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
  32 /**
  33  * DOCUMENT ME!
  34  *
  35  * @author $author$
  36  * @version $Revision$
  37  */
  38 public class Preferences extends GPreferences
  39 {
  40
  41   /**
  42    * Holds name and link separated with | character. Sequence ID must be
  43    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  44    */
  45   public static Vector sequenceURLLinks;
  46
  47   /**
  48    * Holds name and link separated with | character. Sequence IDS and Sequences
  49    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  50    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  51    * 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                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
  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("/=$") == -1)
  74         {
  75           url = url + "|" + st.nextToken();
  76         }
  77         sequenceURLLinks.addElement(name + "|" + url);
  78       }
  79     } catch (Exception ex)
  80     {
  81       System.out.println(ex + "\nError parsing sequence links");
  82     }
  83     {
  84       // upgrade old SRS link
  85       int srsPos = sequenceURLLinks
  86               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  87       if (srsPos > -1)
  88       {
  89         sequenceURLLinks.setElementAt(
  90                 "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
  91                 srsPos);
  92       }
  93     }
  94
  95     /**
  96      * TODO: reformulate groupURL encoding so two or more can be stored in the
  97      * .properties file as '|' separated strings
  98      */
  99
 100     groupURLLinks = new Vector();
 101     // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
 102     // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
 103
 104   }
 105
 106   Vector nameLinks, urlLinks;
 107
 108   JInternalFrame frame;
 109
 110   DasSourceBrowser dasSource;
 111
 112   private WsPreferences wsPrefs;
 113
 114   /**
 115    * Creates a new Preferences object.
 116    */
 117   public Preferences()
 118   {
 119
 120     frame = new JInternalFrame();
 121     frame.setContentPane(this);
 122     dasSource = new DasSourceBrowser();
 123     dasPanel.add(dasSource, BorderLayout.CENTER);
 124     wsPrefs = new WsPreferences();
 125     wsPanel.add(wsPrefs, BorderLayout.CENTER);
 126     int width = 500, height = 420;
 127     if (new jalview.util.Platform().isAMac())
 128     {
 129       width = 570;
 130       height = 460;
 131     }
 132
 133     Desktop.addInternalFrame(frame, "Preferences", width, height);
 134     frame.setMinimumSize(new Dimension(width, height));
 135
 136     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 137     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 138     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 139     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 140
 141     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 142     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 143     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 144     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 145     showUnconserved
 146             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 147     showNpTooltip.setSelected(Cache
 148             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 149     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 150             true));
 151     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 152     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 153     {
 154       colour.addItem(ColourSchemeProperty.getColourName(i));
 155     }
 156
 157     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 158
 159     colour.setSelectedItem(string);
 160
 161     /**
 162      * default min-max colours for annotation shading
 163      */
 164     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 165             Color.orange));
 166     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 167             Color.red));
 168
 169     String[] fonts = java.awt.GraphicsEnvironment
 170             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 171
 172     for (int i = 0; i < fonts.length; i++)
 173     {
 174       fontNameCB.addItem(fonts[i]);
 175     }
 176
 177     for (int i = 1; i < 31; i++)
 178     {
 179       fontSizeCB.addItem(i + "");
 180     }
 181
 182     fontStyleCB.addItem("plain");
 183     fontStyleCB.addItem("bold");
 184     fontStyleCB.addItem("italic");
 185
 186     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 187     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 188     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 189             + ""));
 190
 191     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 192
 193     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 194
 195     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 196
 197     gapSymbolCB.addItem("-");
 198     gapSymbolCB.addItem(".");
 199
 200     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 201
 202     startupCheckbox
 203             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 204     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 205             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 206                     + "/examples/exampleFile_2_3.jar"));
 207
 208     sortby.addItem("No sort");
 209     sortby.addItem("Id");
 210     sortby.addItem("Pairwise Identity");
 211     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 212
 213     epsRendering.addItem("Prompt each time");
 214     epsRendering.addItem("Lineart");
 215     epsRendering.addItem("Text");
 216     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 217             "Prompt each time"));
 218     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 219     userIdWidth.setEnabled(autoIdWidth.isSelected());
 220     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 221     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 222     userIdWidth.setText(wi == null ? "" : wi.toString());
 223     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 224     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 225     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 226     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 227     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 228     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 229     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 230
 231     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 232
 233     autoCalculateConsCheck.setSelected(Cache.getDefault(
 234             "AUTO_CALC_CONSENSUS", true));
 235     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 236             false));
 237     showGroupConservation.setSelected(Cache.getDefault(
 238             "SHOW_GROUP_CONSERVATION", false));
 239     showConsensHistogram.setSelected(Cache.getDefault(
 240             "SHOW_CONSENSUS_HISTOGRAM", true));
 241     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 242             false));
 243
 244     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 245
 246     /***************************************************************************
 247      * Set up Connections
 248      */
 249     nameLinks = new Vector();
 250     urlLinks = new Vector();
 251     for (int i = 0; i < sequenceURLLinks.size(); i++)
 252     {
 253       String link = sequenceURLLinks.elementAt(i).toString();
 254       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 255       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 256     }
 257
 258     updateLinkData();
 259
 260     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 261     proxyServerTB.setEnabled(useProxy.isSelected());
 262     proxyPortTB.setEnabled(useProxy.isSelected());
 263     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 264     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 265
 266     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 267
 268     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 269     questionnaire
 270             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 271                                                                          // antisense
 272                                                                          // here
 273     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 274                                                                        // is
 275                                                                        // true
 276     annotations_actionPerformed(null); // update the display of the annotation
 277                                        // settings
 278     try
 279     {
 280       jbInit();
 281     } catch (Exception ex)
 282     {
 283       ex.printStackTrace();
 284     }
 285
 286   }
 287
 288   /**
 289    * DOCUMENT ME!
 290    *
 291    * @param e
 292    *          DOCUMENT ME!
 293    */
 294   public void ok_actionPerformed(ActionEvent e)
 295   {
 296
 297     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 298             Boolean.toString(seqLimit.isSelected()));
 299     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 300             Boolean.toString(rightAlign.isSelected()));
 301     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 302             Boolean.toString(fullScreen.isSelected()));
 303     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 304             Boolean.toString(openoverv.isSelected()));
 305     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 306             Boolean.toString(annotations.isSelected()));
 307     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 308             Boolean.toString(conservation.isSelected()));
 309     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 310             Boolean.toString(quality.isSelected()));
 311     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 312             Boolean.toString(identity.isSelected()));
 313
 314     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 315             .getSelectedItem().toString());
 316     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 317             .getSelectedItem().toString());
 318
 319     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 320             .getSelectedItem().toString());
 321     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 322             .getSelectedItem().toString());
 323     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 324             .getSelectedItem().toString());
 325
 326     Cache.applicationProperties.setProperty("ID_ITALICS",
 327             Boolean.toString(idItalics.isSelected()));
 328     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 329             Boolean.toString(showUnconserved.isSelected()));
 330     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 331             Boolean.toString(showGroupConsensus.isSelected()));
 332     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 333             Boolean.toString(showGroupConservation.isSelected()));
 334     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 335             Boolean.toString(showConsensHistogram.isSelected()));
 336     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 337             Boolean.toString(showConsensLogo.isSelected()));
 338     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 339             Boolean.toString(smoothFont.isSelected()));
 340     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 341             Boolean.toString(showNpTooltip.isSelected()));
 342     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 343             Boolean.toString(showDbRefTooltip.isSelected()));
 344
 345     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 346             Boolean.toString(wrap.isSelected()));
 347
 348     Cache.applicationProperties.setProperty("STARTUP_FILE",
 349             startupFileTextfield.getText());
 350     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 351             Boolean.toString(startupCheckbox.isSelected()));
 352
 353     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 354             .getSelectedItem().toString());
 355
 356     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 357             minColour.getBackground());
 358     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 359             maxColour.getBackground());
 360
 361     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 362     {
 363       Cache.applicationProperties.remove("EPS_RENDERING");
 364     }
 365     else
 366     {
 367       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 368               .getSelectedItem().toString());
 369     }
 370
 371     if (defaultBrowser.getText().trim().length() < 1)
 372     {
 373       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 374     }
 375     else
 376     {
 377       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 378               defaultBrowser.getText());
 379     }
 380
 381     jalview.util.BrowserLauncher.resetBrowser();
 382
 383     if (nameLinks.size() > 0)
 384     {
 385       StringBuffer links = new StringBuffer();
 386       sequenceURLLinks = new Vector();
 387       for (int i = 0; i < nameLinks.size(); i++)
 388       {
 389         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 390                 + urlLinks.elementAt(i));
 391         links.append(sequenceURLLinks.elementAt(i).toString());
 392         links.append("|");
 393       }
 394       // remove last "|"
 395       links.setLength(links.length() - 1);
 396       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 397               links.toString());
 398     }
 399     else
 400     {
 401       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 402     }
 403
 404     Cache.applicationProperties.setProperty("USE_PROXY",
 405             Boolean.toString(useProxy.isSelected()));
 406
 407     if (proxyServerTB.getText().trim().length() < 1)
 408     {
 409       Cache.applicationProperties.remove("PROXY_SERVER");
 410     }
 411     else
 412     {
 413       Cache.applicationProperties.setProperty("PROXY_SERVER",
 414               proxyServerTB.getText());
 415     }
 416
 417     if (proxyPortTB.getText().trim().length() < 1)
 418     {
 419       Cache.applicationProperties.remove("PROXY_PORT");
 420     }
 421     else
 422     {
 423       Cache.applicationProperties.setProperty("PROXY_PORT",
 424               proxyPortTB.getText());
 425     }
 426
 427     if (useProxy.isSelected())
 428     {
 429       System.setProperty("http.proxyHost", proxyServerTB.getText());
 430       System.setProperty("http.proxyPort", proxyPortTB.getText());
 431     }
 432     else
 433     {
 434       System.setProperty("http.proxyHost", "");
 435       System.setProperty("http.proxyPort", "");
 436     }
 437     Cache.setProperty("VERSION_CHECK",
 438             Boolean.toString(versioncheck.isSelected()));
 439     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 440     {
 441       // default is false - we only set this if the user has actively agreed
 442       Cache.setProperty("USAGESTATS",
 443               Boolean.toString(usagestats.isSelected()));
 444     }
 445     if (!questionnaire.isSelected())
 446     {
 447       Cache.setProperty("NOQUESTIONNAIRES", "true");
 448     }
 449     else
 450     {
 451       // special - made easy to edit a property file to disable questionnaires
 452       // by just adding the given line
 453       Cache.removeProperty("NOQUESTIONNAIRES");
 454     }
 455     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 456             Boolean.toString(blcjv.isSelected()));
 457     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 458             Boolean.toString(clustaljv.isSelected()));
 459     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 460             Boolean.toString(fastajv.isSelected()));
 461     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 462             Boolean.toString(msfjv.isSelected()));
 463     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 464             Boolean.toString(pfamjv.isSelected()));
 465     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 466             Boolean.toString(pileupjv.isSelected()));
 467     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 468             Boolean.toString(pirjv.isSelected()));
 469     Cache.applicationProperties.setProperty("PIR_MODELLER",
 470             Boolean.toString(modellerOutput.isSelected()));
 471     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 472
 473     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 474             Boolean.toString(autoIdWidth.isSelected()));
 475     userIdWidth_actionPerformed();
 476     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 477             userIdWidth.getText());
 478
 479     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 480             Boolean.toString(autoCalculateConsCheck.isSelected()));
 481     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 482             Boolean.toString(sortByTree.isSelected()));
 483     Cache.applicationProperties.setProperty("PAD_GAPS",
 484             Boolean.toString(padGaps.isSelected()));
 485
 486     dasSource.saveProperties(Cache.applicationProperties);
 487     wsPrefs.updateAndRefreshWsMenuConfig(false);
 488     Cache.saveProperties();
 489     try
 490     {
 491       frame.setClosed(true);
 492     } catch (Exception ex)
 493     {
 494     }
 495   }
 496
 497   /**
 498    * DOCUMENT ME!
 499    */
 500   public void startupFileTextfield_mouseClicked()
 501   {
 502     JalviewFileChooser chooser = new JalviewFileChooser(
 503             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 504             new String[]
 505             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 506             new String[]
 507             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 508             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 509     chooser.setFileView(new JalviewFileView());
 510     chooser.setDialogTitle("Select startup file");
 511
 512     int value = chooser.showOpenDialog(this);
 513
 514     if (value == JalviewFileChooser.APPROVE_OPTION)
 515     {
 516       jalview.bin.Cache.applicationProperties.setProperty(
 517               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 518       startupFileTextfield.setText(chooser.getSelectedFile()
 519               .getAbsolutePath());
 520     }
 521   }
 522
 523   /**
 524    * DOCUMENT ME!
 525    *
 526    * @param e
 527    *          DOCUMENT ME!
 528    */
 529   public void cancel_actionPerformed(ActionEvent e)
 530   {
 531     try
 532     {
 533       wsPrefs.updateWsMenuConfig(true);
 534       wsPrefs.refreshWs_actionPerformed(e);
 535       frame.setClosed(true);
 536     } catch (Exception ex)
 537     {
 538     }
 539   }
 540
 541   /**
 542    * DOCUMENT ME!
 543    *
 544    * @param e
 545    *          DOCUMENT ME!
 546    */
 547   public void annotations_actionPerformed(ActionEvent e)
 548   {
 549     conservation.setEnabled(annotations.isSelected());
 550     quality.setEnabled(annotations.isSelected());
 551     identity.setEnabled(annotations.isSelected());
 552     showGroupConsensus.setEnabled(annotations.isSelected());
 553     showGroupConservation.setEnabled(annotations.isSelected());
 554     showConsensHistogram.setEnabled(annotations.isSelected()
 555             && (identity.isSelected() || showGroupConsensus.isSelected()));
 556     showConsensLogo.setEnabled(annotations.isSelected()
 557             && (identity.isSelected() || showGroupConsensus.isSelected()));
 558   }
 559
 560   public void newLink_actionPerformed(ActionEvent e)
 561   {
 562
 563     GSequenceLink link = new GSequenceLink();
 564     boolean valid = false;
 565     while (!valid)
 566     {
 567       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 568               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 569               null) == JOptionPane.OK_OPTION)
 570       {
 571         if (link.checkValid())
 572         {
 573           nameLinks.addElement(link.getName());
 574           urlLinks.addElement(link.getURL());
 575           updateLinkData();
 576           valid = true;
 577         }
 578       }
 579       else
 580       {
 581         break;
 582       }
 583     }
 584   }
 585
 586   public void editLink_actionPerformed(ActionEvent e)
 587   {
 588     GSequenceLink link = new GSequenceLink();
 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
 599     link.setName(nameLinks.elementAt(index).toString());
 600     link.setURL(urlLinks.elementAt(index).toString());
 601
 602     boolean valid = false;
 603     while (!valid)
 604     {
 605
 606       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 607               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 608               null) == JOptionPane.OK_OPTION)
 609       {
 610         if (link.checkValid())
 611         {
 612           nameLinks.setElementAt(link.getName(), index);
 613           urlLinks.setElementAt(link.getURL(), index);
 614           updateLinkData();
 615           valid = true;
 616         }
 617       }
 618
 619       else
 620       {
 621         break;
 622       }
 623     }
 624   }
 625
 626   public void deleteLink_actionPerformed(ActionEvent e)
 627   {
 628     int index = linkNameList.getSelectedIndex();
 629     if (index == -1)
 630     {
 631       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 632               "No link selected!", "No link selected",
 633               JOptionPane.WARNING_MESSAGE);
 634       return;
 635     }
 636     nameLinks.removeElementAt(index);
 637     urlLinks.removeElementAt(index);
 638     updateLinkData();
 639   }
 640
 641   void updateLinkData()
 642   {
 643     linkNameList.setListData(nameLinks);
 644     linkURLList.setListData(urlLinks);
 645   }
 646
 647   public void defaultBrowser_mouseClicked(MouseEvent e)
 648   {
 649     JFileChooser chooser = new JFileChooser(".");
 650     chooser.setDialogTitle("Select default web browser");
 651
 652     int value = chooser.showOpenDialog(this);
 653
 654     if (value == JFileChooser.APPROVE_OPTION)
 655     {
 656       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 657     }
 658
 659   }
 660
 661   /*
 662    * (non-Javadoc)
 663    *
 664    * @see
 665    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 666    * .ActionEvent)
 667    */
 668   protected void showunconserved_actionPerformed(ActionEvent e)
 669   {
 670     // TODO Auto-generated method stub
 671     super.showunconserved_actionPerformed(e);
 672   }
 673
 674   private void jbInit() throws Exception
 675   {
 676   }
 677
 678   public static Collection getGroupURLLinks()
 679   {
 680     return groupURLLinks;
 681   }
 682
 683   public void minColour_actionPerformed()
 684   {
 685     Color col = JColorChooser.showDialog(this,
 686             "Select Colour for Minimum Value", minColour.getBackground());
 687     if (col != null)
 688     {
 689       minColour.setBackground(col);
 690     }
 691     minColour.repaint();
 692   }
 693
 694   public void maxColour_actionPerformed()
 695   {
 696     Color col = JColorChooser.showDialog(this,
 697             "Select Colour for Maximum Value", maxColour.getBackground());
 698     if (col != null)
 699     {
 700       maxColour.setBackground(col);
 701     }
 702     maxColour.repaint();
 703   }
 704
 705   @Override
 706   protected void userIdWidth_actionPerformed()
 707   {
 708     try
 709     {
 710       String val = userIdWidth.getText().trim();
 711       if (val.length() > 0)
 712       {
 713         Integer iw = Integer.parseInt(val);
 714         if (iw.intValue() < 12)
 715         {
 716           throw new NumberFormatException();
 717         }
 718         userIdWidth.setText(iw.toString());
 719       }
 720     } catch (NumberFormatException x)
 721     {
 722       JOptionPane
 723               .showInternalMessageDialog(
 724                       Desktop.desktop,
 725                       "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
 726                       "Invalid ID Column width",
 727                       JOptionPane.WARNING_MESSAGE);
 728       userIdWidth.setText("");
 729     }
 730   }
 731
 732   @Override
 733   protected void autoIdWidth_actionPerformed()
 734   {
 735     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 736     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 737   }
 738
 739 }