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
 131     for (int i = 0; i < 13; i++)
 132     {
 133       colour.addItem(ColourSchemeProperty.getColourName(i));
 134     }
 135
 136     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 137
 138     colour.setSelectedItem(string);
 139
 140     String[] fonts = java.awt.GraphicsEnvironment
 141             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 142
 143     for (int i = 0; i < fonts.length; i++)
 144     {
 145       fontNameCB.addItem(fonts[i]);
 146     }
 147
 148     for (int i = 1; i < 31; i++)
 149     {
 150       fontSizeCB.addItem(i + "");
 151     }
 152
 153     fontStyleCB.addItem("plain");
 154     fontStyleCB.addItem("bold");
 155     fontStyleCB.addItem("italic");
 156
 157     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 158     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 159     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 160             + ""));
 161
 162     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 163
 164     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 165
 166     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 167
 168     gapSymbolCB.addItem("-");
 169     gapSymbolCB.addItem(".");
 170
 171     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 172
 173     startupCheckbox
 174             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 175     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 176             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 177
 178     sortby.addItem("No sort");
 179     sortby.addItem("Id");
 180     sortby.addItem("Pairwise Identity");
 181     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 182
 183     epsRendering.addItem("Prompt each time");
 184     epsRendering.addItem("Lineart");
 185     epsRendering.addItem("Text");
 186     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 187             "Prompt each time"));
 188
 189     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 190     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 191     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 192     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 193     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 194     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 195     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 196
 197     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 198
 199     autoCalculateConsCheck.setSelected(Cache.getDefault(
 200             "AUTO_CALC_CONSENSUS", true));
 201     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
 202     showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 203     showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
 204     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",false));
 205
 206     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 207
 208     /***************************************************************************
 209      * Set up Connections
 210      */
 211     nameLinks = new Vector();
 212     urlLinks = new Vector();
 213     for (int i = 0; i < sequenceURLLinks.size(); i++)
 214     {
 215       String link = sequenceURLLinks.elementAt(i).toString();
 216       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 217       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 218     }
 219
 220     updateLinkData();
 221
 222     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 223     proxyServerTB.setEnabled(useProxy.isSelected());
 224     proxyPortTB.setEnabled(useProxy.isSelected());
 225     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 226     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 227
 228     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 229
 230     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 231     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
 232     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
 233     annotations_actionPerformed(null); // update the display of the annotation settings
 234     try
 235     {
 236       jbInit();
 237     } catch (Exception ex)
 238     {
 239       ex.printStackTrace();
 240     }
 241
 242   }
 243
 244   /**
 245    * DOCUMENT ME!
 246    *
 247    * @param e
 248    *                DOCUMENT ME!
 249    */
 250   public void ok_actionPerformed(ActionEvent e)
 251   {
 252
 253     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 254             .toString(seqLimit.isSelected()));
 255     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 256             .toString(rightAlign.isSelected()));
 257     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 258             .toString(fullScreen.isSelected()));
 259     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 260             .toString(openoverv.isSelected()));
 261     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 262             .toString(annotations.isSelected()));
 263     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 264             .toString(conservation.isSelected()));
 265     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 266             .toString(quality.isSelected()));
 267     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 268             .toString(identity.isSelected()));
 269
 270     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 271             .getSelectedItem().toString());
 272     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 273             .getSelectedItem().toString());
 274
 275     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 276             .getSelectedItem().toString());
 277     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 278             .getSelectedItem().toString());
 279     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 280             .getSelectedItem().toString());
 281
 282     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 283             .toString(idItalics.isSelected()));
 284     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 285     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
 286     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
 288     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",Boolean.toString(showConsensLogo.isSelected()));
 289     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 290             .toString(smoothFont.isSelected()));
 291
 292     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 293             .toString(wrap.isSelected()));
 294
 295     Cache.applicationProperties.setProperty("STARTUP_FILE",
 296             startupFileTextfield.getText());
 297     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 298             .toString(startupCheckbox.isSelected()));
 299
 300     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 301             .getSelectedItem().toString());
 302
 303     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 304     {
 305       Cache.applicationProperties.remove("EPS_RENDERING");
 306     }
 307     else
 308     {
 309       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 310               .getSelectedItem().toString());
 311     }
 312
 313     if (defaultBrowser.getText().trim().length() < 1)
 314     {
 315       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 316     }
 317     else
 318     {
 319       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 320               defaultBrowser.getText());
 321     }
 322
 323     jalview.util.BrowserLauncher.resetBrowser();
 324
 325     if (nameLinks.size() > 0)
 326     {
 327       StringBuffer links = new StringBuffer();
 328       sequenceURLLinks = new Vector();
 329       for (int i = 0; i < nameLinks.size(); i++)
 330       {
 331         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 332                 + urlLinks.elementAt(i));
 333         links.append(sequenceURLLinks.elementAt(i).toString());
 334         links.append("|");
 335       }
 336       // remove last "|"
 337       links.setLength(links.length() - 1);
 338       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 339               .toString());
 340     }
 341     else
 342     {
 343       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 344     }
 345
 346     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 347             .toString(useProxy.isSelected()));
 348
 349     if (proxyServerTB.getText().trim().length() < 1)
 350     {
 351       Cache.applicationProperties.remove("PROXY_SERVER");
 352     }
 353     else
 354     {
 355       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 356               .getText());
 357     }
 358
 359     if (proxyPortTB.getText().trim().length() < 1)
 360     {
 361       Cache.applicationProperties.remove("PROXY_PORT");
 362     }
 363     else
 364     {
 365       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 366               .getText());
 367     }
 368
 369     if (useProxy.isSelected())
 370     {
 371       System.setProperty("http.proxyHost", proxyServerTB.getText());
 372       System.setProperty("http.proxyPort", proxyPortTB.getText());
 373     }
 374     else
 375     {
 376       System.setProperty("http.proxyHost", "");
 377       System.setProperty("http.proxyPort", "");
 378     }
 379     Cache.setProperty("VERSION_CHECK", Boolean
 380             .toString(versioncheck.isSelected()));
 381     if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) {
 382       // default is false - we only set this if the user has actively agreed
 383       Cache.setProperty("USAGESTATS",Boolean
 384             .toString(usagestats.isSelected()));
 385     }
 386     if (!questionnaire.isSelected())
 387     {
 388       Cache.setProperty("NOQUESTIONNAIRES", "true");
 389     } else {
 390       // special - made easy to edit a property file to disable questionnaires by just adding the given line
 391       Cache.removeProperty("NOQUESTIONNAIRES");
 392     }
 393     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 394             .toString(blcjv.isSelected()));
 395     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 396             .toString(clustaljv.isSelected()));
 397     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 398             .toString(fastajv.isSelected()));
 399     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 400             .toString(msfjv.isSelected()));
 401     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 402             .toString(pfamjv.isSelected()));
 403     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 404             .toString(pileupjv.isSelected()));
 405     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 406             .toString(pirjv.isSelected()));
 407     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 408             .toString(modellerOutput.isSelected()));
 409     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 410
 411     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 412             .toString(autoCalculateConsCheck.isSelected()));
 413     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 414             .toString(padGaps.isSelected()));
 415
 416     dasSource.saveProperties(Cache.applicationProperties);
 417
 418     Cache.saveProperties();
 419     try
 420     {
 421       frame.setClosed(true);
 422     } catch (Exception ex)
 423     {
 424     }
 425   }
 426
 427   /**
 428    * DOCUMENT ME!
 429    */
 430   public void startupFileTextfield_mouseClicked()
 431   {
 432     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 433             .getProperty("LAST_DIRECTORY"), new String[]
 434     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 435             new String[]
 436             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 437             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 438     chooser.setFileView(new JalviewFileView());
 439     chooser.setDialogTitle("Select startup file");
 440
 441     int value = chooser.showOpenDialog(this);
 442
 443     if (value == JalviewFileChooser.APPROVE_OPTION)
 444     {
 445       jalview.bin.Cache.applicationProperties.setProperty(
 446               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 447       startupFileTextfield.setText(chooser.getSelectedFile()
 448               .getAbsolutePath());
 449     }
 450   }
 451
 452   /**
 453    * DOCUMENT ME!
 454    *
 455    * @param e
 456    *                DOCUMENT ME!
 457    */
 458   public void cancel_actionPerformed(ActionEvent e)
 459   {
 460     try
 461     {
 462       frame.setClosed(true);
 463     } catch (Exception ex)
 464     {
 465     }
 466   }
 467
 468   /**
 469    * DOCUMENT ME!
 470    *
 471    * @param e
 472    *                DOCUMENT ME!
 473    */
 474   public void annotations_actionPerformed(ActionEvent e)
 475   {
 476     conservation.setEnabled(annotations.isSelected());
 477     quality.setEnabled(annotations.isSelected());
 478     identity.setEnabled(annotations.isSelected());
 479     showGroupConsensus.setEnabled(annotations.isSelected());
 480     showGroupConservation.setEnabled(annotations.isSelected());
 481     showConsensHistogram.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
 482     showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
 483   }
 484
 485   public void newLink_actionPerformed(ActionEvent e)
 486   {
 487
 488     GSequenceLink link = new GSequenceLink();
 489     boolean valid = false;
 490     while (!valid)
 491     {
 492       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 493               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 494               null) == JOptionPane.OK_OPTION)
 495       {
 496         if (link.checkValid())
 497         {
 498           nameLinks.addElement(link.getName());
 499           urlLinks.addElement(link.getURL());
 500           updateLinkData();
 501           valid = true;
 502         }
 503       }
 504       else
 505       {
 506         break;
 507       }
 508     }
 509   }
 510
 511   public void editLink_actionPerformed(ActionEvent e)
 512   {
 513     GSequenceLink link = new GSequenceLink();
 514
 515     int index = linkNameList.getSelectedIndex();
 516     if (index == -1)
 517     {
 518       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 519               "No link selected!", "No link selected",
 520               JOptionPane.WARNING_MESSAGE);
 521       return;
 522     }
 523
 524     link.setName(nameLinks.elementAt(index).toString());
 525     link.setURL(urlLinks.elementAt(index).toString());
 526
 527     boolean valid = false;
 528     while (!valid)
 529     {
 530
 531       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 532               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 533               null) == JOptionPane.OK_OPTION)
 534       {
 535         if (link.checkValid())
 536         {
 537           nameLinks.setElementAt(link.getName(), index);
 538           urlLinks.setElementAt(link.getURL(), index);
 539           updateLinkData();
 540           valid = true;
 541         }
 542       }
 543
 544       else
 545       {
 546         break;
 547       }
 548     }
 549   }
 550
 551   public void deleteLink_actionPerformed(ActionEvent e)
 552   {
 553     int index = linkNameList.getSelectedIndex();
 554     if (index == -1)
 555     {
 556       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 557               "No link selected!", "No link selected",
 558               JOptionPane.WARNING_MESSAGE);
 559       return;
 560     }
 561     nameLinks.removeElementAt(index);
 562     urlLinks.removeElementAt(index);
 563     updateLinkData();
 564   }
 565
 566   void updateLinkData()
 567   {
 568     linkNameList.setListData(nameLinks);
 569     linkURLList.setListData(urlLinks);
 570   }
 571
 572   public void defaultBrowser_mouseClicked(MouseEvent e)
 573   {
 574     JFileChooser chooser = new JFileChooser(".");
 575     chooser.setDialogTitle("Select default web browser");
 576
 577     int value = chooser.showOpenDialog(this);
 578
 579     if (value == JFileChooser.APPROVE_OPTION)
 580     {
 581       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 582     }
 583
 584   }
 585   /* (non-Javadoc)
 586    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 587    */
 588   protected void showunconserved_actionPerformed(ActionEvent e)
 589   {
 590     // TODO Auto-generated method stub
 591     super.showunconserved_actionPerformed(e);
 592   }
 593
 594   private void jbInit() throws Exception
 595   {
 596   }
 597
 598   public static Collection getGroupURLLinks()
 599   {
 600     return groupURLLinks;
 601   }
 602 }