src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27
  28 import javax.swing.*;
  29
  30 import jalview.bin.*;
  31 import jalview.io.*;
  32 import jalview.jbgui.*;
  33 import jalview.schemes.*;
  34 import jalview.util.MessageManager;
  35
  36 /**
  37  * DOCUMENT ME!
  38  *
  39  * @author $author$
  40  * @version $Revision$
  41  */
  42 public class Preferences extends GPreferences
  43 {
  44
  45   /**
  46    * Holds name and link separated with | character. Sequence ID must be
  47    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  48    */
  49   public static Vector sequenceURLLinks;
  50
  51   /**
  52    * Holds name and link separated with | character. Sequence IDS and Sequences
  53    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  54    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  55    * for first and second token specified after a pipe character at end |,|.
  56    * (TODO: proper escape for using | to separate ids or sequences
  57    */
  58
  59   public static Vector groupURLLinks;
  60   static
  61   {
  62     String string = Cache
  63             .getDefault(
  64                     "SEQUENCE_LINKS",
  65                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
  66     sequenceURLLinks = new Vector();
  67
  68     try
  69     {
  70       StringTokenizer st = new StringTokenizer(string, "|");
  71       while (st.hasMoreElements())
  72       {
  73         String name = st.nextToken();
  74         String url = st.nextToken();
  75         // check for '|' within a regex
  76         int rxstart = url.indexOf("$SEQUENCE_ID$");
  77         while (rxstart == -1 && url.indexOf("/=$") == -1)
  78         {
  79           url = url + "|" + st.nextToken();
  80         }
  81         sequenceURLLinks.addElement(name + "|" + url);
  82       }
  83     } catch (Exception ex)
  84     {
  85       System.out.println(ex + "\nError parsing sequence links");
  86     }
  87     {
  88       // upgrade old SRS link
  89       int srsPos = sequenceURLLinks
  90               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  91       if (srsPos > -1)
  92       {
  93         sequenceURLLinks
  94                 .setElementAt(
  95                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
  96                         srsPos);
  97       }
  98     }
  99
 100     /**
 101      * TODO: reformulate groupURL encoding so two or more can be stored in the
 102      * .properties file as '|' separated strings
 103      */
 104
 105     groupURLLinks = new Vector();
 106   }
 107
 108   Vector nameLinks, urlLinks;
 109
 110   JInternalFrame frame;
 111
 112   DasSourceBrowser dasSource;
 113
 114   private WsPreferences wsPrefs;
 115
 116   /**
 117    * Creates a new Preferences object.
 118    */
 119   public Preferences()
 120   {
 121
 122     frame = new JInternalFrame();
 123     frame.setContentPane(this);
 124     dasSource = new DasSourceBrowser();
 125     dasPanel.add(dasSource, BorderLayout.CENTER);
 126     wsPrefs = new WsPreferences();
 127     wsPanel.add(wsPrefs, BorderLayout.CENTER);
 128     int width = 500, height = 420;
 129     if (new jalview.util.Platform().isAMac())
 130     {
 131       width = 570;
 132       height = 460;
 133     }
 134
 135     Desktop.addInternalFrame(frame,
 136             MessageManager.getString("label.preferences"), width, height);
 137     frame.setMinimumSize(new Dimension(width, height));
 138
 139     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 140     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 141     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 142     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 143
 144     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 145     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 146     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 147     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 148     showUnconserved
 149             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 150     showNpTooltip.setSelected(Cache
 151             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 152     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 153             true));
 154     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 155     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 156     {
 157       colour.addItem(ColourSchemeProperty.getColourName(i));
 158     }
 159
 160     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 161
 162     colour.setSelectedItem(string);
 163
 164     /**
 165      * default min-max colours for annotation shading
 166      */
 167     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 168             Color.orange));
 169     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 170             Color.red));
 171
 172     String[] fonts = java.awt.GraphicsEnvironment
 173             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 174
 175     for (int i = 0; i < fonts.length; i++)
 176     {
 177       fontNameCB.addItem(fonts[i]);
 178     }
 179
 180     for (int i = 1; i < 31; i++)
 181     {
 182       fontSizeCB.addItem(i + "");
 183     }
 184
 185     fontStyleCB.addItem("plain");
 186     fontStyleCB.addItem("bold");
 187     fontStyleCB.addItem("italic");
 188
 189     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 190     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 191     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 192             + ""));
 193
 194     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 195
 196     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 197
 198     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 199
 200     gapSymbolCB.addItem("-");
 201     gapSymbolCB.addItem(".");
 202
 203     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 204
 205     startupCheckbox
 206             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 207     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 208             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 209                     + "/examples/exampleFile_2_3.jar"));
 210
 211     sortby.addItem("No sort");
 212     sortby.addItem("Id");
 213     sortby.addItem("Pairwise Identity");
 214     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 215
 216     epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
 217     epsRendering.addItem(MessageManager.getString("label.lineart"));
 218     epsRendering.addItem(MessageManager.getString("action.text"));
 219     epsRendering.setSelectedIndex(0);
 220     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 221     userIdWidth.setEnabled(autoIdWidth.isSelected());
 222     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 223     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 224     userIdWidth.setText(wi == null ? "" : wi.toString());
 225     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 226     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 227     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 228     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 229     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 230     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 231     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 232
 233     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 234
 235     autoCalculateConsCheck.setSelected(Cache.getDefault(
 236             "AUTO_CALC_CONSENSUS", true));
 237     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 238             false));
 239     showGroupConservation.setSelected(Cache.getDefault(
 240             "SHOW_GROUP_CONSERVATION", false));
 241     showConsensHistogram.setSelected(Cache.getDefault(
 242             "SHOW_CONSENSUS_HISTOGRAM", true));
 243     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 244             false));
 245
 246     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 247
 248     /***************************************************************************
 249      * Set up Connections
 250      */
 251     nameLinks = new Vector();
 252     urlLinks = new Vector();
 253     for (int i = 0; i < sequenceURLLinks.size(); i++)
 254     {
 255       String link = sequenceURLLinks.elementAt(i).toString();
 256       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 257       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 258     }
 259
 260     updateLinkData();
 261
 262     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 263     proxyServerTB.setEnabled(useProxy.isSelected());
 264     proxyPortTB.setEnabled(useProxy.isSelected());
 265     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 266     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 267
 268     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 269
 270     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 271     questionnaire
 272             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 273                                                                          // antisense
 274                                                                          // here
 275     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 276                                                                        // is
 277                                                                        // true
 278     annotations_actionPerformed(null); // update the display of the annotation
 279                                        // settings
 280     try
 281     {
 282       jbInit();
 283     } catch (Exception ex)
 284     {
 285       ex.printStackTrace();
 286     }
 287
 288   }
 289
 290   /**
 291    * DOCUMENT ME!
 292    *
 293    * @param e
 294    *          DOCUMENT ME!
 295    */
 296   public void ok_actionPerformed(ActionEvent e)
 297   {
 298
 299     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 300             Boolean.toString(seqLimit.isSelected()));
 301     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 302             Boolean.toString(rightAlign.isSelected()));
 303     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 304             Boolean.toString(fullScreen.isSelected()));
 305     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 306             Boolean.toString(openoverv.isSelected()));
 307     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 308             Boolean.toString(annotations.isSelected()));
 309     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 310             Boolean.toString(conservation.isSelected()));
 311     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 312             Boolean.toString(quality.isSelected()));
 313     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 314             Boolean.toString(identity.isSelected()));
 315
 316     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 317             .getSelectedItem().toString());
 318     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 319             .getSelectedItem().toString());
 320
 321     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 322             .getSelectedItem().toString());
 323     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 324             .getSelectedItem().toString());
 325     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 326             .getSelectedItem().toString());
 327
 328     Cache.applicationProperties.setProperty("ID_ITALICS",
 329             Boolean.toString(idItalics.isSelected()));
 330     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 331             Boolean.toString(showUnconserved.isSelected()));
 332     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 333             Boolean.toString(showGroupConsensus.isSelected()));
 334     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 335             Boolean.toString(showGroupConservation.isSelected()));
 336     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 337             Boolean.toString(showConsensHistogram.isSelected()));
 338     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 339             Boolean.toString(showConsensLogo.isSelected()));
 340     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 341             Boolean.toString(smoothFont.isSelected()));
 342     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 343             Boolean.toString(showNpTooltip.isSelected()));
 344     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 345             Boolean.toString(showDbRefTooltip.isSelected()));
 346
 347     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 348             Boolean.toString(wrap.isSelected()));
 349
 350     Cache.applicationProperties.setProperty("STARTUP_FILE",
 351             startupFileTextfield.getText());
 352     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 353             Boolean.toString(startupCheckbox.isSelected()));
 354
 355     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 356             .getSelectedItem().toString());
 357
 358     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 359             minColour.getBackground());
 360     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 361             maxColour.getBackground());
 362
 363     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 364     {
 365       Cache.applicationProperties.remove("EPS_RENDERING");
 366     }
 367     else
 368     {
 369       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 370               .getSelectedItem().toString());
 371     }
 372
 373     if (defaultBrowser.getText().trim().length() < 1)
 374     {
 375       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 376     }
 377     else
 378     {
 379       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 380               defaultBrowser.getText());
 381     }
 382
 383     jalview.util.BrowserLauncher.resetBrowser();
 384
 385     if (nameLinks.size() > 0)
 386     {
 387       StringBuffer links = new StringBuffer();
 388       sequenceURLLinks = new Vector();
 389       for (int i = 0; i < nameLinks.size(); i++)
 390       {
 391         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 392                 + urlLinks.elementAt(i));
 393         links.append(sequenceURLLinks.elementAt(i).toString());
 394         links.append("|");
 395       }
 396       // remove last "|"
 397       links.setLength(links.length() - 1);
 398       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 399               links.toString());
 400     }
 401     else
 402     {
 403       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 404     }
 405
 406     Cache.applicationProperties.setProperty("USE_PROXY",
 407             Boolean.toString(useProxy.isSelected()));
 408
 409     if (proxyServerTB.getText().trim().length() < 1)
 410     {
 411       Cache.applicationProperties.remove("PROXY_SERVER");
 412     }
 413     else
 414     {
 415       Cache.applicationProperties.setProperty("PROXY_SERVER",
 416               proxyServerTB.getText());
 417     }
 418
 419     if (proxyPortTB.getText().trim().length() < 1)
 420     {
 421       Cache.applicationProperties.remove("PROXY_PORT");
 422     }
 423     else
 424     {
 425       Cache.applicationProperties.setProperty("PROXY_PORT",
 426               proxyPortTB.getText());
 427     }
 428
 429     if (useProxy.isSelected())
 430     {
 431       System.setProperty("http.proxyHost", proxyServerTB.getText());
 432       System.setProperty("http.proxyPort", proxyPortTB.getText());
 433     }
 434     else
 435     {
 436       System.setProperty("http.proxyHost", "");
 437       System.setProperty("http.proxyPort", "");
 438     }
 439     Cache.setProperty("VERSION_CHECK",
 440             Boolean.toString(versioncheck.isSelected()));
 441     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 442     {
 443       // default is false - we only set this if the user has actively agreed
 444       Cache.setProperty("USAGESTATS",
 445               Boolean.toString(usagestats.isSelected()));
 446     }
 447     if (!questionnaire.isSelected())
 448     {
 449       Cache.setProperty("NOQUESTIONNAIRES", "true");
 450     }
 451     else
 452     {
 453       // special - made easy to edit a property file to disable questionnaires
 454       // by just adding the given line
 455       Cache.removeProperty("NOQUESTIONNAIRES");
 456     }
 457     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 458             Boolean.toString(blcjv.isSelected()));
 459     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 460             Boolean.toString(clustaljv.isSelected()));
 461     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 462             Boolean.toString(fastajv.isSelected()));
 463     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 464             Boolean.toString(msfjv.isSelected()));
 465     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 466             Boolean.toString(pfamjv.isSelected()));
 467     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 468             Boolean.toString(pileupjv.isSelected()));
 469     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 470             Boolean.toString(pirjv.isSelected()));
 471     Cache.applicationProperties.setProperty("PIR_MODELLER",
 472             Boolean.toString(modellerOutput.isSelected()));
 473     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 474
 475     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 476             Boolean.toString(autoIdWidth.isSelected()));
 477     userIdWidth_actionPerformed();
 478     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 479             userIdWidth.getText());
 480
 481     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 482             Boolean.toString(autoCalculateConsCheck.isSelected()));
 483     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 484             Boolean.toString(sortByTree.isSelected()));
 485     Cache.applicationProperties.setProperty("PAD_GAPS",
 486             Boolean.toString(padGaps.isSelected()));
 487
 488     dasSource.saveProperties(Cache.applicationProperties);
 489     wsPrefs.updateAndRefreshWsMenuConfig(false);
 490     Cache.saveProperties();
 491     try
 492     {
 493       frame.setClosed(true);
 494     } catch (Exception ex)
 495     {
 496     }
 497   }
 498
 499   /**
 500    * DOCUMENT ME!
 501    */
 502   public void startupFileTextfield_mouseClicked()
 503   {
 504     JalviewFileChooser chooser = new JalviewFileChooser(
 505             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 506             new String[]
 507             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 508             new String[]
 509             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 510             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 511     chooser.setFileView(new JalviewFileView());
 512     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 513
 514     int value = chooser.showOpenDialog(this);
 515
 516     if (value == JalviewFileChooser.APPROVE_OPTION)
 517     {
 518       jalview.bin.Cache.applicationProperties.setProperty(
 519               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 520       startupFileTextfield.setText(chooser.getSelectedFile()
 521               .getAbsolutePath());
 522     }
 523   }
 524
 525   /**
 526    * DOCUMENT ME!
 527    *
 528    * @param e
 529    *          DOCUMENT ME!
 530    */
 531   public void cancel_actionPerformed(ActionEvent e)
 532   {
 533     try
 534     {
 535       wsPrefs.updateWsMenuConfig(true);
 536       wsPrefs.refreshWs_actionPerformed(e);
 537       frame.setClosed(true);
 538     } catch (Exception ex)
 539     {
 540     }
 541   }
 542
 543   /**
 544    * DOCUMENT ME!
 545    *
 546    * @param e
 547    *          DOCUMENT ME!
 548    */
 549   public void annotations_actionPerformed(ActionEvent e)
 550   {
 551     conservation.setEnabled(annotations.isSelected());
 552     quality.setEnabled(annotations.isSelected());
 553     identity.setEnabled(annotations.isSelected());
 554     showGroupConsensus.setEnabled(annotations.isSelected());
 555     showGroupConservation.setEnabled(annotations.isSelected());
 556     showConsensHistogram.setEnabled(annotations.isSelected()
 557             && (identity.isSelected() || showGroupConsensus.isSelected()));
 558     showConsensLogo.setEnabled(annotations.isSelected()
 559             && (identity.isSelected() || showGroupConsensus.isSelected()));
 560   }
 561
 562   public void newLink_actionPerformed(ActionEvent e)
 563   {
 564
 565     GSequenceLink link = new GSequenceLink();
 566     boolean valid = false;
 567     while (!valid)
 568     {
 569       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 570               MessageManager.getString("label.new_sequence_url_link"),
 571               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 572       {
 573         if (link.checkValid())
 574         {
 575           nameLinks.addElement(link.getName());
 576           urlLinks.addElement(link.getURL());
 577           updateLinkData();
 578           valid = true;
 579         }
 580       }
 581       else
 582       {
 583         break;
 584       }
 585     }
 586   }
 587
 588   public void editLink_actionPerformed(ActionEvent e)
 589   {
 590     GSequenceLink link = new GSequenceLink();
 591
 592     int index = linkNameList.getSelectedIndex();
 593     if (index == -1)
 594     {
 595       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 596               MessageManager.getString("label.no_link_selected"),
 597               MessageManager.getString("label.no_link_selected"),
 598               JOptionPane.WARNING_MESSAGE);
 599       return;
 600     }
 601
 602     link.setName(nameLinks.elementAt(index).toString());
 603     link.setURL(urlLinks.elementAt(index).toString());
 604
 605     boolean valid = false;
 606     while (!valid)
 607     {
 608
 609       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 610               MessageManager.getString("label.new_sequence_url_link"),
 611               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 612       {
 613         if (link.checkValid())
 614         {
 615           nameLinks.setElementAt(link.getName(), index);
 616           urlLinks.setElementAt(link.getURL(), index);
 617           updateLinkData();
 618           valid = true;
 619         }
 620       }
 621
 622       else
 623       {
 624         break;
 625       }
 626     }
 627   }
 628
 629   public void deleteLink_actionPerformed(ActionEvent e)
 630   {
 631     int index = linkNameList.getSelectedIndex();
 632     if (index == -1)
 633     {
 634       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 635               MessageManager.getString("label.no_link_selected"),
 636               MessageManager.getString("label.no_link_selected"),
 637               JOptionPane.WARNING_MESSAGE);
 638       return;
 639     }
 640     nameLinks.removeElementAt(index);
 641     urlLinks.removeElementAt(index);
 642     updateLinkData();
 643   }
 644
 645   void updateLinkData()
 646   {
 647     linkNameList.setListData(nameLinks);
 648     linkURLList.setListData(urlLinks);
 649   }
 650
 651   public void defaultBrowser_mouseClicked(MouseEvent e)
 652   {
 653     JFileChooser chooser = new JFileChooser(".");
 654     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 655
 656     int value = chooser.showOpenDialog(this);
 657
 658     if (value == JFileChooser.APPROVE_OPTION)
 659     {
 660       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 661     }
 662
 663   }
 664
 665   /*
 666    * (non-Javadoc)
 667    *
 668    * @see
 669    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 670    * .ActionEvent)
 671    */
 672   protected void showunconserved_actionPerformed(ActionEvent e)
 673   {
 674     // TODO Auto-generated method stub
 675     super.showunconserved_actionPerformed(e);
 676   }
 677
 678   private void jbInit() throws Exception
 679   {
 680   }
 681
 682   public static Collection getGroupURLLinks()
 683   {
 684     return groupURLLinks;
 685   }
 686
 687   public void minColour_actionPerformed()
 688   {
 689     Color col = JColorChooser.showDialog(this,
 690             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 691     if (col != null)
 692     {
 693       minColour.setBackground(col);
 694     }
 695     minColour.repaint();
 696   }
 697
 698   public void maxColour_actionPerformed()
 699   {
 700     Color col = JColorChooser.showDialog(this,
 701             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 702     if (col != null)
 703     {
 704       maxColour.setBackground(col);
 705     }
 706     maxColour.repaint();
 707   }
 708
 709   @Override
 710   protected void userIdWidth_actionPerformed()
 711   {
 712     try
 713     {
 714       String val = userIdWidth.getText().trim();
 715       if (val.length() > 0)
 716       {
 717         Integer iw = Integer.parseInt(val);
 718         if (iw.intValue() < 12)
 719         {
 720           throw new NumberFormatException();
 721         }
 722         userIdWidth.setText(iw.toString());
 723       }
 724     } catch (NumberFormatException x)
 725     {
 726       JOptionPane
 727               .showInternalMessageDialog(
 728                       Desktop.desktop,
 729                       MessageManager.getString("warn.user_defined_width_requirements"),
 730                       MessageManager.getString("label.invalid_id_column_width"),
 731                       JOptionPane.WARNING_MESSAGE);
 732       userIdWidth.setText("");
 733     }
 734   }
 735
 736   @Override
 737   protected void autoIdWidth_actionPerformed()
 738   {
 739     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 740     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 741   }
 742
 743 }