src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26
  27 import jalview.bin.*;
  28 import jalview.io.*;
  29 import jalview.jbgui.*;
  30 import jalview.schemes.*;
  31 import jalview.ws.EnfinEnvision2OneWay;
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class Preferences extends GPreferences
  40 {
  41
  42   /**
  43    * Holds name and link separated with | character. Sequence ID must be
  44    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  45    */
  46   public static Vector sequenceURLLinks;
  47
  48   /**
  49    * Holds name and link separated with | character. Sequence IDS and Sequences
  50    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  51    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  52    * for first and second token specified after a pipe character at end |,|.
  53    * (TODO: proper escape for using | to separate ids or sequences
  54    */
  55
  56   public static Vector groupURLLinks;
  57   static
  58   {
  59     String string = Cache
  60             .getDefault(
  61                     "SEQUENCE_LINKS",
  62                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  63     sequenceURLLinks = new Vector();
  64
  65     try
  66     {
  67       StringTokenizer st = new StringTokenizer(string, "|");
  68       while (st.hasMoreElements())
  69       {
  70         String name = st.nextToken();
  71         String url = st.nextToken();
  72         // check for '|' within a regex
  73         int rxstart = url.indexOf("$SEQUENCE_ID$");
  74         while (rxstart == -1 && url.indexOf("/=$") == -1)
  75         {
  76           url = url + "|" + st.nextToken();
  77         }
  78         sequenceURLLinks.addElement(name + "|" + url);
  79       }
  80     } catch (Exception ex)
  81     {
  82       System.out.println(ex + "\nError parsing sequence links");
  83     }
  84     /**
  85      * TODO: reformulate groupURL encoding so two or more can be stored in the
  86      * .properties file as '|' separated strings
  87      */
  88
  89     groupURLLinks = new Vector();
  90     // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
  91     // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
  92
  93   }
  94
  95   Vector nameLinks, urlLinks;
  96
  97   JInternalFrame frame;
  98
  99   DasSourceBrowser dasSource;
 100
 101   /**
 102    * Creates a new Preferences object.
 103    */
 104   public Preferences()
 105   {
 106
 107     frame = new JInternalFrame();
 108     frame.setContentPane(this);
 109     dasSource = new DasSourceBrowser();
 110     dasPanel.add(dasSource, BorderLayout.CENTER);
 111
 112     int width = 500, height = 420;
 113     if (new jalview.util.Platform().isAMac())
 114     {
 115       width = 570;
 116       height = 460;
 117     }
 118
 119     Desktop.addInternalFrame(frame, "Preferences", width, height);
 120     frame.setMinimumSize(new Dimension(width, height));
 121
 122     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 123     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 124     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 125     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 126
 127     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 128     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 129     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 130     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 131     showUnconserved
 132             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 133     showNpTooltip.setSelected(Cache
 134             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 135     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 136             true));
 137
 138     for (int i = 0; i < 13; i++)
 139     {
 140       colour.addItem(ColourSchemeProperty.getColourName(i));
 141     }
 142
 143     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 144
 145     colour.setSelectedItem(string);
 146
 147     String[] fonts = java.awt.GraphicsEnvironment
 148             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 149
 150     for (int i = 0; i < fonts.length; i++)
 151     {
 152       fontNameCB.addItem(fonts[i]);
 153     }
 154
 155     for (int i = 1; i < 31; i++)
 156     {
 157       fontSizeCB.addItem(i + "");
 158     }
 159
 160     fontStyleCB.addItem("plain");
 161     fontStyleCB.addItem("bold");
 162     fontStyleCB.addItem("italic");
 163
 164     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 165     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 166     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 167             + ""));
 168
 169     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 170
 171     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 172
 173     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 174
 175     gapSymbolCB.addItem("-");
 176     gapSymbolCB.addItem(".");
 177
 178     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 179
 180     startupCheckbox
 181             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 182     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 183             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 184
 185     sortby.addItem("No sort");
 186     sortby.addItem("Id");
 187     sortby.addItem("Pairwise Identity");
 188     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 189
 190     epsRendering.addItem("Prompt each time");
 191     epsRendering.addItem("Lineart");
 192     epsRendering.addItem("Text");
 193     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 194             "Prompt each time"));
 195
 196     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 197     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 198     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 199     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 200     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 201     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 202     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 203
 204     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 205
 206     autoCalculateConsCheck.setSelected(Cache.getDefault(
 207             "AUTO_CALC_CONSENSUS", true));
 208     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 209             false));
 210     showGroupConservation.setSelected(Cache.getDefault(
 211             "SHOW_GROUP_CONSERVATION", false));
 212     showConsensHistogram.setSelected(Cache.getDefault(
 213             "SHOW_CONSENSUS_HISTOGRAM", true));
 214     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 215             false));
 216
 217     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 218
 219     /***************************************************************************
 220      * Set up Connections
 221      */
 222     nameLinks = new Vector();
 223     urlLinks = new Vector();
 224     for (int i = 0; i < sequenceURLLinks.size(); i++)
 225     {
 226       String link = sequenceURLLinks.elementAt(i).toString();
 227       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 228       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 229     }
 230
 231     updateLinkData();
 232
 233     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 234     proxyServerTB.setEnabled(useProxy.isSelected());
 235     proxyPortTB.setEnabled(useProxy.isSelected());
 236     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 237     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 238
 239     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 240
 241     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 242     questionnaire
 243             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 244                                                                          // antisense
 245                                                                          // here
 246     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 247                                                                        // is
 248                                                                        // true
 249     annotations_actionPerformed(null); // update the display of the annotation
 250                                        // settings
 251     try
 252     {
 253       jbInit();
 254     } catch (Exception ex)
 255     {
 256       ex.printStackTrace();
 257     }
 258
 259   }
 260
 261   /**
 262    * DOCUMENT ME!
 263    *
 264    * @param e
 265    *          DOCUMENT ME!
 266    */
 267   public void ok_actionPerformed(ActionEvent e)
 268   {
 269
 270     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 271             .toString(seqLimit.isSelected()));
 272     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 273             .toString(rightAlign.isSelected()));
 274     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 275             .toString(fullScreen.isSelected()));
 276     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 277             .toString(openoverv.isSelected()));
 278     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 279             .toString(annotations.isSelected()));
 280     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 281             .toString(conservation.isSelected()));
 282     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 283             .toString(quality.isSelected()));
 284     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 285             .toString(identity.isSelected()));
 286
 287     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 288             .getSelectedItem().toString());
 289     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 290             .getSelectedItem().toString());
 291
 292     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 293             .getSelectedItem().toString());
 294     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 295             .getSelectedItem().toString());
 296     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 297             .getSelectedItem().toString());
 298
 299     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 300             .toString(idItalics.isSelected()));
 301     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
 302             .toString(showUnconserved.isSelected()));
 303     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
 304             .toString(showGroupConsensus.isSelected()));
 305     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 306             Boolean.toString(showGroupConservation.isSelected()));
 307     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 308             Boolean.toString(showConsensHistogram.isSelected()));
 309     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
 310             .toString(showConsensLogo.isSelected()));
 311     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 312             .toString(smoothFont.isSelected()));
 313     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
 314             .toString(showNpTooltip.isSelected()));
 315     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
 316             .toString(showDbRefTooltip.isSelected()));
 317
 318     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 319             .toString(wrap.isSelected()));
 320
 321     Cache.applicationProperties.setProperty("STARTUP_FILE",
 322             startupFileTextfield.getText());
 323     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 324             .toString(startupCheckbox.isSelected()));
 325
 326     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 327             .getSelectedItem().toString());
 328
 329     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 330     {
 331       Cache.applicationProperties.remove("EPS_RENDERING");
 332     }
 333     else
 334     {
 335       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 336               .getSelectedItem().toString());
 337     }
 338
 339     if (defaultBrowser.getText().trim().length() < 1)
 340     {
 341       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 342     }
 343     else
 344     {
 345       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 346               defaultBrowser.getText());
 347     }
 348
 349     jalview.util.BrowserLauncher.resetBrowser();
 350
 351     if (nameLinks.size() > 0)
 352     {
 353       StringBuffer links = new StringBuffer();
 354       sequenceURLLinks = new Vector();
 355       for (int i = 0; i < nameLinks.size(); i++)
 356       {
 357         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 358                 + urlLinks.elementAt(i));
 359         links.append(sequenceURLLinks.elementAt(i).toString());
 360         links.append("|");
 361       }
 362       // remove last "|"
 363       links.setLength(links.length() - 1);
 364       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 365               .toString());
 366     }
 367     else
 368     {
 369       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 370     }
 371
 372     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 373             .toString(useProxy.isSelected()));
 374
 375     if (proxyServerTB.getText().trim().length() < 1)
 376     {
 377       Cache.applicationProperties.remove("PROXY_SERVER");
 378     }
 379     else
 380     {
 381       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 382               .getText());
 383     }
 384
 385     if (proxyPortTB.getText().trim().length() < 1)
 386     {
 387       Cache.applicationProperties.remove("PROXY_PORT");
 388     }
 389     else
 390     {
 391       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 392               .getText());
 393     }
 394
 395     if (useProxy.isSelected())
 396     {
 397       System.setProperty("http.proxyHost", proxyServerTB.getText());
 398       System.setProperty("http.proxyPort", proxyPortTB.getText());
 399     }
 400     else
 401     {
 402       System.setProperty("http.proxyHost", "");
 403       System.setProperty("http.proxyPort", "");
 404     }
 405     Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
 406             .isSelected()));
 407     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 408     {
 409       // default is false - we only set this if the user has actively agreed
 410       Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
 411               .isSelected()));
 412     }
 413     if (!questionnaire.isSelected())
 414     {
 415       Cache.setProperty("NOQUESTIONNAIRES", "true");
 416     }
 417     else
 418     {
 419       // special - made easy to edit a property file to disable questionnaires
 420       // by just adding the given line
 421       Cache.removeProperty("NOQUESTIONNAIRES");
 422     }
 423     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 424             .toString(blcjv.isSelected()));
 425     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 426             .toString(clustaljv.isSelected()));
 427     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 428             .toString(fastajv.isSelected()));
 429     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 430             .toString(msfjv.isSelected()));
 431     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 432             .toString(pfamjv.isSelected()));
 433     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 434             .toString(pileupjv.isSelected()));
 435     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 436             .toString(pirjv.isSelected()));
 437     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 438             .toString(modellerOutput.isSelected()));
 439     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 440
 441     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 442             .toString(autoCalculateConsCheck.isSelected()));
 443     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 444             .toString(padGaps.isSelected()));
 445
 446     dasSource.saveProperties(Cache.applicationProperties);
 447
 448     Cache.saveProperties();
 449     try
 450     {
 451       frame.setClosed(true);
 452     } catch (Exception ex)
 453     {
 454     }
 455   }
 456
 457   /**
 458    * DOCUMENT ME!
 459    */
 460   public void startupFileTextfield_mouseClicked()
 461   {
 462     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 463             .getProperty("LAST_DIRECTORY"), new String[]
 464     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 465             new String[]
 466             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 467             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 468     chooser.setFileView(new JalviewFileView());
 469     chooser.setDialogTitle("Select startup file");
 470
 471     int value = chooser.showOpenDialog(this);
 472
 473     if (value == JalviewFileChooser.APPROVE_OPTION)
 474     {
 475       jalview.bin.Cache.applicationProperties.setProperty(
 476               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 477       startupFileTextfield.setText(chooser.getSelectedFile()
 478               .getAbsolutePath());
 479     }
 480   }
 481
 482   /**
 483    * DOCUMENT ME!
 484    *
 485    * @param e
 486    *          DOCUMENT ME!
 487    */
 488   public void cancel_actionPerformed(ActionEvent e)
 489   {
 490     try
 491     {
 492       frame.setClosed(true);
 493     } catch (Exception ex)
 494     {
 495     }
 496   }
 497
 498   /**
 499    * DOCUMENT ME!
 500    *
 501    * @param e
 502    *          DOCUMENT ME!
 503    */
 504   public void annotations_actionPerformed(ActionEvent e)
 505   {
 506     conservation.setEnabled(annotations.isSelected());
 507     quality.setEnabled(annotations.isSelected());
 508     identity.setEnabled(annotations.isSelected());
 509     showGroupConsensus.setEnabled(annotations.isSelected());
 510     showGroupConservation.setEnabled(annotations.isSelected());
 511     showConsensHistogram.setEnabled(annotations.isSelected()
 512             && (identity.isSelected() || showGroupConsensus.isSelected()));
 513     showConsensLogo.setEnabled(annotations.isSelected()
 514             && (identity.isSelected() || showGroupConsensus.isSelected()));
 515   }
 516
 517   public void newLink_actionPerformed(ActionEvent e)
 518   {
 519
 520     GSequenceLink link = new GSequenceLink();
 521     boolean valid = false;
 522     while (!valid)
 523     {
 524       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 525               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 526               null) == JOptionPane.OK_OPTION)
 527       {
 528         if (link.checkValid())
 529         {
 530           nameLinks.addElement(link.getName());
 531           urlLinks.addElement(link.getURL());
 532           updateLinkData();
 533           valid = true;
 534         }
 535       }
 536       else
 537       {
 538         break;
 539       }
 540     }
 541   }
 542
 543   public void editLink_actionPerformed(ActionEvent e)
 544   {
 545     GSequenceLink link = new GSequenceLink();
 546
 547     int index = linkNameList.getSelectedIndex();
 548     if (index == -1)
 549     {
 550       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 551               "No link selected!", "No link selected",
 552               JOptionPane.WARNING_MESSAGE);
 553       return;
 554     }
 555
 556     link.setName(nameLinks.elementAt(index).toString());
 557     link.setURL(urlLinks.elementAt(index).toString());
 558
 559     boolean valid = false;
 560     while (!valid)
 561     {
 562
 563       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 564               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 565               null) == JOptionPane.OK_OPTION)
 566       {
 567         if (link.checkValid())
 568         {
 569           nameLinks.setElementAt(link.getName(), index);
 570           urlLinks.setElementAt(link.getURL(), index);
 571           updateLinkData();
 572           valid = true;
 573         }
 574       }
 575
 576       else
 577       {
 578         break;
 579       }
 580     }
 581   }
 582
 583   public void deleteLink_actionPerformed(ActionEvent e)
 584   {
 585     int index = linkNameList.getSelectedIndex();
 586     if (index == -1)
 587     {
 588       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 589               "No link selected!", "No link selected",
 590               JOptionPane.WARNING_MESSAGE);
 591       return;
 592     }
 593     nameLinks.removeElementAt(index);
 594     urlLinks.removeElementAt(index);
 595     updateLinkData();
 596   }
 597
 598   void updateLinkData()
 599   {
 600     linkNameList.setListData(nameLinks);
 601     linkURLList.setListData(urlLinks);
 602   }
 603
 604   public void defaultBrowser_mouseClicked(MouseEvent e)
 605   {
 606     JFileChooser chooser = new JFileChooser(".");
 607     chooser.setDialogTitle("Select default web browser");
 608
 609     int value = chooser.showOpenDialog(this);
 610
 611     if (value == JFileChooser.APPROVE_OPTION)
 612     {
 613       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 614     }
 615
 616   }
 617
 618   /*
 619    * (non-Javadoc)
 620    *
 621    * @see
 622    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 623    * .ActionEvent)
 624    */
 625   protected void showunconserved_actionPerformed(ActionEvent e)
 626   {
 627     // TODO Auto-generated method stub
 628     super.showunconserved_actionPerformed(e);
 629   }
 630
 631   private void jbInit() throws Exception
 632   {
 633   }
 634
 635   public static Collection getGroupURLLinks()
 636   {
 637     return groupURLLinks;
 638   }
 639 }