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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.io.JalviewFileChooser;
  26 import jalview.io.JalviewFileView;
  27 import jalview.jbgui.GPreferences;
  28 import jalview.jbgui.GSequenceLink;
  29 import jalview.schemes.ColourSchemeProperty;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Font;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.MouseEvent;
  38 import java.util.Collection;
  39 import java.util.StringTokenizer;
  40 import java.util.Vector;
  41
  42 import javax.swing.JColorChooser;
  43 import javax.swing.JFileChooser;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JOptionPane;
  46
  47 /**
  48  * DOCUMENT ME!
  49  *
  50  * @author $author$
  51  * @version $Revision$
  52  */
  53 public class Preferences extends GPreferences
  54 {
  55
  56   /**
  57    * Holds name and link separated with | character. Sequence ID must be
  58    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  59    */
  60   public static Vector sequenceURLLinks;
  61
  62   /**
  63    * Holds name and link separated with | character. Sequence IDS and Sequences
  64    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  65    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  66    * for first and second token specified after a pipe character at end |,|.
  67    * (TODO: proper escape for using | to separate ids or sequences
  68    */
  69
  70   public static Vector groupURLLinks;
  71   static
  72   {
  73     String string = Cache
  74             .getDefault(
  75                     "SEQUENCE_LINKS",
  76                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
  77     sequenceURLLinks = new Vector();
  78
  79     try
  80     {
  81       StringTokenizer st = new StringTokenizer(string, "|");
  82       while (st.hasMoreElements())
  83       {
  84         String name = st.nextToken();
  85         String url = st.nextToken();
  86         // check for '|' within a regex
  87         int rxstart = url.indexOf("$SEQUENCE_ID$");
  88         while (rxstart == -1 && url.indexOf("/=$") == -1)
  89         {
  90           url = url + "|" + st.nextToken();
  91         }
  92         sequenceURLLinks.addElement(name + "|" + url);
  93       }
  94     } catch (Exception ex)
  95     {
  96       System.out.println(ex + "\nError parsing sequence links");
  97     }
  98     {
  99       // upgrade old SRS link
 100       int srsPos = sequenceURLLinks
 101               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 102       if (srsPos > -1)
 103       {
 104         sequenceURLLinks
 105                 .setElementAt(
 106                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 107                         srsPos);
 108       }
 109     }
 110
 111     /**
 112      * TODO: reformulate groupURL encoding so two or more can be stored in the
 113      * .properties file as '|' separated strings
 114      */
 115
 116     groupURLLinks = new Vector();
 117   }
 118
 119   Vector nameLinks, urlLinks;
 120
 121   JInternalFrame frame;
 122
 123   DasSourceBrowser dasSource;
 124
 125   private WsPreferences wsPrefs;
 126
 127   /**
 128    * Creates a new Preferences object.
 129    */
 130   public Preferences()
 131   {
 132
 133     frame = new JInternalFrame();
 134     frame.setContentPane(this);
 135     dasSource = new DasSourceBrowser();
 136     dasPanel.add(dasSource, BorderLayout.CENTER);
 137     wsPrefs = new WsPreferences();
 138     wsPanel.add(wsPrefs, BorderLayout.CENTER);
 139     int width = 500, height = 420;
 140     if (new jalview.util.Platform().isAMac())
 141     {
 142       width = 570;
 143       height = 460;
 144     }
 145
 146     Desktop.addInternalFrame(frame,
 147             MessageManager.getString("label.preferences"), width, height);
 148     frame.setMinimumSize(new Dimension(width, height));
 149
 150     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 151     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 152     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 153     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 154
 155     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 156     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 157     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 158     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 159     showUnconserved
 160             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 161     showNpTooltip.setSelected(Cache
 162             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 163     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 164             true));
 165     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 166     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 167     {
 168       colour.addItem(ColourSchemeProperty.getColourName(i));
 169     }
 170
 171     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 172
 173     colour.setSelectedItem(string);
 174
 175     /**
 176      * default min-max colours for annotation shading
 177      */
 178     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 179             Color.orange));
 180     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 181             Color.red));
 182
 183     String[] fonts = java.awt.GraphicsEnvironment
 184             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 185
 186     for (int i = 0; i < fonts.length; i++)
 187     {
 188       fontNameCB.addItem(fonts[i]);
 189     }
 190
 191     for (int i = 1; i < 31; i++)
 192     {
 193       fontSizeCB.addItem(i + "");
 194     }
 195
 196     fontStyleCB.addItem("plain");
 197     fontStyleCB.addItem("bold");
 198     fontStyleCB.addItem("italic");
 199
 200     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 201     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 202     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 203             + ""));
 204
 205     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 206
 207     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 208
 209     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 210
 211     gapSymbolCB.addItem("-");
 212     gapSymbolCB.addItem(".");
 213
 214     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 215
 216     startupCheckbox
 217             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 218     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 219             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 220                     + "/examples/exampleFile_2_3.jar"));
 221
 222     sortby.addItem("No sort");
 223     sortby.addItem("Id");
 224     sortby.addItem("Pairwise Identity");
 225     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 226
 227     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 228     sortAnnBy
 229             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 230     sortAnnBy
 231             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 232     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 233             .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
 234                     SequenceAnnotationOrder.NONE.name()));
 235     sortAnnBy.setSelectedItem(savedSort.toString());
 236
 237     sortAutocalc.addItem("Autocalculated first");
 238     sortAutocalc.addItem("Autocalculated last");
 239
 240     final boolean showAbove = Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
 241             true);
 242     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 243             : sortAutocalc.getItemAt(1));
 244
 245     epsRendering.addItem(MessageManager.getString("label.prompt_each_time"));
 246     epsRendering.addItem(MessageManager.getString("label.lineart"));
 247     epsRendering.addItem(MessageManager.getString("action.text"));
 248     epsRendering.setSelectedIndex(0);
 249     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 250     userIdWidth.setEnabled(autoIdWidth.isSelected());
 251     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 252     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 253     userIdWidth.setText(wi == null ? "" : wi.toString());
 254     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 255     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 256     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 257     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 258     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 259     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 260     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 261
 262     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 263
 264     autoCalculateConsCheck.setSelected(Cache.getDefault(
 265             "AUTO_CALC_CONSENSUS", true));
 266     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 267             false));
 268     showGroupConservation.setSelected(Cache.getDefault(
 269             "SHOW_GROUP_CONSERVATION", false));
 270     showConsensHistogram.setSelected(Cache.getDefault(
 271             "SHOW_CONSENSUS_HISTOGRAM", true));
 272     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 273             false));
 274
 275     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 276
 277     /***************************************************************************
 278      * Set up Connections
 279      */
 280     nameLinks = new Vector();
 281     urlLinks = new Vector();
 282     for (int i = 0; i < sequenceURLLinks.size(); i++)
 283     {
 284       String link = sequenceURLLinks.elementAt(i).toString();
 285       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 286       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 287     }
 288
 289     updateLinkData();
 290
 291     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 292     proxyServerTB.setEnabled(useProxy.isSelected());
 293     proxyPortTB.setEnabled(useProxy.isSelected());
 294     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 295     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 296
 297     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 298
 299     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 300     questionnaire
 301             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
 302                                                                          // antisense
 303                                                                          // here
 304     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
 305                                                                        // is
 306                                                                        // true
 307     annotations_actionPerformed(null); // update the display of the annotation
 308                                        // settings
 309     try
 310     {
 311       jbInit();
 312     } catch (Exception ex)
 313     {
 314       ex.printStackTrace();
 315     }
 316
 317   }
 318
 319   /**
 320    * DOCUMENT ME!
 321    *
 322    * @param e
 323    *          DOCUMENT ME!
 324    */
 325   public void ok_actionPerformed(ActionEvent e)
 326   {
 327
 328     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 329             Boolean.toString(seqLimit.isSelected()));
 330     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 331             Boolean.toString(rightAlign.isSelected()));
 332     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 333             Boolean.toString(fullScreen.isSelected()));
 334     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 335             Boolean.toString(openoverv.isSelected()));
 336     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 337             Boolean.toString(annotations.isSelected()));
 338     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 339             Boolean.toString(conservation.isSelected()));
 340     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 341             Boolean.toString(quality.isSelected()));
 342     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 343             Boolean.toString(identity.isSelected()));
 344
 345     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 346             .getSelectedItem().toString());
 347     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 348             .getSelectedItem().toString());
 349
 350     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 351             .getSelectedItem().toString());
 352     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 353             .getSelectedItem().toString());
 354     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 355             .getSelectedItem().toString());
 356
 357     Cache.applicationProperties.setProperty("ID_ITALICS",
 358             Boolean.toString(idItalics.isSelected()));
 359     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 360             Boolean.toString(showUnconserved.isSelected()));
 361     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 362             Boolean.toString(showGroupConsensus.isSelected()));
 363     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 364             Boolean.toString(showGroupConservation.isSelected()));
 365     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 366             Boolean.toString(showConsensHistogram.isSelected()));
 367     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 368             Boolean.toString(showConsensLogo.isSelected()));
 369     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 370             Boolean.toString(smoothFont.isSelected()));
 371     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 372             Boolean.toString(showNpTooltip.isSelected()));
 373     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 374             Boolean.toString(showDbRefTooltip.isSelected()));
 375
 376     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 377             Boolean.toString(wrap.isSelected()));
 378
 379     Cache.applicationProperties.setProperty("STARTUP_FILE",
 380             startupFileTextfield.getText());
 381     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 382             Boolean.toString(startupCheckbox.isSelected()));
 383
 384     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 385             .getSelectedItem().toString());
 386
 387     // convert description of sort order to enum name for save
 388     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 389             .forDescription(sortAnnBy.getSelectedItem().toString());
 390     if (annSortOrder != null)
 391     {
 392       Cache.applicationProperties.setProperty(Cache.SORT_ANNOTATIONS,
 393               annSortOrder.name());
 394     }
 395
 396     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 397     Cache.applicationProperties.setProperty(Cache.SHOW_AUTOCALC_ABOVE,
 398             Boolean.valueOf(showAutocalcFirst).toString());
 399
 400     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 401             minColour.getBackground());
 402     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 403             maxColour.getBackground());
 404
 405     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 406     {
 407       Cache.applicationProperties.remove("EPS_RENDERING");
 408     }
 409     else
 410     {
 411       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 412               .getSelectedItem().toString());
 413     }
 414
 415     if (defaultBrowser.getText().trim().length() < 1)
 416     {
 417       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 418     }
 419     else
 420     {
 421       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 422               defaultBrowser.getText());
 423     }
 424
 425     jalview.util.BrowserLauncher.resetBrowser();
 426
 427     if (nameLinks.size() > 0)
 428     {
 429       StringBuffer links = new StringBuffer();
 430       sequenceURLLinks = new Vector();
 431       for (int i = 0; i < nameLinks.size(); i++)
 432       {
 433         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 434                 + urlLinks.elementAt(i));
 435         links.append(sequenceURLLinks.elementAt(i).toString());
 436         links.append("|");
 437       }
 438       // remove last "|"
 439       links.setLength(links.length() - 1);
 440       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 441               links.toString());
 442     }
 443     else
 444     {
 445       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 446     }
 447
 448     Cache.applicationProperties.setProperty("USE_PROXY",
 449             Boolean.toString(useProxy.isSelected()));
 450
 451     if (proxyServerTB.getText().trim().length() < 1)
 452     {
 453       Cache.applicationProperties.remove("PROXY_SERVER");
 454     }
 455     else
 456     {
 457       Cache.applicationProperties.setProperty("PROXY_SERVER",
 458               proxyServerTB.getText());
 459     }
 460
 461     if (proxyPortTB.getText().trim().length() < 1)
 462     {
 463       Cache.applicationProperties.remove("PROXY_PORT");
 464     }
 465     else
 466     {
 467       Cache.applicationProperties.setProperty("PROXY_PORT",
 468               proxyPortTB.getText());
 469     }
 470
 471     if (useProxy.isSelected())
 472     {
 473       System.setProperty("http.proxyHost", proxyServerTB.getText());
 474       System.setProperty("http.proxyPort", proxyPortTB.getText());
 475     }
 476     else
 477     {
 478       System.setProperty("http.proxyHost", "");
 479       System.setProperty("http.proxyPort", "");
 480     }
 481     Cache.setProperty("VERSION_CHECK",
 482             Boolean.toString(versioncheck.isSelected()));
 483     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 484     {
 485       // default is false - we only set this if the user has actively agreed
 486       Cache.setProperty("USAGESTATS",
 487               Boolean.toString(usagestats.isSelected()));
 488     }
 489     if (!questionnaire.isSelected())
 490     {
 491       Cache.setProperty("NOQUESTIONNAIRES", "true");
 492     }
 493     else
 494     {
 495       // special - made easy to edit a property file to disable questionnaires
 496       // by just adding the given line
 497       Cache.removeProperty("NOQUESTIONNAIRES");
 498     }
 499     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 500             Boolean.toString(blcjv.isSelected()));
 501     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 502             Boolean.toString(clustaljv.isSelected()));
 503     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 504             Boolean.toString(fastajv.isSelected()));
 505     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 506             Boolean.toString(msfjv.isSelected()));
 507     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 508             Boolean.toString(pfamjv.isSelected()));
 509     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 510             Boolean.toString(pileupjv.isSelected()));
 511     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 512             Boolean.toString(pirjv.isSelected()));
 513     Cache.applicationProperties.setProperty("PIR_MODELLER",
 514             Boolean.toString(modellerOutput.isSelected()));
 515     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 516
 517     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 518             Boolean.toString(autoIdWidth.isSelected()));
 519     userIdWidth_actionPerformed();
 520     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 521             userIdWidth.getText());
 522
 523     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 524             Boolean.toString(autoCalculateConsCheck.isSelected()));
 525     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 526             Boolean.toString(sortByTree.isSelected()));
 527     Cache.applicationProperties.setProperty("PAD_GAPS",
 528             Boolean.toString(padGaps.isSelected()));
 529
 530     dasSource.saveProperties(Cache.applicationProperties);
 531     wsPrefs.updateAndRefreshWsMenuConfig(false);
 532     Cache.saveProperties();
 533     try
 534     {
 535       frame.setClosed(true);
 536     } catch (Exception ex)
 537     {
 538     }
 539   }
 540
 541   /**
 542    * DOCUMENT ME!
 543    */
 544   public void startupFileTextfield_mouseClicked()
 545   {
 546     JalviewFileChooser chooser = new JalviewFileChooser(
 547             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 548             new String[]
 549             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 550             new String[]
 551             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 552             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 553     chooser.setFileView(new JalviewFileView());
 554     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 555
 556     int value = chooser.showOpenDialog(this);
 557
 558     if (value == JalviewFileChooser.APPROVE_OPTION)
 559     {
 560       jalview.bin.Cache.applicationProperties.setProperty(
 561               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 562       startupFileTextfield.setText(chooser.getSelectedFile()
 563               .getAbsolutePath());
 564     }
 565   }
 566
 567   /**
 568    * DOCUMENT ME!
 569    *
 570    * @param e
 571    *          DOCUMENT ME!
 572    */
 573   public void cancel_actionPerformed(ActionEvent e)
 574   {
 575     try
 576     {
 577       wsPrefs.updateWsMenuConfig(true);
 578       wsPrefs.refreshWs_actionPerformed(e);
 579       frame.setClosed(true);
 580     } catch (Exception ex)
 581     {
 582     }
 583   }
 584
 585   /**
 586    * DOCUMENT ME!
 587    *
 588    * @param e
 589    *          DOCUMENT ME!
 590    */
 591   public void annotations_actionPerformed(ActionEvent e)
 592   {
 593     conservation.setEnabled(annotations.isSelected());
 594     quality.setEnabled(annotations.isSelected());
 595     identity.setEnabled(annotations.isSelected());
 596     showGroupConsensus.setEnabled(annotations.isSelected());
 597     showGroupConservation.setEnabled(annotations.isSelected());
 598     showConsensHistogram.setEnabled(annotations.isSelected()
 599             && (identity.isSelected() || showGroupConsensus.isSelected()));
 600     showConsensLogo.setEnabled(annotations.isSelected()
 601             && (identity.isSelected() || showGroupConsensus.isSelected()));
 602   }
 603
 604   public void newLink_actionPerformed(ActionEvent e)
 605   {
 606
 607     GSequenceLink link = new GSequenceLink();
 608     boolean valid = false;
 609     while (!valid)
 610     {
 611       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 612               MessageManager.getString("label.new_sequence_url_link"),
 613               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 614       {
 615         if (link.checkValid())
 616         {
 617           nameLinks.addElement(link.getName());
 618           urlLinks.addElement(link.getURL());
 619           updateLinkData();
 620           valid = true;
 621         }
 622       }
 623       else
 624       {
 625         break;
 626       }
 627     }
 628   }
 629
 630   public void editLink_actionPerformed(ActionEvent e)
 631   {
 632     GSequenceLink link = new GSequenceLink();
 633
 634     int index = linkNameList.getSelectedIndex();
 635     if (index == -1)
 636     {
 637       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 638               MessageManager.getString("label.no_link_selected"),
 639               MessageManager.getString("label.no_link_selected"),
 640               JOptionPane.WARNING_MESSAGE);
 641       return;
 642     }
 643
 644     link.setName(nameLinks.elementAt(index).toString());
 645     link.setURL(urlLinks.elementAt(index).toString());
 646
 647     boolean valid = false;
 648     while (!valid)
 649     {
 650
 651       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 652               MessageManager.getString("label.new_sequence_url_link"),
 653               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 654       {
 655         if (link.checkValid())
 656         {
 657           nameLinks.setElementAt(link.getName(), index);
 658           urlLinks.setElementAt(link.getURL(), index);
 659           updateLinkData();
 660           valid = true;
 661         }
 662       }
 663
 664       else
 665       {
 666         break;
 667       }
 668     }
 669   }
 670
 671   public void deleteLink_actionPerformed(ActionEvent e)
 672   {
 673     int index = linkNameList.getSelectedIndex();
 674     if (index == -1)
 675     {
 676       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 677               MessageManager.getString("label.no_link_selected"),
 678               MessageManager.getString("label.no_link_selected"),
 679               JOptionPane.WARNING_MESSAGE);
 680       return;
 681     }
 682     nameLinks.removeElementAt(index);
 683     urlLinks.removeElementAt(index);
 684     updateLinkData();
 685   }
 686
 687   void updateLinkData()
 688   {
 689     linkNameList.setListData(nameLinks);
 690     linkURLList.setListData(urlLinks);
 691   }
 692
 693   public void defaultBrowser_mouseClicked(MouseEvent e)
 694   {
 695     JFileChooser chooser = new JFileChooser(".");
 696     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 697
 698     int value = chooser.showOpenDialog(this);
 699
 700     if (value == JFileChooser.APPROVE_OPTION)
 701     {
 702       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 703     }
 704
 705   }
 706
 707   /*
 708    * (non-Javadoc)
 709    *
 710    * @see
 711    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 712    * .ActionEvent)
 713    */
 714   protected void showunconserved_actionPerformed(ActionEvent e)
 715   {
 716     // TODO Auto-generated method stub
 717     super.showunconserved_actionPerformed(e);
 718   }
 719
 720   private void jbInit() throws Exception
 721   {
 722   }
 723
 724   public static Collection getGroupURLLinks()
 725   {
 726     return groupURLLinks;
 727   }
 728
 729   public void minColour_actionPerformed()
 730   {
 731     Color col = JColorChooser.showDialog(this,
 732             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 733     if (col != null)
 734     {
 735       minColour.setBackground(col);
 736     }
 737     minColour.repaint();
 738   }
 739
 740   public void maxColour_actionPerformed()
 741   {
 742     Color col = JColorChooser.showDialog(this,
 743             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 744     if (col != null)
 745     {
 746       maxColour.setBackground(col);
 747     }
 748     maxColour.repaint();
 749   }
 750
 751   @Override
 752   protected void userIdWidth_actionPerformed()
 753   {
 754     try
 755     {
 756       String val = userIdWidth.getText().trim();
 757       if (val.length() > 0)
 758       {
 759         Integer iw = Integer.parseInt(val);
 760         if (iw.intValue() < 12)
 761         {
 762           throw new NumberFormatException();
 763         }
 764         userIdWidth.setText(iw.toString());
 765       }
 766     } catch (NumberFormatException x)
 767     {
 768       JOptionPane
 769               .showInternalMessageDialog(
 770                       Desktop.desktop,
 771                       MessageManager.getString("warn.user_defined_width_requirements"),
 772                       MessageManager.getString("label.invalid_id_column_width"),
 773                       JOptionPane.WARNING_MESSAGE);
 774       userIdWidth.setText("");
 775     }
 776   }
 777
 778   @Override
 779   protected void autoIdWidth_actionPerformed()
 780   {
 781     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 782     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 783   }
 784
 785 }