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.MouseEvent;
  39 import java.util.Collection;
  40 import java.util.StringTokenizer;
  41 import java.util.Vector;
  42
  43 import javax.swing.JColorChooser;
  44 import javax.swing.JFileChooser;
  45 import javax.swing.JInternalFrame;
  46 import javax.swing.JOptionPane;
  47 import javax.swing.JPanel;
  48
  49 /**
  50  * DOCUMENT ME!
  51  *
  52  * @author $author$
  53  * @version $Revision$
  54  */
  55 public class Preferences extends GPreferences
  56 {
  57
  58   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  59
  60   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  61
  62   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  63
  64   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  65
  66   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  67
  68   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  69
  70   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  71
  72   private static final int MIN_FONT_SIZE = 1;
  73
  74   private static final int MAX_FONT_SIZE = 30;
  75
  76   /**
  77    * Holds name and link separated with | character. Sequence ID must be
  78    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  79    */
  80   public static Vector sequenceURLLinks;
  81
  82   /**
  83    * Holds name and link separated with | character. Sequence IDS and Sequences
  84    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  85    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  86    * for first and second token specified after a pipe character at end |,|.
  87    * (TODO: proper escape for using | to separate ids or sequences
  88    */
  89
  90   public static Vector groupURLLinks;
  91   static
  92   {
  93     String string = Cache
  94             .getDefault(
  95                     "SEQUENCE_LINKS",
  96                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
  97     sequenceURLLinks = new Vector();
  98
  99     try
 100     {
 101       StringTokenizer st = new StringTokenizer(string, "|");
 102       while (st.hasMoreElements())
 103       {
 104         String name = st.nextToken();
 105         String url = st.nextToken();
 106         // check for '|' within a regex
 107         int rxstart = url.indexOf("$SEQUENCE_ID$");
 108         while (rxstart == -1 && url.indexOf("/=$") == -1)
 109         {
 110           url = url + "|" + st.nextToken();
 111         }
 112         sequenceURLLinks.addElement(name + "|" + url);
 113       }
 114     } catch (Exception ex)
 115     {
 116       System.out.println(ex + "\nError parsing sequence links");
 117     }
 118     {
 119       // upgrade old SRS link
 120       int srsPos = sequenceURLLinks
 121               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 122       if (srsPos > -1)
 123       {
 124         sequenceURLLinks
 125                 .setElementAt(
 126                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 127                         srsPos);
 128       }
 129     }
 130
 131     /**
 132      * TODO: reformulate groupURL encoding so two or more can be stored in the
 133      * .properties file as '|' separated strings
 134      */
 135
 136     groupURLLinks = new Vector();
 137   }
 138
 139   Vector nameLinks, urlLinks;
 140
 141   JInternalFrame frame;
 142
 143   DasSourceBrowser dasSource;
 144
 145   private WsPreferences wsPrefs;
 146
 147   /**
 148    * Creates a new Preferences object.
 149    */
 150   public Preferences()
 151   {
 152     super();
 153     frame = new JInternalFrame();
 154     frame.setContentPane(this);
 155     dasSource = new DasSourceBrowser();
 156     dasTab.add(dasSource, BorderLayout.CENTER);
 157     wsPrefs = new WsPreferences();
 158     wsTab.add(wsPrefs, BorderLayout.CENTER);
 159     int width = 500, height = 420;
 160     if (new jalview.util.Platform().isAMac())
 161     {
 162       width = 570;
 163       height = 460;
 164     }
 165
 166     Desktop.addInternalFrame(frame,
 167             MessageManager.getString("label.preferences"), width, height);
 168     frame.setMinimumSize(new Dimension(width, height));
 169
 170     /*
 171      * Set Visual tab defaults
 172      */
 173     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 174     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 175     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 176     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 177
 178     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 179     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 180     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 181     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 182     showUnconserved
 183             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 184     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 185             false));
 186     showGroupConservation.setSelected(Cache.getDefault(
 187             "SHOW_GROUP_CONSERVATION", false));
 188     showConsensHistogram.setSelected(Cache.getDefault(
 189             "SHOW_CONSENSUS_HISTOGRAM", true));
 190     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 191             false));
 192     showNpTooltip.setSelected(Cache
 193             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 194     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 195             true));
 196
 197     String[] fonts = java.awt.GraphicsEnvironment
 198             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 199     for (int i = 0; i < fonts.length; i++)
 200     {
 201       fontNameCB.addItem(fonts[i]);
 202     }
 203
 204     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 205     {
 206       fontSizeCB.addItem(i + "");
 207     }
 208
 209     fontStyleCB.addItem("plain");
 210     fontStyleCB.addItem("bold");
 211     fontStyleCB.addItem("italic");
 212
 213     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 214     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 215     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 216             + ""));
 217
 218     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 219
 220     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 221
 222     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 223
 224     gapSymbolCB.addItem("-");
 225     gapSymbolCB.addItem(".");
 226
 227     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 228
 229     sortby.addItem("No sort");
 230     sortby.addItem("Id");
 231     sortby.addItem("Pairwise Identity");
 232     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 233
 234     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 235     sortAnnBy
 236             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 237     sortAnnBy
 238             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 239     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 240             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 241                     SequenceAnnotationOrder.NONE.name()));
 242     sortAnnBy.setSelectedItem(savedSort.toString());
 243
 244     sortAutocalc.addItem("Autocalculated first");
 245     sortAutocalc.addItem("Autocalculated last");
 246     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
 247             true);
 248     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 249             : sortAutocalc.getItemAt(1));
 250     startupCheckbox
 251             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 252     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 253             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 254                     + "/examples/exampleFile_2_3.jar"));
 255
 256     /*
 257      * Set Colours tab defaults
 258      */
 259     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 260     {
 261       colour.addItem(ColourSchemeProperty.getColourName(i));
 262     }
 263     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 264     colour.setSelectedItem(string);
 265     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 266             Color.orange));
 267     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 268             Color.red));
 269
 270     /*
 271      * Set Structure tab defaults.
 272      */
 273     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 274     structFromPdb.setSelected(structSelected);
 275     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 276     useRnaView.setEnabled(structSelected);
 277     addSecondaryStructure
 278             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 279     addSecondaryStructure.setEnabled(structSelected);
 280     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 281     addTempFactor.setEnabled(structSelected);
 282     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 283             Viewer.JMOL.name()));
 284
 285     /*
 286      * Set Connections tab defaults
 287      */
 288     nameLinks = new Vector();
 289     urlLinks = new Vector();
 290     for (int i = 0; i < sequenceURLLinks.size(); i++)
 291     {
 292       String link = sequenceURLLinks.elementAt(i).toString();
 293       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 294       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 295     }
 296
 297     updateLinkData();
 298
 299     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 300     proxyServerTB.setEnabled(useProxy.isSelected());
 301     proxyPortTB.setEnabled(useProxy.isSelected());
 302     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 303     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 304
 305     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 306
 307     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 308     // note antisense here: default is true
 309     questionnaire
 310             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 311     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 312
 313     /*
 314      * Set Output tab defaults
 315      */
 316     epsRendering
 317             .addItem(MessageManager.getString("label.prompt_each_time"));
 318     epsRendering.addItem(MessageManager.getString("label.lineart"));
 319     epsRendering.addItem(MessageManager.getString("action.text"));
 320     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 321             "Prompt each time"));
 322     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 323     userIdWidth.setEnabled(autoIdWidth.isSelected());
 324     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 325     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 326     userIdWidth.setText(wi == null ? "" : wi.toString());
 327     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 328     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 329     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 330     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 331     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 332     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 333     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 334     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 335
 336     /*
 337      * Set Editing tab defaults
 338      */
 339     autoCalculateConsCheck.setSelected(Cache.getDefault(
 340             "AUTO_CALC_CONSENSUS", true));
 341     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 342     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 343
 344     annotations_actionPerformed(null); // update the display of the annotation
 345                                        // settings
 346   }
 347
 348   /**
 349    * Save user selections on the Preferences tabs to the Cache and write out to
 350    * file.
 351    *
 352    * @param e
 353    */
 354   public void ok_actionPerformed(ActionEvent e)
 355   {
 356     /*
 357      * Save Visual settings
 358      */
 359     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 360             Boolean.toString(seqLimit.isSelected()));
 361     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 362             Boolean.toString(rightAlign.isSelected()));
 363     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 364             Boolean.toString(fullScreen.isSelected()));
 365     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 366             Boolean.toString(openoverv.isSelected()));
 367     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 368             Boolean.toString(annotations.isSelected()));
 369     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 370             Boolean.toString(conservation.isSelected()));
 371     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 372             Boolean.toString(quality.isSelected()));
 373     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 374             Boolean.toString(identity.isSelected()));
 375
 376     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 377             .getSelectedItem().toString());
 378
 379     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 380             .getSelectedItem().toString());
 381     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 382             .getSelectedItem().toString());
 383     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 384             .getSelectedItem().toString());
 385
 386     Cache.applicationProperties.setProperty("ID_ITALICS",
 387             Boolean.toString(idItalics.isSelected()));
 388     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 389             Boolean.toString(showUnconserved.isSelected()));
 390     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 391             Boolean.toString(showGroupConsensus.isSelected()));
 392     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 393             Boolean.toString(showGroupConservation.isSelected()));
 394     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 395             Boolean.toString(showConsensHistogram.isSelected()));
 396     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 397             Boolean.toString(showConsensLogo.isSelected()));
 398     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 399             Boolean.toString(smoothFont.isSelected()));
 400     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 401             Boolean.toString(showNpTooltip.isSelected()));
 402     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 403             Boolean.toString(showDbRefTooltip.isSelected()));
 404
 405     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 406             Boolean.toString(wrap.isSelected()));
 407
 408     Cache.applicationProperties.setProperty("STARTUP_FILE",
 409             startupFileTextfield.getText());
 410     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 411             Boolean.toString(startupCheckbox.isSelected()));
 412
 413     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 414             .getSelectedItem().toString());
 415
 416     // convert description of sort order to enum name for save
 417     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 418             .forDescription(sortAnnBy.getSelectedItem().toString());
 419     if (annSortOrder != null)
 420     {
 421       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 422               annSortOrder.name());
 423     }
 424
 425     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 426     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 427             Boolean.valueOf(showAutocalcFirst).toString());
 428
 429     /*
 430      * Save Colours settings
 431      */
 432     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 433             .getSelectedItem().toString());
 434     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 435             minColour.getBackground());
 436     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 437             maxColour.getBackground());
 438
 439     /*
 440      * Save Structure settings
 441      */
 442     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 443             Boolean.toString(addTempFactor.isSelected()));
 444     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 445             Boolean.toString(addSecondaryStructure.isSelected()));
 446     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 447             Boolean.toString(useRnaView.isSelected()));
 448     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 449             Boolean.toString(structFromPdb.isSelected()));
 450     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 451             .getSelectedItem().toString());
 452
 453     /*
 454      * Save Output settings
 455      */
 456     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 457     {
 458       Cache.applicationProperties.remove("EPS_RENDERING");
 459     }
 460     else
 461     {
 462       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 463               .getSelectedItem().toString());
 464     }
 465
 466     /*
 467      * Save Connections settings
 468      */
 469     if (defaultBrowser.getText().trim().length() < 1)
 470     {
 471       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 472     }
 473     else
 474     {
 475       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 476               defaultBrowser.getText());
 477     }
 478
 479     jalview.util.BrowserLauncher.resetBrowser();
 480
 481     if (nameLinks.size() > 0)
 482     {
 483       StringBuffer links = new StringBuffer();
 484       sequenceURLLinks = new Vector();
 485       for (int i = 0; i < nameLinks.size(); i++)
 486       {
 487         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 488                 + urlLinks.elementAt(i));
 489         links.append(sequenceURLLinks.elementAt(i).toString());
 490         links.append("|");
 491       }
 492       // remove last "|"
 493       links.setLength(links.length() - 1);
 494       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 495               links.toString());
 496     }
 497     else
 498     {
 499       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 500     }
 501
 502     Cache.applicationProperties.setProperty("USE_PROXY",
 503             Boolean.toString(useProxy.isSelected()));
 504
 505     if (proxyServerTB.getText().trim().length() < 1)
 506     {
 507       Cache.applicationProperties.remove("PROXY_SERVER");
 508     }
 509     else
 510     {
 511       Cache.applicationProperties.setProperty("PROXY_SERVER",
 512               proxyServerTB.getText());
 513     }
 514
 515     if (proxyPortTB.getText().trim().length() < 1)
 516     {
 517       Cache.applicationProperties.remove("PROXY_PORT");
 518     }
 519     else
 520     {
 521       Cache.applicationProperties.setProperty("PROXY_PORT",
 522               proxyPortTB.getText());
 523     }
 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
 594     Cache.saveProperties();
 595
 596     try
 597     {
 598       frame.setClosed(true);
 599     } catch (Exception ex)
 600     {
 601     }
 602   }
 603
 604   /**
 605    * DOCUMENT ME!
 606    */
 607   public void startupFileTextfield_mouseClicked()
 608   {
 609     JalviewFileChooser chooser = new JalviewFileChooser(
 610             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 611             new String[]
 612             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 613             new String[]
 614             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 615             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 616     chooser.setFileView(new JalviewFileView());
 617     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 618
 619     int value = chooser.showOpenDialog(this);
 620
 621     if (value == JalviewFileChooser.APPROVE_OPTION)
 622     {
 623       jalview.bin.Cache.applicationProperties.setProperty(
 624               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 625       startupFileTextfield.setText(chooser.getSelectedFile()
 626               .getAbsolutePath());
 627     }
 628   }
 629
 630   /**
 631    * DOCUMENT ME!
 632    *
 633    * @param e
 634    *          DOCUMENT ME!
 635    */
 636   public void cancel_actionPerformed(ActionEvent e)
 637   {
 638     try
 639     {
 640       wsPrefs.updateWsMenuConfig(true);
 641       wsPrefs.refreshWs_actionPerformed(e);
 642       frame.setClosed(true);
 643     } catch (Exception ex)
 644     {
 645     }
 646   }
 647
 648   /**
 649    * DOCUMENT ME!
 650    *
 651    * @param e
 652    *          DOCUMENT ME!
 653    */
 654   public void annotations_actionPerformed(ActionEvent e)
 655   {
 656     conservation.setEnabled(annotations.isSelected());
 657     quality.setEnabled(annotations.isSelected());
 658     identity.setEnabled(annotations.isSelected());
 659     showGroupConsensus.setEnabled(annotations.isSelected());
 660     showGroupConservation.setEnabled(annotations.isSelected());
 661     showConsensHistogram.setEnabled(annotations.isSelected()
 662             && (identity.isSelected() || showGroupConsensus.isSelected()));
 663     showConsensLogo.setEnabled(annotations.isSelected()
 664             && (identity.isSelected() || showGroupConsensus.isSelected()));
 665   }
 666
 667   public void newLink_actionPerformed(ActionEvent e)
 668   {
 669
 670     GSequenceLink link = new GSequenceLink();
 671     boolean valid = false;
 672     while (!valid)
 673     {
 674       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 675               MessageManager.getString("label.new_sequence_url_link"),
 676               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 677       {
 678         if (link.checkValid())
 679         {
 680           nameLinks.addElement(link.getName());
 681           urlLinks.addElement(link.getURL());
 682           updateLinkData();
 683           valid = true;
 684         }
 685       }
 686       else
 687       {
 688         break;
 689       }
 690     }
 691   }
 692
 693   public void editLink_actionPerformed(ActionEvent e)
 694   {
 695     GSequenceLink link = new GSequenceLink();
 696
 697     int index = linkNameList.getSelectedIndex();
 698     if (index == -1)
 699     {
 700       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 701               MessageManager.getString("label.no_link_selected"),
 702               MessageManager.getString("label.no_link_selected"),
 703               JOptionPane.WARNING_MESSAGE);
 704       return;
 705     }
 706
 707     link.setName(nameLinks.elementAt(index).toString());
 708     link.setURL(urlLinks.elementAt(index).toString());
 709
 710     boolean valid = false;
 711     while (!valid)
 712     {
 713
 714       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 715               MessageManager.getString("label.new_sequence_url_link"),
 716               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 717       {
 718         if (link.checkValid())
 719         {
 720           nameLinks.setElementAt(link.getName(), index);
 721           urlLinks.setElementAt(link.getURL(), index);
 722           updateLinkData();
 723           valid = true;
 724         }
 725       }
 726
 727       else
 728       {
 729         break;
 730       }
 731     }
 732   }
 733
 734   public void deleteLink_actionPerformed(ActionEvent e)
 735   {
 736     int index = linkNameList.getSelectedIndex();
 737     if (index == -1)
 738     {
 739       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 740               MessageManager.getString("label.no_link_selected"),
 741               MessageManager.getString("label.no_link_selected"),
 742               JOptionPane.WARNING_MESSAGE);
 743       return;
 744     }
 745     nameLinks.removeElementAt(index);
 746     urlLinks.removeElementAt(index);
 747     updateLinkData();
 748   }
 749
 750   void updateLinkData()
 751   {
 752     linkNameList.setListData(nameLinks);
 753     linkURLList.setListData(urlLinks);
 754   }
 755
 756   public void defaultBrowser_mouseClicked(MouseEvent e)
 757   {
 758     JFileChooser chooser = new JFileChooser(".");
 759     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 760
 761     int value = chooser.showOpenDialog(this);
 762
 763     if (value == JFileChooser.APPROVE_OPTION)
 764     {
 765       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 766     }
 767
 768   }
 769
 770   /*
 771    * (non-Javadoc)
 772    *
 773    * @see
 774    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 775    * .ActionEvent)
 776    */
 777   protected void showunconserved_actionPerformed(ActionEvent e)
 778   {
 779     // TODO Auto-generated method stub
 780     super.showunconserved_actionPerformed(e);
 781   }
 782
 783   public static Collection getGroupURLLinks()
 784   {
 785     return groupURLLinks;
 786   }
 787
 788   @Override
 789   public void minColour_actionPerformed(JPanel panel)
 790   {
 791     Color col = JColorChooser.showDialog(this,
 792             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 793     if (col != null)
 794     {
 795       panel.setBackground(col);
 796     }
 797     panel.repaint();
 798   }
 799
 800   @Override
 801   public void maxColour_actionPerformed(JPanel panel)
 802   {
 803     Color col = JColorChooser.showDialog(this,
 804             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 805     if (col != null)
 806     {
 807       panel.setBackground(col);
 808     }
 809     panel.repaint();
 810   }
 811
 812   @Override
 813   protected void userIdWidth_actionPerformed()
 814   {
 815     try
 816     {
 817       String val = userIdWidth.getText().trim();
 818       if (val.length() > 0)
 819       {
 820         Integer iw = Integer.parseInt(val);
 821         if (iw.intValue() < 12)
 822         {
 823           throw new NumberFormatException();
 824         }
 825         userIdWidth.setText(iw.toString());
 826       }
 827     } catch (NumberFormatException x)
 828     {
 829       JOptionPane
 830               .showInternalMessageDialog(
 831                       Desktop.desktop,
 832                       MessageManager.getString("warn.user_defined_width_requirements"),
 833                       MessageManager.getString("label.invalid_id_column_width"),
 834                       JOptionPane.WARNING_MESSAGE);
 835       userIdWidth.setText("");
 836     }
 837   }
 838
 839   @Override
 840   protected void autoIdWidth_actionPerformed()
 841   {
 842     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 843     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 844   }
 845
 846 }