X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=facc826d1dda70aca91672780a46690b92dc4600;hb=ad1f4306281b0894fa42394b9a68da834cf14af6;hp=6a558d5e1615057ef69e4c5911993672e10687c1;hpb=f5d6c0018555b2c453c2c0354c84cd5d2d81e3b9;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6a558d5..facc826 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -22,9 +22,9 @@ package jalview.gui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
-import jalview.bin.Jalview;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -37,6 +37,7 @@ import jalview.urls.UrlLinkTableModel;
 import jalview.urls.api.UrlProviderFactoryI;
 import jalview.urls.api.UrlProviderI;
 import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -80,6 +81,7 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  * @author $author$
  * @version $Revision$
  */
+@SuppressWarnings("serial")
 public class Preferences extends GPreferences
 {
   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
@@ -126,9 +128,9 @@ public class Preferences extends GPreferences
    * Holds name and link separated with | character. Sequence ID must be
    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
    */
-  public static UrlProviderI sequenceUrlLinks;
+  public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
 
-  public static UrlLinkTableModel dataModel;
+  public final static UrlLinkTableModel dataModel;
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
@@ -138,7 +140,8 @@ public class Preferences extends GPreferences
    * (TODO: proper escape for using | to separate ids or sequences
    */
 
-  public static List<String> groupURLLinks;
+  public static final List<String> groupURLLinks; // not implemented
+
   static
   {
     // get links selected to be in the menu (SEQUENCE_LINKS)
@@ -164,7 +167,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<>();
+    groupURLLinks = new ArrayList<>(); // not implemented
   }
 
   JInternalFrame frame;
@@ -189,7 +192,12 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
       wsPrefs = new WsPreferences();
       wsTab.add(wsPrefs, BorderLayout.CENTER);
@@ -328,7 +336,7 @@ public class Preferences extends GPreferences
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
     showHiddenAtStart
-            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 
     /*
      * Set Structure tab defaults.
@@ -536,6 +544,12 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
+    
+    
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
   }
 
   /**
@@ -555,7 +569,7 @@ public class Preferences extends GPreferences
     /*
      * JalviewJS doesn't support Lineart so force it to Text
      */
-    String defaultOption = Jalview.isJS() ? "Text"
+    String defaultOption = Platform.isJS() ? "Text"
             : Cache.getDefault(propertyKey, "Prompt each time");
     if (defaultOption.equalsIgnoreCase("Text"))
     {
@@ -588,65 +602,65 @@ public class Preferences extends GPreferences
     /*
      * Save Visual settings
      */
-    Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+    Cache.setPropertyNoSave("SHOW_JVSUFFIX",
             Boolean.toString(seqLimit.isSelected()));
-    Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+    Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
             Boolean.toString(rightAlign.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+    Cache.setPropertyNoSave("SHOW_FULLSCREEN",
             Boolean.toString(fullScreen.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+    Cache.setPropertyNoSave("SHOW_OVERVIEW",
             Boolean.toString(openoverv.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
             Boolean.toString(annotations.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.toString(conservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+    Cache.setPropertyNoSave("SHOW_QUALITY",
             Boolean.toString(quality.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+    Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.toString(identity.isSelected()));
 
-    Cache.applicationProperties.setProperty("GAP_SYMBOL",
+    Cache.setPropertyNoSave("GAP_SYMBOL",
             gapSymbolCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("FONT_NAME",
+    Cache.setPropertyNoSave("FONT_NAME",
             fontNameCB.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_STYLE",
+    Cache.setPropertyNoSave("FONT_STYLE",
             fontStyleCB.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_SIZE",
+    Cache.setPropertyNoSave("FONT_SIZE",
             fontSizeCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("ID_ITALICS",
+    Cache.setPropertyNoSave("ID_ITALICS",
             Boolean.toString(idItalics.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+    Cache.setPropertyNoSave("SHOW_UNCONSERVED",
             Boolean.toString(showUnconserved.isSelected()));
-    Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+    Cache.setPropertyNoSave(SHOW_OCCUPANCY,
             Boolean.toString(showOccupancy.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+    Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
             Boolean.toString(showGroupConsensus.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
             Boolean.toString(showGroupConservation.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+    Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
             Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+    Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
             Boolean.toString(showConsensLogo.isSelected()));
-    Cache.applicationProperties.setProperty("ANTI_ALIAS",
+    Cache.setPropertyNoSave("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
-    Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+    Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
             Boolean.toString(scaleProteinToCdna.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+    Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
             Boolean.toString(showNpTooltip.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+    Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
             Boolean.toString(showDbRefTooltip.isSelected()));
 
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+    Cache.setPropertyNoSave("WRAP_ALIGNMENT",
             Boolean.toString(wrap.isSelected()));
 
-    Cache.applicationProperties.setProperty("STARTUP_FILE",
+    Cache.setPropertyNoSave("STARTUP_FILE",
             startupFileTextfield.getText());
-    Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+    Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
             Boolean.toString(startupCheckbox.isSelected()));
 
-    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+    Cache.setPropertyNoSave("SORT_ALIGNMENT",
             sortby.getSelectedItem().toString());
 
     // convert description of sort order to enum name for save
@@ -654,20 +668,20 @@ public class Preferences extends GPreferences
             .forDescription(sortAnnBy.getSelectedItem().toString());
     if (annSortOrder != null)
     {
-      Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+      Cache.setPropertyNoSave(SORT_ANNOTATIONS,
               annSortOrder.name());
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+    Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
             Boolean.valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
      */
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
             protColour.getSelectedItem().toString());
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
             nucColour.getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
@@ -679,73 +693,77 @@ public class Preferences extends GPreferences
      */
     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
-    Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+    Cache.setPropertyNoSave(USE_LEGACY_GAP,
             Boolean.toString(useLegacyGap.isSelected()));
-    Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+    Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
             Boolean.toString(showHiddenAtStart.isSelected()));
 
     /*
      * Save Structure settings
      */
-    Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+    Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
             Boolean.toString(addTempFactor.isSelected()));
-    Cache.applicationProperties.setProperty(ADD_SS_ANN,
+    Cache.setPropertyNoSave(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.applicationProperties.setProperty(USE_RNAVIEW,
+    Cache.setPropertyNoSave(USE_RNAVIEW,
             Boolean.toString(useRnaView.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+    Cache.setPropertyNoSave(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
-    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+    Cache.setPropertyNoSave("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
     /*
      * Save Output settings
      */
-    Cache.applicationProperties.setProperty("EPS_RENDERING",
+    Cache.setPropertyNoSave("EPS_RENDERING",
             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
-    Cache.applicationProperties.setProperty("HTML_RENDERING",
+    Cache.setPropertyNoSave("HTML_RENDERING",
             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
-    Cache.applicationProperties.setProperty("SVG_RENDERING",
+    Cache.setPropertyNoSave("SVG_RENDERING",
             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 
-    /*
-     * Save Connections settings
+    if (!Platform.isJS())
+    /**
+     * @j2sNative
      */
-    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
-
-    jalview.util.BrowserLauncher.resetBrowser();
+    {
+      // Java only
+      // Save Connections settings
+      Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+      BrowserLauncher.resetBrowser();
+    }
 
     // save user-defined and selected links
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
     if (menuLinks.isEmpty())
     {
-      Cache.applicationProperties.remove("SEQUENCE_LINKS");
+      Cache.removePropertyNoSave("SEQUENCE_LINKS");
     }
     else
     {
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+      Cache.setPropertyNoSave("SEQUENCE_LINKS",
               menuLinks.toString());
     }
 
     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
     if (nonMenuLinks.isEmpty())
     {
-      Cache.applicationProperties.remove("STORED_LINKS");
+      Cache.removePropertyNoSave("STORED_LINKS");
     }
     else
     {
-      Cache.applicationProperties.setProperty("STORED_LINKS",
+      Cache.setPropertyNoSave("STORED_LINKS",
               nonMenuLinks.toString());
     }
 
-    Cache.applicationProperties.setProperty("DEFAULT_URL",
+    Cache.setPropertyNoSave("DEFAULT_URL",
             sequenceUrlLinks.getPrimaryUrlId());
 
-    Cache.applicationProperties.setProperty("USE_PROXY",
+    Cache.setPropertyNoSave("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
@@ -784,48 +802,67 @@ public class Preferences extends GPreferences
     /*
      * Save Output settings
      */
-    Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+    Cache.setPropertyNoSave("BLC_JVSUFFIX",
             Boolean.toString(blcjv.isSelected()));
-    Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+    Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
             Boolean.toString(clustaljv.isSelected()));
-    Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+    Cache.setPropertyNoSave("FASTA_JVSUFFIX",
             Boolean.toString(fastajv.isSelected()));
-    Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+    Cache.setPropertyNoSave("MSF_JVSUFFIX",
             Boolean.toString(msfjv.isSelected()));
-    Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+    Cache.setPropertyNoSave("PFAM_JVSUFFIX",
             Boolean.toString(pfamjv.isSelected()));
-    Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+    Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
             Boolean.toString(pileupjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+    Cache.setPropertyNoSave("PIR_JVSUFFIX",
             Boolean.toString(pirjv.isSelected()));
-    Cache.applicationProperties.setProperty("PIR_MODELLER",
+    Cache.setPropertyNoSave("PIR_MODELLER",
             Boolean.toString(modellerOutput.isSelected()));
-    Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+    Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
             Boolean.toString(embbedBioJSON.isSelected()));
-    jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
-
-    Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+    Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
+    Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
      * Save Editing settings
      */
-    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+    Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
             Boolean.toString(autoCalculateConsCheck.isSelected()));
-    Cache.applicationProperties.setProperty("SORT_BY_TREE",
+    Cache.setPropertyNoSave("SORT_BY_TREE",
             Boolean.toString(sortByTree.isSelected()));
-    Cache.applicationProperties.setProperty("PAD_GAPS",
+    Cache.setPropertyNoSave("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    if (!Jalview.isJS())
+    if (!Platform.isJS())
     {
       wsPrefs.updateAndRefreshWsMenuConfig(false);
     }
+
+    /*
+     * Save Backups settings
+     */
+    Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
+            Boolean.toString(backupfilesConfirmDelete.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.NO_MAX,
+            Boolean.toString(backupfilesKeepAll.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
+            Boolean.toString(suffixReverse.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX,
+            suffixTemplate.getText());
+    Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
+            Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
+            Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+    Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
+            Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+
     Cache.saveProperties();
-    Desktop.instance.doConfigureStructurePrefs();
+    Desktop.getInstance().doConfigureStructurePrefs();
     try
     {
       frame.setClosed(true);
@@ -878,7 +915,7 @@ public class Preferences extends GPreferences
       FileFormatI format = chooser.getSelectedFormat();
       if (format != null)
       {
-        Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+        Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
                 format.getName());
       }
       startupFileTextfield
@@ -897,7 +934,7 @@ public class Preferences extends GPreferences
   {
     try
     {
-      if (!Jalview.isJS())
+      if (!Platform.isJS())
       {
         wsPrefs.updateWsMenuConfig(true);
         wsPrefs.refreshWs_actionPerformed(e);
@@ -936,7 +973,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
               MessageManager.getString("label.new_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -988,7 +1025,7 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
               MessageManager.getString("label.edit_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1,
               null) == JvOptionPane.OK_OPTION)
@@ -1041,8 +1078,11 @@ public class Preferences extends GPreferences
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     // TODO: JAL-3048 not needed for j2s
-    /*
-     * @j2sNative
+    if (!Platform.isJS()) // BH 2019
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
      */
     {
       JFileChooser chooser = new JFileChooser(".");
@@ -1072,6 +1112,11 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
+  /**
+   * not implemented -- returns empty list
+   * 
+   * @return
+   */
   public static List<String> getGroupURLLinks()
   {
     return groupURLLinks;
@@ -1135,7 +1180,7 @@ public class Preferences extends GPreferences
   {
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
-    showHiddenAtStart.setSelected(true);
+    showHiddenAtStart.setSelected(false);
     hiddenColour.setBackground(
             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
   }
@@ -1158,7 +1203,7 @@ public class Preferences extends GPreferences
     } catch (NumberFormatException x)
     {
       userIdWidth.setText("");
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager
                       .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
@@ -1177,14 +1222,14 @@ public class Preferences extends GPreferences
    * Returns true if chimera path is to a valid executable, else show an error
    * dialog.
    */
-  private boolean validateChimeraPath()
+  protected boolean validateChimeraPath()
   {
     if (chimeraPath.getText().trim().length() > 0)
     {
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
                 JvOptionPane.ERROR_MESSAGE);
@@ -1223,7 +1268,7 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
@@ -1296,7 +1341,7 @@ public class Preferences extends GPreferences
     }
   }
 
-  private class UrlListSelectionHandler implements ListSelectionListener
+  protected class UrlListSelectionHandler implements ListSelectionListener
   {
 
     @Override