src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27
  28 import jalview.bin.*;
  29 import jalview.io.*;
  30 import jalview.jbgui.*;
  31 import jalview.schemes.*;
  32 import jalview.ws.EnfinEnvision2OneWay;
  33
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class Preferences extends GPreferences
  41 {
  42
  43   /**
  44    * Holds name and link separated with | character. Sequence ID must be
  45    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  46    */
  47   public static Vector sequenceURLLinks;
  48   /**
  49    * Holds name and link separated with | character. Sequence IDS and Sequences must be
  50    * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$
  51    * and separation character for first and second token specified after a pipe character at end |,|.
  52    * (TODO: proper escape for using | to separate ids or sequences
  53    */
  54
  55   public static Vector groupURLLinks;
  56   static
  57   {
  58     String string = Cache
  59             .getDefault(
  60                     "SEQUENCE_LINKS",
  61                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  62     sequenceURLLinks = new Vector();
  63
  64     try
  65     {
  66       StringTokenizer st = new StringTokenizer(string, "|");
  67       while (st.hasMoreElements())
  68       {
  69         String name = st.nextToken();
  70         String url = st.nextToken();
  71         // check for '|' within a regex
  72         int rxstart = url.indexOf("$SEQUENCE_ID$");
  73         while (rxstart == -1 && url.indexOf("/=$") == -1)
  74         {
  75           url = url + "|" + st.nextToken();
  76         }
  77         sequenceURLLinks.addElement(name + "|" + url);
  78       }
  79     } catch (Exception ex)
  80     {
  81       System.out.println(ex + "\nError parsing sequence links");
  82     }
  83     /**
  84      * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings
  85      */
  86
  87     groupURLLinks = new Vector();
  88     //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
  89     //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
  90
  91   }
  92
  93   Vector nameLinks, urlLinks;
  94
  95   JInternalFrame frame;
  96
  97   DasSourceBrowser dasSource;
  98
  99   /**
 100    * Creates a new Preferences object.
 101    */
 102   public Preferences()
 103   {
 104
 105     frame = new JInternalFrame();
 106     frame.setContentPane(this);
 107     dasSource = new DasSourceBrowser();
 108     dasPanel.add(dasSource, BorderLayout.CENTER);
 109
 110     int width = 500, height = 420;
 111     if (new jalview.util.Platform().isAMac())
 112     {
 113       width = 570;
 114       height = 460;
 115     }
 116
 117     Desktop.addInternalFrame(frame, "Preferences", width, height);
 118     frame.setMinimumSize(new Dimension(width, height));
 119
 120     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 121     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 122     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 123     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 124
 125     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 126     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 127     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 128     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 129     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 130     showNpTooltip.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 131     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 132
 133     for (int i = 0; i < 13; i++)
 134     {
 135       colour.addItem(ColourSchemeProperty.getColourName(i));
 136     }
 137
 138     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 139
 140     colour.setSelectedItem(string);
 141
 142     String[] fonts = java.awt.GraphicsEnvironment
 143             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 144
 145     for (int i = 0; i < fonts.length; i++)
 146     {
 147       fontNameCB.addItem(fonts[i]);
 148     }
 149
 150     for (int i = 1; i < 31; i++)
 151     {
 152       fontSizeCB.addItem(i + "");
 153     }
 154
 155     fontStyleCB.addItem("plain");
 156     fontStyleCB.addItem("bold");
 157     fontStyleCB.addItem("italic");
 158
 159     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 160     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 161     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 162             + ""));
 163
 164     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 165
 166     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 167
 168     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 169
 170     gapSymbolCB.addItem("-");
 171     gapSymbolCB.addItem(".");
 172
 173     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 174
 175     startupCheckbox
 176             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 177     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 178             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 179
 180     sortby.addItem("No sort");
 181     sortby.addItem("Id");
 182     sortby.addItem("Pairwise Identity");
 183     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 184
 185     epsRendering.addItem("Prompt each time");
 186     epsRendering.addItem("Lineart");
 187     epsRendering.addItem("Text");
 188     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 189             "Prompt each time"));
 190
 191     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 192     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 193     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 194     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 195     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 196     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 197     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 198
 199     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 200
 201     autoCalculateConsCheck.setSelected(Cache.getDefault(
 202             "AUTO_CALC_CONSENSUS", true));
 203     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
 204     showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 205     showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
 206     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",false));
 207
 208     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 209
 210     /***************************************************************************
 211      * Set up Connections
 212      */
 213     nameLinks = new Vector();
 214     urlLinks = new Vector();
 215     for (int i = 0; i < sequenceURLLinks.size(); i++)
 216     {
 217       String link = sequenceURLLinks.elementAt(i).toString();
 218       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 219       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 220     }
 221
 222     updateLinkData();
 223
 224     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 225     proxyServerTB.setEnabled(useProxy.isSelected());
 226     proxyPortTB.setEnabled(useProxy.isSelected());
 227     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 228     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 229
 230     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 231
 232     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 233     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
 234     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
 235     annotations_actionPerformed(null); // update the display of the annotation settings
 236     try
 237     {
 238       jbInit();
 239     } catch (Exception ex)
 240     {
 241       ex.printStackTrace();
 242     }
 243
 244   }
 245
 246   /**
 247    * DOCUMENT ME!
 248    *
 249    * @param e
 250    *                DOCUMENT ME!
 251    */
 252   public void ok_actionPerformed(ActionEvent e)
 253   {
 254
 255     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 256             .toString(seqLimit.isSelected()));
 257     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 258             .toString(rightAlign.isSelected()));
 259     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 260             .toString(fullScreen.isSelected()));
 261     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 262             .toString(openoverv.isSelected()));
 263     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 264             .toString(annotations.isSelected()));
 265     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 266             .toString(conservation.isSelected()));
 267     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 268             .toString(quality.isSelected()));
 269     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 270             .toString(identity.isSelected()));
 271
 272     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 273             .getSelectedItem().toString());
 274     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 275             .getSelectedItem().toString());
 276
 277     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 278             .getSelectedItem().toString());
 279     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 280             .getSelectedItem().toString());
 281     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 282             .getSelectedItem().toString());
 283
 284     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 285             .toString(idItalics.isSelected()));
 286     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
 288     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
 289     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
 290     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",Boolean.toString(showConsensLogo.isSelected()));
 291     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 292             .toString(smoothFont.isSelected()));
 293     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected()));
 294     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean.toString(showDbRefTooltip.isSelected()));
 295
 296     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 297             .toString(wrap.isSelected()));
 298
 299     Cache.applicationProperties.setProperty("STARTUP_FILE",
 300             startupFileTextfield.getText());
 301     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 302             .toString(startupCheckbox.isSelected()));
 303
 304     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 305             .getSelectedItem().toString());
 306
 307     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 308     {
 309       Cache.applicationProperties.remove("EPS_RENDERING");
 310     }
 311     else
 312     {
 313       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 314               .getSelectedItem().toString());
 315     }
 316
 317     if (defaultBrowser.getText().trim().length() < 1)
 318     {
 319       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 320     }
 321     else
 322     {
 323       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 324               defaultBrowser.getText());
 325     }
 326
 327     jalview.util.BrowserLauncher.resetBrowser();
 328
 329     if (nameLinks.size() > 0)
 330     {
 331       StringBuffer links = new StringBuffer();
 332       sequenceURLLinks = new Vector();
 333       for (int i = 0; i < nameLinks.size(); i++)
 334       {
 335         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 336                 + urlLinks.elementAt(i));
 337         links.append(sequenceURLLinks.elementAt(i).toString());
 338         links.append("|");
 339       }
 340       // remove last "|"
 341       links.setLength(links.length() - 1);
 342       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 343               .toString());
 344     }
 345     else
 346     {
 347       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 348     }
 349
 350     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 351             .toString(useProxy.isSelected()));
 352
 353     if (proxyServerTB.getText().trim().length() < 1)
 354     {
 355       Cache.applicationProperties.remove("PROXY_SERVER");
 356     }
 357     else
 358     {
 359       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 360               .getText());
 361     }
 362
 363     if (proxyPortTB.getText().trim().length() < 1)
 364     {
 365       Cache.applicationProperties.remove("PROXY_PORT");
 366     }
 367     else
 368     {
 369       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 370               .getText());
 371     }
 372
 373     if (useProxy.isSelected())
 374     {
 375       System.setProperty("http.proxyHost", proxyServerTB.getText());
 376       System.setProperty("http.proxyPort", proxyPortTB.getText());
 377     }
 378     else
 379     {
 380       System.setProperty("http.proxyHost", "");
 381       System.setProperty("http.proxyPort", "");
 382     }
 383     Cache.setProperty("VERSION_CHECK", Boolean
 384             .toString(versioncheck.isSelected()));
 385     if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) {
 386       // default is false - we only set this if the user has actively agreed
 387       Cache.setProperty("USAGESTATS",Boolean
 388             .toString(usagestats.isSelected()));
 389     }
 390     if (!questionnaire.isSelected())
 391     {
 392       Cache.setProperty("NOQUESTIONNAIRES", "true");
 393     } else {
 394       // special - made easy to edit a property file to disable questionnaires by just adding the given line
 395       Cache.removeProperty("NOQUESTIONNAIRES");
 396     }
 397     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 398             .toString(blcjv.isSelected()));
 399     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 400             .toString(clustaljv.isSelected()));
 401     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 402             .toString(fastajv.isSelected()));
 403     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 404             .toString(msfjv.isSelected()));
 405     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 406             .toString(pfamjv.isSelected()));
 407     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 408             .toString(pileupjv.isSelected()));
 409     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 410             .toString(pirjv.isSelected()));
 411     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 412             .toString(modellerOutput.isSelected()));
 413     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 414
 415     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 416             .toString(autoCalculateConsCheck.isSelected()));
 417     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 418             .toString(padGaps.isSelected()));
 419
 420     dasSource.saveProperties(Cache.applicationProperties);
 421
 422     Cache.saveProperties();
 423     try
 424     {
 425       frame.setClosed(true);
 426     } catch (Exception ex)
 427     {
 428     }
 429   }
 430
 431   /**
 432    * DOCUMENT ME!
 433    */
 434   public void startupFileTextfield_mouseClicked()
 435   {
 436     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 437             .getProperty("LAST_DIRECTORY"), new String[]
 438     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 439             new String[]
 440             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 441             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 442     chooser.setFileView(new JalviewFileView());
 443     chooser.setDialogTitle("Select startup file");
 444
 445     int value = chooser.showOpenDialog(this);
 446
 447     if (value == JalviewFileChooser.APPROVE_OPTION)
 448     {
 449       jalview.bin.Cache.applicationProperties.setProperty(
 450               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 451       startupFileTextfield.setText(chooser.getSelectedFile()
 452               .getAbsolutePath());
 453     }
 454   }
 455
 456   /**
 457    * DOCUMENT ME!
 458    *
 459    * @param e
 460    *                DOCUMENT ME!
 461    */
 462   public void cancel_actionPerformed(ActionEvent e)
 463   {
 464     try
 465     {
 466       frame.setClosed(true);
 467     } catch (Exception ex)
 468     {
 469     }
 470   }
 471
 472   /**
 473    * DOCUMENT ME!
 474    *
 475    * @param e
 476    *                DOCUMENT ME!
 477    */
 478   public void annotations_actionPerformed(ActionEvent e)
 479   {
 480     conservation.setEnabled(annotations.isSelected());
 481     quality.setEnabled(annotations.isSelected());
 482     identity.setEnabled(annotations.isSelected());
 483     showGroupConsensus.setEnabled(annotations.isSelected());
 484     showGroupConservation.setEnabled(annotations.isSelected());
 485     showConsensHistogram.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
 486     showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
 487   }
 488
 489   public void newLink_actionPerformed(ActionEvent e)
 490   {
 491
 492     GSequenceLink link = new GSequenceLink();
 493     boolean valid = false;
 494     while (!valid)
 495     {
 496       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 497               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 498               null) == JOptionPane.OK_OPTION)
 499       {
 500         if (link.checkValid())
 501         {
 502           nameLinks.addElement(link.getName());
 503           urlLinks.addElement(link.getURL());
 504           updateLinkData();
 505           valid = true;
 506         }
 507       }
 508       else
 509       {
 510         break;
 511       }
 512     }
 513   }
 514
 515   public void editLink_actionPerformed(ActionEvent e)
 516   {
 517     GSequenceLink link = new GSequenceLink();
 518
 519     int index = linkNameList.getSelectedIndex();
 520     if (index == -1)
 521     {
 522       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 523               "No link selected!", "No link selected",
 524               JOptionPane.WARNING_MESSAGE);
 525       return;
 526     }
 527
 528     link.setName(nameLinks.elementAt(index).toString());
 529     link.setURL(urlLinks.elementAt(index).toString());
 530
 531     boolean valid = false;
 532     while (!valid)
 533     {
 534
 535       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 536               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 537               null) == JOptionPane.OK_OPTION)
 538       {
 539         if (link.checkValid())
 540         {
 541           nameLinks.setElementAt(link.getName(), index);
 542           urlLinks.setElementAt(link.getURL(), index);
 543           updateLinkData();
 544           valid = true;
 545         }
 546       }
 547
 548       else
 549       {
 550         break;
 551       }
 552     }
 553   }
 554
 555   public void deleteLink_actionPerformed(ActionEvent e)
 556   {
 557     int index = linkNameList.getSelectedIndex();
 558     if (index == -1)
 559     {
 560       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 561               "No link selected!", "No link selected",
 562               JOptionPane.WARNING_MESSAGE);
 563       return;
 564     }
 565     nameLinks.removeElementAt(index);
 566     urlLinks.removeElementAt(index);
 567     updateLinkData();
 568   }
 569
 570   void updateLinkData()
 571   {
 572     linkNameList.setListData(nameLinks);
 573     linkURLList.setListData(urlLinks);
 574   }
 575
 576   public void defaultBrowser_mouseClicked(MouseEvent e)
 577   {
 578     JFileChooser chooser = new JFileChooser(".");
 579     chooser.setDialogTitle("Select default web browser");
 580
 581     int value = chooser.showOpenDialog(this);
 582
 583     if (value == JFileChooser.APPROVE_OPTION)
 584     {
 585       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 586     }
 587
 588   }
 589   /* (non-Javadoc)
 590    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 591    */
 592   protected void showunconserved_actionPerformed(ActionEvent e)
 593   {
 594     // TODO Auto-generated method stub
 595     super.showunconserved_actionPerformed(e);
 596   }
 597
 598   private void jbInit() throws Exception
 599   {
 600   }
 601
 602   public static Collection getGroupURLLinks()
 603   {
 604     return groupURLLinks;
 605   }
 606 }