JAL-2527 Started adding overview preferences
[jalview.git] / src / jalview / gui / Preferences.java
index 8048efe..6fdaa0d 100755 (executable)
@@ -24,15 +24,18 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.urls.DesktopUrlProviderFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
 import jalview.urls.UrlLinkTableModel;
-import jalview.urls.UrlProviderFactoryI;
-import jalview.urls.UrlProviderI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -51,10 +54,10 @@ import java.util.ArrayList;
 import java.util.List;
 
 import javax.help.HelpSetException;
+import javax.swing.JButton;
 import javax.swing.JColorChooser;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.ListSelectionModel;
 import javax.swing.RowFilter;
@@ -105,6 +108,8 @@ public class Preferences extends GPreferences
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 
+  public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
   private static final int MIN_FONT_SIZE = 1;
 
   private static final int MAX_FONT_SIZE = 30;
@@ -151,7 +156,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<String>();
+    groupURLLinks = new ArrayList<>();
   }
 
   JInternalFrame frame;
@@ -208,18 +213,19 @@ public class Preferences extends GPreferences
     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
     showUnconserved
             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
-    showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
-            false));
-    showGroupConservation.setSelected(Cache.getDefault(
-            "SHOW_GROUP_CONSERVATION", false));
-    showConsensHistogram.setSelected(Cache.getDefault(
-            "SHOW_CONSENSUS_HISTOGRAM", true));
-    showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
-            false));
-    showNpTooltip.setSelected(Cache
-            .getDefault("SHOW_NPFEATS_TOOLTIP", true));
-    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
-            true));
+    showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
+    showGroupConsensus
+            .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+    showGroupConservation.setSelected(
+            Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+    showConsensHistogram.setSelected(
+            Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+    showConsensLogo
+            .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+    showNpTooltip
+            .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip
+            .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
@@ -239,12 +245,12 @@ public class Preferences extends GPreferences
 
     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
-    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
-            + ""));
+    fontStyleCB.setSelectedItem(
+            Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
-    scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
-            false));
+    scaleProteinToCdna
+            .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
@@ -284,20 +290,28 @@ public class Preferences extends GPreferences
     /*
      * Set Colours tab defaults
      */
-    for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+    protColour.addItem(ResidueColourScheme.NONE);
+    nucColour.addItem(ResidueColourScheme.NONE);
+    for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
     {
-      protColour.addItem(ColourSchemeProperty.getColourName(i));
-      nucColour.addItem(ColourSchemeProperty.getColourName(i));
+      String name = cs.getSchemeName();
+      protColour.addItem(name);
+      nucColour.addItem(name);
     }
-    String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+    String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+            ResidueColourScheme.NONE);
     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
-    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
-            Color.orange));
-    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
-            Color.red));
+    minColour.setBackground(
+            Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(
+            Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+    gapColour.setBackground(
+            Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
+    hiddenColour.setBackground(
+            Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
 
     /*
      * Set Structure tab defaults.
@@ -310,8 +324,8 @@ public class Preferences extends GPreferences
     addSecondaryStructure.setEnabled(structSelected);
     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
     addTempFactor.setEnabled(structSelected);
-    structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
-            ViewerType.JMOL.name()));
+    structViewer.setSelectedItem(
+            Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
     chimeraPath.addActionListener(new ActionListener()
     {
@@ -346,16 +360,16 @@ public class Preferences extends GPreferences
     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 
     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
-    sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(),
+    sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
             SortOrder.DESCENDING));
     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
             SortOrder.DESCENDING));
-    sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
-            SortOrder.ASCENDING));
+    sortKeys.add(
+            new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 
     sorter.setSortKeys(sortKeys);
     sorter.sort();
-    
+
     // set up filtering
     ActionListener onReset;
     onReset = new ActionListener()
@@ -377,9 +391,7 @@ public class Preferences extends GPreferences
       public boolean include(
               Entry<? extends TableModel, ? extends Object> entry)
       {
-        int col = ((UrlLinkTableModel) entry.getModel()).getIdColumn();
-        String id = entry.getStringValue(col);
-        return sequenceUrlLinks.isUserEntry(id);
+        return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
       }
     };
 
@@ -406,35 +418,35 @@ public class Preferences extends GPreferences
       @Override
       public void changedUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
 
       @Override
       public void removeUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
 
       @Override
       public void insertUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
     });
 
     // set up list selection functionality
-    linkUrlTable.getSelectionModel().addListSelectionListener(
-            new UrlListSelectionHandler());
+    linkUrlTable.getSelectionModel()
+            .addListSelectionListener(new UrlListSelectionHandler());
 
     // set up radio buttons
     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
-            .getDefaultColumn();
+            .getPrimaryColumn();
     String onClickName = linkUrlTable.getColumnName(onClickCol);
-    linkUrlTable.getColumn(onClickName).setCellRenderer(
-               new RadioButtonRenderer());
+    linkUrlTable.getColumn(onClickName)
+            .setCellRenderer(new RadioButtonRenderer());
     linkUrlTable.getColumn(onClickName)
             .setCellEditor(new RadioButtonEditor());
 
@@ -444,8 +456,8 @@ public class Preferences extends GPreferences
       if (linkUrlTable.getModel().getColumnClass(column)
               .equals(Boolean.class))
       {
-        TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
-                column);
+        TableColumn tableColumn = linkUrlTable.getColumnModel()
+                .getColumn(column);
         int preferredWidth = tableColumn.getMinWidth();
 
         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
@@ -461,8 +473,6 @@ public class Preferences extends GPreferences
 
     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
-    proxyServerTB.setEnabled(useProxy.isSelected());
-    proxyPortTB.setEnabled(useProxy.isSelected());
     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 
@@ -507,14 +517,14 @@ public class Preferences extends GPreferences
     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
-    embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
-            true));
+    embbedBioJSON
+            .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 
     /*
      * Set Editing tab defaults
      */
-    autoCalculateConsCheck.setSelected(Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
+    autoCalculateConsCheck
+            .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 
@@ -556,20 +566,22 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.toString(identity.isSelected()));
 
-    Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("GAP_SYMBOL",
+            gapSymbolCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_NAME",
+            fontNameCB.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_STYLE",
+            fontStyleCB.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_SIZE",
+            fontSizeCB.getSelectedItem().toString());
 
     Cache.applicationProperties.setProperty("ID_ITALICS",
             Boolean.toString(idItalics.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
             Boolean.toString(showUnconserved.isSelected()));
+    Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+            Boolean.toString(showOccupancy.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
             Boolean.toString(showGroupConsensus.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
@@ -595,8 +607,8 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
             Boolean.toString(startupCheckbox.isSelected()));
 
-    Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+            sortby.getSelectedItem().toString());
 
     // convert description of sort order to enum name for save
     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
@@ -608,16 +620,16 @@ public class Preferences extends GPreferences
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
-            .valueOf(showAutocalcFirst).toString());
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+            Boolean.valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
      */
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+            protColour.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+            nucColour.getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
@@ -634,8 +646,8 @@ public class Preferences extends GPreferences
             Boolean.toString(useRnaView.isSelected()));
     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+            structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
@@ -678,7 +690,7 @@ public class Preferences extends GPreferences
     }
 
     Cache.applicationProperties.setProperty("DEFAULT_URL",
-            sequenceUrlLinks.getDefaultUrlId());
+            sequenceUrlLinks.getPrimaryUrlId());
 
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
@@ -796,24 +808,25 @@ public class Preferences extends GPreferences
   @Override
   public void startupFileTextfield_mouseClicked()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
-                "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
-                "PIR", "BLC", "Jalview" },
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    JalviewFileChooser chooser = JalviewFileChooser
+            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager
-            .getString("label.select_startup_file"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_startup_file"));
 
     int value = chooser.showOpenDialog(this);
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.applicationProperties.setProperty(
-              "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
-      startupFileTextfield.setText(chooser.getSelectedFile()
-              .getAbsolutePath());
+      FileFormatI format = chooser.getSelectedFormat();
+      if (format != null)
+      {
+        Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+                format.getName());
+      }
+      startupFileTextfield
+              .setText(chooser.getSelectedFile().getAbsolutePath());
     }
   }
 
@@ -848,6 +861,7 @@ public class Preferences extends GPreferences
     conservation.setEnabled(annotations.isSelected());
     quality.setEnabled(annotations.isSelected());
     identity.setEnabled(annotations.isSelected());
+    showOccupancy.setEnabled(annotations.isSelected());
     showGroupConsensus.setEnabled(annotations.isSelected());
     showGroupConservation.setEnabled(annotations.isSelected());
     showConsensHistogram.setEnabled(annotations.isSelected()
@@ -863,15 +877,25 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
-          ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
-                  link.getName(), link.getURL());
-          valid = true;
+          if (((UrlLinkTableModel) linkUrlTable.getModel())
+                  .isUniqueName(link.getName()))
+          {
+            ((UrlLinkTableModel) linkUrlTable.getModel())
+                    .insertRow(link.getName(), link.getURL());
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
       else
@@ -894,21 +918,37 @@ public class Preferences extends GPreferences
       return;
     }
 
-    link.setName(linkUrlTable.getValueAt(index, 0).toString());
-    link.setURL(linkUrlTable.getValueAt(index, 1).toString());
+    int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getNameColumn();
+    int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getUrlColumn();
+    String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
+    link.setName(oldName);
+    link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.edit_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
-          linkUrlTable.setValueAt(link.getName(), index, 0);
-          linkUrlTable.setValueAt(link.getURL(), index, 1);
-          valid = true;
+          if ((oldName.equals(link.getName()))
+                  || (((UrlLinkTableModel) linkUrlTable.getModel())
+                          .isUniqueName(link.getName())))
+          {
+            linkUrlTable.setValueAt(link.getName(), index, nameCol);
+            linkUrlTable.setValueAt(link.getURL(), index, urlCol);
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
       else
@@ -938,13 +978,12 @@ public class Preferences extends GPreferences
     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
   }
 
-
   @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(MessageManager
-            .getString("label.select_default_browser"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_default_browser"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -1001,6 +1040,32 @@ public class Preferences extends GPreferences
   }
 
   @Override
+  public void gapColour_actionPerformed(JButton btn)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_gap_colour"),
+            gapColour.getForeground());
+    if (col != null)
+    {
+      btn.setForeground(col);
+    }
+    btn.repaint();
+  }
+
+  @Override
+  public void hiddenColour_actionPerformed(JButton btn)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_hidden_colour"),
+            hiddenColour.getForeground());
+    if (col != null)
+    {
+      btn.setForeground(col);
+    }
+    btn.repaint();
+  }
+
+  @Override
   protected void userIdWidth_actionPerformed()
   {
     try
@@ -1017,10 +1082,11 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
-              .getString("warn.user_defined_width_requirements"),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager
+                      .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -1043,10 +1109,10 @@ public class Preferences extends GPreferences
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
-                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.ERROR_MESSAGE);
         return false;
       }
     }
@@ -1082,13 +1148,12 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JOptionPane.showInternalOptionDialog(
-              Desktop.desktop,
+      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
               null, options, options[0]);
-      if (showHelp == JOptionPane.NO_OPTION)
+      if (showHelp == JvOptionPane.NO_OPTION)
       {
         try
         {
@@ -1155,7 +1220,7 @@ public class Preferences extends GPreferences
       return name.hashCode() + code.hashCode();
     }
   }
-  
+
   private class UrlListSelectionHandler implements ListSelectionListener
   {
 
@@ -1174,30 +1239,26 @@ public class Preferences extends GPreferences
       }
       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
 
-      // determine if the new selection is a custom url or not
-      int col = ((UrlLinkTableModel) linkUrlTable.getModel())
-              .getNameColumn();
-      if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable.getModel()
-              .getValueAt(modelIndex, col)))
+      // enable/disable edit and delete link buttons
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowDeletable(modelIndex))
       {
-        // entry is not a user-defined url and so should not be edited
-        // disable edit and delete buttons
-        deleteLink.setEnabled(false);
-        editLink.setEnabled(false);
+        deleteLink.setEnabled(true);
       }
       else
       {
-        deleteLink.setEnabled(true);
-        editLink.setEnabled(true);
+        deleteLink.setEnabled(false);
       }
 
-      // BUT if it's the default url, don't allow deletion
-      col = ((UrlLinkTableModel) linkUrlTable.getModel())
-              .getDefaultColumn();
-      if ((boolean) linkUrlTable.getValueAt(index, col))
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowEditable(modelIndex))
       {
-        deleteLink.setEnabled(false);
+        editLink.setEnabled(true);
+      }
+      else
+      {
+        editLink.setEnabled(false);
       }
     }
-}
+  }
 }