src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27
  28 import jalview.bin.*;
  29 import jalview.io.*;
  30 import jalview.jbgui.*;
  31 import jalview.schemes.*;
  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    * Holds name and link separated with | character. Sequence IDS and Sequences must be
  49    * $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$
  50    * and separation character for first and second token specified after a pipe character at end |,|.
  51    * (TODO: proper escape for using | to separate ids or sequences
  52    */
  53
  54   public static Vector groupURLLinks;
  55   static
  56   {
  57     String string = Cache
  58             .getDefault(
  59                     "SEQUENCE_LINKS",
  60                     "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
  61     sequenceURLLinks = new Vector();
  62
  63     try
  64     {
  65       StringTokenizer st = new StringTokenizer(string, "|");
  66       while (st.hasMoreElements())
  67       {
  68         String name = st.nextToken();
  69         String url = st.nextToken();
  70         // check for '|' within a regex
  71         int rxstart = url.indexOf("$SEQUENCE_ID$");
  72         while (rxstart == -1 && url.indexOf("/=$") == -1)
  73         {
  74           url = url + "|" + st.nextToken();
  75         }
  76         sequenceURLLinks.addElement(name + "|" + url);
  77       }
  78     } catch (Exception ex)
  79     {
  80       System.out.println(ex + "\nError parsing sequence links");
  81     }
  82     /**
  83      * TODO: reformulate groupURL encoding so two or more can be stored in the .properties file as '|' separated strings
  84      */
  85
  86     groupURLLinks = new Vector();
  87     groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
  88     groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
  89
  90   }
  91
  92   Vector nameLinks, urlLinks;
  93
  94   JInternalFrame frame;
  95
  96   DasSourceBrowser dasSource;
  97
  98   /**
  99    * Creates a new Preferences object.
 100    */
 101   public Preferences()
 102   {
 103
 104     frame = new JInternalFrame();
 105     frame.setContentPane(this);
 106     dasSource = new DasSourceBrowser();
 107     dasPanel.add(dasSource, BorderLayout.CENTER);
 108
 109     int width = 500, height = 420;
 110     if (new jalview.util.Platform().isAMac())
 111     {
 112       width = 570;
 113       height = 460;
 114     }
 115
 116     Desktop.addInternalFrame(frame, "Preferences", width, height);
 117     frame.setMinimumSize(new Dimension(width, height));
 118
 119     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 120     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 121     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 122     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 123
 124     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 125     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 126     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 127     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 128     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 129
 130     for (int i = 0; i < 13; i++)
 131     {
 132       colour.addItem(ColourSchemeProperty.getColourName(i));
 133     }
 134
 135     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 136
 137     colour.setSelectedItem(string);
 138
 139     String[] fonts = java.awt.GraphicsEnvironment
 140             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 141
 142     for (int i = 0; i < fonts.length; i++)
 143     {
 144       fontNameCB.addItem(fonts[i]);
 145     }
 146
 147     for (int i = 1; i < 31; i++)
 148     {
 149       fontSizeCB.addItem(i + "");
 150     }
 151
 152     fontStyleCB.addItem("plain");
 153     fontStyleCB.addItem("bold");
 154     fontStyleCB.addItem("italic");
 155
 156     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 157     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 158     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 159             + ""));
 160
 161     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 162
 163     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 164
 165     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 166
 167     gapSymbolCB.addItem("-");
 168     gapSymbolCB.addItem(".");
 169
 170     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 171
 172     startupCheckbox
 173             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 174     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 175             "http://www.jalview.org/examples/exampleFile_2_3.jar"));
 176
 177     sortby.addItem("No sort");
 178     sortby.addItem("Id");
 179     sortby.addItem("Pairwise Identity");
 180     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 181
 182     epsRendering.addItem("Prompt each time");
 183     epsRendering.addItem("Lineart");
 184     epsRendering.addItem("Text");
 185     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 186             "Prompt each time"));
 187
 188     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 189     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 190     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 191     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 192     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 193     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 194     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 195
 196     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 197
 198     autoCalculateConsCheck.setSelected(Cache.getDefault(
 199             "AUTO_CALC_CONSENSUS", true));
 200     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
 201     showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 202     showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
 203     showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",false));
 204
 205     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 206
 207     /***************************************************************************
 208      * Set up Connections
 209      */
 210     nameLinks = new Vector();
 211     urlLinks = new Vector();
 212     for (int i = 0; i < sequenceURLLinks.size(); i++)
 213     {
 214       String link = sequenceURLLinks.elementAt(i).toString();
 215       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 216       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 217     }
 218
 219     updateLinkData();
 220
 221     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 222     proxyServerTB.setEnabled(useProxy.isSelected());
 223     proxyPortTB.setEnabled(useProxy.isSelected());
 224     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 225     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 226
 227     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 228
 229     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 230     questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
 231     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
 232     annotations_actionPerformed(null); // update the display of the annotation settings
 233     try
 234     {
 235       jbInit();
 236     } catch (Exception ex)
 237     {
 238       ex.printStackTrace();
 239     }
 240
 241   }
 242
 243   /**
 244    * DOCUMENT ME!
 245    *
 246    * @param e
 247    *                DOCUMENT ME!
 248    */
 249   public void ok_actionPerformed(ActionEvent e)
 250   {
 251
 252     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
 253             .toString(seqLimit.isSelected()));
 254     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
 255             .toString(rightAlign.isSelected()));
 256     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
 257             .toString(fullScreen.isSelected()));
 258     Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
 259             .toString(openoverv.isSelected()));
 260     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
 261             .toString(annotations.isSelected()));
 262     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
 263             .toString(conservation.isSelected()));
 264     Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
 265             .toString(quality.isSelected()));
 266     Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
 267             .toString(identity.isSelected()));
 268
 269     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 270             .getSelectedItem().toString());
 271     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 272             .getSelectedItem().toString());
 273
 274     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 275             .getSelectedItem().toString());
 276     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 277             .getSelectedItem().toString());
 278     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 279             .getSelectedItem().toString());
 280
 281     Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
 282             .toString(idItalics.isSelected()));
 283     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
 284     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
 285     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
 286     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
 287     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_PROFILE",Boolean.toString(showConsensProfile.isSelected()));
 288     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
 289             .toString(smoothFont.isSelected()));
 290
 291     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
 292             .toString(wrap.isSelected()));
 293
 294     Cache.applicationProperties.setProperty("STARTUP_FILE",
 295             startupFileTextfield.getText());
 296     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
 297             .toString(startupCheckbox.isSelected()));
 298
 299     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 300             .getSelectedItem().toString());
 301
 302     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 303     {
 304       Cache.applicationProperties.remove("EPS_RENDERING");
 305     }
 306     else
 307     {
 308       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 309               .getSelectedItem().toString());
 310     }
 311
 312     if (defaultBrowser.getText().trim().length() < 1)
 313     {
 314       Cache.applicationProperties.remove("DEFAULT_BROWSER");
 315     }
 316     else
 317     {
 318       Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
 319               defaultBrowser.getText());
 320     }
 321
 322     jalview.util.BrowserLauncher.resetBrowser();
 323
 324     if (nameLinks.size() > 0)
 325     {
 326       StringBuffer links = new StringBuffer();
 327       sequenceURLLinks = new Vector();
 328       for (int i = 0; i < nameLinks.size(); i++)
 329       {
 330         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 331                 + urlLinks.elementAt(i));
 332         links.append(sequenceURLLinks.elementAt(i).toString());
 333         links.append("|");
 334       }
 335       // remove last "|"
 336       links.setLength(links.length() - 1);
 337       Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
 338               .toString());
 339     }
 340     else
 341     {
 342       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 343     }
 344
 345     Cache.applicationProperties.setProperty("USE_PROXY", Boolean
 346             .toString(useProxy.isSelected()));
 347
 348     if (proxyServerTB.getText().trim().length() < 1)
 349     {
 350       Cache.applicationProperties.remove("PROXY_SERVER");
 351     }
 352     else
 353     {
 354       Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
 355               .getText());
 356     }
 357
 358     if (proxyPortTB.getText().trim().length() < 1)
 359     {
 360       Cache.applicationProperties.remove("PROXY_PORT");
 361     }
 362     else
 363     {
 364       Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
 365               .getText());
 366     }
 367
 368     if (useProxy.isSelected())
 369     {
 370       System.setProperty("http.proxyHost", proxyServerTB.getText());
 371       System.setProperty("http.proxyPort", proxyPortTB.getText());
 372     }
 373     else
 374     {
 375       System.setProperty("http.proxyHost", "");
 376       System.setProperty("http.proxyPort", "");
 377     }
 378     Cache.setProperty("VERSION_CHECK", Boolean
 379             .toString(versioncheck.isSelected()));
 380     if (Cache.getProperty("USAGESTATS")!=null || usagestats.isSelected()) {
 381       // default is false - we only set this if the user has actively agreed
 382       Cache.setProperty("USAGESTATS",Boolean
 383             .toString(usagestats.isSelected()));
 384     }
 385     if (!questionnaire.isSelected())
 386     {
 387       Cache.setProperty("NOQUESTIONNAIRES", "true");
 388     } else {
 389       // special - made easy to edit a property file to disable questionnaires by just adding the given line
 390       Cache.removeProperty("NOQUESTIONNAIRES");
 391     }
 392     Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
 393             .toString(blcjv.isSelected()));
 394     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
 395             .toString(clustaljv.isSelected()));
 396     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
 397             .toString(fastajv.isSelected()));
 398     Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
 399             .toString(msfjv.isSelected()));
 400     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
 401             .toString(pfamjv.isSelected()));
 402     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
 403             .toString(pileupjv.isSelected()));
 404     Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
 405             .toString(pirjv.isSelected()));
 406     Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
 407             .toString(modellerOutput.isSelected()));
 408     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 409
 410     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
 411             .toString(autoCalculateConsCheck.isSelected()));
 412     Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
 413             .toString(padGaps.isSelected()));
 414
 415     dasSource.saveProperties(Cache.applicationProperties);
 416
 417     Cache.saveProperties();
 418     try
 419     {
 420       frame.setClosed(true);
 421     } catch (Exception ex)
 422     {
 423     }
 424   }
 425
 426   /**
 427    * DOCUMENT ME!
 428    */
 429   public void startupFileTextfield_mouseClicked()
 430   {
 431     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 432             .getProperty("LAST_DIRECTORY"), new String[]
 433     { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 434             new String[]
 435             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 436             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 437     chooser.setFileView(new JalviewFileView());
 438     chooser.setDialogTitle("Select startup file");
 439
 440     int value = chooser.showOpenDialog(this);
 441
 442     if (value == JalviewFileChooser.APPROVE_OPTION)
 443     {
 444       jalview.bin.Cache.applicationProperties.setProperty(
 445               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 446       startupFileTextfield.setText(chooser.getSelectedFile()
 447               .getAbsolutePath());
 448     }
 449   }
 450
 451   /**
 452    * DOCUMENT ME!
 453    *
 454    * @param e
 455    *                DOCUMENT ME!
 456    */
 457   public void cancel_actionPerformed(ActionEvent e)
 458   {
 459     try
 460     {
 461       frame.setClosed(true);
 462     } catch (Exception ex)
 463     {
 464     }
 465   }
 466
 467   /**
 468    * DOCUMENT ME!
 469    *
 470    * @param e
 471    *                DOCUMENT ME!
 472    */
 473   public void annotations_actionPerformed(ActionEvent e)
 474   {
 475     conservation.setEnabled(annotations.isSelected());
 476     quality.setEnabled(annotations.isSelected());
 477     identity.setEnabled(annotations.isSelected());
 478     showConsensHistogram.setEnabled(annotations.isSelected());
 479     showConsensProfile.setEnabled(annotations.isSelected());
 480     showGroupConsensus.setEnabled(annotations.isSelected());
 481     showGroupConservation.setEnabled(annotations.isSelected());
 482   }
 483
 484   public void newLink_actionPerformed(ActionEvent e)
 485   {
 486
 487     GSequenceLink link = new GSequenceLink();
 488     boolean valid = false;
 489     while (!valid)
 490     {
 491       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 492               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 493               null) == JOptionPane.OK_OPTION)
 494       {
 495         if (link.checkValid())
 496         {
 497           nameLinks.addElement(link.getName());
 498           urlLinks.addElement(link.getURL());
 499           updateLinkData();
 500           valid = true;
 501         }
 502       }
 503       else
 504       {
 505         break;
 506       }
 507     }
 508   }
 509
 510   public void editLink_actionPerformed(ActionEvent e)
 511   {
 512     GSequenceLink link = new GSequenceLink();
 513
 514     int index = linkNameList.getSelectedIndex();
 515     if (index == -1)
 516     {
 517       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 518               "No link selected!", "No link selected",
 519               JOptionPane.WARNING_MESSAGE);
 520       return;
 521     }
 522
 523     link.setName(nameLinks.elementAt(index).toString());
 524     link.setURL(urlLinks.elementAt(index).toString());
 525
 526     boolean valid = false;
 527     while (!valid)
 528     {
 529
 530       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 531               "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
 532               null) == JOptionPane.OK_OPTION)
 533       {
 534         if (link.checkValid())
 535         {
 536           nameLinks.setElementAt(link.getName(), index);
 537           urlLinks.setElementAt(link.getURL(), index);
 538           updateLinkData();
 539           valid = true;
 540         }
 541       }
 542
 543       else
 544       {
 545         break;
 546       }
 547     }
 548   }
 549
 550   public void deleteLink_actionPerformed(ActionEvent e)
 551   {
 552     int index = linkNameList.getSelectedIndex();
 553     if (index == -1)
 554     {
 555       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 556               "No link selected!", "No link selected",
 557               JOptionPane.WARNING_MESSAGE);
 558       return;
 559     }
 560     nameLinks.removeElementAt(index);
 561     urlLinks.removeElementAt(index);
 562     updateLinkData();
 563   }
 564
 565   void updateLinkData()
 566   {
 567     linkNameList.setListData(nameLinks);
 568     linkURLList.setListData(urlLinks);
 569   }
 570
 571   public void defaultBrowser_mouseClicked(MouseEvent e)
 572   {
 573     JFileChooser chooser = new JFileChooser(".");
 574     chooser.setDialogTitle("Select default web browser");
 575
 576     int value = chooser.showOpenDialog(this);
 577
 578     if (value == JFileChooser.APPROVE_OPTION)
 579     {
 580       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 581     }
 582
 583   }
 584   /* (non-Javadoc)
 585    * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
 586    */
 587   protected void showunconserved_actionPerformed(ActionEvent e)
 588   {
 589     // TODO Auto-generated method stub
 590     super.showunconserved_actionPerformed(e);
 591   }
 592
 593   private void jbInit() throws Exception
 594   {
 595   }
 596 }