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     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 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     /**
 151      * default min-max colours for annotation shading
 152      */
 153     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 154     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 155
 156     String[] fonts = java.awt.GraphicsEnvironment
 157             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 158
 159     for (int i = 0; i < fonts.length; i++)
 160     {
 161       fontNameCB.addItem(fonts[i]);
 162     }
 163
 164     for (int i = 1; i < 31; i++)
 165     {
 166       fontSizeCB.addItem(i + "");
 167     }
 168
 169     fontStyleCB.addItem("plain");
 170     fontStyleCB.addItem("bold");
 171     fontStyleCB.addItem("italic");
 172
 173     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 174     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 175     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 176             + ""));
 177
 178     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 179
 180     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 181
 182     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 183
 184     gapSymbolCB.addItem("-");
 185     gapSymbolCB.addItem(".");
 186
 187     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 188
 189     startupCheckbox
 190             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 191     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 192             Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
 193
 194     sortby.addItem("No sort");
 195     sortby.addItem("Id");
 196     sortby.addItem("Pairwise Identity");
 197     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 198
 199     epsRendering.addItem("Prompt each time");
 200     epsRendering.addItem("Lineart");
 201     epsRendering.addItem("Text");
 202     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 203             "Prompt each time"));
 204
 205     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 206     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 207     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 208     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 209     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 210     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 211     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 212
 213     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 214
 215     autoCalculateConsCheck.setSelected(Cache.getDefault(
 216             "AUTO_CALC_CONSENSUS", true));
 217     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 218             false));
 219     showGroupConservation.setSelected(Cache.getDefault(
 220             "SHOW_GROUP_CONSERVATION", false));
 221     showConsensHistogram.setSelected(Cache.getDefault(
 222             "SHOW_CONSENSUS_HISTOGRAM", true));
 223     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 224             false));
 225
 226     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 227
 228     /***************************************************************************
 229      * Set up Connections
 230      */
 231     nameLinks = new Vector();
 232     urlLinks = new Vector();
 233     for (int i = 0; i < sequenceURLLinks.size(); i++)
 234     {
 235       String link = sequenceURLLinks.elementAt(i).toString();
 236       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 237       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 238     }
 239
 240     updateLinkData();
 241
 242     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 243     proxyServerTB.setEnabled(useProxy.isSelected());
 244     proxyPortTB.setEnabled(useProxy.isSelected());
 245     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 246     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 247
 248     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 249
 250     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 251     questionnaire
 252             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 253                                                                          // antisense
 254                                                                          // here
 255     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 256                                                                        // is
 257                                                                        // true
 258     annotations_actionPerformed(null); // update the display of the annotation
 259                                        // settings
 260     try
 261     {
 262       jbInit();
 263     } catch (Exception ex)
 264     {
 265       ex.printStackTrace();
 266     }
 267
 268   }
 269
 270   /**
 271    * DOCUMENT ME!
 272    *
 273    * @param e
 274    *          DOCUMENT ME!
 275    */
 276   public void ok_actionPerformed(ActionEvent e)
 277   {
 278
 279     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 280             Boolean.toString(seqLimit.isSelected()));
 281     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 282             Boolean.toString(rightAlign.isSelected()));
 283     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 284             Boolean.toString(fullScreen.isSelected()));
 285     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 286             Boolean.toString(openoverv.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 288             Boolean.toString(annotations.isSelected()));
 289     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 290             Boolean.toString(conservation.isSelected()));
 291     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 292             Boolean.toString(quality.isSelected()));
 293     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 294             Boolean.toString(identity.isSelected()));
 295
 296     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 297             .getSelectedItem().toString());
 298     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 299             .getSelectedItem().toString());
 300
 301     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 302             .getSelectedItem().toString());
 303     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 304             .getSelectedItem().toString());
 305     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 306             .getSelectedItem().toString());
 307
 308     Cache.applicationProperties.setProperty("ID_ITALICS",
 309             Boolean.toString(idItalics.isSelected()));
 310     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 311             Boolean.toString(showUnconserved.isSelected()));
 312     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 313             Boolean.toString(showGroupConsensus.isSelected()));
 314     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 315             Boolean.toString(showGroupConservation.isSelected()));
 316     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 317             Boolean.toString(showConsensHistogram.isSelected()));
 318     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 319             Boolean.toString(showConsensLogo.isSelected()));
 320     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 321             Boolean.toString(smoothFont.isSelected()));
 322     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 323             Boolean.toString(showNpTooltip.isSelected()));
 324     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 325             Boolean.toString(showDbRefTooltip.isSelected()));
 326
 327     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 328             Boolean.toString(wrap.isSelected()));
 329
 330     Cache.applicationProperties.setProperty("STARTUP_FILE",
 331             startupFileTextfield.getText());
 332     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 333             Boolean.toString(startupCheckbox.isSelected()));
 334
 335     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 336             .getSelectedItem().toString());
 337
 338     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground());
 339     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground());
 340
 341     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 342     {
 343       Cache.applicationProperties.remove("EPS_RENDERING");
 344     }
 345     else
 346     {
 347       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 348               .getSelectedItem().toString());
 349     }
 350
 351     if (defaultBrowser.getText().trim().length() < 1)
 352     {
 353       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 354     }
 355     else
 356     {
 357       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 358               defaultBrowser.getText());
 359     }
 360
 361     jalview.util.BrowserLauncher.resetBrowser();
 362
 363     if (nameLinks.size() > 0)
 364     {
 365       StringBuffer links = new StringBuffer();
 366       sequenceURLLinks = new Vector();
 367       for (int i = 0; i < nameLinks.size(); i++)
 368       {
 369         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 370                 + urlLinks.elementAt(i));
 371         links.append(sequenceURLLinks.elementAt(i).toString());
 372         links.append("|");
 373       }
 374       // remove last "|"
 375       links.setLength(links.length() - 1);
 376       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 377               links.toString());
 378     }
 379     else
 380     {
 381       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 382     }
 383
 384     Cache.applicationProperties.setProperty("USE_PROXY",
 385             Boolean.toString(useProxy.isSelected()));
 386
 387     if (proxyServerTB.getText().trim().length() < 1)
 388     {
 389       Cache.applicationProperties.remove("PROXY_SERVER");
 390     }
 391     else
 392     {
 393       Cache.applicationProperties.setProperty("PROXY_SERVER",
 394               proxyServerTB.getText());
 395     }
 396
 397     if (proxyPortTB.getText().trim().length() < 1)
 398     {
 399       Cache.applicationProperties.remove("PROXY_PORT");
 400     }
 401     else
 402     {
 403       Cache.applicationProperties.setProperty("PROXY_PORT",
 404               proxyPortTB.getText());
 405     }
 406
 407     if (useProxy.isSelected())
 408     {
 409       System.setProperty("http.proxyHost", proxyServerTB.getText());
 410       System.setProperty("http.proxyPort", proxyPortTB.getText());
 411     }
 412     else
 413     {
 414       System.setProperty("http.proxyHost", "");
 415       System.setProperty("http.proxyPort", "");
 416     }
 417     Cache.setProperty("VERSION_CHECK",
 418             Boolean.toString(versioncheck.isSelected()));
 419     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 420     {
 421       // default is false - we only set this if the user has actively agreed
 422       Cache.setProperty("USAGESTATS",
 423               Boolean.toString(usagestats.isSelected()));
 424     }
 425     if (!questionnaire.isSelected())
 426     {
 427       Cache.setProperty("NOQUESTIONNAIRES", "true");
 428     }
 429     else
 430     {
 431       // special - made easy to edit a property file to disable questionnaires
 432       // by just adding the given line
 433       Cache.removeProperty("NOQUESTIONNAIRES");
 434     }
 435     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 436             Boolean.toString(blcjv.isSelected()));
 437     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 438             Boolean.toString(clustaljv.isSelected()));
 439     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 440             Boolean.toString(fastajv.isSelected()));
 441     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 442             Boolean.toString(msfjv.isSelected()));
 443     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 444             Boolean.toString(pfamjv.isSelected()));
 445     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 446             Boolean.toString(pileupjv.isSelected()));
 447     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 448             Boolean.toString(pirjv.isSelected()));
 449     Cache.applicationProperties.setProperty("PIR_MODELLER",
 450             Boolean.toString(modellerOutput.isSelected()));
 451     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 452
 453     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 454             Boolean.toString(autoCalculateConsCheck.isSelected()));
 455     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 456             Boolean.toString(sortByTree.isSelected()));
 457     Cache.applicationProperties.setProperty("PAD_GAPS",
 458             Boolean.toString(padGaps.isSelected()));
 459
 460     dasSource.saveProperties(Cache.applicationProperties);
 461     wsPrefs.updateAndRefreshWsMenuConfig(false);
 462     Cache.saveProperties();
 463     try
 464     {
 465       frame.setClosed(true);
 466     } catch (Exception ex)
 467     {
 468     }
 469   }
 470
 471   /**
 472    * DOCUMENT ME!
 473    */
 474   public void startupFileTextfield_mouseClicked()
 475   {
 476     JalviewFileChooser chooser = new JalviewFileChooser(
 477             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 478             new String[]
 479             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 480             new String[]
 481             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 482             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 483     chooser.setFileView(new JalviewFileView());
 484     chooser.setDialogTitle("Select startup file");
 485
 486     int value = chooser.showOpenDialog(this);
 487
 488     if (value == JalviewFileChooser.APPROVE_OPTION)
 489     {
 490       jalview.bin.Cache.applicationProperties.setProperty(
 491               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 492       startupFileTextfield.setText(chooser.getSelectedFile()
 493               .getAbsolutePath());
 494     }
 495   }
 496
 497   /**
 498    * DOCUMENT ME!
 499    *
 500    * @param e
 501    *          DOCUMENT ME!
 502    */
 503   public void cancel_actionPerformed(ActionEvent e)
 504   {
 505     try
 506     {
 507       wsPrefs.updateWsMenuConfig(true);
 508       wsPrefs.refreshWs_actionPerformed(e);
 509       frame.setClosed(true);
 510     } catch (Exception ex)
 511     {
 512     }
 513   }
 514
 515   /**
 516    * DOCUMENT ME!
 517    *
 518    * @param e
 519    *          DOCUMENT ME!
 520    */
 521   public void annotations_actionPerformed(ActionEvent e)
 522   {
 523     conservation.setEnabled(annotations.isSelected());
 524     quality.setEnabled(annotations.isSelected());
 525     identity.setEnabled(annotations.isSelected());
 526     showGroupConsensus.setEnabled(annotations.isSelected());
 527     showGroupConservation.setEnabled(annotations.isSelected());
 528     showConsensHistogram.setEnabled(annotations.isSelected()
 529             && (identity.isSelected() || showGroupConsensus.isSelected()));
 530     showConsensLogo.setEnabled(annotations.isSelected()
 531             && (identity.isSelected() || showGroupConsensus.isSelected()));
 532   }
 533
 534   public void newLink_actionPerformed(ActionEvent e)
 535   {
 536
 537     GSequenceLink link = new GSequenceLink();
 538     boolean valid = false;
 539     while (!valid)
 540     {
 541       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 542               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 543               null) == JOptionPane.OK_OPTION)
 544       {
 545         if (link.checkValid())
 546         {
 547           nameLinks.addElement(link.getName());
 548           urlLinks.addElement(link.getURL());
 549           updateLinkData();
 550           valid = true;
 551         }
 552       }
 553       else
 554       {
 555         break;
 556       }
 557     }
 558   }
 559
 560   public void editLink_actionPerformed(ActionEvent e)
 561   {
 562     GSequenceLink link = new GSequenceLink();
 563
 564     int index = linkNameList.getSelectedIndex();
 565     if (index == -1)
 566     {
 567       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 568               "No link selected!", "No link selected",
 569               JOptionPane.WARNING_MESSAGE);
 570       return;
 571     }
 572
 573     link.setName(nameLinks.elementAt(index).toString());
 574     link.setURL(urlLinks.elementAt(index).toString());
 575
 576     boolean valid = false;
 577     while (!valid)
 578     {
 579
 580       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 581               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 582               null) == JOptionPane.OK_OPTION)
 583       {
 584         if (link.checkValid())
 585         {
 586           nameLinks.setElementAt(link.getName(), index);
 587           urlLinks.setElementAt(link.getURL(), index);
 588           updateLinkData();
 589           valid = true;
 590         }
 591       }
 592
 593       else
 594       {
 595         break;
 596       }
 597     }
 598   }
 599
 600   public void deleteLink_actionPerformed(ActionEvent e)
 601   {
 602     int index = linkNameList.getSelectedIndex();
 603     if (index == -1)
 604     {
 605       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 606               "No link selected!", "No link selected",
 607               JOptionPane.WARNING_MESSAGE);
 608       return;
 609     }
 610     nameLinks.removeElementAt(index);
 611     urlLinks.removeElementAt(index);
 612     updateLinkData();
 613   }
 614
 615   void updateLinkData()
 616   {
 617     linkNameList.setListData(nameLinks);
 618     linkURLList.setListData(urlLinks);
 619   }
 620
 621   public void defaultBrowser_mouseClicked(MouseEvent e)
 622   {
 623     JFileChooser chooser = new JFileChooser(".");
 624     chooser.setDialogTitle("Select default web browser");
 625
 626     int value = chooser.showOpenDialog(this);
 627
 628     if (value == JFileChooser.APPROVE_OPTION)
 629     {
 630       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 631     }
 632
 633   }
 634
 635   /*
 636    * (non-Javadoc)
 637    *
 638    * @see
 639    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 640    * .ActionEvent)
 641    */
 642   protected void showunconserved_actionPerformed(ActionEvent e)
 643   {
 644     // TODO Auto-generated method stub
 645     super.showunconserved_actionPerformed(e);
 646   }
 647
 648   private void jbInit() throws Exception
 649   {
 650   }
 651
 652   public static Collection getGroupURLLinks()
 653   {
 654     return groupURLLinks;
 655   }
 656   public void minColour_actionPerformed()
 657   {
 658     Color col = JColorChooser.showDialog(this,
 659             "Select Colour for Minimum Value", minColour.getBackground());
 660     if (col != null)
 661     {
 662       minColour.setBackground(col);
 663     }
 664     minColour.repaint();
 665   }
 666
 667   public void maxColour_actionPerformed()
 668   {
 669     Color col = JColorChooser.showDialog(this,
 670             "Select Colour for Maximum Value", maxColour.getBackground());
 671     if (col != null)
 672     {
 673       maxColour.setBackground(col);
 674     }
 675     maxColour.repaint();
 676   }
 677
 678 }