src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   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   private WsPreferences wsPrefs;
 102
 103   /**
 104    * Creates a new Preferences object.
 105    */
 106   public Preferences()
 107   {
 108
 109     frame = new JInternalFrame();
 110     frame.setContentPane(this);
 111     dasSource = new DasSourceBrowser();
 112     dasPanel.add(dasSource, BorderLayout.CENTER);
 113     wsPrefs = new WsPreferences();
 114     wsPanel.add(wsPrefs, BorderLayout.CENTER);
 115     int width = 500, height = 420;
 116     if (new jalview.util.Platform().isAMac())
 117     {
 118       width = 570;
 119       height = 460;
 120     }
 121
 122     Desktop.addInternalFrame(frame, "Preferences", width, height);
 123     frame.setMinimumSize(new Dimension(width, height));
 124
 125     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 126     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 127     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 128     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 129
 130     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 131     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 132     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 133     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 134     showUnconserved
 135             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 136     showNpTooltip.setSelected(Cache
 137             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 138     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 139             true));
 140
 141     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 142     {
 143       colour.addItem(ColourSchemeProperty.getColourName(i));
 144     }
 145
 146     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 147
 148     colour.setSelectedItem(string);
 149
 150     String[] fonts = java.awt.GraphicsEnvironment
 151             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 152
 153     for (int i = 0; i < fonts.length; i++)
 154     {
 155       fontNameCB.addItem(fonts[i]);
 156     }
 157
 158     for (int i = 1; i < 31; i++)
 159     {
 160       fontSizeCB.addItem(i + "");
 161     }
 162
 163     fontStyleCB.addItem("plain");
 164     fontStyleCB.addItem("bold");
 165     fontStyleCB.addItem("italic");
 166
 167     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 168     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 169     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 170             + ""));
 171
 172     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 173
 174     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 175
 176     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 177
 178     gapSymbolCB.addItem("-");
 179     gapSymbolCB.addItem(".");
 180
 181     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 182
 183     startupCheckbox
 184             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 185     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 186             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 187
 188     sortby.addItem("No sort");
 189     sortby.addItem("Id");
 190     sortby.addItem("Pairwise Identity");
 191     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 192
 193     epsRendering.addItem("Prompt each time");
 194     epsRendering.addItem("Lineart");
 195     epsRendering.addItem("Text");
 196     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 197             "Prompt each time"));
 198
 199     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 200     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 201     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 202     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 203     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 204     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 205     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 206
 207     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 208
 209     autoCalculateConsCheck.setSelected(Cache.getDefault(
 210             "AUTO_CALC_CONSENSUS", true));
 211     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 212             false));
 213     showGroupConservation.setSelected(Cache.getDefault(
 214             "SHOW_GROUP_CONSERVATION", false));
 215     showConsensHistogram.setSelected(Cache.getDefault(
 216             "SHOW_CONSENSUS_HISTOGRAM", true));
 217     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 218             false));
 219
 220     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 221
 222     /***************************************************************************
 223      * Set up Connections
 224      */
 225     nameLinks = new Vector();
 226     urlLinks = new Vector();
 227     for (int i = 0; i < sequenceURLLinks.size(); i++)
 228     {
 229       String link = sequenceURLLinks.elementAt(i).toString();
 230       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 231       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 232     }
 233
 234     updateLinkData();
 235
 236     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 237     proxyServerTB.setEnabled(useProxy.isSelected());
 238     proxyPortTB.setEnabled(useProxy.isSelected());
 239     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 240     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 241
 242     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 243
 244     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 245     questionnaire
 246             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 247                                                                          // antisense
 248                                                                          // here
 249     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 250                                                                        // is
 251                                                                        // true
 252     annotations_actionPerformed(null); // update the display of the annotation
 253                                        // settings
 254     try
 255     {
 256       jbInit();
 257     } catch (Exception ex)
 258     {
 259       ex.printStackTrace();
 260     }
 261
 262   }
 263
 264   /**
 265    * DOCUMENT ME!
 266    *
 267    * @param e
 268    *          DOCUMENT ME!
 269    */
 270   public void ok_actionPerformed(ActionEvent e)
 271   {
 272
 273     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 274             .toString(seqLimit.isSelected()));
 275     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 276             .toString(rightAlign.isSelected()));
 277     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 278             .toString(fullScreen.isSelected()));
 279     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 280             .toString(openoverv.isSelected()));
 281     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 282             .toString(annotations.isSelected()));
 283     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 284             .toString(conservation.isSelected()));
 285     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 286             .toString(quality.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 288             .toString(identity.isSelected()));
 289
 290     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 291             .getSelectedItem().toString());
 292     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 293             .getSelectedItem().toString());
 294
 295     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 296             .getSelectedItem().toString());
 297     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 298             .getSelectedItem().toString());
 299     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 300             .getSelectedItem().toString());
 301
 302     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 303             .toString(idItalics.isSelected()));
 304     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
 305             .toString(showUnconserved.isSelected()));
 306     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
 307             .toString(showGroupConsensus.isSelected()));
 308     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 309             Boolean.toString(showGroupConservation.isSelected()));
 310     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 311             Boolean.toString(showConsensHistogram.isSelected()));
 312     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
 313             .toString(showConsensLogo.isSelected()));
 314     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 315             .toString(smoothFont.isSelected()));
 316     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
 317             .toString(showNpTooltip.isSelected()));
 318     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
 319             .toString(showDbRefTooltip.isSelected()));
 320
 321     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 322             .toString(wrap.isSelected()));
 323
 324     Cache.applicationProperties.setProperty("STARTUP_FILE",
 325             startupFileTextfield.getText());
 326     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 327             .toString(startupCheckbox.isSelected()));
 328
 329     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 330             .getSelectedItem().toString());
 331
 332     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 333     {
 334       Cache.applicationProperties.remove("EPS_RENDERING");
 335     }
 336     else
 337     {
 338       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 339               .getSelectedItem().toString());
 340     }
 341
 342     if (defaultBrowser.getText().trim().length() < 1)
 343     {
 344       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 345     }
 346     else
 347     {
 348       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 349               defaultBrowser.getText());
 350     }
 351
 352     jalview.util.BrowserLauncher.resetBrowser();
 353
 354     if (nameLinks.size() > 0)
 355     {
 356       StringBuffer links = new StringBuffer();
 357       sequenceURLLinks = new Vector();
 358       for (int i = 0; i < nameLinks.size(); i++)
 359       {
 360         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 361                 + urlLinks.elementAt(i));
 362         links.append(sequenceURLLinks.elementAt(i).toString());
 363         links.append("|");
 364       }
 365       // remove last "|"
 366       links.setLength(links.length() - 1);
 367       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 368               .toString());
 369     }
 370     else
 371     {
 372       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 373     }
 374
 375     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 376             .toString(useProxy.isSelected()));
 377
 378     if (proxyServerTB.getText().trim().length() < 1)
 379     {
 380       Cache.applicationProperties.remove("PROXY_SERVER");
 381     }
 382     else
 383     {
 384       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 385               .getText());
 386     }
 387
 388     if (proxyPortTB.getText().trim().length() < 1)
 389     {
 390       Cache.applicationProperties.remove("PROXY_PORT");
 391     }
 392     else
 393     {
 394       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 395               .getText());
 396     }
 397
 398     if (useProxy.isSelected())
 399     {
 400       System.setProperty("http.proxyHost", proxyServerTB.getText());
 401       System.setProperty("http.proxyPort", proxyPortTB.getText());
 402     }
 403     else
 404     {
 405       System.setProperty("http.proxyHost", "");
 406       System.setProperty("http.proxyPort", "");
 407     }
 408     Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
 409             .isSelected()));
 410     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 411     {
 412       // default is false - we only set this if the user has actively agreed
 413       Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
 414               .isSelected()));
 415     }
 416     if (!questionnaire.isSelected())
 417     {
 418       Cache.setProperty("NOQUESTIONNAIRES", "true");
 419     }
 420     else
 421     {
 422       // special - made easy to edit a property file to disable questionnaires
 423       // by just adding the given line
 424       Cache.removeProperty("NOQUESTIONNAIRES");
 425     }
 426     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 427             .toString(blcjv.isSelected()));
 428     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 429             .toString(clustaljv.isSelected()));
 430     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 431             .toString(fastajv.isSelected()));
 432     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 433             .toString(msfjv.isSelected()));
 434     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 435             .toString(pfamjv.isSelected()));
 436     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 437             .toString(pileupjv.isSelected()));
 438     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 439             .toString(pirjv.isSelected()));
 440     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 441             .toString(modellerOutput.isSelected()));
 442     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 443
 444     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 445             .toString(autoCalculateConsCheck.isSelected()));
 446     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 447             .toString(padGaps.isSelected()));
 448
 449     dasSource.saveProperties(Cache.applicationProperties);
 450     wsPrefs.updateAndRefreshWsMenuConfig(false);
 451     Cache.saveProperties();
 452     try
 453     {
 454       frame.setClosed(true);
 455     } catch (Exception ex)
 456     {
 457     }
 458   }
 459
 460   /**
 461    * DOCUMENT ME!
 462    */
 463   public void startupFileTextfield_mouseClicked()
 464   {
 465     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 466             .getProperty("LAST_DIRECTORY"), new String[]
 467     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 468             new String[]
 469             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 470             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 471     chooser.setFileView(new JalviewFileView());
 472     chooser.setDialogTitle("Select startup file");
 473
 474     int value = chooser.showOpenDialog(this);
 475
 476     if (value == JalviewFileChooser.APPROVE_OPTION)
 477     {
 478       jalview.bin.Cache.applicationProperties.setProperty(
 479               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 480       startupFileTextfield.setText(chooser.getSelectedFile()
 481               .getAbsolutePath());
 482     }
 483   }
 484
 485   /**
 486    * DOCUMENT ME!
 487    *
 488    * @param e
 489    *          DOCUMENT ME!
 490    */
 491   public void cancel_actionPerformed(ActionEvent e)
 492   {
 493     try
 494     {
 495       wsPrefs.updateWsMenuConfig(true);
 496       frame.setClosed(true);
 497     } catch (Exception ex)
 498     {
 499     }
 500   }
 501
 502   /**
 503    * DOCUMENT ME!
 504    *
 505    * @param e
 506    *          DOCUMENT ME!
 507    */
 508   public void annotations_actionPerformed(ActionEvent e)
 509   {
 510     conservation.setEnabled(annotations.isSelected());
 511     quality.setEnabled(annotations.isSelected());
 512     identity.setEnabled(annotations.isSelected());
 513     showGroupConsensus.setEnabled(annotations.isSelected());
 514     showGroupConservation.setEnabled(annotations.isSelected());
 515     showConsensHistogram.setEnabled(annotations.isSelected()
 516             && (identity.isSelected() || showGroupConsensus.isSelected()));
 517     showConsensLogo.setEnabled(annotations.isSelected()
 518             && (identity.isSelected() || showGroupConsensus.isSelected()));
 519   }
 520
 521   public void newLink_actionPerformed(ActionEvent e)
 522   {
 523
 524     GSequenceLink link = new GSequenceLink();
 525     boolean valid = false;
 526     while (!valid)
 527     {
 528       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 529               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 530               null) == JOptionPane.OK_OPTION)
 531       {
 532         if (link.checkValid())
 533         {
 534           nameLinks.addElement(link.getName());
 535           urlLinks.addElement(link.getURL());
 536           updateLinkData();
 537           valid = true;
 538         }
 539       }
 540       else
 541       {
 542         break;
 543       }
 544     }
 545   }
 546
 547   public void editLink_actionPerformed(ActionEvent e)
 548   {
 549     GSequenceLink link = new GSequenceLink();
 550
 551     int index = linkNameList.getSelectedIndex();
 552     if (index == -1)
 553     {
 554       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 555               "No link selected!", "No link selected",
 556               JOptionPane.WARNING_MESSAGE);
 557       return;
 558     }
 559
 560     link.setName(nameLinks.elementAt(index).toString());
 561     link.setURL(urlLinks.elementAt(index).toString());
 562
 563     boolean valid = false;
 564     while (!valid)
 565     {
 566
 567       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 568               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 569               null) == JOptionPane.OK_OPTION)
 570       {
 571         if (link.checkValid())
 572         {
 573           nameLinks.setElementAt(link.getName(), index);
 574           urlLinks.setElementAt(link.getURL(), index);
 575           updateLinkData();
 576           valid = true;
 577         }
 578       }
 579
 580       else
 581       {
 582         break;
 583       }
 584     }
 585   }
 586
 587   public void deleteLink_actionPerformed(ActionEvent e)
 588   {
 589     int index = linkNameList.getSelectedIndex();
 590     if (index == -1)
 591     {
 592       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 593               "No link selected!", "No link selected",
 594               JOptionPane.WARNING_MESSAGE);
 595       return;
 596     }
 597     nameLinks.removeElementAt(index);
 598     urlLinks.removeElementAt(index);
 599     updateLinkData();
 600   }
 601
 602   void updateLinkData()
 603   {
 604     linkNameList.setListData(nameLinks);
 605     linkURLList.setListData(urlLinks);
 606   }
 607
 608   public void defaultBrowser_mouseClicked(MouseEvent e)
 609   {
 610     JFileChooser chooser = new JFileChooser(".");
 611     chooser.setDialogTitle("Select default web browser");
 612
 613     int value = chooser.showOpenDialog(this);
 614
 615     if (value == JFileChooser.APPROVE_OPTION)
 616     {
 617       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 618     }
 619
 620   }
 621
 622   /*
 623    * (non-Javadoc)
 624    *
 625    * @see
 626    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 627    * .ActionEvent)
 628    */
 629   protected void showunconserved_actionPerformed(ActionEvent e)
 630   {
 631     // TODO Auto-generated method stub
 632     super.showunconserved_actionPerformed(e);
 633   }
 634
 635   private void jbInit() throws Exception
 636   {
 637   }
 638
 639   public static Collection getGroupURLLinks()
 640   {
 641     return groupURLLinks;
 642   }
 643 }