = true;
 723         }
 724       }
 725
 726       else
 727       {
 728         break;
 729       }
 730     }
 731   }
 732
 733   public void deleteLink_actionPerformed(ActionEvent e)
 734   {
 735     int index = linkNameList.getSelectedIndex();
 736     if (index == -1)
 737     {
 738       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 739               MessageManager.getString("label.no_link_selected"),
 740               MessageManager.getString("label.no_link_selected"),
 741               JOptionPane.WARNING_MESSAGE);
 742       return;
 743     }
 744     nameLinks.removeElementAt(index);
 745     urlLinks.removeElementAt(index);
 746     updateLinkData();
 747   }
 748
 749   void updateLinkData()
 750   {
 751     linkNameList.setListData(nameLinks);
 752     linkURLList.setListData(urlLinks);
 753   }
 754
 755   public void defaultBrowser_mouseClicked(MouseEvent e)
 756   {
 757     JFileChooser chooser = new JFileChooser(".");
 758     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 759
 760     int value = chooser.showOpenDialog(this);
 761
 762     if (value == JFileChooser.APPROVE_OPTION)
 763     {
 764       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 765     }
 766
 767   }
 768
 769   /*
 770    * (non-Javadoc)
 771    *
 772    * @see
 773    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 774    * .ActionEvent)
 775    */
 776   protected void showunconserved_actionPerformed(ActionEvent e)
 777   {
 778     // TODO Auto-generated method stub
 779     super.showunconserved_actionPerformed(e);
 780   }
 781
 782   public static Collection getGroupURLLinks()
 783   {
 784     return groupURLLinks;
 785   }
 786
 787   @Override
 788   public void minColour_actionPerformed(JPanel panel)
 789   {
 790     Color col = JColorChooser.showDialog(this,
 791             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 792     if (col != null)
 793     {
 794       panel.setBackground(col);
 795     }
 796     panel.repaint();
 797   }
 798
 799   @Override
 800   public void maxColour_actionPerformed(JPanel panel)
 801   {
 802     Color col = JColorChooser.showDialog(this,
 803             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 804     if (col != null)
 805     {
 806       panel.setBackground(col);
 807     }
 808     panel.repaint();
 809   }
 810
 811   @Override
 812   protected void userIdWidth_actionPerformed()
 813   {
 814     try
 815     {
 816       String val = userIdWidth.getText().trim();
 817       if (val.length() > 0)
 818       {
 819         Integer iw = Integer.parseInt(val);
 820         if (iw.intValue() < 12)
 821         {
 822           throw new NumberFormatException();
 823         }
 824         userIdWidth.setText(iw.toString());
 825       }
 826     } catch (NumberFormatException x)
 827     {
 828       JOptionPane
 829               .showInternalMessageDialog(
 830                       Desktop.desktop,
 831                       MessageManager.getString("warn.user_defined_width_requirements"),
 832                       MessageManager.getString("label.invalid_id_column_width"),
 833                       JOptionPane.WARNING_MESSAGE);
 834       userIdWidth.setText("");
 835     }
 836   }
 837
 838   @Override
 839   protected void autoIdWidth_actionPerformed()
 840   {
 841     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 842     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 843   }
 844
 845 }