src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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",
 154             Color.orange));
 155     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 156             Color.red));
 157
 158     String[] fonts = java.awt.GraphicsEnvironment
 159             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 160
 161     for (int i = 0; i < fonts.length; i++)
 162     {
 163       fontNameCB.addItem(fonts[i]);
 164     }
 165
 166     for (int i = 1; i < 31; i++)
 167     {
 168       fontSizeCB.addItem(i + "");
 169     }
 170
 171     fontStyleCB.addItem("plain");
 172     fontStyleCB.addItem("bold");
 173     fontStyleCB.addItem("italic");
 174
 175     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 176     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 177     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 178             + ""));
 179
 180     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 181
 182     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 183
 184     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 185
 186     gapSymbolCB.addItem("-");
 187     gapSymbolCB.addItem(".");
 188
 189     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 190
 191     startupCheckbox
 192             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 193     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 194             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 195                     + "/examples/exampleFile_2_3.jar"));
 196
 197     sortby.addItem("No sort");
 198     sortby.addItem("Id");
 199     sortby.addItem("Pairwise Identity");
 200     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 201
 202     epsRendering.addItem("Prompt each time");
 203     epsRendering.addItem("Lineart");
 204     epsRendering.addItem("Text");
 205     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 206             "Prompt each time"));
 207     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 208     userIdWidth.setEnabled(autoIdWidth.isSelected());
 209     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 210     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 211     userIdWidth.setText(wi == null ? "" : wi.toString());
 212     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 213     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 214     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 215     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 216     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 217     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 218     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 219
 220     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 221
 222     autoCalculateConsCheck.setSelected(Cache.getDefault(
 223             "AUTO_CALC_CONSENSUS", true));
 224     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 225             false));
 226     showGroupConservation.setSelected(Cache.getDefault(
 227             "SHOW_GROUP_CONSERVATION", false));
 228     showConsensHistogram.setSelected(Cache.getDefault(
 229             "SHOW_CONSENSUS_HISTOGRAM", true));
 230     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 231             false));
 232
 233     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 234
 235     /***************************************************************************
 236      * Set up Connections
 237      */
 238     nameLinks = new Vector();
 239     urlLinks = new Vector();
 240     for (int i = 0; i < sequenceURLLinks.size(); i++)
 241     {
 242       String link = sequenceURLLinks.elementAt(i).toString();
 243       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 244       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 245     }
 246
 247     updateLinkData();
 248
 249     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 250     proxyServerTB.setEnabled(useProxy.isSelected());
 251     proxyPortTB.setEnabled(useProxy.isSelected());
 252     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 253     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 254
 255     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 256
 257     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 258     questionnaire
 259             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 260                                                                          // antisense
 261                                                                          // here
 262     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 263                                                                        // is
 264                                                                        // true
 265     annotations_actionPerformed(null); // update the display of the annotation
 266                                        // settings
 267     try
 268     {
 269       jbInit();
 270     } catch (Exception ex)
 271     {
 272       ex.printStackTrace();
 273     }
 274
 275   }
 276
 277   /**
 278    * DOCUMENT ME!
 279    *
 280    * @param e
 281    *          DOCUMENT ME!
 282    */
 283   public void ok_actionPerformed(ActionEvent e)
 284   {
 285
 286     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 287             Boolean.toString(seqLimit.isSelected()));
 288     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 289             Boolean.toString(rightAlign.isSelected()));
 290     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 291             Boolean.toString(fullScreen.isSelected()));
 292     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 293             Boolean.toString(openoverv.isSelected()));
 294     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 295             Boolean.toString(annotations.isSelected()));
 296     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 297             Boolean.toString(conservation.isSelected()));
 298     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 299             Boolean.toString(quality.isSelected()));
 300     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 301             Boolean.toString(identity.isSelected()));
 302
 303     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 304             .getSelectedItem().toString());
 305     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 306             .getSelectedItem().toString());
 307
 308     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 309             .getSelectedItem().toString());
 310     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 311             .getSelectedItem().toString());
 312     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 313             .getSelectedItem().toString());
 314
 315     Cache.applicationProperties.setProperty("ID_ITALICS",
 316             Boolean.toString(idItalics.isSelected()));
 317     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 318             Boolean.toString(showUnconserved.isSelected()));
 319     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 320             Boolean.toString(showGroupConsensus.isSelected()));
 321     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 322             Boolean.toString(showGroupConservation.isSelected()));
 323     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 324             Boolean.toString(showConsensHistogram.isSelected()));
 325     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 326             Boolean.toString(showConsensLogo.isSelected()));
 327     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 328             Boolean.toString(smoothFont.isSelected()));
 329     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 330             Boolean.toString(showNpTooltip.isSelected()));
 331     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 332             Boolean.toString(showDbRefTooltip.isSelected()));
 333
 334     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 335             Boolean.toString(wrap.isSelected()));
 336
 337     Cache.applicationProperties.setProperty("STARTUP_FILE",
 338             startupFileTextfield.getText());
 339     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 340             Boolean.toString(startupCheckbox.isSelected()));
 341
 342     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 343             .getSelectedItem().toString());
 344
 345     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 346             minColour.getBackground());
 347     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 348             maxColour.getBackground());
 349
 350     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 351     {
 352       Cache.applicationProperties.remove("EPS_RENDERING");
 353     }
 354     else
 355     {
 356       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 357               .getSelectedItem().toString());
 358     }
 359
 360     if (defaultBrowser.getText().trim().length() < 1)
 361     {
 362       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 363     }
 364     else
 365     {
 366       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 367               defaultBrowser.getText());
 368     }
 369
 370     jalview.util.BrowserLauncher.resetBrowser();
 371
 372     if (nameLinks.size() > 0)
 373     {
 374       StringBuffer links = new StringBuffer();
 375       sequenceURLLinks = new Vector();
 376       for (int i = 0; i < nameLinks.size(); i++)
 377       {
 378         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 379                 + urlLinks.elementAt(i));
 380         links.append(sequenceURLLinks.elementAt(i).toString());
 381         links.append("|");
 382       }
 383       // remove last "|"
 384       links.setLength(links.length() - 1);
 385       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 386               links.toString());
 387     }
 388     else
 389     {
 390       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 391     }
 392
 393     Cache.applicationProperties.setProperty("USE_PROXY",
 394             Boolean.toString(useProxy.isSelected()));
 395
 396     if (proxyServerTB.getText().trim().length() < 1)
 397     {
 398       Cache.applicationProperties.remove("PROXY_SERVER");
 399     }
 400     else
 401     {
 402       Cache.applicationProperties.setProperty("PROXY_SERVER",
 403               proxyServerTB.getText());
 404     }
 405
 406     if (proxyPortTB.getText().trim().length() < 1)
 407     {
 408       Cache.applicationProperties.remove("PROXY_PORT");
 409     }
 410     else
 411     {
 412       Cache.applicationProperties.setProperty("PROXY_PORT",
 413               proxyPortTB.getText());
 414     }
 415
 416     if (useProxy.isSelected())
 417     {
 418       System.setProperty("http.proxyHost", proxyServerTB.getText());
 419       System.setProperty("http.proxyPort", proxyPortTB.getText());
 420     }
 421     else
 422     {
 423       System.setProperty("http.proxyHost", "");
 424       System.setProperty("http.proxyPort", "");
 425     }
 426     Cache.setProperty("VERSION_CHECK",
 427             Boolean.toString(versioncheck.isSelected()));
 428     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 429     {
 430       // default is false - we only set this if the user has actively agreed
 431       Cache.setProperty("USAGESTATS",
 432               Boolean.toString(usagestats.isSelected()));
 433     }
 434     if (!questionnaire.isSelected())
 435     {
 436       Cache.setProperty("NOQUESTIONNAIRES", "true");
 437     }
 438     else
 439     {
 440       // special - made easy to edit a property file to disable questionnaires
 441       // by just adding the given line
 442       Cache.removeProperty("NOQUESTIONNAIRES");
 443     }
 444     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 445             Boolean.toString(blcjv.isSelected()));
 446     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 447             Boolean.toString(clustaljv.isSelected()));
 448     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 449             Boolean.toString(fastajv.isSelected()));
 450     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 451             Boolean.toString(msfjv.isSelected()));
 452     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 453             Boolean.toString(pfamjv.isSelected()));
 454     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 455             Boolean.toString(pileupjv.isSelected()));
 456     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 457             Boolean.toString(pirjv.isSelected()));
 458     Cache.applicationProperties.setProperty("PIR_MODELLER",
 459             Boolean.toString(modellerOutput.isSelected()));
 460     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 461
 462     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 463             Boolean.toString(autoIdWidth.isSelected()));
 464     userIdWidth_actionPerformed();
 465     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 466             userIdWidth.getText());
 467
 468     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 469             Boolean.toString(autoCalculateConsCheck.isSelected()));
 470     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 471             Boolean.toString(sortByTree.isSelected()));
 472     Cache.applicationProperties.setProperty("PAD_GAPS",
 473             Boolean.toString(padGaps.isSelected()));
 474
 475     dasSource.saveProperties(Cache.applicationProperties);
 476     wsPrefs.updateAndRefreshWsMenuConfig(false);
 477     Cache.saveProperties();
 478     try
 479     {
 480       frame.setClosed(true);
 481     } catch (Exception ex)
 482     {
 483     }
 484   }
 485
 486   /**
 487    * DOCUMENT ME!
 488    */
 489   public void startupFileTextfield_mouseClicked()
 490   {
 491     JalviewFileChooser chooser = new JalviewFileChooser(
 492             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 493             new String[]
 494             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 495             new String[]
 496             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 497             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 498     chooser.setFileView(new JalviewFileView());
 499     chooser.setDialogTitle("Select startup file");
 500
 501     int value = chooser.showOpenDialog(this);
 502
 503     if (value == JalviewFileChooser.APPROVE_OPTION)
 504     {
 505       jalview.bin.Cache.applicationProperties.setProperty(
 506               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 507       startupFileTextfield.setText(chooser.getSelectedFile()
 508               .getAbsolutePath());
 509     }
 510   }
 511
 512   /**
 513    * DOCUMENT ME!
 514    *
 515    * @param e
 516    *          DOCUMENT ME!
 517    */
 518   public void cancel_actionPerformed(ActionEvent e)
 519   {
 520     try
 521     {
 522       wsPrefs.updateWsMenuConfig(true);
 523       wsPrefs.refreshWs_actionPerformed(e);
 524       frame.setClosed(true);
 525     } catch (Exception ex)
 526     {
 527     }
 528   }
 529
 530   /**
 531    * DOCUMENT ME!
 532    *
 533    * @param e
 534    *          DOCUMENT ME!
 535    */
 536   public void annotations_actionPerformed(ActionEvent e)
 537   {
 538     conservation.setEnabled(annotations.isSelected());
 539     quality.setEnabled(annotations.isSelected());
 540     identity.setEnabled(annotations.isSelected());
 541     showGroupConsensus.setEnabled(annotations.isSelected());
 542     showGroupConservation.setEnabled(annotations.isSelected());
 543     showConsensHistogram.setEnabled(annotations.isSelected()
 544             && (identity.isSelected() || showGroupConsensus.isSelected()));
 545     showConsensLogo.setEnabled(annotations.isSelected()
 546             && (identity.isSelected() || showGroupConsensus.isSelected()));
 547   }
 548
 549   public void newLink_actionPerformed(ActionEvent e)
 550   {
 551
 552     GSequenceLink link = new GSequenceLink();
 553     boolean valid = false;
 554     while (!valid)
 555     {
 556       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 557               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 558               null) == JOptionPane.OK_OPTION)
 559       {
 560         if (link.checkValid())
 561         {
 562           nameLinks.addElement(link.getName());
 563           urlLinks.addElement(link.getURL());
 564           updateLinkData();
 565           valid = true;
 566         }
 567       }
 568       else
 569       {
 570         break;
 571       }
 572     }
 573   }
 574
 575   public void editLink_actionPerformed(ActionEvent e)
 576   {
 577     GSequenceLink link = new GSequenceLink();
 578
 579     int index = linkNameList.getSelectedIndex();
 580     if (index == -1)
 581     {
 582       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 583               "No link selected!", "No link selected",
 584               JOptionPane.WARNING_MESSAGE);
 585       return;
 586     }
 587
 588     link.setName(nameLinks.elementAt(index).toString());
 589     link.setURL(urlLinks.elementAt(index).toString());
 590
 591     boolean valid = false;
 592     while (!valid)
 593     {
 594
 595       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 596               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 597               null) == JOptionPane.OK_OPTION)
 598       {
 599         if (link.checkValid())
 600         {
 601           nameLinks.setElementAt(link.getName(), index);
 602           urlLinks.setElementAt(link.getURL(), index);
 603           updateLinkData();
 604           valid = true;
 605         }
 606       }
 607
 608       else
 609       {
 610         break;
 611       }
 612     }
 613   }
 614
 615   public void deleteLink_actionPerformed(ActionEvent e)
 616   {
 617     int index = linkNameList.getSelectedIndex();
 618     if (index == -1)
 619     {
 620       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 621               "No link selected!", "No link selected",
 622               JOptionPane.WARNING_MESSAGE);
 623       return;
 624     }
 625     nameLinks.removeElementAt(index);
 626     urlLinks.removeElementAt(index);
 627     updateLinkData();
 628   }
 629
 630   void updateLinkData()
 631   {
 632     linkNameList.setListData(nameLinks);
 633     linkURLList.setListData(urlLinks);
 634   }
 635
 636   public void defaultBrowser_mouseClicked(MouseEvent e)
 637   {
 638     JFileChooser chooser = new JFileChooser(".");
 639     chooser.setDialogTitle("Select default web browser");
 640
 641     int value = chooser.showOpenDialog(this);
 642
 643     if (value == JFileChooser.APPROVE_OPTION)
 644     {
 645       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 646     }
 647
 648   }
 649
 650   /*
 651    * (non-Javadoc)
 652    *
 653    * @see
 654    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 655    * .ActionEvent)
 656    */
 657   protected void showunconserved_actionPerformed(ActionEvent e)
 658   {
 659     // TODO Auto-generated method stub
 660     super.showunconserved_actionPerformed(e);
 661   }
 662
 663   private void jbInit() throws Exception
 664   {
 665   }
 666
 667   public static Collection getGroupURLLinks()
 668   {
 669     return groupURLLinks;
 670   }
 671
 672   public void minColour_actionPerformed()
 673   {
 674     Color col = JColorChooser.showDialog(this,
 675             "Select Colour for Minimum Value", minColour.getBackground());
 676     if (col != null)
 677     {
 678       minColour.setBackground(col);
 679     }
 680     minColour.repaint();
 681   }
 682
 683   public void maxColour_actionPerformed()
 684   {
 685     Color col = JColorChooser.showDialog(this,
 686             "Select Colour for Maximum Value", maxColour.getBackground());
 687     if (col != null)
 688     {
 689       maxColour.setBackground(col);
 690     }
 691     maxColour.repaint();
 692   }
 693
 694   @Override
 695   protected void userIdWidth_actionPerformed()
 696   {
 697     try
 698     {
 699       String val = userIdWidth.getText().trim();
 700       if (val.length() > 0)
 701       {
 702         Integer iw = Integer.parseInt(val);
 703         if (iw.intValue() < 12)
 704         {
 705           throw new NumberFormatException();
 706         }
 707         userIdWidth.setText(iw.toString());
 708       }
 709     } catch (NumberFormatException x)
 710     {
 711       JOptionPane
 712               .showInternalMessageDialog(
 713                       Desktop.desktop,
 714                       "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
 715                       "Invalid ID Column width",
 716                       JOptionPane.WARNING_MESSAGE);
 717       userIdWidth.setText("");
 718     }
 719   }
 720
 721   @Override
 722   protected void autoIdWidth_actionPerformed()
 723   {
 724     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 725     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 726   }
 727
 728 }