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",
 274             Boolean.toString(seqLimit.isSelected()));
 275     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 276             Boolean.toString(rightAlign.isSelected()));
 277     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 278             Boolean.toString(fullScreen.isSelected()));
 279     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 280             Boolean.toString(openoverv.isSelected()));
 281     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 282             Boolean.toString(annotations.isSelected()));
 283     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 284             Boolean.toString(conservation.isSelected()));
 285     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 286             Boolean.toString(quality.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 288             Boolean.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",
 303             Boolean.toString(idItalics.isSelected()));
 304     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 305             Boolean.toString(showUnconserved.isSelected()));
 306     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 307             Boolean.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",
 313             Boolean.toString(showConsensLogo.isSelected()));
 314     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 315             Boolean.toString(smoothFont.isSelected()));
 316     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 317             Boolean.toString(showNpTooltip.isSelected()));
 318     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 319             Boolean.toString(showDbRefTooltip.isSelected()));
 320
 321     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 322             Boolean.toString(wrap.isSelected()));
 323
 324     Cache.applicationProperties.setProperty("STARTUP_FILE",
 325             startupFileTextfield.getText());
 326     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 327             Boolean.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",
 368               links.toString());
 369     }
 370     else
 371     {
 372       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 373     }
 374
 375     Cache.applicationProperties.setProperty("USE_PROXY",
 376             Boolean.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",
 385               proxyServerTB.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",
 395               proxyPortTB.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",
 409             Boolean.toString(versioncheck.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",
 414               Boolean.toString(usagestats.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",
 427             Boolean.toString(blcjv.isSelected()));
 428     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 429             Boolean.toString(clustaljv.isSelected()));
 430     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 431             Boolean.toString(fastajv.isSelected()));
 432     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 433             Boolean.toString(msfjv.isSelected()));
 434     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 435             Boolean.toString(pfamjv.isSelected()));
 436     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 437             Boolean.toString(pileupjv.isSelected()));
 438     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 439             Boolean.toString(pirjv.isSelected()));
 440     Cache.applicationProperties.setProperty("PIR_MODELLER",
 441             Boolean.toString(modellerOutput.isSelected()));
 442     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 443
 444     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 445             Boolean.toString(autoCalculateConsCheck.isSelected()));
 446     Cache.applicationProperties.setProperty("PAD_GAPS",
 447             Boolean.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(
 466             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 467             new String[]
 468             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 469             new String[]
 470             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 471             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 472     chooser.setFileView(new JalviewFileView());
 473     chooser.setDialogTitle("Select startup file");
 474
 475     int value = chooser.showOpenDialog(this);
 476
 477     if (value == JalviewFileChooser.APPROVE_OPTION)
 478     {
 479       jalview.bin.Cache.applicationProperties.setProperty(
 480               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 481       startupFileTextfield.setText(chooser.getSelectedFile()
 482               .getAbsolutePath());
 483     }
 484   }
 485
 486   /**
 487    * DOCUMENT ME!
 488    *
 489    * @param e
 490    *          DOCUMENT ME!
 491    */
 492   public void cancel_actionPerformed(ActionEvent e)
 493   {
 494     try
 495     {
 496       wsPrefs.updateWsMenuConfig(true);
 497       frame.setClosed(true);
 498     } catch (Exception ex)
 499     {
 500     }
 501   }
 502
 503   /**
 504    * DOCUMENT ME!
 505    *
 506    * @param e
 507    *          DOCUMENT ME!
 508    */
 509   public void annotations_actionPerformed(ActionEvent e)
 510   {
 511     conservation.setEnabled(annotations.isSelected());
 512     quality.setEnabled(annotations.isSelected());
 513     identity.setEnabled(annotations.isSelected());
 514     showGroupConsensus.setEnabled(annotations.isSelected());
 515     showGroupConservation.setEnabled(annotations.isSelected());
 516     showConsensHistogram.setEnabled(annotations.isSelected()
 517             && (identity.isSelected() || showGroupConsensus.isSelected()));
 518     showConsensLogo.setEnabled(annotations.isSelected()
 519             && (identity.isSelected() || showGroupConsensus.isSelected()));
 520   }
 521
 522   public void newLink_actionPerformed(ActionEvent e)
 523   {
 524
 525     GSequenceLink link = new GSequenceLink();
 526     boolean valid = false;
 527     while (!valid)
 528     {
 529       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 530               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 531               null) == JOptionPane.OK_OPTION)
 532       {
 533         if (link.checkValid())
 534         {
 535           nameLinks.addElement(link.getName());
 536           urlLinks.addElement(link.getURL());
 537           updateLinkData();
 538           valid = true;
 539         }
 540       }
 541       else
 542       {
 543         break;
 544       }
 545     }
 546   }
 547
 548   public void editLink_actionPerformed(ActionEvent e)
 549   {
 550     GSequenceLink link = new GSequenceLink();
 551
 552     int index = linkNameList.getSelectedIndex();
 553     if (index == -1)
 554     {
 555       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 556               "No link selected!", "No link selected",
 557               JOptionPane.WARNING_MESSAGE);
 558       return;
 559     }
 560
 561     link.setName(nameLinks.elementAt(index).toString());
 562     link.setURL(urlLinks.elementAt(index).toString());
 563
 564     boolean valid = false;
 565     while (!valid)
 566     {
 567
 568       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 569               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 570               null) == JOptionPane.OK_OPTION)
 571       {
 572         if (link.checkValid())
 573         {
 574           nameLinks.setElementAt(link.getName(), index);
 575           urlLinks.setElementAt(link.getURL(), index);
 576           updateLinkData();
 577           valid = true;
 578         }
 579       }
 580
 581       else
 582       {
 583         break;
 584       }
 585     }
 586   }
 587
 588   public void deleteLink_actionPerformed(ActionEvent e)
 589   {
 590     int index = linkNameList.getSelectedIndex();
 591     if (index == -1)
 592     {
 593       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 594               "No link selected!", "No link selected",
 595               JOptionPane.WARNING_MESSAGE);
 596       return;
 597     }
 598     nameLinks.removeElementAt(index);
 599     urlLinks.removeElementAt(index);
 600     updateLinkData();
 601   }
 602
 603   void updateLinkData()
 604   {
 605     linkNameList.setListData(nameLinks);
 606     linkURLList.setListData(urlLinks);
 607   }
 608
 609   public void defaultBrowser_mouseClicked(MouseEvent e)
 610   {
 611     JFileChooser chooser = new JFileChooser(".");
 612     chooser.setDialogTitle("Select default web browser");
 613
 614     int value = chooser.showOpenDialog(this);
 615
 616     if (value == JFileChooser.APPROVE_OPTION)
 617     {
 618       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 619     }
 620
 621   }
 622
 623   /*
 624    * (non-Javadoc)
 625    *
 626    * @see
 627    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 628    * .ActionEvent)
 629    */
 630   protected void showunconserved_actionPerformed(ActionEvent e)
 631   {
 632     // TODO Auto-generated method stub
 633     super.showunconserved_actionPerformed(e);
 634   }
 635
 636   private void jbInit() throws Exception
 637   {
 638   }
 639
 640   public static Collection getGroupURLLinks()
 641   {
 642     return groupURLLinks;
 643   }
 644 }